Computational protocol: MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity

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Protocol publication

[…] After immunoprecipitation of the chromatin, ChIP-seq libraries were generated and sequenced. Alignment was performed using Bowtie [] v0.12.7 on Arabidopsis thaliana genome TAIR10. Default Bowtie parameters were used except for: -best -strata (used to get the best mapping position with the minimum of mismatches). Peak calling was performed with MACS (http://liulab.dfci.harvard.edu/MACS/) []. Gene annotation and peak distribution relative to annotated Arabidopsis transcription start site was performed with GPAT [].Global clustering of the H3K9ac ChIP-seq data and quantitative comparisons were performed using the seqMINER program (http://bips.u-strasbg.fr/seqminer/) []. As reference coordinates, we used the MACS determined peaks for H3K9ac. Tag densities from each ChIP-seq dataset were collected in a window of 1 kb around the reference peak. The collected values were subjected to k-means clustering coupled to linear-based normalization. The normalization procedure reduces bias in the clustering due to inherent differences between ChIP-seq experiments. […]

Pipeline specifications

Software tools Bowtie, seqMINER
Databases TAIR
Application ChIP-seq analysis
Organisms Arabidopsis thaliana