chip_galonska {DChIPRep} | R Documentation

## Another example ChIP data set that can be used with `importDataFromMatrices` from rom Galonska et. al., 2015.

### Description

The containes the H3Kme3 data in the serum and 24h_2i conditions from Galonska et. al., 2015 as well as the whole cell extract data, which is treated as input for all four samples. The data were downloaded from the SRA at the european nucleotide archive (ENA, accession PRJNA242892). The reads were aligned ot the mm9 reference genome using bowtie2 (Langmead and Salzberg, 2012) with default options. Then, filtering of unmapped, low mapping quality (< 10), duplicated and multi-mapping reads was performed with Picard tools. The fragment length was inferred using cross correlation plots from SPP (Kharchenko, et. al., 2008).

### Usage

    data(chip_galonska)

### Format

a matrix

### Value

a matrix

### References

Galonska, Christina, Michael J. Ziller, Rahul Karnik, and Alexander Meissner. 2015. "Ground State Conditions Induce Rapid Reorganization of Core Pluripotency Factor Binding Before Global Epigenetic Reprogramming." Cell Stem Cell 17 (4). Elsevier BV: 462-70. http://dx.doi.org/10.1016/j.stem.2015.07.005. Kharchenko, Peter V, Michael Y Tolstorukov, and Peter J Park. 2008. "Design and Analysis of ChIP-Seq Experiments for DNA-Binding Proteins." Nat Biotechnol 26 (12). Nature Publishing Group: 1351-9. http://dx.doi.org/10.1038/nbt.1508. Langmead, Ben, and Steven L Salzberg. 2012. "Fast Gapped-Read Alignment with Bowtie 2." Nature Methods 9 (4). Nature Publishing Group: 357-59. http://dx.doi.org/10.1038/nmeth.1923. Picard Tools - by Broad Institute. 2016. http://broadinstittue.github.io/picard/.

### See Also

sample_table_galonska input_galonska TSS_galonska

[Package DChIPRep version 1.18.0 Index]