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Series GSE42810 Query DataSets for GSE42810
Status Public on Feb 14, 2014
Title Chronic cocaine-regulated epigenome in mouse [ChIP-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Increasing evidence supports a role for altered gene expression in mediating the lasting effects of cocaine on the brain, and recent work has demonstrated the involvement of chromatin modifications in these alterations. However, all such studies to date have been restricted by their reliance on microarray technologies which have intrinsic limitations. Here, we used advanced sequencing methods, RNA-seq and ChIP-seq, to obtain an unprecedented view of cocaine-induced changes in gene expression and associated adaptations in numerous modes of chromatin regulation in the nucleus accumbens, a key brain reward region. We identify unique combinations of chromatin changes, or signatures, that accompany cocaine’s regulation of gene expression, including the dramatic involvement of pre-mRNA alternative splicing in cocaine action. Together, this delineation of the cocaine-induced epigenome in the nucleus accumbens reveals several novel modes of drug regulation, thereby providing new insight into the biological basis of cocaine addiction. More broadly, the combinatorial chromatin and transcriptional approaches that we describe serve as an important resource for the field, as they can be applied to other systems to reveal novel transcriptional and epigenetic mechanisms of neuronal regulation.
Overall design ChIP-seq of 6 marks (H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9me2, RNApolII) were done on mouse nucleus accumbens 24 hr after 7 day daily cocaine ip injection with saline as control. Three replicates for each condition.
Contributor(s) Shen L, Feng J
Citation(s) 24758366
Submission date Dec 08, 2012
Last update date May 15, 2019
Contact name Li Shen
Organization name Icahn School of Medicine at Mount Sinai
Department Neuroscience
Lab Shen
Street address 1425 Madison Ave
City New York
State/province NY
ZIP/Postal code 10029
Country USA
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (41)
GSM1050334 H3K27me3 ChIP-seq Coc Rep1
GSM1050335 H3K27me3 ChIP-seq Coc Rep2
GSM1050336 H3K27me3 ChIP-seq Coc Rep3
This SubSeries is part of SuperSeries:
GSE42811 Chronic cocaine-regulated epigenome in mouse
BioProject PRJNA183443
SRA SRP017479

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE42810_RAW.tar 29.9 Gb (http)(custom) TAR (of BED, BW, TXT)
GSE42810_diff.k27m3.res.annotated.txt.gz 371.7 Kb (ftp)(http) TXT
GSE42810_diff.k36m3.res.annotated.txt.gz 99.0 Kb (ftp)(http) TXT
GSE42810_diff.k4m1.res.annotated.txt.gz 58.2 Kb (ftp)(http) TXT
GSE42810_diff.k4m3.res.annotated.txt.gz 427.0 Kb (ftp)(http) TXT
GSE42810_diff.k9m2.res.annotated.txt.gz 506.6 Kb (ftp)(http) TXT
GSE42810_diff.k9m3.res.annotated.txt.gz 160.5 Kb (ftp)(http) TXT
GSE42810_diff.pol2.res.annotated.txt.gz 377.5 Kb (ftp)(http) TXT
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Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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