Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NUP98

Cell type

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

Attributes by original data submitter

Sample

source_name
Neural progenitor cells, Nup98 ChIP
cell line
HUES6-derived
cell type
neural progenitor cells
chip antibody
Nup98 (Cell Signaling #2292 )

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed in 1% formaldehyde (Polysciences) for 10min. Fixation was stopped by adding glycine to a final concentration of 125mM. Fixed cells were lysed and sonicated. DNA was immunoprecipitated, eluted, de-crosslinked, treated with RNase and protease, and purified. Library was constructed using Illumina ChIP-Seq DNA sample prep kit and sequencing was done on Illumina GAII.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
27184945
Reads aligned (%)
78.1
Duplicates removed (%)
16.3
Number of peaks
1081 (qval < 1E-05)

hg38

Number of total reads
27184945
Reads aligned (%)
79.9
Duplicates removed (%)
15.1
Number of peaks
923 (qval < 1E-05)

Base call quality data from DBCLS SRA