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| Status |
Public on Dec 07, 2015 |
| Title |
BAF180 ChIP-seq CT22 Bethyl antibody |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
Sex: Male
age: 10-20 weeks
genotype: Wild-type
chip antibody: BAF180 (Bethyl A301-591A)
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| 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).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Apr 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Bokai Zhu |
| E-mail(s) |
bzhu@bcm.edu
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| Phone |
2192085319
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| Organization name |
Baylor College of Medicine
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| Department |
MCB
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| Lab |
Post-doc
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| Street address |
One Baylor Plaza, M813
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN03481940 |
| SRA |
SRX994722 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1657174_BAF180_ChIP-Seq_CT22_Bethyl_antibody.bw |
65.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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