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
strain
C57BL/6
tissue
Mammary gland
state
lactation day 1
genotype
wild type
chip antibody
H3K27ac (Abcam, ab4729)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Frozen-stored mammary tissues from L1 and p13 were broken into powder with mortar and pestle. Nuclei were extracted in Farnham lysis buffer (5mM PIPES pH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitors). Mammary epithelial cells were isolated from fresh L1 and p13 mammary tissues. Antibodies against STAT5A (Santa Cruz, sc-1081), GR (Thermo Scientific, PA1-511A), MED1 (Bethyl laboratory, A300-793A), H3K27ac (Abcam, Ab4729), NFIB (Santa Cruz, sc-5567), ELF5 (Santa Cruz, sc-9645), RNA Pol II (Abcam, Ab5408) and H3K4me3 (Milllipore, 17-614) were used for ChIP. Libraries were prepared for sequencing using standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
68231982
Reads aligned (%)
96.5
Duplicates removed (%)
18.1
Number of peaks
73563 (qval < 1E-05)

mm9

Number of total reads
68231982
Reads aligned (%)
96.4
Duplicates removed (%)
18.2
Number of peaks
73622 (qval < 1E-05)

Base call quality data from DBCLS SRA