EMBO/sd-character-level-ner huggingface dataset:
LPS induced miRNA export from mammalian macrophage cells. A schematic diagram of the experiments has been described in left panel of (A). Characterization and quantification of exosomes derived from Control and LPS-activated RAW 264.7 cells by Nanoparticle Tracking Analysis (NTA) done for isolated exosomes. Relative size distributions are shown (A, right panel).
(e) A549 cells infected with adenovirus harbouring shRNA for Rubicon and control (luciferase) were cultured in N or S medium for 4 h and cell lysates were subjected to immunoblotting with the antibodies indicated. Full scans of the blots in b and e are available in Supplementary Information, Fig. S6.
B HCC827 NSCLC cells carrying dox-inducible GFP-Usp27xC87A, GFP-Usp27x, or two separate lines established from these GFP-Usp27x-cells where the Bim-locus had been targeted for deletion using CRISPR/Cas9 (Bim-KO), were treated with combinations of dox and the EGFR-inhibitor gefitinib as indicated. Apoptosis was measured after 72h of treatment by staining for active caspase-3, followed by flow cytometric analysis. Data (means/SEM) are from n=≥15 (maternal GFP-Usp27x line) or from n≥5 (for Bim1KO) or from n≥6 (for Bim2KO), or n=4 (for GFP-Usp27xC87A) separate experiments. P-values (t-test) for statistically significant differences are shown. Again, the addition of QVD inhibited cells from active Caspase-3 positive staining (not shown). The inset shows Bim-knock-out-efficiency (n=2).
Control or CEP41-deficient HUVECs cultivated under laminar shear stress and immunostained with ARL13b-specific antibodies to measure deciliation. Representative images are indicated by rectangles with numbers and shown in magnified images in the right panels. The resulting data were compared to those of cells under static conditions in (F). Scale bars, 20 μm. Quantification of ARL13b-positive ciliary cells (G) and of relative intensity of GT335/ARL13b signals in the cilia (H) in images (F) is the results of three independent experiments with ≥ 200 cells per condition (mean ± SD (G), median (H)). *
C. After sucrose gradient fractionation of lysates of tunicamycin-treated H9c2 cells, GADD34, PP1 and Nox4 co-eluted in fractions 12 and 13 (F12, F13).
Kaplan-Meier survival curves based on datasets from GEO, EGA and TCGA, demonstrating that high expression of both mDia2/DIAPH3 and INHBA in patients with liver, stomach and breast cancer correlates with poor overall survival. Data and statistical analyses were collected from KMPlotter.
F Representative images of 31-32 week old WT and NYKO mice showing aberrant positioning of hind limbs.
(C) The relative enrichment of KDMs targeting ribosomal protein-coding genes in 786-0 cells. The outer circle represents the enrichment value of ribosomal protein-coding genes by each KDM. The inner circles represent the sum of the indicated values. The IgG was used as a control.
Cells analyzed using QIBC. I. Quantification of EU incorporation in cells in (H) (red bars, mean; n>2000 cells per condition).
Microtubular transport speed is reduced by the presence of aggresome-like structures in HEK293T cells and is improved upon 4-PBA treatment. The mean velocity of lysosomes was measured on time-lapse recordings of HEK293T cells labelled with LysoTracker®. (E): siCtl/+4PBA n=622/677; siElp3/+4PBA n=674/577; siAlkbh8/+4PBA n=460/484, pooled from 4 experiments, ***p<0.001. All data analysed with Kruskal-Wallis ANOVA, Dunn's multiple comparisons test. Box/whisker plots depict minimum, first quartile, median, third quartile, and maximum.
Effects of Fus-silencing (pink line) and U1-inhibition (yellow line) on read distributions of RNAPII-FUS-tRIP (left) and RNAPII-U1C-tRIP (right) around APA sites repressed by both FUS and U1 snRNP [the first quadrant in (A)]. The p-values for the differences between contAS and U1AS (left panel), as well as those between siCont and siFus (right panel), are indicated by circles.
A) HT29 cells were treated with or without 300 nM 5-AZA-CdR for 2 days and subsequently washed and transfected with the indicated siRNAs. Cells were harvested 72h post-transfection and the type I IFN response was analyzed by RT-qPCR analysis of IFN-β, IFIT1, and ISG15 transcript expression, normalized to ACTB. B) LIM1215 cells were treated with or without 300 nM 5-AZA-CdR for 2 days and subsequently washed and transfected with the indicated siRNAs. Cells were harvested 72h post-transfection and the type I IFN response was analyzed as in (A). C) LIM1215 cells were treated with 250 nM palbociclib or a DMSO control for 7 days. Three days after treatment initiation, cells were transfected with the indicated siRNAs and cultured for an additional 72h. The type I IFN response was monitored as in (A). Data information: Data from three biological independent experiments are shown with mean ± s.d.. Statistical analysis was performed using ordinary two-way ANOVA with Tukey's post hoc test. ns, not significant; *, p<0.05; **, p<0.01; ***, p<0.001; ****, p<0.0001.
Kaplan-Meier curves showing mammary tumor-specific survival for the different models. WB1P-BE3 females injected with Lenti-sgPik3caE542K-Myc (n=10), Lenti-sgPik3caE545K-Myc (n=10) and Lenti-sgPik3caE453K-Myc (n=10) showed a reduced mammary tumor-specific survival compared to WB1P-BE3 female mice injected with Lenti-sgNT-Myc (n=11) vectors (respectively 47, 44 and 49 days after injection vs 72 days after injection, P < 0.0001 by Mantel-Cox test).
(F) Quantification of γ-H2AX foci in HeLa cells where POGZ has been targeted by CRISPR technology (POGZ∆-1 or -2) and in control HeLa cells (sgCtrl). Cells were exposed to 1 Gy before being pulsed with Edu for 1hr and were recovered at the indicated time points. Cells were fixed, stained, and imaged via confocal microscopy. Data are the total number of γ-H2AX foci in EdU+ cells and represented as a bar graph showing the mean ± SD (n = 3 biological replicates, with at least 100 cells analyzed for each time point). Significance was determined by two-way ANOVA followed by a Dunnett's test. *P<0.05, **P<0.0005. (G) Representative images used for quantification in (F). Scale bar = 5 μm.
Summary of the possible disease mechanisms in neuronal cells with POLG mutations.
FLT3 signaling was detected by Western blotting in 293FT cells-transfected with FLT3/ITD mRNA (I)
D, E, Left: 3D reconstruction of two-photon (D) and light sheet microscopy images of intact cleared ROSAmT/mG eye showing that GFP+-donor and -acceptor photoreceptors are in the same area. D, Right: A high magnification image showing GFP+-donor and -acceptor photoreceptors connected by protrusions (pink arrows). E, Right: In detail, donor and acceptor photoreceptors also appear connected through cell protrusions (pink arrow).
(B) Alignment of Atg8 predicted three‐dimensional structure with its mammalian homologues. SWISS MODEL was used to predict Atg8 structure and PyMol was used for presentation. Orange represents the predicted Atg8 structure, and red, blue and green represent GATE‐16, GABARAP and LC3, respectively.
(B-D) Flow cytometry analysis of the number of CD45 positive cells (B), percentage of neutrophils (C) and of inflammatory macrophages (CD38+Egr2-) and tissue-repair macrophages (CD38-Egr2+) (D) in forepaw skin of RDEB mice treated as in A. Data information: individual data points, mean ± S.E.M are shown. The data were analyzed by one-way ANOVA with Tukey's correction, P values < 0.05 are considered significant and shown; n = 5-14 biological replicates.
B. Quantification of EYFP-Parkin translocation to mitochondria. The percentage of PC6 cells with EYFP-Parkin translocated to mitochondria in response to PINK1 overexpression is lower in the Miro shRNAs-expressing groups when compared with the scrambled shRNA-expressing group (scr shRNA). ****P < 0.0001, n = 6 dishes per group, 20 fields per dish, one-way ANOVA
A. Immunoassay-based quantification of neurofilament-light chain (NfL) protein levels in CSF of 6-month-old Grn-/- (n=4), Trem2-/-(n=4), Double-/- (n=4) and WT (n=5) male mice. B. Immunoassay-based quantification of NfL levels in CSF of 14-month-old Grn-/-, Trem2-/-, Double-/- and WT female mice (n=3 per genotype). Data information: Data in A, B represent mean ± SEM. For statistical analysis in A-B two-way ANOVA with Dunnett`s post hoc test was used the unpaired
(a,b) Effects of G120A and F52A mutations, which perturbed C18-ceramide binding of LC3B, on targeting of mitochondria by LC3B-containing autophagosomes (visualized by confocal microscopy using anti-Flag and anti-Tom20) (a) or mitochondrial function (measurement of OCR) (b). V, vector.
Isomerase activities of phosphorylated PDI WT and S357A by Fam20C for indicated times (N) measured by scrambled RNase A reactivation assay. The activity of PDI WT was taken as 100%. Data information: All data were shown as mean ± SEM of three independent experiments. , ***p < 0.001 (two-way ANOVA, the post hoc Tukey's HSD test).
(H) Scattering profiles, their normalised pair-distribution functions P(r) and low-resolution ab initio models for the RBCC domains of TRIM25 and TRIM32. The curves and envelopes are reported using the same colour scheme in all respective panels and the envelopes for the constructs are drawn to scale.
(A) LPS/ATP treated wild type microglia were stained for NLRP3 (green) and CALCOCO2 (red) and analysed by confocal microscopy. Colocalizations of NLRP3 aggregates (arrows) and CALCOCO2 (arrowheads) are apparent; scale bar: 10 µm.
(D) The presence of cytosolic PPM1D puncta in etoposide-treated PPM1D+/+MEFs. PPM1D+/+MEFs were treated with etoposide (10 µM) for 6 hr, immunostained with an anti-PPM1D antibody, and their nuclei stained with Hoechst 33342 (50 ng/ml). Representative images of anti-PPM1D (green; upper panels) and Hoechst 33342 (blue; lower panels) are shown. Arrowheads indicate cytoplasmic PPM1D puncta.
D, Scatterplots for the differentially expressed genes (DEGs) highlighting the inflammatory/immune genes that are most significantly downregulated in the inhibiter-treated cultures.
Data derived from the gels presented in (A) and (B) presenting binding of RPA and SUMO-RPA to DNA in binding and displacement conditions.
(A) Analysis for genome-wide SRCAP binding regions in ISCs from ChIP-seq was shown. Coordinate information for sequence alignment was from UCSC (intron and exon), Ensemble GRCM38 (mm10, release-90) (upstream 2000bp, downstream 2000bp, distal intergenic region, TSS (transcription start site), TES and promoter), GSE57919 (Dnase-seq peaks, liftover to mm10), and GSE34568 (H3K4me2, liftover to mm10). Distribution of SRCAP peaks in ChIP-seq and its overlap with each kind of region was analyzed by bedtools.
d, e, Representative confocal images of primary cilia with variable length formed in C19 cells subject to 72 hserum starvation. Data shown represent 100 cells per well in triplicate samples.
B6.K18-hACE2IP-THV mice were primed (i.m.) at wk 0 and boosted (i.n.) at wk 5 (n = 5) with non-integrative LV::S. Control mice were injected with an empty LV (sham). (A) Representative IFN-γ response by lung CD8+ T cells of as studied at wk 7 after in vitro stimulation with the indicated SCoV-2-derived peptides.
Percentage level m.3243A>G in blood, urinary sediment and skeletal muscle. No differences were detected by using the two-sided Wilcoxon signed-rank test with an empirical level of significance. W = week of the study.
Volcano plot highlighting significantly (P < 0.05, > three‐fold change) up‐regulated (red) and down‐regulated (green) phosphopeptides identified in each screen. Rab GTPases are marked in purple.
(B) LPS/ATP treated wild type microglia were immunolabeled for NLRP3 (green) and LC3 (red) and analysed by super resolution microscopy (SIM). NLRP3 aggregates of different sizes coclustering with LC3-positive autophagosomes are clearly visible. 3D volume rendering of large (I) and small (II) NLRP3 aggregates from the magnified ROIs showed engulfment of NLRP3 by autophagosomes; scale bar: 10 µm; magnified ROIs: 1 µm.
(A, B) Ability of serial C‐terminal deletions of TMEM59 to activate LC3. 293 cells were transfected with the indicated TMEM59 C‐terminal deletions, HA-LC3A (A) or HA-LC3B (B) and GST, and lysed for western blotting against the indicated molecules.
I. Cortical neurons were transfected at day in vitro (DIV) 3 with control vector, a functional or a non-functional FBXO7 shRNA plasmid together with a transfection marker. At DIV6 apoptotic neurons were counted. Four independent experiments were included in the analysis (ANOVA, ** p<0.01, mean +s.e.m.).
Putative Siz2 E2~SUMO interaction interface modeled by aligning PINIT and SP-RING domains of Siz2 to those of Siz1 in the context of the PCNA/Siz1/Ubc9~SUMO complex (pdb 5JNE) (Streich & Lima, 2016) (D) and Siz1 E2~SUMO interactions present in the PCNA/Siz1/Ubc9~SUMO complex (E). Contact forming residues are shown in stick representation and Siz1/Siz2 residues that make contacts with SUMO and E2 are additionally colored in cyan and magenta, respectively.
A Genetic interactions between irc5-Δ1 and HR mutants. Logarithmically growing cultures of wild type (W303-1a), irc5-Δ1 (IL012), rad51Δ (MC002), irc5-Δ1 rad51Δ (TB046), rad52Δ (MC006) and irc5-Δ1 rad52Δ (TB047) strains were 10-fold serially diluted and plated onto YPD plates with or without MMS
C. Impact of TMPRSS2 on S and ACE2, measured by Western Blot. 293T cells were transfected with or without IFITM1, TMPRSS2, S or ACE2 plasmids, and analyzed 18h later.
Quantification of the protein levels of ER lumenal proteins in the cytosolic fraction as shown in (A). n = 5 biological replicates, the horizontal line represent the sample ﻿mean. ﻿Differences were analyzed by Unpaired Student's t-test using Prism 9 (GraphPad), except when otherwise indicated. P-values < 0.05 were considered significant).
(B, C) Percentages of GFP+ cells within 5.2+ pDC (B) or of GFP+ (green) vs GFP- (white) cells within 5.2+ IFN-I-producing pDC (C) isolated from indicated MCMV-GFP-infected MBMC. Data shown (mean±SEM) are from 2 pooled independent experiments each with 3 mice per group
a. Joint cell segmentation and cell type annotation (JSTA) overview. Initially, watershed based segmentation is performed and a cell level type classifier is trained based on the Neocortical Cell Type Taxonomy (NCTT) data. The deep neural network (DNN) parameterized cell level classifier then assigns cell (sub) types (red and blue in this cartoon example). Based on the current assignment of pixels to cell (sub) types, a new DNN is trained to estimate the probabilities that each pixel comes from each of the possible (sub) types given the local RNA density at each pixel. In this example, two pixels that were initially assigned to the "red" cells got higher probability to be of a blue type. Since the neighbor cell is of type "blue" they were reassigned to that cell during segmentation update. Using the updated segmentation and the cell type classifier cell types are reassigned. The tasks of training, segmentation, and classification are repeated over many iterations until convergence.
G Quantitative analysis of CD31 / Ki67-positive cells in FI, CI, PI and PI+MVF in % of all endothelial cells (n = 10 each). Mean ± SD. One-way ANOVA and Tukey's multiple comparisons post hoc test were used for statistical analysis. *P < 0.05 vs. FI; #P < 0.05 vs. CI; +P < 0.05 vs. PI.
Heatmaps showing GO terms associated with differentially-expressed genes in two TAD groups from panel C; SASP-related GO terms are highlighted. The number of genes (N) behind each heatmap are indicated.
B. Real Time PCR quantification of 5'-ETS steady-state levels in HeLa cells expressing PNRC1W300A or GFP control. The average of 3 independent experiments ± SD is reported.
LCI assays showing that CBF1 inhibits phyB interaction with PIF4 (C) in plant cells. Different letters represent significant differences by one-way ANOVA with Duncan's post hoc test (P < 0.05).
A-C Wild‐type and atg‐2 hermaphrodites have a single vulva (arrow). (B) let‐60(n1046gf) mutants show a Muv phenotype. Black arrows indicate pseudovulvae.
(C, D) Efficiency of Ctcflos KD by (C) LNA Gapmer ASO1, ASO3 and ASO4 targeting Ctcflos transcript 1 and (D) LNA Gapmer ASO2, ASO5 and ASO6 targeting Ctcflos transcript 3 and 4 compared to nontargeting controls, assessed by qPCR. Mean values ± SD, n=3 (biological replicates), one-way ANOVA (Šídák-test ), ***p<0.001, ****p<0.0001.
(B) (C) Analysis of DNA content by flow cytometry of G1 phase synchronized wild type, rad3-102, rad3-102 rad51∆, rad3-102 mus81 and rad3-102 mus81-dd cells and further released into S phase. Cells were synchronized in G1 with α-factor, untreated or irradiated with 20 J/m2 UV-C, let in G1 for 2h, and released into S phase. Three biological replicates have been performed.
The engraftment of MOLM-13 after FST knockout was detected by flow cytometry of human CD45 and mouse CD45.1 positive cells in recipient mouse BM aspiration at week 2 post transplantation. Data information: data were presented as mean ± SEM. *P<0.05, **P<0.01 (Student's t-test).
(c) Potential confounders in half-life analyses. Top, total protein ideally decreases over time in a predictable manner (top right panel). Middle, toxicity reduces the amount of measured protein, potentially shortening the calculated half-life (middle right panel). Bottom, protein aggregation might also shorten half-life estimations if the protein cannot be immunoprecipitated (black arrows, bottom right panel) or lengthen it if the protein is more stable and successfully immunoprecipitated (gray arrows, bottom right panel).
J: Compared to littermate controls, sCA1 neurons of NexCre cTKO animals show no significant reduction in total dendritic length in basal dendrites (Mann-Whitney test, nsp = 0.5601).
Western blot bands for YAP, pS127 YAP and total protein. (E) Quantification of YAP and pYAP Ser127 normalised to total protein, expressed relative to unstimulated control (n=8)
D. Dot plot representation of flagellum length in the indicated cell lines and conditions. For each condition, 100 flagella were measured and statistical analysis was performed with the ANOVA test. Significant differences are indicated with a star (P<0.0001
(F,G) Migration (F) and Matrigel invasion (G) of LM2 cells transduced with a retroviral vector overexpressing PIP5K1A or control vector. Data normalized to control values. N = 5 inserts/group.
Immunofluorescence images (left) of α-actinin and cTNT in CTR and DCM single cardiomyocytes, illustrating 3 different levels of sarcomeric organization (perinuclear, fully and peripherally organized). Percentage of cells with different levels of sarcomeric organization (right) under basal and stress conditions. Statistical difference was tested using the chi-squared test (CTR1 basal: n = 283, CTR2 basal: n = 250, DCM1 basal: n = 255, DCM2 basal: n = 236, CTR1 Iso: n = 245, CTR2 Iso: n = 230; DCM1 Iso: n = 242 and DCM2 Iso: n = 269; ***P = 1.93E−16 CTR basal versus DCM basal; ***P = 9.61E−34 CTR Iso versus DCM Iso, **P = 0.001 DCM basal versus DCM Iso). No significant differences were observed comparing CTR basal and CTR Iso groups. Scale bars, 25 μm.
(E) TEM images of a single ommatidium from photoreceptors of (i) rdgB9-day1 and (iii) rdgB9;dEsytKO - day 1 flies reared in dark, scale bar: 1 µm (red asterisk indicates R7 photoreceptor). (E-ii, iv) Magnified image showing a single photoreceptor from the ommatidium image shown on the left. Scale bar: 200 nm. (F) Quantification of the number of MCS per photoreceptor for R1-R6 in 1 day old dark reared wild type (from Figure 5B i), rdgB9 and rdgB9;dEsytKO flies. n=30 photoreceptors from 3 separate flies.
Left: Representative immunofluorescent staining of GM130 (yellow), F-actin (gray) and DAPI (blue) in negative control and CAMSAP2 siRNA transfected hRPEs at the edge of the wound after 8 h. Scale bar: 50 μm. Middle: Schematic diagram of Golgi-nucleus orientation towards the front (45°-135°) or the rear (-45°- -135°). Right: Quantification of the percentage of Golgi-nucleus orientation towards the front or rear of the cell.
(E) Mass spectrum analysis of IREB2-associated proteins. Mock or IREB2-FLAG was transfected into HEK293T cells and FLAG-tagged proteins were enriched by anti-FLAG M2 beads and incubated with lysates from normal mice colon tissues. Five matched peptides corresponding to OTUD1 were shown on the right panel.
A, Co-IP analysis was performed in 293T cells with antibodies against p53 or H2Bub1.
Frequencies of all possible dipeptide sequences in S3-LCEs. Fold changes and P-values are shown as in Fig 1E. The color code indicates the number of P or S in a dipeptide.
D. Comparative analysis of GOBP enrichment for hHSC and hLSEC from Cluster 3 and Cluster 4 from Panel (A) A, with blue terms specific for hHSC and pink specific for hLSEC and gray terms shared between them. Significance was same as Panel (B).
Cells were incubated in 0.5% ambient oxygen for 16 hours. Immunoblots show HIF-1α, HIF-2α and HIF-1β protein levels in the wild type and single clones of CRISPR-Cas9 engineered cell lines
C, E, G, I Immunohistochemical staining for Snai1/2 (Abcam ab85931) (C) E14.5midgut, (E) E14.5hind gut, (G) postnatal day 14 SI, (I) postnatal day 14 colon. Snai1immunohistochemistry peptide competition controls are shown as inserts (C', E', G', I'). Scale bars: 20 mm.D, F, H, J, K X‐gal staining for β‐galactosidase activity in tissue from Snai2LacZ mice stained in whole mount, sectioned and counterstained with nuclear fast red (D) E14.5midgut, (F) E14.5hind gut, (H) postnatal day 14 SI, (J) postnatal day 14 colon, (K) adult SI. Controls for X‐gal staining are shown as inserts (D', F', H', J').L, M, N Double immunostaining of small intestinalcrypts for Snai1/2 (red) and (M) Lgr5‐GFP (green); (N) merge shows Snai1 is present in both CBCstem cells and proliferating transit amplifying cells. Scale bars: 10 mm.O, P Immunohistochemistry for Snai1 using a different primary antibody (Genetex GTX125918) shows minimal expression of Snai1 in villi. (P) Expression of Snai1 is detected at the base of crypts (P) with strong nuclear expression in CBCstem cells indicated by arrows. Scale bars: 20 mm (O), 10 mm (P).Q Schematic diagram showing Snai1 expression (red) within different cell types in the crypt. SI = small intestine. See also Supplementary Fig S1.
(e,f) DHE and DAPI fluorescence in the dentate gyrus (e) and SVZ (f) of Ctrl and FIP200GFAP cKO mice at P28 (n = 5 mice for each). Dotted lines indicate the boundaries of the GZ (e) and SVZ (f). Arrows mark cells in the SGZ (e) and SVZ (f), and arrowheads mark cells in surround regions (the GZ in e and the ST in f). LV, lateral ventricle; ML, molecular layer. Full-length blots are presented in Supplementary Figure 11.
A. Scatter plot showing the expression of EP300 and BAZ2A in two large cohorts of metastatic and primary PCa.
B. LNA efficiently mediated LincGET knockdown. LNA was injected at phCG 25 hours and embryos were collected at phCG 48 hours at late 2-cell stage for TM-qPCR analysis. The error bars represent s.e.m. About 50 embryos of each stage were used and three experimental replicates were performed.
RT-PCR analysis of constitutive expression and splicing of XBP1 in glioblastoma cells transduced with RGD4C/AAVP-Grp78, in the presence of TMZ. Sizes of the PCR products were 289 bp for unspliced XBP1 and 263 bp for spliced XBP1, the lower size band is not specific. Time points were selected among those tested in the Western blot in (A), subsequently the image containing 0, 1 and 2 hours was juxtaposed to images of 6, 12 and 24 hours. A white line has been added between the gel pieces that have been juxtaposed.
E, F, Number (E) and size (F) of SnRK1α1- and SnRK1α2-foci in root tip cells of WT and tsn1 tsn2 seedling expressing ProUBQ:GFP-SnRK1α1 or ProUBQ:GFP-SnRK1α2, respectively, after HS (60 min at 39ºC). Data represent means ± SD of at least 16 replicate measurements from three independent experiments. P values denote statistically significant differences for comparisons to WT plants (two-tailed t-test).