Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD1

Cell type

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

Attributes by original data submitter

Sample

source_name
hES HUES64
cell line
HUES64
chip antibody
anti-BRD1 (Abcam, ab71877)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed in HUES64 cells using the Myers lab ChIP-seq protocol (http://myers.hudsonalpha.org/documents/Myers%20Lab%20ChIP-seq%20Protocol%20v041610.pdf) with the following modifications. Nuclei were sonicated using a BioRuptor (Diagenode) for 20 cycles (30 sec on/30 sec off) on high power. After centrifugation at 4°C for 15 min at 20,000 rcf., 5% of total chromatin was set aside for input and the remainder was incubated with 10 ug of anti-BRD1 (Abcam, ab71877) or anti-RING1B (Abcam, ab3832) overnight at 4° C. Chromatin/antibody complexes were captured by incubation with Protein A Dynabeads (Invitrogen) for 2 hr at 4° with rotation. After cross-link reversal, DNA was purified by phenol-chloroform exctraction and ethanol precipitation. Illumina ChIP-seq libraries were prepared using the NEBNext ChIP-seq library preparation kit (New England Biolabs) and sequenced as described above. ChIP

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
27838653
Reads aligned (%)
92.8
Duplicates removed (%)
4.9
Number of peaks
1717 (qval < 1E-05)

hg38

Number of total reads
27838653
Reads aligned (%)
95.0
Duplicates removed (%)
3.3
Number of peaks
2704 (qval < 1E-05)

Base call quality data from DBCLS SRA