New online tools, avalable for free download, for analysis of chromatin and gene data:

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:
Lists of Genes Regulated in Brain Reward Regionss in Addiction Models

McClung, Nat Neurosci, 2003
Regulation of gene expression in nucleus accumbens by cocaine, ΔFosB, and CREB

McClung, J Neurosci, 2005
Regulation of gene expression in ventral tegmental area and locus coeruleus by morphine

Renthal, Neuron, 2007
Regulation of gene expression in nucleus accumbens by cocaine and HDAC5

Winstanley, J Neurosc–i, 2007
Regulation of gene expression in orbitofrontal cortex by cocaine and ΔFosB

Renthal, Neuron, 2009
Regulation of chromatin binding of acetylated and methylated histones, and of ΔFosB and CREB, in nucleus accumbens by cocaine

Maze, Science, 2010
Regulation of gene expression in nucleus accumbens by acute vs. chronic cocaine

Maze, PNAS, 2011
Regulation of chromatin binding of H3K9me3 in nucleus accumbens by cocaine
The sequence data reported in this paper are available in the GenBank
database (accession no. GSE24850)

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, 2013
Supplementary tables of chromatin changes induced by chronic cocaine

Ferguson, J Neurosci, 2015
Supplementary tables of SIRT1 binding in NAc after chronic cocaine

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.


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