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

Sample

source_name

OTX2 ChIP-seq in D341 cell line infected with CRISPR.GFP2

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

hg38

Number of total reads

26038812

Reads aligned (%)

98.8

Duplicates removed (%)

11.8

Number of peaks

57749 (qval < 1E-05)

hg19

Number of total reads

26038812

Reads aligned (%)

98.3

Duplicates removed (%)

12.4

Number of peaks

57694 (qval < 1E-05)