Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TP63

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC H9
NA
NA

Attributes by original data submitter

Sample

source_name
Surface Ectoderm Cells
cell line
H9
genotype
wild-type
treatment strategy
Day 7 of differentiation with RA/BMP4 (surface ectoderm)
chip-seq antibody
p63 (Active Motif 39739)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed in 1% formaldehyde, chromatin lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with the indicated antibody. 60x10^6 and 10x10^6 cross-linked cells were used per assay for p63 or histone marks, respectively. DNA was quantified using Qubit (Invitrogen). Between 5 and 10 ng of pooled DNA were used for library preparation using the NEBNext kit (New England Biolabs) and Agencourt AMPure XP beads (Beckman), both according to the manufacturer's protocol.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
61450916
Reads aligned (%)
66.6
Duplicates removed (%)
16.0
Number of peaks
5407 (qval < 1E-05)

hg38

Number of total reads
61450916
Reads aligned (%)
67.6
Duplicates removed (%)
15.1
Number of peaks
4799 (qval < 1E-05)

Base call quality data from DBCLS SRA