{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Kohei Kumegawa"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16244"],"description":["RNA-seq of colorectal cancer PDOs treated with AMG510 and control."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic 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)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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)."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Kohei Kumegawa"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of PDOs treated with AMG510","description":"RNA-seq of colorectal cancer PDOs treated with AMG510 and control.","dates":{"release":"2025-11-22T00:00:00Z","modification":"2025-11-22T11:14:30.44Z","creation":"2025-11-21T10:17:46.366Z"},"accession":"E-MTAB-16244","cross_references":{"ENA":["ERP185461"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}