EMBO/sd-character-level-ner huggingface dataset:
A. Induced 3T3-L1 cells stably expressing Flag-WDTC1 were subjected to subcellular fractionation. Aliquots of total cell extract (TCE) and subcellular fractions were analyzed by immunoblot as indicated; fraction purity was assessed by α-Tubulin and histone H3 antibodies.
D. Colocalization (Mander's overlap) between Arl8b and Rab7 as a function of the indicated effector perturbations, n≥5 images (3≥ cells per image) analysed per condition from 2 independent experiments.
The cRQ values from RT-qPCR of indicated cells. Total RNA was extracted and CD137 mRNA levels measured relative to that from HEK293T cells. Conjugated OptoCARCD19‑T cells were also assayed either before or after 24 hours stimulation in the dark state. Individual values from three biological replicates are shown, with mean depicted by bar plot.
A) Schematic depicting Hh auto-processing, which starts with the cleavage of the protein into a C-terminal part (Hh.C, yellow) and a N-terminal part (Hh.N, blue), with simultaneous covalent addition of cholesterol. Palmitate, from either diet or de novo lipogenesis (via ACC and Fasn), is added onto Hh-N, in a reaction catalysed by an acyltransferase, encoded by rasp.
F Quantification of data presented in E. Error bars represent mean value ± standard deviations of mean for the intensity values of three distinct chromosome bands representing chromosome XII or III (n=3). Values for G1-synchronized cells were set to 100
CRTH2 subcellular localization in GFP-fused CRTH2 expressing plasmid-transfected cells. Red arrows indicate CRTH2 localized in the ER and white arrows indicate CRTH2 localized in the plasma membrane. Green, GFP-CRTH2; blue, DAPI; red, Calnexin; Scale bar, 20 μm.
E, Immunoblot analysis of protein lysates from Raw 264.7 cells treated with 1 μg/ml LPS for the indicated times and run under non-reducing conditions. Immunoblots are representative of at least three independent experiments.
SRF reporter showing dose dependent suppression of the GPR56-CTF induced SRF signal by the CDK7 inhibitor YKL-5-124, but not by the CDK12/13 inhibitor THZ531. Four technical replicates. One of four individual experiments. Unpaired t-test, bars and error bars represent mean and standard deviation, *** p<0.0005, ** p<0.005, * p<0.05.
E. Human iPSC-derived NSCs (day 0) immunostained for Trim46, γ-Tubulin and Centrin. Zoom represents centrosome structure. Scale bar = 5µm in overview, 2µm in zooms.
I Western blot analysis of phosphorylated and total extracellular signal-regulated kinase (ERK) and AKT 2 days after PHx.
C Morphology of inguinal WAT, BAT, and liver from WT and FADD-D mice fed a HFD for 20 days. WAT and BAT were stained with hematoxylin and eosin. Liver tissues were stained with Oil red O to demonstrate lipid accumulation and counterstained with hematoxylin. Scale bars = 50 μm. Shown are typical results from four different fields and three different experiments.
I. Geometric Mean Fluorescence Intensity (gMFI) IFN-γ levels following of stimulation with increasing amount of NP 366-374 peptide.
C-E IRE1α, XBP-1S, and XBP-1U mRNA in CWR22xenografts grown in nude mice and collected at the indicated times after castration. The value at t = 0 was set to 1. Columns represent the mean of at least three independent tumors for each time point, and bars represent SE. P-values ranged between 5.7  ×  10−10 and 0.0002. IRE1α expression at 48 h post-castration was 3.17 × 10−6 with respect to t = 0 using unpaired Student's t-test.
(B) Kaplan Meier survival curve of mice treated as in A, P values as indicated, the data were tested with log-rank test - PBS treated vs. 0.1 mg/kg Ang-(1-7) treated and PBS treated vs. 1.0 mg/kg Ang-(1-7) treated; n = 12-15 mice as indicated in the figure.
(C) Energy expenditure of 16-week-old Ftoflox/flox and FtoAKO mice fed a HFD. White and gray areas in the graphs indicate day and night, respectively. Data information: The data were presented as the mean ± SD of n = 6 mice per group or triplicate tests (n = 3). Statistical analyses were performed using Student t‐test. ∗∗p < 0.01, ∗∗∗p < 0.001.
(C) Scatter plot showing RNA-seq data from Stat3+/+ cells cultured in 2i and stimulated with LIF for 1h (Martello et al, 2013). Absolute expression is shown in RPKM. Green dots indicate known LIF targets that serve as positive controls. Mitochondrial encoded transcripts are represented as orange dots. Only genes with FC>1.7 and a p-value <0.05 are shown.
Analysis of RAE expression by ddPCR in aged (75-week-old) mice. Data are presented as the percentage of positive drops normalized to the mean control value. Each point represents an individual mouse and shows the mean amplification from two independent experiments n = 7 (R26AID+/+p48CRE+/KI); 9 (R26AID+/KIp48CRE+/KI). *P = 0.012.
(E) Effect of HA-HuR expression on miRNA levels on EV and non-EV fractions of the culture supernatant collected from control and HA-HuR encoding plasmid transfected Huh7 cells. For isolation of non-EV fraction, supernatant obtained after removal of EVs by ultracentrifugation was used for RNA preparation (left panel) (mean+/- s.e.m., n=3). Effect of HuR expression on CD63, Alix and HuR levels in EVs. Extracts from EVs isolated from control or HA-HuR expressing Huh7 cells were western blotted for respective proteins (right panel).
(I) Analysis of TJP1 exon 20 inclusion by RT-PCR upon transfection of HUVECs with a control SSO or an SSO masking the exon 20 - intron 20 boundary (E20 SSO) (n = 9 independent biological replicates). Representative agarose gel on the right. Schematic outline at the top right. Data information: data are represented as mean ± S.E.M. n.s.: non-significant, *p < 0.05, **p < 0.01. two-tailed unpaired t-test,
Colocalization of CRTH2, LARP6 and GRP78 in NIH 3T3 cells. White arrow indicates colocalization of CRTH2, LARP6 and GRP78. Scale bar, 20 μm.
Bead uptake in BMDMs with and without loading of 25 µM EGTA/AM and 10 μM Ned-19. EGTA-insensitive phagocytosis of beads was inhibited by Ned-19 (n= 75-102 cells) in WT BMDM; ***P<0.001.
ssDNA accumulation analysis in STN1-deficient U2OS cells with and without mirin treatment. Representative images of native BrdU staining are shown.
(H) Quantification of mCerulean lifetimes of control and Hs578T CEP55 knockdow ncells and in response to treatment with nocodazole at indicated time points as shown in G. Blue: 1 ns; red: 3 ns. Graph represents the mean±SEM of three independent experiments.
Quantifications of the number and fluorescence intensities of intracellular Transferrin puncta (n=28-30 fields from 3 independent experiments). Colored horizontal bars indicate median values and whiskers 5 and 95 percentiles.
Ratio of genotypes obtained of 1 week-old pups from crossing Malt1fl/fl K5creTg/+ CARD1414E138A+/+ male mice with Malt1fl/fl K5cre+/+ CARD14E138Atg/+ female mice.
A. Representative immunoblots from GluA2 coIP probed for Sec23, Sec13, and GluA2 after no DHPG, 10, 30, and 60 minutes of treatment with DHPG. B. Graph depicting the kinetics of the association between GluA2 and Sec23 as well as GluA2 and Sec13 after treatment with DHPG for the same points in time as in A. For Sec23, 10 min DHPG, n = 16; 30 min DHPG, n = 15; 60 min DHPG, n = 7, p < 0.0001, ANOVA. For Sec13, 10 min DHPG, n = 7; 30 min DHPG, n = 14; 60 min DHPG, n = 6, p < 0.01, ANOVA.
A RT-PCR analysis of ApoER2 exon 19 splicing in RNA isolated from hippocampus of 4 month old AD and WT mice treated with ASO-21 or ASO-C at P1-2.B Quantitation of exon 19 splicing. (mean s.e.m.; Kruskal-Wallis test with Dunn's multiple comparison test.
(E) Schematic representation of the BIR assay. Two fragments of the LYS2 gene sharing 2.1 kb of homology (lys and ys2) were integrated on chromosomes V and XI, respectively. Induction of HO endonuclease expression under control of the GAL1 promoter produces a DSB next to the lys fragment that can be repaired by BIR. BIR events can be scored by selecting survivor colonies, which harbor a functional LYS2 gene.
C Western blot analysis for Orc2 and Mcm2‐7 in the nuclear chromatin fraction and Orc2, Mcm2‐7, Dup/Cdt1, and cyclin E in the cytoplasmic fraction for each condition assayed.
G WT and IOB MEFs were grown in 1% FBS, 15% FBS media with or without 2 μmol MHY1485 for 4 days. Relative cell number is the ratio of cells on day 4 normalized to day 1, three independent experiments. ****, #### P < 0.0001, calculated by two-way ANOVA.
Cellular cholesterol content (left panel) and glucose uptake (right panel) of HUVECs treated with de novo cholesterol synthesis inhibitor simvastatin. Data presented as mean ± SEM from a representative experiment performed in triplicates. Statistical evaluation using one-way ANOVA and Tukey´s multiple comparisons test, p-value: * <0.05, ** <0.01, *** <0.001 (compared to untreated control). p-value: # <0.05, ### <0.001 (compared to simvastatin control).
(c) Subcellular fractionation and immunoblotting of the nuclear fraction. Jurkat T cells, either treated with etoposide, or overexpressing ATG5 following lentiviral gene transfer, were cultured in the presence and absence of leptomycin B for 72 h. Leptomycin B increased relative ATG5 and Beclin 1 levels in the nucleus.
Western blot of the indicated proteins in T-inducible PSCs stimulated as indicated for 24 hr. GAPDH was used as a loading control.
Polysome profiles of HCT116 cells with or without YTHDF1 knockdown. The right panels show the distributions of TCF7L2, and ACTB in polysome fractions. Data are represented as mean ± SEM. *p<0. 05, **p<0. 01 (3 biological replicates, t-test).
C. Schematic representation of the strategy of tamoxifen treatment and timepoint of analysis in Casp8WT/MLKLko or Casp8ECko/MLKLko mice.
(G) Anti-HBHA serum IgG ELISA reactivity for TB patients and HCW (black lines) compared to two representative HD (red lines). Dashed line indicates the threshold OD405nm for positive reactivity (left). Asterisks indicate serum responses of donors selected for single sorting of HBHA-reactive memory B cells. Data are representative of two independent experiments.
(I) Representative high-resolution confocal images of C. elegans expressing mitochondria-targeted GFP in the body wall muscle cells (scale bar= 10 μm). Quantification of mitochondrial morphology (elongation) is reported in the right panel (one-way ANOVA with Holm-Sidak's correction, n=37-47 animals from 3 independent experiments). Data information: , middle line represents the median, and the upper and lower lines represent the upper and lower quartiles, respectively. Across experiments, p value summary is ns= not significant, *p<0.05, **p < 0.01; ***p < 0.001, ****p<0.0001.
A Heatmap depiction of the dependence of AGO4‐ and AGO6‐bound siRNAs on Pol IV. Identities of siRNAs were retrieved from Havecker et al (), and siRNAs were grouped into 1,210 AGO4‐bound clusters and 1,486 AGO6‐bound clusters (see Materials and Methods for details), each of which corresponds to a colored horizontal bar; the bars are stacked numerically into a column (y‐axis). Information on siRNA levels in Pol IV mutant and wild‐type plants was retrieved from Zhang et al ().
(D) WT, COUP-TFII overexpression (OE) and COUP-TFII knockout (KO) cells were seeded in Seahorse XF-24 cell culture microplates. The cells were rendered quiescent in 0.5% FBS DMEM overnight and then treated with or without 10 ng/ml TGFβ1 for 24 hours. All the cells were incubated in the glycolysis stress test medium without glucose and pyruvate, followed by sequential treatments with glucose (10mM), oligomycin (5μg/ml) and 2-DG (50mM). Real-time extracellular acidification rate (ECAR) was recorded as the baseline (before glucose), the rate of glycolysis (after glucose), glycolytic capacity (after oligomycin), and glycolytic reserve (after 2-DG) (n = 10).
(B and C) qRT-PCR of SUMO mRNAs from 12-week-old WT and R6/2 mouse cortex (B) and striatum (C). SUMO enzyme mRNAs are differentially expressed in R6/2 versus control with statistically significant increases in SENP1 (p = 0.01), SENP3 (p = 0.02), and SUMO-1 (p = 0.003) in cortex and SENP1 (p = 0.02), SENP6 (p = 0.04), PIAS3 (p = 0.007), SUMO-1 (p = 0.02), and SUMO-2 (p = 0.02) in striatum. Samples were analyzed in quadruplicate and normalized to mouse β-actin. Data are shown as R6/2 expression relative to WT levels set at 1 for each enzyme with ± SD (n = 4). *p < 0.05. n.s., not significant.
A. Detection of de novo Ty1 insertions upstream of the SUF16 and SEO1 genes by PCR using a primer in HIS3 (red triangle) and a primer in the locus of interest (blue triangle). Ty1 retrotransposition was induced in cells transformed with plasmids expressing WT or mutant (IN1 K617A, S621A and L622A) Ty1his3AI from the GAL1 promoter. Total genomic DNA was extracted from His+ cells obtained from independent cultures.
(L) (L) Schematic presentation of the domain structures of Sqa and deletion mutants. (M-N) Atg1 physically interacted with Sqa.
Effect of PP2A knock-down on Ago2 phosphorylation and its miRNA association. Ago2 associated IL-1β mRNA level was estimated in siCon and siPP2A treated cells which were stimulated with LPS for 24hrs (mean+/- s.e.m., n=3) (L).
D. The intracellular survival of 188SLO(Y255A) was significantly lower than that of its parental strain, 188, and similar to that of 188SLO-. *, P<0.01.
(C) Effects of RNF26 and its mutant on SeV-triggered activation of the IFN-β promoter. The 293 cells (2×105) were transfected with the IFN-β promoter reporter (0.1 µg) and RNF26 or its mutant (0.1 µg each). Twenty hours after transfection, cells were infected with SeV for 12 hours or left uninfected before reporter assays were performed.
A. VEAL2 RNA levels significantly increased upon overexpression of VEAL2 plasmid compared to control. Bar graph representing relative expression of VEAL2 in control pcDNA3.1 plasmid (1μg) and VEAL2 in pcDNA3.1 plasmid (1μg) for overexpression in HUVECs. GAPDH was taken as normalization control. Data is acquired from 3 different biological replicates and shown as mean fold change values ± standard deviation.
B. Determination of the viral load in organs by standard plaque assay. HDAC6+/+ and HDAC6-/- mice were intravenously infected with VSV-Indiana, and the brain and spleen were collected at 5 dpi (2 × 108 pfu/mouse; n = 6 per group; Mann-Whitney test).
C Four possible scenarios where kinase activity of HERK1/ANJ are not required for signal transduction during pollen tube reception. Red components indicate proteins active in signal transduction while black proteins act as scaffolds for complex assembly. Each scenario is discussed in more detail in the discussion section.
(L) Relative expressions of miR-342-3p and Socs6 in PBMCs from healthy individuals (n=27) and TB patients (n=34) were detected by qRT-PCR. The correlation between miR-342-3p and Socs6 was analyzed by Spreaman test. Spearman rank correlation: r = -0.532, p < 0.001, n = 61.
C. Following surgical denervation of wild type or CHOP−/− mice, LC3 and p62 expression was assessed by western blot. Right panels show quantification of signal relative to GAPDH. ***p<0.001 by ANOVA, n. s. = not significant.
A-C. mRNA expression of Sufu, Gli1 and Fbxl17 detected in 285 medulloblastoma samples (GEO accession: GSE37382), stratified by tumor subtype. Level of significance (p) for Kruskal-Wallis (KW) rank test is p<10-8. Analysis using one-way anova gave comparable results.
(D) XO8 GSCs were treated with MG132, salinosporamide A, epoxomicin, or bortezomib for 24 hrs. Cell lysates were subjected to immunoblot analysis with anti-PARP-1, anti-CHOP, anti-ATF3, anti-ATF3, and anti-BiP antibodies.
SENP3 knockdown increases endogenous Fis1 SUMO-2/3-ylation in HeLa cells. SUMO-2/3 conjugates were immunoprecipitated (IP) from whole cell lysates prepared from HeLa cells using SUMO-2/3 affinity beads. IP and lysate samples were blotted as indicated.
D. Averaged percentage of MEFs with different types of mitochondria were determined according to the mitochondrial morphology by MitoTracker (Red) staining in wild-type MEFs, or MEFs containing MFN null mutations transfected with empty vector control (Ctrl) or a GASZ expressing plasmid.
(A) WT (pdr5∆) cells expressing FLAG-Orm2 and Sec61-GFP (integral ER membrane protein) treated with MG-132 were fractionated into insoluble membrane (P100) and soluble cytoplasmic (S100) fractions and analyzed by SDS-PAGE and Western blot with the indicated antibodies.
G) PLA assay using anti-RB and anti-MDM2 antibodies, H1299 cell were treated or not with etoposide to induce stress, the endogenous proteins were visualised. Cell nuclei were visualised with DAPI blue. The red dots show the interaction between the two proteins. The scale bar corresponds to 20 μm.
RNA-seq of upregulation of RET, IL2RA and CCL5 after FST344 overexpression in ML-2 cells.
2-NBD-glucose uptake in murine pancreatic endothelial cells (MS1) and primary human umbilical vein endothelial cells (HUVEC) treated for 2 h with VEGF-B167 (B167) or VEGF-B186 (B186) compared to control treated cells. Data presented as mean ± SEM from representative experiments performed in triplicates. Statistical evaluation using one-way ANOVA and Dunnett´s multiple comparisons test, p-value: * <0.05, ** <0.01, *** <0.001 (compared to untreated control). Scale bar, 20 μm.
A-C Tethering assay using the R-Luc-6xMS2-A95-MALAT1 reporters containing the indicated 5'-UTRs and MS2-HA-tagged DDX6 or a DDX6 mutant (Mut1) that does not bind to NOT1 in HEK293T cells. R-Luc activity and mRNA levels were normalized to those of the F-Luc control and analyzed as described in Fig 2C,D.
(A) Consequence of miR-124 on EOC cell viability (as in 2A). N, normal cell lines (IHH and HOSE). In the screen, miR-124 was found to significantly reduce cell viability (Z-score < -2) in 6 cell lines, and TCGA expression data revealed no significant change in expression of this miRNA in ovarian tumors.
A. Gene ontology (GO) analysis of microarray data from the trachea and oviduct. GO scores (negative enrichment) of differentially expressed genes from the trachea and oviduct of Gemc1-/- mice (additional information in Dataset EV2).
F. Representative images of transwell migration and invasion assays in Hela PTENε+/- cells at 200× magnification (left panel, the scale bars represent 50 μm). (right panel) Migrated or invaded cells were counted at five random fields at 100× magnification per well to assess cell migration and invasion ability.
(d,e) CN1.4 cortical cells were transfected with the mock or HA-mNDP52 plasmid (d) or with mNDP52 siRNA or scramble RNA as a control (e). The cells transfected with siRNA or scramble RNA were treated with SFN (10 μM) for 24 h. The levels of tau phosphorylated at Ser262/Ser356 and Ser396/Ser404 were analysed by immunoblotting using 12E8 and PHF1 antibodies, respectively. Total tau was detected with a polyclonal tau-specific antibody (Tau). The relative molecular masses (kDa) are indicated to the left of each blot.
A SARS-CoV-2 genome annotation. Two-thirds of the viral RNA, mainly located in the first open reading frame (ORF 1a/b), encodes 16 nonstructural proteins (NSPs). The rest of the viral genome encodes four main structural proteins, namely, the spike (S), envelope (E), nucleocapsid (N), membrane (M) proteins, and several accessory factors. SARS‐CoV‐2 enters the cell primarily via binding to ACE2, followed by its priming by TMPRSS2. In addition to ACE2 and TMPRSS2, other potential SARS-CoV-2 receptors, proteases, and cofactors for infection are indicated.
B. Radar charts comparing clinicopathological features for the patients classified according to the expression of the metagene from the subnetwork-5, -6, -9 and the combination of subnteworks-6 and -9. Each axis of the diagrams represents a scale of proportions for a specific feature, ranging from 0 to 1. *, chi-square test, p<0.0001.
B. The average level of CpG methylation at the targeted regions was 33.3%-34.6% and 27.7%-36.2% in sperm datasets from young and aged mice, respectively. The average depth of each sample was 11.3-27.6, which covered 44.2%-62.9% of the target regions at a depth of 10.
A. Time-lapse images of Tpm-saturated actin filament depolymerizing from their barbed end (BE), with or without MICAL1. Depolymerization is initiated at time t=0 from a non-oxidized actin filament. The increase in the depolymerization rate reflects the oxidation of actin with time. Tpm is labeled with neonGreen (nGr), and actin is unlabeled.
Simultaneous expression of Y701F-STAT1 rescued the hTau-induced suppression of NMDARs mRNA expression measured by qRT-PCR in hippocampal CA3 of C57 mice (n=4). Data information: Data were presented as mean ± SD , two-way analysis of variance (ANOVA) followed by Bonferroni' s post hoc test *, p<0.05, **, p<0.01, ***, p<0.001 vs eGFP or hTau; #, p<0.05, ##, p<0.01 vs hTau.
(A) To the left, representative immunofluorescence microscopy/confocal images showing that the number of TH+cells is reduced in Pbx1-/- embryos. Deletion of Pbx1 decreases the proportion of NURR1+neuroblasts that become TH+neurons at E12.5, indicating that Pbx1 is required for the proper maturation of NURR1+neuroblasts. To the right, quantification of these experiments.
A) Expression levels of the cluster markers in the hemolymph of WI larvae compared to NI larvae. The left panel indicates the distribution of each marker across all clusters (as in Figure 2D), the graph on the right panel, indicates the Log2 of the ratio between the expression level in WI versus NI. Positive values indicate an up-regulation upon wasp infestation and negative values a down-regulation (n=3, pool of 10 larvae per replicate, mean +/- SD are represented on the graph). The p-value are estimated by bilateral student test and indicated as follow: ns = not-significant (>0.05), "*" = p[0.05 - 0.01[, "**" = p[0.01-0.001[.
qRT-PCR analyses of miR-9 expression in control (shCTR) and antimiR-9 FaDu cells. Data represent the mean (±SD) of three independent experiments performed in duplicate and unpaired t-test was used to verify the statistical significance.
Average ratios of amino acids in all human internal exons, which are evenly divided as in (A). The numbers in parentheses indicate the ratio of C-nucleotides in the codons considering codon usage in humans. The mean and SE (semi-transparent shade) are indicated. Note that proline and serine are frequently used in IDRs and are rich in C-nucleotides in their codons.   Violin plots showing the fractions of disordered residues in all human internal exons, which are evenly divided as in (A). The mean (green) with standard error (SE, semi-transparent shade) and the median (red) of the fractions of disordered residues are indicated.
(C) HT29 cells were infected with Shigella WT, ∆ospD3, or ∆ospC1. Cell lysates obtained at the indicated time points were subjected to immunoblotting.
(E) Alcian blue staining of the chicken limb bud micromasses treated with GRK2 inhibitor CMPD101. Note the gradual inhibition of the cartilage nodules with increasing concentration of CMPD101, quantified below. Mean ± SEM. Mann-Whitney U test; number of micromasses is indicated. A representative experiment of four (pH 2.5) and three (pH 1.0) is shown. Scale bar, 100 μm. (F) Alcian blue staining of the micromasses generated from Grk2+/+ and Grk2-/- NIH3T3 cells. Note the mildly weaker staining by alcian blue pH 2.5 and the nearly absent sulfation stained by alcian blue pH 1.0 in the Grk2-/- micromasses. Central band, median. Box, 1st-3rd quartile. Whiskers, 10%-90% percentile. Mann-Whitney U test; number of micromasses is indicated. Scale bar, 1 mm.
(G) Cells were transfected with control or BRG1 and BRM (B/B) siRNAs and treated with 10 nM R5020 as indicated, and the levels of repressed genes was measured by RT-PCR. * P-value < 0.05. BC: BCAS1, KR: KRT23 and IG: IGFBP5 genes.
B Survival analysis of the SCOTROC4 cohort. Kaplan-Meier plots for PFS (left) and OS (right) stratified according to quartiles of RAD51NES. Log-rank test, shading denotes 95% confidence intervals.
(G) Mitochondrial respiration rates were determined from the plantaris muscle of the indicated genotypes using pyruvate/malate as substrate. Pyruvate/malate (Py/M)-stimulated, ADP-dependent respiration, oligomycin-induced (oligo) and the respiratory control ratio (RC) are shown. NTG, n = 6; MCK-miR-499, n = 4. *p = 0.015 (Py/M), *p = 0.017 (ADP), *p = 0.001 (Oligo).