Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
OTX2

Cell type

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

Attributes by original data submitter

Sample

source_name
D283 Cell line
cell line
D283
antibody
ChIP Grade OTX2 - Abcam - ab21990

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation was performed as previously described (Kaur et al., Disease Models & Mechanisms, 2015). D283 tumorspheres were crosslinked for 10 minutes in 1% formaldehyde and quenched by 0.125M glycine for 5 minutes. Using 500 μl of sonification buffer [50 mM HEPES, pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% (w/v) Triton X-100, 0.1% (v/v) sodium deoxycholate, 1% (w/v) SDS and protease inhibitors] cell pellets were resuspended and sonicated into ∼400 bp with a bioruptor. Samples were incubated with protein A-Dynabeads ovalbumin and salmon sperm for 1 hour at 4°C to preclear the chromatin. OTX2 antibody was coupled to protein A-Dynabeads with protein A (rabbit antibody) in immunoprecipitation buffer. The precleared-chromatin and antibody bound beads were incubated overnight at 4°C. Unbound chromatin was washed away while the bound fraction was eluted in 400 μl of elution buffer and reverse crosslinked with 5 M NaCl (0.2 M final) and 4 μl of RNAse A (1 mg/ml) overnight at 55°C. Samples were treated with proteinase K (20 μg/μl), DNA was extracted using phenol:chloroform and suspended in 50 μl elution buffer 27 NextFlex Illumina Chip-seq kit

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
90527535
Reads aligned (%)
122.5
Duplicates removed (%)
36.4
Number of peaks
84826 (qval < 1E-05)

hg38

Number of total reads
90527535
Reads aligned (%)
123.8
Duplicates removed (%)
36.1
Number of peaks
86145 (qval < 1E-05)

Base call quality data from DBCLS SRA