|
| Status |
Public on Oct 03, 2024 |
| Title |
sgUSP22_H2BK120ub_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
HepG2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: human hepatocellular carcinoma cell
antibody: H2BK120ub
treatment: HepG2 cells were infected with lentiviruses expressing cas9 and USP22 sgRNA to establish USP22 knockout cells, followed by treatment with Sorafenib for 24 hours.
|
| Treatment protocol |
HepG2 cells were infected with lentiviruses expressing Cas9 together with control sgRNA or USP22 sgRNA to establish control and USP22 knockout HepG2 cells, followed by treatment with Sorafenib for 24 hours.
|
| Growth protocol |
HepG2 cells were cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum at 37℃ in a humidified atmosphere with 5% CO2. Drosophila Schneider 2 cells (S2 cells) were cultured in SFX-Insect medium supplemented with 10% fetal bovine serum at 27℃.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
HepG2 cells were cross-linked with 1% formaldehyde for 10 minutes and quenched with 0.125 M glycine. Cells were then resuspended in SDS buffer. The resulting cell pellets were resuspended in ice-cold immunoprecipitation (IP) buffer, and subjected to sonication. Drosophila Schneider 2 cells (S2 cells) were prepared and processed in the same manner. Depending on the DNA concentration of each sample, chromatin from HepG2 cells was mixed with S2 cell chromatin at a ratio of 5:1. Subsequently, the chromatin was incubated overnight at 4°C with H2BK120ub antibodies. Protein A/G beads were then added at 4℃ for 4 hours. After thorough washes, samples were incubated in de-cross-linking buffer at 65°C for 6 hours, and DNA was extracted.
The DNA fragments were repaired and dA-tailed, after which they were ligated to sequencing adaptors. The final DNA library was obtained by size selection and PCR amplification.
Spike-in ChIP-seq
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were aligned to the human genome (UCSC hg38) and Drosophila melanogaster genome (UCSC dm3) using Bowtie2 (v2.4.5).
Dupulicates were removed by Sambamba (v1.0).
Mapped reads with high confidence were sorted, indexed, and transformed to bam format using SAMtools (v1.6).
Spike-in normalized bigwig files were generated using the deepTools (v3.5.4)
Peak was called by MACS2 (v2.2.9.1).
Assembly: hg38 and dm3
Supplementary files format and content: bigWig files
|
| |
|
| Submission date |
Oct 03, 2024 |
| Last update date |
Oct 03, 2024 |
| Contact name |
Bei Lan |
| E-mail(s) |
lanbei@tmu.edu.cn
|
| Organization name |
Tianjin Medical University
|
| Street address |
No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China
|
| City |
Tianjin |
| State/province |
天津Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE278685 |
USP22 promotes the proliferation and inhibits Sorafenib-induced ferroptosis of hepatocellular carcinoma cells through its deubiquitinase activity [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN44047940 |
| SRA |
SRX26268299 |
