Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Meningioma
MeSH Description
A relatively common neoplasm of the CENTRAL NERVOUS SYSTEM that arises from arachnoidal cells. The majority are well differentiated vascular tumors which grow slowly and have a low potential to be invasive, although malignant subtypes occur. Meningiomas have a predilection to arise from the parasagittal region, cerebral convexity, sphenoidal ridge, olfactory groove, and SPINAL CANAL. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, pp2056-7)

Attributes by original data submitter

Sample

source_name
meningioma
tissue type
meningioma
mutation subtype
TRAF7/KLF4
grade
benign
chip antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
10 to 15 frozen sections of each tumor block or dura sample were collected for each experiment. 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 Q800R2 Sonicator by QSonica (60 minutes total, amplitude 30, 10 second pulses, 10 second rest). Soluble chromatin was incubated with magnetic beads coated with either H3K27ac antibody (ab4729) overnight at 4°C. Chromatin was precipitated using a magnet, washed extensively, and eluted with TE+1% SDS. Crosslinks were reversed, and samples were purified. Prior to sequencing, the enrichment of each sample was calculated using qPCR and well-established control primers for H3K27ac.. Samples were subjected to 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
50239838
Reads aligned (%)
99.5
Duplicates removed (%)
2.3
Number of peaks
1636 (qval < 1E-05)

hg19

Number of total reads
50239838
Reads aligned (%)
99.1
Duplicates removed (%)
4.0
Number of peaks
1533 (qval < 1E-05)

Base call quality data from DBCLS SRA