Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Arabidopsis thaliana) | ECT2 | TAIR10 | AT3G13460 | EVOLUTIONARILY CONSERVED C-TERMINAL REGION 2 |
| Gene (Arabidopsis thaliana) | ECT3 | TAIR10 | AT5G61020 | EVOLUTIONARILY CONSERVED C-TERMINAL REGION 3 |
| Gene (Arabidopsis thaliana) | ECT4 | TAIR10 | AT1G55500 | EVOLUTIONARILY CONSERVED C-TERMINAL REGION 4 |
| Gene (Arabidopsis thaliana) | WIP1 | TAIR10 | AT4G26455 | WPP DOMAIN INTERACTING PROTEIN 1 |
| Gene (Drosophila melanogaster) | ADAR Isoform N | Genebank, FlyBase, NCBI | CG12598 NM_001297862 | Adenosine deaminase acting on RNA |
| Genetic reagent (A. thaliana) | SALK_002225 C (ect2-1) | NASC | N657472, N2110120 | |
| Genetic reagent (A. thaliana) | SALK_077502 (ect3-1) | NASC | N577502, N2110123 | |
| Genetic reagent (A. thaliana) | te234 (ect2-1/ect3-1/ect4-2) | Arribas-Hernández et al., 2018 | N2110132 | Donated to NASC and ABRC |
| Genetic reagent (A. thaliana) | ECT3pro:FLAG-DmADAR E488Q cd-ECT3ter | This paper (see Methods) | Seed requests to pbrodersen@bio.ku.dk | |
| Genetic reagent (A. thaliana) | ect3-1/ECT3pro:ECT3-FLAG-DmADAR E488Q cd-ECT3ter | This paper (see Methods) | Seed requests to pbrodersen@bio.ku.dk | |
| Genetic reagent (A. thaliana) | te234/ECT3pro:ECT3-FLAG-DmADAR E488Q cd-ECT3ter | This paper (see Methods) | Seed requests to pbrodersen@bio.ku.dk | |
| Genetic reagent (A. thaliana) | ect2-1/ECT2pro:ECT2-FLAG-DmADAR E488Q cd-ECT2ter | Arribas-Hernández et al., 2021 | ||
| Genetic reagent (A. thaliana) | te234/ECT2pro:ECT2-FLAG-DmADAR E488Q cd-ECT2ter | Arribas-Hernández et al., 2021 | ||
| Genetic reagent (A. thaliana) | ect2-1/ECT2pro:ECT2-mCherry-ECT2ter | Arribas-Hernández et al., 2018; Arribas-Hernández et al., 2020 | N2110839, N2110840 | Donated to NASC and ABRC |
| Genetic reagent (A. thaliana) | te234/ECT2pro:ECT2 W464A -mCherry-ECT2ter | Arribas-Hernández et al., 2018; Arribas-Hernández et al., 2020 | N2110847, N2110848 | Donated to NASC and ABRC |
| Genetic reagent (A. thaliana) | GFP:WIP1 | Xu et al., 2007 | ||
| Genetic reagent (A. thaliana) |
ect2-1/+ GFP: WIP1ECT2pro:ECT2- mCherry-ECT2ter |
This paper (see Methods) | Seed requests to pbrodersen@bio.ku.dk | |
| Antibody | anti-mCherry (rabbit polyclonal) | Abcam | ab183628 | Used for WB (1:1000) |
| Chemical compound, drug | Glufosinate-ammonium (PESTANAL) | Sigma | 45520 77182-82-2 | Used for selection of transgenic lines |
| Sequence-based reagent | USER cloning primers | This paper (Appendix) | Used for cloning. Sequences are in the Appendix | |
| Commercial assay or kit | RNeasy Plus Micro kit (inc RLT buffer) | QIAGEN | Cat. # 74,034 | Used for RNA-extraction of FACS-sorted protoplasts |
| Commercial assay or kit | Illumina DNA Nextera Flex kit (now called Illumina DNA Prep) | Illumina | Cat. # 20018704 | Used for Smart-seq2 library preparation |
| Commercial assay or kit | NEBNext small RNA library prep set for Illumina | NEB | Cat. # E7330S | Used for sRNA-seq library preparation |
| Software, algorithm | R | https://www.R-project.org/ | Used for data analyses | |
| Software, algorithm | hyperTRIBER | Rennie et al., 2021; https://github.com/sarah-ku/hyperTRIBER; https://github.com/sarah-ku/targets_arabidopsis | Used for calling significant ADAR-edited sites | |
| Software, algorithm | cutadapt | Kechin et al., 2017 | Used for trimming Smart-seq2, mRNAseq and sRNA-seq reads | |
| Software, algorithm | STAR | Dobin et al., 2013 | Used for mapping Smart-seq2, mRNAseq and sRNA-seq reads | |
| Software, algorithm | nanoPARE and PAS analysis pipelines | Schon et al., 2018; https://github.com/Gregor-Mendel-Institute/nanoPARE; https://github.com/maschon0/ect_polyA_analysis | Used for PAS/PAC analyses | |
| Software, algorithm | bedtools | Quinlan and Hall, 2010 | Used to merge polyadenylation clusters | |
| Software, algorithm | Salmon | Patro et al., 2017 | Used for transcript quantification (Smart-seq2 and mRNAseq) | |
| Software, algorithm | featureCounts | Liao et al., 2014 | Used for sRNA-seq quantification | |
| Software, algorithm | DESeq2 | Love et al., 2014 | Used for DEA (Smart-seq2, mRNAseq and sRNA-seq) | |
| Software, algorithm | gprofiler2 | Raudvere et al., 2019 | Used for GO-term enrichment analysis | |
| Software, algorithm | ggplot2 | https://ggplot2.tidyverse.org | Used to generate plots | |
| Software, algorithm | ImageJ | Schindelin et al., 2012 | Used to generate fluorescence intensity plots | |
| Software, algorithm | IGV (Integrative Genomics Viewer) | Robinson et al., 2011 | Used to navigate and represent genomic data |