Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Breast
Cell type
3134
Tissue
Mammary
Lineage
cellLine
Description
Mammary

Attributes by original data submitter

Sample

source_name
3134 cells
cell line
3134 murine mammary epithelial cell line
treatment
untreated
replicate
replicate 1
chip antibody
NA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Expression of dominant-negative variant proteins was induced by removal of tetracycline for 48 hrs prior to harvest by trypsinization. Nuclei from harvested cells were isolated and digested with 60-80 U/ml DNase I (Roche, Indianapolis, IN) for 3 min at 37°C. Digested DNA were incubated at 55°C with 10 μg/ml RNase A (Roche) for a few hours to overnight followed by addition of 25 μg/ml Proteinase K (Ambion, Austin, TX) and incubation at 55°C for at least 4 hrs. DNA fragments were purified by phenol/chloroform extraction and ultracentrifugation through a sucrose gradient. After purification, fragments (between 100 and 500 bp in size) were then pooled, precipitated and assembled into libraries for sequencing.

Sequencing Platform

instrument_model
Illumina Genome Analyzer

mm10

Number of total reads
9309890
Reads aligned (%)
77.7
Duplicates removed (%)
7.8
Number of peaks
154 (qval < 1E-05)

mm9

Number of total reads
9309890
Reads aligned (%)
77.6
Duplicates removed (%)
8.1
Number of peaks
173 (qval < 1E-05)

Base call quality data from DBCLS SRA