{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Mingxia Li"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-10587"],"description":["To assess the role of Bap1 genes in MC38 colon carcinoma cell linewe knocked out the Bap1 gene in the MC38 cell line through CRISPR-Cas9 technology, MC38-Bap1-Wildtype and MC38-Bap1-Knockout tumor cells expressing BFP fluorescent protein were injected into Rag2-deficient mice subcutaneously. On the 10th day of tumor growth, BFP positive tumor cells were isolated and sorted by flow Cytometer. Bulk RNA-seq was performed on MC38-Bap1-Wildtype and MC38-Bap1-Knockout tumor cells for different gene signatures."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - MC38-Bap1-Wildtype and MC38-Bap1-Knockout tumor cells expressing BFP fluorescent protein were injected into Rag2-/- mice subcutaneously. On the 10th day of tumor growth, the tumor cell was dissociated into single cells with Tumor Dissociation Kit (Miltenyi,130-096-730), and red blood cells were removed with ACK lysis buffer (Gibco,492-01). The dead cells in tumor cells were removed with Dead Cell Removal kit (Miltenyi,130-090-101), Then the tumor cells were resuspended with Facs buffer and BFP positive tumor cells were sorted by flow cytometry.","Nucleic Acid Extraction - Then RNA was extracted with TRIzol reagent (Ambion 15596-026)follow the instructions.","Library Construction - RNA was breaken into smart fragments with fragment buffer, and cDNAs were synthesized using the RNA fragments as templates, after which NEBNext Adaptor with hairpin loop structure were ligated ,and 3 µl USER Enzyme (NEB, USA) was used with purified adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.","Sequencing - Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations, the library preparations were sequenced on an Illumina Novaseq platform."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Mingxia Li"],"additional_accession":[]},"is_claimable":false,"name":"Bulk RNA-Seq analysis of  MC38 colon carcinoma cells isolated from Rag2-deficient mice","description":"To assess the role of Bap1 genes in MC38 colon carcinoma cell linewe knocked out the Bap1 gene in the MC38 cell line through CRISPR-Cas9 technology, MC38-Bap1-Wildtype and MC38-Bap1-Knockout tumor cells expressing BFP fluorescent protein were injected into Rag2-deficient mice subcutaneously. On the 10th day of tumor growth, BFP positive tumor cells were isolated and sorted by flow Cytometer. Bulk RNA-seq was performed on MC38-Bap1-Wildtype and MC38-Bap1-Knockout tumor cells for different gene signatures.","dates":{"release":"2025-07-06T00:00:00Z","modification":"2023-07-10T16:17:00.163Z","creation":"2023-07-10T16:17:00.163Z"},"accession":"E-MTAB-10587","cross_references":{"ENA":["ERP149372"],"Biostudies":["E-MTAB-10588","E-MTAB-10610","E-MTAB-10593","E-MTAB-10585","E-MTAB-10584"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}