Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Breast
Cell type
Mammary glands
NA
NA

Attributes by original data submitter

Sample

source_name
L1 mammary gland
tissue
Mammary gland
time
Lactation day 1
genotype
MutA
chip antibody
H3K4me3 (Millipore, 17-614)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Frozen-stored mammary tissues 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). Antibodies against H3K27ac (Abcam, Ab4729), H3K4me3 (Millipore, 17-614), PolII (Abcam, ab5408) were used for ChIP. Libraries were prepared for sequencing using standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
23441948
Reads aligned (%)
97.9
Duplicates removed (%)
21.7
Number of peaks
20732 (qval < 1E-05)

mm9

Number of total reads
23441948
Reads aligned (%)
97.5
Duplicates removed (%)
21.7
Number of peaks
20778 (qval < 1E-05)

Base call quality data from DBCLS SRA