|
| Status |
Public on Aug 22, 2017 |
| Title |
786-O NFkb ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
ccRCC cell line
|
| Organism |
Homo sapiens |
| Characteristics |
transcription factor: NFkB
chip antibody: NFĸB p65 (sc-372, Santa Cruz)
source: 786-O (ATCC CRL1932)
|
| Growth protocol |
786-O cells were grown in RPMI-1640 medium (Sigma) supplemented with 10% fetal bovine serum (Gibco). Cells were maintained in a 5% CO2-humidified incubator at 37°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For each transcription factor, ~3x107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and stopped by adding glycine to a final concentration of 0.2M. Chromatin was extracted and sonicated to ~500bp (Vibra cell, SONICS). The total volume of immunoprecipitation was 1.5 ml and the amount of antibody used was 15 µg. The input DNA was precleared with protein G Dynabeads (LifeTechnologies) for 2 hr at 4°C and then incubated with antibodies conjugated protein G beads overnight at 4°C. The beads were washed 6 times with wash buffer at room temperature.
Amplified DNA was used with NEBNext ChIP-Seq library prep reagent set (NEB)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing reads were trimmed (10bp from front and back) and mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) 'mem' algorithm. Only reads with mapQ >10 and with duplicates removed by rmdup were used in the subsequent analysis.
Significant peaks were called using MACS2 (q-value < 0.01).
Genome_build: hg19
Supplementary_files_format_and_content: bed format for ucsc genome browser, including 5 columns: "chromosome" "start of region" "end of region" "peak name" "peak enrichment"
|
| |
|
| Submission date |
Aug 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaosai Yao |
| E-mail(s) |
xiaosai.yao@gmail.com, yao.xiaosai@gene.com
|
| Phone |
+65 68088271
|
| Organization name |
Genome Institute of Singapore
|
| Street address |
60 Biopolis Street, Genome, #02-01
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE86092 |
Transcription factors enriched in tumor-associated enhancers in VHL-deficient ccRCC |
| GSE86095 |
VHL deficiency drives enhancer activation of oncogenes in clear cell renal cell carcinoma |
|
| Relations |
| BioSample |
SAMN05710714 |
| SRA |
SRX2055843 |
