Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

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
cell line
MCF7
cell type
breast cancer cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
MCF7 were crosslinked with 1% formaldehyde for 10min and then incubated with nuclear extraction buffer (20mM Hepes-KOH ph7.5, 10mM KCl, 1mM EDTA, 0.2% NP40, 1mM DTT and 10% glycerol) to isolate nuclei. The nulei in sonication buffer (20mM Tris-HCl pH8, 150mM NaCl, 2mM EDTA, 0.1% SDS, 1% TritonX-100) was sheared in Misonix Sonicator. The further chromatin immunoprecipitation was implimented with RNAP2 antibody (05-623 Millipore) . The library construction followed the protocol in kit of NEBNext® ChIP-Seq Library Prep Reagent Set (E6200, New England Biolab) with the modfication that single index primer in place of dual primers was used in the final step of PCR amplication. The libraries were indexed with Illumina barcode. Five indexed libraries were finally pooled into one lane and sequenced in Hiseq2500.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
11330163
Reads aligned (%)
93.4
Duplicates removed (%)
1.8
Number of peaks
195 (qval < 1E-05)

hg19

Number of total reads
11330163
Reads aligned (%)
92.6
Duplicates removed (%)
2.8
Number of peaks
551 (qval < 1E-05)

Base call quality data from DBCLS SRA