Innate, translation-dependent silencing of an invasive transposon in Arabidopsis
Creators: name: Oberlin, Stefan
name: Rajendran, Rajeswaran
name: Trasser, Marieke
name: Barragán-Borrero, Verónica
name: Schon, Michael A.
name: Plotnikova, Alexandra
name: Loncsek, Lukas
name: Nodine, Michael D.
name: Marí-Ordóñez, Arturo
name: Voinnet, Olivier
Publisher: name: Zenodo
Year: 2021

description: The dataset contains all the original raw files for protein and RNA blots, qPCR and Sanger sequencing trace data and additional raw data, sorted by figure and figure panel. NGS data has been deposited on GEO, accession numbers of datasets used in each figure are rlisted accordingly in the list at the end. The content of each file is: <strong>FIGURE 1:</strong> <strong>1C:</strong> Northern blots raw TIFF image files for the detection of <em>35S:EVD</em> RNA isoforms in WT and <em>rdr6</em> backgrounds. <strong>1D:</strong> qPCR data for the quantification of <em>35S:EVD</em> RNA isoforms in WT and <em>rdr6</em> backgrounds. <strong>1E:</strong> Western blots and Coomassie staining raw TIFF image files for the detection of RDR6 and <em>35S:EVD</em> GAG proteins in WT and <em>rdr6</em> backgrounds. <strong>FIGURE 2:</strong> <strong>2B</strong>: qPCR data for the quantification of <em>35S:GFP-EVDin/ter-GUS</em> RNA isoforms in WT and <em>rdr6</em> backgrounds. <strong>2D:</strong> Northern blots raw TIFF image files for the detection of <em>35S:GFP-EVDin/ter-GUS</em> derived siRNAs in WT and <em>rdr6</em>backgrounds <strong>FIGURE 3:</strong> <strong>3D:</strong> qPCR data for the quantification of RNA isoforms produced by <em>EVD</em> splicing mutants in WT and <em>rdr6</em> backgrounds. <strong>3E:</strong> Northern blots raw TIFF image files for the detection of RNA isoforms and siRNAs produced by <em>EVD </em>mutants in WT and <em>rdr6</em> backgrounds. <strong>3F:</strong> Western blot and Coomassie staining raw TIFF image files for the detection of GAG proteins from <em>EVD</em> mutants in WT and <em>rdr6</em> backgrounds. <strong>FIGURE 5:</strong> <strong>5A:</strong> Northern blots raw TIFF image files for the detection of <em>35S:GFP-GUS</em> and <em>35S:GFP-EVDin/ter-GUS</em> mRNA isoforms and siRNAs in WT and <em>rdr6</em> backgrounds. <strong>5B:</strong> Western blots and Coomassie staining raw TIFF image files for the detection of GFP and GFP-GUS fusion proteins from <em>35S:GFP-GUS</em> and <em>35S:GFP-EVDin/ter-GUS</em> in WT and <em>rdr6</em> backgrounds. <strong>5C:</strong> qPCR data for the quantification of <em>EVD</em> and <em>GFP-EVDin/ter-GUS </em>RNA isoform abundance in total RNA from total, nuclear and cytoplasmic fractions. <strong>5D:</strong> qPCR data for the quantification of <em>EVD</em> and <em>GFP-EVDin/ter-GUS </em>polyA+ RNA isoform abundance in RNA from total, nuclear and cytoplasmic fractions. <strong>FIGURE 6</strong>: <strong>6G:</strong> 5’-OH RACE raw sanger sequencing trace data (ab1) and annotated files (gbk) mapping to <em>EVD</em>. Also used for Supplementary Figure 9D. <strong>SUPP FIGURE 1:</strong> <strong>S1A:</strong> Northern blots raw TIFF image files for the detection of <em>35S:EVD</em> derived siRNA in WT and <em>rdr6</em> backgrounds. <strong>S1B:</strong> Northern blots raw TIFF image files for the detection of <em>EVD</em> derived siRNA in <em>ddm1</em> and <em>ddm1 rdr6</em> backgrounds. <strong>S1D:</strong> qPCR data for the quantification of <em>EVD </em>RNA isoforms in <em>ddm1</em> and <em>ddm1 rdr6</em> backgrounds. <strong>S1E:</strong> Western blots and Coomassie staining raw TIFF image files for the detection of RDR6 and <em>EVD</em> GAG proteins in <em>ddm1</em>and <em>ddm1 rdr6</em> backgrounds. <strong>S1F+H:</strong> qPCR data for the quantification of <em>EVD </em>RNA isoforms in <em>met1-</em>derived<em> epiRIL#15 </em>(epi15) generations <strong>S1G:</strong> Northern blots raw TIFF image files for the detection of <em>EVD</em> derived siRNA in <em>met1</em>-derived<em> epiRIL#15 </em>(epi15) generations. <strong>SUPP FIGURE 2:</strong> <strong>S2A:</strong> Northern blots raw TIFF image files for the detection of <em>EVD</em> siRNAs in WT and <em>dcl1</em> F2 populations derived from crosses between <em>35S:EVD </em>and <em>dcl1.</em> <strong>S2B:</strong> Western blots and Coomassie staining raw TIFF image files for the detection of DCL1 and <em>EVD</em> GAG protein in WT and <em>dcl1</em> F2 populations derived from crosses between <em>35S:EVD </em>and <em>dcl1.</em> <strong>S2C:</strong> Northern blots raw TIFF image files for the detection of <em>EVD</em> siRNAs in WT and <em>hyl1</em> F2 populations derived from crosses between <em>35S:EVD </em>and <em>hyl1.</em> <strong>S2D:</strong> Western blots and Coomassie staining raw TIFF image files for the detection of HYL1 and <em>EVD</em> GAG protein in WT and <em>hyl1</em> F2 populations derived from crosses between <em>35S:EVD </em>and <em>hyl1.</em> <strong>S2F:</strong> qPCR data for the quantification of expression levels of miRNA and tasiRNA targets in <em>ddm1 </em>and <em>ddm1 rdr6</em>. Raw data for <em>EVD </em>RNA isoform levels in the same samples is located in the S1D folder. <strong>S2G:</strong> qPCR data for the quantification of expression levels of miRNA and tasiRNA targets in <em>35S:EVD WT </em>and <em>35S:EVD rdr6</em>. Raw data for <em>EVD </em>RNA isoform levels in the same samples is located in 1D. <strong>S2H:</strong> qPCR data for the quantification of expression levels of miRNA and tasiRNA targets and <em>EVD</em> isoforms in <em>35S:EVD WT </em>and <em>35S:EVD dcl1</em>. <strong>S2I:</strong> qPCR data for the quantification of expression levels of miRNA and tasiRNA targets and <em>EVD</em> isoforms in <em>35S:EVD WT </em>and <em>35S:EVD hyl1</em>. <strong>SUPP FIGURE 3:</strong> <strong>S3A-D-E:</strong> qPCR data for the quantification of <em>EVD</em> isoforms in total and polyA+ and polyA- RNA fractions from <em>35S:EVD WT, 35S:EVD rdr6, ddm1 </em>and <em>ddm1 rdr6</em>. <strong>S3B</strong>: Northern blots raw TIFF image files for the detection of <em>EVD</em> RNA isoforms in polyA+ and polyA- RNA fractions from <em>35S:EVD WT, 35S:EVD rdr6, ddm1 </em>and <em>ddm1 rdr6</em>. <strong>S3C</strong>: Northern blots raw TIFF image files for the detection of <em>EVD</em> RNA isoforms in polyA+ and polyA- RNA fractions from (1X) <em>35S:EVD rdr6, (</em>10X<em>) ddm1 </em>and (10X) <em>ddm1 rdr6</em>. <strong>SUPP FIGURE 4: </strong> <strong>S4A:</strong> Northern blot raw TIFF image files for the detection of <em>35S:GFP-EVDin/ter-GUS</em> RNA isoforms in WT and <em>rdr6</em>backgrounds. <strong>S4C:</strong> Western blot and Coomassie staining raw TIFF image files for the detection of GFP and GFP-GUS fusion proteins from <em>35S:GFP-EVDin/ter-GUS</em> in WT and <em>rdr6</em> backgrounds. <strong>S4D:</strong> Western blot and Coomassie staining raw TIFF image files for the detection of GUS and GFP-GUS fusion proteins from <em>35S:GFP-EVDin/ter-GUS</em> in WT and <em>rdr6</em> backgrounds. <strong>SUPP FIGURE 5:</strong> <strong>S5A:</strong> Northern blots raw TIFF image files for the detection of RNA isoforms and siRNAs produced by <em>EVD </em>mutants in WT and <em>rdr6</em> backgrounds from the POL region from the same blots as in 3E. <strong>S5B:</strong> Western blot and Coomassie staining raw TIFF image files for the extended detection of GAG proteins from <em>EVD</em> mutants in WT and <em>rdr6</em> backgrounds from 3F. <strong>S5C:</strong> Western blots and Coomassie staining raw TIFF image files for the detection of cytoplasmic (UGPase) and nuclear (H3) markers in total, nuclear and cytoplasmic fractions used for 5C and 5D. <strong>S5D:</strong> qPCR data for the quantification of <em>EVD</em> and <em>GFP-EVDin/ter-GUS </em>RNA full length mRNA abundance in total, nuclear and cytoplasmic RNA fractions. <strong>S5E:</strong> qPCR data for the quantification of <em>EVD</em> RNA isoform abundance in total, nuclear and cytoplasmic RNA fractions in <em>met1-</em>derived<em> epiRIL#15 </em>(epi15) F11 generation. <strong>S5F:</strong> Western blots and Coomassie staining raw TIFF image files for the detection of cytoplasmic (UGPase) and nuclear (H3) markers in total, nuclear and cytoplasmic fractions used for S5E. <strong>SUPP FIGURE 6:</strong> <strong>6C:</strong> Northern blots raw TIFF image files for the detection of <em>EVD</em> siRNAs in WT and <em>xrn4</em> F2 populations derived from e<em>pi15</em>crosses to <em>xrn4</em>. <strong>6D: </strong>qPCR data for the quantification of <em>EVD</em> RNA isoforms in WT and <em>xrn4</em> F2 populations derived from e<em>pi15</em> crosses to <em>xrn4</em>. <strong>6E:</strong> qPCR data for the quantification of <em>EVD</em> DNA copy number in WT and <em>xrn4</em> F2 populations derived from e<em>pi15</em> crosses to <em>xrn4</em>. <strong>6F:</strong> Northern blots raw TIFF image files for the detection of <em>EVD</em> siRNAs in WT and <em>rdr6</em> F2 populations derived from e<em>pi15</em>crosses to <em>rdr6</em>. <strong>6G:</strong> qPCR data qPCR data for the quantification of <em>EVD</em> RNA isoforms in WT and <em>rdr6</em> F2 populations derived from e<em>pi15</em>crosses to <em>rdr6</em>. <strong>6H:</strong> qPCR data for the quantification of <em>EVD</em> DNA copy number in WT and <em>xrn4</em> F2 populations derived from e<em>pi15</em> crosses to <em>rdr6</em>. <strong>S6I:</strong> Northern blots raw TIFF image files for the detection of <em>EVD</em> siRNAs in WT and <em>xrn2</em> F2 populations derived from e<em>pi15</em>crosses to <em>xrn2</em>. <strong>S6J:</strong> qPCR data for the quantification of <em>EVD</em> RNA isoforms in WT and <em>xrn2</em> F2 populations derived from e<em>pi15</em> crosses to <em>xrn2</em>. <strong>S6K:</strong> qPCR data for the quantification of <em>EVD</em> DNA copy number in WT and <em>xrn2</em> F2 populations derived from e<em>pi15</em> crosses to <em>xrn2</em>. <strong>S6L:</strong> Northern blots raw TIFF image files for the detection of <em>EVD</em> siRNAs in WT and <em>xrn3</em> F2 populations derived from e<em>pi15</em>crosses to <em>xrn3</em>. <strong>S6M:</strong> qPCR data for the quantification of <em>EVD</em> RNA isoforms in WT and <em>xrn3</em> F2 populations derived from e<em>pi15</em> crosses to <em>xrn3</em>. <strong>S6N:</strong> qPCR data for the quantification of <em>EVD</em> DNA copy number in WT and <em>xrn3</em> F2 populations derived from e<em>pi15</em> crosses to <em>xrn3</em>. <strong>SUPP FIGURE 10:</strong> <strong>S10C-D:</strong> Northern blots raw TIFF image files for the detection of siRNAs produced by <em>35S:HA-EVD-FLAG<sup>PGm</sup> </em>and <em>35S:GFP-EVDin/ter-GUS<sup>dG4</sup></em> mutants in T1 pools of WT and <em>rdr6</em> backgrounds. <strong>S10E:</strong> Western blot and Coomassie staining raw TIFF image files for the detection of HA-GAG protein from <em>35S:HA-EVD-FLAG<sup>PGm</sup></em> mutants in WT and <em>rdr6</em> backgrounds. <strong>S10F:</strong> Western blot and Coomassie staining raw TIFF image files for the detection of GFP protein from <em>35S:GFP-EVDin/ter-GUS<sup>dG4</sup></em> mutants in WT and <em>rdr6</em> backgrounds. <strong>SUPP FIGURE 11:</strong> <strong>S11B:</strong> Raw image file of EtBr staining of agarose gel electrophoresis of 5’OH-RACE prior to gel excision and cloning. <strong>SUPP FIGURE 12:</strong> <strong>S12A:</strong> Northern blots raw TIFF image files for the detection of <em>EVD</em> transcripts in <em>rdr6 </em>through PAGE. <strong>S12B:</strong> Raw data for total seed count per plant from epi15 F8 x <em>rdr6 </em>F2 populations. All the NGS data generated for this study can be found under the GEO accession GSE167484. The data was used to generate the following figure panels: Figure 1B. Figure 2C. Figure 6B. Figure 7A-D. Supplementary Figure 4B. Supplementary Figure 6B. Supplementary Figure 7A-F. Supplementary Figure 8B-E. Supplementary Figure 9. Supplementary Figure 10 A-B. Supplementary Figure 13 Publicly available sequencing data (from indicated datasets) was used to generate the following panels: Figure 1F, G: GSE52952 Figure 4A, B: GSE52952 + GSE93584 Supplementary Figure 1C: GSE41755 Supplementary Figure 8A: SRX7482974 + SRX7482974