Correction 2026-11-11: 12 samples replaced by re-converted versions (GSE205707 x6, GSE275125 x4, GSM8933093, GSM5643203); 6 samples withdrawn (GSE298115 GSM9008651/GSM9008653, GSE244723 x4) - sample files

samples/GSE244723/GSM7825036/sample.json

@@ -1,279 +0,0 @@
-{
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-  "gse": [
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-  "published_gse": "GSE244723",
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-    "tissue": "embryonic heart",
-    "platform": "ST (legacy)",
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-      "age": "CS16",
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-      "technology": "Spatial Transcriptomics",
-      "platform": "GPL24676",
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-      "publication_pmid": "38011284",
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samples/GSE244723/GSM7825037/sample.json

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-{
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-  "gsm": "GSM7825037",
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+        "path": "_meta/geo_metadata.json",
+        "input_root": "source-reference://public-storage/sda_work/sda_all_root/inputs-v2/GSE294965",
+        "members": null,
+        "sha256": "d0fb0c021fa8a2de0172d82d9e3a17b46f9629a4f41aa1fbdd161a0208478c69"
       },
       {
-        "role": "hesrt_metadata.normalized.json",
-        "path": "source-reference://public-storage/sda_work/hesrt-v1.3-expanded/GSE294965/GSM8933093/metadata.normalized.json",
-        "sha256": "d5acfd77304a1850995855eb102dc0e8450248e2b3e69c07e58b2b66464c00e9"
+        "role": "modality_manifest",
+        "path": "source-reference://public-storage/sda_work/sda_all_root/release/_modality/GSE294965/GSM8933093/modality_manifest.json",
+        "sha256": "131d41a2ff6ec998af521f30cb6448559883a94caea26704e825a91b4dd68509"
       },
       {
-        "role": "hesrt_manifest.json",
-        "path": "source-reference://public-storage/sda_work/hesrt-v1.3-expanded/GSE294965/GSM8933093/manifest.json",
-        "sha256": "25a4be30d1905224395ef9767571e32f6ae86fe48f81ad92197cacb0f2cf2f9e"
+        "role": "modality_acceptance",
+        "path": "source-reference://public-storage/sda_work/sda_all_root/release/_modality/GSE294965/GSM8933093/acceptance.json",
+        "sha256": "b63929a30199b144bdcb143ba0a65a1faf2af18dd3d0f236ac2be3ab1264c4b5"
       }
     ]
   }

samples/GSE294965/GSM8933093/spatial.h5ad

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:49731c5977d2c6fe5fffea88906cb9db24c1c0b47405d9d15871c7ae58130c90
-size 130374312
+oid sha256:2ed265ff4ca61397f5967c5a67ec598ad67cf4952c5f28593d9d961534d42f01
+size 120213608

starter/starter.json

@@ -2,7 +2,7 @@
  "schema": "sda-db-starter-1",
  "release": "v1.0.0-20261025",
  "release_commit": "999566bf516169ba8c9cf1ad9e5a2b722bb8a97a",
- "description": "88 samples of the paper release, chosen to represent its platforms, organs and species; files are byte-identical to the gated dataset and need no login.",
+ "description": "86 samples of the paper release, chosen to represent its platforms, organs and species; files are byte-identical to the gated dataset and need no login.",
  "selection": "train/val split only; at most 2 samples per study; verified counts, no QC flags; images only when registration verified and review PASS (or HESRT human review); at most 200 MB per sample",
  "gsms": [
   "GSM5907084",
@@ -26,7 +26,6 @@
   "GSM9331988",
   "GSM4284327",
   "GSM7574424",
-  "GSM7825036",
   "GSM9232562",
   "GSM8284978",
   "GSM5841553",
@@ -39,7 +38,6 @@
   "GSM9556004",
   "GSM8563706",
   "GSM4284320",
-  "GSM7825037",
   "GSM4459917",
   "GSM9525786",
   "GSM9448988",
@@ -347,18 +345,6 @@
    "sha256": "1db1fc1b0abab948b01b78577492b2c94f39c55fd98c03fad39065492abac762",
    "bytes": 4804758
   },
-  "samples/GSE244723/GSM7825036/sample.json": {
-   "sha256": "2a853e795146a226fc6e042d360704ea237d16254b727def86740b524340aadf",
-   "bytes": 9693
-  },
-  "samples/GSE244723/GSM7825036/spatial.h5ad": {
-   "sha256": "6696e53908e1b77097bb6886753f1f8d8a1ebb3c182af90ba457c68407814d66",
-   "bytes": 9086206
-  },
-  "samples/GSE244723/GSM7825036/image.tif": {
-   "sha256": "bc868dd62027415de8b77fe9ac9f9d4bc6974ea38c149d7ba2a04984908d7712",
-   "bytes": 5587892
-  },
   "samples/GSE297058/GSM9232562/sample.json": {
    "sha256": "5c80563321cec1875d639db6bb27918c7e115094b1e02d85d3236f777ec9eb06",
    "bytes": 7675
@@ -503,18 +489,6 @@
    "sha256": "1f6b7aacb4d98855ab6a623d8f6f9f9b975cb4a4e626611595bee3f0c03a4999",
    "bytes": 126443572
   },
-  "samples/GSE244723/GSM7825037/sample.json": {
-   "sha256": "b132f3f471f764a7f300dd2ee538acba4da32de4b23f27fbe1ab946264472256",
-   "bytes": 9695
-  },
-  "samples/GSE244723/GSM7825037/spatial.h5ad": {
-   "sha256": "f4ecdd3862087c30e2b3f7d12a51c1881feccfb11877c56e5e38fdcfce29833a",
-   "bytes": 9265414
-  },
-  "samples/GSE244723/GSM7825037/image.tif": {
-   "sha256": "fccb624e617ce44ee73d7ce7a15682b3d7bbfd68c11e5357fa344e61e2545a2c",
-   "bytes": 5674237
-  },
   "samples/GSE147747/GSM4459917/sample.json": {
    "sha256": "156ea0d2b5a886c418c58d48db8cc672eb260e4e57828bb46dc5a4da366ad0bd",
    "bytes": 9969
@@ -636,16 +610,16 @@
    "bytes": 23801661
   },
   "samples/GSE294965/GSM8933093/sample.json": {
-   "sha256": "df1dd9d835caf8f418e1c49ebb9fa307d224ab33da1969d1aaa3b3ff7f6cbb23",
-   "bytes": 9114
+   "sha256": "8ea9b4301c56241fe762e4a8f409a8447173b29c93d1e2428d11e9bf7b5f35a0",
+   "bytes": 10062
   },
   "samples/GSE294965/GSM8933093/spatial.h5ad": {
-   "sha256": "49731c5977d2c6fe5fffea88906cb9db24c1c0b47405d9d15871c7ae58130c90",
-   "bytes": 130374312
+   "sha256": "2ed265ff4ca61397f5967c5a67ec598ad67cf4952c5f28593d9d961534d42f01",
+   "bytes": 120213608
   },
   "samples/GSE294965/GSM8933093/image.tif": {
-   "sha256": "01ef1cd43a0695094645e4d298f18bc26bef173f2a5192809450ad32cc156c26",
-   "bytes": 35536764
+   "sha256": "93f170f7d2fb6d2e66e30487acea741b1810b00934c98f800a88aac7fb3c1326",
+   "bytes": 687006734
   },
   "samples/GSE328700/GSM9687902/sample.json": {
    "sha256": "6c30ffb0d072cef320093afb31ab2db9a59ad72552db87e54155c1fdc8381496",
@@ -1058,6 +1032,17 @@
     "GSM6963121"
    ],
    "reason": "swap 5 low-resolution Visium H&E (4.7-7.3 um/px) for 5 cell-resolution Visium H&E (0.73-0.93 um/px)"
+  },
+  {
+   "date": "2026-11-11",
+   "removed": [
+    "GSM7825036",
+    "GSM7825037"
+   ],
+   "corrected": [
+    "GSM8933093"
+   ],
+   "reason": "removed: withdrawn from the dataset (deposit has no gene names); corrected: re-converted from the deposit, files equal the gated dataset after the 2026-11-11 correction, not the paper tag"
   }
  ]
 }