biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsMingxia LiIllumina NovaSeq 6000DNA-seqMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-10584In recent years,Bap1 has been reported to be involved in the process of tumorigenesis. Bap1 gene mutations frequently occur in tumors such as uveal melanoma, mesothelioma, and kidney cancer. In our study,we found that Bap1 deletion in MC38 colon carcinoma cells can promote anti-tumor immune response. To investigate how the genetic mutational landscape,whole exome sequencing of MC38 colon carcinoma cells and MC38 Bap1-knockout cells were performed.biostudies-arrayexpressNucleic Acid Extraction - DNA extraction were performed follow the steps below: An equal volume of saturated phenol was added to the above sample treatment solution, then centrifuged at 5000g for 10 minutes. The upper aqueous phase was taked into a new tube, and repeat the step until the water phase was clear. Then 1/10 volume of 3M sodium acetate (PH5.2) and 2.5 times volume of absolute ethanol were added and centrifuged to discard the supernatant. Last 75% ethanol was used to wash for DNA extraction.Library Construction - For library Preparation, the genomic DNA was randomly broken into fragments about 180-280 bp in length by the Covaris sonicator. Then DNA fragments were end repaired and phosphorylated, T4 DNA ligase was used to ligate the Illumina sequencing adapter to both ends of the library DNA , and size selection was captured with magnetic beads. Captured libraries were enriched by PCR Amplification.Sequencing - Samples underwent exome capture using SureSelect XT Mouse All Exon Kit (Agilent, 5190-4642) according to the manufacturer’s protocols. Whole-exome sequencing were performed on an Illumina platform for pairedend 150bp reads .Sample Collection - The cells were washed once with TBS, then centrifuged at 4000g to discard the supernatant, added 10 times the volume of lysis buffer, and water bathed for 2 hours at 55℃.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesMingxia LifalseWhole exome sequencing of MC38 colon carcinoma cells and MC38 Bap1-knockout cellsIn recent years,Bap1 has been reported to be involved in the process of tumorigenesis. Bap1 gene mutations frequently occur in tumors such as uveal melanoma, mesothelioma, and kidney cancer. In our study,we found that Bap1 deletion in MC38 colon carcinoma cells can promote anti-tumor immune response. To investigate how the genetic mutational landscape,whole exome sequencing of MC38 colon carcinoma cells and MC38 Bap1-knockout cells were performed.2025-06-30T00:00:00Z2023-07-11T02:00:31.073Z2023-07-10T15:45:37.813ZE-MTAB-10584ERP149300E-MTAB-10588E-MTAB-10610E-MTAB-10587E-MTAB-10593E-MTAB-10585EFO_0002944EFO_0004170EFO_0002693EFO_0005518EFO_0004184