Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Breast
Cell type
Mammary glands
NA
NA

Attributes by original data submitter

Sample

source_name
Mammary
strain
C57BL/6
tissue
Mammary gland
state
lactation day 1
genotype
Wap-delE1c

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
DNase-seq: L1 mammary gland was isolated and snap frozen in liquid nitrogen. Frozen tissue was grinded into powder and homogenized with buffer A (15 mM Tris–HCl pH 8.0, 15 mM NaCl, 60 mM KCl, 1 mM EDTA, 0.5 mM EGTA, 0.15 mM Spermine, 0.5 mM Spermidine, 0.5 mM DTT, 1 mM PMSF with proteinase inhibitors). After cells were lysed in buffer A supplemented with 0.2% NP40, nuclei were collected, counted and re-suspended in DNase buffer. 10 U DNase I (New England Biolab) was used to digest 10 million nuclei at 37◦C for 5 min followed by proteinase K digestion. Genomic DNA was then purified. Approximately, 50–100 bp DNA fragments were selected for further library construction and sequencing. Libraries were prepared for sequencing using standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
36176410
Reads aligned (%)
70.9
Duplicates removed (%)
7.1
Number of peaks
19328 (qval < 1E-05)

mm9

Number of total reads
36176410
Reads aligned (%)
70.8
Duplicates removed (%)
7.2
Number of peaks
19228 (qval < 1E-05)

Base call quality data from DBCLS SRA