Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Nucleus Accumbens
MeSH Description
Collection of pleomorphic cells in the caudal part of the anterior horn of the LATERAL VENTRICLE, in the region of the OLFACTORY TUBERCLE, lying between the head of the CAUDATE NUCLEUS and the ANTERIOR PERFORATED SUBSTANCE. It is part of the so-called VENTRAL STRIATUM, a composite structure considered part of the BASAL GANGLIA.

Attributes by original data submitter

Sample

source_name
Nucleus accumbens tissue
tissue
Nucleus accumbens
treatment
Control
antibody
none
strain
C57BL/6

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For each ChIP-seq replicate, bilateral 14-gauge NAc punches were pooled from 10 mice. 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 (Invitrogen) conjugated to an antibody that specifically recognizes PARP-1 (ab6079). Immunoprecipitated DNA and total (input) genomic DNA were prepared for ChIP-seq using an Illumina kit according to the manufacturer’s instructions. Each experimental condition was analyzed with independent biological triplicates. 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 2% agarose gel. The range of excision was 250–350 bp. After DNA clean up, samples were amplified with 21 cycles of PCR. Amplification and size selection were confirmed with a BioAnalyzer. The resulting libraries were sequenced on an Illumina HiSeq 2500 with 100 bp read length.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
52124646
Reads aligned (%)
99.8
Duplicates removed (%)
37.6
Number of peaks
165 (qval < 1E-05)

mm9

Number of total reads
52124646
Reads aligned (%)
99.7
Duplicates removed (%)
37.6
Number of peaks
167 (qval < 1E-05)

Base call quality data from DBCLS SRA