GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM999806 Query DataSets for GSM999806
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
SRA SRX185716
BioSample SAMN01163714

Supplementary file Size Download File type/resource
GSM999806_Th0_42hr_background_normalized.profile.wig.gz 2.3 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap