Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Breast
Cell type
Mammary cells
NA
NA

Attributes by original data submitter

Sample

source_name
mammary tissues, p13, no treatment, input
strain/background
outbred
tissue
mammary
developmental stage
day 13 of pregnancy
treatment
none
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Frozen-stored mammary tissues from p13 were broken into powder with mortar and pestle. With MECs, cells were cross-linked with 1% formaldehyde for 10 min at RT. Nuclei were extracted in Farnham lysis buffer (5mM PIPES PH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitor). Antibodies against STAT5 (Santa Cruz Biotechnology, cat# sc-1081; L-20, lot# L2012, 10ug) and H3K4me3 (Millipore, cat# 17-164, lot# JBC1793805, 5ug) were used for ChIP. Active Motif performed ChIP with in-house H3K27me3 antibody using pooled tissues from three individual mice of p13. Libraries were prepared for sequencing using standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
14112850
Reads aligned (%)
93.8
Duplicates removed (%)
3.4
Number of peaks
145 (qval < 1E-05)

mm9

Number of total reads
14112850
Reads aligned (%)
93.7
Duplicates removed (%)
3.5
Number of peaks
158 (qval < 1E-05)

Base call quality data from DBCLS SRA