EMBO/sd-character-level-ner huggingface dataset:
D MBTPS1 knockout led to a decrease in global ATP production in HaCaT cells. Control and MBTPS1-KO HaCaT cells were cultured in 6-well dishes. A standard curve was generated to calculate the sample ATP concentrations using an ATP Lite Luminescence Assay Kit (n = 4 biological replicates).
D RT-PCR analysis of DUXAP8 expression in RNA extracted from GS∆44, GS∆44's mother (GSM) and GS∆44's father (F) fibroblasts. GAPDH was used as control. Lane (-) indicates the negative control. Representative results are shown (n=3).
(b,c) Immunoglobulin assembly (b) and total intracellular (IC) and secreted (Sec) IgM heavy chain (IgM-H, c) in Atg5f/f and Atg5f/fCD19-CreB cells stimulated for 3 d with LPS, then pulse-labeled and chased (time, above lanes), followed by immunoprecipitation of the μ-chain from lysates and SDS-PAGE (left) in nonreducing conditions (b) or reducing conditions (c). Right, quantification of intracellular IgM polymers by densitometry (b) and of secretion efficiency, estimated as the amount of radioactive secreted μ-chain at the end of the chase relative to intracellular μ-chain at the end of the pulse (c). AU, arbitrary units.
(C-E) Ctcflos meets the three selection criteria for positively regulated lncRNAs in brite adipogenesis. (C) Correlation of Ctcflos (mean of transcript 1; 2; 3) with Ucp1 transcript levels across differentiated brite adipocytes derived from the five mouse strains (transcript levels in RPKM). Mean values, n=3 (biological replicates), pearson correlation, *p<0.05. (D) Ctcflos transcript levels (mean of transcript 1; 2; 3) in differentiated compared to undifferentiated brite adipocytes of 129S6 mice (transcript levels in RPKM). Mean and individual values, n=3 (biological replicates), unpaired t test, ****p< 0.0001. (E) Ctcflos transcript levels (mean of transcript 1; 2; 3) in differentiated brite (+rosi) compared to differentiated white (-rosi) adipocytes of 129S6 mice (transcript levels in RPKM). Mean and individual values, n=3 (biological replicates), unpaired t test, *p< 0.05.
C 5' RACE analysis of the tiTERRA transcription start site using total RNA from cells carrying two tiTELs (CAF110) maintained in YES medium. Nucleotides boxed in blue overlap with the 5' UTR of the nmt1+ transcript while the ones in green correspond to subtelomeric sequences. tiTERRA and TERRA transcription start sites (TSS) are indicated.
Cell number and category of BALF samples were from wild-type (WT) and EphA2-kockout (KO) mice (n=3 per strain) on day 1 and day 3 after intranasal infection with reovirus (4×104 PFU per mouse). Shown is mean ± SD. Data information: Each symbol represents an independent experiment; small horizontal lines indicate the average of triplicates. *P<0.05, **P <0.01 and ***P<0.001 (unpaired t test). Data represent three independent biological replicates.
A-C. Wild type embryos injected with control MO, subphenotypic doses of shox MO, cyp26c1 MO or a combination of shox + cyp26c1 MOs. (B, C) Dorsal view and magnification on the pectoral fins of col2a1expression at 55 hpf. Arrow and dotted line indicate the pectoral fin.
(B) Western Blot (WB) showing the levels of USP7, MPM-2, histone H3S10P and histone H3 in whole nuclear extracts of HCT-116 cells treated with 50 μM P22077 for 2-4 hrs (USP7i), 10 μM RO3306 for 8 hrs (CDK1i) or DMSO as a control. Ponceau staining is shown as a loading control.
C: Organisation of functional NTH domains I-III (coloured bars) in T. thermophilis, E. coli, mammals, and Plasmodium. Linker connecting functional domains is indicated by dotted line. Prokaryotic nth genes are segmented into three (T. thermophilis) or two (E. coli) segments, encoding NTH subunits α1, α2 and β (T. thermophilis) or α and β (E. coli). Eukaryotic nth genes are unsegmented and encode single polypeptide NTH of different orientations, either corresponding to an αβ linkage (mammal), or to a βα linkage (Plasmodium). The amino (N) and carboxy (C) termini of the eukaryotic NTH polypeptides are indicated.
(B). The mRNA expression of OXGR1 in different tissues of 12-weeks male C57BL/6 mice (n = 3 per group).
FLAG-tagged CYLD or catalytically inactive FLAG-CYLD (C598A), respectively, were stably expressed in CYLD-/-MEF, followed by infection with control retrovirus, or retrovirus encoding SPATA2, and purified by FLAG-IP. Purified CYLD or the inactive mutant were added to recombinant di-ubiquitin for 0, 20 or 40 min at 37°C as indicated. After electrophoresis, the gel was cut and the lower part was silver stained to visualize mono-and di-ubiquitin, while the upper part was transferred to a membrane and probed for FLAG and V5. In (A), the experiment was done with M1-linked di-ubiquitin substrate, in (B) K63-linked di-ubiquitin substrate was subjected to the assay, and in (C) K48-linked di-ubiquitin substrate was analyzed.
(G) HeLa cells transfected with GFP-ATG16L1 were fixed, labeled for mATG9, and then analyzed by TIRF microscopy. Control cells were cotransfected with GFP-ATG16L1 and Straw-ATG16L1. Pictures are at the same magnification and brightness. See Figure S1J for quantification.
(B, C) Flow cytometry (B) and scatter plots (C) represent CD8+ T cells derived from peripheral blood co-stained with IFN-γ and CD11a, following ex vivo restimulation with SIINFEKL. Data information: Data are representative of two experiments performed with scatter plots showing mean values (±SEM).
A. Nuclear fractionation followed by simple western analysis (Peggy Sue) shows an increase in nuclear actin in AECs exposed to TGFβ1 for 48 h. Quantification (right panel) shows mean + s.d., n = 3 biological replicates , ns = non-significant, *p = 0.014, ANOVA/Tukey's).
(C) PercevalHR is a ratiometric fluorescent protein that changes its excitation spectrum based on its binding to ATP (930 nm) or ADP (840 nm).
(C) Structure of the TRIM25 RING/E2~Ub complex with the RING domains in the same colour scheme as in (A), UBE2D1 in grey and the ubiquitin molecules in salmon and red.
ChIP-qPCR results show the association of Flag-tagged chromo-domain depleted HP1c mutant (HP1c △CD) with Notch target genes. The amount of immunoprecipitated DNA in each sample is represented as signal relative to the total amount of input chromatin (equivalent to 1). HA antibody is used as a control. Error bars indicate SEM. n=3 technical replicates. Data are evaluated with two-tailed Student's t-test (*p < 0.05, **p < 0.01, ***p < 0.001).
qRT-PCR analysis with RNA isolated from control or ATG5 siRNA transfected THP-1 cells expressing 3X-Flag epitope or Flag-IRGM as indicated.
qRT-PCR analysis of mRNA levels of Skp2, Aurka, Dll1, and Hey1 in control, Shp2 ko, and Shp2‐inhibited cells. Error bars represent SEM (n = 3).
A. Diagram explaining how codon/amino acid expression bias was computed: correlation was calculated between the frequency of each codon/amino acid and mRNA levels per gene. Orange means correlation and purple anti-correlation.
(H) Distribution of death times in TNF-treated L929 wildtype (wt) cells (representative data of three independent experiments).
s. (B) Cell cycle analysis of HCT116 p53-/- or p53+/+ cells untreated or treated with 50 µM etoposide for 24 hrs. Cell cycle was determined by FACS analysis of propidium iodide stained cells.
D, miRNA or mRNA levels as determined by quantitative PCR of the indicated transcripts at different time points during cardiomyocyte differentiation in the indicated samples. Data are represented as mean ± s.d. (n=2 independent experiments with 6 replicates each).
a, Representative flow cytometry data of CD69 and Celltrace violet (CTV) staining on gated living CD8 T cells. The purified CD8 Tn were isolated from young mice and stimulated by different doses of anti-CD3 ab for 72 hours. Enlarged number representing the percentage of the corresponding gate.
(I) Confirmation of cyclin B1 and B2 depletion 48 hours after siRNA (pool of four different siRNAs) depletion by immunoblotting in WT RPE-1 cells. Asterisks indicate non-specific bands that are not targeted by siRNAs.
D) Putative pathway of regulation of Piezo2 currents by Gi-coupled receptors; activation of Gi-coupled receptors promotes the release of Gβγ activating PI3K and MAPK kinase, thus indirectly potentiating Piezo2 currents.
(E) Western blotting of iNOS, tubulin, phospho-Thr172 AMPKα (pAMPK), total AMPKα (AMPK), phospho-Ser79-ACC (pACC) and total ACC. Quantification represents the levels of iNOS protein normalized to tubulin and relative to the IFNγ/TNFα control Data information: All quantifications are of three independent experiments (n = 3) and error bars represent the SEM For panels E through G, p-values were calculated using the Student"s t-test. *, p < 0.05; **, p < 0.01 from DMSO controls; ††, p < 0.01 from IFNγ/TNFα treated controls
a-b, Representative images of cilia (a) and dot plots (b) showing primary cilia length variation at different time points after serum starvation (SS). Markers in (a) show ARL13B (cilia) and PCNT (Basal body). The graph shows individual length of cilia from 3 biological replicates (n>150 cilia per sample and experiment). Scale bar: 1µm. Data shown in include mean ±s.d. are calculated by two-tailed unpaired student t-test.
B Basal mitochondrial calcium levels in WT and Nox4KO MEFs after serum starvation. Representative photomicrographs are shown at the top. The spectrum color scale represents the ratio of emitted fluorescence (YFP/CFP). Mean data at the bottom. Scale bars: 10 µm. n=3/group (with >100 cells per individual experiment).
B. Representative FACS readout of EdU/Propidium iodide cell cycle staining of PeTa cells after 6 days of 100 nM GSK-LSD1 or DMSO treatment. C. Quantification of EdU/Propidium iodide staining depicted in Fig 3B. n = 3 biological replicates. Data are represented as means ±SD. **p<0.01; ****p<0.0001; ns, non-significant (G1 phase: DMSO vs GSK-LSD1 p = 0.0059; S phase: DMSO vs GSL-LSD1 p<0.0001; G2/M phase: DMSO vs GSK-LSD1 p = 0.2338; unpaired Student's t-test).
B) WRKY29 transcripts measured by qRT-PCR in flg22 treated leaf material. Leaf strips of Col-0 and mkkk7 were treated with 1 µM flg22 for t=0, 1, 2, and 4h. WRKY29 transcripts were normalized against Ubiquitin transcript as described before [62]. Bars represent mean value and error bars show SE (n=3). (* p<0.05, ** p<0.01, student t-test).
(K, L) Correlation of IKBKE (IKKε) and PSAT1 (K) or IKBKE (IKKε) and ATF4 (L) expression in the ER negative sample subset.
Confocal imaging of 5DO fat body nuclei expressing UAS transgenes and labeled by mAb414, or expressing Nup107RFP.
F. Immunisation with cGAMP-VLPs increases production of antibody-secreting cells. Cells from draining lymph nodes and spleens were seeded in ELISPOT plates coated with cGAMP-VLP lysates. After overnight incubation, cells producing VLP-specific IgG antibodies were identified using an anti-IgG Fc antibody.
WT and pc-ak-2KO cells were transfected with a combination of three siRNAs against CEP192, fixed and triple labelled for EB1, CEP192 and CAP350, as a centrosomal marker. Scramble siRNA was used as a control.
Left panel: Representative blots showing protein levels of YAP and phosphorylated YAP (Ser127) in control (si-Ctrl), YAP knockdown (si-YAP), TAZ knockdown (si-TAZ) and YAP/TAZ double knockdown (si-YAP/TAZ) hOSE Cells. β-Actin was used as a protein loading control. Right panel: Cell proliferation (cell number) of control (si-Ctrl), YAP knockdown (si-YAP), TAZ knockdown (si-TAZ) and YAP/TAZ double knockdown (si-YAP&si-TAZ) hOSE cells.
Western blot of tunica media-intimathoracic aorta lysates from mice culled after a minimum 4-h fast. Following exsanguination after surgery, mouse tissues were rapidly harvested and the tunica adventitia removed before storage, and later, the samples were homogenised, clarified and quantified prior to SDS-PAGE. Western blot analysis confirmed the expression of KLHL3 and CUL3. Similar to the kidney, the aorta of CUL3WT/Δ403-459 showed slightly lower levels of CUL3 compared to CUL3WT without any change in KLHL3 levels.
Flow cytometric analysis of mitochondrial volume (MTG) (F, n=6, technical replicates for control; n=5, technical replicates for WS5A and CP2A), total MMP (TMRE) (G, n=5, technical replicates for control; n=4, technical replicates for WS5A and CP2A) in Detroit 551, WS5A and CP2A fibroblasts.
In normal condition, FTO demethylases m6A modification of Hif1a mRNA, which in turn prevents YTHDC2-mediated mRNA translation and thermogenic gene expression, thereby increasing white adipocytes differentiation and lipid accumulation, leading to HFD-induced obesity. FTO deficiency in adipose tissue increases mRNA m6A level of Hif1a transcript, leading to YTHDC2-mediated transltion and enhanced protein expression of HIF1A. Subsequently, HIF1A promotes transcription and expression of thermogenic genes, including Ppargc1a, Prdm16, Pparg, which results in white adipocytes browning and thermogenesis, thereby resisting obesity.
(H) Western blot detection of p-ATM Ser1981, ATM, p-CHK2 Thr68, CHK2, p-AMPKα Thr172 and AMPKα in H1299 cells in normal medium or after 2DG (5mM) and oligomycin (2.5μM) treatment.
(A-D) Ki67 (green; mitotically active progenitors) and Tuj1 (red; post-mitotic neurons) IF at E14.5 (A,A'), E16.5 (B,B') and E18.5 (C,C') of lateral pallia of wild-type (WT) versus mutant (KO) brains. Ki67+ proliferating cells (quantified in D) accumulate in mutant cortices. n ≥ 3 brains. Data information: Nuclei (blue) were stained with DAPI. the number of positive cells was quantified in 100µm-width boxes, randomly placed across the LP. 2-way ANOVA (*P<0.05, **P<0.01, ***P<0.001). Scale bars: 50µm. CP: cortical plate; IZ: intermediate zone; SVZ: subventricular zone; VZ: ventricular zone.
Western blot analysis of the supernatant (S) and insoluble pellet (P) fractions of vehicle- or rapamycin (Rapa., 1 μM for 4 h)-treated Hek293T cell mitochondria following carbonate extraction at pH 11.5. Akt, phosphorylated (S473) Akt (p-Akt), MICU1, the established integral membrane proteins TIM23 and MCU, and the soluble protein cytochrome c (Cyt. c) was analyzed
F Schematic representation of the IMT1 binding region on the human POLRMT sequence, adapted from Previously identified mutations conferring resistance to IMT1 are reported in red Representative results of n=3 independent sequencing experiments of the POLRMT gene in RKO and IMT1-resistant RKO cells at the region of interest.
D Average frequency distribution of nucleosome positions relative to each other. Data was aligned to each mapped nucleosome in the genome and plotted for a 600 bp window for pl-iPSC, NPC and the chronic myelogenous leukaemia (Cml) derived cell line, K562. In all cases, a prominent single nucleosome is presented with only minor flanking peaks, indicating that the majority of nucleosomes do not occur as evenly spaced arrays in human cells.
(A) Left panel, Mice, treated as indicated, were sacrificed and the indicated tissues were collected and stained for PG (arrows) with PAS following diastase treatment. Scale bars, 200 µm (liver, muscle), 50 µm (cortex, heart, peripheral nerve). Right panel, PAS staining was quantified based on analysis of 4 sections from each tissue in n=3 wt, n=7 Gbeys/ys vehicle-treated, and n=9 144DG11-treated mice.
A. Eigen value of the 3-microRNA signature measured in the mice that performed longitudinal water maze training. Note the significantly increased expression of the signature already at 15 months of age, suggesting that increased expression levels precede detectable cognitive impairment. Number of biological replicates = 10/group, unpaired two-sided Wilcox rank test.
in vitro angiogenesis assay was performed in static or shear stress-exposed HUVECs transfected with the indicated siRNAs for 18 h in (C).
B: Control or ELDR plasmid DNA overexpressed NOK (3×102) were seeded and allowed to form colonies. After two weeks, colonies were stained with crystal violet and counted. Representative images of colonies in control and ELDR overexpressed cells are presented. The right panel shows quantitation. n = 3 biological replicates. Data are represented as the mean ± SD,
(B) Oxygen consumption rates (OCR) in primary myoblasts and differentiated myotubes. Basal OCR was first measured, followed by administration of 10 mM sodium pyruvate, and 2 μM oligomycin (to inhibit ATP synthase), uncoupler FCCP (2 μM), or rotenone/antimycin (Rot/A) (1 μM) as indicted. n = 3 separate experiments done with 10 biological replicates. *p < 0.0001 (FCCP).
A. Schematic representation of the experimental strategy. Four-month-old lethally irradiated mdx mice were transplanted with either GFP-CriptoMy-LOF (mdx-CriptoMy-LOF) or GFP-Control (mdx-Control) bone marrow and sacrificed at 16 weeks (wks) after transplantation.
1x106 primary DLBCL cells obtained by passaging through a MISTRG6 mouse were intravenously injected into MISTRG or MISTRG6 recipients. with representative H&E-stained spleen (MISTRG6) and lymph node (patient) sections in C
(J) Western blot bands for protein expression in PSCs (p-Tmod is post-translational modification). The plot shows the quantification of the sum of band intensities corresponding to isoform 1, isoform 2, isoform 3, and post-transcriptionally modified HIF-1A (n=8 control and n=8 tam)
(H) Relative HCV RNA levels as measured by real-time RT-PCR. HCV replicon cells transfected with either the control vector or the flag-UVRAG plasmid for two days were lysed for quantification of HCV RNA by real-time RT-PCR. In (F) and (H), *, p<0.05.
(A) Top hit selected candidates are listed. The plot shows relative S9.6 nuclear intensity values for cells transformed with each of the indicated pool of siRNAs.
Analysis of transferrin uptake in fibroblasts transduced with the indicated lentiviruses. Representative confocal micrographs of fibroblasts fed with Alexa488-conjugated Transferrin for 30 min. Scale bar, 10 μm.
E-F. Representative hematoxylin and eosin (H&E) staining and statistical results of the micro-metastatic nodules in the liver from mice injected with the indicated cells into the spleen for 45 days. N=8 per group. **P < 0.01, Student's t-test, mean ± SD.
E. Bodyweight in STO (n=49) and ATO (n=36). Data information: All data are presented in the box plot format. The central band in each box represents the median, boxes indicate the middle quartiles, whiskers extended to the minimum and maximum values. *p<0.05 and **p<0.01, determined using Student's or Welch t-test.
A Click-iT AHA labeling assay to detect newly synthesized glycolytic enzymes. The level of HSP90 in total cell lysates was used as a loading control.
(B) Flp-In T-REx 293 cells with induced MIA40FLAG expression were solubilized, and the affinity purification of MIA40FLAG was performed. Fractions were analyzed by SDS-PAGE and Western blot. Load: 2.5 %. Eluate: 100 %. Unbound: 2.5 %.
qPCR (D, n = 3 biological replicates) analysis of Eno1, Slc2a6, Txn1, and Txnip gene expression in pMΦ and fetal Mo from E14.5 WT fetal liver.
A. Colony forming assays show increased proliferative potential of cells cultured in 3C compared to freshly isolated epidermal cells (Epi d0; control) (mean ±SEM; n=5; *p ≤ 0.05, Mann-Whitney U-test). 3C: 3D-Matrigel in KGM + Y27632 + VEGF-A + FGF-2.
C. Real-time qRT-PCR analyses of fold changes in transcript levels for each cytokine/chemokine gene in D-THP-1 cells following Stx2a (10 ng/mL) intoxication for various time-points in the presence or absence of OSMI-1 (10 µM, final). Data are normalized using GAPDH as a loading control (n = 3, biological replicates). Data information: For graphs error bar represents mean ± S.E.M. Statistical analysis was performed using two-tailed Student's t-test. *P < 0.05; **P < 0.01; and ***P < 0.001. The effects of OSMI-1 were compared with those of the vehicle (DMSO) control at each time-point.
E, F Levels of viral genome, protein, and progeny of VSV (E) or HSV-1 (F) from virus-infected 293T cells transfected with RBM47 shRNA or shNC at the indicated time points. The PCR and viral titer data are represented as the means ± SD of n = 3 biological replicates. Data information: The data shown are representative of n = 3 independent experiments.**P ≤ 0.01, and ***P ≤ 0.001 (Student's t-test).
(A) smFISH images showing nuclear Gadd45b mRNA in latent (UL36-negative) neurons and nuclear/cytoplasmic Gadd45b mRNA in viral UL36-positive neurons. Latently-infected SCG neurons treated with LY294002 and WAY-150138 for 48 hrs were processed using smFISH to detect Gadd45b (green) and viral UL36 (red) mRNA levels and colocalization. Nuclei were stained with DAPI (blue). Scale bar, 10 μm. (B) smFISH images processed as in (A) showing nuclear Gadd45b mRNA in uninfected neurons at 48 hrs post treatment with LY294002. Scale bar, 10 μm.
Seedling length of WT, pldα6, COM, and PA-treated plants grown on 0, 0.1, 1 and 10 μM GA3 for 7 days. Values are means ± SD (n = 15 plants) from one representative of three independent experiments.
(A and B) FACS-sorted T cell populations and Monocyte-derived Macrophages were treated with the indicated stimuli: Nigericin (Nig. 4h), NeedleTox (4h), Val-boroPro (VbP 22h), ABT737/S63845 (A/S 22h). When indicated, cells were primed with LPS for 2 hours prior to stimulation. When indicated, MCC950 was added to the media 30 minutes prior to the addition of Nigericin. LDH-activity (A) and IL-1β and IL-18 concentration (B and C, respectively) in the supernatant were determined by LDH cytotoxicity assay and ELISA respectively. Individual data points ± SEM from three independent donors are shown. Statistics indicate significance by two-way ANOVA: ***p ≤ 0.001; **p ≤ 0.01; *p ≤ 0.05; ns, not significant. P-values were corrected for multiple comparisons (Dunnett).
C. Representative flow cytometry plots showing the relative surface density for B220 (CD45R) after four days of stimulation with LPS either in the presence of DOT1L inhibitor, Pinometostat or DMSO as a control (left panel) and statistical analysis of MFI of B220 for each treatment (right panel). Results represent the data from one experiment and numbers represent biological replicates for each treatment (n = 4).
Relative expression of indicated genes in Rvtreated with 50 µM CHP for 24 h as compared with Rv as measured by qRT-PCR. Data were normalized with respect to 16s rRNA and results are expressed as mean log2 fold change ± SD of three independent replicates and is representative of one of two biological replicates. Statistical significance was analysed using student's t-test (two-tailed, unpaired). Early log-phase cultures of indicated strains were subjected to 50 µM of CHP for 24 h and the CFUs (mean ±SEM; n=3) were enumerated.
Identification of several STXBP4 missense mutations that disrupt its interaction with α-catenin and AMOT. The missense mutations within the STXBP4 α-catenin-binding region and the 9-amino acid sequence of the STXBP4 WW domain were indicated and annotated (F).
B. AKT phosphorylation in myogenic C2C12 cells treated with different doses of insulin. n=3, data represent mean ± SEM, unpaired t-test.
D The expression of endogenous ENTREP in HMEC. ENTREP co-localized with Clathrin, RAB5, RAB7 and RAB11. Inserts, the ring-shaped structures of the marked areas. The images are representative of at least two independent experiments. Scale bar 10mm.