Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
OTX2

Cell type

Cell type Class
Neural
Cell type
D341 Med
Primary Tissue
Brain: Cerebellum
Tissue Diagnosis
Medulloblastoma

Attributes by original data submitter

Sample

source_name
OTX2 ChIP-seq in D341 cell line infected with shGFP
cell line
D341
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
22129761
Reads aligned (%)
75.2
Duplicates removed (%)
12.8
Number of peaks
42781 (qval < 1E-05)

hg38

Number of total reads
22129761
Reads aligned (%)
75.9
Duplicates removed (%)
12.4
Number of peaks
42906 (qval < 1E-05)

Base call quality data from DBCLS SRA