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
prefrontal cortex (BA9)
tissue
brain prefrontal cortex (Brodmann Area 9)
condition
HD
gender
female
onset age
unknown
age at death
56
cag repeat
45
post-mortem interval
19
chip antibody
H3K4me3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Neuronal nuclei from prefrontal cortex BA9 were NeuN+ labeled and fluorescence activated sorted (FACS) for subsequent H3K4me3 ChIP-seq. Briefly, approximately 300mg to 500mg of -80oC frozen grey matter dissected from BA9 was homogenized in 5ml lysis buffer and ultracentrifuged over sucrose solution at 24,400 rpm for two hours at 4oC. The resulting pellet was suspended in 550ul PBS, and immunolabeled with NeuN for 60 minutes while rotated in darkness. NeuN+ and NeuN- fractions were separated and collected by FACS. ChIP sequencing was performed for the NeuN+ fraction. Briefly, genomic regions with H3K4me3 modification were extracted by chromatin immunoprecipitation using anti-H3K4me3 antibody and further prepared into ChIP-seq library for sequencing. For each brain sample, 1 ug of DNA was used to construct sequencing libraries using Illumina’s TruSeq Sample Prep Kit, according to the manufacturer’s protocol (Illumina, San Diego, CA), and sequenced using 36nt single-end reads on Illumina’s GA II.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg38

Number of total reads
5694304
Reads aligned (%)
100.0
Duplicates removed (%)
21.6
Number of peaks
24853 (qval < 1E-05)

hg19

Number of total reads
5694304
Reads aligned (%)
100.0
Duplicates removed (%)
21.8
Number of peaks
24852 (qval < 1E-05)

Base call quality data from DBCLS SRA