Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
D283 Med
Primary Tissue
Brain
Tissue Diagnosis
Medulloblastoma

Attributes by original data submitter

Sample

source_name
American Type Culture Collection
antibody
IgG control
cell line
D283
otx2 silencing
OTX2low

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The reaction was then quenched with 0.125 M Glycine for 10 minutes. Cells were washed twice with 1X PBS. Chromatin was mechanically sheered in sonication buffer (HEPES pH 7.9 (50 mM), NaCl (140 mM, EDTA (1 mM), Triton (1%), Na-deoxycholate (0.1%), SDS (1%), PIC (1X)). Immunoprecipitation was carried out with H3K27me3 (07-449, Millipore) and H3K4me3 (07-473, Millipore) antibodies overnight at 4°C. Antibody complexes were captured on Dynabeads (Invitrogen) for 4 hours at 4°C then washed with Low Salt buffer (SDS (0.1%), Triton (1%), EDTA (2mM), Tris-HCl pH 8.1 (20 mM), NaCl (150 mM)), High Salt buffer (SDS (0.1%), Triton (1%), EDTA (2mM), Tris-HCl pH 8.1 (20 mM), NaCl (500 mM)), LiCl buffer (LiCl (0.25M), Na-deoxycholate (1%), EDTA (1mM), Tris-HCl pH 8.1 (10mM), NP-40 (1%)) and TE. Antibody complexes were eluted from the beads and reverse cross-linked for 12-16 hours at 65°C. Chromatin was then incubated in RNase A (0.2mg/mL) and NaCl (0.2 M/mL) for 2 hours. Proteinase K (0.2 mg/mL) was then added for an additional 2 hours. Chromatin was then cleaned using the Qiagen PCR Purification Kit according to manufacturer's instructions. NextFlex Illumina Chip-seq kit

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
61224201
Reads aligned (%)
97.0
Duplicates removed (%)
7.3
Number of peaks
1731 (qval < 1E-05)

hg19

Number of total reads
61224201
Reads aligned (%)
96.0
Duplicates removed (%)
9.0
Number of peaks
1445 (qval < 1E-05)

Base call quality data from DBCLS SRA