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Sample GSM884978 Query DataSets for GSM884978
Status Public on Sep 19, 2012
Title Unstimulated macrophages Foxo3a Wildtype ChIP-Seq
Sample type SRA
Source name Unstimulated macrophages, wildtype, Foxo3a ChIP
Organism Mus musculus
Characteristics background strain: C57BL/6
genotype: wildtype
cell type: unstimulated bone marrow macrophages
chip antibody: anti-Foxo3a (FKHRL1 (H-144))
antibody vendor: Santa Cruz Biotechnology
antibody catalog #: sc-11351
antibody lot#: H0210
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:
Foxo3_BMM_export.txt: NCBI37/mm9 (July 2007)
Foxo3_BMM.bed: NCBI37/mm9 (July 2007) NCBI37/mm9 (July 2007)
Submission date Mar 02, 2012
Last update date May 15, 2019
Contact name Ayush Raman
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
SRA SRX125261
BioSample SAMN00794601

Supplementary file Size Download File type/resource
GSM884978_Foxo3_BMM.bed.gz 24.0 Mb (ftp)(http) BED 96.8 Mb (ftp)(http) BAR
GSM884978_Foxo3_BMM_export.txt.gz 530.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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