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Sample GSM999804 Query DataSets for GSM999804
Status Public on Sep 13, 2012
Title BMDC 6hr LPS IRF4
Sample type SRA
 
Source name Bone marrow derived dendritic cells stimulated with LPS
Organism Mus musculus
Characteristics strain: C57BL/6
cell type/growth condition: Bone marrow derived dendritic cells stimulated with LPS for 6hrs
timepoint: 6 hrs
chip antibody: IRF-4 Antibody (M-17)
chip antibody vendor: Santa Cruz Biotechnologies
chip antibody cat. #: sc-6059
chip antibody lot #: L1010
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 HiSeq 2000
 
Description Sample 5
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 GPL13112
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 SRX185714
BioSample SAMN01163712

Supplementary file Size Download File type/resource
GSM999804_BMDC_aIRF4_ChIP_normalized.profile.wig.gz 23.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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