Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
JMJD6

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
Michigan Cancer Foundation-7 cells(MCF-7 cells)
cell line
MCF7
treatment
E2
chip antibody
ab10526(Abcam)

Sequenced DNA Library

library_name
GSM5658232
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with disuccinimidyl glutarate (DSG) (2 mM) (Proteochem) for 45 mins at RT, washed twice with PBS and then double-fixed with 1% formaldehyde for another 10 mins at RT. Fixation was stopped by adding glycine (0.125 M) and incubated for 5 mins at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300~500 bp average in size through sonication. The resultant protein was immunoprecipitated with anti-BRD4 antibody overnight at 4 °C, followed by incubation with protein G magnetic beads (Bio-Rad) for an additional 4 hrs. After washing and elution, the protein-DNA complex was reversed by heating at 65 °C overnight. Immunoprecipitated DNA was purified by using QIAquick spin columns and subjected to high throughput sequencing. The libraries were constructed following Illumina's Chip-Seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an 'A' base so the adaptors from Illumina with a 'T' can ligate on the ends. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
27731898
Reads aligned (%)
98.2
Duplicates removed (%)
31.0
Number of peaks
504 (qval < 1E-05)

hg19

Number of total reads
27731898
Reads aligned (%)
97.4
Duplicates removed (%)
32.8
Number of peaks
578 (qval < 1E-05)

Base call quality data from DBCLS SRA