KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
H3K27ac	Abeam	Cat# ab4729; RRID:AB_2118291
H3K27me3	Abeam	Cat# ab6002; RRID:AB_305237
Chemicals, Peptides, and Recombinant Proteins
pA-MNase conjugated to protein A	Steven Henikoff’s Lab
TRIzol®	Invitrogen	Cat# 15596026
MagMAX mirVana Total RNA Isolation Kit	Applied Biosystems	Cat# A27828
Papain	Worthington Biochemical	Cat# LS003118
Superscript II reverse transcriptase	Invitrogen	Cat# 18064
PowerUp SYBR Green Master Mix	Applied Biosystems	Cat# A25741
Etomoxir (Seahorse XF Mito Fuel Flex Test Kit)	Agilent	Cat# 103260
BAM 15	Timtec	Cat# ST056388
Rotenone	Sigma	Cat# R8875
Critical Commercial Assays
PureLink Genomic DNA Mini Kit	Invitrogen	Cat# K182001
EZ DNA Methylation-Gold Kit	Zymo	Cat# D5005
Accel-NGS Methyl-Seq DNA Library Kit	Swift Biosciences	Cat# 30024
RNeasy Plus Micro Kit	QIAGEN	Cat# 74034
QIAquick PCR Purification Kit	QIAGEN	Cat# 28104
SMARTer® ThruPLEX® DNA-Seq Kit	Takara Bio	Cat# R400674
SMARTer Stranded Total RNA-Seq Kit v2- Pico Input Mammalian	Takara Bio	Cat# 634411
Oligonucleotides
Prdm1 Forward ATTAAGCCTATCCCTGCCAAC	This paper	N/A
Prdm1 Reverse CTACTGTATTGCTTTGGGTTGC	This paper	N/A
Hk2 Forward TCAAAGAGAACAAGGGCGAG	This paper	N/A
Hk2 Reverse AGGAAGCGGACATCACAATC	This paper	N/A
Irs1 Forward GGATCGTCAATAGCGTAACT	This paper	N/A
Irs1 Reverse GAAATAGTTCGAGTCTGGGT	This paper	N/A
Hnrnpd Forward CTCCAGACACACCTGAAGAAA	This paper	N/A
Hnrnpd Reverse CAGAACCCACGCCTCTTATT	This paper	N/A
Plekh2 Forward AGAGACAAGTTATCGATGCAGAG	This paper	N/A
Plekh2 Reverse ACTGGTCTGAATATTAGCTGCTT	This paper	N/A
Prok1 Forward GCCTGCGGTTGTGTACC	This paper	N/A
Prok1 Reverse AGGTATGGTGTTGGCGTTTC	This paper	N/A
Immpl2 Forward AAATTGGGCGAGGGTACAATA	This paper	N/A
Immpl2 Reverse AGGCCTTGAAGCATCTTCTC	This paper	N/A
Deposited Data
Raw and analyzed data	This paper	GEO: GSE134873; https://neicommons.nei.nih.gov/#/.
Retina topological domains	Norrie et al., 2019	https://pecan.stjude.cloud/retinalnucleome
ATAC-Seq data in mouse rods	Mo et al., 2016	GEO: GSE72550
Nrl ChIP-Seq in mouse rods	Hao et al., 2012	https://datashare.nei.nih.gov/nnrlMain.jsp
Crx ChIP-Seq in mouse rods	Corbo et al., 2010	GEO: GSE20012
WGBS in mouse rods, cones, and rd7 model	Mo et al., 2016	GEO: GSE72550
WGBS in mouse ES cells and NPCs	Stadler et al., 2011	GEO: GSE30202
WGBS in mouse hepatocytes	Cole et al., 2017	GEO: GSE89274
WGBS in mouse beta cells	Avrahami et al., 2015	GEO: GSE68618
WGBS in mouse frontal cortex	Lister et al., 2013	GEO: GSE47966
WGBS in mouse cerebellum	Hon et al., 2013	GEO: GSE42836
Mouse genome assembly GRCm38.p4	Ensembl	http://mar2016.archive.ensembl.org/Mus_musculus/lnfo/lndex
Experimental Models: Organisms/Strains
Nrlp-GFP	Akimoto et al., 2006	N/A
C57BL/6J	National Inst of Aging	https://www.nia.nih.gov/research/dab/aged-rodent-colonies-handbook
Software and Algorithms
R version 3.4.4	R Core Team	https://www.r-project.org/
samtools version 1.9	Li et al., 2009	http://www.htslib.org/
deepTools version 3.1.1	Max Planck Institute for Immunobiology and Epigenetics	https://deeptools.readthedocs.io/en/develop/
Trim Galore! version 0.4.5	Babraham Bioinformatics	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Trimmomatic version 0.36	Bolger et al., 2014	http://www.usadellab.org/cms/?page=trimmomatic
FastQC version 0.11.5	Babraham Bioinformatics	http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Bismark version 0.19.1	Krueger and Andrews, 2011	https://www.bioinformatics.babraham.ac.uk/projects/bismark/
bowtie2 version 2.3.4.1	Langmead and Salzberg, 2012	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
bsseq version 1.14.0	Hansen et al., 2012	https://www.bioconductor.org/packages/release/bioc/html/bsseq.html
ggplot2 version 3.2.1	Hadley Wickham	https://github.com/tidyverse/ggplot2
csaw version 1.10.0	Lun and Smyth, 2016	https://bioconductor.org/packages/release/bioc/html/csaw.html
DSS version 2.26.0	Wu et al., 2015	http://bioconductor.org/packages/release/bioc/html/DSS.html
eulerr version 5.1.0	Larsson J	https://cran.r-project.org/web/packages/eulerr/index.html
circlize version 0.4.5	Gu et al, 2016	https://cran.r-project.org/web/packages/circlize/index.html
apcluster version 1.4.7	Bodenhofer et al., 2011	https://cran.r-project.org/web/packages/apcluster/index.html
ComplexHeatmap version 1.17.1	Gu et al., 2016	https://www.bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html
pheatmap version 1.0.10	Raivo Kolde	https://cran.r-project.org/web/packages/pheatmap/index.html
Gviz version 1.22.3	Hahne and Ivanek, 2016	https://bioconductor.org/packages/release/bioc/html/Gviz.html
karyoploteR version 1.2.2	Bernat Gel	https://bioconductor.org/packages/release/bioc/html/karyoploteR.html
methylSeekR version 1.16.0	Burger et al., 2013	https://bioconductor.org/packages/release/bioc/html/MethylSeekR.html
Stats version 0.1.0	Kartikeya Bolar	https://cran.r-project.org/web/packages/STAT/index.html
MASS version 7.3–50	Brian Ripley	https://cran.r-project.org/web/packages/MASS/index.html
countreg version 0.2–1	Achim Zeileis	https://r-forge.r-project.org/R/?group_id=522
gProfileR version 0.6.7	Reimand et al., 2007	https://cran.r-project.org/web/packages/gProfileR/index.html
questionr version 0.7.0	Barnier et al., 2018	https://cran.r-project.org/web/packages/questionr/index.html
Cytoscape version 3.7.1	Shannon et al., 2003	https://cytoscape.org/
ClueGO version 2.5.4	Bindea et al., 2009	http://apps.cytoscape.org/apps/cluego
toRun_Imputation.R	Stubbs et al., 2017	https://github.com/EpigenomeClock/MouseEpigeneticClock