Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC derived neural cells
NA
NA

Attributes by original data submitter

Sample

source_name
Neuroepithelilal cells
cell type
Neuroepithelilal cells
age
day 10
genotype
PAX6A-FLAG
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
the cultures were digested with TrypLE to become single cells and then were crosslinked using 1% formaldehyde provided by the kit. The cells were incubated at room temperature for 10 mins in a chemical fume hood. After incubation, the cells were treated with glycine solution for 5 mins at room temperature. After washing with cold PBS twice, the cells were lysed with the lysis buffer in the presence of protease inhibitors and MNase (provided by the kit to digest DNA). They were then sonicated (three 20-second pulses at 3 watts power) to yield DNA fragments of about 150bp to 1000bp. After taking 10 µl samples as an INPUT the rest samples were incubated with 1 µg FLAG antibody in 100 µl IP buffer provided by the kit overnight at 2-8 °C. The pull-downs were harvested by ChIP Grade Protein A/G Magnetic Beads. The DNAs were recovered from the INPUTs and IPs RNA libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
32009513
Reads aligned (%)
97.3
Duplicates removed (%)
11.5
Number of peaks
618 (qval < 1E-05)

hg19

Number of total reads
32009513
Reads aligned (%)
96.7
Duplicates removed (%)
12.7
Number of peaks
518 (qval < 1E-05)

Base call quality data from DBCLS SRA