|
| Status |
Public on Sep 13, 2012 |
| Title |
Th0 42hr Input |
| Sample type |
SRA |
| |
|
| Source name |
Th0 polarized cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type/growth condition: Naïve T-cells from spleen activated by anti-CD3 and anti-CD28
timepoint: 42 hrs
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
20000000 cells were harvested, crosslinked with formaldehyde, sonicated, IPed with appropriate antibodies and reverse-crosslinked to obtain 300-500 bp DNA fragments. These DNA fragments were ligated to Illumina TruSeq adapters for sequencing on the Illumina GAIIx.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Sample 7
|
| Data processing |
Illumina Casava1.7 software used for basecalling and generating eland extended files mapped onto mm9
Sequenced reads for the BMDCs were mapped to mm9 whole genome using gsnap with parameter s-d mm9 -Q -n 2 -A sam
QuEST was used for peak calling on the aligned eland extended or SAM files with the recommended 30 -fold enrichment used as threshold.
Genome_build: mm9
Supplementary_files_format_and_content: wig files indicating the reads aligned to the mm9 genome
|
| |
|
| Submission date |
Sep 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Smita Agrawal |
| Organization name |
Genentech Inc.
|
| Department |
Immunology
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE40483 |
A genomic regulatory element that directs assembly and function of immunespecific AP-1-IRF complexes |
| GSE40727 |
ChIPseq analysis of IRF4 and BATF in immune cells |
|
| Relations |
| SRA |
SRX185716 |
| BioSample |
SAMN01163714 |
