Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GATA3

Cell type

Cell type Class
Neural
Cell type
NGP
NA
NA

Attributes by original data submitter

Sample

source_name
Neuroblastoma
cell line
NGP
chip antibody
GATA3
antibody catalog
sc-22206X
system
Brain

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified. Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
12999942
Reads aligned (%)
89.2
Duplicates removed (%)
5.2
Number of peaks
4948 (qval < 1E-05)

hg38

Number of total reads
12999942
Reads aligned (%)
90.6
Duplicates removed (%)
4.5
Number of peaks
4891 (qval < 1E-05)

Base call quality data from DBCLS SRA