Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CHD4

Cell type

Cell type Class
Neural
Cell type
Glioblastoma
MeSH Description
A malignant form of astrocytoma histologically characterized by pleomorphism of cells, nuclear atypia, microhemorrhage, and necrosis. They may arise in any region of the central nervous system, with a predilection for the cerebral hemispheres, basal ganglia, and commissural pathways. Clinical presentation most frequently occurs in the fifth or sixth decade of life with focal neurologic signs or seizures.

Attributes by original data submitter

Sample

source_name
glioblastoma tumor intiating cells, 0308 line
chip antibody
anti-CHD4, Abcam, ab72418
number of replicates
2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
20-100 million target cells were cross-linked at room temperature for 10 min with fresh 11% formaldehyde, quenched with 2.5M glycine, and processed through the DNA elution steps following the Agilent Technologies Mammalian ChIP-on-chip protocol (version 10.2, March 2011, http://www.chem.agilent.com/Library/usermanuals/Public/G4481-90010_MammalianProtocol_10.2.pdf), with the following modifications: sonication buffer composition 20 mM Tris-HCl , 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100; sonication in 3 mL was performed on a Bioruptor Standard (Diagenode, Denville, NJ) high setting at 4°C for 30 min total (cycles: 30 seconds on/30 seconds off); after sonication and centrifugation at 1400g, supernatant underwent immunoprecipitation with 10 ug antibody [anti-ZFXH4 (Abnova, H00079776-M11), mouse IgG2A (R&D Systems, AB003), anti-CHD4 (Abcam, ab72418), or rabbit polyclonal (Abcam, ab27478) antibodies] for four days for ZFHX4/mouse isotype control IP or overnight for CHD4/rabbit polyclonal control IP; protein G Dynabeads (Life Technologies, 1007D) were incubated with the IP lysates for 45 min and washed with sonication buffer x 2, buffer 1 (20 mM Tris HCl, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) x 2, buffer 2 (10 mM Tris HCl, 250 mM LiCl, 2 mM EDTA, 1% Igepal) x 2, and buffer 3 (10 mM Tris HCl, 1 mM EDTA, 50 mM NaCl) x 2. Immunoprecipitated DNA was quantified by picogreen and size was evaluated on a HighSense BioAnalyzer chip. Fragments between 100 and 600 bp were collected using an automated system (Pippin Prep, Sage Science) then end repaired, ligated and amplified for 15 cycles using reagents included in the Truseq DNA Sample Preparation kit from Illumina. Experimental conditions followed strictly the instructions of the manufacturer, with the exception of the adaptors being diluted 1/10 for the input DNA and 1/50 for all other samples. 7 barcoded libraries were run on 2 lanes of a Hiseq 2000 in a 50bp/50bp paired end run, using the TruSeq SBS Kit v3 (Illumina). The average number of read pairs per sample was 48 million

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
49242116
Reads aligned (%)
171.5
Duplicates removed (%)
4.9
Number of peaks
6346 (qval < 1E-05)

hg38

Number of total reads
49242116
Reads aligned (%)
173.5
Duplicates removed (%)
4.7
Number of peaks
6750 (qval < 1E-05)

Base call quality data from DBCLS SRA