|
| Status |
Public on Jan 22, 2009 |
| Title |
Input |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
no treatment
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Normal culture conditions. Subconfluent cells were grown in DMEM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was fixed in 1% formaldehyde, sheared to 200-800bp, immunoprecipitated using Oct1 antibodies, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
input DNA, both 26 and 36bp reads, 5 lanes.
variable: no treatment
|
| Data processing |
The standard Illumina GAPipeline-0.3.0 was run to convert images to quality scored sequences and aligned reads. The USeq package http://useq.sourceforge.net was then used to identify enriched Oct1 binding peaks.
Each processed file contains a list of genomic regions (NCBI 36.1, H_sapiens_Mar_2006, hg18) enriched for Oct1 binding.
These files were generated by running the EnrichedRegionMaker on ScanSeqs window scored data, see http://useq.sourceforge.net/ .
Adjacent and overlapping windows with a q-value FDR of 0.0001 were joined into larger enriched regions.
The best scoring window's scores are used to represent the enriched region.
|
| |
|
| Submission date |
Jan 05, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Dean Tantin |
| E-mail(s) |
dean.tantin@path.utah.edu
|
| Phone |
(801) 587-3035
|
| Organization name |
University of Utah
|
| Department |
Department of Pathology
|
| Street address |
15 North Medical Drive East
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE14283 |
A general mechanism for transcription regulation by Oct1 and Oct4 in response to genotoxic and oxidative stress |
|
| Relations |
| SRA |
SRX003181 |
| BioSample |
SAMN02195539 |
