Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TFAP2A

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPS cells
NA
NA

Attributes by original data submitter

Sample

source_name
WT p2hNCC
cell line
WT hiPSC#1
genotype
WT
treatment
hiPSC differentiation into hNCC (passage 2)
chip antibody
TFAP2A (sc-12726, Santa Cruz)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies againts the specific proteins of interest in each case. DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
31405768
Reads aligned (%)
49.0
Duplicates removed (%)
17.5
Number of peaks
34605 (qval < 1E-05)

hg38

Number of total reads
31405768
Reads aligned (%)
49.4
Duplicates removed (%)
17.2
Number of peaks
34667 (qval < 1E-05)

Base call quality data from DBCLS SRA