Computational protocol: Dynamic chromatin accessibility modeled by Markov process of randomly-moving molecules in the 3D genome

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Protocol publication

[…] Hi-C raw data were firstly mapped to hg19 (Human) or dm3 (Drosophila) reference genome and binned into contact matrix by HiC-Pro version 2.7.2b (). The ICE normalization was performed by HiTC version 1.14.0 (). To filter out the noise from repetitive regions in the chromosome, we removed regions from each centromere's upstream 500 to downstream 500 kb. [...] Reads were mapped to hg19 reference genome and gene expression was quantified by RSEM version 1.2.25 (). Differential expression analysis was conducted by EBSeq version 1.10.0 (). Differentially expressed genes were defined as having posterior probability of differential expression equal to 1. Gene ontology (GO) analysis was conducted by BiNGO version 3.0.3 (). [...] Because compartment A/B was a qualitative description of genome, we also used compartment score (first or second principal component of Hi-C matrix ()) to represent compartment A/B. Genome was divided into 50 kb non-overlapping bins and then compartment score and directionality index () were computed by HiTC version 1.14.0 (). Hubs and median bins were defined as in Huang et al. (). Whole genome's SSD were ranked and the top 10 and 45% quantiles were taken as the thresholds for SSD hubs and SSD median, respectively. Histone mark signatures were computed around the center of each hub or median and the computation of normalized signals is the same as Huang et al. (). Insulation score was defined as in Crane et al. (). We computed using custom scripts which are available at compartment score, the difference between GM12878 and NHEK cell lines were computed. Here we used difference instead of fold change because compartment score contained negative values. The thresholds of high and low differential features were defined as 5 and 95% quantiles of the fold change or difference. We also labeled each bin as compartment A or B and tracked the change of compartment when correlating it with differential expression data. […]

Pipeline specifications

Software tools RSEM, EBSeq, BiNGO
Application RNA-seq analysis