EMBO/sd-character-level-ner huggingface dataset:
(d) Representative images of HepG2 cells transfected with control or TSC2 siRNA immunostained for TSC2 (green) and PMP70 (red). Individual boundaries are shown to identify cells with TSC2 knockdown (white) versus cells that retain TSC2 (yellow). Scale bars, 10 μm. (e) Corresponding immunoblots for HepG2 cells transfected with control or TSC2 siRNA showing the extent of knockdown (average over population of cells). (f) HepG2 cells from d were analysed for Pearson's correlation coefficient of TSC2 co-localization with PMP70 using Imaris software. Quantification was performed on 8-12 cells from each of the 4 independent experiments, giving rise to a total of 40 cells. All error bars represent s.e.m., ***P0.001. Uncropped images of western blots are shown in Supplementary Fig. S6. Source data for the statistical analysis are shown in Supplementary Table S1.
G, Significantly enriched biological processes and cellular components from SYNGO enrichment analysis.
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.
Percentage of cells undergoing cell division (D) within the 40 h imaging in response to the low, natural, and high frequency Nutlin-3 dosing regimens
Mouse xenograft model to assess tumor growth of WM3734 with stable TMX1 knockdown (TMX1 kds; two clones) in immunodeficient mice. (I) Tumor growth in the first 19 days after injection; (J) the corresponding tumor volume quantified after 19 days and (K) after 45 days.
All analyses were performed using AhCre Eed+/+ and AhCre Eedfl/fl mice (n=5) injected with β-naphthoflavone and sacrificed after 15 days.A) Immunohistochemistry analysis of small intestinal sections, using the indicated antibodies.
(f) HEK293 cells were transfected with GFP-Atg14L with or without mCherry-linked dominant-negative ULK1, and these cells were cultured in complete or starvation medium for 60 min. Bars, 10 µm.
A time-lapse imaging of a representative MII oocyte with visible lagging chromatid at midzone during anaphase II expressing CENP-C- EGFP (centromeres, green) and H2B-mCherry (chromatin, red). Upper row shows maximum intensity z projection images from representative timepoints at metaphase II and anaphase II. A lagging chromatid is indicated by a blue arrowhead. Number next to the circles enclosing the segregating chromatids denotes number of chromatids at each pole. The bottom row depicts 3D positions for centromeres of normally segregating chromosomes as black dots, and centromeres of laggard-producing chromosome as red dots in a side view along the spindle equator. One of the centromeres is left behind at anaphase (blue arrowhead), but will segregate equationally. Tracks of individual centromeres are color-coded according to the speed, as indicated by the colour bar. Time is shown relative to anaphase II onset (min:sec). Scale bars, 5 μm.
(E) Silencing UHMK1 in SGC7901 cells via UHMK1-siRNA. NCOA3 phosphorylation at S1062/T1067 was measured with a special Ab that recognizes phosphorylated NCOA3-S1062/T1067.
F Immunofluorescence images of KLF10 and nephrin in renal sections of wild-type or KDM6A-KO mice with or without STZ treatment. Scale bars, 20 μm. *P < 0.05 versus the untreated wild-type group, #P < 0.05 versus the STZ-treated wild-type group (Parametric ANOVA and a Bonferroni post hoc test; n = 3).
(G) Upper panel, confirmation of Cdc27 depletion by immunoblotting 72 hours after siRNA transfection in B1dd/B2ko cells. Lower panel, following 40-hour siRNA transfection B1dd/B2ko cells were treated for 24 hours with Thymidine, released for 10 hours and treated with proTAME and Apcin for additional four hours. At this point, the cells were fixed and stained with tubulin and pericentrin for immunofluorescence analysis.
HEK293 Tet-off experiments showing the degradation of IL6-OPT, IL6-WT and IL6-DE transcripts (D), under vehicle (PBS)- and anisomycin (ANI)-treatment, post-doxycycline addition. data is representative of 3 independent experiments each with 3 replicates. The data represents the mean ± SD for 3 replicates. A two-way ANOVA with Holm-Sidak multiple comparisons was performed. P-values are denoted as follows: p < 0.05 (*), p<0.01 (**) and p<0.001 (***).
(A) Representative western blot showing level of ATF4 in ATF4-silenced Flp-In 293 HA-IKKε cells treated with doxycycline (16 hours).
LSM images of cross-sections through the heart of an adult control and ILK K.O. mouse four weeks after myocardial ischemia and reperfusion (MI/R), showing the outer lateral region of the LV. Scale bars: 100 µm Overall cardiac lymph vessel and blood vessel density in heart sections as determined by Lyve1-positive and CD31-positive area (normalised to total analysed myocardial area), respectively. (n = 5 control and n = 7 ILK K.O. mice), P = 0.051 (cardiac lymph vessel density in adult control versus adult ILK K.O.), *P = 0.025 (cardiac blood vessel density in adult control versus adult ILK K.O.)
(B) A slice through the central wheel of fungal FAS. The pitch of α-helices is resolved.
(c) Cytokine secretion by LPS-primed wild-type (WT) and NALP3-deficient (NALP3-KO) macrophages incubated with rotenone, followed by stimulation for 1 h with ATP.
A. Endogenous LRP6 and OGT interact with each other. HEK293T cells were lysed and the cell lysates were immunoprecipitated with anti-LRP6 antibody and blotted with OGT. WCL, whole-cell lysates.
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)
(E) Bone metastasis-free survival in WT C57BL/6 mice harboring RM1 BD Irf- cells ± MS275, poly I:C or combination treatment (n = 6 per group; log-rank (Mantel-Cox) test).
(a) Graphic representation of a transverse section from an E6.5 embryo. The epiblast is divided in three distinct regions: anterior (red), posterior (green) and PS (blue). The PS region is defined as the area where the basement membrane (yellow) is degraded.
B) t-distributed stochastic neighbor embedding (t-SNE) analysis of the proteome data corrected via a linear regression model. The different growth patterns are color-coded as in panel A.
(D) Quantification of weekly proliferation rate in cells treated as in B. A total of 60,000 cells of each cell line were cultured in 10cm dishes with 1uM palbociclib for a total of 3 weeks. Every 7 days, cells were trypsinised and total cell counts were determined. The 0-week timepoint shows the 7-day fold increase of untreated cells. The data points show fold increase in cell count over each 7-day period, and bars represent the mean from 2 experiments.
D, E Immunoblot analysis of HeLa cells transfected with the indicated siRNAs and treated with Baf A1 as indicated. In D, the panels are from more than one western blot experiment but only a single GAPDH loading control is shown. In E, the bars represent the mean±sd of band intensities of three independent experiments as quantified using ImageJ. Statistical comparison was analyzed by one-way ANOVA followed by Tukey multiple comparison test and significance displayed as ***p ˂ 0.001, **p ˂ 0.005; ns is not significant.
Tumor formation on chicken CAM of MLS cell lines following shRNA-mediated YAP1 knockdown. The number of tumors is given above each bar, Fisher exact test; ns, not significant.
C. Scatter plots comparing the si6B-NT and NT-2 genes expression. The higher expression genes in siRNA-6B and NT-2 are colored with red and blue, respectively (FC > 5, FPKM >5).
(B) Representative wt (top) and FLNAΔECS (below) mouse showing the blood flow just above the aortic valve. Note: Reduced blood flow in FLNAΔECS mouse as depicted by pseudocoloring. The red circle represents the time window at which the images are shown.
B. Graph showing the decreased fold change of CD41+CD61+ megakaryocytes cultured in 4D7 compared to IgG. FACS-sorted CD34+ from myelofibrosis patients with CALR or JAK2 mutation were cultured over 12 days without TPO in the presence of SCF, IL-6 and IL-9. Black columns show JAK2V617F mutation positive samples (n= 4 technical replicates of samples from different patients). Data information: Unpaired students t-test used to determine statistical significance Bars represent standard deviations *, P = 0.05 - 0.01, **, P = 0.01 - 0.001, ***, P = 0.001 - 0.0001, ****, P <0.0001, n.s, not significant.
Neonates were obtained by caesarean delivery. a, b, Successfully resuscitated pups were monitored in a humidified chamber without milk feeding (a) or with artificial milk feeding provided every 3-6 h through a tube inserted into the stomach (b).
F UCSC genome browser views of sequencing data at CPEB4 locus under different conditions. The blue region represents antagonist‐responsive AR location, while the two pink regions indicate agonist‐responsive AR locations.
(C) Schematic illustration of target protein depletion using the AID system to analyze the requirement of dynein for acentrosomal spindle pole formation.
B. Immunoblot assay of RKIP+/+, RKIP+/- and RKIP-/- peritoneal macrophage cells treated with intracellular poly(I:C) (1 μg/ml).
B-D. Representative confocal images of the microdroplets without (B) and with GTP (C and D). The concentrations of FtsZ, SlmA and SBS were 12, 5 and 1 μM, respectively (B and C) or 6, 3 and 0.5 μM respectively (D). 1 mM (C) or 2 mM GTP (D). Scale bars: 40 μm except in images on the far right (20 μm), which are either a magnification of the indicated region in the merged image (B) or independent images at higher magnification (C, D).
B. Quantification of shRNA-Control and shRNA-Pten organoid morphology upon treatment with DMSO, EZH2 (GSK126) and BAZ2A-BRD inhibitors (BAZ2-ICR and GSK2801).
A Schematic illustration of the experiment. C57Bl/6 mice (7 weeks old) received AAV expressing PLTP or GFP (as control) at the viral titer of 5x1012 GC/mouse via tail-vein. High fat diet (HFD) started one week after AAV administration for both groups. Metabolic studies and euthanasia were performed after 10 weeks of HFD.
G Plasma bile acids composition of mice in (B). Pool of samples from mice on HFD that received GFP or PLTP. n=5 for both groups.
(K Proximal protrusion length of the cartwheel beyond the microtubule triplets in C. reinhardtii, P. tetraurelia, N. gruberi, and H. sapiens. Internal cartwheel inside the microtubule barrel, dark blue (INT); external cartwheel beyond the microtubule wall, light blue (EXT). Mean values are displayed above each bar plot with the black lines indicating the standard deviation (K). Mature C. reinhardtii, n = 4, external cartwheel length = 37.6 +/- 3.4, internal cartwheel length 74.2 +/- 16.6; C. reinhardtii procentriole, n = 2, external cartwheel mean length = 52.8 +/- 22.0, internal cartwheel length 26.5 +/- 29.7; P. tetraurelia, n = 23, external cartwheel mean length = 11.5 +/- 9.2, internal cartwheel length 66.6 +/- 15.7; N. gruberi, n = 19, external cartwheel mean length = 41.0 +/- 22.5, internal cartwheel length 259.0 +/- 87.2; human procentriole, n = 7, external cartwheel length 23.1 +/- 10.3, internal cartwheel length 154.7 +/- 47.7. Error reported is standard deviation. Scale bar, 50 nm.
(a) ELISA of cytokines in supernatants (left) and immunoblot analysis of caspase-1 and IL-1β in lysates (right) of J774A.1 macrophages exposed to EtBr (0, 10, 100 or 500 ng/ml; wedges) and left unstimulated or stimulated with LPS alone or with LPS and ATP.
Metascape analysis of differentially expressed Spindle-related genes between wildtype H9 hCOs and RGCC-KO hCOs. (adjusted absolute log2(FC)>0.5, padj <0.05). List of DEGs under the GO term Spindle from 3D RNAseq results were clustered into sub-terms to make enrichment network. The top 20 significantly enriched sub-terms were showed in the right panel. Each color of the node represents a sub-term. The size of the node corresponds to the number of genes within this sub-term were shown in the middle panel. Sub-terms with with smaller p-value was shown in the right panel. Nodes with kappa similarity over 0.3 are linked by edges.
G-I. Summarized differential module behavior between B6 and D2 (3 biological replicates) upon transition from ESCs to EpiLCs represented by PC1 of transcript abundance for all genes within each module. G. D2 retained proliferation in EpiLCs. H. Up regulation of neurogenesis in B6 EpiLCs. I. Increased regulation of cell cycle M phase in B6 ESCs.
(C) Dot plot showing the proportion of neural stem cells (GFAP+) out of DAPI+ cells in primary SEZ/ChP co-culture with or without treatment with GW4869 inhibitor or AntimiR204.
Autophagy components promote CHIKV infection and control virus‐induced cell death in HeLa cells. Cells were mock infected or infected and immunoblotted for actin, p62 (A) or LC3 (B).
(e) Western blot analysis of DICER in HeLa cells treated with control siRNA or either of two independent siRNAs targeting ATG7. Cells were also treated with nonspecific antagomir or let-7 targeting antagomir.
E The distributions of endogenous TFG and Sec31A were examined using immunogold EM. Large arrowheads highlight 15 nm gold particles bound to α‐TFG antibodies. The small arrowhead highlights 5 nm gold particles bound to α‐Sec31A antibodies. At least 15 different cells were examined, and representative images are shown. Scale bar, 100 nm.
Dose-dependent viability assays of BRCA2-proficient (+BRCA2) or -deficient (-BRCA2) human DLD1 cells treated with drugs at the indicated concentrations for six days.
(D) flg22-induced MAPK activation in Col-0 and ddl-6. Ten-day-old seedlings were treated with 100 nM flg22 and collected at the indicted time points. MAPK activation was analyzed by an immunoblot (IB) with -pERK antibody (top panel), and the protein loading is shown by Ponceau S staining for RuBisCo (RBC) (bottom panel).
PDTCs derived from breast cancer samples as previously described (Bruna et al, 2016) were treated with chlorambucil at the indicated doses. Cell survival is represented relative to DMSO control. AB521, ER-negative tumour, no BRCA1 alteration; STG201, tumour with BRCA1 promoter methylation and loss of BRCA1 expression; VHIO179, tumour with BRCA1 germline mutation and MAD2L2 inactivating mutation (olaparib-resistant)
(B) HEK293FT cells were transfected with the indicated constructs, subjected to co- immunoprecipitation and immunoblotted with the indicated antibodies.
O A model illustrating the signal transduction between scar-forming cells and post-traumatic axons mediated by trans-homophilic NB-3 interactions.
Body weights of WT and Rcan1-KO mice fed normal chow diet (NC) for 20 weeks starting at 8-10 weeks of age (male, n=15 each). Data information: values shown are mean ±SD * = p < 0.05; ** = p < 0.01; *** = p < 0.001 (two-way ANOVA with multiple comparisons, except for A and B, which used multiple t-tests).
Wildtype SIRT7, but not its RF mutant, downregulates SIRT7 target genes involved in mitochondria biogenesis SIRT7 target gene expression was determined and presented as a heatmap on a log2 scale (F)
Western blot for CSF-1R in HEK293 cells transfected with native and ΔA781_N783 (top) or P824R (bottom) CSF-1R and treated with rapamycin. Horizontal line indicates untreated cells, with concentrations 0.1, 0.5, 1, 5, 10μM. Corresponding densitometry (below) displays the fold change of CSF-1R relative to the untreated control for each transfection (**** p < 0.0001, one-way ANOVA with Sidak's post-test for multiple comparison to untreated, n = 3 biological replicates, error bars indicate SEM). Western blot for CSF-1R in HEK293 cells transfected with native and ΔA781_N783 (top) or P824R (bottom) CSF-1R and treated with 3-methyladenosine. Horizontal line indicates untreated cells, with increasing concentrations 0.1, 0.2, 0.5, 1mM. Corresponding densitometry (below) displays the fold change of CSF-1R relative to the untreated control for each transfection (**** p < 0.0001, * p = 0.0114, one-way ANOVA with Sidak's post-test for multiple comparison to untreated, n = 3 biological replicates, error bars indicate SEM). Western blot for CSF-1R and Actin in HEK293 cells transfected with native and ΔA781_N783 (top) or P824R (bottom) CSF-1R and treated with MG132 or PLX3397. Horizontal line indicates untreated cells, 20μM PLX3397, with increasing concentrations 0.1, 0.5, 0.1, 5μM. Corresponding densitometry (below) displays the fold change of CSF-1R relative to the untreated control for each transfection (*** p = 0.0002, ** p = 0.002, one-way ANOVA with Sidak's post-test for multiple comparison to untreated, n = 3 biological replicates, error bars indicate SEM).
D Duramycin sensitivity in ApoE ACM-treated fibroblasts. Note increased sensitivity after 20 min to 5 μM duramycin in ApoE4-treated cells, which was blocked upon the addition of 15 μM exogenous PtdEtn (mean±SD; n=3, with 3 replicates/experiment).
(A-B) Sequential frames of time-lapse confocal microscopy sequence of LLO-treated HeLa cells expressing (A) GFP-NMHCIIA . LLO was added to culture medium 10 seconds before t0. DIC - differential interference contrast. (A) Arrows indicate NMHCIIA bundles at PM blebbing sites.
(G) Western blot analyses of H3K27ac, H3K56ac, H3K36me3, H3K4me3 and H3K27me3 expression protein levels in WT and KO cortices at E13.5.
G Western blot analysis showing release of cytochrome c (Cyto c) into the cytosol in DM. Representative figure from n=3.
Zonation of human hepatocytes. Left - Max normalized expression over the reconstructed six lobule layers (L1 to L6), sorted by center of mass from the central vein (cv) to the portal node (pn). Right - selected pericentrally (top), and periportally (bottom) zonated genes. Blue patches are standard errors of the mean.
(c,d) Immunofluorescence of HeLa cells coexpressing HA-Nod1 (red; c) or HA-Nod2 (red; d) and Myc-FL-ATG16L1 (green). Blue, DAPI.
(O) Western blot analysis of Ubb and Ube2n siRNA transfected cell lysates with antibodies as indicated.
ChIP-seq data show enrichment of ISWI (blue) in clonal ISWI-3HA parasites at 12 hpi relative to regions of accessible chromatin ("ATAC," red). Chromatin accessibility (ATAC-seq) data were taken from the 15 hpi time point in (Toenhake et al, 2018; Data ref: Toenhake et al, 2018). Genome location is indicated at the top of the panel. The x-axis is DNA sequence, with genes represented by black boxes indented to delineate introns and labeled with white arrowheads to indicate transcription direction. The y-axis is enrichment (ChIP/Input or ATAC-seq/genomic DNA). One replicate was used for the ISWI ChIP-seq.
(c,d) Molecular model of interaction sites for CL binding to LC3 by docking analysis. CL is coloured magenta in the top-ranked binding site conformation (c), and cyan in the alternative conformation (d), with the phosphates as spheres (oxygen, red; phosphorus, orange). Amino acids interacting with CL are represented as spheres along the LC3 ribbon structure, coloured blue>orange from N>C terminus.
(A) Schematic of SRPK1 signaling pathway that regulates subcellular SRSF1 localization, which in turns can impact export and translation of repeat RNAs in the cytoplasm. SRPK1 may also act directly on protein translation pathways (dotted arrow). Known pharmacological compounds that inhibit SRPK1 can disrupt this pathway.
Western blot analysis of MRP1 (Cell Signaling), xCT and GAPDH of OVCAR-3 cells treated with APR-246 +/- MK-571 for 24h.
(B) Representative pictures of ZEB1 and MITF immunostaining in primary melanomas. Scale bar = 40 µm. The aberrant activation of ZEB1 in melanomas is correlated with a MITFlow phenotype.
(A) Preparations of chromatin-bound proteins were prepared in triplicate and subjected to SDS-PAGE and immunoblotting with the indicated antibodies in a strain that either does or does not express Rpb3-TAP Quantification of chromatin-bound Rpb1-S2P and Rpb1-S5P is shown on the right. Mcm2 is used as a loading control.
B) Five-fold serial dilutions of strains of the indicated genotypes grown on YPD plates at 30 °C or at 16 °C. Growth assays are representative images of biological replicates.
F. The knockdown efficiency of YTHDF1 in HK1, CNE2EBV and C666 cells, transfected with YTHDF1-specific siRNAs (siY1-1 and siY1-2) or the siNC control for 24 h, was determined by qRT-PCR. The mRNA levels of YTHDF1 were normalized to the housekeeping gene ACTB.
Different expression of proteins in samples collected at the first timepoint. The heatmap (left panel) indicated expression patterns of proteins overrepresented (fold change > 2) in healthy control (1,656 proteins), mild (1,547 proteins) and severe (2,362 proteins) patient groups. The top categories enriched for clusters are shown. Values for each protein in each sample (columns) are color-coded based on expression level, low (blue) and high (red) z-scored FOT. The line plots (middle panel) indicated selected gene sets with up-up (upregulation in both mild and severe patients compared with healthy controls) or up-down or down-down regulation trend during disease progression. The bar plot (right panel) indicated Gene Ontology annotations with up-up or up-down or down-downregulation trend during disease progression (Fisher-exact test, p <0.05).
C. Total AURKA and p-AURKA levels in control and PCM1-depleted cells. RPE1 cells were transfected with control or PCM1 siRNA#1 for 48 h. Following 24 h serum starvation, cell lysates were prepared and run on an SDS-PAGE gel. Proteins were detected by immunoblotting with antibodies against AURKA, p-AURKA and GAPDH (loading control).
(G) Representative photographs of fly eyes expressing GMR-GAL4 driven (GGGGCC) 28-EGFP at 29˚C along with the quantifications of necrosis and eye width. n=28-30/genotype. Error bars represent mean +/- SD.
e, BECN1-induced autophagy requires AMBRA1. After AMBRA1 downregulation, GFP-LC3-expressing 2FTGH cells were transduced with a BECN1-encoding retrovirus. Occurrence of autophagy was analysed 48 h later by appearance of GFP-LC3 punctate staining.
Mitochondrial DNA copy numbers were determined by real-time PCR and normalized to nuclear DNA standards (D).
Schema of the mouse wild type and mutant Tmem106b locus. The tm2a allele carries a LacZ-Neo selection cassette in intron 3 and a loxP-flanked exon 4. Upon Cre recombinase expression in the germline, exon 4 is deleted and Tmem106b expression abolished (tm2b allele).
Experimental set-up for global proteomic analysis of 5-azadC-induced SUMOylation changes.
EVs were isolated from CCM of uninfected Jurkat cells by differential ultracentrifugation SD). (B) Whole-mount EM analysis showing representative images and size distribution of particles in 2K, 10K and 100K pellets (Scale bar, 200 nm). The diameter (nm) of particles was determined with ImageJ for five different experiments. 387, 363 and 385 particles were counted for 2K, 10K and 100K pellets, respectivelly.
(F) Per cell Pearson Correlation between RAB21 and the various markers. Error bars are SEM, n=2 independent experiments.
Histopathological analysis of mice, which were intranasally treated with bipNb NM1267 or control Nb NM1251 and subsequently infected with 3*103 PFU SARS-CoV-2 B.1. C Quantification of lung damage was done in n = 3 animals per group and grading score of individual animals is presented as mean ± SD with **P < 0.01, by unpaired t test.
Micrographs of maximum intensity projections of forebrain sections from 3 mo old C57BL/6J mice after EdU application for 4 weeks in drinking water (F) immunostained as indicated on top of the panels. Double-positive cells are indicated by arrowheads. CTX: cerebral cortex; DIE: diencephalon; HC: hippocampus. Scale bars: 10 µm (F).