REAGENT or RESOURCE	SOURCE	IDENTIFIER
Software and algorithms
STAR v2.7.1a	Dobin et al.69	https://github.com/alexdobin/STAR
RNA-SeQC73 v2.3.4	DeLuca et al.70	https://github.com/francois-a/rnaseqc
R package: DESeq2 v1.30.0	Love et al.71	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
BCFtools v1.6	Danecek et al.72	https://www.htslib.org/download/
PLINK v1.90b6.10	Purcell et al.73	https://www.cog-genomics.org/plink/
R package: edgeR v3.32.1	Robinson et al.74	https://bioconductor.org/packages/release/bioc/html/edgeR.html
R package: topGO	Alexa et al.75	https://bioconductor.org/packages/release/bioc/html/topGO.html
BisqueRNA R package	Jew et al.27	https://github.com/cran/BisqueRNA
APEX toolkit	Quick et al.76	https://github.com/corbinq/apex
R package: coloc	Giambartolomei et al.77	https://cloud.r-project.org/web/packages/coloc/index.html
R package: mashR	Urbut et al.40	https://github.com/stephenslab/mashr
BURST version 0.99.7f96	Al-Ghalith et al.78	https://github.com/knights-lab/BURST
MetaPhlAn v3.0.7	Beghini et al.79	https://huttenhower.sph.harvard.edu/metaphlan/
Sparse canonical components analysis code	Priya et al.53	https://github.com/blekhmanlab/host_gene_microbiome_interactions
CoPTR	Joseph et al.61	https://github.com/tyjo/coptr
Deposited data
Milk RNA-sequencing data	This paper	dbGaP: phs003408.v1.p1
Milk DNA-sequencing data and genotypes	This paper	dbGaP: phs003408.v1.p1
Infant fecal metagenomic sequencing data	This paper	SRA: PRJNA1019702
Milk transcriptome quantifications, infant fecal metagenome abundances, milk eQTL summary statistics, HMO concentrations, additional metadata	This paper	https://figshare.com/collections/Johnson_et_al_human_milk_multi-omics/7371256
GTEx RNA-sequencing quantifications and eQTL summary statistics	GTEx Portal25	https://gtexportal.org/home/downloads/adult-gtex/overview
1000 Genomes genotypes	Byrska-Bishop et al.80	https://www.internationalgenome.org/data-portal/data-collection/30x-grch38
Single-cell human milk RNA-seq data	Nyquist et al.17	https://singlecell.broadinstitute.org/single_cell/study/SCP1671/cellular-and-transcriptional-diversity-over-the-course-of-human-lactation
Breast cancer GWAS summary statistics	Zhang et al.43	http://bcac.ccge.medschl.cam.ac.uk/