{"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-17082"],"description":["Colon from mouse with genetic background VBPN was extracted and wild-type organoid culture was created. Afterwards, the organoids were treated with 4-OHT and cancerous organoids with BPN mutations were created. Subsequently, 2 Apc and 2 Rnf43 cell lines were created via CRIPSR knock-out. Additionally, Ctnnb1 gene was edited via CRISPR base editing and the edit S33F was created. Finally, also non-nargeting conrotl cell lines for conventional knock-out (NT) and base editing (NTBE) were generated. From these cell lines RNA-seq was performed."],"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).","Sample Collection - Organoids were grown in cell culture dish in BME gel and growth medium. Organoids with BME gel and growth medium were taken from the culture dish and centrifuged. Supernatant was aspirated and organoids were transfered to a separate tube for nucleic acid extraction.","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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - 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.","Data Transformation - Raw gene-level counts were normalized using DESeq2. Genes with low total counts were filtered, and sample-specific size factors were estimated using DESeq2’s median-of-ratios method to correct for library size and composition differences. Normalized counts were obtained by dividing raw counts by these size factors."],"omics_type":["Metabolomics","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 cancerous organoid cell lines from the colon of VBPN mice and genome engineered with CRISPR","description":"Colon from mouse with genetic background VBPN was extracted and wild-type organoid culture was created. Afterwards, the organoids were treated with 4-OHT and cancerous organoids with BPN mutations were created. Subsequently, 2 Apc and 2 Rnf43 cell lines were created via CRIPSR knock-out. Additionally, Ctnnb1 gene was edited via CRISPR base editing and the edit S33F was created. Finally, also non-nargeting conrotl cell lines for conventional knock-out (NT) and base editing (NTBE) were generated. From these cell lines RNA-seq was performed.","dates":{"release":"2026-06-26T00:00:00Z","modification":"2026-06-26T01:00:44.948Z","creation":"2026-05-26T13:04:12.4Z"},"accession":"E-MTAB-17082","cross_references":{"ENA":["ERP193968"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}