Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CHD8

Cell type

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

Attributes by original data submitter

Sample

source_name
human control NPCs
cell type
iPSC (GM8330-8)-derived NPC
passages
11
shRNA target gene
GFP
chip antibody
CHD8 (Novus Biological NB100-60417)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Complexes were precipitated with Dynabeads Protein A beads (Invitrogen), and immunoprecipitated chromatin was eluted in elution buffer de-crosslinked at 65°C for 8 hr (or O/N), and treated with proteinase K (Roche). DNA was purified by extracting with phenol and chloroform and precipitating in ethanol. Library preparation was carried out using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB Cat#E73705), according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
66121585
Reads aligned (%)
182.5
Duplicates removed (%)
5.8
Number of peaks
20910 (qval < 1E-05)

hg38

Number of total reads
66121585
Reads aligned (%)
184.4
Duplicates removed (%)
5.5
Number of peaks
21530 (qval < 1E-05)

Base call quality data from DBCLS SRA