|
| Status |
Public on Nov 24, 2012 |
| Title |
p300S4KO |
| Sample type |
SRA |
| |
|
| Source name |
primary CD4+ T cells from spleen and lymph nodes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
genotype/variation: STAT4<tm1> (STAT4KO)
cell type: in vitro polarized T helper1 cells for 7 days
passages: FACS sorted naive CD4+T cells cultured in vitro for 7 days under Th1 condition and restimulated with plate-bound CD3/28 +IL12 for 2 hrs
chip antibody: anti-p300
antibody vendor/catalog#: sc-585, Santa Cruz Biotechnology
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell lysates were made by sonication and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3 end. After adapter ligation, DNA was PCR amplified with Illumina primers for 16 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIX following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Chromatin IP against p300
|
| Data processing |
For H3K4me1: the unique tags were mapped into non-overlapping 200 bp windows of the mouse genome. Significant islands were identified based on window tag-count threshold determined from a p-value=0.05 defined by Poisson background model using SICER, a method appropriate for broad peaks
For p300 and STATs CisGenome v2.0, an extension of the earlier version (Ji et al., 2008), was utilized based on the normal rabbit serum as the control IP. The parameters used for seq-peak command were c=2 or 3, b=100, and e=0.
RNA-seq: tophat and cufflinks. Sequence reads from each cDNA library were mapped onto the mouse genome build mm9 using tophat and the mappable data were then processed by Cufflinks (Trapnell et al.). The obtained data were normalized based on RPKM (reads per kilobase exon model per million mapped reads).
Genome_build: mm9
|
| |
|
| Submission date |
Aug 29, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Golnaz Vahedi |
| Organization name |
National Institutes of Health
|
| Department |
NIAMS
|
| Lab |
Lymphocyte Cell Biology Section
|
| Street address |
9000 Rockville Pike Bldg 10 Rm 13C101A
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE40463 |
STATs Shape the Active Enhancer Landscape of T Cell Populations |
|
| Relations |
| SRA |
SRX183935 |
| BioSample |
SAMN01162773 |
