Diffreps
Finding differential chromatin modification sites from ChIP-seq data
Ngsplot
An easy-to-use visualization tool for global enrichment of next-generation sequencing data
Chromatin and Gene Databases:
Published genome-wide datasets—not included within the relevant publications due to journal policy—are provided here:
Sun, J Neurosci, 2012
Regulation of chromatin binding of H3K9me2 in nucleus accumbens by morphine
Robison, J Neurosci, 2013
Supplementary table of protein changes in nucleus accumbens after cocaine
Ferguson, J Neurosci, 2015
Supplementary tables of SIRT1 binding in NAc after chronic cocaine:
Table 1A SIRT1 Differential Binding Gene List Down
Table 1B SIRT1 Differential Binding Gene List Up
Table 2 SIRT1 ChIP-Seq + RNA-Seq Targets
Table 1A SIRT1 Differential Binding Gene List Down
Table 1B SIRT1 Differential Binding Gene List Up
Table 2 SIRT1 ChIP-Seq + RNA-Seq Targets
Sun, Neuroscience, 2017
Supplementary Table 1. Nucleosome occupancy events after repeated cocaine exposure. Nucleosome occupancy events were computed from total H3 ChIP–seq data using DANPOS as described in Methods. The chromosomal locations of these events are shown in the Table as Start to Finish, and were then annotated to the genome accordingly.
Supplementary Table 2. Nucleosome shift events after repeated cocaine exposure. Nucleosome shift events were computed from total H3 ChIP–seq data using DANPOS as described in Methods. The chromosomal locations of these events are shown in the Table as Start to Finish, and were then annotated to the genome accordingly.