|
| Status |
Public on Apr 19, 2014 |
| Title |
mouse_e11.5_forebrain_inputforH3K4me1H3K4me3H3K27mme3 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic day 11.5 (e11.5) forebrain
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: e11.5
tissue: forebrain
chip antibody: input
strain: CD1
Sex: pooled male and female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryonic heart and hindbrain was isolated from CD1 mouse embryos at e11.5 .Tissue samples were cross linked and cells were dissociated and subject to chromatin isolation, sonication and immunoprecipitation. ChIP DNA was sheared by sonication, end-repaired, ligated to illumina sequencing adapters. ChIP and input DNA between 300 and 500bp was sequenced on the Illumina HiSeq 2000 to generate 50 or 36bp reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Tissue pooled from ~150 embryos sonicated input DNA
|
| Data processing |
Bam: 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: Unique BWA-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 FLAG ChIP samples was performed using MACS1.4 with the appropriate matched control sample where present. Parameters were: macs14 -t chip.bam –control=input.bam –name=chip_output –format=BAM –gsize=mm –tsize=36 –bw=300 –mfold=10,30 –nolambda –nomodel –shiftsize=150 -p 0.00001. Peaks overlapping repeats, or duplicated regions of the genome were removed as likely mapping artifacts.
Genome_build: mm9
Supplementary_files_format_and_content: bed and wig
|
| |
|
| Submission date |
Apr 18, 2014 |
| 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 |
GPL11002 |
| Series (1) |
| GSE37151 |
Expanding the Catalog of Enhancer Marks In Vivo |
|
| Relations |
| BioSample |
SAMN02729872 |
| SRA |
SRX521633 |
