|
| Status |
Public on Jun 19, 2024 |
| Title |
HA ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cell line
cell line: B16
cell type: Melanoma
genotype: Tdg HA knockin
chip antibody: HA (CST, 3724)
|
| Growth protocol |
B16 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, cells were crosslinked with 1% formaldehyde for 10 min at room temperature and quenched with 0.125 M glycine. The final DNA length was approximately 300 bp sonicated using a COVARIS S220.
For IP, 1/10 of the supernatant was incubated with the HA (CST, 3724) or p53 (CST, 2524) antibody at 4 °C overnight and immunoprecipitation was performed with Protein G magnetic beads. Immunoprecipitated chromatin (ChIP DNA) was eluted in TE buffer. Following end-repair, A-tailing, adaptor ligation, library amplification was performed with the VAHTS Universal DNA Library Prep Kit for Illumina kit (Vazyme, ND607).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
For ChIP seq Data analysis, raw data were trimmed by Trim Galore with default settings. Then, the clean data were mapped to mouse reference genome mm10 using bowtie2 with the parameters --no-unal --no-mixed --no-discordant -X 2000. Duplicates were removed using Picard. Metaplot and heatmap were generated using deepTools. Peaks were called using MACS2 callpeak and annotated with ChIPseeker package. Those overlapped with promoters were further subject to STREME for motif discovery.
Assembly: mm10
Supplementary files format and content: bigwig files for Tdg and Trp53 enrichment
Supplementary files format and content: tab-seperated files indicating Tdg and Trp53 peaks
|
| |
|
| 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
|
| Department |
Center for Excellence in Molecular Cell Science
|
| Street address |
Yueyang Road 320
|
| City |
shanghai |
| State/province |
--- Select a state --- |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE236719 |
Synthetic essentiality of thymine DNA glycosylase in p53-deficient cancer [ChIP-seq] |
| GSE236728 |
Synthetic essentiality of thymine DNA glycosylase in p53-deficient cancer |
|
| Relations |
| BioSample |
SAMN36344200 |
| SRA |
SRX20927692 |
