REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
5-mC monoclonal antibody cl.b Classic	Diagenode	C15200006-500
Magnetic beads (Dynabeads M−280 Sheep anti-Mouse IgG; 11201D)	Life technologies	11202D
Biological samples
Female and male rats of an outbred strain	Harlan/Envigo (Indianapolis, IN)	Hsd:Sprague Dawley SD
Aspen Sani chips	Harlan
8640 Teklad 22/5 Rodent Diet	Harlan	8640
Chemicals, peptides, and recombinant proteins
Protein precipitation solution	Promega	A7953
Bovine serum albumen (BSA)	Sigma	A2153
Collagenase (Sigma C1639)	Sigma	C1639
F-12 culture medium	Gibco-Life Technologies, USA.	Ref 11765-054
Glycoblue	Life Technologies	AM 9516
Proteinase K	Bio Basic	PB0451
Buffered Phenol-Chloroform-Isoamylalcohol solution	Fisher Scientific	327111000
Dimethyl sulfoxide (DMSO)	J. T. Baker	9224-01
Oligonucleotides
NEBNext Multiplex Oligos for Illumina	NEB, San Diego, CA	E7335L
NEBNext Multiplex Oligos for Illumina	NEB, San Diego, CA	E7500L
Critical commercial kits
Qubit ssDNA kit (Molecular Probes Q10212)	Life Technologies	Q10212
NEBNext Ultra II RNA Library Prep Kit for Illumina	NEB, San Diego, CA	E7770L
Deposited data
The public database at NCBI GEO	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117995 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151458 https://www.ncbi.nlm.nih.gov/geo/	GEO # GSE117995
The public database at NCBI GEO	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117995 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151458 https://www.ncbi.nlm.nih.gov/geo/	GEO # GSE151458
The public database at NCBI GEO	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117995 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151458 https://www.ncbi.nlm.nih.gov/geo/	GEO # GSE121585
Software and algorithms
FastQC program	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Trimmomatic	http://www.usadellab.org/cms/?page=trimmomatic	PMID: 24695404
Bowtie2	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml	PMID: 22388286
MEDIPS	https://bioconductor.org/packages/release/bioc/html/MEDIPS.html	PMID: 24227674
BiomaRt R package	https://bioconductor.org/packages/release/bioc/html/biomaRt.html	PMID: 19617889 PMID: 16082012
Ensembl database	https://www.ensembl.org/index.html	PMID: 31691826
KEGG pathway search	https://www.genome.jp/kegg/mapper/search.html	PMID: 31423653
DAVID	https://david.ncifcrf.gov/home.jsp	PMID: 19131956 PMID: 19033363
WGCNA R package	https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/	PMID: 19114008
Pathway Studio	https://www.pathwaystudio.com