REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-5-methylcytosine antibody	Diagenode	C15200006-100
Biological Samples
CTVT biopsies (see STAR Methods for details)	Department of Veterinary Sciences, University of Messina, Italy and Veterinary Hospital ”Dr Halim Atique” - Centro Universitário de Rio Preto (UNIRP), São José do Rio Preto, São Paulo, Brazil	N/A
Chemicals, Peptides, and Recombinant Proteins
Vincristine (Italy) Vincristine (Brazil)	Teva Italia Libbs	038549010 7896094202870
Lidocaine	Zoetis	100319019
Proteinase K (ChIP grade)	Diagenode	C06050002
Critical Commercial Assays
SYBR® Green Mix	LifeTechnologies/Thermo Fisher	4309155
DNAse I kit	Thermo Fisher	AM1906
High-Capacity cDNA Reverse Transcription Kit	Applied Biosystems/Thermo Fisher	4368814
QuantiTect SYBR Green RT-PCR Kit	Qiagen	204243
AmpureXT magnetic beads	AutoQ Biosciences	AQ 60050
Illumina TruSeq RNA Library Prep kit v2	Illumina	RS-122-2001
KAPA Stranded mRNA-Seq Kit	KAPA Bioscience	KK8420
Auto-MeDIP kit	Diagenode	AF-Auto01-0016
End repair module	New England Biolabs	E6050L
A-tail module	New England Biolabs	E6053L
Adapter ligation module	New England Biolabs	E6056L
MESA BLUE qPCR MasterMix Plus	Eurogentec	RT-SY2X-03+WOUB
High-fidelity Phusion polymerase (5×)	New England Biolabs	M0530L
dNTP mix	New England Biolabs	N0447L
Deposited Data
RNAseq for CTVT-5 and CTVT-6	This paper	ArrayExpress E-MTAB-5488
RNAseq for 7xx CTVTs	This paper	ArrayExpress E-MTAB-5889
MeD-IP	This paper	ArrayExpress E-MTAB-5495
CTVT genome 1	Murchison et al., 2014	European Nucleotide Archive SAMEA2358413
CTVT genome 2	Murchison et al., 2014	European Nucleotide Archive SAMEA2358415
Cancer cells transcriptomes	ArrayExpress	E-GEOD-32474
Oligonucleotides
β-ACTIN Forward: CTCCATCATGAAGTGTGACGTTG	Murgia et al., 2006	N/A
β-ACTIN Reverse: CGATGATCTTGATCTTCATTGTGC	Murgia et al., 2006	N/A
DLA DQA-1 tumour. Forward: GAATTTGATGGCGATGAGTT	Murgia et al., 2006	N/A
DLA DQA-1 tumour Reverse: TCAGGATGTTCAAGTTTTGT TTTAT	Murgia et al., 2006	N/A
DLA DQA-1 common. Forward ACTACGGCATAAATGTCTA CCAGTC	Murgia et al., 2006	N/A
DLA DQA-1 common Reverse: CAAGTTTCTCAGTGCAC CCTGT	Murgia et al., 2006	N/A
LINE-MYC Forward: AGGGTTTCCCATCCTTTAACATT	Murgia et al., 2006	N/A
LINE-MYC Reverse: AGATAAGAAGCTTTTGCACAGCAA	Murgia et al., 2006	N/A
PE.Adapter.1.0: ACACTCTTTCCCTACACGACGCTCTTCCGATC∗T (∗) = phosphothiolate modification	This Paper	N/A
PE.Adapter.2.0: [Phos]GATCGGAAGAGCGGTTCAGCA GGAATGCCGAG [Phos] = 3′phosphate group	This Paper	N/A
Methylated qPCR Forward: GGTGAACTTCCGATAGTG	This Paper	N/A
Methylated qPCR Reverse: CAGTCATAGATGGTCGGT	This Paper	N/A
Unmethylated Forward: GTTAGAGCCTGCATAACG	This Paper	N/A
Unmethylated Reverse: GAAAGAGCACTGGCTAAC	This Paper	N/A
PCR_primer_PE_1.0: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCT ACACGACGCTCTTCCGATC∗T; (∗) = phosphothiolate modification	This Paper	N/A
PCR_primer_PE_2.0: CAAGCAGAAGACGGCATACGAGA TCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATC∗T [Phos] = 3′phosphate group	This Paper	N/A
Software and Algorithms
Ingenuity Pathway Analysis (IPA®)	Qiagen	www.qiagen.com/ingenuity
MEV software suite	TM4 MeV	http://www.tm4.org/mev.html
PicardTools	Broad Institute	http://broadinstitute.github.io/picard/
HTSeq-count	Anders et al., 2015	http://www-huber.embl.de/users/anders/HTSeq
TopHat v2.0.13	Trapnell et al., 2009	https://ccb.jhu.edu/software/tophat/index.shtml
R/BioConductor	Gentleman et al., 2004	https://www.bioconductor.org/
MeDUSA	Wilson et al., 2012	https://www.ucl.ac.uk/cancer/research/department-cancer-biology/medical-genomics-group/past-projects/medusa-project/medusa
DESeq BioConductor library	Anders and Huber, 2010	https://bioconductor.org/packages/release/bioc/html/DESeq.html
DESeq2 BioConductor library	Love et al., 2014.	http://bioconductor.org/packages/release/bioc/html/DESeq2.html