Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Breast
Cell type
Mammary glands
NA
NA

Attributes by original data submitter

Sample

source_name
Mammary gland
strain/background
C57BL/6
genotype/variation
Enhancer-delS1-4
Stage
Lactation day 1
tissue
Mammary gland
chip-antibody
H3K27ac (Abcam, ab4729)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Mammary tissues from specific stages during pregnancy and lactation were harvested, and stored at -80°C. The frozen-stored tissues were ground into powder in liquid nitrogen. Chromatin was fixed with formaldehyde (1% final concentration) for 15 min at room temperature, and then quenched with glycine (0.125 M final concentration). Samples were processed as previously described. The following antibodies were used for ChIP-seq: STAT5A (Santa Cruz Biotechnology, sc-1081), GR (Thermo Fisher Scientific, PA1-511A), H3K27ac (Abcam, ab4729), H3K4me3 (Millipore, 17-614), NFIB (Santa Cruz Biotechnology, sc-5567), and RNA polymerase II (Abcam, ab5408). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 2500 instrument (Illumina). Libraries for sequencing were prepared using standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
27892469
Reads aligned (%)
99.0
Duplicates removed (%)
4.4
Number of peaks
35012 (qval < 1E-05)

mm9

Number of total reads
27892469
Reads aligned (%)
98.9
Duplicates removed (%)
4.5
Number of peaks
35030 (qval < 1E-05)

Base call quality data from DBCLS SRA