Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Saccharomyces cerevisiae) | Various | This paper | NCBITaxon:4932 | W303 Background; see Supplementary file 1 |
| Antibody | Anti-V5 (mouse monoclonal) | Thermo Fisher Scientific | Cat # R960-25 | (5 µl for ChIP, 1:5000 for Western) |
| Antibody | Anti-Hexokinase (rabbit polyclonal) | Rockland | Cat # 100-4159 | (1:20,000) |
| Antibody | Anti-m6A (rabbit polyclonal) | Synaptic Systems | Cat # 202-003 | 300 ng per 1 μg IP DNA |
| Antibody | Anti-Pgk1 (mouse monoclonal) | Invitrogen | Cat # 459,250 | (1:40,000) |
| Antibody | Anti-Sir3 (rabbit polyclonal) | N. Dhillon & R. Kamakaka |
(10 μl for ChIP, 1:1000 for Western) | |
| Recombinant DNA reagent | SIR2-M.ECOGII | This paper | Fusion of SIR2 and bacterial adenine methyltransferase M.ECOGII | |
| Recombinant DNA reagent | SIR3-M.ECOGII | This paper | Fusion of SIR3 and bacterial adenine methyltransferase M.ECOGII | |
| Recombinant DNA reagent | SIR4-M.ECOGII | This paper | Fusion of SIR4 and bacterial adenine methyltransferase M.ECOGII | |
| Recombinant DNA reagent | YEp24 | doi:https://doi.org/10.1016/0378-1119(79)90004-0 | Empty 2 μm overexpression plasmid; see Supplementary file 2 | |
| Recombinant DNA reagent | pMB34 | This paper | M.ECOGII inserted into pFA6a-natMX6; see Supplementary file 2 | |
| Recombinant DNA reagent | pMB54 | This paper | SIR3-M.ECOGII inserted into YEp24; see Supplementary file 2 | |
| Recombinant DNA reagent | pFA6a-natMX6 | doi:10.1002/yea.1291 | natMX6 marker integration cassette; see Supplementary file 2 | |
| Sequence-based reagent | Various oligonucleotides | This paper | qPCR and cloning primers |
See Supplementary file 3 |
| Commercial assay or kit | NEBNext Ultra II Library Prep Kit for Illumina | New England Biolabs | Cat # E7645 | |
| Commercial assay or kit | NEBNext Multiplex Oligos for Illumina | New England Biolabs | Cat # E7335/E7500 | |
| Commercial assay or kit | Qubit dsDNA HS | Invitrogen | Cat # Q32854 | |
| Commercial assay or kit | Qiaquick PCR Purification Kit | Qiagen | Cat # 28,104 | |
| Commercial assay or kit | Accel-NGS 1S Plus DNA Library Kit | Swift Biosciences | Cat # 10,024 | |
| Commercial assay or kit | Swift Single Indexing Primers Set A | Swift Biosciences | Cat # X6024 | |
| Commercial assay or kit | YeaStar Genomic DNA Kit | Genesee Scientific | Cat # 11-323 | |
| Commercial assay or kit | Covaris g-TUBE | Covaris | Cat # 520,079 | |
| Commercial assay or kit | NEB Oxford Nanopore Companion | New England Biolabs | Cat # E7180S | |
| Commercial assay or kit | NEBNext Quick Ligation Reaction Master Mix | New England Biolabs | Cat # B6058 | |
| Commercial assay or kit | NEB Blunt/TA Ligase Master Mix | New England Biolabs | Cat # M0367 | |
| Commercial assay or kit | Oxford Ligation Sequencing Kit | Oxford Nanopore Technologies |
Cat # SQK-LSK109 | |
| Commercial assay or kit | Oxford Native Barcoding Expansion 1–12 | Oxford Nanopore Technologies |
Cat # EXP-NBD104 | |
| Commercial assay or kit | Qiagen RNeasy kit | Qiagen | Cat # 74,104 | |
| Commercial assay or kit | SuperScript III First-Strand Synthesis System | Invitrogen | Cat # 18080051 | |
| Commercial assay or kit | DyNAmo HS SYBR Green kit | Thermo Fisher | Cat # F410L | |
| Commercial assay or kit | RNase-free DNase set | Qiagen | Cat # 79,254 | |
| Software, algorithm | SAMtools | doi:10.1093/bioinformatics/btp352 | ||
| Software, algorithm | Bowtie2 | doi:10.1038/nmeth.1923 | ||
| Software, algorithm | IGV | doi:10.1093/bib/bbs017 | ||
| Software, algorithm | Guppy Basecaller | Oxford Nanopore Technologies | ||
| Software, algorithm | Megalodon | Oxford Nanopore Technologies | https://github.com/nanoporetech/megalodon | |
| Software, algorithm | All-context rerio model | Oxford Nanopore Technologies | res_dna_r941_ min_modbases-all-context_v001.cfg |
For Megalodon modified base-calling; https://github.com/nanoporetech/rerio |
| Peptide, recombinant protein | Protein A Dynabeads | Thermo Fisher | Cat # 10,002D | |
| Peptide, recombinant protein | Proteinase K | New England Biolabs |
Cat # P8107S | |
| Peptide, recombinant protein | RNase A | Thermo Fisher | Cat # EN0531 |