biostudies-arrayexpressHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13803Colorectal 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).biostudies-arrayexpressSequencing - 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 adaptersMINSEQE ScoreAssays and DataProcessed DataorganisationMAGE-TAB FilesData 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).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensE-MTAB-13799William DalleywaterfalseRNAseq 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.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).2026-03-02T00:00:00Z2026-03-02T02:02:03.96Z2024-02-12T23:25:13.825ZE-MTAB-13803ERP157417E-MTAB-13799E-MTAB-13785EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184