octsox_peaks: Sox2 and Oct4 binding sites
In teunbrand/tornadoplot: Tornado Plot

Description Format Details Source References

This dataset contains a sample of genomic binding sites of the Sox2 and Oct4 proteins in mouse embryonic stem cells.

A GRangesList with 3 elements, each having 500 genomic locations of binging sites.

Sox2: 500 genomic loci where Sox2 binds
Oct4: 500 genomic loci where Oct4 binds
Both: 500 genomic loci where both Sox2 and Oct4 bind

The genomic loci were obtained by chromatin immunoprecipitation followed by sequencing (ChIP-seq) with antibodies against the Sox2 and Oct4 proteins. The model system used were wildtype mouse embryonic stem cells.

The original data was deposited in the gene expression omnibus (GEO) under accession GSE74112.

The data were aligned against the "mm10" reference genome by Cistrome. Other preprocessing steps are described at the Cistrome website.

Finally, locations in standard chromosomes were reduced to unique sites and categorised based on overlap with Sox2 binding sites and Oct4 binding sites or both. From each of the three resultant categories, 500 locations were randomly sampled without replacement.

The files used to construct this data were downloaded as bed files from http://cistrome.org/db/#/ (accessed at 2021-08-18). The files can be unambiguously found by entering the following numbers in the search bar: "73468" for the Sox2 sample and "73466" for the Oct4 sample.

Liu, Ziying et al. Catalytic-Independent Functions of PARP-1 Determine Sox2 Pioneer Activity at Intractable Genomic Loci (2017) Molecular Cell 65 4 p589-603 https://doi.org/10.1016/j.molcel.2017.01.017

teunbrand/tornadoplot documentation built on Dec. 23, 2021, 8:48 a.m.