|
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 |