EMBO/sd-character-level-ner huggingface dataset:
Figure 4(A) IPA analysis of RNA-seq data showing the 14 top-predicted upstream regulators of differentially expressed genes. Positive Z-scores (orange) represent activated upstream regulators, negative Z-scores (blue) represent inhibited upstream regulators. (B) Known regulators of differentially expressed genes in the ESM1-NLS cells giving rise to the prediction of CTNNB1 as an upstream regulator. Observed upregulation and downregulation of mRNA are shown in red and green, respectively. The predicted relationships were shown as arrow lines with different color. The detail of predicted relationships of all the genes to the upstream regulator and the color intensity scale were described in the prediction legend. (C) GSEA of RNA seq data demonstrating the enrichment of gene sets related to Wnt signaling in 22Rv1-P cells expressing ESM1-NLS. NES, normalized enrichment score. The p values for the GSEA test statistics are calculated by permutation. (D) GSEA analysis identified β-catenin oncogenic signatures as the top induced pathways of PRAD in the PubMed GEO datasets (GSE3325 and GSE7930). NES, normalized enrichment score. The p values for the GSEA test statistics are calculated by permutation. (E) The transcriptional activity of β-catenin in 22Rv1-P cells with different patterns of ESM1 overexpression. Bars are the mean ± SD of three independent experiments. (F) Manipulating ESM1 expression impacts transcriptional activity of NFκB. Bars are the mean ± SD of three independent experiments.
Figure 6Dose-response to EV20/MMAF after 5 days of treatment in BT474 cells resistant to neratinib (BTRN#5 and BTRN#24) Levels of HER2, pHER2, HER3, pHER3, pAKT and calnexin of (B) cells resistant to neratinib Dose-response to EV20/MMAF after 5 days of treatment in BT474 cells resistant to lapatinib (BTRL, BTRL#109 and BTRL#3) Levels of HER2, pHER2, HER3, pHER3, pAKT and calnexin of cells resistant to lapatinib Dose-response to EV20/MMAF after 5 days of treatment in BT474 cells resistant to T-DM1 (BT-TDM1R#1 and BT-TDM1R#6). Levels of HER2, pHER2, HER3, pHER3, pAKT and calnexin of cells resistant to TDM1.
Figure 1(A, B) Representative Western blot (A) and quantification (B) of p62 associated with mitochondria from spinal cords. Protein levels are normalized by subunit ATPβ of mitochondria (Complex V). Mitochondrial p62 levels are increased at 120 days (symptomatic stage) in SOD1-G93A spinal cord relative to Non Tg and wild type SOD1 (wtSOD1). Results are expressed as mean ± SEM relative to Non Tg at 30 days; n=8 mice (4 males and 4 females). At 120 days, **p= 0.0018 (Non Tg vs. SOD1-G93A) and **p= 0.0011 (SOD1-G93A vs. wtSOD1) by paired one-way ANOVA with Tukey's correction. No other statistically significant differences were found (paired Friedman's test with Dunn's correction at 30 days and paired one-way ANOVA with Tukey's correction at 60 and 90 days). (C, D) Representative Western blot (C) and quantification (D) of Tim23 in homogenates from spinal cords using β-actin as normalizer. Results are expressed as mean ± SEM and relative to Non Tg at 30 days; n=6 mice (3 males and 3 females). ***p= 0.0002 (Non Tg vs. SOD1-G93A at 120 days) by paired one-way ANOVA with Tukey's correction. No other statistically significant differences were found (paired Friedman's test with Dunn's correction at 30 days and paired one-way ANOVA with Tukey's correction at 60 and 90 days). Tim23 is decreased in SOD1-G93A spinal cord relative to Non Tg at 120 days. (E, F) Western blot (E) and quantification (F) of COXI in homogenates from spinal cords. Protein levels are normalized by β-actin. Results are expressed as mean ± SEM and relative to Non Tg at 30 days; n=6 mice (3 males and 3 females). *p= 0.017 (Non Tg vs. SOD1-G93A at 120 days) by paired Friedman's test with Dunn's correction. No other statistically significant differences were found (paired Friedman's test with Dunn's correction at 30 and 60 days and paired one-way ANOVA with Tukey's correction at 90 days). COX1 is decreased in SOD1-G93A spinal cord relative to Non Tg at 120 days. G) qPCR (fold change) of PGC1α mRNA normalized by β-actin mRNA. Results are expressed as mean ± SEM and fold change of Non Tg at 30 days; n= 6 (3 males and 3 females) for 30 and 120 days, n= 4 (2 males and 2 females) for 60 days and n= 5 (3 males and 2 females) for 90 days. *p= 0.035 at 90 days and ***p= 0.0007 at 120 days. Paired Student's t test (for 60, 90 and 120 days) and paired Wilcoxon's test (for 30 days) were used for comparisons.
Manipulations of miR-29a levels promote changes in PNNs a) Images of WFA-labeled PNNs of scrambled treated visual cortex (left) and miR-29a mimic (right) in young mice.Figure 6a) Images of WFA-labeled PNNs of scrambled treated visual cortex (left) and miR-29a mimic (right) in young mice. Scale bar 60 µm. (b,c) Quantification of PNN density (scr vs mim29a, N=3 mice per group; t-test, p=0.20) and intensity for each animal (scr vs mim29a, N=3 mice per group; t-test, p=0.014). d) Cumulative frequency of PNNs staining intensity in scrambled and mimic treated young mice scr (N=1438 cells vs mim29a N=1749 cells, Kolmogorov-Smirnov test, p<0.0001). e) PNN distribution in classes of intensity in mice treated with scrambled and mimic 29a. f) Images of WFA-labeled PNNs of scrambled treated visual cortex (left) and amiR-29a LNA (right) in adult mice. Scale bar 60 µm. (g,h) Quantification of PNN density (scr vs amiR-29a, N=3 mice per group; t-test, p=0.03) and intensity for each animal scr vs amiR-29a, N=3 mice per group; t-test, p=0.047. i) Cumulative frequency of PNNs intensity in scrambled and amiR-29a treated adult mice. scr N=1883 cells vs amiR-29a N=1937 cells, Kolmogorov-Smirnov test, p< 0.0001. j) PNN distribution in classes of intensity in mice treated with scrambled and amiR-29a. k) Biochemical quantification of C4S in adult amiR-29a treated mice (N=5) as compared to scrambled animals (N=4). t test, p=0.0008. l) Example of Arylsulfatase B (ArsB) western blot. Left: The lanes corresponding to the treated (treat scr or treat amiR-29a) and untreated (untreat scr or untreat amiR-29a) cortex (ctx) of two amiR-29a treated and two scr treated mice are reported. Right: quantification of the data shows ArsB upregulation by amiR-29a. The results are expressed as fold change normalized to untreated cortex. Each symbol represents the result of one animal. N=4, scr vs amiR-29a treated cortex, unpaired t test, p=0.043
Figure 3A, Oil-red-O staining of control (healthy) and steatotic liver. Scale bar: 100 µm. B, Reconstructed MSOT image (800 nm) with linear unmixing and difference value of lipid in lower abdominal section. Unmixing result: blue for Hb, red for HbO2, yellow for lipid, jet for 700 nm - 930 nm difference. The colour bar shows the colour coding of MSOT a.u. from 0 to maximum (bottom to top) (Maximum value control/steatosis: Hb: 1.1/0.5; HbO2: 1.9/0.8; Lipid: 21000/24000; 700-900nm: 3000/3000) Scale bar: 4 mm. C, Normalized spectra of livers and kidneys from a control (healthy) and a subject with hepatic steatosis. Each spectrum is from the same animal. Data information: In the figure, A.U. = arbitrary units D, Reconstructed MSOT image (800 nm) with difference values of lipid in control (healthy) and steatotic liver ex vivo. The colour bar shows the colour coding of MSOT a.u. from 0 to maximum (bottom to top) (Maximum value control/steatosis: 10000/10000) Scale bar: 4 mm. E, Linear unmixing readouts of lipids and difference values from control and steatotic (grade 3) livers. Control: n = 6, Steatosis n = 9. Each dot represents data from one animal (control: n = 6, steatosis n = 9). Data represent the mean (+/- 95% confidence). The Mann-Whitney test and the unpaired t test were used to verify the statistical significance in linear and difference data, respectively. Linear liver control vs steatosis: P = 0.0004; Difference liver control vs steatosis: P = 6.62E-06 Data information: In the figure, A.U. = arbitrary units
Figure 2Live imaging of a rescue transgene expressing an eGFP-tagged version of Integrator subunit 6 (INTS-6) in the germline of C. elegans. M=mitotic region, TZ=transition zone. Co-localization between INTS-6::eGFP and mCherry::PRDE-1 in germ cells. PRDE-1 and INTS-6 co-localize in early stages of meiosis (1,2) and up to mid-pachytene (3), where an additional INTS-6 focus appears (3). When PRDE-1 foci are about to disappear, co-localization is lost (4), and the additional INTS-6 focus remains present well after the loss of PRDE-1 foci (5).
Figure 5A) Heat and oxidative stress cause a Tf2 TSS shift in WT cells, resulting in the production of reverse transcription competent Tf2 transcripts. Transcription fold change as in Figure 1D, but relative to act1 transcription and to transcription in the same culture immediately prior to stress, as measured by qPCR. Error bars represent standard deviation of reverse transcriptions of biological duplicates. B) Heat shock-associated TSS shift is accompanied by a reduction in LTR nucleosome occupancy. The degree of nucleosome loss is greater in WT cells than in fft2Δ fft3Δ cells, where nucleosome occupancy is already very low (Fig 2B, Fig S3). LTR nucleosome occupancy shown relative to occupancy of the Tf2 ORF +1 nucleosome, measured by MNase-qPCR. C) Exposure to stress conditions does not increase Tf2 transcript levels further in fft2Δ fft3Δ cells. Transcription fold change as in Figure 1D, but relative to act1 transcription and to transcription in the same culture immediately prior to stress, as measured by qPCR. Error bars represent standard deviation of reverse transcriptions of biological duplicates
marks co-associating TAD clusters harbouring SASP-related genes.Figure 3Overview of TiLO using a subregion of HUVEC chr5 as an example. TADs along each chromosome are treated as nodes in an interaction network and inter-TAD Hi-C signal is used to infer network connections. Inferred connections are then sliced and network robustness is assessed iteratively to obtain the final clustering. TAD clusters are visualized in the space of the nucleus using Chrom3D. Chrom3D visualisation of the whole genome (top) and of TAD clustering in chr10 from proliferating IMR90 (middle); each sphere represents one TAD. Violin plots (bottom) show 3D distances amongst TADs in three randomly-selected clusters (0, 1, and 4) or between TADs from different clusters. *: significantly different to inter-cluster distances, Wilcoxon-Mann-Whitney test. Chrom3D visualisation of TAD clustering in chr14 from proliferating (top) and senescent IMR90 (bottom). TADs (spheres) are coloured by the cluster they belong to (left) or according to their HMGB1 ChIP-seq content (middle; grey - zero peaks, blue - 1 or 2 peaks, purple - 3 or 4 peaks, red - 5 or more peaks). Violin plots (right) show 3D distances amongst TADs in each subgroup or between HMGB1-containing and non-containing TADs. *: significantly different to inter-cluster distances, Wilcoxon-Mann-Whitney test. 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. Heatmap showing protein (SASP, from http://www.saspatlas.com/; log fold ratio) and gene expression levels (log2FC) of IMR90 SASP-related genes embedded in high-HMGB1 (red) TADs like those in panel C. **: genes bound by HMGB1 in ChIP-seq data are more than expected by chance; P>0.001, hypergeometric test.
Figure 1(A) Schematic diagram of the two-photon intravital imaging and 2PLIM. (B) Representative intravital image of calvarial bone marrow of Tcirg1EGFP/+ male mice treated with BTPDM1 showing osteoclasts (left, EGFP fluorescence) and 2PLIM image for pO2 changes (right, phosphorescence lifetime of BTPDM1). Scale bar, 20 μm. (C) Phosphorescence lifetime in each osteoclast of calvarial bone marrow of mice upon exposure to ambient air (n = 91 from six mice). (D, E) Change in pO2 of osteoclasts in the mice upon exposure to various concentration of oxygen from 21% to 14% pO2. Magnified PLIM images of osteoclasts under different peripheral oxygen saturation (SpO2, D). The pO2 of each osteoclast in these mice was plotted (E, n = 47 from three mice for each SpO2). Scale bar, 20 μm. (F) Effect of physioxia (5% pO2) or physiological hypoxia (2% pO2) on osteoclastogenesis. TRAP-stained cells (left panel) and the number of TRAP-positive cells with more than three nuclei (right). Scale bar, 100 μm.
Figure 2(A) Adult phenotypes of the ash122/ash19011 flies supplemented with transgenic constructs expressing either the full-length Ash1 (Ash1FL) or the truncated variants lacking the PHD (Ash1∆PHD) or the SET (Ash1∆SET) domains. Note the third leg (L3) to second leg (L2), haltere (H) to wing (black arrows), t5 to t4 and t6 to t5 transformations in the Ash1∆PHD and the Ash1∆SET but not in the Ash1FL flies. The latter are evident from the partial loss of pigmentation in t6 and t5, or the appearance of small bristles (trichomas) on t6 of the Ash1∆PHD and the Ash1∆SET flies in the area that is normally naked (Ash1FL, yellow dashed line). (B) Two-fold dilutions of total nuclear protein extracts from the third instar larvae of the ash122/ash19011 mutants supplemented with various transgenic constructs and wild type flies were analyzed by western blot with anti-Ash1 antibodies. Arrowhead indicates the position of Ash1 protein. Note that transgenic proteins are expressed at comparable level. (C) Coomassie staining of SDS-PAGE separated protein extracts from (B) was used to control the loading.
Differential regulation of scaffold RNAs by AGO4 and AGO6AGO6 dysfunction reduces levels of Pol V‐dependent transcripts.Figure 6A AGO6 dysfunction reduces levels of Pol V‐dependent transcripts. RNA levels were measured by RT-qPCR. Means ± SD are shown, n = 3. B AGO6 dysfunction decreases Pol V occupancy at chromatin of loci where Pol V transcript levels are affected by AGO6. Anti‐NRPE1 antibody was used for ChIP assays. Means ± SD are shown, n = 3.
Figure 4A. Spermatocytes were immunolabeled against CETN3 (green), CEP164 (red), SYCP3 (blue), and stained with DAPI (upper right inset). Zoomed images of the centrosome are shown in the bottom and top left insets. Scale bars = 5 μm. B. The percent of centrioles containing CEP164 distal appendages was quantified from three biological replicates (n = 30 total cells) in control, Aurka cKO, Plk1 cHet, and Plk1 cKO spermatocytes at the pachytene-stage of meiotic prophase and metaphase I. C. Quantification of gamma-tubulin positive centrosomes per metaphase I spermatocyte. Immunolabeling was performed on three biological replicates, with ≥20 spermatocytes quantified per replicate. The total number of cells quantified for control, Aurka cKO, Plk1 cHet, and Plk1 cKO mice were 137, 169, 198, and 198, respectively. D. Spermatocytes were immunolabeled against gamma-tubulin (green), alpha-tubulin (red), and stained with DAPI (blue). Plk1 and Aurka cKO spermatocytes arrest at a prometaphase stage. Scale bars = 5 μm. Western blots of gamma-tubulin from protein extracts obtained from 19dpp and 22dpp control, Aurka cKO, and Plk1 cKO spermatocytes (E). Total protein stained with 2,2,2-Trichloroethanol (TCE) display protein loading. Western blots of gamma-tubulin from Protein extracts from control and Plk1 cHet spermatocytes at 16, 19 and 22 dpp (F). Total protein stained with 2,2,2-Trichloroethanol (TCE) display protein loading.
Figure 1(A) Immunofluorescence staining against Iba-1 in cortex (Cx), hippocampus (Hip) and cerebellum (Cb) of NPA affected and control 3 year-old children. Scale bars, 50 μm. (B) Magnified image showing ramified (left) versus amoeboid (right) morphology in control and NPA microglia. Scale bars, 10 μm. (C) Mean ± SEM area of Iba-1 positive cells in different brain regions from a NPA affected and a control child (n = 20 cells, Student´s t-test). (D) Immunofluorescence staining against Iba-1 in Cx, Hip and Cb of 3 month-old ASMko and wt mice. DAPI staining shows cell nuclei. Scale bars, 50 μm. (E) Mean ± SEM number of Iba-1 positive cells in different brain regions from ASMko and wt mice (n = 5 mice per group, Student´s t-test). (F) 3D rendered images obtained with Imaris Surface software from high magnification images of immunofluorescence staining against Iba-1 showing representative microglial morphology in Cx, Hip and Cb of ASMko and wt mice. Scale bars, 10 μm. (G) Mean ± SEM area of Iba-1 positive cells in the different brain regions from ASMko and wt mice (n = 5 mice per group, >10 cells per mouse, Student´s t-test). Scale bars, 15 μm. (H) Example of projection detection by the Filament Imaris software. (I) Mean ± SEM branch point number per process and process length in iba1+ cells obtained with the Imaris Filament software (Student´s t-test).
Figure 6A) Volcano plot showing the transcriptional effects of KLF5 deletion in CFPAC-1 cells. Differentially expressed genes were identified by comparing two KLF5-deleted clones with two wt clones. The Y-axis shows the -log10 of the q-values determined by Cuffdiff. The genes indicated in green are part of the signature of classical PDACs (Collisson et al, 2011). B) Gene-ontology analysis on the set of differentially expressed genes in KLF5-KO cells. Bubble color indicates the FDR (color scale shown on the right) while size indicates the frequency of the GO term in the GOA database (bubbles of more general GO terms are larger). C) Scatter plots showing H3K27Ac (left) and H3K4me1 (right) levels at putative enhancers (TSS-distal genomic regions) in control vs. KLF5-KO cells. The box-plots in the insets show KLF5 tag counts in the hypo- and hyper-acetylated or methylated regions.D) Genomic distribution of common and differential acetylation in control and KLF5-KO cells.E) Histogram showing the percentage of hypo- and hyper-acetylated peaks (divided in TSS-proximal and distal) that contain a KLF5 peak. F) Representative RNA-seq and ChIP-seq snapshots centered on a KLF5-dependent gene (MUC4) and a KLF5-repressed gene (VIM). G) Subcutaneous xenografts of wild type or KLF5-deleted CFPAC-1 cells were stained with the indicated antibodies. MiaPaCa-2 xenografts are shown for comparison (n = 4 animals analyzed per group).
Figure 4(A) Schematics of construction and screening platform to characterize a library of CRISPRa-mediated inducible promoters by targeted RNAseq and DNAseq. (B) Promoters significantly activated by CasTA2.1 using gRNA-H23 (left) or gRNA-H22 (right) are plotted with basal expression level on x-axis against fold activation by CRISPRa on y-axis. N is the total number of promoters shown. Red box corresponds to highly activated promoters (fold change >10).  (C) Highly activated promoters (>10-fold) using gRNA-H23 (left) or gRNA-H22 (right) are plotted. Basal expression levels (purple lines), induced expression level (orange lines on left or red lines on right, activated with gRNA-H23 or gRNA-H22, respectively) and induced fold changes (gray bars) are shown. Promoters were first ranked and grouped by basal expression levels. Within each group, promoters were ranked by activation fold changes.
Figure 2A Pulldown and Western blot analysis validated the interaction between the viral protein ORF3a and its interactors, VPS11 and CLCC1, and the binding of S protein to SPCS2. HEK293T cells with SFB-tagged bait expression were collected and lysed. Cell lysates were subjected to pulldown assay using S-protein beads. Western blot analysis was conducted with the indicated antibodies. Cells transfected with vector or construct encoding control genes were included as controls in these experiments. B Immunostaining analysis of protein localization. U2OS cells were transfected with construct encoding ORF3a. Cells were fixed and stained with the indicated antibodies. The green signal is CLCC1 or lysosome marker LAMP1, the red signal is flag (for SFB-ORF3a), and the blue signal indicates DAPI/nuclei. Scale bar: 10 µm. C Overlap of HCIPs identified from SFB-tandem affinity purification and second-generation biotin ligase (BioID2) labeling experiments. D Overlap of HCIPs reported previously and those identified in the current study.
Figure 5(A-C) Actograms show mean locomotor activity in wild-type under a medium (dark blue line) and low (light blue line) intensity LD regime at (A) 5 dpf, (B) 6 dpf and (C) 7 dpf. Spectrum and photoperiod is the same under both conditions. The band on each side of the mean indicates the 95% confidence interval. The bar under the chart indicates the 12:12 hour LD interval. (D) Box plot shows a significant reduction in locomotor activity during the wake state under a low (light blue box) than a medium (dark blue box) intensity LD regime on the 5th, 6th and 7th dpf. (E) As in D for the rest state (dark phase). No difference in locomotor activity was detected. Data information: boxplot divides the data in quartiles: the box indicates the interquartile range, with the horizontal line in the box denoting the median of the data set, the whiskers extend to the minimum and maximum, and meet the box at the median of the lower (quartile 1) and median of the upper (quartile 3) half of the dataset. Black dots indicate biological replicates (n=18), the red dot indicates the mean, red error bars indicate the confidence interval (95%) and asterisks indicate significance (0.01<p(✱)<0.05, 0.001<p(✱✱)<0.01, p(✱✱✱)<0.001, ns = not significant). (F) Larvae show significant less displacement in large-angle turns at the onset of the dark interval under a low intensity LD regime than under a medium intensity LD regime on the 6th and 7th dpf Data information: boxplot divides the data in quartiles: the box indicates the interquartile range, with the horizontal line in the box denoting the median of the data set, the whiskers extend to the minimum and maximum, and meet the box at the median of the lower (quartile 1) and median of the upper (quartile 3) half of the dataset. Black dots indicate biological replicates (n=18), the red dot indicates the mean, red error bars indicate the confidence interval (95%) and asterisks indicate significance (0.01<p(✱)<0.05, 0.001<p(✱✱)<0.01, p(✱✱✱)<0.001, ns = not significant).
Activation of thermoregulatory brain regions in Cdk4-/- mice.Figure 6A-D Confocal illustrations of frontal hypothalamic sections from Cdk4+/+ mice (A, C, N=3) and Cdk4-/- mice (B, D, N=3). Low magnification showing nuclei (Hoechst, left pannel) and c-Fos activated-cells (white, right pannel) in the mPOA (A1-2, B1-2) and the ARC, the VMH, the DMH, the LH (C1-2, D1-2). High magnifications corresponding to the frame area in A1-2, B1-2, C2, D2 and showing c-Fos-IR cells (A3-4, B3-4, C3-6, D3-6). Scale bars (A1-2, B1-2, C1-2, D1-2): 200μm, (A3-4, B3-4, C3-4, D3-4): 50μm. E Quantification of c-Fos IR cells in brain sections of Cdk4+/+ and Cdk4-/- mice (n=15-24 slices according hypothalamic nucleus and genotype).
Figure 8(a) Design of the transgene construct, consisting of an enhanced green fluorescent protein (EGFP) transcript, marked at its 3' end by a random barcode (purple bar) and driven by the human PGK promoter. The construct is flanked by the terminal repeats (5'TR and 3'TR) of the Piggybac transposon that are used for random integration in the genome. (b) Summary of the mapped locations of integrations in the genomes of two F1 hybrid mES cell clonal cell lines. LAD and iLAD integrations are shown in orange and black, respectively. (c) Average DamID profiles across 17 transgene integration sites inside LADs. Blue curve shows alleles without integrations, red curve shows the corresponding alleles with integrations. Shading between the lines shows which curve has the highest value. (d) Relative expression levels of individual barcoded transgenes in LADs and iLADs. (e) Estimated expression levels of integrated transgenes in LADs (vertical orange lines; median value indicated by arrowhead), compared to the distribution of expression levels of all active endogenous genes (black curve).