Dataset features

Specifications


Application: ChIP-seq analysis
Number of samples: 11
Release date: Jan 18 2011
Last update date: Jul 20 2018
Access: Public
Chemicals: Cocaine
Genes: XK
Dataset link ChIP-Seq reveals regulation of the heterochromatic mark, H3K9me3, in NAc following repeated cocaine administration

Experimental Protocol


Animals received daily i.p. injections of either 'saline' (7 treatments of saline) or 'repeated' cocaine (7 treatments of 20 mg/kg cocaine). 24 hours after the last dose, chromatin immunoprecipitation was performed utilizing previously validated methods. Each experimental condition was performed in either duplicate or triplicate (2 cocaine, 3 saline). Briefly, for each ChIP, bilateral 14-gauge NAc punches (anterior and posterior) were pooled from 5 mice (20 punches). Tissue was lightly fixed to cross-link DNA with associated proteins and the material was further sheared and immunoprecipitated using sheep anti-rabbit magnetic beads conjugated to an antibody that specifically recognizes H3K9me3. Resulting immunoprecipitated DNA and total (input) genomic DNA were prepared for ChIP-sequencing using an Illumina kit according to manufacturer’s instructions. 20 ng of starting material, as determined by PicoGreen concentrations, was used in each case. Briefly, each sample underwent end repair followed by addition of an A base to the 3’ end. Proprietary adapters were then ligated to the ends, followed by size selection on a 3% agarose gel. The range of excision was 175-225 bp. Following DNA clean up, samples were amplified with 21 cycles of PCR. Amplification and size selection were confirmed with a BioAnalyzer. 5 pM concentrations were used to generate clusters for sequencing analysis.

Repositories


GEO

GSE24850

ArrayExpress

E-GEOD-24850

ENA

SRP003900

BioProject

PRJNA132069

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Contact


Li Shen