chip_galonska: 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).
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/.