Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZNF92

Cell type

Cell type Class
Neural
Cell type
HRPEpiC
Tissue
epithelium
Lineage
ectoderm
Description
retinal pigment epithelial cells

Attributes by original data submitter

Sample

source_name
Retinal pigment cells, science cell
chip-seq antibody
ZNF92
antibody catalog number
Abgent AP4646A
cell type
Retinal pigment cells #6540

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
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. 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.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
35287382
Reads aligned (%)
76.7
Duplicates removed (%)
12.6
Number of peaks
25331 (qval < 1E-05)

hg38

Number of total reads
35287382
Reads aligned (%)
78.3
Duplicates removed (%)
11.4
Number of peaks
24785 (qval < 1E-05)

Base call quality data from DBCLS SRA