|
| Status |
Public on Dec 19, 2013 |
| Title |
Forebrain P21 input |
| Sample type |
SRA |
| |
|
| Source name |
forebrain
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD-1
developmental stage: P21
chip antibody: none
|
| Growth protocol |
Tissues were collected from CD1 mice at each stage. For all but P56 stage, samples represent pooled tissues from multiple embryos/mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissues were cross-linked, lysed, and sonicated and immunoprecipation was performed using H3K27ac (Abcam Ab4729). Input samples represent sonicated DNA before immunoprecipitation
Libraries were constructed using standard protocols and the Illumina TruSeq kit with index barcodes.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Forebrain P21 input
|
| Data processing |
Basecalls performed using standard Illumina pipeline
ChIP-seq reads were aligned to the mm9 genome assembly using BWA with the following call: bwa aln -t 6 -l 25 mm9 sample.fastq.gz
Peaks were called using MACS (version 1.4) incoporating matched input data with the following call: macs14 -t chip.bam --control=input.bam –name=chip_output --format=BAM --gsize=mm --tsize=50 --bw=300 --mfold=10,30 --nolambda --nomodel --shiftsize=150 -p 0.00001
Peaks were filtered to remove regions where a significant proportion of the reads mapped within repetitive regions
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated by extending reads to 300bp and calculating the number of reads per 25bp bins across the genome; .bed files represent filtered peaks ranked by significance
|
| |
|
| Submission date |
Nov 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Alex S Nord |
| E-mail(s) |
asnord@lbl.gov
|
| Organization name |
Lawrence Berkeley National Laboratory
|
| Department |
Genomics Divsion
|
| Street address |
1 Cyclotron Road, Mail Stop 84-171
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE52386 |
Rapid and Pervasive Changes in Genome-Wide Enhancer Usage During Mammalian Development |
|
| Relations |
| BioSample |
SAMN02402724 |
| SRA |
SRX377675 |
