|
| Status |
Public on Dec 18, 2009 |
| Title |
Jurkat_InputDNA |
| Sample type |
SRA |
| |
|
| Source name |
Input DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Jurkat, clone E6-1 T lymphocyte
antibody: None
|
| Growth protocol |
Jurkat T cells were grown in RPMI media with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked nuclei were prepared from 1E7 Jurkat T cells. Chromatin was sheared by sonication and partitioned by immunoprecipitation with antibodies bound to magentic beads. Crosslinks were revered by heating and DNA was purified by a Qiagen PCR cleanup kit. ChIP and Input DNA was prepared for sequencing using Illumina’s ChIP-seq kit. Each ChIP DNA sample was pooled from three independent replicates. 36 bp reads were generated using Illumina’s Genome Analyzer II and standard pipeline software.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Sheared Input DNA
|
| Data processing |
Alignment (*sorted.txt files): Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. See GSE17954 supplementary readme file for column descriptions (GSE17954_README_Sorted.txt).
Peak detection (*EmpFDR* files) was performed using the Useq application package (http://useq.sourceforge.net). File descriptions are available at http://useq.sourceforge.net/outputFileTypeDescriptions.html
|
| |
|
| Submission date |
Sep 03, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Hollenhorst |
| E-mail(s) |
[email protected]
|
| Organization name |
Indiana University
|
| Street address |
1001 E Third St, Jordan Hall 104
|
| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE17954 |
DNA specificity determinants associate with distinct transcription factor functions |
|
| Relations |
| SRA |
SRX015828 |
| BioSample |
SAMN00007541 |
