Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Agrobacterium tumefaciens) | C58C1 | other | Dr. Robert Schmitz (University of Georgia) | |
| Strain, strain background (Eutrema salsugineum) | Shandong | https://www.arabidopsis.org | CS22504 | |
| Strain, strain background (E. salsugineum) | Shandong AtCMT3 lineages | This paper | Dr. Robert Schmitz (University of Georgia) | |
| Strain, strain background (E. salsugineum) | Yukon | https://www.arabidopsis.org | CS22664 | |
| Antibody | anti-H3K9me2 | Cell Signaling Technology | Cat# 9753 s; RRID: AB_659848 | Polyclonal, 5 μg |
| Antibody | anti-H3K9me1 | Abcam | Cat# 8896; RRID: AB_732929 | Polyclonal, 5 μg |
| Recombinant DNA reagent | pEarleyGate 302 pAtCMT3::gAtCMT3 | PMID: 23021223 | ||
| Peptide, recombinant protein | T4 DNA Ligase | NEB | Cat# M0202 | |
| Peptide, recombinant protein | Klenow Fragment | NEB | Cat# M0210 | |
| Peptide, recombinant protein | Phusion DNA Polymerase | NEB | Cat# M0530 | |
| Peptide, recombinant protein |
SuperScript III Reverse Transcriptase | Invitrogen | Cat# 18080044 | |
| Commercial assay or kit | Qiagen DNeasy Plant Mini Kit |
Qiagen | Cat# 69106 | |
| Commercial assay or kit | EZ DNA-methylation Gold Kit |
Zymogen | Cat# D5006 | |
| Commercial assay or kit | AMPure beads | Beckman Coulter | Cat# A63880 | |
| Commercial assay or kit | NEXTFLEX Bisulfite Sequencing Library Prep Kit | Bioo Scientific | Cat# NOVA-5119–01 | |
| Commercial assay or kit | KAPA HiFi Uracil+ | Roche | Cat #07959079001 | |
| Commercial assay or kit | Direct-Zol RNA Mini-prep plus |
Zymogen | Cat# R2071 | |
| Commercial assay or kit | Illumina TruSeq mRNA Stranded Library Kit | Illumina | Cat# 20020594 | |
| Commercial assay or kit | Protein A Dynabeads | Invitrogen | Cat# 10001D | |
| Commercial assay or kit | LightCycler 480 SYBR green master mix | Roche | Cat# 04707516001 | |
| Chemical compound, drug | Silwet L-77 | Phyto Technology Laboratories | Cat#:S7777 | |
| Chemical compound, drug | Pierce Protease Inhibitors | ThermoFisher | Cat# A32963 | |
| Chemical compound, drug | NEBNext dA-Tailing Reaction Buffer | NEB | Cat# B6059 | |
| Chemical compound, drug | proteinase K | ThermoFisher | Cat# 26160 | |
| Software, algorithm | methylpy | PMID: 26030523 | https://github.com/yupenghe/methylpy | |
| Software, algorithm | cutadapt v1.9.dev1 | DOI: https://doi.org/10.14806/ej.17.1.200 | RRID:SCR_011841 | https://cutadapt.readthedocs.io/en/stable/ |
| Software, algorithm | bowtie 2.2.4 | PMID: 22388286 | RRID:SCR_005476 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Software, algorithm | Intervene v.0.6.1 | PMID: 28569135 | https://intervene.readthedocs.io/en/latest/ | |
| Software, algorithm | Bedtools v2.27.1 | PMID: 20110278 | RRID:SCR_006646 | https://bedtools.readthedocs.io/en/latest/ |
| Software, algorithm | HISAT2 v2.0.5 | PMID: 25751142 | RRID:SCR_015530 | https://ccb.jhu.edu/software/hisat2/index.shtml |
| Software, algorithm | StringTie v1.3.3b | PMID: 25690850 | RRID:SCR_016323 | https://ccb.jhu.edu/software/stringtie/#pub |
| Software, algorithm | HOMER 4.10 | PMID: 20513432 | RRID:SCR_010881 | http://homer.ucsd.edu/homer/ |
| Software, algorithm | Trimmomatic v0.33 | PMID: 24695404 | RRID:SCR_011848 | http://www.usadellab.org/cms/?page=trimmomatic |
| Software, algorithm | Bowtie v1.1.1 | PMID: 19261174 | RRID:SCR_005476 | http://bowtie-bio.sourceforge.net/index.shtml |
| Software, algorithm | SAMtools v1.2 and v0.1.19 | PMID: 19505943 | RRID:SCR_00210 | http://samtools.sourceforge.net |
| Software, algorithm | R v3.44 | other | RRID:SCR_001905 | https://www.r-project.org |