data ArrayExpress/E-MTAB-11981

.gitattributes

@@ -1256,3 +1256,4 @@ data/ArrayExpress/E-MTAB-16918/raw_count_matrix.txt filter=lfs diff=lfs merge=lf
 data/ArrayExpress/E-MTAB-13655/CRC08_LM_VISIUM.tif filter=lfs diff=lfs merge=lfs -text
 data/ArrayExpress/E-MTAB-13655/CRC09_LM_VISIUM.tif filter=lfs diff=lfs merge=lfs -text
 data/ArrayExpress/E-MTAB-13655/CRC11_LM_VISIUM.tif filter=lfs diff=lfs merge=lfs -text
+data/ArrayExpress/E-MTAB-11981/micromets_counts_matrix.txt filter=lfs diff=lfs merge=lfs -text

data/ArrayExpress/E-MTAB-11981/E-MTAB-11981.idf.txt

@@ -0,0 +1,70 @@
+MAGE-TAB Version	1.1
+Investigation Title	CRC micrometastasis generated by AKP MTOs resolved by single cell RNAseq
+
+Experimental Design	cell type comparison design
+Experimental Design Term Source REF	EFO
+Experimental Design Term Accession Number	EFO:0001745
+
+Experimental Factor Name	single cell identifier
+Experimental Factor Type	single cell identifier
+Experimental Factor Term Source REF	EFO
+Experimental Factor Term Accession Number	EFO_0010197
+
+Person Last Name	Batlle	Mateo	Attolini
+Person First Name	Eduard	Lidia	Camille Stephan-Otto
+Person Mid Initials			
+Person Email	eduard.batlle@irbbarcelona.org	lidia.mateo@irbbarcelona.org	camille.stephan@irbbarcelona.org
+Person Phone
+Person Fax
+Person Affiliation	IRB Barcelona / BIST	IRB Barcelona / BIST	IRB Barcelona / BIST
+Person Address	C. Baldiri Reixac 10, Barcelona, 08028, Spain	C. Baldiri Reixac 10, Barcelona, 08028, Spain	C. Baldiri Reixac 10, Barcelona, 08028, Spain
+Person Roles		submitter
+Person Roles Term Source REF
+Person Roles Term Accession Number
+
+Quality Control Type
+Quality Control Term Source REF
+Quality Control Term Accession Number
+
+Replicate Type
+Replicate Term Source REF
+Replicate Term Accession Number
+
+Normalization Type
+Normalization Term Source REF
+Normalization Term Accession Number
+
+Date of Experiment	2022-04-26
+Public Release Date	2022-11-18
+
+PubMed ID	36352230
+Publication DOI	10.1038/s41586-022-05402-9 
+Publication Author List	Cañellas-Socias A, Cortina C, Hernando-Momblona X, Palomo-Ponce S, Mulholland EJ, Turon G, Mateo L, Conti S, Roman O, Sevillano M, Slebe F, Stork D, Caballé-Mestres A, Berenguer-Llergo A, Álvarez-Varela A, Fenderico N, Novellasdemunt L, Jiménez-Gracia L, Sipka T, Bardia L, Lorden P, Colombelli J, Heyn H, Trepat X, Tejpar S, Sancho E, Tauriello DVF, Leedham S, Attolini CS, Batlle E.
+Publication Title	Metastatic recurrence in colorectal cancer arises from residual EMP1+ cells.
+Publication Status
+Publication Status Term Source REF
+Publication Status Term Accession Number
+
+Experiment Description	Longitudinal single cell RNA-expression analysis of tumor cells along metastatic relapse. AKP mouse tumor organoids (MTOs) were implanted in the caecum and left to metastasize into the liver. Livers were collected at different timepoints post-injection and GFP+ CD45- cells were sorted in 96-well smart-seq plates. Tumor cells were collected from liver with colorectal cancer (CRC) micrometastatic stage disease.
+
+Protocol Name	P-MTAB-125238	P-MTAB-125239	P-MTAB-125236	P-MTAB-125237	P-MTAB-125235	P-MTAB-125240
+Protocol Type	nucleic acid library construction protocol	nucleic acid sequencing protocol	sample collection protocol	nucleic acid extraction protocol	treatment protocol	high throughput sequence alignment protocol
+Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO
+Protocol Term Accession Number	EFO_0004184	EFO_0004170	EFO_0005518	EFO_0002944		EFO_0004917
+Protocol Description	Full-length single-cell RNA-seq libraries were prepared using the SMART-Seq v5 Ultra Low Input RNA Kit for Sequencing (Takara Bio). All reactions were downscaled to one quarter of the original protocol and performed following thermal cycling manufacturer’s conditions.	Pooled sequencing of Nextera libraries was carried out using a HiSeq4000 (Illumina) to an average sequencing depth of 0.5 million reads per cell. Sequencing was carried out as paired-end (PE75) reads with library indexes corresponding to cell barcodes.	For isolation of low numbers of tumour cells from mice without visible metastases, whole livers were thoroughly minced with razor blades. After an initial 30-minute digestion with 200 U/ml collagenase IV, samples were filtered through 100 μm meshes. Although most cells flowed through, a small fraction of the samples - highly enriched for tumour cells - was retained in the filter (Supplementary Figure 5c). Filters were then laid into a 6-well plate and covered with HBSS containing collagenase IV, Dispase II and DNase I. After re-digestion in a water bath for 30 minutes al 37 °C, most cells now seeped through the filters. Single-cell preparations were first blocked with anti-CD16/32 (clone 93; eBioscience) and then stained with APC anti-Epcam (118214; Biolegend) and BV605 anti-CD45 (103155, Biolegend) antibodies. Finally, cells were resuspended in HBSS with 0.5% FBS and DAPI (Sigma Aldrich).	Freshly harvested GFP+ single cells were sorted into 96-well plates containing 2.5 µl of the Reaction buffer (1x Lysis Buffer, RNase Inhibitor 1U/µl).	MTOs were established from primary tumors arising in genetically engineered mouse models bearing mutations in Apc, Kras, and p53 (AKP mouse model, Apc fl/fl, KrasG12D and Trp53 fl/fl). We analyzed by scRNAseq micro-dissected liver metastases generated by implantation of AKP MTOs in the caecum of c57BL/6 mice. The PGK is driven by a constitutive PGK promoter and therefore expressed in all tumor cells. GFP was used thus to separate tumor cells from the rest of healthy cells.	The raw output of Smart-seq2 single-cell RNA sequencing were analyzed with the zUMIs pipeline.
+Protocol Parameters
+Protocol Hardware		Illumina HiSeq 4000
+Protocol Software
+Protocol Contact
+
+Term Source Name	EFO	ArrayExpress
+Term Source File	http://www.ebi.ac.uk/efo/	http://www.ebi.ac.uk/arrayexpress/
+Term Source Version	http://www.ebi.ac.uk/efo/
+
+SDRF File	E-MTAB-11981.sdrf.txt
+Comment [Submitted Name]	CRC micrometastasis generated by AKP MTOs resolved by single cell RNAseq
+Comment [TemplateType]	Animal - Single-cell sequencing
+Comment [SecondaryAccession]	ERP140462
+Comment [SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/ERR10109828-ERR10110511
+Comment [AEExperimentType]	RNA-seq of coding RNA from single cells
+Comment[ArrayExpressAccession]	E-MTAB-11981

data/ArrayExpress/E-MTAB-11981/micromets_counts_matrix.txt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f581742d9cf829d0b631ecc7bc8314f1ea4218747ce4b1cdfeeadc1a69403d1d
+size 33033207