Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Neural
Cell type
Meninges
MeSH Description
The three membranes that cover the BRAIN and the SPINAL CORD. They are the dura mater, the arachnoid, and the pia mater.

Attributes by original data submitter

Sample

source_name
meninges_normal control
tissue
meninges
who grade
n/a
histology
n/a
radiated
N
age
not determined
gender
not determined

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
10-15 frozen sections of each tumor block or dura sample were collected for ChIPseq experiments. Tissue was crosslinked with 1% formaldehyde, quenched with glycine, and washed with PBS. Nuclei were extracted by dounce homogenization and resuspended in nuclear lysis buffer containing 0.3% SDS. Chromatin was sheared by sonication with a Misonix S4000 in a 430A cup horn (60 minutes total, amplitude 30, 10 second pulses, 10 second rest). Soluble chromatin was incubated with magnetic beads coated with H3K27ac antibody (Abcam ab4729) overnight at 4°C. Chromatin was precipitated with magnet, washed extensively, and eluted with TE+1%SDS. Crosslinks were reversed and DNA was purified. Standard Illumina paired-end multiplexed library construction. H3K27ac ChIP and input samples were sequenced for each tumor (1x75bp, HiSeq 2000).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
38723709
Reads aligned (%)
98.1
Duplicates removed (%)
1.3
Number of peaks
952 (qval < 1E-05)

hg19

Number of total reads
38723709
Reads aligned (%)
97.6
Duplicates removed (%)
1.9
Number of peaks
874 (qval < 1E-05)

Base call quality data from DBCLS SRA