Antigen

Antigen Class

Histone

Antigen

H3K4me3

Cell type

Cell type Class

Breast

Cell type

Mammary glands

NA

NA

Sample

source_name

Mammary gland (during lactation)

tissue

Mammary gland (during lactation)

strain

FVB/NJxCAST/EiJ

age

adult (12 weeks) - 3 days post natal

chip antibody

H3K4me3 (Millipore, 07-473, lot 2384705)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Total RNA and DNA were extracted using TRI-reagent (Sigma-Aldrich T9424) according to the manufacturers protocol. Total RNA was DNaseI treated using the DNA-FreeTM kit (Ambion). RNA-seq: 3ug Ribosomal RNA was depleted from total DNaseI-treated RNA using the RiboZero rRNA removal kit (Human/Mouse/Rat) (Epicentre). Strand-specific RNA-seq libraries were prepared employing the TruSeq RNA Sample Prep Kit v2 (Illumina) modified as described in Sultan et al. 2012 for strand-specific sequencing. ChIP-seq: Native ChIP was conducted as described in Regha et al. 2007. ChIP-seq libraries were prepared using the TruSeq ChIP Sample Prep Kit (Illumina).

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

66525557

Reads aligned (%)

92.1

Duplicates removed (%)

12.0

Number of peaks

443 (qval < 1E-05)

mm9

Number of total reads

66525557

Reads aligned (%)

91.9

Duplicates removed (%)

11.9

Number of peaks

494 (qval < 1E-05)