Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Breast
Cell type
Mammary epithelial cells
NA
NA

Attributes by original data submitter

Sample

source_name
Luminal mammary epithelial cells_input
background strain
Wildtype FVB
gender
female
tissue
Mammary gland
age
Adult (8-12 weeks)
protocol
Ovariectomy + 2 weeks 17β-oestradiol + progesterone

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Mammary glands were dissociated and cells purified using previously established protocols (PMID: 20445538). Lysates were extracted from sorted nuclei using a nuclei lysis buffer (according to ATAC-seq protocol from Buenrostro et al 2013). Transposase reaction was carried out following the protocol of the Nextera DNA library preparation kit (illumina). Libraries were prepared using the NeBNext buffer and appropriate ATAC-seq libraries adaptors (Illumina, Buenrostro et al, 2013). The llibrary was size-selected using the DNA on a ChIP technology.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
49733515
Reads aligned (%)
95.8
Duplicates removed (%)
8.6
Number of peaks
437 (qval < 1E-05)

mm9

Number of total reads
49733515
Reads aligned (%)
95.6
Duplicates removed (%)
8.6
Number of peaks
436 (qval < 1E-05)

Base call quality data from DBCLS SRA