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Sample GSM1011086 Query DataSets for GSM1011086
Status Public on Apr 16, 2014
Title mouse_e11.5_heart_control
Sample type SRA
 
Source name mouse_e11.5_heart_control
Organism Mus musculus
Characteristics strain: 129/C57BL/6
genotype/variation: SMARCA4/FLAG knock-in
Sex: pooled male and female
tissue: Mouse embryonic day 11.5 (e11.5) heart
Extracted molecule genomic DNA
Extraction protocol Embryonic heart and hindbrain was isolated from 129/C57BL/6 (smarca4/FLAG knock-in) mouse embryos at e11.5. ESCs from the same line were cultured as per standard protocols. Tissue samples and ESCs were cross linked and cells were dissociated and subject to chromatin isolation, sonication and immunoprecipitation using an anti-FLAG antibody [Sigma- F1804 [ 1mg/ml ]-Monoclonal ANTI-FLAG M2 antibody produced in mouse. Lot #: 088K6018]. ANTI-FLAG bound chromatin is treated with proteinase K and RNAse followed by clean up using QIAGEN QIAquick PCR Purification Kit (28104). ChIP DNA was sheared by sonication, end-repaired, ligated to illumina sequencing adapters. Gel purified amplified ChIP DNA between 300 and 500bp was sequenced on the Illumina HiSeq 2000 to generate 50 or 36 bp reads
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Bed: Sequence reads were mapped to the mouse (mm9) genome using bwa with default parameters. Reads mapping to multiple sites in the genome with an equivalent score, and duplicate reads with identical start sites were discarded.
Wig: Aligned read coordinates were extended to 300bp in the direction of the alignment. Coverage depth was calculated from extended reads at 25bp intervals throughout the genome.
peaks: Peak detection in SMARCA4-FLAG ChIP samples was performed using MACS1.4 with the appropriate matched control sample where present. Parameters were: gsize=2260035739 --tsize=50 or 36 --bw=300 --pvalue=1e-5 --mfold=10,30 --llocal=20000 --shiftsize=100. Peaks overlapping repeats, or duplicated regions of the genome were removed as likely mapping artifacts.
Genome_build: mm9
 
Submission date Sep 28, 2012
Last update date May 15, 2019
Contact name Matthew James Blow
E-mail(s) mjblow@lbl.gov
Phone 510-486-6590
Fax 510-486-7004
Organization name Lawrence Berkeley National Laboratory
Department Genomics Division
Lab Rubin / Pennacchio
Street address 1 Cyclotron Road
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platform ID GPL13112
Series (1)
GSE37151 Expanding the Catalog of Enhancer Marks In Vivo
Relations
SRA SRX190172
BioSample SAMN01731601

Supplementary file Size Download File type/resource
GSM1011086_mouse_e11.5_heart_control.wig.gz 261.7 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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