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
differentiated neural progenitor cells at day 28
cell line/strain
H1
cell type
differentiated neural progenitor cells at day 28 with deletion of UTX and JMJD3
genotype
UTX and JMJD3 knockout
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, 1×107 cells of each sample were crosslinked in 1% formaldehyde with rotation for 10 minutes at room temperature. And then these crosslinked reactions were stopped by 0.125 M glycine with rotation for 5 minutes at room temperature. and cell sample were sonicated, and then ChIPed with H3K27me3 antibodies. DNA libraries were prepared for sequencing using standard Illumina protocols.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
26277864
Reads aligned (%)
98.4
Duplicates removed (%)
4.3
Number of peaks
1145 (qval < 1E-05)

hg19

Number of total reads
26277864
Reads aligned (%)
97.5
Duplicates removed (%)
5.7
Number of peaks
977 (qval < 1E-05)

Base call quality data from DBCLS SRA