biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsMingxia LiIllumina NovaSeq 6000RNA-seq of coding RNAMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-10587To 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.biostudies-arrayexpressSample 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.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesMingxia LifalseBulk RNA-Seq analysis of MC38 colon carcinoma cells isolated from Rag2-deficient miceTo 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.2025-07-06T00:00:00Z2023-07-10T16:17:00.163Z2023-07-10T16:17:00.163ZE-MTAB-10587ERP149372E-MTAB-10588E-MTAB-10610E-MTAB-10593E-MTAB-10585E-MTAB-10584EFO_0002944EFO_0004170EFO_0005518EFO_0003738EFO_0004184