MurEpi.RRBS.small: Example data set: Murine methylation status data set of...

In annikabuerger/Cogito: Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets

Example data set: Murine methylation status data set of GSE77004

Description

This murine data from King et al. was downloaded from the NCBI GEO database under accession number GSE77004.

The methylation status, mesured by RRBS, was similarly taken from the published files (accession number GSE84103), which contain the fraction of methylated cytosine for every CpG context supported by a minimum of 5 reads.

To reduce the storage size and complexity of the murine example data, the data only contains data of chr5 and four sample conditions (3x TFX and 1x mut) were removed.

Usage

MurEpi.RRBS.small

Format

A GRanges Object containing a lot of Ranges with methylation status.

Source

NCBI GEO database accession number GSE84103 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84103

References

King AD, Huang K, Rubbi L, Liu S, Wang CY, Wang Y, Pellegrini M, Fan G. Reversible Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Mouse Embryonic Stem Cells. Cell Rep. 2016 Sep 27;17(1):289-302. doi: 10.1016/j.celrep.2016.08.083

annikabuerger/Cogito documentation built on July 7, 2022, 4:38 p.m.