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
MCF7
antibody
JMJD6
treatment
none
cell line
Michigan Cancer Foundation-7 cells(MCF-7 cells)
antibody catalog/vendor
ab10526(Abcam)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were then fixed with 1% formaldehyde (Sigma) for 10 mins at room temperature (RT) (for MED12 and Pol II ChIP), or fixed with disuccinimidyl glutarate (DSG) (2mM) (Proteochem) for 45 min at RT, washed twice with PBS and then double-fixed with 1% formaldehyde for another 10 min at RT (for JMJD6 ChIP). Fixation was stopped by adding glycine (0.125M) 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. Resultant was immunoprecipitated with anti-MED12, anti-Pol II or anti-JMJD6 antibody overnight at 4°C, followed by incubation with protein G magnetic beads (Invitrogen) for an additional 2 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 (Qiagen) 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

hg19

Number of total reads
26222856
Reads aligned (%)
55.5
Duplicates removed (%)
7.5
Number of peaks
756 (qval < 1E-05)

hg38

Number of total reads
26222856
Reads aligned (%)
56.7
Duplicates removed (%)
6.3
Number of peaks
471 (qval < 1E-05)

Base call quality data from DBCLS SRA