|
| Status |
Public on Apr 04, 2020 |
| Title |
Tcp- and Dex-treated H3 ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
A549 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lung adenocarcinoma
passages: immortalized
chip antibody: Abcam (ab1791)
|
| Treatment protocol |
Cells were treated with 100nM Dex for 2 hours for ChIP-seq and for 24 hours for microarry. For TCP cells were treated with 150 uM for 24 hours.
|
| Growth protocol |
A549 cells were cultured in DMEM supplemented with 20% FBS for maintenance. For experiments cells were to being grown in media supplemented with charcoal striped serum for 16-24 hours to hormone deplete prior to ethanol or Dex treatment.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v1.2.1.1 with parameters -m 1 -p 10
mapped data were smoothed with spp (http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.html)
ChIP signal was normalizated by excluting Input signal
For histone modification ChIP-Seq, ChIP signal was further normalized with H3 signal.
GR peaks were identified using the Model based Analysis of ChIP-Seq (MACS v1.4) package regions of significant enrichment were determined against sample input at p < 1E-5.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using KentUtils
|
| |
|
| Submission date |
Dec 27, 2017 |
| Last update date |
Apr 04, 2020 |
| Contact name |
Feizhen Wu |
| E-mail(s) |
wufz@fudan.edu.cn
|
| Phone |
86-21-54237821
|
| Organization name |
Fudan Univ, Shanghai, China
|
| Department |
Institutes of Biomedical Sciences
|
| Lab |
Epigenetics lab
|
| Street address |
Dongan Road 131, Rm 511 Mingdao Building
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE108588 |
GR and LSD1/KDM1A-targeted gene activation requires selective H3K4me2 demethylation at enhancers |
|
| Relations |
| BioSample |
SAMN08271872 |
| SRA |
SRX3517829 |
