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
OTX2 ChIP-seq in D283 cell line infected with shOTX2.1393
cell line
D283
chip antibody
OTX2
source type
cell line

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin from formaldehyde-fixed cells (3-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads(Beckman Coulter) after crosslink reversal, RNAse A and Proteinase K treatment. ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
34321319
Reads aligned (%)
73.0
Duplicates removed (%)
24.7
Number of peaks
77233 (qval < 1E-05)

hg38

Number of total reads
34321319
Reads aligned (%)
73.8
Duplicates removed (%)
24.2
Number of peaks
77362 (qval < 1E-05)

Base call quality data from DBCLS SRA