{"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-13803"],"description":["Colorectal cancer (CRC) cell lines (LS1034 and HCT116, representing different genetic backgrounds of CRC) were co-cultured with iPSC-derived intestinal stroma (described in other protocols). Control conditions were each cell line cultured separately. A dose response for HCT116 on stroma was tested using a varying seeding density. After culture, cells were separated using MACS based on EpCAM expression (EpCAM+: CRC cell line / EpCAM-: stroma) and then measured for reciprocal changes in gene expression by RNAseq (i.e. CRC effect on stromal expression and vice verse on cell lines)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Illumina NovaSeq 6000 Sequencing System, 150bp, paired-end. Performed by Novogene Ltd.","Sample Collection - Cells were washed with PBS 1x and then dissociated with TrypLE Select. Cells were labelled with anti-EpCAM magnetic beads and separated using a MACS column into EpCAM+ and EpCAM- populations. Cells were lysed with the lysis buffer (see extraction kit details)","Nucleic Acid Extraction - RNA was extracted using GenElute™ Mammalian Total RNA Miniprep Kit following manufacturer’s instructions (Cat no. RTN70 - Sigma Aldrich)","Library Construction - PolyA enrichment of mRNA, RT first-strand cDNA library with ligation of sequencing adapters"],"figure_sub":["MINSEQE Score","Assays and Data","Processed Data","organisation","MAGE-TAB Files"],"data_protocol":["Data Transformation - fastq files aligned with the reference genome to create BAM files (STARalign v2.6.1d). Raw transcript counts quantified using FeatureCounts (v1.5.0-p3)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"additional_accession":["E-MTAB-13799"],"pubmed_authors":["William Dalleywater"]},"is_claimable":false,"name":"RNAseq of colorectal cancer cell lines (LS1034/HCT116) cultured with iPSC-derived intestinal stroma, separated by EpCAM expression (MACS). Monocultures of each cell line and co-cultures with LS1034 or HCT116 with stroma.","description":"Colorectal cancer (CRC) cell lines (LS1034 and HCT116, representing different genetic backgrounds of CRC) were co-cultured with iPSC-derived intestinal stroma (described in other protocols). Control conditions were each cell line cultured separately. A dose response for HCT116 on stroma was tested using a varying seeding density. After culture, cells were separated using MACS based on EpCAM expression (EpCAM+: CRC cell line / EpCAM-: stroma) and then measured for reciprocal changes in gene expression by RNAseq (i.e. CRC effect on stromal expression and vice verse on cell lines).","dates":{"release":"2026-03-02T00:00:00Z","modification":"2026-03-02T02:02:03.96Z","creation":"2024-02-12T23:25:13.825Z"},"accession":"E-MTAB-13803","cross_references":{"ENA":["ERP157417"],"Biostudies":["E-MTAB-13799","E-MTAB-13785"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}