{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14227"],"description":["3 Cancer associated fibroblasts (CAFs) and one corresponding Normal associated fibroblasts (NAFs) were isolated from human treatment-naive CRC patients, propagated under culture conditions and potential heterogeneity was assesed using single cell RNA-sequencing."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Cultivated fibroblasts were trypsinized, counted and loaded onto a 10x Chromium Next GEM Chip following the Chromium Next GEM Single Cell 3´user guide (10x Genomics).","Growth Protocol - Fibroblasts were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum (FCS, Sigma-Aldrich, #S0615) 1% L-Glutamin (Thermo Fisher, #25030-024) and 1% Penicillin/Streptomycin (Gibco, #15140-122) at 37°C, with 8.5% CO2 and 95% humidity.","Library Construction - Amplified cDNA was used for 3’ RNA-seq library generation, RNA-seq libraries were prepared following the manufacturer’s user guide (10x Genomics).","Sample Collection - 3 human CAF lines from human CRC and one matching NAFs from uninvolved healthy colon were isolated as described in Naschberger et al, JoVE2018 and Schellerer et al, Oncol Rep 2014 and propagated in culture for up to three passages prior to scRNA-sequencing.","Sequencing - Each single-cell RNA-seq library was sequenced on a NovaSeq 6000 (Illumina)"],"figure_sub":["MINSEQE Score","Assays and Data","Processed Data","organisation","MAGE-TAB Files"],"data_protocol":["Data Transformation - The individual samples were combined using the aggr function of cellranger version 6.0.0."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"additional_accession":["ERP161674"],"pubmed_authors":["Elisabeth Naschberger"]},"is_claimable":false,"name":"ScRNA-seq analysis of cultured primary CAFs (n=3) and NAFs (n=1)","description":"3 Cancer associated fibroblasts (CAFs) and one corresponding Normal associated fibroblasts (NAFs) were isolated from human treatment-naive CRC patients, propagated under culture conditions and potential heterogeneity was assesed using single cell RNA-sequencing.","dates":{"release":"2025-12-30T00:00:00Z","modification":"2026-05-27T15:08:23.805Z","creation":"2024-07-04T11:30:08.876Z"},"accession":"E-MTAB-14227","cross_references":{"ENA":["ERP161674"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}