Innate, translation-dependent silencing of an invasive transposon in Arabidopsis

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:

FIGURE 1:

• 1C: Northern blots raw TIFF image files for the detection of 35S:EVD RNA isoforms in WT and rdr6 backgrounds.
• 1D: qPCR data for the quantification of 35S:EVD RNA isoforms in WT and rdr6 backgrounds.
• 1E: Western blots and Coomassie staining raw TIFF image files for the detection of RDR6 and 35S:EVD GAG proteins in WT and rdr6 backgrounds. 

FIGURE 2:

• 2B: qPCR data for the quantification of 35S:GFP-EVDin/ter-GUS RNA isoforms in WT and rdr6 backgrounds.
• 2D: Northern blots raw TIFF image files for the detection of 35S:GFP-EVDin/ter-GUS derived siRNAs in WT and rdr6backgrounds

FIGURE 3:

• 3D: qPCR data for the quantification of RNA isoforms produced by EVD splicing mutants in WT and rdr6 backgrounds.
• 3E: Northern blots raw TIFF image files for the detection of RNA isoforms and siRNAs produced by EVD mutants in WT and rdr6 backgrounds.
• 3F: Western blot and Coomassie staining raw TIFF image files for the detection of GAG proteins from EVD mutants in WT and rdr6 backgrounds.

FIGURE 5:

• 5A: Northern blots raw TIFF image files for the detection of 35S:GFP-GUS and 35S:GFP-EVDin/ter-GUS mRNA isoforms and siRNAs in WT and rdr6 backgrounds.
• 5B: Western blots and Coomassie staining raw TIFF image files for the detection of GFP and GFP-GUS fusion proteins from 35S:GFP-GUS and 35S:GFP-EVDin/ter-GUS in WT and rdr6 backgrounds.
• 5C: qPCR data for the quantification of EVD and GFP-EVDin/ter-GUS RNA isoform abundance in total RNA from total, nuclear and cytoplasmic fractions. 
• 5D: qPCR data for the quantification of EVD and GFP-EVDin/ter-GUS polyA+ RNA isoform abundance in RNA from total, nuclear and cytoplasmic fractions.

FIGURE 6:

• 6G: 5’-OH RACE raw sanger sequencing trace data (ab1) and annotated files (gbk) mapping to EVD. Also used for Supplementary Figure 9D.

SUPP FIGURE 1:

• S1A: Northern blots raw TIFF image files for the detection of 35S:EVD derived siRNA in WT and rdr6 backgrounds.
• S1B: Northern blots raw TIFF image files for the detection of EVD derived siRNA in ddm1 and ddm1 rdr6 backgrounds.
• S1D: qPCR data for the quantification of EVD RNA isoforms in ddm1 and ddm1 rdr6 backgrounds.
• S1E: Western blots and Coomassie staining raw TIFF image files for the detection of RDR6 and EVD GAG proteins in ddm1and ddm1 rdr6 backgrounds.
• S1F+H: qPCR data for the quantification of EVD RNA isoforms in met1-derived epiRIL#15 (epi15) generations
• S1G: Northern blots raw TIFF image files for the detection of EVD derived siRNA in met1-derived epiRIL#15 (epi15) generations.

SUPP FIGURE 2:

• S2A: Northern blots raw TIFF image files for the detection of EVD siRNAs in WT and dcl1 F2 populations derived from crosses between 35S:EVD and dcl1.
• S2B: Western blots and Coomassie staining raw TIFF image files for the detection of DCL1 and EVD GAG protein in WT and dcl1 F2 populations derived from crosses between 35S:EVD and dcl1.
• S2C: Northern blots raw TIFF image files for the detection of EVD siRNAs in WT and hyl1 F2 populations derived from crosses between 35S:EVD and hyl1.
• S2D: Western blots and Coomassie staining raw TIFF image files for the detection of HYL1 and EVD GAG protein in WT and hyl1 F2 populations derived from crosses between 35S:EVD and hyl1.
• S2F: qPCR data for the quantification of expression levels of miRNA and tasiRNA targets in ddm1 and ddm1 rdr6. Raw data for EVD RNA isoform levels in the same samples is located in the S1D folder.
• S2G: qPCR data for the quantification of expression levels of miRNA and tasiRNA targets in 35S:EVD WT and 35S:EVD rdr6. Raw data for EVD RNA isoform levels in the same samples is located in 1D.
• S2H: qPCR data for the quantification of expression levels of miRNA and tasiRNA targets and EVD isoforms in 35S:EVD WT and 35S:EVD dcl1.
• S2I: qPCR data for the quantification of expression levels of miRNA and tasiRNA targets and EVD isoforms in 35S:EVD WT and 35S:EVD hyl1.

SUPP FIGURE 3:

• S3A-D-E: qPCR data for the quantification of EVD isoforms in total and polyA+ and polyA- RNA fractions from 35S:EVD WT, 35S:EVD rdr6, ddm1 and ddm1 rdr6.
• S3B: Northern blots raw TIFF image files for the detection of EVD RNA isoforms in polyA+ and polyA- RNA fractions from 35S:EVD WT, 35S:EVD rdr6, ddm1 and ddm1 rdr6.
• S3C: Northern blots raw TIFF image files for the detection of EVD RNA isoforms in polyA+ and polyA- RNA fractions from (1X) 35S:EVD rdr6, (10X) ddm1 and (10X) ddm1 rdr6.

SUPP FIGURE 4: 

• S4A: Northern blot raw TIFF image files for the detection of 35S:GFP-EVDin/ter-GUS RNA isoforms in WT and rdr6backgrounds.
• S4C: Western blot and Coomassie staining raw TIFF image files for the detection of GFP and GFP-GUS fusion proteins from 35S:GFP-EVDin/ter-GUS in WT and rdr6 backgrounds.
• S4D: Western blot and Coomassie staining raw TIFF image files for the detection of GUS and GFP-GUS fusion proteins from 35S:GFP-EVDin/ter-GUS in WT and rdr6 backgrounds.

SUPP FIGURE 5:

• S5A: Northern blots raw TIFF image files for the detection of RNA isoforms and siRNAs produced by EVD mutants in WT and rdr6 backgrounds from the POL region from the same blots as in 3E.
• S5B: Western blot and Coomassie staining raw TIFF image files for the extended detection of GAG proteins from EVD mutants in WT and rdr6 backgrounds from 3F.
• S5C: 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. 
• S5D: qPCR data for the quantification of EVD and GFP-EVDin/ter-GUS RNA full length mRNA abundance in total, nuclear and cytoplasmic RNA fractions.
• S5E: qPCR data for the quantification of EVD RNA isoform abundance in total, nuclear and cytoplasmic RNA fractions in met1-derived epiRIL#15 (epi15) F11 generation.
• S5F: 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.

SUPP FIGURE 6:

• 6C: Northern blots raw TIFF image files for the detection of EVD siRNAs in WT and xrn4 F2 populations derived from epi15crosses to xrn4.
• 6D: qPCR data for the quantification of EVD RNA isoforms in WT and xrn4 F2 populations derived from epi15 crosses to xrn4.
• 6E: qPCR data for the quantification of EVD DNA copy number in WT and xrn4 F2 populations derived from epi15 crosses to xrn4.
• 6F: Northern blots raw TIFF image files for the detection of EVD siRNAs in WT and rdr6 F2 populations derived from epi15crosses to rdr6.
• 6G: qPCR data qPCR data for the quantification of EVD RNA isoforms in WT and rdr6 F2 populations derived from epi15crosses to rdr6.
• 6H: qPCR data for the quantification of EVD DNA copy number in WT and xrn4 F2 populations derived from epi15 crosses to rdr6.
• S6I: Northern blots raw TIFF image files for the detection of EVD siRNAs in WT and xrn2 F2 populations derived from epi15crosses to xrn2.
• S6J: qPCR data for the quantification of EVD RNA isoforms in WT and xrn2 F2 populations derived from epi15 crosses to xrn2.
• S6K: qPCR data for the quantification of EVD DNA copy number in WT and xrn2 F2 populations derived from epi15 crosses to xrn2.
• S6L: Northern blots raw TIFF image files for the detection of EVD siRNAs in WT and xrn3 F2 populations derived from epi15crosses to xrn3.
• S6M: qPCR data for the quantification of EVD RNA isoforms in WT and xrn3 F2 populations derived from epi15 crosses to xrn3.
• S6N: qPCR data for the quantification of EVD DNA copy number in WT and xrn3 F2 populations derived from epi15 crosses to xrn3.

SUPP FIGURE 10:

• S10C-D: Northern blots raw TIFF image files for the detection of siRNAs produced by 35S:HA-EVD-FLAG^PGm and 35S:GFP-EVDin/ter-GUS^dG4  mutants in T1 pools of WT and rdr6 backgrounds. 
• S10E: Western blot and Coomassie staining raw TIFF image files for the detection of HA-GAG protein from 35S:HA-EVD-FLAG^PGm mutants in WT and rdr6 backgrounds.
• S10F: Western blot and Coomassie staining raw TIFF image files for the detection of GFP protein from 35S:GFP-EVDin/ter-GUS^dG4 mutants in WT and rdr6 backgrounds.

SUPP FIGURE 11:

• S11B: Raw image file of EtBr staining of agarose gel electrophoresis of 5’OH-RACE prior to gel excision and cloning.

SUPP FIGURE 12:

• S12A: Northern blots raw TIFF image files for the detection of EVD transcripts in rdr6 through PAGE.
• S12B: Raw data for total seed count per plant from epi15 F8 x rdr6 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