Sample information curated by ChIP-Atlas

Antigen

Antigen Class
DNase-seq
Antigen
DNase-Seq

Cell type

Cell type Class
Breast
Cell type
Mammary glands
NA
NA

Attributes by original data submitter

Sample

source_name
Dnase-seq_WT_I1
strain
C57BL/6
tissue
Mammary gland
time
Involution day 1
genotype/variation
wild type

Sequenced DNA Library

library_strategy
DNase-Hypersensitivity
library_source
GENOMIC
library_selection
DNase
library_construction_protocol
Frozen tissue was ground into powder and homogenized with buffer A (15mM Tris-HCl PH 8.0, 15 mM NaCl, 60 mM KCl, 1mM EDTA, 0.5mM EGTA, 0.15mM Spermine, 0.5mM Spermidine, 0.5mM DTT, 1mM PMSF with proteinase inhibitors). After cells were lysated, nucleuses were collected, counted and re-suspended in Dnase buffer. 10U Dnase I (New England Biolab) was used to digest 10 million nucleuses at 37C0 for 5 minutes followed by proteinase K digestion. Genomic DNA was then purified. 50 bp and -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
48085729
Reads aligned (%)
96.2
Duplicates removed (%)
8.8
Number of peaks
19017 (qval < 1E-05)

mm9

Number of total reads
48085729
Reads aligned (%)
96.0
Duplicates removed (%)
8.8
Number of peaks
19063 (qval < 1E-05)

Base call quality data from DBCLS SRA