Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Ventral Tegmental Area
MeSH Description
A region in the MESENCEPHALON which is dorsomedial to the SUBSTANTIA NIGRA and ventral to the RED NUCLEUS. The mesocortical and mesolimbic dopaminergic systems originate here, including an important projection to the NUCLEUS ACCUMBENS. Overactivity of the cells in this area has been suspected to contribute to the positive symptoms of SCHIZOPHRENIA.

Attributes by original data submitter

Sample

source_name
Ventral tegmental area (brain)
strain
C57BL/6
chip antibody
none
stress conditions
Std - Ctl

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
All tissue was taken from adult male mice during the light cycle, 24 hours after behavioral testing. RNA was purified first by TriZol extraction followed by column purification sing Rneasy micro kits (Qiagen) according to manufacturer's protocol. All samples were found to have a high RIN value (>9; BioAnalyzer, Agilent). Chromatin was briefly crosslinked in 1% formaldehyde and sonicated to 200-600bp fragments. Samples were pooled by group to immunoprecipitate 1 microgram of chromatin with ChIP-grade H3K4me1 antibody (AbCam Ab8895) overnight at 4C. DNA from ChIP or Input (5%) was de-crosslinked overnight, RNA and protein degraded enzymatically, and purified by PCR purification kit (Qiagen). RNA-seq libraries were prepared using Illumina TruSeq unstranded kit A and B for poly-A selected transcripts, according to protocol. ChIP-seq/Input libraries were prepared by NEBNext Ultra DNA kit with Illumina adaptors according to protocol. RNA-seq samples counterbalanced across groups for multiplexing and sequenced on an Illumina Hi-Seq machine with 100-bp single-end reads in the Mount Sinai Genomics Core Facilities. Multiplexing produced >30 million reads per sample. ChIP and corresponding Input samples were multiplexed separately to achieve >80-million reads/sample on Illumina Hi-Seq V4 chemsitry with 100-bp single-end reads in the Mount Sinai Genomics Core Facilities.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
12801909
Reads aligned (%)
67.2
Duplicates removed (%)
11.4
Number of peaks
275 (qval < 1E-05)

mm9

Number of total reads
12801909
Reads aligned (%)
67.0
Duplicates removed (%)
11.6
Number of peaks
225 (qval < 1E-05)

Base call quality data from DBCLS SRA