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

Similar protocols

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 ( []. 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 ( []. 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