EMBO/sd-character-level-ner huggingface dataset:
C Fraction of expressed genes (genes with non-zero counts in DESeq2) were calculated which exhibit individual or combinations of differential gene expression (DGE), differential transcript usage (DTU) and/or alternative splicing (AS) events in HEK293 and HeLa WT cells overexpressing UPF3A using the respective computational analysis (cutoffs are indicated). AS and DTU events were collapsed on the gene level. For DGE, p-values were calculated by DESeq2 using a two-sided Wald test and corrected for multiple testing using the Benjamini-Hochberg method. For DTU, p-values were calculated by IsoformSwitchAnalyzeR (ISAR) using a DEXSeq-based test and corrected for multiple testing using the Benjamini-Hochberg method. For AS, p-values were calculated by LeafCutter using an asymptotic Chi-squared distribution and corrected for multiple testing using the Benjamini-Hochberg method.
Mass spectrometry analysis of cytosolically located soluble ER glycoproteins in HEK293T cells treated with Tg compared to that found in human GBM tumor cells-derived cytosols.
IL-6 mRNA expression by DC cells. C57BL/6, MyD88−/− and Tlr9−/− mice were inoculated intraperitoneally with fdWT or fdsc-αDEC bacteriophages or, as a control, with LPS. Mice were sacrificed 2 h later, and purified spleen dendritic cells were analyzed for IL-6 mRNA levels by quantitative real-time PCR. Bars represent the mean fold increase ± SD. The experiments were performed three times (n = 2 per group). Comparative analyses were performed using Student's t-test for unpaired samples.
(D) Coimmunoprecipitation of Pex3 with Atg36. IP was performed in background strains of C13 abyss or C13-Atg36-PtA using plasmids expressing Pex3-GFP or Pex13-GFP under control of their endogenous promoters. Cells grown for 24 h to post‐log phase in glucose medium. IgGSepharose beads were used to immobilise Atg36-PtA from spheroplastyeast lysates. SDS-PAGE gels were probed with anti‐GFP and PAP. Yeast lysates represent 5% of the lysate added to the beads and analysed by immunoblotting. TL, total lysate; IP, immunoprecipitate.
(a) Endogenous immunoprecipitation of NCOA4 with ferritin heavy (FTH1) and light (FTL) chains from DLD1 cell lysates.
Spearman's correlation between single-cell RecA-mCherrywt fluorescence range and fluorescence VMR over the lifetime of the cell (n = 360). The data shown are from 3 independent experiments. Dashed lines separate different levels of dispersion, and colors denote subpopulations that are underdispersed (gray), dispersed (plum), or highly dispersed (magenta). RecA-mCherrywt fluorescence of subpopulations segregated by fluorescence VMR (58 < n < 159). The data shown are from 3 independent experiments. Black lines indicate means ± SD. Asterisks denote significant difference by Kruskal-Wallis and Dunn's multiple comparison test: ****p < 0.0001.
D) Western blot analysis of Ub-K48 proteins in the insoluble fraction of intestine lysates from mice plus or minus heat shock. E) Quantification of D. Each central line and error bar indicate mean +/- SEM of a biological replicates (n=3 biological replicates per group) Data information: * indicates p<0.05, ** indicates p<0.005, and *** indicates p<0.0005 by unpaired two tailed students t-test comparing male and female samples or samples with or without heat shock.
a) Trajectory analysis reveals alterations in gene expression pattern over time and disease state (d0, d3, d7). Above: Trajectory heat map depicting loss of homeostatic microglial gene expression signatures (P2ry12, Tmem119, Csf1r, SiglecH) and induction of genes involved in cytoskeleton modifications (Actb, Tuba1c), cell cycle progression (Cdk1, Ptma) and antigen-presentation (Cd74, H2-Aa). Highlighted molecules (asterisks) were confirmed by immunohistochemistry shown in b-d). Below: Trajectory plot showing the trajectory followed by myeloid cells upon CNV progress.
CAF-PC2 cells were treated with TGFβ (30 ng/ml) for 24 hours with siRNA-mediated knockdown of JUNB, JUND, SMAD4 or RELA. CM was collected and subjected to human IL-6 ELISA.
(D) A time course of dLGN synapse density (vGlut2+/Homer1+) between WT and controls.
(a) Magnified view showing the detailed interaction around Leu374(p). (b) Magnified view showing the detailed interaction around Tyr380(p). (c) Magnified view showing the importance of main-chain hydrogen bonds of the Galbi peptide. (a-c) Red dashed lines designate hydrogen bonds.
(F) siRNA depletion of SCOC reduces FEZ1-ULK1 complex. HEK293 cells treated with either SCOC or ULK1 siRNAs were transfected with FEZ1-GFP. FEZ1-GFP was detected with anti‐GFP in both BN-PAGE and SDS-PAGE. Endogenous ULK1 was detected with anti‐ULK1 antibody. Arrowheads indicate a FEZ1-GFP and endogenous ULK1 complex at 200 kDa and a larger MW complex >1236 kDa also detected in (D) in the triple transfection. The 200 KDa complex is sensitive to loss of SCOC and ULK1.
(c) Percentages of germination of C. albicans untreated (vehicle-treated, open circle) or treated with IL-17A at 1 (black triangle) or 10 ng ml−1 (black square) for 4 or 24 h. Data are mean±s.d. P 0.05, IL-17A-treated versus vehicle-treated cells, at 4 h; P 0.01 (1 ng) and P 0.001 (10 ng) at 24 h (one-way analysis of variance Bonferroni post-test) (n=3).
B. The direct correlation between RNA (TPM) and protein abundances (copy number) for all quantified genes in the same tissues and cell lines. Spearman (ρ) and Pearson (r) correlation between the two values across the quantified genes are shown. The other seven tissues and five cell lines are shown in Figure EV4.
(D) Heatmap of transcription factor binding motifs in each K-means cluster. The significance of enrichment (-log10(FDR)) is denoted by color scale. Transcription factor families of particular interest are highlighted on top of the heatmap.
(H) EI24 cannot bind to the phospho-mimicking (3SE) IRE1 mutant. HeLa cells transfected with wild-type HA-IRE1 or the 3SE mutant were treated as in (B). Protein-protein interactions were analyzed by IP.
A, B PBMC-derived macrophages were treated with GBS WT, ΔcylE, ΔcovR, or ΔcovRΔcylE at an MOI of 1 and incubated for 4 h. Cytotoxicity was measured by LDH release (A), and IL1β release in supernatants was measured by ELISA (B).Data information: Data shown are the average of four independent experiments performed in triplicate, error bars ± SEM. Significance was determined using Bonferroni's multiple comparison test following ANOVA. (A) n = 4, *P = 0.021 for WT versus ΔcovR; *P = 0.01 for ΔcovR versus ΔcovRΔcylE. (B) n = 4, *P = 0.031 for WT versus ΔcovR; *P = 0.036 for ΔcovR versus ΔcovRΔcylE. (C) n = 4, ****P < 0.0001, **P = 0.002. (D) n = 4, **P = 0.005.
B Immunoblot detection of PDGFRα levels in MLg cells after treatment with scrambled microRNA (SCR) or a miR-34a (MIM34a) mimic (n = 3 separate cell cultures for each group).
Representative immunofluorescence of primary cilium in WT and Mecp2 null primary cortical neurons at DIV7 and DIV14. Scale bar 10 µm, and 5 µm in the enlarged image. Arrows indicate not ciliated cells.
(O) Western blot of CathB levels (for both the precursor (pro-CathB) and the cleaved-mature forms) in the culture media from ASMko and wt cerebellar organotypic cultures from mice fed with vehicle (veh) or PLX (PLX). Below, Western blots of organotypic culture lysates against Iba-1, to confirm microglia depletion, and against GAPDH as loading control.
(E) qRT-PCR for ZIKV RNA expression in brain, mean ± SEM, n=3 biological replicates, *p < 0.05, **p < 0.001 by Student's t test.
Influence of Ctcflos KD on Prdm16 alternative splicing. (T) Relative Prdm16 total, (U) Relative Prdm16 long and (V) Relative Prdm16 short transcript levels 72 hours after Ctcflos KD, comparing Ctcflos tr1 (ASO 1) KD and control samples, assessed by qPCR, Mean values ± SD, n=3-4 (biological replicates), unpaired t tests, *p<0.05, ***p<0.001.
Bone marrow-derived myeloid cells were treated with BSA-control (Con) or oleate in the presence or absence of 10 nM rapamycin (Rapa). The polarization of myeloid cells was detected via flow cytometry as indicated by CD11b and CD206 expression.
C. FACS analysis of control and PD fibroblast show the M6PR amount at plasma membrane before and after antioxidants treatments (NAC and IDE).
Figure 7a. Longer genes tend to have a larger fraction of differentially used exons. Box plot shows the fraction of exons significantly differentially used for 9026 expressed genes grouped into deciles based on the genomic length (including exons and introns) of their longest transcripts. n=3 replicates.
(E) Lysates from control (WT) or CRISPR generated TRIP6 null (TRIP6-KO) HEK293A cells were analyzed by western blotting using the indicated antibodies (quantification shown in (G)).
HeLa cells expressing a doxycycline-inducible shRNA targeting PRMT1 were treated or not with doxycycline (Dox) for 6 days. PRMT1 depletion was monitored by immunoblotting using the indicated antibodies (E). The p14ARF signals were densitometrically quantified and normalized to the respective β-TUBULIN signal, as specified by the numbers below the blot, with the -Dox condition set to 1.
F) Dwell time histogram for different N's with the MI-AA helix-7 mutant. The dwell time histogram for N = 6 fit with double exponential decay (green; R2 = 0.98); The dwell time for N = 6 with single exponential fit was 15.2 ± 3.41 sec, R2 = 0.96).
(D) Normalization of excessive climbing frequency (but not duration) by treatment of synapses in PtenΔC/ΔC mice (2-5 months) with DCS (20 mg/kg). (n = 17 mice for WT-V, 17 for WT-D, 16 for ΔC-V, 16 for ΔC-D, *P < 0.05, **P < 0.01, ns, not significant, two-way ANOVA with Tukey's test). The error bars represent SEM.
AFF4 (green) and FOXN1 (red) are shown by immunofluorescence in the following wild-type tissue samples: (C) developing murine epidermis, E16.5; (D) human epidermis, adult; (E) murine thymus, P0, outer region. DNA is stained by Hoechst dye 33258 (blue). Co-localization of AFF4 and FOXN1 generates yellow color, visible in cell nuclei of all samples. In panel C, the fluorescent signal in the periderm (P) is nonspecific, as it is present when primary antibodies are omitted from the staining. Inner regions of the murine thymus (not shown) yielded the same extensive overlap of FOXN1 and AFF4 staining as that shown in panel E. Arrowheads mark the dermal/epidermal border (C, D). CT, cortex of the thymus. Scale bars, 20 µm.
(B) Wild type mice received strain GFP-K79 via the tail vein and 1 hr later, animals were perfused and the meninges, cortex and choroid plexus were obtained for demonstration of intravenously injected bacteria. The arrows represent bacteria co-localized with capillaries (e.g., within capillaries) and arrowheads represent bacteria outside the capillaries (e.g., exited from the capillaries). A few bacteria were successfully passed through the meningeal and cortex capillaries, but no bacteria were demonstrated in the choroid plexus at this time.
(B) Dot plots represent intracellular IFN-I staining in 5.2+ vs 5.1+ pDC isolated from indicated MCMV-infected MBMC. Isotype control (IC) staining was performed on a mixture of cells isolated from both types of MCMV-infected MBMC.
A Control of mammary stem cell activity by Wnt4 during development. Schematic representation of mammary gland development (bottom) and control of mammary stem/progenitor cells by hormones (top). Model showing Wnt4 expression during mammary gland development. Wnt4 is important for stem cell activation throughout postnatal mammary gland development. Perinatal Wnt4 expression is independent of ER and PR, yet unknown factors control it. PR signaling is required for Wnt4 expression in puberty and adulthood. PR expression is induced by ER signaling.
(A) To generate MITOL-3Flag knock-in (KI) HCT116 cell lines, 3xFlag gene cassettes were inserted upstream of the MITOL stop codon using CRISPR/Cas9-based gene editing. Insertion of the 3Flag-tag was verified by immunoblotting with an anti-Flag antibody. Asterisk indicates a cross-reacting band.
U2OS LacR-Fok1 cells were transfected with GFP or GFP-SHLD2 and 24 h later DNA damage was induced using Shield-1 and 4-OHT. The cells were then processed for GFP and mCherry immunofluorescence. Shown are representative micrographs. Scale bar = 5µm. Quantification of the experiments shown in (C). Data are represented as the mean ± SD (n=3). At least 100 cells per condition were counted.
A, BVRAC currents (ICl,vol) of the HAP1 (A) and KBM7 (B) haploid cell lines. Left panels, example current traces of ICl,vol fully activated by hypotonic cell swelling measured with the voltage‐clamp protocol shown in (A). Dashed lines indicate zero current. Right panels, averaged current/voltage relationships of maximally activated ICl,vol. Consistent with VRAC currents, they needed hypotonic swelling for activation, displayed an I− > Cl− permeability sequence, and were blocked by DCPIB (Appendix Fig S2A-H). The difference in current inactivation between HAP1 and KBM7 cells can be explained by the fact that KBM7 cells hardly express LRRC8E (Fig EV1) which accelerates VRAC inactivation (Voss et al, 2014). At potentials > +100 mV, also KBM7 currents inactivated (Appendix Fig S2I). Data are presented as mean ± SEM; n = 5-10.C
The Y-maze test was performed using 12-month-old male Mgat3+/+, Mgat3−/−, hAPP/Mgat3+/+, or hAPP/Mgat3−/− mice (n = 8-10). **P = 0.004 for Mgat3+/+ versus hAPP/Mgat3+/+, *P = 0.022 for hAPP/Mgat3+/+ versus hAPP/Mgat3−/−.
(D) The distribution of histone reads in 5' UTR, CDS and 3' UTR in rRNA-depleted nuclear RNA-seq and ALYREF-iCLIP-seq.
(b) Thr 145 phosphorylation of EndoB1 facilitates its dimerization in 293T cells.
(E) STIM1 protein expression in expanded human T cells analyzed by immunoblotting. One representative Western blot of 3 is shown. Bar graphs are the mean ± SEM of STIM1 expression normalized to actin from 3 independent experiments.
C, Differentially methylated CpGs were depleted at promoters and CpG islands but enriched at gene bodies and enhancers compared to all CpGs covered by RRBS. Stars indicate FDR adjusted p < 0.05 (linear regression).
[b] Heatplots of cumulative SLEs: WT (n=11 slices from 3 mice), Xrcc1Nes-Cre (n=12 slices from 4 mice), Parp1+/-/Xrcc1Nes-Cre (n=12 slices from 3 mice) and Parp1-/-/Xrcc1Nes-Cre (n=10 slices from 3 mice). Each horizontal bar corresponds to one slice with the colour code indicating cumulative SLEs.
Cryo-TEM images demonstrate the lipid bilayer EV purified from Molm-14 and U-937 cells. Scale bars are 100nm.
(g) HEK293 cells were transfected with ATG14L, VPS34 and Beclin-1 and grown under nutrient-rich conditions. ATG14L-containing VPS34 complexes were immunoprecipitated and lipid kinase activity was assayed as described in Fig. 1j. Inputs were immunoblotted with the indicated antibodies. Representative of four unique experiments.
Immunostaining for CCN1 (green) in the adult brain coronal section. Scale bar: 50 μm. The insert refers to the same image with DAPI staining to show cell nuclei (blue). LV, lateral ventricle.
C) Semi-transparent surface representation of our Ctf19D-RWD-Mcm21D-RWD-Okp1295-360 crystal structure, with secondary structure cartoon-diagram underneath; left: in a similar orientation as Ctf19-Mcm21 in B.
(f) Wortmannin treatments delayed the initial LC3 recruitment times onto parkin-labelled mitochondria in HeLa cells expressing KR-dMito, EGFP-LC3B and EBFP2-parkin. Each '+' marks the times measured in individual HeLa cells (the red '□' (square) denotes the average from five cells). P=0.0172 (Student's t-test).
(J-L) Tg(ins:kaede);Tg(ins:CFP-NTR) transgenics, with or without Tg(bactin:igfbp1a), were injected with a control morpholino or a morpholino that knocked down arx, which is necessary for α-cell differentiation and thus glucagon expression (J-K). Scale bars: 20 μm. (L) Quantification of the total number of regenerating β cells at 4 dpf (after β-cell ablation at 2-3 dpf). ****P<0.0001, *P<0.05, ns=nonsignificant. n=42, 20, 48 and 20, respectively.
A. Localization of GFP2-IN1 bNLS variants in yeast cells by direct fluorescence microscopy. Nup49-mCherry signal was used to visualize the location of the nuclear envelope. Corresponding DIC images are shown. Scale bar is 5 μm.
ELISA of TNFα and IL-6 in the supernatants from untreated or LPS-stimulated WT or Spata2-KO BMDMs. Bars and error bars represent the mean ± S.D. of triplicate experiments. Statistical analysis was performed using unpaired two-tailed Student's t-test.
(A) Multiple HKC strains (passage 2,3) from individuals of the two ancestries were stably infected with a lentivirus expressing dominant negative mutant TP53 (TP53R248W) and superinfected with a H-RasV12 expressing virus, followed, 24 hours later, by parallel intradermal injections into the back of NOD-SCID female mice. 7 strains per ancestry, 4-5 mice per assays were used. Tumors were excised 15 days post-injection. Shown is size quantification of all individual tumors (dots) by digital caliper. **p<0.01. n(tumors by White HKCs) =28, n(tumors by Black HKCs)=31, n((tumors by Black HKCs with <20% genome admixture)=13. Two-tailed unpaired Mann-Whitney test. In the plot, bars represent mean +/- SD.
(A) Structure of ScPrx1 (PDB ID: 5YKJ). The positions of relevant amino acids are indicated and the applied modifications in Prx1-P233stop and Prx1-C91A are shown. The C-terminal region absent in the Prx1-P233stop mutant is highlighted in green.
G. Immunofluorescence analyses of GSC differentiation. To stimulate differentiation BT168FO were grown as monolayer in the presence of serum and treated with doxycycline for up to 7 days. The upper panel displays immunofluorescence images of NESTIN, GFAP, ß-tubulin III, SOX2, and FlagOmomyc expression. FlagOmomyc blunted SOX2 expression and decreased GFAP and NESTIN protein levels, while inducing the onset of ß-tubulin III. The lower panel shows the percentage of positive cells for each cell marker evaluated (n = 4; mean ± SD). 16 fields for each assay were examined; scale bar = 100 μm.
A) Left panel: plasma total cholesterol in the different lipoprotein fractions of WT and Pkp2+/- mice fed a 3-month HFD (blue line) or a 3-month HFD+atorvastatin (red line). Right panel: plasma total cholesterol quantity in fractions 29-32, corresponding to low, very-low and intermediate-density lipoproteins, of WT and Pkp2+/- mice fed a 3-month HFD (blue line; n=7) or a 3-month HFD+atorvastatin (red line; n=9; Two-tailed Student's t-test). Data information: mean ± SEM. * p<0.05; ** p<0.01; *** p<0.001.
(D) YFP or YFP-Fis1 was co-overexpressed with HA-TBC1D15 or HA-TBC1D17 in HEK293 cells. The cell extracts were subjected to pull down assays with GFP-Trap. 5% input and bound fractions were analyzed by immunoblotting with anti-HA (upper panel) and anti-GFP (lower panel) antibodies.
(A) Knockdown of FEZ1 enhances LC3 lipidation but does not affect p62 degradation. Anti‐Actin and ‐LC3 blot after siRNA treatment in HEK293 cells. Quantification of LC3II/actin of averaged duplicates; error bars represent s.e.m. (n=3). Significance was determined using a two‐tailed paired t‐test: RISCfree ES versus siFEZ1‐01 ES, P=0.034. Quantification of p62/actin ( Supplementary Figure S5) performed as in Figure 4B; error bars represent s.e.m. (n=3); RISCfree FM versus RISCfree 2 and 4 hP>0.0001 and P=0.0014, respectively. qRT-PCR showing FEZ1 mRNA levels after indicated knockdown in GFP-LC3‐HEK cells (error bars represent s.d.).
(C Representative immunoblots of total PKCα and p-PKCα in primary human pPMNs that were treated by PMA (C) for 0, 0.5, 1, 2, 3 h.
A-D The localization of Twi1p in wild‐type (A, C) and COI12KO (B, D) cells at the early (meiotic prophase; A, B) and mid‐ (nuclear exchange; C, D) conjugation stages was analyzed by immunofluorescence microscopy staining using an anti‐Twi1p antibody. Twi1p was localized in the parental MACs at both stages in wild‐type cells (A, C). In contrast, in COI12KO cells, Twi1p was localized in the cytoplasm at the early stage (B) and became undetectable at the mid‐stage (D). All pictures share the scale bar (10 μm) shown in (A).
A, The caspase-3-reporter cell line (labelled DEVD) and the control cell line (DEVG; see methods) were infected and analysed at various time points post-infection by flow cytometry (Chlamydia trachomatis (Ctr; MOI=1, 30 h); Salmonella Typhimurium (STy; MOI=50, 24h); Toxoplasma gondii (MOI=5, 16 h); MVA (MOI=10, 16h); Influenza A virus (IAV; MOI=1, 16h); Herpes simplex virus 1 (HSV-1; MOI=1, 16h). Staurosporine treated cells (1 μM, 3h) were used as a positive control. Percentages of cells positive for caspase-3-activation (FRET-loss) were determined. Data are means/SEM of three independent experiments. (n=3)
D ChIP DNA samples from wild type (untagged) and abo1-GFP cells were analysed by qPCR for Tf2 LTR. Data are the mean of four independent biological repeats and error bars represent ±SEM.
G, Two examples of protein-metabolite pairs are shown with their respective Pearson correlation coefficients
(C) Proximal ligation assay monitoring (left) and quantification (right) of UBTD1 associated with YAP of DU145 and A549 cells transfected with the indicated siRNA (control, siCTRL; UBTD1: siUBTD1pool). Nuclei were stained with DAPI (Blue) on the MERGE image.
C) Venn diagram showing the overlap between the sets of genes with significant differences between WT and mdx mice at different weeks.
E H4 Cas9 cells and H4 Cas9 cells stably expressing Myc-TMEM41B or TMEM41B-Myc were lysed and subjected to anti-Myc IP. Eluates were analyzed by mass spectrometry. Enrichment of proteins in IPs from Myc-TMEM41B or TMEM41B-Myc cells versus H4 Cas9 cells is depicted as log2 fold changes. Entire data is reported in Dataset EV2
Under low-sugar conditions, KIN10 is activated by GRIK1, and phosphorylates PIF4. The phosphorylation induces the degradation of PIF4 through 26S proteasome, suppressing PIF4-mediated thermoresponsive hypocotyl growth. An increase in sucrose results in a rise in T6P. T6P inhibits the GRIK1-mediated KIN10 activation, which allows an increase in PIF4 protein in response to high temperatures. The increased PIF4 induces hypocotyl elongation by activating auxin signaling.
(D and E) Immunoprecipitation with anti-Flag M2 affinity agarose gel and immunoblotting with anti-Myc antibody shows that NO donors increased the interaction of Flag-Beclin 1 with WT Myc-Bcl-2 (D), but not with AAA Myc-Bcl-2 (E), in HeLa cells transfected with WT Myc-Bcl-2 (D) or AAA Myc-Bcl-2 (E) along with either empty Flag or Flag-Beclin 1. Asterisk denotes IgG band (E).
I-J. AdOx treatment decreases R388 methylation of SIRT7. MEF and L02 cells were treated with AdOx for 24 hrs. Methylation of immunoprecipitated endogenous SIRT7 was determined by western blot (I). The band intensity of western blots was measured to quantify relative R388 methylation ratio (J) (mean ± SD, n=3 experimental replicates, ***p < 0.001, unpaired two-tailed t-test)
(C) Structural comparison between the HsAtg4B-LC3 precursor and SENP2-SUMO‐3 precursor complexes. Left, structure of the HsAtg4B-LC3 precursor complex; right, structure of the SENP2-SUMO‐3 precursor complex. HsAtg4B and SENP2 are shown as a ribbon model, whereas LC3 and SUMO‐3 precursors are shown as a stick model. The side chains of the important residues at the catalytic site are also shown as a stick model. Atom colouring is the same as in (A, B).