Computational protocol: The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity

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Protocol publication

[…] ChIP-seq and ChIP-qPCR were performed at three different life stages using antibodies against H3K4me3, H3K4me1, H3K27ac, H3K36me3, RNApolII, and CoBra as detailed in the . 50 bp single-end Illumina sequencing reads were aligned to the Capsaspora genome (v.2) using Bowtie (), and regions of enrichment were determined using MACS2 (), correcting for genome mappability. Chromatin state definition and genomic feature enrichment was performed using ChromHMM (). Capsaspora genome was reannotated as described in the . […]

Pipeline specifications

Software tools Bowtie, MACS, ChromHMM
Application ChIP-seq analysis
Organisms Capsaspora owczarzaki