Package 'MMDiffBamSubset'

Utilities returning the paths to the sample sheet Cfp1.csv, to the BAM files WT_2.bam, Null_2.bam, Resc_2.bam and Input.bam, as well as corresponding peak files WT_2_Macs_peaks.xls, Null_2_Macs_peaks.xls Resc_2_Macs_peaks.xls

Description

Cfp1.csv Sample Sheet containing meta information about the experiment.

BAM files each containing subsets of original files with reads mapping to region ch1:3000000...75000000. The data is available as part of ArrayExpress Experiment E-ERAD-79, which contains ChIP-Seq of mice cells to assess the link between histone modification states of H3K4me3 with respect to the mediator proteins Cfp1.

WT_2.bam: organism: Mus musculus; Cell type: ES cells, Immunoprecipitate: H3K4me3

Null_2.bam: organism: Mus musculus; Cell type: Cfp1 -/- ES cells, Immunoprecipitate: H3K4me3

Resc_2.bam: organism: Mus musculus; Cell type: Cfp1-/- ES cells and wtCfp1 rescue cDNA, Immunoprecipitate: H3K4me3

Input.bam: organism: Mus musculus; input_DNA (pooled from different cell types)

WT.AB2, Null.AB2, Resc.AB2 and Input return the path to those files.

Additionally, subsets of peaks called by MACS[2] are provided.

WT.AB2.Peaks, Null.AB2.Peaks and Resc.AB2.Peaks return the path to the respective peak files.

Usage

Cfp1.Exp()
WT.AB2()
Null.AB2()
Resc.AB2()
Input()
WT.AB2.Peaks()
Null.AB2.Peaks()
Resc.AB2.Peaks()

Details

See the MMDiff package or [1] for details about the experiment (ChIP-seq, H3K4me3, Mus musculus). BAM files contain single-end reads aligned to reference genome NBCI37/mm9

References

[1] Clouaire T et al. (2012). Cfp1 integrates both CpG content and gene activity for accurate H3K4me3 deposition in embryonic stem cells. Genes Dev. August 1, 2012 26: 1714–1728

[2] Zhang Y et al. (20078). Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008, 9(9):R137.

Examples

Cfp1.Exp()
WT.AB2()
Null.AB2()
Resc.AB2()
Input()
WT.AB2.Peaks()
Null.AB2.Peaks()
Resc.AB2.Peaks()

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