|
| Status |
Public on Oct 15, 2014 |
| Title |
p-KDM3A_HS(-) |
| Sample type |
SRA |
| |
|
| Source name |
Jurkat cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Jurkat
cell type: Acute T Cell Leukemia T lymphocyte
treatment: 37℃ 1h
chip antibody: p-KDM3A
antibody manufacturer: customized from Beijing B&M Biotech (Beijing, China)
|
| Treatment protocol |
1×10^7 Jurkat cells were treated with or without Heat Shock (42℃ water bath for 1 hour)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with KDM3A or p-KDM3A antibody.The sonicated DNA fragments were purified as Input control.
The DNA fragments were end-repaired, adenylated,ligated to adaptors and PCR-amplified for 18 cycles. The PCR products corresponding to bp 250-450 were gel-purified, quantified and stored at -80°C until use for sequencing
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Illumina GAIIx system for 80-nt single-end sequencing
ChIP-seq reads were aligned to the hg19 genome assembly using BWA algorithm with the default settings
SICER V1.1 for peak calling(results were uncorrelated with our data in GEO)
Input control of the HS(-) and HS(+) were added into "input_pool_clean"
Genome_build: hg19
Supplementary_files_format_and_content: .wig files which show our aligned reads in line graphics
|
| |
|
| Submission date |
Oct 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ye Zhang |
| E-mail(s) |
yezhang@pumc.edu.cn
|
| Phone |
861069155939
|
| Organization name |
Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College
|
| Street address |
5 Dongdan Santiao
|
| City |
Beijing |
| State/province |
Not applicable |
| ZIP/Postal code |
100005 |
| Country |
China |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE62309 |
Specific phosphorylation of histone demethylase KDM3A determines target gene expression in response to heat shock |
|
| Relations |
| BioSample |
SAMN03107085 |
| SRA |
SRX732510 |
