Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EBF3

Cell type

Cell type Class
Neural
Cell type
SK-N-SH
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
SK-N-SH, p.P177L EBF3-FLAG, FLAG ChIP
cell line
SK-N-SH (ATCC HTB-11)
stable expression
p.P177L EBF3-FLAG
chip antibody
anti-FLAG(M2) (Sigma-1804, Lot# SLBK1346V)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
20x10e6 cells for two biological replicates for each vector were crosslinked in 1% formaldehyde, sonicated to fragment chromatin using the BioRuptor Twin Sonicator (Diagenode), and immunoprecipitated using monoclonal anti-FLAG M2 antibody (Sigma). Samples were reverse-crosslinked and recovered DNA was used as input for Illumina sequencing library preparation. ChIP-seq was performed as previously described (Reddy et al. 2009).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
33943277
Reads aligned (%)
65.2
Duplicates removed (%)
21.3
Number of peaks
3858 (qval < 1E-05)

hg38

Number of total reads
33943277
Reads aligned (%)
66.7
Duplicates removed (%)
20.2
Number of peaks
3906 (qval < 1E-05)

Base call quality data from DBCLS SRA