|
| Status |
Public on Jun 25, 2023 |
| Title |
si_αKG_input |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cell line
cell line: SK-Hep1 cells
chip antibody: none
treatment: sime2+αKG
|
| Growth protocol |
DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP–seq analysis, briefly, reads from ChIP-seq data for polymerase II antibodies were aligned to the hg19 genome using bowtie2 (v2.3.5.1). Peaks were called using MACS2(v2.2.6) for polymerase II. Different peaks were generated using bdgdiff. The ChIP-seq pileup heatmaps were generated using plotHeatmap. GO/KEGG enrichment analysis was performed using the R package clusterProfiler(v4.0). Visualization was realized by IGV(v2.8.9). Motifs were found to analyze the DNA sequence of poly II protein binding through motifmatchr(v 1.20.0)[1].
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads from ChIP-seq data for polymerase II antibodies were aligned to the hg19 genome using bowtie2 (v2.3.5.1).
Peaks were called using MACS2(v2.2.6).
Different peaks were generated using bdgdiff.
Motifs were found to analyze the DNA sequence of poly II protein binding through motifmatchr(v 1.20.0).
Visualization was realized by IGV(v2.8.9).
Assembly: hg19
Supplementary files format and content: bigWig,
Supplementary files format and content: narrowPeak
|
| |
|
| Submission date |
Dec 24, 2022 |
| Last update date |
Jun 25, 2023 |
| Contact name |
zhenxi zhang |
| E-mail(s) |
liwei@ibms.pumc.edu.cn
|
| Organization name |
PUMC
|
| Street address |
Dongdan Santiao No. 5
|
| City |
beijing |
| ZIP/Postal code |
10005 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE221723 |
αKG-driven RNA polymerase II transcription of cyclin D1 licenses malic enzyme 2 to promote cell cycle progression |
|
| Relations |
| BioSample |
SAMN32398596 |
| SRA |
SRX18847377 |
