REAGENT or RESOURCE	SOURCE	IDENTIFIER
Critical commercial assays
E.Z.N.A.® Total RNA Kit II	Omega Bio-Tek	R6934
Qiagen Gel Extraction Kit	Qiagen	28706
Illumina DNA Prep Kit	Illumina	20060059
RNA Nano 6000 Assay Kit	Agilent	5067–1511
NEBNext® UltraTM RNA Library Prep Kit	Illumina	E7770
Triglycerides content kit	Michybio	M1009A
Total cholesterol content kit	Michybio	M1010A
Deposited data
Raw data of 16S rRNA sequencing and metagenomics	This paper	SRA: PRJNA881293
Raw and processed data of RNA-seq	This paper	GEO: GSE240147
GH induced genes in male GF mice	Weger et al.66	GEO: GSE77221
Liver gene expression in female offspring from obese mother	Savva et al.67	SRA: PRJNA723771
Liver gene expression in female mice treated with dihydrotestosterone, a PCOS model	Roy et al.74	GEO: GSE197765
Transcription factors ChIP-Atlas data	Oki et al.119	https://chip-atlas.org/
ChIP-seq IRF9 in male mouse macrophages	Platanitis et al.120	SRA: SRX4178758
ChIP-seq STAT2 in male mouse macrophages	Platanitis et al.120	SRA: SRX4178757
ChIP-seq SUZ12 in male mouse ES cells	Hu et al.121	SRA: SRX111886
Experimental models: Organisms/strains
Mouse: C57BL/6J	Huafukang Biological Technology	SCXK-2020-0026
Oligonucleotides
Forward_16S_rRNA: 5′-CCTAYGGGRBGCASCAG-3′	Xing et al.122	N/A
Reverse_16S_rRNA: 5′-GGACTACNNGGGTATCTAAT-3′	Xing et al.122	N/A
Software and algorithms
R	R Foundation123	https://www.r-project.org
DESeq2	Love et al.124	https://doi.org/10.18129/B9.bioc.DESeq2
Enrichr	Kuleshov et al.125	http://amp.pharm.mssm.edu/Enrichr/
dryR	Weger et al.38	https://github.com/naef-lab/dryR
QIIME 2	Bolyen et al.126	https://qiime2.org/
Silva	Quast et al.127	http://www.arb-silva.de/
Microeco	Liu et al.128	https://github.com/ChiLiubio/microeco
Readfq	Chen et al.129	https://github.com/cjfields/readfq
MetaGeneMark	Zhu et al.130	http://topaz.gatech.edu/GeneMark/
MEGAHIT	Karlsson et al.131	N/A
CD-HIT	Li et al.132	http://www.bioinformatics.org/cd-hit/
Bowtie2	Langmead et al.133	https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.4/
DIAMOND	Buchfink et al.134	https://github.com/bbuchfink/diamond/
Hisat2	Kim et al.135	https://daehwankimlab.github.io/hisat2/