EMBO/sd-character-level-ner huggingface dataset:
Effect of Ctcflos KD on Serine/Arginine rich Splicing factor 2 (SC35/SRSF2) and nuclear speckle abundance in Ctcflos tr1 (ASO 1) KD and control cells (KD day 1 of differentiation, analysis after 48h). (E) Immunocytochemistry of SC35. SC35 signal (blue) alone (middle images) and SC35 (blue), DNA staining by DAPI (green) and phase contrast (PC) (gray) combined (outer images).
HUVECs were transfected with ADAR1-targeting siRNAs and subjected to hypoxia treatment for 5 hrs. The 3'-end extension of HIF1A-AS2 RNA transcription in ADAR1 knockdown cells (GFP, control) was examined by PCR with primers corresponding to the depicted regions of HIF1A-AS2 locus. GAPDH serves as an internal control. Sequence locations are shown in kbp and relative to the transcription start site.
D. Bar graph representing the number of animals which displayed the hemorrhage phenotype across the progeny derived from breeding of two control gib004Tg(fli1a:EGFP;gata1a:DsRed) zebrafish and progeny derived from an outcross of veal2gib005Δ8/+ zebrafish. Data from three different experiments plotted as mean percentage values ± standard deviation.
(A) Representative image of the intestinal populations purified in the cell sorting experiments.
(d) The same cells imaged in the cyan channel, before and at the indicated times after photoconversion (arrow) by exposure to 405 nm light. Top: Representative images of the cyan fluorescence. Bottom: Quantification of the intensity of the cyan fluorescence. Values are expressed as times the intensity before photoconversion that was given an arbitrary value of 1. Values are mean+s.e. of 3 different experiments with >10 cells counted per experiment. Scale bars, 5 μm.
VSV-eGFP infection induces ACE2 expression.HEK293 cells were cultured in six-well plates and infected with VSV-eGFP as indicated above. 6 hrs later, HEK293 cells were collected for RNA isolation and RT-qPCR analysis. Results in each panel are representative of three independent experiments.
D Identification of target gene modules - groups of genes with common regulatory patterns by TFs. Colour indicates the fold change (adjusted for significance) of gene expression following each TF perturbation. Rows (perturbed TFs) and columns (target genes) are hierarchically clustered. 44 modules for target genes are shown. Below examples. Selected modules with highlighted overall regulation pattern and example genes listed below.
(D) Schematic illustrating the rescue DKO NPC differentiation defect with the GSK3 inhibitor CHIR99021 (chemical name: 6-[2-[[4-(2,4-dichlorophenyl)-5-(5-methyl-1H-imidazol-2-yl) pyrimidin-2-yl]amino]ethylamino]pyridine-3-carbonitrile). Created with Biorender.com.
Endogenous METTL14 interacts with RNAPII. Endogenous co-immunoprecipitation (IP) was performed using the METTL14 antibody for IP and the RNAPII antibody for Western blot detection (left panel) and using the RNAPII antibody for IP and the METTL14 antibody for Western blot detection (right panel).
(B) Immunofluorescence (IF) validation of mintbody specificity. Mouse MC12 cells, which stably express H3K27me3-mintbody (sfGFP), are labelled with antibodies specific for H3K27me3 (Cy5) and H3K9me3 (Cy3). DNA is stained with Hoechst33342. Single confocal sections are shown. Arrows mark Xi. Scale bar = 10 μm.
(B) Schematic of the uncoupled fork and uncoupled product generated by persistent stalling of leading-strand synthesis.
Cells depleted of Rod using RNAi and transfected with the indicated Bub1 constructs. (D) Representative immunofluorescence images of cells stained for YFP and Mad1 in each condition. Scale bar, 5 μm.
(E) Immunoblot of SCOT, BDH1, CD31 and the loading control VCP in murine endothelial cells isolated from heart, muscle, lung and adipose tissue.
Rescue of angiogenic sprouting by Myc overexpression in E11.5 C57Bl/6 Vegfr2Y1212F /Y1212F explant tissue. Quantification as fold-increase of vessel sprouting area compared to WT MycOE/Cre -. Scale bar, 250 µm. Error bars: SD; unpaired T test, ** p <0.01, **** p <0.0001. n=4-11 explants, one explant/embryo.
B. Expression of notch1b after treatment with DMSO vehicle control (left) or Wortmannin (WM, middle). Graph displays quantitation of results. Shown are the percentages of embryos with normal or decreased notch1b expression for each condition.
(D) BN-PAGE analysis of mitochondria lacking SLP2, YME1L or PARL. Mitochondria isolated from corresponding MEFs were solubilized using 1.5% (w/v) digitonin at a protein concentration of 2.5 mg/ml. Solubilized proteins were separated by a 3-13% blue native gradient gel and analyzed using SLP2-, YME1L- and PARL-specific antibodies.
A, Schematic overview of antiviral function of EVs. Briefly, EVs from naïve or NoVΔB2-infected BALB/c suckling mice were extracted 3 days post infection, and then injected into AG6 suckling mice. After 12 hours post immunization, AG6 suckling mice were challenged by WT NoV and then sacrificed at 1dpi.
(c) Representative images from colon cancer tissues by immunohistochemistry staining. Negative correlation between Beclin1 and Dvl was observed in late stages of tumours, whereas positive correlation between p62 and Dvl in late stages of tumours. Scale bar, 25 μm.
Model depicting the molecular and physiological barrier function of NTRAS. By sequestering hnRNPL, NTRAS promotes TJP1 exon 20 inclusion and expression of TJP1α+, this way maintaining endothelial barrier function. In the absence of NTRAS, hnRNPL represses exon 20, thereby favoring TJP1α- expression and hyperpermeability. TJP1 alternative exon 20 and the alpha domain are highlighted in green, hnRNPL binding motifs are depicted as red boxes.
C) ELISA binding results of mAbs specific for hRSV F (left panels) or hMPV F (right panels) with the proteins indicated at left. mAbs specific of hRSV F bind to epitopes of antigenic site Ø (D25), antigenic site II (Mz and 47F) or antigenic site IV (101F and 107F). mAs specific of hMPV F bind to epitopes of antigenic site II (MF14), antigenic site IV (MF11, MF16 and MF29) or an epitope shared by hRSV F and hMPV F (MPE8).
ChIP-qPCR detection of PCAF (D) occupancies at the indicated promoters in Myoparr-depleted C2C12 cells. n = 3, mean ± SD. *p < 0.05. **p < 0.01.
(g) Changes in safranine fluorescence after addition of ADP, Ca2+ or FCCP to -Tet and +Tet PCF trypanosomes (means±s.d., n=3, **P0.001, Student's t-test).
(C) Quantification of detailed morphology of CMs in MICOS mutants (left). TEM recordings were assigned to 8 classes (right). Data information: n: number of mitochondrial sections
(B) Overview of the adapted PGCLC differentiation timeline. Stages of the culture system are shown.
E, PCA analysis of RNA-seq and microarray data from miiPSCs and known already-published PSC types. Log2 expression values were normalized to mESCs in each study. Data from miiPSCs (this study), mES cells (each study), 2C-like cells (MacFarlan et al, 2012) and epiblast stem cells (Najm et al, 2011) were analyzed and a total of 17,243 genes were selected. For miiPSCs, clones 1 and 2 were analyzed 10 days after miR-203 exposure, while clones 3 and 4 were analyzed 25 days after miR-203 exposure (see schematic shown in Figure 1B). For Tomato PSCs, Tomato fluorescence is associated to 2C-like retrotransposon expression, thus Tomato-positive cells are identified as 2C-like cells (MacFarlan et al, 2012).
(B) HEK293 cells were co-transfected with an INPPL1 3` UTR-luciferase plasmid and scrambled miRNA mimic (40 nM), miR-2137 mimic (40 nM) or miR-205 mimic (40 nM) for 24 hours. Protein lysates were analyzed for luciferase activity and normalized to secreted embryonic alkaline phosphatase (SEAP) reporter activity (n=3 biological replicates).
Removal of CDK12 inhibitor in early G1/S rescues cell cycle progression. Western blotting of , protein levels Western blotting were performed 7, 12 and 15 h post-release, respectively. CTRL=control samples without the 3-MB-PP1. In b, n=3 and error bars indicate SEM. In c, d representative images from 3 biological replicates are shown.
(c) The 124 genes with a known role in the lipid metabolic process, whose expression was perturbed by TFEB overexpression, are represented as coloured circles and assigned to specific lipid breakdown (left) or lipid biosynthesis (right) sub-categories. The percentages of upregulated (red circles) and downregulated genes (green circles) are shown both for the two main groups and for each sub-category. *Note that in calculating these percentages, genes assigned to the negative regulation of lipid catabolic process and to the negative regulation of lipid biosynthetic process have been included in the lipid breakdown and in the lipid biosynthesis groups, respectively.
G. Box and whisker plot indicating direction of change for histone modifications between WT and Chr 4 KO cells.
From the differentially expressed genes in (E), mitochondrion-localized and redox-related proteins were more than by chance downregulated after NFAT1 knockdown.
L Structural organization of BSP chimeric subconstructs. S (red), signal peptide; module 1 (magenta); module 2 (orange); module 3 (green); module 4 (blue); module 5 (cyan); R-ClfA (yellow), clumping factor R domain; W (purple), cell wall anchor.
B. BALB/c mice bearing Mettl3 or Mettl14 deficient and control tumors were treated with IFNγ -blocking antibody and PD-1 antibody as indicated. Tumor size was measured over time. n, the numbers of mice. Data are mean ± s.e.m of the indicated number of mice. * P < 0.05; * * P < 0.01; * * * P < 0.001 by Student's t-tests.
H, Complementation analysis of H3K14ac. Total cell extracts of siRNA treated lacZ-V5 and BRPF3-V5 (siBRPF3/a resistant) expressing cells were analysed by western blotting. One representative experiment out of four biological replicas is shown.
Venn diagram demonstrating the significant enrichment of QKI-mediated change genes in the set of QKI binding genes determined by RIP-seq experiment. Only 30 genes identified by microarray analysis were also QKI binding targets. Schematic diagram of search strategy to identify genes, which contained QRE motif sites and involved in controlling adipose thermogenic metabolism. The following publicly available datasets were used for the comparisons: brown versus white adipose tissues (WAT) (NCBI GEO: GSE51080), BAT following cold exposure (NCBI GEO: GSE40486) and WAT following cold exposure (NCBI GEO: GSE51080).
(F-G) Quantification of cholesterol uptake and esterification in the indicated cells was measured by 4h incubation with 3H-cholesterol and subsequent analysis of radiolabel incorporation. The dashed line indicates control levels. Graphs represent fold change over controls. Treatment with Sandoz 58-035, a specific ACAT1 inhibitor, caused a ~95% reduction in cholesterol esterification. EV, empty vector. One-sample t-test. (n=3-4; * p< 0.05).
(g) Representative traces of mitochondrial membrane potential of digitonin-permeabilized BSF trypanosomes grown in the presence (+Tet) or absence (−Tet) of tetracycline. The reactions were incubated as in Fig. 3c. CaCl2 (50 μM), EGTA (200 μM) and FCCP (10 μM) were added where indicated.
Rv::pN and Rv::pN-F-sigH were either subjected to none or 50 µM of CHP for 6 h followed by cross-linking. 1 mg WCL was used to immunoprecipitate FLAG-SigH and 1/10th IP was probed with α-FLAG and 9/10th IP with α-AosR. 50 µg WCLs were probed with α-FLAG,α-AosR, and α-SigA as controls.
M Following transfection with LacZ or polyQ79, HEK293T cells were grown under different concentrations of glucose for 5 days before measuring aggregate size.
(E) Auxin activity as visualized by the constitutively expressed inverse DII-NLS-VENUS marker (green) in root meristems of 5-day-old seedlings.
Representative immunoblot of WT, LUZP1 KO, and Venus-LUZP1-expressing LUZP1 knockout (REV) Eph4 cells treated with 100 nM calyculin A for 30 min. Quantification of the ppMLC/MLC ratio relative to WT control, confirming the reversal of the difference in ppMLC levels within CRs between WT and LUZP1 KO cells by calyculin A [WT, 1.00 (control) vs. 1.40 ± 0.06 (calyculin A) vs. 1.14 ± 0.33 (washout); KO, 0.09 ± 0.04 (control) vs. 1.49 ± 0.06 (calyculin A) vs. 0.81 ± 0.99 (washout); REV, 2.06 ± 1.78 (control) vs. 1.82 ± 1.50 (calyculin A) vs. 1.80 ± 1.14 (washout)]. n = 3. Bars and error bars represent the mean ± SD.
(A) Murine Krt86 is shown schematically with exons as rectangles and the transcription start site marked by an arrow. Sites assayed in the pre-mRNA or ChIP studies of panels B-G are indicated.
A. Morphological observation of small peptides and LncBMP4 backbone chains, promoting PGC formation in vitro, Scale bar: 60 µm (n =3 independent experiments).
B Clustering of the antagonist‐responsive AR locations based on dynamic signal shifting of H3K4me2 affected by DHT treatment.
(B) In vitro kinase assay for auto-phosphorylated LRRK2 using isolated LRRK2 mutants and [γ-32P]ATP with or without LRRK2-IN-1 (1 μM). Mutant LRRK2 precipitated with antibody against V5 was subjected to SDS/PAGE. Blots were with antibody against V5 or phosphoserine. [γ-32P]ATP-incorporated LRRK2 visualized by autoradiography.
D Histogram showing expression levels of the top 10 astrocyte specific markers genes in DIE (blue bars) and CTX GM (red bars) samples. Data information: CTX GM: cerebral cortex grey matter; DIE: diencephalon; n=3 biological replicates, tissue from 3 mice was pooled
(B) Kinetics of internalization of triple mutant hAPP in hippocampal neurons from wild type, p75NTR knock-out (KO), ΔDD and C259A mice. Shown is mean ± SEM of percentage internalization of total surface APP (set to 100%). N=3 independent experiments each performed in duplicate; *, P<0.05 knock-in vs. KO mutants; **, P<0.01, WT vs. all other genotypes (2-way ANOVA). (C) Linear transformation of hAPP internalization kinetics shown in (B). IMAX denotes maximal internalization in %. T1/2 denotes time for half maximal internalization in minutes.
The low bi-allelic expression of Tsix in mESCs allows the association of RIF1 with P2 on both Xist alleles. However, the presence of pluripotency-dependent inhibitors will not allow Xist up-regulation, despite the presence of RIF1. (1) Upon differentiation, the increase of Tsix levels weakens the association of RIF1 with P2. This opens the opportunity for a stochastic KAP1 binding to P2 of one of the two alleles (2). KAP1 is required for sustained high levels of Tsix, further reinforcing RIF1 exclusion from the KAP1-bound/Tsix high allele and establishing the asymmetry. It is not known whether KAP1 gains access to P2 to promote the increase of Tsix levels first, or whether the increase of Tsix levels is initially triggered by a differentiation-dependent factor. (3). The pluripotency Xist inhibitors having been silenced, RIF1 promotes Xist expression on the future Xi. A self-sustainable binary switch is thus created and it consolidates the choice of the future Xi and Xa.
(C) Correlation statistics for the localization of 3Flag-MITOL and catalase in the presence of GFP-Parkin wild-type or an inactive C431S mutant. Dots indicate individual Pearson correlation coefficient data points. In the box-plots, the center lines indicate the medians, the box limits indicate the 25th and 75th percentiles as determined in the R software package, and the whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles. Means and the number of samples are shown on the box and X-axis, respectively. Statistical significance was calculated using a one-tailed Welch's t-test. MITOL overlapped with catalase only in the presence of wild-type Parkin in wild-type HeLa cells. In PINK1 knockout (KO) HeLa cells, wild-type Parkin was unable to induce the peroxisomal translocation of MITOL.
B, Gene ranking based on siRNA scores from two independent screens. 219 genes were targeted by three individual siRNAs and ranked based on P-values derived from RSA and Fisher's analysis. Selected hits are highlighted.
F Placensin stimulation of HTR-8/SVneo cell invasion. After placensin treatment for 24h, cell invasiveness was determined using the Transwell assay (left panel: micrographs of cells; right panel: fold changes in number of migrated cells, biological replicates, n=4). Cells were incubated with mitomycin C to rule out effects on cell proliferation. Scale bars: 100μm. C: control.
b-c, Percentages of CD44low CD62Lhigh (Tn) (b) and CD44high CD62Llow (Tem) (c) cells among total CD8 T cells of spleen and pLNs from young and 45-wk-old Dj-1 KO and WT littermates (young KO, n=5; young WT, n=5; 45-wk-old KO, n=8; 45-wk-old WT, n=6; for 45-wk-old mice, data pooled from 2 independent experiments).
C, D. Representative confocal images and plots show that ccdc108 morphants displayed ciliogenesis defects in neuromasts (C) and olfactory placodes (D). Zebrafish embryos were fixed and stained with the Ac-tub antibody (green), phalloidin (purple) and Hoechst (blue). Data information: Quantitative data were from three independent repeats. Unpaired two-tailed t-test was performed (*** p<0.001; * p<0.05). Mean ± s.e.m values are presented.
C Food consumption per gram of body weight gained (g/g ∆BW) over the first 15 weeks on NC or HFD, starting at 8 weeks of age (male, n=9 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).
(A) Representative image of quadriceps from WTFlx and Ndufs3 smKO animals of 8 months of age. Muscle weight from Ndufs3 smKO males (black bar) and wild-type mice (white bar) from 6, and 8 months of age (n=5 each group). Bars represent means ± standard error (SEM).
igure 1. SLFN11 is a DNA damage responsive protein. (A) Expression analysis of SLFN11 in human cell lines.
C, Quantification of difference analysis readouts in liver. Same subjects as in B. Each dot represents data from one animal (grade 0: n = 14; grade 1: n = 11; grade 2 & 3: n = 9). Data represent the mean (+/- 95% confidence). The unpaired t test was used to verify the statistical significance. Grade 0 vs grade 1: P = 9.93E-05; grade 0 vs grade 2: P = 0.0004; grade 0 vs grade 3: P = 4.90E-05 Data information: In the figure, A.U. = arbitrary units.
EB formation from WT and the two hnRNPLL-KO ES cell clones. WT ES cell-derived EBs formed cystic structures by day 8 of differentiation; While both hnRNPLL-KO ES cell clones-derived EBs were more compact. Scale bar, 200 μm.
(F) Bioluminescence imaging quantification of lung colonization by 40,000 MDA-MB-231 cells overexpressing PTPRN2, PTPRN2C945A, or control vector. N = 5 mice/group. Right, H&amp;amp;E staining of representative lung sections.
(A) WT, MFF−/− or DRP1−/− cells stably expressing YFP-LC3 and mCherry-Parkin were treated with valinomycin for 3 hr and subjected to immunofluorescence microscopy with anti-TOMM20 antibody. Scale bars, 10 μm. (B) Quantification of mCherry-Parkin translocation to mitochondria after 3 hr of valinomycin treatment. Partial and complete denote that Parkin translocates to some of and all mitochondria, respectively. The error bars represent ±SD from three independent replicates. Over 50 cells were counted in each replicate. (C) YFP-LC3 morphologies of cells in (A) were quantified. Percentages of cells harboring diffuse, punctate or accumulated YFP-LC3 are shown. The error bars represent ±SD from three independent replicates. Over 100 cells were counted in each replicate.
Flow cytometric analysis of the percentage of tumor infiltrating CD8+ T cells (n = 4 biological replicates, mean ± s.e.m., *P = 0.0433, ***P = 0.0001, two-tailed unpaired Student's t-test) of mock or OTUD1 expressing CT26 tumors treated with or without NP-VE.
B Time-lapse images of GFP-Pst DC3000 and Pst DC3000 (AvrRpt2) captured at 0 (magenta), 15, (yellow), and 30 (green) sec Time in seconds in the movies is shown at the top of images. Blue color was used for chlorophyll autofluorescence. Data information: Leaves were inoculated with GFP-labeled bacteria at 108 cfu/ml for 2 days. Scale bars, 10 μm
SRSF3-responsive alternative 3′ ends of the Med1 gene. (Top panel) Disorder analysis for MED1 using PONDR VL-XT (deep blue) and IUPred2 (light blue). The scores in the ordinate indicate disordered tendencies between 0 and 1 (a score of more than 0.5 indicates disordered). (Middle panel) Protein and gene structures of MED1. The protein structure was segmented into individual exonic regions. The SRSF3-responsive last exon is indicated in pink. (Bottom panel) Sashimi plots of RNA-seqs from Srsf3- and/or Hnrnpk-silenced cells.
(D) Kymographs showing fluorescently-tagged MTs co-imaged with fluorescently-tagged Klp5/Klp6 in control (top panels, repeated from 1C) or ∆tea2 cells (bottom panels). Dashed yellow line indicates the cell end
The graph is representing the percentage of RA-SVs around the whole ribbon at wild-type under inhib, rest and stim. Upon stimulation, the percentage of SVs without filaments and ribbon-attached SVs are significantly reduced, while interconnected SVs increased significantly.
Expression of a SUMOylation-deficient Flag-Fis1 K149R mutant in HeLa cells induces LC3-II. Flag-Fis1 WT or Flag-Fis1 K149R mutant was transfected into HeLa cells in which endogenous Fis1 was depleted using siRNA for 48 h. Lysate samples were blotted as indicated.
STAT1 occupied cTAZ promoter in an IFN-α-sensitive manner. RKO cells were treated with or without IFN-α (50 ng/ml) for 1 hour and subjected to ChIP assays. cTAZ PCR primers were designed to target STAT1/2 binding site. ISG15 promoter was included as a positive control.
A. Representative pictures showing Peyer´s Patches in Casp8WT mice, and different severities of hemorrhage formation in Casp8ECko mice at an early disease stage. Scale bars: 1mm.
(D) Total number of GnRH neurons that migrated out of nasal explants isolated from control and mutant embryos, quantified after 8 days in culture. Mann-Whitney U test, n=3 to 5 embryos from at least 3 litters.
A, overview of the NodLabel procedure, using a viSNE layout of CyTOF single-cell events. Left side, point color indicates channel values for four example channels. Right side, traditional hierarchical gating was used on a subset of samples to identify 8 major immune compartments, which was then used to train a logistic regression classifier (Nod) that applied labels for canonical leukocyte phenotypes to all samples (NodLabel).
EC-miR-483-Tg and WT rats were injected with saline or MCT. Analysis of RV hypertrophy [RV/(LV+S)] for the indicated groups (7 rats per group) Data information: Values are expressed as mean ± SEM. Statistical test: t-test (*P < 0.05 vs. respective controls or between the indicated groups).
Figure 7. The RPA1-binding ability of SLFN11 is required for its function in DNA damage response. (A-C) A SLFN11-deficient SF268 cell line to express Flag-tagged wild-type SLFN11, the K605M/D668A mutant, or the Δ5 mutant was generated. The resulting cell line was treated with CPT (1 μM) for 1 hr. Cells were then washed and shifted to fresh medium. 24 hr later, cells were fixed and processed for RPA2 or RAD51 immunofluorescence. Scale bar, 10 μm. Error bars are s.d.; n=3.
(C) Positive correlation between fadA gene copy numbers (x-axis) and ANXA1 mRNA levels (y- axis) in F. nucleatum-induced Apcmin/+ mouse colonic tumors (n=34; Pearson's correlation). Each dot represents the average of qPCR results performed in duplicates
A. Schematic domain organization of Drosophila PlexA and Sema1b (SS, signal sequence; TM, transmembrane region, red symbols represent the position of N-linked glycosylation sites)
D. Binding affinities calculated from titration data of co-sedimentation assays of lifeAct-14 (1.2µM) and lifeAct-17 (2.2µM) as indicated. Data points for each concentration were averaged from 3 independent experiments, error bars represent S.D between independent experiments.
D. Hematoxilin/eosin staining of C57/Bl6 mice brain coronal sections sacrificed after 14 days of treatment with prazosin. Scale bar = 2 mm.