Activated p53 ChIP-seq depth and (SISSR) peaks datasets
Description
This composite track is a compilation of the 41 ChIP-seq data sets that contain activated or overexpressed p53 from published studies. The data for the human p53 transcription factor binding sites were generated by various labs. The tracks represent peak calls and signals that were generated based on a uniform processing pipeline of all published raw data.
Data Statistics
The ChIP-seq data sets came from 21 publications. Included in the data sets are results from 13 cell types and 12 methods of inducing or activating p53 that span nine timepoints (from 1 to 48 hr after treatment).
Display Conventions and Configuration
The individual ChIP-seq tracks are organized by cell and condition by which p53 is induced or activated, where samples can be selected from a cell vs. condition matrix. Additionally, we include subtracks to indicate p53 peaks that appear in 2+ or 20+ data sets. Each track can be turned on/off individually.
p53 peaks in 2+ data sets subtrack is defined as peaks that appeared in at least (≥) 2 independent data sets.
p53 peaks in 20+ data sets subtrack is defined as peaks that appeared in at least (≥) 20 independent data sets.
The colors for each classification are as follows:
coverage track depth
SISSRs peak calls
p53 peaks in 2+ data sets
p53 peaks in 20+ data sets
Methods
Please note: For a full description of the methods used, refer to Nguyen et al. (2018) in the References section below.
ChIP-seq analysis workflow
Relevant ChIP-seq and associated input data sets were downloaded from publicly-available resources as listed in Supplemental Table ST1. All reads were clipped to a maximum length of 36 nucleotides (nt), then filtered to retain only sequences with a mean base quality score of at least 20. Filtered reads were aligned against the hg19 reference genome (excluding haplotype chromosomes) via Bowtie v0.12.8 with parameters “-m1 -v2” to accept only uniquely-mapped hits with a maximum of 2 mismatched bases. Multiple replicates from the same sample were merged, then duplicate reads were removed with MergeSamFiles.jar and MarkDuplicates.jar from the Picard tool suite v1.86 (http://broadinstitute.github.io/picard). Depth tracks were generated with BEDTools genomeCoverageBed v2.17.0 and UCSC utility bedGraphToBigWig, after extending each uniquely-mapped, non-duplicate read to a length of 200 nt.
p53 peak calls
The SISSRs program was used to identify p53 bound peaks for each p53 ChIP-seq data set using its associated input data set (or a surrogate input) as a control at default parameters (p<0.001). The SISSRs output peaks were subsequently redefined as 200-mers centered on the called peak’s midpoint. Merged peak lists were generated for the 41 activated p53 ChIP-seq data sets and for the 17 control p53 ChIP-seq data sets by BEDTools mergeBed v2.24.0, where regions that had at least one nt overlap or were book-ended were merged.
Credit
These data were analyzed by Nguyen et al., at the National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) in Research Triangle Park, North Carolina, USA. Please direct all questions to menendez@niehs.nih.gov.
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