Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Neural
Cell type
Prefrontal Cortex
MeSH Description
The rostral part of the frontal lobe, bounded by the inferior precentral fissure in humans, which receives projection fibers from the MEDIODORSAL NUCLEUS OF THE THALAMUS. The prefrontal cortex receives afferent fibers from numerous structures of the DIENCEPHALON; MESENCEPHALON; and LIMBIC SYSTEM as well as cortical afferents of visual, auditory, and somatic origin.

Attributes by original data submitter

Sample

source_name
30 y old Male NeuN+
tissue type
postmortem prefrontal cortex
chip antibody
H3K4me3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Libraries were prepared according to Illumina's instructions accompanying the ? Kit (#). Briefly, ChIP DNA was end repaired (End-it DNA Repair kit, Epicentre) and A-tailed (Klenow Exo-minus; Epicentre). Adaptors (Genomic Adaptor Oligo Mix; Illumina, San Diego, CA) were ligated to the ChIP-DNA (Fast-Link kit, Epicentre) for PCR amplification and PCR products were gel extracted. Here, the region of 200 – 300 bps was cut out of the gel, containing the expected DNA fragment, consisting of the 150 bp mononucleosomal ChIP-DNA plus 100 bp adaptors. Between each step the samples were cleaned with column based PCR purification kits (Qiagen). The prepared DNA was run on bioanalyzer to determine concentration and size distribution of the library. Libraries were sequenced with the Genome Analyzer II (Illumina). All sequencing libraries contained single-end 36-bp raw reads were mapped to the human genome (UCSC version hg19) using Bowtie (version 0.12.8).

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg38

Number of total reads
12857103
Reads aligned (%)
98.4
Duplicates removed (%)
21.5
Number of peaks
29901 (qval < 1E-05)

hg19

Number of total reads
12857103
Reads aligned (%)
98.0
Duplicates removed (%)
22.2
Number of peaks
29999 (qval < 1E-05)

Base call quality data from DBCLS SRA