|
| Status |
Public on Nov 07, 2023 |
| Title |
B16_F10 cells, PRMT1_sg1,H3K27ac, ChIP |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cell line
cell line: B16-F10
cell type: melanoma cells
genotype: PRMT1 knockout
treatment: H3K27ac(abcam, #ab4729)
|
| Growth protocol |
B16-F10 and A375 cells were maintained in DMEM medium containing 1% Penicillin/Streptomycin and 10% FBS andcultured in 37°C incubator with 5%CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The total RNA from B16-F10 or A375 cells was extracted by trizol(Vazyme) according to manufacturer’s protocol for RNA-seq. For chip-seq, B16-F10 cells were fixed by 1% formaldehyde for 10 minutes. Then, chromatin from cells lysate was digested by Micrococcal Nuclease into DNA fragments between 150-900 bp in length and released by sonication for antibody enrichment.
DNA libraries for chip-seq were estabished using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme) following the manufacturer’s guidelines. Equal amount of each library was sequencing on lIIumina NovaSeq 6000. The first sequencing data was not sufficient for data analysis, the second sequencing was performed.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The skewer(0.2.2) was used to remove low quality, splice fragments and too short sequences (less than 50bp) of raw paired-end reads and FastQC were then used to qualified the reads.
The filtered reads were mapped on mouse genome mm10 by Bowtie (2.4.3) and Picard (2.26.5) was used to further remove duplicates due to PCR amplification.
To validate the distribution of H3K27ac signaling in genome, reads were extended to 200bp and normalized(reads per kilobase per million) to genarate bigwig files using deepTools. The bigwig files were visualized using IGV.
To analyze the enhancer signal intensity changes, the bam files were used to determine enhancers using ROSE_main.py and the enhancers of nearby genes were annotated with ROSE_geneMapper.py. The intensity curves of ChIP-seq signals for H3K27ac on enhancer regions were generated by deepTools (2.0).
Assembly: mm10
Supplementary files format and content: bigWig,bam
|
| |
|
| Submission date |
Aug 07, 2023 |
| Last update date |
Nov 07, 2023 |
| Contact name |
Liyuan Zhou |
| E-mail(s) |
zhouliyaun21@mails.ucas.ac.cn
|
| Organization name |
University of Chinese Academy of Sciences
|
| Street address |
国科大杭州高等研究院
|
| City |
Hangzhou |
| State/province |
杭州市 |
| ZIP/Postal code |
310024 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE240258 |
PRMT1 inhibition activates the interferon pathway to potentiate antitumor immunity and enhance checkpoint blockade efficacy in melanoma |
|
| Relations |
| BioSample |
SAMN36873420 |
| SRA |
SRX21282172 |
