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| Status |
Public on Jun 19, 2024 |
| Title |
B16_Trp53KO Bisulfite-Seq |
| Sample type |
SRA |
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| Source name |
cell line
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| Organism |
Mus musculus |
| Characteristics |
tissue: cell line
cell line: B16
cell type: Melanoma
genotype: Trp53 KO
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| Growth protocol |
KP and B16 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was extracted from cells using Phenol-chloroform DNA extraction protocol.
Briefly, 200-1000 ng genomic DNA was used for WGBS library construction. DNA was sonicated to ~250 bp fragments with the Diagenode Bioruptor Pico. Then DNA was subjected to end-repair, A-tailing, and ligation using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) and methylated adaptor (Roche) according to the manufacturer’s instructions. DNA was purified with VAHTS DNA Clean Beads. Subsequently, library was bisulfite modified using QIAGEN EpiTect Fast DNA Bisulfite Kit (59824) and amplified with KAPA2G Robust HotStart PCR Kits with dNTPs (Sigma-Aldrich). Library was finally subjected to 150 bp paired-end sequencing using the Illumina Novaseq6000 instrument.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
For data processing, raw data were trimmed by Trim Galore with default settings. Then, the clean data were mapped to mm10 mouse reference genome using Bismark (v0.20.1) with the parameters -X 2000 --score_min L,0,-0.6. Duplicates were removed using Picard (v2.22.4). Bigwig files were generated using bedGraphToBigWig (v4) and visualized in Integrative Genomics Viewer (IGV). CGmapTools (v0.1.2) was used for DMR calling, for which only the CpG sites with at least 3×coverage were kept. DMRs were defined by a dynamic fragment strategy: the length (the maximal distance between two adjacent common cytosines is 100 bp, and the maximal DMR size is 1000 bp), methylation level difference (at least 25% absolute methylation level difference), P value (less than 0.05) and CpG number (at least 6 CpG sites) were considered. All the annotated information was downloaded from the UCSC Genome Browser (mm10). Promoters were defined as ± 2.5 kb from the TSS (Transcription Start Site).
Assembly: mm10
Supplementary files format and content: bedgraph files for level and sequencing depth of 5mC
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| Submission date |
Jul 06, 2023 |
| Last update date |
Jun 19, 2024 |
| Contact name |
Zhenyu Shao |
| Organization name |
Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
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| Department |
Center for Excellence in Molecular Cell Science
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| Street address |
Yueyang Road 320
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| City |
shanghai |
| State/province |
--- Select a state --- |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE236722 |
Synthetic essentiality of thymine DNA glycosylase in p53-deficient cancer [WGBS] |
| GSE236728 |
Synthetic essentiality of thymine DNA glycosylase in p53-deficient cancer |
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| Relations |
| BioSample |
SAMN36344305 |
| SRA |
SRX20927811 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7574473_B16_Trp53KO.bedgraph.gz |
221.3 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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