Antigen

Antigen Class

TFs and others

Antigen

TFAP2A

Cell type

Cell type Class

Pluripotent stem cell

Cell type

iPS cells

NA

NA

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

hg38

Number of total reads

33393835

Reads aligned (%)

48.5

Duplicates removed (%)

18.4

Number of peaks

29958 (qval < 1E-05)

hg19

Number of total reads

33393835

Reads aligned (%)

48.4

Duplicates removed (%)

18.7

Number of peaks

29900 (qval < 1E-05)