Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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, DAC+455 treatment
cell line
MCF-7 Breast adenocarcinoma cell line
chip antibody
Input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP DNA was prepared as described previously by our group (O’Hagan et al. 2011). Briefly, following drug treatment, cells were crosslinked with 37% formaldehyde and nuclei were subsequently extracted. Nuclear lysate was sonicated on Diagenode Bioruptor until majority of chromatin fragments were in the 100-300 bp range. Antibodies were incubated with sonicated chromatin overnight at 4°C, followed by capturing primary antibodies by adding ProteinA/G magnetic beads (DynaBeads) and incubating at room temperature for 3 hrs. Captured antibody complexes were then washed with low and hi-salt buffers. Chromatin was eluted off of the beads in elution buffer and cross-linking was reversed with an overnight incubation at 65°C. Chromatin fragments were then incubated with Rnase A for 1 hr at 37°C, and then Proteinase-K for 2 hrs at 55°C. Libraries were constructed according to the protocol provided by Illumina’s TruSeq DNA Sample Preparation v2 Kit

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
30032446
Reads aligned (%)
99.2
Duplicates removed (%)
2.2
Number of peaks
840 (qval < 1E-05)

hg19

Number of total reads
30032446
Reads aligned (%)
98.2
Duplicates removed (%)
3.6
Number of peaks
1007 (qval < 1E-05)

Base call quality data from DBCLS SRA