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Sample GSM722994 Query DataSets for GSM722994
Status Public on Jul 01, 2012
Title RenLab-Input-spleen (Illumina GA IIx)
Sample type SRA
 
Source name Mouse spleen
Organism Mus musculus
Characteristics strain: C57Bl/6
chip antibody: none (Input)
chip antibody details: None
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 http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description Input
Data processing RenLab-Input-spleen-DM340.bam: Alignment to mm9 using Illumina's ELAND 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
E-mail(s) biren@ucsd.edu
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]
Relations
SRA SRX062982
BioSample SAMN00618927
Named Annotation GSM722994_RenLab-Input-spleen.bigwig

Supplementary file Size Download File type/resource
GSM722994_RenLab-Input-spleen-DM340.bam 783.7 Mb (ftp)(http) BAM
GSM722994_RenLab-Input-spleen.bigwig 73.0 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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