Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3R26cit

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF-7
cell line
MCF-7 breast cancer cells
agent
E2
time
10min
chip antibody
H3R26Cit (AbCam, catalog# ab19847, lot# 135757)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
To achieve high temporal resolution, ChIP crosslinking concentration of formaldehyde was 2% and crosslinking was quenched after 1 minute with 250mM glycine. The H3R26Cit antibody we used for IP was AbCam: ab19847. The H3K27ac antibody we used for IP was Millipore: 07-360. The ends of the ChIP DNA were blunted and phosphorylated in 1X END Repair Buffer (Epicentre Biotechnologies, #ER0720), 250nM dNTPs, 1mM ATP, and 1X END-IT enzyme mix (Epicentre Biotechnologies, #ER0720) for 45 minutes. An A overhang was achieved in 1xNEB2 buffer, 200nM dATP (Invitrogen), 3units of Klenow (3¢-5¢ exo-) 5U/ml (from New England BioLabs), in 50ul volume for 30 minutes. 10nM of adapter was ligated to the DNA in 1X ligation buffer, 5ml (3000units) of UltraPure Ligase from enzymatics (Enzymatics T4 DNA Ligase #L603-HC-L) in a total volume of 50ul. Thirteen cycles of PCR with Phusion polymerase were performed to acquire the final library.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
10886878
Reads aligned (%)
69.7
Duplicates removed (%)
1.3
Number of peaks
1503 (qval < 1E-05)

hg19

Number of total reads
10886878
Reads aligned (%)
69.0
Duplicates removed (%)
1.7
Number of peaks
1371 (qval < 1E-05)

Base call quality data from DBCLS SRA