{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Manuel Mastel"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17076"],"description":["Mice 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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Manuel Mastel"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of mouse tumors from the intestinal tract of mice with genetic background VBPN, VBPNA or VBPNC","description":"Mice 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.","dates":{"release":"2026-06-11T00:00:00Z","modification":"2026-06-11T01:00:44.174Z","creation":"2026-05-26T10:55:51.153Z"},"accession":"E-MTAB-17076","cross_references":{"ENA":["ERP193818"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}