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Sample GSM1264391 Query DataSets for GSM1264391
Status Public on Dec 19, 2013
Title Liver E17.5 input
Sample type SRA
 
Source name liver
Organism Mus musculus
Characteristics strain: CD-1
developmental stage: E17.5
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 Liver E17.5 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 SAMN02402750
SRA SRX377701

Supplementary file Size Download File type/resource
GSM1264391_Liver_E17.5_input.bed.gz 687 b (ftp)(http) BED
GSM1264391_Liver_E17.5_input.wig.gz 220.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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