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Sample GSM722992 Query DataSets for GSM722992
Status Public on Jul 01, 2012
Title RenLab-H3K4me3-spleen (Illumina GA IIx)
Sample type SRA
Source name Mouse spleen
Organism Mus musculus
Characteristics strain: C57Bl/6
chip antibody: H3K4me3
chip antibody details: Millipore, 05-745
Treatment protocol None
Growth protocol Adult liver, kidney, bone marrow, lung, heart, cortex, cerebellum, spleen were dissected from 8-week old male C57Bl/6 mice (Charles River). Mouse embryonic fibroblast (MEF) MEF cells were derived from E13.5 C57Bl/6 mouse embryos and genotyping was performed to select male MEF cells used for this study. mESC line Bruce4 was maintained on mitomycin C-inactivated MEF feeder layers in DME containing 15% fetal calf serum, leukemia inhibiting factor, penicillin/streptomycin, L-glutamine and non-essential amino acids. All ES cells were passaged on 0.2 % gelatin twice to deplete feeder cells before harvest for experiments.
Extracted molecule genomic DNA
Extraction protocol See
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description H3K4me3 IP
Data processing RenLab-H3K4me3-spleen-DM425.bam: Alignment to mm9 using Bowtie software with a seed length of 25 bases and up to 2 mismatches. Only sequences mapping to exactly one location were kept. If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq: Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.
Submission date May 11, 2011
Last update date May 15, 2019
Contact name Bing Ren
Organization name University of California, San Diego
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
Platform ID GPL11002
Series (2)
GSE29184 A draft map of cis-regulatory sequences in the mouse genome
GSE29218 A draft map of cis-regulatory sequences in the mouse genome [ChIP-Seq]
SRA SRX062980
BioSample SAMN00618925
Named Annotation GSM722992_RenLab-H3K4me3-spleen.bigwig

Supplementary file Size Download File type/resource
GSM722992_RenLab-H3K4me3-spleen-DM425.bam 323.9 Mb (ftp)(http) BAM
GSM722992_RenLab-H3K4me3-spleen.bigwig 33.0 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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