DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse

. 2022 Jul 13;2(7):100144. doi: 10.1016/j.xgen.2022.100144

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples

Patient-derived xenografts (PDXs)	Van Andel Research Institute	Human Colorectal Cancer PDX models: VARI PDX-026 VARI PDX-034 VARI PDX-047 VARI PDX-048 VARI PDX-050 VARI PDX-065 VARI PDX-066 VARI PDX-067 VARI PDX-069 VARI PDX-075 VARI PDX-079 VARI PDX-081 VARI PDX-084 VARI PDX-104 VARI PDX-106 VARI PDX-085 VARI PDX-144
Mouse DNA methylation calibration standards	EpigenDx	Cat# 80-8060M-PreMix
Rat DNA methylation calibration standards	EpigenDx	Cat# 80-8060R-PreMix
Human blood DNA	Bloodbank	Anonymous Donor

Chemicals, peptides, and recombinant proteins

2’-deoxy-5-azacytidine (Decitabine, DAC)	Sigma-Aldrich	A3656

Critical commercial assays

DNeasy Blood & Tissue Kit	Qiagen	Cat# 69506
AllPrep DNA/RNA Mini Kit	Qiagen	Cat# 80204
Mouse Methylation BeadChip	Illumina	Cat# 20041558
Infinium HD FFPE DNA Restore Kit	Illumina	Cat# WG-321-1002
EZ DNA Methylation Kit	Zymo Research	Cat# D5001

Deposited data

Raw and analyzed data	This paper	GEO: GSE184410

Experimental models: Cell lines

Hamster: CHO cells	ATCC	CRL-11268
Mouse: NIH/3T3 cells	ATCC	CRL-1658
Mouse: C3H 10T1/2 cells	ATCC	Clone 8, CCL-226
Mouse: B16 melanoma cells	ATCC	CRL-6322
Mouse: J1 ES cells and Dnmt1 gene-targeted derivatives	Jaenisch Laboratory, Whitehead Institute for Biomedical Research	J1, N/N Cl52, N/N Cl10, S/S Li et al., 1992³⁸
Mouse: Dnmt1 gene-targeted J1 ES Cells	Jaenisch Laboratory, Whitehead Institute for Biomedical Research	J1 C/C Lei et al., 1996⁴⁹
Mouse: Dnmt1 gene-targeted J1 ES Cells	Laird Laboratory, University of Southern California	J1 R/+ Eads et al., 2002⁴⁷
Mouse: Dnmt1 gene-targeted J1 ES Cells	Laird Laboratory, University of Southern California	J1 PH/+, P/H Chan et al., 2001⁴⁸

Experimental models: Organisms/strains

Mouse: 25 strains	The Jackson Laboratory	JAX # 002448 129S1/SvlmJ JAX # 000646 A/J JAX # 000648 AKR/J JAX # 000651 Balb/Cj JAX # 002282 BTBR_T+ ITpr3tf/J JAX # 000659 C3H/HeJ JAX # 002020 C57BL/6J JAX # 000665 C57BL/10J JAX # 005304 C57BL/6NJ JAX # 000668 C57L/J JAX # 000669 C58/J JAX # 000928 CAST/EiJ JAX # 000656 CBA/J JAX # 000670 DBA/1J JAX # 000671 DBA/2J JAX # 001800 FVB/NJ JAX # 002106 KK/HiJ JAX # 000676 LP/J JAX # 000550 MOLF/EiJ JAX # 001976 NOD/ShiLtJ JAX # 000684 NZB/BINJ JAX # 002105 NZO/HILtJ JAX # 001058 NZW/LacJ JAX # 003715 PWK/PhJ JAX # 001145 WSB/EiJ
Rat: CD® (Sprague Dawley) IGS Rat	Charles River Laboratories	Strain Code 001

Software and algorithms

SeSAMe	Zhou et al., 2018²⁰	https://bioconductor.org/packages/release/bioc/html/sesame.html
LOLA	Sheffield et al., 2016⁷⁵	https://bioconductor.org/packages/release/bioc/html/LOLA.html
BEDTools	Quinlan et al., 2010¹⁷⁸	https://github.com/arq5x/bedtools2

Other

Mouse Methylation BeadChip Manifest and Probe Annotation	This paper	http://zwdzwd.github.io/InfiniumAnnotation
Comparison of the Illumina and SeSAMe probe Manifests	This paper	https://github.com/zhou-lab/InfiniumAnnotationV1/blob/main/Anno/MM285/MM285.manifest.comparison.tsv.gz
Mouse Genome ChromHMM Segmentation	Van der Velde et al., 2021	https://www.encodeproject.org/
ENCODE mouse WGBS and human MethylationEPIC data	ENCODE Project Consortium et al., 2020	https://www.encodeproject.org/
Ensembl Mouse Gene Model version 99	Zerbino et al., 2018	https://useast.ensembl.org/Mus_musculus/Info/Index
Transcription factor binding sites and histone modification data from the Cistrome Database	Liu et al., 2011	http://cistrome.org/Cistrome/Cistrome_Project.html
Mouse strain genetic variation from The Mouse Genome Project	Keane et al., 2011	https://www.sanger.ac.uk/data/mouse-genomes-project/
Curation of the mouse array probes from imprinting control regions	This paper	https://github.com/zhou-lab/ImprintingAnno
176 WGBS datasets	ENCODE, GEO	176 Accession numbers listed in Table S1
H3K27me3 ChIP-seq peaks	ENCODE	ENCODE accession numbers listed in Table S7
Probes used to estimate human/mouse contribution in PDX data.	This paper	Table S6
Genes predicted to escape X-inactivation based on Mouse Methylation BeadChip	This paper	Table S2
Inbred mouse strain genealogy	Beck et al., 2000	https://www.nature.com/articles/ng0100_23