biostudies-arrayexpressKohei KumegawaHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16244RNA-seq of colorectal cancer PDOs treated with AMG510 and control.biostudies-arrayexpressNucleic Acid Extraction - Total RNA was extracted using an RNeasy mini kit (Qiagen) and quantified using 2100 Expert Bioanalyzer software (Agilent).Sequencing - Sequencing of 150 bp paired-end reads was performed using the Illumina NovaSeq6000 system (Illumina).Sample Collection - Patient derived organoids were treated with 100 nM AMG510 for 24 h.Library Construction - RNA-seq analysis was outsourced to Macrogen Japan Corp. (Tokyo, Japan). Following the manufacturer’s instructions, total RNA with an RIN>7 was used to generate a barcode-labeled library using an Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Salmon was used for quantifying transcript abundance from RNA-seq reads. Tximport package was used to import transcript-level abundances and summarizes abundances, counts, and transcript length s to gene-level matrix (https://github.com/thelovelab/tximport). Gene enrichment analysis was performed using the fgsea package with nperm=1000 97 (https://bioconductor.org/packages/release/bioc/html/fgsea.html). Tidy format gene sets were retrieved using msigdbr package (https://cran.r-project.org/web/packages/msigdbr/vignettes/msigdbr-intro.html), and the rnk file was generated using wilcoxauc function in presto package (https://rdrr.io/github/immunogenomics/presto/man/wilcoxauc.html).UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensKohei KumegawafalseRNA-seq of PDOs treated with AMG510RNA-seq of colorectal cancer PDOs treated with AMG510 and control.2025-11-22T00:00:00Z2025-11-22T11:14:30.44Z2025-11-21T10:17:46.366ZE-MTAB-16244ERP185461EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184