EMBO/sd-character-level-ner huggingface dataset:
Figure 5A. Small RNAs extracted from ovaries of different genotypes were sequenced. Size histograms of normalized RNA populations matching Transposable Elements (TE) are shown. Red: sense. Blue: antisense. endo-siRNA (21nt) and piRNAs (23-28 nt) are indicated. Rpp30 mutations in two different genetic backgrounds (Rpp3018.2 and Rpp3018.2/Rpp30PE) specifically alters piRNA populations, compared to heterozygous control ovaries. white virgin ovaries were used as developmental control. Rpp3018.2 carrying the ubiRpp30GFP transgene (genetic background control) rescues general piRNA populations. aubHN/aubQC42 was used as positive control. B. Specific normalized unique mapper piRNA populations (23-28nt) from the major piRNA clusters are shown for the indicated genotypes. The scale of reads is indicated on the left. C. The ping-pong signal calculated on multi-mappers piRNA populations is shown for the different genotypes. . D. Nuage specific markers (Aub, Ago3 and Mael) are shown in stage 3 wild-type and germline mutant clones for Rpp3018.2. Scale bar, 10µm. E-H. Double mutant ovaries for Rpp30 and chk2 (Rpp3018.2, mnkp6) rescued the specific and general piRNA populations, nuage morphology and the characteristic ping-pong signal. Scale bar, 10µm.
Figure 3(A) RNA-seq expression profile at the Pax5 locus in Pax5Jak2/+ B-ALL cells (black) and Pax5+/+ pro-B cells (grey). The exon-intron structure and the two alternative promoters at exons 1A and 1B of Pax5 are shown below. (B) Immunoblot analysis of nuclear extracts isolated from Pax5+/+ (WT) pro-B cells and Pax5Jak2/+ lymph node tumor cells. The wild-type Pax5 and Pax5-Jak2 proteins were detected with an antibody raised again the N-terminal (N-term) paired domain of Pax5. The size of marker proteins is indicated in kilodaltons (kDa) to the left. (C) Flow-cytometric analysis of Pax5 protein expression by intracellular Pax5 staining of lymph node B220+CD19+ B cells from a Pax5+/+ mouse (grey filled) and B220lowCD19+ B-ALL cells from a 10-week-old Pax5Jak2/+ tumor mouse (black). The full-length Pax5 protein was detected with an antibody that recognizes C-terminal Pax5 sequences that are absent in the Pax5-Jak2 protein. (D) Flow-cytometric analysis of bone marrow cells from 4-week-old Pax5ihCd2/+ and Pax5Jak2/ihCd2 mice. The expression of human (h) CD2 from the Pax5ihCd2 allele is shown for CD19+B220+ (grey) and CD19+B220low (black) B cells. (E) Loss of the wild-type Pax5 allele in CD19+B220low B cells from the bone marrow of 6-week-old Pax5Jak2/+ mice. Genomic DNA isolated from flow cytometry-sorted CD19+B220+ (+) and CD19+B220low (low) B cells was analyzed by PCR with primers amplifying exon 4 of the wild-type Pax5 allele and unique sequences of the Pax5Jak2 allele as shown in the schematic diagram of the two Pax5 alleles. The positions of the PCR fragments corresponding to the two Pax5 alleles are indicated to the right of the agarose gel. (F) Copy number analysis of the Pax5Jak2 allele by quantitative PCR analysis with primers amplifying unique sequences across the Pax5 exon 5-Jak2 exon 19 junction of the Pax5Jak2 allele. The PCR analysis was performed with genomic DNA isolated from lymph node (LN) Pax5Jak2/+ B-ALL cells (3 experiments), from flow cytometry-sorted CD19+B220+ and CD19+B220low B cells from the bone marrow (BM) of 6-week-old Pax5Jak2/+ mice (2 experiments each) and from CD19+B220+ B cells from Pax5+/+ bone marrow (2 experiments). The PCR data were normalized to the product amplified from a control region located 35 Mb upstream of Pax5, and the ratio obtained for B220+ B cells from Pax5Jak2/+ bone marrow was set to 1 copy number of the Pax5Jak2 allele. (G) Kaplan-Meier survival analysis of Cd79a-Cre Ikzf1neo/+ Pax5LSL-Jak2/+ (black) and Cd79a-Cre Pax5LSL-Jak2/+ (grey) mice. Statistical analysis of the survival curves was performed with the log-rank (Mantel-Cox) test; ****P < 0.0001. n, number of mice analyzed. (H) Flow-cytometric analysis of B220 and CD19 expression in B-ALL tumor cells from the lymph node of a Cd79a-Cre Ikzf1neo/+ Pax5LSL-Jak2/+ mouse (black; left). Pax5 expression in these B-ALL tumor cells (black line) and control Pax5+/+ lymph node B cells (grey filled) was determined by intracellular Pax5 staining (right).
Figure 2Weight loss of wild-type (WT) (n=6) or Stat4 knockout(Stat4-KO) (n=6) mice receiving intraperitoneal injection of PBS or LIF during challenge with 3% DSS. wild-type (WT) (n=6) or Stat4 knockout(Stat4-KO) (n=6) mice receiving intraperitoneal injection of PBS or LIF during challenge with 3% DSS. Macroscopic changes in the colon of the mice on day 10 of colitis induction Comparison of the colon length in the mice on day 10 of colitis induction wild-type (WT) (n=6) or Stat4 knockout(Stat4-KO) (n=6) mice receiving intraperitoneal injection of PBS or LIF during challenge with 3% DSS. DAI (stool consistency and bleeding score) of colitis mice treated wild-type (WT) (n=6) or Stat4 knockout(Stat4-KO) (n=6) mice receiving intraperitoneal injection of PBS or LIF during challenge with 3% DSS. H&E histology of representative colons from colitis mice. Scale bar, 20μm. Weight loss of Rag1-/- (n=6) mice transferred with CD45RBhi CD4+ T cells and intraperitoneally injected with PBS or LIF for 8 weeks. Rag1-/- (n=6) mice transferred with CD45RBhi CD4+ T cells and intraperitoneally injected with PBS or LIF for 8 weeks. Macroscopic changes in the colon of Rag1-/- mice treated Comparison of colon lengths in the Rag1-/- mice at week 8 (n=5). Rag1-/- (n=6) mice transferred with CD45RBhi CD4+ T cells and intraperitoneally injected with PBS or LIF for 8 weeks. H&E histology of representative mouse colons on day 54 of colitis induction
Figure 1Schematics of the Arabidopsis root-tip; relevant cell layers are highlighted. Representative confocal images of cell-type-specific promoter::GFP:AGO1 translational fusions. Immunoblot analysis of FLAG:AGO1 IPed in each root-tip layer. Scale bars: 50μM, NT: Non-transformed. CB: Coomassie blue. Left: input and IPed AGO1 following post-lysis addition of a radiolabeled siRNA duplex (siGFP). Right: northern analysis of AGO1-bound sRNAs. Layer-specific distribution of all AGO1-loaded miRNAs. Northern analysis of layer-specific AGO1-loaded miRNAs using sRNAs IPed independently from that used for deep-sequencing. Bar-plots underneath each panel display the deep-sequencing results as normalized reads counts. Origins, proportions and conservation of previously uncharacterized AGO1-loaded miRNAs.
Nrg3 locates to synapses on ErbB4+ interneurons in vitro.Figure 2 A) Hippocampal neurons cultured for 21 days were analyzed by immunocytochemistry using antibodies against Nrg3, ErbB4 and vGlut1, demonstrating co-clustering of Nrg3 and ErbB4 in excitatory synapses. Note that (A) displays Nrg3/vGlut1 and (A') Nrg3/ErbB4 signals of the same triple-stained image  B) Quantification of the proportions of vGlut1/2+ and vGAT+ presynaptic boutons that are positive for Nrg3 (two-tailed Wilcoxon test, ****P<0.0001, n=18 from 2 independent experiments). C) Quantification of Nrg3 immunofluorescence levels in vGlut1/2+ and vGAT+ presynaptic boutons that are positive for Nrg3 (A.U., arbitrary units, two-tailed Wilcoxon test, ****P<0.0001, n=17 from 2 independent experiments)  D) Quantification of vGlut1/2+ synapse numbers on secondary dendrites of PV interneurons in cultures from wildtype (wt) and Nrg3-/- mice (21-24 days in culture). Data from n=27 (wt) and n=26 (Nrg3-/-) neurons from 3 independent experiments were analyzed using two-tailed Mann-Whitney U-test, ****P<0.0001 E) Immunocytochemical analysis of a mixed culture containing neurons of wildtype and ErbB4-/-; Gad1/Gad67-GFP animals triple-stained against ErbB4, GFP and Nrg3. To improve the visibility, ErbB4 and Nrg3 signals are also shown separately (E', E''). ErbB4+ interneurons from wildtype animals are indicated by filled arrowheads, interneurons from ErbB4-/- mice were identified by GFP and are indicated by open arrowheads  F) Immunocytochemical analysis of a mixed culture containing neurons from wildtype and Nrg3-/-; Gad1/Gad67-GFP animals triple-stained against ErbB4, GFP and Nrg3. To improve visibility, ErbB4 and Nrg3 signals are also shown separately (F', F''). ErbB4+ interneurons from Nrg3-/- animals are GFP-positive and are indicated by open arrowheads; ErbB4+ interneurons from wildtype animals are GFP-negative and are indicated by filled arrowheads
Figure 6(A) Survival curves of XBP1fl/flIRE1fl/fl and XBP1ΔDC IRE1truncDC mice infected intraperitoneally with 500 Pru parasites. Log-rank (Mantel-Cox) test, p=0,0004; n=10 mice per genotype. (B) Number of parasite genomes per spleen and PEC from XBP1fl/flIRE1fl/fl and XBP1ΔDC IRE1truncDC infected intraperitoneally with 500 Pru parasites 6 days post-infection. Unpaired Student T-test **: p<0.01; mean ± S.E.M (n=2 independent experiments combined). (C) mRNA relative expression of Il-6, Il-12, Ifn-g and Tnf-a by splenocytes from XBP1fl/flIRE1fl/fl and XBP1ΔDC IRE1truncDC mice infected or not (NI) with 500 Pru parasites for 6 days. Results are normalized to the housekeeping gene Gapdh. Two-way ANOVA Tukey's multiple comparisons, ns: p>0.05; *: p<0.05; **: p<0.01; ****: p<0.0001; mean ± S.E.M (n=2 independent experiments combined). (D, E) Quantification of the number of total (left histogram) and activated (right histogram) (IFNγ-positive) CD4+ T cells (D) and CD8+ T cells (E) in the spleen of control mice (XBP1fl/flIRE1fl/fl) and XBP1ΔDC IRE1truncDC infected for 6 days. Two-way ANOVA Tukey's multiple compare, ns: p> 0.05; *: p <0.05; **: p <0.01; ***: p <0.001; ****: p <0.0001; mean ± S.E.M (n=2 independent experiments combined). (F) Frequency and number of cDC2 (left) and cDC1 (right) in the spleen of control mice and XBP1ΔDC IRE1truncDC infected for 6 days. Two-way ANOVA Tukey's multiple compare, ns: p> 0.05; ****: p <0.0001; mean ± S.E.M (n=2 independent experiments combined).
a) Co-localization between ATG12 and VAMP2-HA in control and CALM knockdown HeLa cells stably.f5(a) Co-localization between ATG12 and VAMP2-HA in control and CALM knockdown HeLa cells stably expressing VAMP2-HA. Confocal pictures are shown with magnified areas on the right showing co-localization between ATG12 and VAMP2 in control cells and no co-localization in CALM knockdown cells. Quantification of ATG12-VAMP2 co-localization is shown on the graph as the Pearson's coefficient (data are mean ±s.d.;*P0.05; two-tailed t-test). Scale bars, 5 μm. (b) Western blot analysis of VAMP2, actin and LC3-II in HeLa cells where VAMP2 was knocked down, as indicated. The cells were starved in Hanks balanced salt solution (HBSS) and treated with Baf A1 as indicated. (SE, short exposure; LE, longer exposure.) Quantification of LC3-II/actin ratio is shown. Data are representative of three independent experiments and shown as mean ±s.d. (*P0.05; NS, not significant, two-tailed t-test). (c) LC3 dot counting in CALM and VAMP2 knockdown cells. CALM or VAMP2 were knocked down in cells expressing GFP-LC3. The cells were kept in full medium or starved in HBSS for 4 h, fixed and subjected to automated fluorescence microscopy to score the number of LC3 dots per cell. The number of LC3 dots per cell (shown as mean ±s.d.) is shown on the graph for each condition (n≥300 cells per condition; BC, basal conditions). (*P0.01; NS, not significant, two-tailed t-test). (d) Number of p62 dots per cell in VAMP2 knockdown. HeLa cells where VAMP2 was knocked down were fixed and subjected to microscopy after labelling endogenous p62 using specific antibody. The data represent the number of p62 dots per cell shown as mean ±s.d. (*P0.05; two-tailed t-test; n≥300 cells per condition). (e) Percentage of huntingtinQ74-expressing cells with aggregates in VAMP2 knockdown HeLa cells. Data are from one representative experiments performed in triplicate, out of three independent experiments and shown as mean ±s.d. (*P0.05; two-tailed t-test). (f) Western blot analysis of VAMP2, actin and LC3-II in HeLa cells stably expressing VAMP2-HA wild type or VAMP2-HA mutated in the CALM-binding site at different levels (wild-type clone 6, wt Cl6: low level; wild-type clone 11, wt Cl11: high level; mutant clone 11, AA Cl11: low level; mutant clone 12, AA Cl12: high level). The cells were treated with Baf A1 as indicated. (SE, short exposure; LE, longer exposure). Quantification of LC3-II/actin ratio is shown. Data are representative of three independent experiments and shown as mean ±s.d. (*P0.05; two-tailed t-test).
Figure 1ISRE-luciferase reporter assay in 293T cells infected with BTV-8 or mock-infected (Control) and treated with 1000 U/ml of universal-IFN Luminescence fold induction was measured at different time points p.i. Mean luciferase activity fold inductions in control or BTV-infected in three experiments are presented. * GAS-luciferase reporter assay in Vero cells infected with BTV-8 or mock-infected (Control) and treated wit 5 ng/ml of IFN-γ. Luminescence fold induction was measured at different time points p.i. Mean luciferase activity fold inductions in control or BTV-infected in three experiments are presented qRT-PCR analysis of ISGs induction in mock- or BTV-8-infected 293T cells after type I IFN treatment for 8 hr. Mean mRNA fold inductions for 3 experiments are presented. qRT-PCR analysis of ISGs induction in mock- or BTV-8-infected Vero cells after type II IFN treatment for 8 hr. Mean mRNA fold inductions for 3 experiments are presented.
Figure 3Recombinant phosphorylated Tau expressed in insect cells (p-Tau) de-mixes in the presence of PEG but fails to coacervate with RNA (5 μM p-Tau, 10% PEG). In the presence of PEG, polyA-Cy3 co-condensates with p-Tau (arrow heads). Scale bar=10 μm. Tau phospho-variants generated by in vitro phosphorylation of non-phosphorylated Tau from E. coli with different kinases (PKA, GSK3β, or Cdk5) show differences in phosphorylation at specific phospho-site (pT205, pS262/pS356, pS324 and pS404) tested by Western blot. Non-phosphorylated Tau and p-Tau from insect cells are loaded for comparison. Position of tested p-sites is indicated in the Tau sequence cartoon. Western blot for total Tau (Tau13 antibody) confirms equal loading (0.2 μg Tau per lane) of the Tau preparations. Phos-tag gel shows degree and heterogeneity of phosphorylation in the different Tau phospho-variants. Intensity along the lanes are plotted as colored lines next to gel image. Condensation of Tau phospho-variants in the Tau:PEG, Tau:RNA (polyA), and pTau:PEG:RNA systems was determined by turbidity measurements for condensates in solution (absorption at 600 nm) and by microscopy for surface attached condensates (surface coverage; top left). Turbidity measurements are shown on the left y-axis (blue circles), and surface coverage in % on right y-axis (black data points). Scale bars=20 μm. N=4 experiments, data points represent the average of 5 data points from turbidity measurements taken at 20±5 min after LLPS induction. Top right panel shows turbidity measurements of Tau alone as negative control for LLPS detection. One-way ANOVA with Tukey test for multiple comparison. *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001.
Figure 1(A) Total lysates from the indicated cell lines cultured in regular conditions at a steady state were subjected to western blotting. s.e., short exposure; l.e., long exposure. The major Merlin band is indicated by an asterisk. The ratio of mono-ubiquitinated to native Merlin in each lane of the short exposure blot was quantified by Image J and is shown under the blot. The same lysates were also used in Figure EV1A. Asterisks indicate native Merlin, arrows show ubiquitinated Merlin. (B) Total lysates from LN229 cells in which Merlin was or was not knocked out (KO) were subjected to western blotting. LN229 (C) cells were detached (denoted by sus., referring to suspension) by trypsinization (see Methods) and reseeded (attach) for two (LN229) hours. Total lysates from these cells were subjected to western blotting. The ratio of mono-ubiquitinated to native Merlin in each lane was quantified by Image J and is shown under the blot. Ubiquitinated Merlin is marked with arrows. Met5-A (D) cells were detached (denoted by sus., referring to suspension) by trypsinization (see Methods) and reseeded (attach) for four (Met5-A) hours. Total lysates from these cells were subjected to western blotting. The ratio of mono-ubiquitinated to native Merlin in each lane was quantified by Image J and is shown under the blot. Ubiquitinated Merlin is marked with arrows. (E) LN229 cells transduced with a Merlin or scrambled shRNA were treated with DMSO, ionomycin (Iono) or thapsigargin (TG). Total lysates of these cells were subjected to western blotting. The major Merlin band is indicated by an asterisk. The ratio of mono-ubiquitinated to native Merlin in each lane was quantified by Image J and is shown under the blot. Ubiquitinated Merlin is marked with an arrow. (F) LN229 cells treated with DMSO or thapsigargin (TG) were lysed and subjected to immunoprecipitation with a Merlin antibody or IgG. The immunoprecipitated products were subjected to western blotting. The number of conjugated ubiquitin (Ub) moieties was marked. Tetra-ubiquitinated Merlin is indicated by an arrow. (G) LN229 cells stably transduced with 6x-Histidine-tagged ubiquitin (His-Ubi) were treated with DMSO or thapsigargin (TG). These cells were lysed and subjected to nickel-charged affinity purification followed by western blotting for endogenous Merlin. Both arrowhead and arrow point to the mono-ubiquitinated Merlin. The ratio of mono-ubiquitinated to native Merlin in each lane of the lysate blot was quantified by Image J and is shown under the blot. (H) LN229 cells stably transduced with 6x-Histidine-tagged ubiquitin (His-Ubi) were detached or reseeded as in (C). These cells were lysed and subjected to nickel-charged affinity purification followed by western blotting for endogenous Merlin. Arrowheads and arrows point to the mono- or di-ubiquitinated Merlin (see a longer exposed blotting results in Figure EV1D). The ratio of mono-ubiquitinated to native Merlin in each lane of the lysate blot was quantified by Image J and is shown under the blot.
Figure 7Images of mESCs transduced with Rptor or Rictor shRNAs in SL. Scale bar, 400 µm.   Relative proliferation of mESCs as in (A) (mean values ± SD). n = 3 biological replicates.   Western blotting for RPTOR, RICTOR and the indicated pluripotency proteins as in (A) (left) and quantification (right) (mean values ± SD). n = 3 biological replicates. Images of mESCs transduced with Eif4a1, Eif4e and Eif4g1 shRNAs in SL. Scale bar, 400 µm. Relative proliferation of mESCs as in (D) (mean values ± SD). n = 3 biological replicates. Western blotting for EIF4A1, EIF4E, EIF4G1 and the indicated pluripotency proteins as in (D) (left) and quantification (right) (mean values ± SD). n = 3 biological replicates. Western blotting for EIF4E, EIF4G1 and the indicated pluripotency proteins in cells with the indicated KD in the indicated culture conditions.
Figure 1A Schematic overview of the scRNA-seq workflow. B t-SNE plots showing integrated analysis of Prrx1-Cre- (8-week-old mice, n=3 males) and Lepr-Cre-traced (8-week-old mice, n=4 males) cells. Cells were colored by clusters (left) or samples (right). Top 20 PCs were chosen for the clustering. C Heatmap showing the relative expression levels (row-wide Z score) of the 20 most significant markers for each cluster (rows) across cells in the 9 clusters (columns). Bars on the top were colored as in (B). D Violin plots showing the expression of feature genes for each cluster. E In situ hybridization of Col3a1 on femur sections. Col3a1 was expressed in the perichondral (a) and periosteal (b) regions, but not in the bone marrow. B: Bone; BM: Bone marrow; Peri: Periosteum; Endo: Endosteum. Scale bars were 100 µm. Arrowheads indicated the periosteum. F Relative contribution to each cluster by Prrx1-Cre- and Lepr-Cre-traced cells after normalization to total cells (4170 cells in Prrx1-Cre, 3050 cells in Lepr-Cre). G UMAP plot showing the inferred trajectories by RNA velocity analysis.
Figure 3A. Quantification of cytokines and other mediators in plasma obtained from COVID-19 patients (COVID, n=15) and healthy controls (CTR, n=15). Data represent individual values, mean ± standard error of the mean. Mann-Whitney test was used for statistical analysis. Exact p values are reported in the figure. B. Representative dot plots showing percentages of immature and mature circulating monocytes in CTR and COVID-19 patients. Scatter plots showing the quantification of immature and mature monocytes in healthy controls (CTR, n=6) and COVID-19 patients (COVID, n=7) are reported. Mann-Whitney test was used for statistical analysis. Exact p values are reported in the figure.
Figure 4(A) Knockdown of SIRT1 abolished CSAG2-mediated decrease in ac-p53 K382. CSAG2 over-expressing HCT116 were transfected with SIRT1 siRNA for 72 hr before doxorubicin/TSA treatment for 6 hr. Cell lysates were blotted for the indicated proteins. (B) Inhibition of SIRT1 enzymatic activity blocked CSAG2-induced decrease in p53 ac-K382. CSAG2 over-expressing HCT116 cells were treated with 1 μM doxorubicin/ 0.4 μM TSA with or without 1 μM EX-527 for 6 hr. Cell lysates were blotted for the indicated proteins. Inhibition of SIRT1 enzymatic activity prevents CSAG2-knockdown increase in p53 ac-K382. CSAG2-knockdown stable cells were treated by 1 μM doxorubicin/ 0.4 μM TSA with or without 1 μM EX-527 for 6 hr. Cells were then harvested and blotted for the indicated proteins (C) Inhibition of SIRT1 enzymatic activity prevents CSAG2-knockdown increase in p53 ac-K382. CSAG2-knockdown stable cells were treated by 1 μM doxorubicin/ 0.4 μM TSA with or without 1 μM EX-527 for 6 hr. Cells were then harvested and blotted for the indicated proteins and quantitated (D; n=3 biological replicates). Data shown as mean ± SD. (E) CSAG2 binds catalytically inactive SIRT1 H363Y. Cells were transfected with the indicated constructs before anti-Myc IP and blotting for the indicated proteins. (F) SIRT1 H363Y blocks CSAG2 regulation of p53 ac-K382 levels. HCT116 cells were transfected with the indicated constructs and blotted for the indicated proteins. (G) Inhibition of SIRT1 activity abolished CSAG2-induced anchorage-independent growth. Soft agar colony formation assays were performed in control or CSAG2 over-expressing HCT116 cells with or without EX-527 treatment. Data are represented as the mean ± SD, n=3 biological replicates. (H) Summary of region on CSAG2 required for SIRT1 interaction. HEK293FT cells stably expressing HA-SIRT1 were transfected with indicated CSAG2 constructs for 48 h before IP with anti-HA followed by SDS-PAGE and immunoblotting for anti-Myc. (I) CSAG2 Δ37 mutant fails to interact with SIRT1 in vitro. Myc-tagged CSAG2 38-127 fragment was in vitro translated and followed by in vitro binding assay with recombinant GST-SIRT1, SDS-PAGE, and immunoblotting for anti-Myc. (J) CSAG2 Δ37 mutant does not regulate p53 ac-K382 levels. Cells were transfected with the indicated Myc-CSAG2 constructs for 48 hr before being treated with 1 μM doxorubicin/ 0.4 μM TSA. Cell lysates were blotted for the indicated proteins. (K) CSAG2 Δ37 fails to promote anchorage-independent growth of H460 cells. Soft agar colony formation assays were performed in CSAG2-negative H460 cells stably expressing CSAG2 wild-type or CSAG2 Δ37 mutant (n=3 biological replicates). Data are represented as the mean ± SD.