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| Status |
Public on Jun 05, 2018 |
| Title |
TAC-Yap1ChIPSeq |
| Sample type |
SRA |
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| Source name |
heart tissue
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| Organism |
Mus musculus |
| Characteristics |
phenotype: wild-type
surgical procedure: transverse aortic constriction
days post-surgery: 7
antibody: anti-YAP1 (US Biological; Y1200-01D)
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| Treatment protocol |
Wild type C57BL/6J male mice were subjected to a sham or a transverse aortic constriction surgery. Hearts were removed 7 days post-surgery
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Heart were surgically removed and snap frozen and shipped to Active Motif for ChIP-Seq
Library was constructed by Active Motif (https://www.activemotif.com/)
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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 |
Sequence Analysis: The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
Determination of Fragment Density: Since the 5´-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp). To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can be visualized in genome browsers. bigWig files also provide the peak metrics in the Active Motif analysis program described below.
“Peak Finding”: MACS v.1.4.2 was used to identify the binding sites of Yap1
Normalization: The tag number of all samples (within a comparison group) is reduced by random sampling to the number of tags present in the smallest sample. This normalization method works well for most assays and can detect site-specific as well as most global differences in target enrichments between samples.
Merged Region Analysis: To compare peak metrics between 2 or more samples, overlapping Intervals are grouped into “Merged Regions”, which are defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping Intervals; “merged peaks”). In locations where only one sample has an Interval, this Interval defines the Merged Region. The use of Merged Regions is necessary because the locations and lengths of Intervals are rarely exactly the same when comparing different samples. 6. Annotations: After defining the Intervals and Merged Regions, their genomic locations along with their proximities to gene annotations and other genomic features are determined and presented in Excel spreadsheets. In addition, average and peak (i.e. at “summit”) fragment densities within Intervals and Merged Regions are compiled.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files show peak shapes in the form of a signal histogram and cand be visualized in the UCSC browser
Supplementary_files_format_and_content: Excel file of Active Regions (Merged Regions), which are genomic regions containing 1 or multiple overlapping Intervals
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| Submission date |
Jun 04, 2018 |
| Last update date |
Jun 05, 2018 |
| Contact name |
Maha Abdellatif |
| E-mail(s) |
abdellma@njms.rutgers.edu
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| Phone |
9739721254
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| Organization name |
Rutgers-University
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| Department |
Cell Biology and Molecular Medicine
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| Street address |
185 S. Orange Ave.
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| City |
Newark |
| State/province |
NJ |
| ZIP/Postal code |
07103 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE115294 |
Genome-wide mapping of Yap1 in the normal and hypertrophied hearts |
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| Relations |
| BioSample |
SAMN09323806 |
| SRA |
SRX4159427 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3173911_TAC_YAP1_mm10_i78_uniqnorm_signal.bw |
113.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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