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Sample GSM1657176 Query DataSets for GSM1657176
Status Public on Dec 07, 2015
Title Input CT10 sonication
Sample type SRA
Source name liver
Organism Mus musculus
Characteristics strain: C57BL/6
Sex: Male
age: 10-20 weeks
genotype: Wild-type
chip antibody: None
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated (for BAF180 ChIP-Seq) or MNase-digested (for REV-ERBα ChIP-Seq) nuclei and Protein-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina NextSeq 500 (75 nt reads, single-end for BAF180 ChIP-Seq). The resulting DNA libraries were quantified and sequenced on Illumina HiSeq 2500 Sequencing system (50nt reads, single end for REV-ERBα ChIP-Seq).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Data processing The sequences identified were mapped to the mouse genome (NCBI37/UCSC mm9) using BOWTIE function in Galaxy. Only the sequences uniquely mapped with no more than 2 mismatches were kept and used as valid reads. PCR duplicates were also removed. Mapped sequences from different replicates of REV-ERBα ChIP-Seq were pooled together for subsequent analysis
Peak calling was carried out by MACS (version 1.4.2 20120305) in Galaxy/Cistrome (options --mfold 10, 30 --pvalue 1e-5), on each ChIP-seq file against the matching input file.
To account for the different sequencing depths between samples, the signal files generated from MACS were normalized by Signal Extraction Scaling (SES) method (Meyer and Liu, 2014). The peak summits were used as the binding site centers, and the normalized signal files were used as the binding strength for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated by Galaxy/cistrome
Submission date Apr 14, 2015
Last update date May 15, 2019
Contact name Bokai Zhu
Phone 2192085319
Organization name Baylor College of Medicine
Department MCB
Lab Post-doc
Street address One Baylor Plaza, M813
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
Platform ID GPL19057
Series (2)
GSE67852 Genome-wide maps of BAF180 and REV-ERBα binding
GSE67860 Coactivator-Dependent Oscillation of Chromatin Accessibility Dictates Circadian Gene Amplitude through REV-ERB Loading
BioSample SAMN03481942
SRA SRX994724

Supplementary file Size Download File type/resource
GSM1657176_Input_CT10_sonication.bigwig 247.1 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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