Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
KhES-3
Primary Tissue
Embryo
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
Human Embryonic Stem Cells_input
chip antibody
none (input)
cell line
HES-3 (46 X,X) (ES Cell International)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
HES-3 Cells were crosslinked with 1% formaldehyde and treated with 1% SDS-based cell lysis buffer. The lysates were sonicated using branson sonifier 250. Ring1B-bound DNA was enriched using antibodies. Libraries were prepared using NEBNext Ultra DNA library Prep Kit for Illumina (New England Biolabs, Catalog # - E7370S) as per the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina MiSeq

hg38

Number of total reads
5094736
Reads aligned (%)
97.0
Duplicates removed (%)
0.8
Number of peaks
87 (qval < 1E-05)

hg19

Number of total reads
5094736
Reads aligned (%)
96.2
Duplicates removed (%)
1.6
Number of peaks
356 (qval < 1E-05)

Base call quality data from DBCLS SRA