KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Cyclin D1	Biocare Medical	Cat# CP236B
Estrogen receptor	Santa Cruz Biotechnology	Cat# SC-542; RRID:AB_631470
pAKT S473	Cell Signaling Technologies	Cat# 3787; RRID:AB_331170
pERK1/2	Cell Signaling Technologies	Cat# 9101; RRID:AB_331646
STAT5A	Santa Cruz Biotechnology	Cat# SC-1081; RRID:AB_632448
CD8	ThermoFisher	Cat# 14008185; RRID:AB_467088
F4/80	Biolegend	Cat#123102; AB_893506
Progesterone Receptor	Dako	Cat#A0098; RRID:AB_2315192
Biological Samples
Mammary cell preparations from NRL-PRL mammary glands	This Paper	N/A
Critical Commercial Assays
Blood & Cell Culture DNA Mini Kit	QIAGEN	13323
TruSeq PCR free WGS library preparation kit	Illumina	20015962
RNEasy Midi Kit	QIAGEN	75142
TruSeq Stranded Total RNA library preparation kit	Illumina	20020596
Phusion Hot Start Flex DNA polymerase	New England Biolabs	M0535
QIAquick PCR Purification Kit	QIAGEN	28104
M-MLV reverse transcriptase	Promega	M1705
SYBR Green	ThermoFisher	4309155
Deposited Data
Mouse reference genome (NCBI build 38, GRCm38)	Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26
Ensembl reference transcriptome v84	Ensembl	ftp://ftp.ensembl.org/pub/release-84/gtf/mus_musculus/
Mouse Genomes Project v142	Keane et al., 2011	ftp://ftp-mouse.sanger.ac.uk/REL-1505-SNPs_lndels/
Human breast cancer sequencing dataset	Banerji et al., 2012	http://www.cbioportal.org/
Human breast cancer sequencing dataset	Cancer Genome Atlas Network, 2012	http://www.cbioportal.org/
Human breast cancer sequencing dataset	Curtis et al., 2012	http://www.cbioportal.org/
Human breast cancer sequencing dataset	Lefebvre et al., 2016	http://www.cbioportal.org/
Human breast cancer sequencing dataset	Stephens et al., 2012	http://www.cbioportal.org/
Human breast cancer sequencing dataset	Griffith et al., 2018	phs001234.v1.p1
Raw and analyzed data	This Paper	SRP189110
Experimental Models: Organisms/Strains
Mouse: NRL-PRL [lines 1647–13, TgN(Nrl-Prl)23EPS; 1655–8, TgN(Nrl-Prl)24EPS]	Rose-Hellekant et al., 2003	N/A
Oligonucleotides
Primers for Real Time PCR, see Table S6	This Paper	N/A
Primers for Sanger Sequencing, see Table S6	This Paper	N/A
Software and Algorithms
Codon Code Aligner [v 7.0.1]	CodonCode Corporation	https://www.codoncode.com/aligner/
Genome Modeling System	Griffith et al., 2015	https://github.com/genome/gms
BWA-MEMvO.7.10	Li, 2013	https://github.com/lh3/bwa
SAMBLASTERvO.1.22	Faust and Hall, 2014	https://github.com/GregoryFaust/samblaster
SomaticSniper v1.0.4	Larson et al., 2012	http://gmt.genome.wustl.edu/packages/somatic-sniper/
VarScan2 V2.3.6	Koboldt et al.,2012	http://varscan.sourceforge.net/
Strelkav1.0.11	Saunders et al., 2012	https://github.com/lllumina/strelka
Mutect v1.1.4	Cibulskis et al., 2013	https://software.broadinstitute.org/cancer/cga/mutect
GATK Somatic Indel Detector v5336	McKenna et al., 2010	https://software.broadinstitute.org/gatk/
Samtools r982	Li et al., 2009	http://samtools.sourceforge.net/
CopyCat v0.1	N/A	https://github.com/chrisamiller/copyCat
Manta	Chen et al., 2016	https://github.com/lllumina/manta
Integrate	Zhang et al., 2016	https://sourceforge.net/projects/integrate-fusion/
cBioPortal	Gaoet et al., 2013	http://www.cbioportal.org
Kallisto	Zerbino et al., 2018	https://pachterlab.github.io/kallisto/
TopHat	Trapnell et al., 2009	https://github.com/infphilo/tophat
Cufflinks	Trapnell et al., 2010	https://github.com/cole-trapnell-lab/cufflinks
HTSeq-count	Anders and Huber, 2010	https://htseq.readthedocs.io/en/release_0.11.1/
DESeq2	Love et al., 2014	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Gene set enrichment analysis (fgsea)	Sergushichev, 2016	https://bioconductor.org/packages/release/bioc/html/fgsea.html
Ggplot2	Wickham, 2009	https://ggplot2.tidyverse.org/
GenVisR	Skidmore et al., 2016	https://bioconductor.org/packages/release/bioc/html/GenVisR.html
Seq-lmmuCC	Chen et al., 2018	http://218.4.234.74:3200/immune/
Other
Manual review standard operating procedures	Barnell et al., 2018	N/A