EMBO/SourceData huggingface dataset:
Figure legend: "B.  Glucose tolerance Test  (GTT) demonstrating progressive defect in clearance of blood glucose in Rb∆K7 mice. 6-7 week (left) or 6 month (right) old fasting  Rb∆K7 mice and control  littermates (n=5-6 each per group) were injected with  glucose, and blood glucose was determined at indicated intervals. Error bars represent SD."
NCBI gene IDs:
"Rb: 19645"
Figure legend: "F. Loss of  pancreatic islet area in Rb∆K7 mice correlates with reduced proliferation and H3K36me3 histone marks, but not with increased cell death. TUNEL analysis showing apoptosis in 10 day-old Rb∆K7 islets  is even lower than in control littermates. Arrow points to a rare  apoptotic  cell in control islet. Serine800/804 phosphorylation of pRb in β-cells from 10 day-old control but not Rb∆K7 islets with a Ser-to-Ala substitution at this site. BrdU incorporation and  PH3 staining showing reduced S-phase and mitotic cells, respectively, in 2- and 3-week old Rb∆K7 vs control islets. Reduced H3K36me3 staining in  pancreatic islets from 3-week old Rb∆K7 mice  compared to control littermates (n&gt;3 for each experiment). Scale bar, 100 μm."
NCBI gene IDs:
"Rb: 19645"
Figure legend: "H. Reduced ability of  Rb∆K7 β-cell  to re-enter the cell cycle in response to pregnancy (top) or mitogenic (bottom) signals. Top, cell proliferation in P14.5 pregnant  Rb∆K7 islet β-cell  vs. control was determined by double  immunostaining with BrdU  and insulin  (left); quantification (right). Results were normalized for the number of BrdU/Insulin positive cells in control islets. An independent experiment using ki67 to quantify cell cycle re-entry top. Bottom, cell proliferation in Rb∆K7 β-cell vs. control  islets following  Exendin4  treatment was determined by  immunostaining for  Ki67; results were normalized for the number of positive cells in control islets. Mean ±SD, P values by two-tailed unpaired student's t-test. Scale bar, 100 μm."
NCBI gene IDs:
"Rb: 19645"
Figure legend: "I. Representative immunostaining showing induction of PDX1 (islet), SOX9 (pancreatic epithelium) and MCM4 (islet) expression  in Rb∆K7 vs control mice. Scale bar, 100 μm."
NCBI gene IDs:
"Rb: 19645"
Figure legend: "D. Representative image of a  pancreatic islet  from a 9-month old  Rb∆K7 mouse immunestained for the SASP marker IL-6 (red) and  insulin (green). DAPI was used to stain nuclei (blue). Arrows point to IL-6+,  insulin+  pancreatic β-cells. Scale bar, 20 μm."
NCBI gene IDs:
"Rb: 19645"
Figure legend: "E. Representative  immunostaining for the DDR marker γ-H2A  in islets from 3-week old Rb∆K7 and control  mice (left); statistical analysis (right; n=5 each). Arrows point to pancreatic γ-H2A-positive Rb∆K7 islet cells. Error bars represent SD; P value calculated by one-way ANOVA, Tukey's multiple comparisons test. Scale bar, 100 μm."
NCBI gene IDs:
"Rb: 19645"
Figure legend: "H. Vitamin C diet increases 5hmC  expression and improves  β-cell  morphology and islet size in  Rb∆K7 mice. Scale bar, 100 μm. I. Vitamin C diet reduces the difference in γ−H2A+ β-cells  in  Rb∆K7 vs control pancreatic islets relative to regular diet by 3.74 folds. Bars indicate mean ±SD. Adjusted P values by one-way ANOVA, Tukey's multiple comparisons test. J. Vitamin C diet increases  pancreatic islet cell cycle  re-entry during pregnancy of Rb∆K7 mice relative to control pregnant mice (no statistical difference, n.s.) or relative to pregnant  Rb∆K7 vs control mice fed on regular diet (P&lt;0.0001) by 3.8 folds. Bars represent mean ±SD. Adjusted P values by one-way ANOVA, Tukey's multiple comparisons test."
NCBI gene IDs:
"Rb: 19645"
Figure legend: "B. Left, top, effect of retrovirus-mediated transduction of under-phosphorylated Rb∆K11 (rRb∆K11) on   Rb-deficient mammary tumor cell proliferation as determined by  MTT  assay (n=4-5 technical replicates). Left, bottom, quantification of SA-βGAL in rRb∆K11-transduced cells. Bars represent mean ±SD; P value calculated by two-tailed unpaired student's t-test. Right, representative images of SA-βGAL staining showing robust senescence (arrows) in rRb∆K11-transduced cells. Original magnification: 200x."
NCBI gene IDs:
"Rb: 19645"
Figure legend: "F. Vitamin C  reduces cellular senescence induced by  retroviral-mediated over-expression of Rb∆K11. Top - images of SA-βGAL staining in human diploid cells, IMR90, transduced with control or rRb∆K11 virus with or without vitamin C added at the time of infection. Arrows point to  SA-βGAL-positive cells. Bottom left, quantification of SA-βGAL staining (bars represent mean ±SEM; n=4 biological replicates). P values by one-way ANOVA, Tukey's multiple comparisons test. Bottom right, dot-blot  analysis with antibody for 5hmC on DNA extracted from  IMR90 cells treated or not with vitamin C. Original magnification: 200x."
NCBI gene IDs:
"Rb: 5925"
Figure legend: "B Western blot  analysis of lysates of HEK293  cells 72 hours post-transfection with the various F8  variants. Neg, non-transfected cells."
NCBI gene IDs:
"F8: 2157"
Figure legend: "A  Western blot  (WB) of protein lysates of HEK293  cells 72 hours post-transfection (n=3; biological replicates) with either Npu inteins   or Heterologous (N-intein DnaB   + C-intein DnaE) split-inteins. I + II, N6 split-intein  proteins; I+II (Het.), heterologous split-intein  proteins; I, 5'N6 coding sequence (CDS)-N-DnaE  protein; I (N-int  B), 5'N6 CDS-N-DnaB. II, C-DnaE-3'N6 CDS protein. Excised inteins  (∼12kDa) are present only in the down part of the blot  when I + II (Npu inteins) are provided. Arrows indicate the full-length N6 protein, single halves and excised inteins."
NCBI gene IDs:
"DnaB: 
DnaE: "
Figure legend: "A Western blot  (WB) of protein lysates of HEK293  cells 72 hpt with the AAV-N6  split- intein  plasmids and with the codon-optimised set. I + II, N6   split-intein  proteins; I, 5' N6 CDS-N-DnaE  protein; II, C-DnaE-3'N6 CDS protein. (n=3; biological replicates). Arrows indicate the full-length N6 protein, excised inteins and both single halves. Codop: codon-optimised."
NCBI gene IDs:
"DnaE: "
Figure legend: "C Chromogenic assay performed on the medium from transfected cells to measure F8  activity levels reported as International Units/deciliter (IU/dl) (n=3; biological replicates).Data are presented as mean ±SEM. Significant differences between groups were assessed using Kruskal-Wallis test p value = 0.027. *indicates the significant difference between the I+II (N6 split-intein) and the II (C-DnaE-3'N6 CDS) groups: p value ≤ 0.05. **indicates the significant difference between the Codop I+II and the I (5' N6 CDS-N-DnaE) codop groups: p value ≤ 0.01. **indicates the significant difference between the Codop I+II and the II (C-DnaE-3'N6 CDS) codop groups: p value ≤ 0.01."
NCBI gene IDs:
"DnaE: "
Figure legend: "A Bisulfite DNA methylation sequencing of the Athila6ATE transcriptional start site (TSS) in genotypes with silenced TEs (left of the dashed line) or transcriptionally active TEs (right of the dashed line). Methylation in the CG (red), CHG (blue) and CHH (green) sequence contexts are shown (H = C, T, or A). Error bars represent Wilson score interval 95% confidence limits. For multiple statistical tests, one‐way ANOVA was performed using Tukey's multiple comparison test. ns, not significant."
NCBI gene IDs:
"Athila6A: "
Figure legend: "B The reads‐per‐million‐(RPM)‐normalized accumulation of Athila6ATE siRNAs from TE‐silenced epigenomes (left) and ddm1TE‐active epigenomes (right). Inset line graphs reflecting the same values are shown for select genotypes. All line graphs have the same y‐axis scale and are shown for increased resolution in genotypes with low siRNA levels."
NCBI gene IDs:
"Athila6A: 
ddm1: 836808"
Figure legend: "AGO6 relative enrichment of small RNAs (solid lines) and total small RNAs (dashed lines) are shown for each small RNA size class (21, 22 and 24nt) at four genomic loci.A A representative microRNA, miR158B. The location of miR158B from this locus is shown in orange."
NCBI gene IDs:
"miR158B: 6240876"
Figure legend: "AGO6 relative enrichment of small RNAs (solid lines) and total small RNAs (dashed lines) are shown for each small RNA size class (21, 22 and 24nt) at four genomic loci.B The SimpleHat2 non‐autonomous TE targeted by Pol IV‐RdDM.C The RDR6‐RdDM target locus TAS3a."
NCBI gene IDs:
"Pol IV: 
SimpleHat2: 
RDR6: 824112
TAS3a: 3768766"
Figure legend: "AGO6 relative enrichment of small RNAs (solid lines) and total small RNAs (dashed lines) are shown for each small RNA size class (21, 22 and 24nt) at four genomic loci.D The Athila6A consensus element in the wt Col epigenome.E The same Athila6A consensus element as in (D) upon transcriptional activation in the ddm1 epigenome."
NCBI gene IDs:
"Athila6A: 
ddm1: 836808"
Figure legend: "AGO6 relative enrichment of small RNAs (solid lines) and total small RNAs (dashed lines) are shown for each small RNA size class (21, 22 and 24nt) at four genomic loci.F The total small RNAs produced in the wt Col TE‐silenced epigenome.G The total small RNAs in ddm1 mutants."
NCBI gene IDs:
"ddm1: 836808"
Figure legend: "AGO6 relative enrichment of small RNAs (solid lines) and total small RNAs (dashed lines) are shown for each small RNA size class (21, 22 and 24nt) at four genomic loci.H Bisulfite sequencing of different regions of the Athila6A element. Error bars represent Wilson score interval 95% confidence limits. Differences in the methylation status were analyzed with a two‐tailed unpaired Student's t‐test."
NCBI gene IDs:
"Athila6A: "
Figure legend: "AGO6 relative enrichment of small RNAs (solid lines) and total small RNAs (dashed lines) are shown for each small RNA size class (21, 22 and 24nt) at four genomic loci.I A second biological replicate of the FLAG‐AGO6‐IP and no‐antigen control followed by deep sequencing shown for the Athila6A consensus element in ddm1 mutants. The transcriptional start sites of the LTR TSS‐ and IR‐driven transcripts are shown."
NCBI gene IDs:
"Athila6A: 
ddm1: 836808"
Figure legend: "AGO6 relative enrichment of small RNAs (solid lines) and total small RNAs (dashed lines) are shown for each small RNA size class (21, 22 and 24nt) at four genomic loci.J Analysis of the first base of AGO6‐enriched siRNAs from the wt Col TE‐silenced epigenome (left) and the ddm1 TE‐transcriptionally active epigenome (right)."
NCBI gene IDs:
"ddm1: 836808"
Figure legend: "B H3Ac control ChIP from the same chromatin used in the AGO6‐IP for the At1g08200 constitutively expressed gene and the Athila6A TSS. Enrichment of H3Ac at the Athila6A TSS is increased upon transcriptional activation in ddm1 mutants, while enrichment of H3Ac at the gene At1g08200 is consistently high in both wt Col and ddm1. Data are represented as mean ± SD of six biological replicates for each genotype."
NCBI gene IDs:
"Athila6A: 
At1g08200: 837341
ddm1: 836808"
Figure legend: "C-E AGO6‐ChIP qPCR analysis of (C) the gene At1g08200 and the Pol IV‐RdDM target SimpleHat2, (D) the Athila6A TSS in wt Col TE‐silenced epigenomes (left) and ddm1 TE‐active epigenomes (right) and (E) TAS3a. ChIP signals in (D) are normalized to the ago6 or ddm1 ago6 no‐antigen controls. ChIP signals in (C) and (E) are normalized to the ago6 no‐antigen control. In (C-E), each biological replicate data point is shown as a gray dot. The data are represented as mean ± SD. For multiple statistical tests, one‐way ANOVA was performed using Tukey's multiple comparison test."
NCBI gene IDs:
"Athila6A: 
Pol IV: 
SimpleHat2: 
ago6: 817856
At1g08200: 837341
ddm1: 836808
TAS3a: 3768766"
Figure legend: "F ChIP qPCR analysis of the FLAG‐tagged POL V protein in wt Col and ddm1. ChIP signals are normalized to the wt Col no‐antigen control."
NCBI gene IDs:
"ddm1: 836808"
Figure legend: "A AGO6 enrichment and depletion of 21-22nt siRNAs for the entire genome in 100‐bp tiles for both wt Col and ddm1. Tiles were categorized by annotation feature."
NCBI gene IDs:
"ddm1: 836808"
Figure legend: "B Of the tiles in (A) in both wt Col and ddm1, we determined the number of tiles with ≥ 2‐fold CHH methylation dependent on RDR6."
NCBI gene IDs:
"ddm1: 836808"
Figure legend: "C Distribution of AGO6 enrichment across TEs (solid lines) and genes (dashed lines) for different sizes of small RNAs in either the wt Col TE‐silenced epigenome or the ddm1 TE‐transcriptionally active epigenome. Dashed lines have the same color codes as the solid lines. 'Start' and 'Stop' represent the edges of the TE and the transcriptional start and stop sites of the genes."
NCBI gene IDs:
"ddm1: 836808"
Figure legend: "D-G Heatmaps of AGO6 enrichment of TE siRNA size classes in wt Col and ddm1 epigenomes. Analyzed were (D) the position of the TE on a chromosome and TE size, (E) the copy number of the TE, (F) the TE type and (G) the TE family name. The color of the TE family name in (G) corresponds to the TE type in (F)."
NCBI gene IDs:
"ddm1: 836808"
Figure legend: "A Bisulfite sequencing of the Athila6A TSS in juvenile leaf tissue."
NCBI gene IDs:
"Athila6A: "
Figure legend: "B qRT-PCR analysis of Athila6A gag/pol steady‐state mRNA transcript levels in inflorescence and leaf tissue."
NCBI gene IDs:
"Athila6A: "
Figure legend: "C qRT-PCR analysis of AGO6 and AGO4 mRNA transcript levels in inflorescence and juvenile leaf tissue."
NCBI gene IDs:
"AGO4: 817246
AGO6: 817856"
Figure legend: "E, F Side view of an inflorescence with (E) or without (F) the AGO6‐GFP transgene.G, H Top‐down view of an inflorescence with (G) or without (H) the AGO6‐GFP transgene."
NCBI gene IDs:
"AGO6: 817856"
Figure legend: "K CHH methylation levels of the RDR6‐RdDM targets TAS3a and Athila6A TSS in whole‐inflorescence‐tissue samples compared to dissected young buds corresponding to floral stages 6-8."
NCBI gene IDs:
"Athila6A: 
RDR6: 824112
TAS3a: 3768766"
Figure legend: "A. Spike-binding  antibodies in serum. Binding  by antibodies of classes M, G, and A is detected with secondary antibodies conjugated to different fluorochromes, and the results are shown on the left, middle, and right plots, respectively. Binding  (geometric mean fluorescence intensity - GMFI- of corresponding secondary antibody) to TE  cells expressing  SARS-CoV-2 spike protein is plotted on the vertical axis, and binding to untransfected cells on the horizontal axis. Each point represents a value from one donor. Samples from donors with no known exposure to  SARS-CoV-2 antigens (n = 86) are plotted with blue circles, recently infected donors (n = 34) with red circles, and vaccinated  donors (n = 14) with green diamonds. Red circles with black triangles correspond to donors from whose  B cells monoclonal antibodies were isolated (n = 5, P values are derived from a two-way analysis of variance followed by Tukey's test to compare the specific binding, i.e., (binding  to spike-expressing cells)/(binding  to untransfected cells) between conditions (convalescent  or vaccinated  against unexposed) within each antibody class. The experiment was independently repeated three times, and results shown come from the third replicate."
NCBI gene IDs:
"spike: 43740568"
Figure legend: "D. Comparison of spike-specific IgM, as measured by  flow cytometry or ELISA. The left two \"FC\" are the results of flow cytometry, and the left verical axis shows the ratio of serum IgM binding  to spike-expressing cells, vs binding  to non-expressing control cells, as plottted in A. The right two columns show spike-RBD-specific IgM  as measured by an IgM-capture ELISA, and the right vertical axis shows the optical densities (OD). P values are calculated by two-way analysis of variance, followed by Sidak's multiple comparisons test. The entire experiment was repeated three times, and the data shown are derived from the third replicate."
NCBI gene IDs:
"spike: 43740568"
Figure legend: "Phenotypes  of blood B cells. B cells from 15 ml of  peripheral blood from each of three convalescent donors were isolated by negative selection with magnetic beads, exposed to adherent cells expressing spike-mCherry  for 3 hours, then retrieved and labeled with fluorescent antibodies and measured by flow cytometry. (A) UMAP algorithm (5000 randomly selected cells/sample) was used to depict the major B cell subsets clustered according to marker expression."
NCBI gene IDs:
"mCherry: 
spike: 43740568"
Figure legend: "Phenotypes  of blood B cells. B cells from 15 ml of  peripheral blood  from each of three convalescent donors were isolated by negative selection with magnetic beads, exposed to adherent cells expressing spike-mCherry  for 3 hours, then retrieved and labeled with fluorescent antibodies and measured by flow cytometry. FlowSOM-based B cell  subpopulations are overlaid as a color dimension, and the colors of the clusters are shown on the left of heatmap (B). B. Heatmap showing mean population expression  levels of markers used for UMAP visualization and FlowSOM-clustering. Colors shown in the legend on the left are also used in the UMAP representation in (A)."
NCBI gene IDs:
"mCherry: 
spike: 43740568"
Figure legend: "Phenotypes  of blood B cells.  B cells  from 15 ml of  peripheral blood  from each of three convalescent donors were isolated by negative selection with magnetic beads, exposed to adherent cells expressing spike-mCherry  for 3 hours, then retrieved and labeled with fluorescent antibodies and measured by flow cytometry. C. Gating strategy to define CD69-high, mCherry-high, spike-capturing B cells (i.e., membrane antigen capture activated cells, MACAC, red box). Dot plot shows CD69  and mCherry fluorescence for  B cells from one of three donors gated by forward and side scatter, and negative for the dye used to mark the antigen donor cells."
NCBI gene IDs:
"mCherry: 
spike: 43740568"
Figure legend: "Phenotypes  of blood B cells. B cells from 15 ml of  peripheral blood  from each of three convalescent donors were isolated by negative selection with magnetic beads, exposed to adherent cells expressing spike-mCherry  for 3 hours, then retrieved and labeled with fluorescent antibodies and measured by  flow cytometry. D. Relative fractions of different B cell subpopulations, from three donors, as shown in A-B, in all B cells compared to within MACAC B cells. P values are based on two-tailed t-tests between the groups. Correlation coefficients (r) were calculated from the z-statistic of the Wilcoxon-Mann-Whitney test. A black horizontal line represents the median. Boxplots represent the interquartile range (IQR). Whiskers extend to the farthest data point within a maximum of 1.5× IQR. Every point represents one donor."
NCBI gene IDs:
"mCherry: "
Figure legend: "E. Gating strategy in MACAC sorting. Single cells are selected based on scatter, antigen-expressing TE spike-mCherry  cells excluded on Cell Trace Violet label, and the spike-capturing (mCherry-high), activated (CD69-high) B cells (population labeled \"MACAC\" in red on the right-most plot) are sorted. The middle plot shows B cells that did not adhere to the TE-spike-cherry  antigen-expressing cells (putatively antigen-irrelevant), and the right plot those that did (putatively antigen-recognizing). Plots show data from one of five convalescent donors Cells in the MACAC  gate were singly distributed into wells of 384-well plates and cultured for 9 days with  IL-21 and CD40L, and then the single well culture supernatants were screened for anti-spike  antibody binding  and virus neutralization as described below. F. Results of single well supernatant screening for antibody binding  to SARS-CoV-2 spike  protein. Results from 3266 wells from 5 donors are shown for IgM  (left), IgG (middle), and IgA  (right)."
NCBI gene IDs:
"spike: 43740568"
Figure legend: "E. Flow cytometric  determination of antibody-dependent complement  deposition on cells. Cells expressing SARS-CoV-2 spike  protein and untransfected control cells were incubated with various concentrations of antibody in the presence of fresh human serum  (from a SARS-CoV-2  unexposed donor). Activation of the complement  cascade was measured by  flow cytometric assessment of complement component C3b  deposition on the surface of the cells. Results for the 3 IgM, (black), 11 IgG, (blue), and 6 IgA  antibodies (red) are shown. P values were calculated by two-way analysis of variance, followed by Tukey's test."
NCBI gene IDs:
"spike: 43740568"
Figure legend: "A. The effect of competition on concentration versus binding  curves of three spike-specific, class-switched antibodies. Antibodies were expressed either as IgM, as originally isolated (black symbols and lines), or artificially switched to IgG1  (blue lines and symbols). For each antibody, identified by name at the top of each plot, the binding  of the antibody alone (\"alone\", open symbols), or the  competitive binding  of the antibody in a mixture of IgM  and IgG1  (\"compet.\", filled symbols) is shown. In the competition scenario, each of the two classes of the antibody were added together at the concentration shown on the horizontal axis. The vertical axis shows the ratio of geometric mean fluorescence of human IgM, or IgG  on spike-expressing cells divided by the corresponding signal on spike-non-expressing control cells. Each point shows the mean of 3 values from three independent experiments. Error bars show standard error. P value was calculated by comparing the area under the curve of each antibody class in the \"alone\" condition with the binding  of the \"competition\" condition by paired, two-tailed t-test."
NCBI gene IDs:
"spike: 43740568"
Figure legend: "C. Flow-cytometric epitope binning of monoclonal IgM, utilizing competitive displacement of IgG  by IgM  with identical variable region Cells expressing SARS-CoV-2 spike  protein and untransfected control cells were incubated with each of 3 neutralizing IgM  antibodies artificially switched  to IgG1, either alone, or mixed with one of the 3 antibodies expressed as IgM. The binding  of each IgG1  alone is shown in the last column of the heatmap, and in competition with each other IgM  in columns 1-3. Color shade represents the specific IgG binding  (ratio of GMFI on TE spike-mCherry  cells to TE 0 cells). Values are mean GMFI ratios from three independent experiments. When IgM binds  the same epitope as the IgG  (automatically the case when the source antibody is the same), the IgM  will displace the IgG, resulting in a reduction in the IgG  signal. Asterisks mark those combinations of antibodies with a statistically significant decrease in binding  of the IgG1  in the presence of IgM, compared to the IgG  alone across 3 independent experiments, (* p&lt;0.05, two-way analysis of variance, followed by Tukey's test)."
NCBI gene IDs:
"spike: 43740568"
Figure legend: "(A) RFP-ATG8g-labeled autophagosomes  were quantified from plants   syringe infected with mock or Xcv ΔxopQ (oD600=0.2) at 2 dpi in the presence or absence of ConA  (bars = 20 μm). Puncta were calculated from z-stacks (15) of n=6 individuals using ImageJ. Central band of boxplots represent the median, the bottom and top represent the 25th and 75th percentiles, whiskers extend to at most 1.5 times the interquartile range. Different letters indicate statistically different groups (P &lt; 0.05) as determined by one-way ANOVA. The experiment was repeated twice with similar results."
NCBI gene IDs:
"xopQ: "
Figure legend: "(B) Immunoblot  analysis of NBR1  and ATG8  protein levels in Xcv ΔxopQ or mock infected  N. benthamiana  plants at 1 and 2dpi. Agrobacterium-mediated transient expression of AIMp-RFP  serves as a control for autophagy   suppression.  Ponceau Staining (PS) served as a loading control. The experiment was repeated three times with similar results."
NCBI gene IDs:
"RFP: 
xopQ: 
AIMp: 9461793"