|
| Status |
Public on Mar 22, 2023 |
| Title |
DMSO-Input |
| Sample type |
SRA |
| |
|
| Source name |
Human hepatoblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human hepatoblastoma
cell line: HepG2
cell type: Human hepatoblastoma
genotype: WT
treatment: DMSO
chip antibody: none (input)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed by VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND604).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
All ChIP-seq raw fastq data was cleaned by removing adaptor sequence.
Cleaned reads were aligned to human reference genome (hg19) using Bowtie2 (-q --phred33 --end-to-end --sensitive -k 1 -p 5 --fr --no-mixed --no-discordant -X 1000)
Peaks calling was finished by MACS2 (v 2.1.1) with the parameters --nomodel --keep-dup all -p 1E-10 --broad --broad-cutoff 1E-10 --extsize 147.
Assembly: hg38
Supplementary files format and content: bigWig files were generated from bam files; Scores represent the RPM value
|
| |
|
| Submission date |
May 10, 2022 |
| Last update date |
Mar 22, 2023 |
| Contact name |
Jie Yao |
| E-mail(s) |
yaojie@whu.edu.cn
|
| Phone |
18771075190
|
| Organization name |
wuhan university
|
| Street address |
wuhan hubei province
|
| City |
wuhan |
| State/province |
湖北 |
| ZIP/Postal code |
430072 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE188535 |
Isoginkgetin induces autophagic cell death in hepatocellular carcinoma |
| GSE202612 |
Isoginkgetin induces autophagic cell death in hepatocellular carcinoma [ChIP-seq 2] |
|
| Relations |
| BioSample |
SAMN28173677 |
| SRA |
SRX15220799 |
