Datasets:
Add the 88-sample starter pack (no login)
Browse files88 samples of release v1.0.0-20261025, byte-identical to the gated dataset (SHA256 in starter/starter.json), under the same samples/<GSE>/<GSM>/ layout.
This view is limited to 50 files because it contains too many changes. See raw diff
- .gitattributes +148 -0
- samples/GSE144239/GSM4284320/image.tif +3 -0
- samples/GSE144239/GSM4284320/sample.json +276 -0
- samples/GSE144239/GSM4284320/spatial.h5ad +3 -0
- samples/GSE144239/GSM4284327/image.tif +3 -0
- samples/GSE144239/GSM4284327/sample.json +276 -0
- samples/GSE144239/GSM4284327/spatial.h5ad +3 -0
- samples/GSE147747/GSM4459917/image.tif +3 -0
- samples/GSE147747/GSM4459917/sample.json +283 -0
- samples/GSE147747/GSM4459917/spatial.h5ad +3 -0
- samples/GSE156862/GSM4745615/sample.json +132 -0
- samples/GSE156862/GSM4745615/spatial.h5ad +3 -0
- samples/GSE178636/GSM5395087/image.tif +3 -0
- samples/GSE178636/GSM5395087/sample.json +275 -0
- samples/GSE178636/GSM5395087/spatial.h5ad +3 -0
- samples/GSE183279/GSM6128246/sample.json +139 -0
- samples/GSE183279/GSM6128246/spatial.h5ad +3 -0
- samples/GSE190094/GSM5713416/sample.json +149 -0
- samples/GSE190094/GSM5713416/spatial.h5ad +3 -0
- samples/GSE195598/GSM5841553/image.tif +3 -0
- samples/GSE195598/GSM5841553/sample.json +287 -0
- samples/GSE195598/GSM5841553/spatial.h5ad +3 -0
- samples/GSE197023/GSM5907084/image.tif +3 -0
- samples/GSE197023/GSM5907084/sample.json +287 -0
- samples/GSE197023/GSM5907084/spatial.h5ad +3 -0
- samples/GSE203612/GSM6177617/image.tif +3 -0
- samples/GSE203612/GSM6177617/sample.json +271 -0
- samples/GSE203612/GSM6177617/spatial.h5ad +3 -0
- samples/GSE209583/GSM6380088/image.tif +3 -0
- samples/GSE209583/GSM6380088/sample.json +283 -0
- samples/GSE209583/GSM6380088/spatial.h5ad +3 -0
- samples/GSE215305/GSM6631766/image.tif +3 -0
- samples/GSE215305/GSM6631766/sample.json +287 -0
- samples/GSE215305/GSM6631766/spatial.h5ad +3 -0
- samples/GSE219120/GSM6774322/image.tif +3 -0
- samples/GSE219120/GSM6774322/sample.json +284 -0
- samples/GSE219120/GSM6774322/spatial.h5ad +3 -0
- samples/GSE221359/GSM6859066/image.tif +3 -0
- samples/GSE221359/GSM6859066/sample.json +283 -0
- samples/GSE221359/GSM6859066/spatial.h5ad +3 -0
- samples/GSE230776/GSM7234197/sample.json +144 -0
- samples/GSE230776/GSM7234197/spatial.h5ad +3 -0
- samples/GSE234199/GSM7454047/image.tif +3 -0
- samples/GSE234199/GSM7454047/sample.json +287 -0
- samples/GSE234199/GSM7454047/spatial.h5ad +3 -0
- samples/GSE234253/GSM7458248/sample.json +144 -0
- samples/GSE234253/GSM7458248/spatial.h5ad +3 -0
- samples/GSE236171/GSM7574424/image.tif +3 -0
- samples/GSE236171/GSM7574424/sample.json +275 -0
- samples/GSE236171/GSM7574424/spatial.h5ad +3 -0
.gitattributes
CHANGED
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# Video files - compressed
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*.mp4 filter=lfs diff=lfs merge=lfs -text
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*.webm filter=lfs diff=lfs merge=lfs -text
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# Video files - compressed
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*.mp4 filter=lfs diff=lfs merge=lfs -text
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*.webm filter=lfs diff=lfs merge=lfs -text
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samples/GSE197023/GSM5907084/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE197023/GSM5907084/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE296582/GSM8972903/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE296582/GSM8972903/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE298286/GSM9011366/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE298286/GSM9011366/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE234199/GSM7454047/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE234199/GSM7454047/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE262430/GSM8169578/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE262430/GSM8169578/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE269875/GSM8329293/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE269875/GSM8329293/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE254652/GSM8047865/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE254652/GSM8047865/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE306288/GSM9759911/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE306288/GSM9759911/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE209583/GSM6380088/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE209583/GSM6380088/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE245388/GSM7841727/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE245388/GSM7841727/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE270678/GSM8349919/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE270678/GSM8349919/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE250138/GSM7974484/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE250138/GSM7974484/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE221359/GSM6859066/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE221359/GSM6859066/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE251693/GSM7986082/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE251693/GSM7986082/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE215305/GSM6631766/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE215305/GSM6631766/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE203612/GSM6177617/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE203612/GSM6177617/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE248517/GSM7916286/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE248517/GSM7916286/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE219120/GSM6774322/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE219120/GSM6774322/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE178636/GSM5395087/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE178636/GSM5395087/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE311783/GSM9331988/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE311783/GSM9331988/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE144239/GSM4284327/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE144239/GSM4284327/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE236171/GSM7574424/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE236171/GSM7574424/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE244723/GSM7825036/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE244723/GSM7825036/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE297058/GSM9232562/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE297058/GSM9232562/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE268049/GSM8284978/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE268049/GSM8284978/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE269875/GSM8329298/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE269875/GSM8329298/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE195598/GSM5841553/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE195598/GSM5841553/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE298286/GSM9011363/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE298286/GSM9011363/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE306288/GSM9759912/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE306288/GSM9759912/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE245388/GSM7841732/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE245388/GSM7841732/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE270678/GSM8349918/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE270678/GSM8349918/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE250138/GSM7974486/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE250138/GSM7974486/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE278936/GSM8558024/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE278936/GSM8558024/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE301265/GSM9078981/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE301265/GSM9078981/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE308929/GSM9256396/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE308929/GSM9256396/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE317226/GSM9467251/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE317226/GSM9467251/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE322640/GSM9556004/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE322640/GSM9556004/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE279181/GSM8563706/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE279181/GSM8563706/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE144239/GSM4284320/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE144239/GSM4284320/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE244723/GSM7825037/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE244723/GSM7825037/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE147747/GSM4459917/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE147747/GSM4459917/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE319755/GSM9525786/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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| 144 |
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samples/GSE319755/GSM9525786/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE296577/GSM9448988/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE296577/GSM9448988/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE345302/GSM10001169/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE345302/GSM10001169/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE311681/GSM9329349/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE311681/GSM9329349/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE311609/GSM9509157/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE311609/GSM9509157/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE290762/GSM8821265/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE290762/GSM8821265/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE297058/GSM9232561/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE297058/GSM9232561/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE298872/GSM9025384/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE298872/GSM9025384/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE288663/GSM8772710/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE288663/GSM8772710/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE294965/GSM8933093/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE294965/GSM8933093/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE328700/GSM9687902/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE328700/GSM9687902/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE304762/GSM9156518/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE304762/GSM9156518/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE320142/GSM9535607/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE320142/GSM9535607/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE281265/GSM8616497/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE281265/GSM8616497/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE312420/GSM9345479/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE312420/GSM9345479/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE289263/GSM8788018/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE289263/GSM8788018/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE319771/GSM9526117/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE319771/GSM9526117/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE294469/GSM8907700/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE313700/GSM9372760/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE313700/GSM9372760/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE293124/GSM8876960/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE298021/GSM9004715/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE305111/GSM9162384/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE268492/GSM8291963/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE253474/GSM8021258/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE333479/GSM9765786/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE281488/GSM9285242/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE190094/GSM5713416/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE294759/GSM8919113/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE298591/GSM9017964/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE325769/GSM9613078/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE294759/GSM8919112/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE230776/GSM7234197/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE283863/GSM8673457/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE313700/GSM9372730/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE313700/GSM9372730/image.tif filter=lfs diff=lfs merge=lfs -text
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samples/GSE289054/GSM8782673/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE329112/GSM9697713/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE293124/GSM8876956/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE273530/GSM8431774/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE313704/GSM9372792/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE288178/GSM8760701/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE315408/GSM9427141/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE344692/GSM9983339/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE183279/GSM6128246/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE234253/GSM7458248/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE156862/GSM4745615/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE325911/GSM9616853/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
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samples/GSE325911/GSM9616845/spatial.h5ad filter=lfs diff=lfs merge=lfs -text
|
samples/GSE144239/GSM4284320/image.tif
ADDED
|
|
Git LFS Details
|
samples/GSE144239/GSM4284320/sample.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"schema": "sda-release-sample-1",
|
| 3 |
+
"release_id": "sda-unified-20261010-v3",
|
| 4 |
+
"gsm": "GSM4284320",
|
| 5 |
+
"gse": [
|
| 6 |
+
"GSE144239",
|
| 7 |
+
"GSE144240"
|
| 8 |
+
],
|
| 9 |
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"published_gse": "GSE144239",
|
| 10 |
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"metadata": {
|
| 11 |
+
"organism": "Homo sapiens",
|
| 12 |
+
"tissue": "skin",
|
| 13 |
+
"platform": "ST (legacy)",
|
| 14 |
+
"technology": "Spatial Transcriptomics",
|
| 15 |
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"fields": {
|
| 16 |
+
"organism": "Homo sapiens",
|
| 17 |
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|
| 18 |
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|
| 19 |
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"sex": null,
|
| 20 |
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|
| 21 |
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|
| 22 |
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|
| 23 |
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"technology": "Spatial Transcriptomics",
|
| 24 |
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"platform": "GPL18573",
|
| 25 |
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|
| 26 |
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|
| 27 |
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"publication_pmid": "32579974",
|
| 28 |
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"repository_id": "GSM4284320"
|
| 29 |
+
},
|
| 30 |
+
"field_sources": {
|
| 31 |
+
"organism": {
|
| 32 |
+
"raw_value": "Homo sapiens",
|
| 33 |
+
"status": "unchanged",
|
| 34 |
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"source": {
|
| 35 |
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"source_path": "metadata/GSE144239_family.soft.gz",
|
| 36 |
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"source_sha256": "6a4cfe0d4db6512b674d9d38410186079020f55ae6305c3002eb31bc62cc2610",
|
| 37 |
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"source_key": "!Sample_organism_ch1"
|
| 38 |
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}
|
| 39 |
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},
|
| 40 |
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"tissue": {
|
| 41 |
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"raw_value": "Skin",
|
| 42 |
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"status": "normalized",
|
| 43 |
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"source": {
|
| 44 |
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"source_path": "metadata/GSE144239_family.soft.gz",
|
| 45 |
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"source_sha256": "6a4cfe0d4db6512b674d9d38410186079020f55ae6305c3002eb31bc62cc2610",
|
| 46 |
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"source_key": "!Sample_source_name_ch1"
|
| 47 |
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}
|
| 48 |
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},
|
| 49 |
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"disease": {
|
| 50 |
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"raw_value": "cSCC",
|
| 51 |
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"status": "unmapped",
|
| 52 |
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"source": {
|
| 53 |
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"source_path": "metadata/GSE144239_family.soft.gz",
|
| 54 |
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"source_sha256": "6a4cfe0d4db6512b674d9d38410186079020f55ae6305c3002eb31bc62cc2610",
|
| 55 |
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"source_key": "!Sample_characteristics_ch1"
|
| 56 |
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|
| 57 |
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|
| 58 |
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|
| 59 |
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|
| 60 |
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|
| 61 |
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|
| 62 |
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|
| 63 |
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|
| 64 |
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|
| 65 |
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|
| 66 |
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|
| 67 |
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|
| 68 |
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|
| 69 |
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"raw_value": "P5",
|
| 70 |
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"status": "unchanged",
|
| 71 |
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"source": {
|
| 72 |
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"source_path": "metadata/GSE144239_family.soft.gz",
|
| 73 |
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"source_sha256": "6a4cfe0d4db6512b674d9d38410186079020f55ae6305c3002eb31bc62cc2610",
|
| 74 |
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|
| 75 |
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|
| 76 |
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|
| 77 |
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|
| 78 |
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|
| 79 |
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|
| 80 |
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|
| 81 |
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},
|
| 82 |
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"technology": {
|
| 83 |
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"raw_value": "Spatial Transcriptomics",
|
| 84 |
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"status": "needs_review",
|
| 85 |
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|
| 86 |
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|
| 87 |
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|
| 88 |
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|
| 89 |
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|
| 90 |
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|
| 91 |
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|
| 92 |
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|
| 93 |
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|
| 94 |
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|
| 95 |
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|
| 96 |
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| 97 |
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| 98 |
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| 99 |
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|
| 100 |
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|
| 101 |
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| 102 |
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| 103 |
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| 104 |
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| 105 |
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| 106 |
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| 107 |
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| 108 |
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| 109 |
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| 110 |
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| 111 |
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| 112 |
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| 113 |
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| 114 |
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| 115 |
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| 116 |
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| 117 |
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| 118 |
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| 119 |
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| 120 |
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| 121 |
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| 122 |
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| 123 |
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| 124 |
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| 125 |
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| 126 |
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| 127 |
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|
| 128 |
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|
| 129 |
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|
| 130 |
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|
| 131 |
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| 132 |
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| 133 |
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| 134 |
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| 135 |
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| 136 |
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|
| 137 |
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|
| 138 |
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},
|
| 139 |
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|
| 140 |
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|
| 141 |
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| 142 |
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|
| 143 |
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| 144 |
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| 145 |
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| 146 |
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|
| 147 |
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| 148 |
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| 149 |
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| 150 |
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| 151 |
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| 153 |
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| 154 |
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| 155 |
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| 156 |
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"R",
|
| 157 |
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| 158 |
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|
| 159 |
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|
| 160 |
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|
| 161 |
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|
| 162 |
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| 163 |
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| 164 |
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[
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| 165 |
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| 166 |
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| 167 |
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| 180 |
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|
| 181 |
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| 182 |
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| 183 |
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| 184 |
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| 185 |
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| 186 |
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| 187 |
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| 188 |
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| 189 |
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| 190 |
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| 1 |
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{
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| 2 |
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|
| 3 |
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|
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|
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|
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|
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|
| 11 |
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|
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|
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samples/GSE147747/GSM4459917/sample.json
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| 1 |
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{
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| 2 |
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|
| 3 |
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|
| 4 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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| 59 |
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samples/GSE178636/GSM5395087/sample.json
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| 1 |
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{
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| 2 |
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|
| 3 |
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|
| 4 |
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|
| 5 |
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|
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|
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|
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|
|
|
|
|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
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|
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|
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|
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|
|
|
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|
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|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
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|
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|
|
| 1 |
+
{
|
| 2 |
+
"schema": "sda-release-sample-1",
|
| 3 |
+
"release_id": "sda-unified-20261010-v3",
|
| 4 |
+
"gsm": "GSM5713416",
|
| 5 |
+
"gse": [
|
| 6 |
+
"GSE190094"
|
| 7 |
+
],
|
| 8 |
+
"published_gse": "GSE190094",
|
| 9 |
+
"metadata": {
|
| 10 |
+
"organism": "Mus musculus",
|
| 11 |
+
"tissue": "kidney cross-section",
|
| 12 |
+
"platform": "Slide-seq",
|
| 13 |
+
"technology": "Slide-seqV2",
|
| 14 |
+
"fields": {
|
| 15 |
+
"organism": "Mus musculus",
|
| 16 |
+
"tissue": "kidney cross-section",
|
| 17 |
+
"disease": "autosomal dominant tubulointersital kidney disease (ADTKD)",
|
| 18 |
+
"sex": null,
|
| 19 |
+
"age": "6 month",
|
| 20 |
+
"donor_id": null,
|
| 21 |
+
"condition": "UMOD-KI/KI",
|
| 22 |
+
"technology": "Slide-seqV2",
|
| 23 |
+
"platform": "GPL24247",
|
| 24 |
+
"stain_type": null,
|
| 25 |
+
"publication_doi": null,
|
| 26 |
+
"publication_pmid": "35372810",
|
| 27 |
+
"repository_id": "GSM5713416",
|
| 28 |
+
"preservation_method": null,
|
| 29 |
+
"panel_name": null,
|
| 30 |
+
"software_version": null
|
| 31 |
+
},
|
| 32 |
+
"field_sources": {
|
| 33 |
+
"organism": {
|
| 34 |
+
"source_id": "geo_meta",
|
| 35 |
+
"pointer": "/samples/GSM5713416/organism",
|
| 36 |
+
"quote": "Mus musculus"
|
| 37 |
+
},
|
| 38 |
+
"platform": {
|
| 39 |
+
"source_id": "geo_meta",
|
| 40 |
+
"pointer": "/samples/GSM5713416/platform_id",
|
| 41 |
+
"quote": "GPL24247"
|
| 42 |
+
},
|
| 43 |
+
"repository_id": {
|
| 44 |
+
"source_id": "geo_meta",
|
| 45 |
+
"pointer": "/samples/GSM5713416/accession",
|
| 46 |
+
"quote": "GSM5713416"
|
| 47 |
+
},
|
| 48 |
+
"tissue": {
|
| 49 |
+
"source_id": "geo_meta",
|
| 50 |
+
"pointer": "/samples/GSM5713416/characteristics/2",
|
| 51 |
+
"quote": "tissue: kidney cross-section"
|
| 52 |
+
},
|
| 53 |
+
"disease": {
|
| 54 |
+
"source_id": "geo_meta",
|
| 55 |
+
"pointer": "/samples/GSM5713416/characteristics/1",
|
| 56 |
+
"quote": "disease state: autosomal dominant tubulointersital kidney disease (ADTKD)"
|
| 57 |
+
},
|
| 58 |
+
"age": {
|
| 59 |
+
"source_id": "geo_meta",
|
| 60 |
+
"pointer": "/samples/GSM5713416/characteristics/3",
|
| 61 |
+
"quote": "age: 6 month"
|
| 62 |
+
},
|
| 63 |
+
"condition": {
|
| 64 |
+
"source_id": "geo_meta",
|
| 65 |
+
"pointer": "/samples/GSM5713416/characteristics/0",
|
| 66 |
+
"quote": "genotype: UMOD-KI/KI"
|
| 67 |
+
},
|
| 68 |
+
"publication_pmid": {
|
| 69 |
+
"source_id": "geo_meta",
|
| 70 |
+
"pointer": "/series/pubmed_ids",
|
| 71 |
+
"quote": "35372810"
|
| 72 |
+
},
|
| 73 |
+
"technology": {
|
| 74 |
+
"source_id": "geo_meta",
|
| 75 |
+
"pointer": "/samples/GSM5713416/description",
|
| 76 |
+
"quote": "Slide-seqV2"
|
| 77 |
+
}
|
| 78 |
+
}
|
| 79 |
+
},
|
| 80 |
+
"expression": {
|
| 81 |
+
"file": "spatial.h5ad",
|
| 82 |
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"sha256": "78f88c826d6bdcf3f5265c5be85461d42ed034343e18bf6fdca837549059f3e1",
|
| 83 |
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"n_obs": 20424,
|
| 84 |
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"n_vars": 20226,
|
| 85 |
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"state": "counts",
|
| 86 |
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"observation_unit": "bead",
|
| 87 |
+
"verification": "VERIFIED"
|
| 88 |
+
},
|
| 89 |
+
"coordinates": {
|
| 90 |
+
"obsm_key": "spatial",
|
| 91 |
+
"units": "pixel",
|
| 92 |
+
"um_basis": "unresolved",
|
| 93 |
+
"um_per_unit": null,
|
| 94 |
+
"um_basis_detail": "frame slideseq_puck_pixel; scorer physical_coordinates UNRESOLVED",
|
| 95 |
+
"spatial_um": false
|
| 96 |
+
},
|
| 97 |
+
"image": null,
|
| 98 |
+
"segmentation": null,
|
| 99 |
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"molecules": null,
|
| 100 |
+
"quality": {
|
| 101 |
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"flags": [],
|
| 102 |
+
"qc_flags": [],
|
| 103 |
+
"drop_features": [],
|
| 104 |
+
"review": null
|
| 105 |
+
},
|
| 106 |
+
"dedup": {
|
| 107 |
+
"content_group": "GSM5713416",
|
| 108 |
+
"group_kind": null,
|
| 109 |
+
"aliases": []
|
| 110 |
+
},
|
| 111 |
+
"split": "train",
|
| 112 |
+
"provenance": {
|
| 113 |
+
"pipeline": "sda-all",
|
| 114 |
+
"source_release": "sda-all-v1.6.3",
|
| 115 |
+
"files": [
|
| 116 |
+
{
|
| 117 |
+
"role": "sample_manifest",
|
| 118 |
+
"path": "source-reference://cw-storage/sda_all_v14/release-p4-v16/GSE190094/GSM5713416/manifest.json",
|
| 119 |
+
"sha256": "a9d3480bb0e7cc3ec90136ece859877e98152ce4edeaf5a22f38e098c94f0117"
|
| 120 |
+
},
|
| 121 |
+
{
|
| 122 |
+
"role": "expression",
|
| 123 |
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"path": "source-reference://cw-storage/sda_all_v14/release-p4-v16/GSE190094/GSM5713416/spatial.h5ad",
|
| 124 |
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"sha256": "78f88c826d6bdcf3f5265c5be85461d42ed034343e18bf6fdca837549059f3e1"
|
| 125 |
+
},
|
| 126 |
+
{
|
| 127 |
+
"role": "source:expression",
|
| 128 |
+
"path": "samples/GSM5713nnn/GSM5713416/GSM5713416_Puck_200210_04.digital_expression.txt.gz",
|
| 129 |
+
"input_root": "source-reference://public-storage/sda_all/inputs-v2/GSE190094",
|
| 130 |
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|
| 131 |
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"sha256": "c68fe0739e9b3be32a92ec80cc37acef1a0a36146d8275857b1b7f67b99820d3"
|
| 132 |
+
},
|
| 133 |
+
{
|
| 134 |
+
"role": "source:coordinates",
|
| 135 |
+
"path": "samples/GSM5713nnn/GSM5713416/GSM5713416_Puck_200210_04_BeadLocationsForR_qc.csv.gz",
|
| 136 |
+
"input_root": "source-reference://public-storage/sda_all/inputs-v2/GSE190094",
|
| 137 |
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"members": null,
|
| 138 |
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|
| 139 |
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},
|
| 140 |
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{
|
| 141 |
+
"role": "source:metadata",
|
| 142 |
+
"path": "_meta/geo_metadata.json",
|
| 143 |
+
"input_root": "source-reference://public-storage/sda_all/inputs-v2/GSE190094",
|
| 144 |
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"members": null,
|
| 145 |
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|
| 146 |
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}
|
| 147 |
+
]
|
| 148 |
+
}
|
| 149 |
+
}
|
samples/GSE190094/GSM5713416/spatial.h5ad
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:78f88c826d6bdcf3f5265c5be85461d42ed034343e18bf6fdca837549059f3e1
|
| 3 |
+
size 50647058
|
samples/GSE195598/GSM5841553/image.tif
ADDED
|
|
Git LFS Details
|
samples/GSE195598/GSM5841553/sample.json
ADDED
|
@@ -0,0 +1,287 @@
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
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|
|
|
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|
|
|
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|
|
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|
|
|
|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
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|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"schema": "sda-release-sample-1",
|
| 3 |
+
"release_id": "sda-unified-20261010-v3",
|
| 4 |
+
"gsm": "GSM5841553",
|
| 5 |
+
"gse": [
|
| 6 |
+
"GSE195598"
|
| 7 |
+
],
|
| 8 |
+
"published_gse": "GSE195598",
|
| 9 |
+
"metadata": {
|
| 10 |
+
"organism": "Mus musculus",
|
| 11 |
+
"tissue": "Popliteal Lymph Nodes",
|
| 12 |
+
"platform": "Visium",
|
| 13 |
+
"technology": "10x Genomics Visium",
|
| 14 |
+
"fields": {
|
| 15 |
+
"organism": "Mus musculus",
|
| 16 |
+
"tissue": "Popliteal Lymph Nodes",
|
| 17 |
+
"disease": "Advanced arthritis",
|
| 18 |
+
"sex": "male",
|
| 19 |
+
"age": "8.5–9 months",
|
| 20 |
+
"donor_id": null,
|
| 21 |
+
"condition": "Advanced arthritis",
|
| 22 |
+
"technology": "10x Genomics Visium",
|
| 23 |
+
"platform": "GPL24247",
|
| 24 |
+
"stain_type": "H&E",
|
| 25 |
+
"publication_doi": null,
|
| 26 |
+
"publication_pmid": "37691918",
|
| 27 |
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| 1 |
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{
|
| 2 |
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|
| 3 |
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|
| 4 |
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|
| 5 |
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|
| 6 |
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"GSE197023"
|
| 7 |
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|
| 8 |
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|
| 9 |
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|
| 10 |
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|
| 11 |
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|
| 12 |
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|
| 13 |
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|
| 14 |
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|
| 15 |
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|
| 16 |
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| 17 |
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| 18 |
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| 19 |
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| 20 |
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|
| 21 |
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| 22 |
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| 23 |
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| 24 |
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| 25 |
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|
| 26 |
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|
| 27 |
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|
| 28 |
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| 29 |
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|
| 30 |
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|
| 31 |
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|
| 32 |
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| 33 |
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| 34 |
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| 35 |
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| 36 |
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| 37 |
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| 38 |
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| 39 |
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|
| 40 |
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| 41 |
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| 42 |
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| 43 |
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| 44 |
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| 45 |
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| 46 |
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| 47 |
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| 48 |
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|
| 49 |
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| 50 |
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| 51 |
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| 52 |
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| 53 |
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| 54 |
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| 55 |
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| 56 |
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| 57 |
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| 58 |
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| 61 |
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| 64 |
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| 65 |
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| 66 |
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| 67 |
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| 68 |
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| 69 |
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| 70 |
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| 71 |
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| 72 |
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| 73 |
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| 74 |
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| 75 |
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| 76 |
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| 77 |
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| 78 |
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| 79 |
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| 80 |
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| 82 |
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| 83 |
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| 84 |
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| 85 |
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| 86 |
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| 87 |
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| 92 |
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| 95 |
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| 101 |
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| 102 |
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| 103 |
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| 104 |
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| 105 |
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| 110 |
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| 111 |
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| 112 |
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| 113 |
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| 114 |
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| 115 |
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| 116 |
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| 118 |
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| 119 |
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| 122 |
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| 149 |
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"role": "hesrt_metadata.normalized.json",
|
| 277 |
+
"path": "source-reference://public-storage/sda_work/hesrt-v1.3-expanded/GSE197023/GSM5907084/metadata.normalized.json",
|
| 278 |
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"sha256": "ba205da21e3c3bcd39f752567554c655abe2e13f35fc83d4b2922a442ab8cadf"
|
| 279 |
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},
|
| 280 |
+
{
|
| 281 |
+
"role": "hesrt_manifest.json",
|
| 282 |
+
"path": "source-reference://public-storage/sda_work/hesrt-v1.3-expanded/GSE197023/GSM5907084/manifest.json",
|
| 283 |
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"sha256": "a831e990849abf8361374e8efc2ff162a14bc78a263a2d48251def298f643796"
|
| 284 |
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|
| 285 |
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]
|
| 286 |
+
}
|
| 287 |
+
}
|
samples/GSE197023/GSM5907084/spatial.h5ad
ADDED
|
@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:1ce4cbefe39ca328c504972f5ca6b44fe6ca210aaa20b9deb6016a0a64d17d51
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| 3 |
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size 4923155
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samples/GSE203612/GSM6177617/image.tif
ADDED
|
|
Git LFS Details
|
samples/GSE203612/GSM6177617/sample.json
ADDED
|
@@ -0,0 +1,271 @@
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|
| 1 |
+
{
|
| 2 |
+
"schema": "sda-release-sample-1",
|
| 3 |
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"release_id": "sda-unified-20261010-v3",
|
| 4 |
+
"gsm": "GSM6177617",
|
| 5 |
+
"gse": [
|
| 6 |
+
"GSE203612"
|
| 7 |
+
],
|
| 8 |
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"published_gse": "GSE203612",
|
| 9 |
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"metadata": {
|
| 10 |
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"organism": "Homo sapiens",
|
| 11 |
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"tissue": "Ovary",
|
| 12 |
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"platform": "Visium",
|
| 13 |
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"technology": "10x Genomics Visium",
|
| 14 |
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"fields": {
|
| 15 |
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"organism": "Homo sapiens",
|
| 16 |
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|
| 17 |
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|
| 18 |
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|
| 19 |
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|
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|
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| 26 |
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|
| 27 |
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|
| 28 |
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|
| 29 |
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|
| 30 |
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|
| 31 |
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"raw_value": "Homo sapiens",
|
| 32 |
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|
| 33 |
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|
| 34 |
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| 35 |
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| 36 |
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"source_key": "!Sample_organism_ch1"
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| 37 |
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}
|
| 38 |
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},
|
| 39 |
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|
| 40 |
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|
| 41 |
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"status": "unmapped",
|
| 42 |
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|
| 43 |
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|
| 47 |
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| 48 |
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|
| 49 |
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|
| 50 |
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|
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| 87 |
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|
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size 19565842
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samples/GSE209583/GSM6380088/image.tif
ADDED
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|
Git LFS Details
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samples/GSE209583/GSM6380088/sample.json
ADDED
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|
| 1 |
+
{
|
| 2 |
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"schema": "sda-release-sample-1",
|
| 3 |
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"release_id": "sda-unified-20261010-v3",
|
| 4 |
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"gsm": "GSM6380088",
|
| 5 |
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|
| 6 |
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"GSE209583"
|
| 7 |
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],
|
| 8 |
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"published_gse": "GSE209583",
|
| 9 |
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|
| 10 |
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|
| 11 |
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|
| 12 |
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|
| 13 |
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"technology": "10x Genomics Visium",
|
| 14 |
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|
| 15 |
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|
| 16 |
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|
| 17 |
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|
| 18 |
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|
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|
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|
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|
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|
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|
| 26 |
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|
| 27 |
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|
| 28 |
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|
| 29 |
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"field_sources": {
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| 30 |
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|
| 31 |
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"raw_value": "Mus musculus",
|
| 32 |
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"status": "unchanged",
|
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"source_key": "!Sample_organism_ch1"
|
| 37 |
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|
| 38 |
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|
| 39 |
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"tissue": {
|
| 40 |
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|
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|
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"source_key": "!Sample_characteristics_ch1 = tissue: Brain"
|
| 46 |
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}
|
| 47 |
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},
|
| 48 |
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"disease": {
|
| 49 |
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|
| 50 |
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|
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"source_key": "!Series_summary = Alzheimer's Disease model 5XFAD"
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|
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|
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|
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|
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|
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|
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}
|
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|
| 85 |
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|
| 86 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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samples/GSE215305/GSM6631766/image.tif
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Git LFS Details
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samples/GSE215305/GSM6631766/sample.json
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|
| 1 |
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{
|
| 2 |
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"schema": "sda-release-sample-1",
|
| 3 |
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"release_id": "sda-unified-20261010-v3",
|
| 4 |
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"gsm": "GSM6631766",
|
| 5 |
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"gse": [
|
| 6 |
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"GSE215305"
|
| 7 |
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],
|
| 8 |
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|
| 9 |
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"metadata": {
|
| 10 |
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|
| 11 |
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"tissue": "Gastrocnemius muscle",
|
| 12 |
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"platform": "Visium",
|
| 13 |
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"technology": "10x Genomics Visium",
|
| 14 |
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"fields": {
|
| 15 |
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"organism": "Mus musculus",
|
| 16 |
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"tissue": "Gastrocnemius muscle",
|
| 17 |
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"disease": "muscular dystrophy",
|
| 18 |
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|
| 19 |
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"age": "8 weeks",
|
| 20 |
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|
| 21 |
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|
| 22 |
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|
| 23 |
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|
| 24 |
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|
| 25 |
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|
| 26 |
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|
| 27 |
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|
| 28 |
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},
|
| 29 |
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|
| 30 |
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|
| 31 |
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|
| 32 |
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"status": "unchanged",
|
| 33 |
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|
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|
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"source_key": "!Sample_organism_ch1: Mus musculus"
|
| 37 |
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|
| 38 |
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},
|
| 39 |
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|
| 40 |
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|
| 41 |
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|
| 42 |
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"source_key": "!Sample_characteristics_ch1 = tissue: Gastrocnemius muscle"
|
| 46 |
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}
|
| 47 |
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|
| 48 |
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"disease": {
|
| 49 |
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|
| 50 |
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|
| 51 |
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"source_key": "!Series_summary: Muscular Dystrophy model (D2-mdx)"
|
| 55 |
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|
| 56 |
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|
| 57 |
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"sex": {
|
| 58 |
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"raw_value": "M",
|
| 59 |
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|
| 60 |
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|
| 64 |
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|
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|
| 66 |
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|
| 67 |
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|
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|
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"source_key": "!Sample_characteristics_ch1 = extraction protocol: 8-week-old D2-Mdx mouse"
|
| 73 |
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|
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|
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|
| 76 |
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|
| 78 |
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|
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|
| 81 |
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|
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samples/GSE219120/GSM6774322/image.tif
ADDED
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|
Git LFS Details
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samples/GSE219120/GSM6774322/sample.json
ADDED
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|
| 1 |
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{
|
| 2 |
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"schema": "sda-release-sample-1",
|
| 3 |
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"release_id": "sda-unified-20261010-v3",
|
| 4 |
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"gsm": "GSM6774322",
|
| 5 |
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"gse": [
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|
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"GSE219122"
|
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|
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| 1 |
+
{
|
| 2 |
+
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|
| 3 |
+
"release_id": "sda-unified-20261010-v3",
|
| 4 |
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|
| 5 |
+
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|
| 6 |
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"GSE221359"
|
| 7 |
+
],
|
| 8 |
+
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|
| 9 |
+
"metadata": {
|
| 10 |
+
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|
| 11 |
+
"tissue": "liver",
|
| 12 |
+
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|
| 13 |
+
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|
| 14 |
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|
| 15 |
+
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|
| 16 |
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|
| 17 |
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|
| 18 |
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|
| 19 |
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|
| 20 |
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|
| 21 |
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|
| 22 |
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|
| 23 |
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|
| 24 |
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|
| 25 |
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|
| 26 |
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|
| 27 |
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|
| 28 |
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},
|
| 29 |
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|
| 30 |
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|
| 31 |
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|
| 32 |
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|
| 33 |
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|
| 34 |
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|
| 35 |
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|
| 36 |
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|
| 37 |
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}
|
| 38 |
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},
|
| 39 |
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|
| 40 |
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|
| 41 |
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|
| 42 |
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|
| 43 |
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| 44 |
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|
| 45 |
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"source_key": "!Sample_characteristics_ch1 = tissue: Liver containing metastases of CRC origin"
|
| 46 |
+
}
|
| 47 |
+
},
|
| 48 |
+
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|
| 49 |
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"raw_value": "liver metastasis of colorectal cancer",
|
| 50 |
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|
| 51 |
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|
| 52 |
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| 53 |
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"source_sha256": "89a830d284b30ca276d07a52aadb7dbe92cfe9734dad7666383208309c4adc00",
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| 54 |
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|
| 55 |
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| 56 |
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| 57 |
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|
| 58 |
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| 59 |
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| 60 |
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| 61 |
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| 62 |
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| 63 |
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| 64 |
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| 65 |
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|
| 66 |
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|
| 67 |
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|
| 68 |
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|
| 69 |
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| 70 |
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|
| 71 |
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| 72 |
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| 73 |
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|
| 74 |
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}
|
| 75 |
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},
|
| 76 |
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|
| 77 |
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|
| 78 |
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| 79 |
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|
| 80 |
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| 81 |
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| 82 |
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"source_key": "!Sample_characteristics_ch1 = condition: Control"
|
| 83 |
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}
|
| 84 |
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},
|
| 85 |
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|
| 86 |
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|
| 87 |
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| 88 |
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|
| 89 |
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| 90 |
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| 91 |
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|
| 92 |
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| 93 |
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| 94 |
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|
| 95 |
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|
| 96 |
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| 97 |
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| 98 |
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| 99 |
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| 100 |
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"source_key": "!Sample_platform_id = GPL24247"
|
| 101 |
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}
|
| 102 |
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},
|
| 103 |
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|
| 104 |
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|
| 105 |
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| 106 |
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| 107 |
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| 108 |
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"source_sha256": "89a830d284b30ca276d07a52aadb7dbe92cfe9734dad7666383208309c4adc00",
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| 109 |
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"source_key": "!Sample_extract_protocol_ch1 = Hematoxilin & Eosin (H&E) staining"
|
| 110 |
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}
|
| 111 |
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},
|
| 112 |
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|
| 113 |
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|
| 114 |
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| 115 |
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|
| 116 |
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},
|
| 117 |
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|
| 118 |
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|
| 119 |
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|
| 120 |
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| 121 |
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| 122 |
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| 123 |
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"source_key": "!Series_pubmed_id = 37863068"
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| 124 |
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}
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| 125 |
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},
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| 126 |
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| 127 |
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| 128 |
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| 129 |
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| 130 |
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| 131 |
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| 132 |
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| 133 |
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| 134 |
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| 135 |
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| 136 |
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| 137 |
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| 138 |
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| 139 |
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| 140 |
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| 141 |
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| 142 |
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| 143 |
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|
| 144 |
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|
| 145 |
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},
|
| 146 |
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|
| 147 |
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| 148 |
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| 149 |
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|
| 150 |
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| 151 |
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| 152 |
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| 153 |
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| 154 |
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| 155 |
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| 156 |
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| 157 |
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| 158 |
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| 159 |
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|
| 160 |
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| 161 |
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| 162 |
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| 163 |
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| 164 |
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| 165 |
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|
| 166 |
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| 167 |
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| 168 |
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| 169 |
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|
| 170 |
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| 171 |
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| 172 |
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| 173 |
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| 174 |
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| 175 |
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| 177 |
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| 184 |
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| 185 |
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| 186 |
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| 188 |
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| 189 |
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| 195 |
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| 198 |
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"sha256": "6384325d2aeaeb150e26f04dcd1b062fa046b37dbe04cfd7589ae4242f45c8ff"
|
| 270 |
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|
| 271 |
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{
|
| 272 |
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"role": "hesrt_metadata.normalized.json",
|
| 273 |
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"path": "source-reference://public-storage/sda_work/hesrt-v1.3-expanded/GSE221359/GSM6859066/metadata.normalized.json",
|
| 274 |
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"sha256": "fc57ffc9b84f8eaeecef2de7ea382f79028dfe0fd9f1804b6d53ea98d7530a18"
|
| 275 |
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|
| 276 |
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{
|
| 277 |
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"role": "hesrt_manifest.json",
|
| 278 |
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"path": "source-reference://public-storage/sda_work/hesrt-v1.3-expanded/GSE221359/GSM6859066/manifest.json",
|
| 279 |
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|
| 280 |
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}
|
| 281 |
+
]
|
| 282 |
+
}
|
| 283 |
+
}
|
samples/GSE221359/GSM6859066/spatial.h5ad
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
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version https://git-lfs.github.com/spec/v1
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oid sha256:04b0d8af58d9565b54a40ef65171a1b283e2032013dd5ae3988c9cad89c9d0af
|
| 3 |
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size 29353721
|
samples/GSE230776/GSM7234197/sample.json
ADDED
|
@@ -0,0 +1,144 @@
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|
|
|
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|
|
|
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|
|
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|
|
|
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|
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|
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|
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|
|
|
|
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|
|
|
|
|
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|
|
|
|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
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|
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|
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|
|
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|
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| 1 |
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{
|
| 2 |
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"schema": "sda-release-sample-1",
|
| 3 |
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"release_id": "sda-unified-20261010-v3",
|
| 4 |
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"gsm": "GSM7234197",
|
| 5 |
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"gse": [
|
| 6 |
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"GSE230776"
|
| 7 |
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],
|
| 8 |
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"published_gse": "GSE230776",
|
| 9 |
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"metadata": {
|
| 10 |
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"organism": "Gallus gallus",
|
| 11 |
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"tissue": "embryonic trunk",
|
| 12 |
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"platform": "Slide-seq",
|
| 13 |
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"technology": "Slide-seq",
|
| 14 |
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"fields": {
|
| 15 |
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"organism": "Gallus gallus",
|
| 16 |
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"tissue": "embryonic trunk",
|
| 17 |
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|
| 18 |
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|
| 19 |
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|
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|
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"condition": "wild-type",
|
| 22 |
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"technology": "Slide-seq",
|
| 23 |
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|
| 24 |
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|
| 25 |
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|
| 26 |
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"publication_pmid": "36840366",
|
| 27 |
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|
| 28 |
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|
| 29 |
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|
| 30 |
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|
| 31 |
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},
|
| 32 |
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"field_sources": {
|
| 33 |
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"organism": {
|
| 34 |
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"source_id": "geo_meta",
|
| 35 |
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"pointer": "/samples/GSM7234197/organism",
|
| 36 |
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"quote": "Gallus gallus"
|
| 37 |
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},
|
| 38 |
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"platform": {
|
| 39 |
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"source_id": "geo_meta",
|
| 40 |
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"pointer": "/samples/GSM7234197/platform_id",
|
| 41 |
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"quote": "GPL19787"
|
| 42 |
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},
|
| 43 |
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"repository_id": {
|
| 44 |
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"source_id": "geo_meta",
|
| 45 |
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"pointer": "/samples/GSM7234197/accession",
|
| 46 |
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"quote": "GSM7234197"
|
| 47 |
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},
|
| 48 |
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"tissue": {
|
| 49 |
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"source_id": "geo_meta",
|
| 50 |
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"pointer": "/samples/GSM7234197/characteristics/0",
|
| 51 |
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"quote": "tissue: embryonic trunk"
|
| 52 |
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},
|
| 53 |
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"condition": {
|
| 54 |
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"source_id": "geo_meta",
|
| 55 |
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"pointer": "/samples/GSM7234197/characteristics/3",
|
| 56 |
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"quote": "genotype: wild-type"
|
| 57 |
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},
|
| 58 |
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"publication_pmid": {
|
| 59 |
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"source_id": "geo_meta",
|
| 60 |
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"pointer": "/series/pubmed_ids",
|
| 61 |
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"quote": "36840366"
|
| 62 |
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},
|
| 63 |
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"technology": {
|
| 64 |
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"source_id": "geo_meta",
|
| 65 |
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"pointer": "/samples/GSM7234197/title",
|
| 66 |
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"quote": "Slide-seq"
|
| 67 |
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},
|
| 68 |
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"preservation_method": {
|
| 69 |
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"source_id": "geo_meta",
|
| 70 |
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"pointer": "/series/overall_design",
|
| 71 |
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"quote": "fresh frozen"
|
| 72 |
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}
|
| 73 |
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}
|
| 74 |
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},
|
| 75 |
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"expression": {
|
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|
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|
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"state": "counts",
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|
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"verification": "VERIFIED"
|
| 83 |
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},
|
| 84 |
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"coordinates": {
|
| 85 |
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"obsm_key": "spatial",
|
| 86 |
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"units": "pixel",
|
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|
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|
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|
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},
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|
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|
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|
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|
| 100 |
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},
|
| 101 |
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"dedup": {
|
| 102 |
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|
| 103 |
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|
| 104 |
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|
| 105 |
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},
|
| 106 |
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|
| 107 |
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|
| 108 |
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|
| 109 |
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|
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"files": [
|
| 111 |
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| 112 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
| 143 |
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|
| 144 |
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}
|
samples/GSE230776/GSM7234197/spatial.h5ad
ADDED
|
@@ -0,0 +1,3 @@
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|
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|
|
|
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|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:1de90dce0876dc6bf0eed35f99cc4bad5adce2427fa7282c471739bd3cd34bcd
|
| 3 |
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size 74010193
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samples/GSE234199/GSM7454047/image.tif
ADDED
|
|
Git LFS Details
|
samples/GSE234199/GSM7454047/sample.json
ADDED
|
@@ -0,0 +1,287 @@
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|
| 1 |
+
{
|
| 2 |
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"schema": "sda-release-sample-1",
|
| 3 |
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"release_id": "sda-unified-20261010-v3",
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|
|
|
|
|
|
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|
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|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
|
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|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"schema": "sda-release-sample-1",
|
| 3 |
+
"release_id": "sda-unified-20261010-v3",
|
| 4 |
+
"gsm": "GSM7458248",
|
| 5 |
+
"gse": [
|
| 6 |
+
"GSE234253"
|
| 7 |
+
],
|
| 8 |
+
"published_gse": "GSE234253",
|
| 9 |
+
"metadata": {
|
| 10 |
+
"organism": "Mus musculus",
|
| 11 |
+
"tissue": "Spleen",
|
| 12 |
+
"platform": "Slide-seq",
|
| 13 |
+
"technology": "Slide-seqV2",
|
| 14 |
+
"fields": {
|
| 15 |
+
"organism": "Mus musculus",
|
| 16 |
+
"tissue": "Spleen",
|
| 17 |
+
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|
| 18 |
+
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|
| 19 |
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|
| 20 |
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|
| 21 |
+
"condition": null,
|
| 22 |
+
"technology": "Slide-seqV2",
|
| 23 |
+
"platform": "GPL19057",
|
| 24 |
+
"stain_type": null,
|
| 25 |
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|
| 26 |
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"publication_pmid": "38944658",
|
| 27 |
+
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|
| 28 |
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|
| 29 |
+
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|
| 30 |
+
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|
| 31 |
+
},
|
| 32 |
+
"field_sources": {
|
| 33 |
+
"organism": {
|
| 34 |
+
"source_id": "geo_meta",
|
| 35 |
+
"pointer": "/samples/GSM7458248/organism",
|
| 36 |
+
"quote": "Mus musculus"
|
| 37 |
+
},
|
| 38 |
+
"platform": {
|
| 39 |
+
"source_id": "geo_meta",
|
| 40 |
+
"pointer": "/samples/GSM7458248/platform_id",
|
| 41 |
+
"quote": "GPL19057"
|
| 42 |
+
},
|
| 43 |
+
"repository_id": {
|
| 44 |
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"source_id": "geo_meta",
|
| 45 |
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"pointer": "/samples/GSM7458248/accession",
|
| 46 |
+
"quote": "GSM7458248"
|
| 47 |
+
},
|
| 48 |
+
"tissue": {
|
| 49 |
+
"source_id": "geo_meta",
|
| 50 |
+
"pointer": "/samples/GSM7458248/characteristics/0",
|
| 51 |
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"quote": "tissue: Spleen"
|
| 52 |
+
},
|
| 53 |
+
"age": {
|
| 54 |
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"source_id": "geo_meta",
|
| 55 |
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"pointer": "/samples/GSM7458248/characteristics/3",
|
| 56 |
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"quote": "age: 6-12 weeks"
|
| 57 |
+
},
|
| 58 |
+
"publication_pmid": {
|
| 59 |
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"source_id": "geo_meta",
|
| 60 |
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"pointer": "/series/pubmed_ids",
|
| 61 |
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"quote": "38944658"
|
| 62 |
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},
|
| 63 |
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"technology": {
|
| 64 |
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"source_id": "geo_meta",
|
| 65 |
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"pointer": "/samples/GSM7458248/description",
|
| 66 |
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"quote": "Slide-seqV2"
|
| 67 |
+
},
|
| 68 |
+
"preservation_method": {
|
| 69 |
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"source_id": "geo_meta",
|
| 70 |
+
"pointer": "/samples/GSM7458248/extract_protocol",
|
| 71 |
+
"quote": "Fresh frozen"
|
| 72 |
+
}
|
| 73 |
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}
|
| 74 |
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},
|
| 75 |
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"expression": {
|
| 76 |
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"file": "spatial.h5ad",
|
| 77 |
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"sha256": "7c7a8ec8733de3d170364d2be552f552af4649d4287f603971937e08b32392cc",
|
| 78 |
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|
| 79 |
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|
| 80 |
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|
| 81 |
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|
| 82 |
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"verification": "VERIFIED"
|
| 83 |
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},
|
| 84 |
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"coordinates": {
|
| 85 |
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"obsm_key": "spatial",
|
| 86 |
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"units": "pixel",
|
| 87 |
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"um_basis": "unresolved",
|
| 88 |
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"um_per_unit": null,
|
| 89 |
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"um_basis_detail": "frame slideseq_puck_pixel; scorer physical_coordinates UNRESOLVED",
|
| 90 |
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"spatial_um": false
|
| 91 |
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},
|
| 92 |
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|
| 93 |
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|
| 94 |
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|
| 95 |
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"quality": {
|
| 96 |
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"flags": [],
|
| 97 |
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|
| 98 |
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"drop_features": [],
|
| 99 |
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"review": null
|
| 100 |
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},
|
| 101 |
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"dedup": {
|
| 102 |
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"content_group": "GSM7458248",
|
| 103 |
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"group_kind": null,
|
| 104 |
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"aliases": []
|
| 105 |
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},
|
| 106 |
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"split": "train",
|
| 107 |
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"provenance": {
|
| 108 |
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"pipeline": "sda-all",
|
| 109 |
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"source_release": "sda-all-v1.3.0",
|
| 110 |
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"files": [
|
| 111 |
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{
|
| 112 |
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"role": "sample_manifest",
|
| 113 |
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"path": "source-reference://public-storage/sda_all/release-p4-v13/GSE234253/GSM7458248/manifest.json",
|
| 114 |
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"sha256": "49c8b45987c38b16890634f2656c698965ec4e89fbee6be766d14d4c40ab834d"
|
| 115 |
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|
| 116 |
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{
|
| 117 |
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"role": "expression",
|
| 118 |
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"path": "source-reference://public-storage/sda_all/release-p4-v13/GSE234253/GSM7458248/spatial.h5ad",
|
| 119 |
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"sha256": "7c7a8ec8733de3d170364d2be552f552af4649d4287f603971937e08b32392cc"
|
| 120 |
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},
|
| 121 |
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{
|
| 122 |
+
"role": "source:expression",
|
| 123 |
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"path": "samples/GSM7458nnn/GSM7458248/GSM7458248_Puck_211217_10.matched.digital_expression.txt.gz",
|
| 124 |
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"input_root": "source-reference://public-storage/sda_all/inputs-v2/GSE234253",
|
| 125 |
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|
| 126 |
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|
| 127 |
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|
| 128 |
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{
|
| 129 |
+
"role": "source:coordinates",
|
| 130 |
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"path": "samples/GSM7458nnn/GSM7458248/GSM7458248_Puck_211217_10_barcode_xy.txt.gz",
|
| 131 |
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|
| 132 |
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| 133 |
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|
| 134 |
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|
| 135 |
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{
|
| 136 |
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"role": "source:metadata",
|
| 137 |
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"path": "_meta/geo_metadata.json",
|
| 138 |
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"input_root": "source-reference://public-storage/sda_all/inputs-v2/GSE234253",
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| 139 |
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| 140 |
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|
| 141 |
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|
| 142 |
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]
|
| 143 |
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}
|
| 144 |
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}
|
samples/GSE234253/GSM7458248/spatial.h5ad
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
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|
|
|
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|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:7c7a8ec8733de3d170364d2be552f552af4649d4287f603971937e08b32392cc
|
| 3 |
+
size 101529904
|
samples/GSE236171/GSM7574424/image.tif
ADDED
|
|
Git LFS Details
|
samples/GSE236171/GSM7574424/sample.json
ADDED
|
@@ -0,0 +1,275 @@
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|
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|
|
|
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|
|
|
|
|
|
|
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|
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|
|
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|
|
|
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|
|
|
|
|
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|
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|
|
|
|
|
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|
|
|
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|
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|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
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|
|
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|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
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|
|
|
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|
|
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|
|
|
|
|
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|
|
|
|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
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|
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|
|
|
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|
|
|
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|
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|
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|
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|
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|
|
|
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|
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|
|
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|
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|
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|
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|
|
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|
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|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
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|
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|
|
|
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|
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|
|
|
|
|
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|
|
|
|
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|
|
|
|
|
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|
|
|
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|
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|
|
|
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|
|
|
|
|
|
|
|
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|
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|
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|
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|
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|
|
|
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|
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|
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|
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|
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|
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|
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|
|
|
|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
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|
|
|
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|
|
|
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|
|
|
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|
|
|
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|
|
|
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|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
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|
|
|
|
|
|
|
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"schema": "sda-release-sample-1",
|
| 3 |
+
"release_id": "sda-unified-20261010-v3",
|
| 4 |
+
"gsm": "GSM7574424",
|
| 5 |
+
"gse": [
|
| 6 |
+
"GSE236171"
|
| 7 |
+
],
|
| 8 |
+
"published_gse": "GSE236171",
|
| 9 |
+
"metadata": {
|
| 10 |
+
"organism": "Mus musculus",
|
| 11 |
+
"tissue": "brain",
|
| 12 |
+
"platform": "ST (legacy)",
|
| 13 |
+
"technology": "Spatial Transcriptomics (legacy)",
|
| 14 |
+
"fields": {
|
| 15 |
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"organism": "Mus musculus",
|
| 16 |
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"tissue": "brain",
|
| 17 |
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"disease": null,
|
| 18 |
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"sex": null,
|
| 19 |
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"age": null,
|
| 20 |
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"donor_id": null,
|
| 21 |
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"condition": "TBI 3 dpi",
|
| 22 |
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"technology": "Spatial Transcriptomics (legacy)",
|
| 23 |
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"platform": "GPL21626",
|
| 24 |
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"stain_type": "H&E",
|
| 25 |
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"publication_doi": null,
|
| 26 |
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"publication_pmid": "38007580",
|
| 27 |
+
"repository_id": "GSM7574424"
|
| 28 |
+
},
|
| 29 |
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"field_sources": {
|
| 30 |
+
"organism": {
|
| 31 |
+
"raw_value": "Mus musculus",
|
| 32 |
+
"status": "unchanged",
|
| 33 |
+
"source": {
|
| 34 |
+
"source_path": "metadata/GSE236171_family.soft.gz",
|
| 35 |
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"source_sha256": "d6567510347d26eb6371221a1570e34e12de6d9ad7e778ca68b47218a2a5b697",
|
| 36 |
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"source_key": "!Sample_organism_ch1"
|
| 37 |
+
}
|
| 38 |
+
},
|
| 39 |
+
"tissue": {
|
| 40 |
+
"raw_value": "Brain",
|
| 41 |
+
"status": "normalized",
|
| 42 |
+
"source": {
|
| 43 |
+
"source_path": "metadata/GSE236171_family.soft.gz",
|
| 44 |
+
"source_sha256": "d6567510347d26eb6371221a1570e34e12de6d9ad7e778ca68b47218a2a5b697",
|
| 45 |
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"source_key": "!Sample_characteristics_ch1 tissue: Brain"
|
| 46 |
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}
|
| 47 |
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},
|
| 48 |
+
"disease": {
|
| 49 |
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"raw_value": null,
|
| 50 |
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"status": "missing",
|
| 51 |
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"source": null
|
| 52 |
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},
|
| 53 |
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"sex": {
|
| 54 |
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"raw_value": null,
|
| 55 |
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"status": "missing",
|
| 56 |
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"source": null
|
| 57 |
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},
|
| 58 |
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"age": {
|
| 59 |
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"raw_value": null,
|
| 60 |
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"status": "missing",
|
| 61 |
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"source": null
|
| 62 |
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},
|
| 63 |
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"donor_id": {
|
| 64 |
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"raw_value": null,
|
| 65 |
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"status": "missing",
|
| 66 |
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"source": null
|
| 67 |
+
},
|
| 68 |
+
"condition": {
|
| 69 |
+
"raw_value": "TBI 3 dpi",
|
| 70 |
+
"status": "unchanged",
|
| 71 |
+
"source": {
|
| 72 |
+
"source_path": "metadata/GSE236171_family.soft.gz",
|
| 73 |
+
"source_sha256": "d6567510347d26eb6371221a1570e34e12de6d9ad7e778ca68b47218a2a5b697",
|
| 74 |
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"source_key": "!Sample_title"
|
| 75 |
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}
|
| 76 |
+
},
|
| 77 |
+
"technology": {
|
| 78 |
+
"raw_value": "Legacy ST",
|
| 79 |
+
"status": "normalized",
|
| 80 |
+
"source": {
|
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