|
| Status |
Public on Feb 12, 2018 |
| Title |
Brd7oe_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
embryonic kidney cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human embryonic kidney cell line transformed with adenovirus 5 DNA
tissue: kidney
genotype: BRD7 overexpression
antibody: Monoclonal ANTI-FLAG® M2 antibody (Sigma Aldrich, Cat# F1804)
cell line: HEK293
|
| Treatment protocol |
Overexpression of BRD7 gene
|
| Growth protocol |
HEK293 cells were grown in DMEM media containing 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and the FLAG fusion Brd7 protein-DNA complexes were isolated with mouse-anti-human, Monoclonal ANTI-FLAG® M2 antibody (Sigma Aldrich, Cat# F1804)
Illumina Paired-End DNA Sample Prep kit (Part#1005063) was used to perform end repair, adenylate 3' ends and to ligate adapters.The purified adapter-ligated DNA fragments were then PCR amplified and the products with length of 100bp - 300bp(including adapters) were used for library construction.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw data was generated and processed through standard Illumina pipeline.
Reads were cleaned by wiping 3' adaptor, empty and low-quality reads, and then were aligned to human genome database hg19 using SOAP 2.21.
Peak-calling using MACS 1.4.0
Genome_build: hg19
Supplementary_files_format_and_content: Wig files for each chromosome were gzipped, separately, and packed into 1 tar file of each lane. Fold enrichment represents reads on peak region against random Poisson distribution with local lambda.
|
| |
|
| Submission date |
Feb 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Xiong |
| E-mail(s) |
xiongwei@csu.edu.cn
|
| Organization name |
Central South University
|
| Department |
Cancer Research Institute
|
| Street address |
110 Xiangya Road
|
| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410078 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE65974 |
Genome-wide maps of Brd7 binding sites in control and BRD7 overexpressed cells. |
| GSE65981 |
BRD7 overexpression cells |
|
| Relations |
| BioSample |
SAMN03351750 |
| SRA |
SRX878830 |
