Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RAD21

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC HUES64
NA
NA

Attributes by original data submitter

Sample

source_name
HUES64
cell type
HUES64 human embryonic stem cells
chip antibody
RAD21 (abcam, ab992)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Approximately 1x107 H9 hESCs were used to make each nasChIP-seq library. Anti-CTCF (Millipore) or -SMC1A (Millipore) antibodies were pre-incubated with Dynabeads Protein A beads (Thermo Fisher). Extracted chromatin was incubated with antibody-beads complex on a rotator at 4 °C for 5 hr. Beads were washed once with Wash Buffer (20 mM Tris-HCl pH 8.1, 500 mM NaCl, 2 mM EDTA pH 8.0, 1% Triton X-100, 0.1% SDS), twice with LiCl Buffer (10 mM Tris-HCl pH 8.1, 250 mM LiCl, 1 mM EDTA pH 8.0, 1% NP-40, 1% sodium deoxycholate), and once with 1x TE pH 8.0 with 50 mM NaCl. DNA was eluted by incubating beads in Elution Buffer at 65 °C for 30 min. Crosslinking-reversal, proteinase K digestion, phenol:chloroform:isoamyl alcohol extraction, ethanol precipitation, click chemistry, ethanol precipitation, streptavidin beads pull-down, and Illumina library preparation steps were the same as described above for nasBS-seq.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
107605519
Reads aligned (%)
193.2
Duplicates removed (%)
2.0
Number of peaks
81234 (qval < 1E-05)

hg38

Number of total reads
107605519
Reads aligned (%)
194.7
Duplicates removed (%)
1.8
Number of peaks
80890 (qval < 1E-05)

Base call quality data from DBCLS SRA