biostudies-arrayexpressManuel MastelMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17076Mice of the genetic background VBPN, VBPNA, VBPNC were injected with tamoxifen systemically (VBPN) or with 4-OHT intra-colonically (VBPNA, VBPNC). After tumor development, the material was processed and RNA-sequencing was conducted.biostudies-arrayexpressLibrary Construction - Whole-transcriptome sequencing libraries were prepared using a modified SMART-seq2-based workflow. Reverse transcription was carried out using 1 µM template-switching oligo (IDT), 1 mM dithiothreitol (Takara Bio Clontech, #707265ML), 1 U/µl RNase inhibitor (Promega, #N2615), Maxima H Minus Reverse Transcriptase (Thermo Fisher/Life Technologies, #EP0753), and 1× Maxima H Minus Reverse Transcriptase buffer. The resulting cDNA was tagmented and further processed for sequencing library generation using the Nextera XT DNA Library Preparation Kit (Illumina, #FC-121-1030).Nucleic Acid Extraction - RNA was extracted from tumor and organoid samples using the RNeasy Mini Kit following the manufacturer’s protocol (Qiagen, #74106). RNA quantity and integrity were evaluated on an Agilent Bioanalyzer using the Agilent RNA Kit (#5067-1513).Sequencing - Next generation sequencing was performed at the German Cancer Research Center Sequencing Facility using an Illumina NovaSeq 6000 SP instrument.Sample Collection - Tumors were collected by surgical excision from the colon or small intestine of mice.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw paired-end RNA-seq reads were provided as gzipped FASTQ files. Sequencing quality was assessed using standard FASTQ quality-control metrics, and adapter sequences and low-quality bases were removed where necessary. Reads were aligned to the mouse reference genome using the splice-aware aligner STAR together with the corresponding gene annotation. Gene-level read counts were generated from the aligned reads using featureCounts. The resulting raw gene count matrix was normalized for sequencing depth and library composition using DESeq2 size-factor normalization. Normalized counts were used for quality control, sample clustering, and visualization, while differential expression analysis was performed using raw gene counts within the DESeq2 framework.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAMus musculusManuel MastelfalseRNA-seq of mouse tumors from the intestinal tract of mice with genetic background VBPN, VBPNA or VBPNCMice of the genetic background VBPN, VBPNA, VBPNC were injected with tamoxifen systemically (VBPN) or with 4-OHT intra-colonically (VBPNA, VBPNC). After tumor development, the material was processed and RNA-sequencing was conducted.2026-06-11T00:00:00Z2026-06-11T01:00:44.174Z2026-05-26T10:55:51.153ZE-MTAB-17076ERP193818EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184