Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RB1

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 cell line, H1.2 knockdown, Rb ChIP
cell line
MCF7
sirna
siH1.2
chip antibody
Rb (4H1; Cell Signalling Technology #9309, lot 9)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were double fixed with DMA followed by formaldehyde. Following lysis and resuspension in RIPA buffer containing 0.1% SDS, cells were sonicated using a Bioruptor Pico (Diagenode). Chromatin was pre-cleared with pre-blocked protein A and G beads overnight prior to incubation with 1ug of antibody. Beads were washed, decrosslinked, treated with proteinase K and then purified using a QIAquick PCR kit (Qiagen). Libraries were constructed using NEBNext Ultra DNA library prep kit according to the manufacturer's instructions.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
112608856
Reads aligned (%)
157.2
Duplicates removed (%)
16.8
Number of peaks
1738 (qval < 1E-05)

hg38

Number of total reads
112608856
Reads aligned (%)
160.1
Duplicates removed (%)
16.0
Number of peaks
2728 (qval < 1E-05)

Base call quality data from DBCLS SRA