|
| Status |
Public on May 02, 2012 |
| Title |
WCE_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Whole Cell Extract_ChIP-seq (input control)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
cell type: human embryonic kidney cells
|
| Growth protocol |
HEK293T cells were cultured in DMEM supplemented with 10% FBS. Cells were maintained at 37 °C under 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked with 1% formaldehyde and incubated with gentle rotation for 10 min at room temperature; cross-linking was quenched by the addition of glycine. Fixed cells were sonicated in lysis buffer using Bioruptor (Diagenode). Sonicated lysates equivalent to 5×10^7 cells were used per immunoprecipitation according to the previously described protocol (Lee et al. 2006). ChIP-seq libraries were prepared with Illumina's ChIP-seq sample prep kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
WCE_ChIP
|
| Data processing |
wce_chip.txt.bam.bed; genome build: hg19
For ChIP-seq analyses, enriched regions were determined by the ‘MACS’ (Zhang et al. 2008) peak-finding program, version 1.4.0rc2. Sequence reads for each ChIP-seq dataset and their associated whole-cell extract controls were used for the input and control file, respectively. The effective genome size was configured appropriately for the human dataset, and the p-value cutoff was set to 1.00e-05 or FDR < 1%, and a fold-change greater than five. All other MACS parameters were left default. Genes were called bound for ChIP-seq sample if an enriched peak region was found within 1kb of the transcription start site of any isoform of a gene from RefSeq (downloaded from UCSC Jan. 21, 2011).
|
| |
|
| Submission date |
Dec 02, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander (Garrett) Garruss |
| E-mail(s) |
asg@stowers.org
|
| Organization name |
Stowers Institute for Medical Research
|
| Lab |
Shilatifard
|
| Street address |
1000 East 50th Street
|
| City |
Kansas CIty |
| State/province |
Missouri |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE34097 |
The SEC family of RNA Polymerase II elongation factors: gene target specificity and transcriptional output |
|
| Relations |
| SRA |
SRX110231 |
| BioSample |
SAMN00761674 |
