IMR90_ChIP_CTCF_reads: plotgardener example CTCF read data

In PhanstielLab/plotgardenerData: Datasets and test data files for the plotgardener package

plotgardener example CTCF read data

Description

A dataset listing aligned sequencing reads for CTCF in the IMR90 cell line as determined by ChIP-seq. Genomic coordinates fall within the region chr21:28000000-30300000 according to the hg19 genome build.

Usage

data("IMR90_ChIP_CTCF_reads")

Format

a dataframe in BED (ranges) format

chrom

The name of the chromosome on which the genome feature exists.

start

The starting position of the feature in the chromosome.

end

The ending position of the feature in the chromosome.

strand

An optional column defining the strand of the feature as either '+' or '-'.

Source

Data from Michael Snyder, Stanford with accession number ENCFF847VPR was downloaded from the ENCODE portal https://www.encodeproject.org/.

References

ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247. PMID: 22955616; PMCID: PMC3439153.

Davis CA, Hitz BC, Sloan CA, Chan ET, Davidson JM, Gabdank I, Hilton JA, Jain K, Baymuradov UK, Narayanan AK, Onate KC, Graham K, Miyasato SR, Dreszer TR, Strattan JS, Jolanki O, Tanaka FY, Cherry JM. The Encyclopedia of DNA elements (ENCODE): data portal update. Nucleic Acids Res. 2018 Jan 4;46(D1):D794-D801. doi: 10.1093/nar/gkx1081. PMID: 29126249; PMCID: PMC5753278.

PhanstielLab/plotgardenerData documentation built on Nov. 8, 2022, 11:20 a.m.