|
| Status |
Public on Sep 19, 2012 |
| Title |
Unstimulated macrophages H4Ac Wildtype ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Unstimulated macrophages, wildtype, H4Ac ChIP
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
genotype: wildtype
cell type: unstimulated bone marrow macrophages
chip antibody: anti-H4Ac (anti-acetyl-histone H4)
antibody vendor: Upstate Biotechnology
antibody catalog #: 06-598
antibody lot#: 32471
|
| Biomaterial provider |
Jackson Laboratory
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-Seq analysis, formalin-fixed cells were sonicated and processed for immunoprecipitation. Briefly, 1.5 X 10^7 BMMs were crosslinked for 10 min. in 1% paraformaldehyde, washed and lysed. Chromatin was sheared by sonication (5 x 60 s at 30% maximum potency) to fragments of approximately 150bp. The sheared chromatin was incubated with anti-rabbit IgG Dynabeads (Invitrogen) pre-conjugated with antibodies to FOXO3 (H-144) or H4Ac, washed and eluted. The eluted chromatin was reverse-cross-linked, and DNA was purified using phenol/chloroform/isoamyl extraction. The purified ChIP DNA was prepared for sequencing with the Illumina ChIPSeq Sample Prep kit and processed in according to the manufacturer’s protocol. Sequencing was performed by Covance, Seattle, WA.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-Seq data was aligned to the mouse genome (NCBI37/mm9; July 2007) using the ELAND alignment software (Illumina). Regions where the ChIP signals were enriched relative to the normal rabbit serum (NRS) control. We have used our in-house pipeline. The peak was identified as a binding location if and only if all the three conditions were simultaneously satisfied: i) the ChIP-Seq signal in the TF-specific IP/H4Ac was at least five times the control ChIP-Seq signal (ii) the ChIP-Seq signal in the TF-specific IP/H4Ac was at least two fragments per million; and (iii) the ChIP-Seq signal in the TF-specific IP/H4Ac corresponded to at least six overlapping fragments (extended reads) at that peak.
Reference: Ramsey,S.A. et al. Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. Bioinformatics 26, 2071-2075 (2010).
*export.txt: ELAND file
*bed: BED file obtained by converting the ELAND file
*bar: BAR file obtained by converting the processed data files; Tags per million; Used for visualizing in the Integrated Genome Browser (IGB)
Genome Build:
H4Ac_WT_BMM_export.txt: NCBI37/mm9 (July 2007)
H4Ac_WT_BMM.bed: NCBI37/mm9 (July 2007)
H4Ac_WT_BMM.tpm.bar: NCBI37/mm9 (July 2007)
|
| |
|
| Submission date |
Mar 02, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Ayush Raman |
| E-mail(s) |
ayush.raman@systemsbiology.org
|
| Phone |
206-732-1473
|
| Organization name |
Institute for Systems Biology
|
| Department |
Computational Dept.
|
| Lab |
Shmulevich Lab
|
| Street address |
401 Terry Avenue North
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98105 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE36241 |
Identification of a FOXO3/IRF7 circuit that limits inflammatory sequelae of antiviral responses (ChIP-Seq) |
| GSE37052 |
Identification of a FOXO3/IRF7 circuit that limits inflammatory sequelae of antiviral responses |
|
| Relations |
| SRA |
SRX125262 |
| BioSample |
SAMN00794602 |
