Sample information curated by ChIP-Atlas

Antigen

Antigen Class
RNA polymerase
Antigen
RNA polymerase II

Cell type

Cell type Class
Breast
Cell type
MCF 10A
Primary Tissue
Breast
Tissue Diagnosis
Fibrocystic Disease

Attributes by original data submitter

Sample

source_name
mammary gland/breast
cell line
MCF10A
cell type
epithelial
cell lineage
ectoderm
treatment
adiramycin
chip antibody
anti-phosphorylated RNA Pol II-S2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclear pellets were washed and resuspended in 1× micrococcal nuclease reaction buffer [10 mM Tris–Cl (pH 7.9), 5 mM CaCl2, 0.5 mM DTT] and the chromatin was digested with micrococcal nuclease (New England Biolabs). The digestion was stopped with EDTA. Histone-DNA complexes were isolated with antibody. DNA fragments were ligated to a pair of adaptors for sequencing on an Illumina Hiseq-2000. The ligation products were size-fractionated to obtain 200–300-bp fragments on a 2% agarose gel and PCR-amplified for 18 cycles. Each library was diluted to 8 pM for 76 cycles of single-read sequencing on the Illumina Hiseq-2000 following the manufacturer's recommended protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
69474371
Reads aligned (%)
97.3
Duplicates removed (%)
12.0
Number of peaks
13267 (qval < 1E-05)

hg19

Number of total reads
69474371
Reads aligned (%)
97.1
Duplicates removed (%)
12.4
Number of peaks
13516 (qval < 1E-05)

Base call quality data from DBCLS SRA