GM12878_ChIP_CTCF_signal: plotgardener example GM12878 CTCF ChIP signal data

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

plotgardener example GM12878 CTCF ChIP signal data

Description

A dataset listing read depths across the genome resulting from CTCF ChIP-seq in the GM12878 cell line. Genomic coordinates fall within the region chr21:28000000-30300000 according to the hg19 genome build.

Usage

data("GM12878_ChIP_CTCF_signal")

Format

a dataframe in BED format with a "score" column

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.

score

Score value of read depth.

Source

Data from Michael Snyder, Stanford with accession number ENCFF312KXX 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 June 15, 2024, 10:38 p.m.