biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsMingxia LiIllumina NovaSeq 6000RNA-seq of coding RNAMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-10588In 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.biostudies-arrayexpressLibrary 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 instructionsSequencing - 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 and MC38 Bap1-knockout cells in vitroIn 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.2025-07-06T00:00:00Z2023-07-10T16:19:09.363Z2023-07-10T16:19:09.363ZE-MTAB-10588ERP149374E-MTAB-10610E-MTAB-10587E-MTAB-10593E-MTAB-10585E-MTAB-10584EFO_0002944EFO_0004170EFO_0005518EFO_0003738EFO_0004184