{"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-10588"],"description":["In order to find out which genes Bap1 regulates to affect the anti-tumor immune response in MC38 colon carcinoma cell linewe knocked out the Bap1 gene in the MC38 cell line through CRISPR-Cas9 technology, RNA was directly isolated for RNA seq and were able to investigate gene expression."],"repository":["biostudies-arrayexpress"],"sample_protocol":["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.","Sample Collection - Cell viability was detected with 0.4% trypan blue staining solution and counted with Countess II (Invitrogen) cell counter, and the cell viability was over 90%.","Nucleic Acid Extraction - RNA was extracted with TRIzol reagent (Ambion 15596-026)follow the instructions","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 and MC38 Bap1-knockout cells in vitro","description":"In order to find out which genes Bap1 regulates to affect the anti-tumor immune response in MC38 colon carcinoma cell linewe knocked out the Bap1 gene in the MC38 cell line through CRISPR-Cas9 technology, RNA was directly isolated for RNA seq and were able to investigate gene expression.","dates":{"release":"2025-07-06T00:00:00Z","modification":"2023-07-10T16:19:09.363Z","creation":"2023-07-10T16:19:09.363Z"},"accession":"E-MTAB-10588","cross_references":{"ENA":["ERP149374"],"Biostudies":["E-MTAB-10610","E-MTAB-10587","E-MTAB-10593","E-MTAB-10585","E-MTAB-10584"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}