EMBO/SourceData huggingface dataset:
Figure legend: "(A)  C-circle assay  for tumor samples. The presence of C-circles was tested in 22 osteosarcomas  by Rolling Circle Amplification  (RCA) assay using Φ29 DNA polymerase. Φ29 DNA polymerase  negative controls and Φ29 DNA polymerase-based reactions starting respectively with 75, 37.5, and 18.75 ng of DNA   were applied to dot blots  and C-circles were detected by hybridization  with a 32P-(CCCTAA)4 telomeric  probe. U2OS  and HeLa  cells correspond to positive and negative control samples, respectively."
NCBI gene IDs:
"DNA polymerase: 6446511"
Figure legend: "(A) Oncoprint graph showing the distribution of mutations  (green rectangles) and copy number variations  (red rectangle, amplification; blue rectangle, copy loss) in all samples. Tumors are distributed according to ALT-positivity (ALT+) or -negativity (ALT-) and ATRX   status (ATRX-mutated or ATRX-wt)."
NCBI gene IDs:
"ATRX: 546"
Figure legend: "(B) Tissue sections of two representative high-grade osteosarcomas  with HES (hematoxylin eosin saffron) staining  (left panel), anti-ATRX  (HPA064684) immunochemistry  (middle panel), and anti-DAXX  (HPA008736) immunochemistry  (right panel), showing ATRX protein expression in two ALT-positive samples. In the top panel, intratumoral ATRX  expression is negative (positive control osteoclasts  are shown). In the bottom panel, intratumoral ATRX  expression is high. Scale bars are 250 μm."
NCBI gene IDs:
"ATRX: 546"
Figure legend: "(A) Copy-number-alteration (CNA) profiles of osteosarcomas. Representation of the GISTIC analysis with false discovery rate (FDR (q-value)) for all cases (n=22; left panel), ALT-positive/ATRX-wt cases (n=11; middle panel), and ALT-positive/ATRX-mutated cases (n=5; right panel)."
NCBI gene IDs:
"ATRX: 546"
Figure legend: "(B) Gain/amplification of TOP3A  gene region (17p11) is a genomic signature of ATRX-wt osteosarcomas. For each ATRX-mutated (top part) and ATRX-wt (bottom part) case, from the left to the right, the chromosome 17 and regional genomic profiles were established, with CGH  Analytics software. A focus was made within the genomic interval (17.25-19.11 Mb) of the short arm of  chromosome 17 (hg38 human genome mapping; Build 38 from NCBI, December 2013 version) including TOP3. Color profiles corresponding to the different tumors are defined at the top of each group. Most ATRX-wt cases show gain or amplification of this region (bottom part), whereas no ATRX-mutated cases display this alteration (top part)."
NCBI gene IDs:
"ATRX: 546
TOP3: 7156
TOP3A: 7156"
Figure legend: "(C) Chromosome 17 copy number variation analysis showing amplification/gain of the TOP3A  region that do not extend into the TP53  gene in ALT ATRX-wt tumors (left panel), and amplification of the TOP3A  region for which TP53  region is at the edge of the amplification/gain in ALT-positive ATRX-wt tumors (right panel)."
NCBI gene IDs:
"ATRX: 546
TOP3A: 7156
TP53: 7157"
Figure legend: "(A) Volcano plot of the supervised analysis of mRNA expression  profiles of osteosarcomas   according to ALT-positive vs. ALT-negative samples, showing upregulated (in red) and downregulated (in green) genes. Twelve tumors had sufficient RNA quality to be analyzed: seven ALT-positive ATRX-wt, two ALT-positive/ATRX-mutated and three ALT-negative."
NCBI gene IDs:
"ATRX: 546"
Figure legend: "(B) TOP3A gene expression  according to ALT  and ATRX  status: ALT+/ATRX-wt (n=7), ALT+/ATRX-mut (n=2) and ALT- (n=3). Box-and-whisker plot were defined with default parameters by median value (central band at the 50th percentile), interquartile ranges (IQR, box limited by 25th and 75th percentile) and whisker boundaries defined by minimum and maximum value. An ANOVA statistical test, and Tukey's range test were used to compare modalities."
NCBI gene IDs:
"ATRX: 546
TOP3A: 7156"
Figure legend: "(B)  Western blot  showing TOP3A protein expression in nine osteosarcoma  cell lines and NY  siTOP3A as control."
NCBI gene IDs:
"TOP3A: 7156"
Figure legend: "(D) C-circle assay showing inverse effect of ATRX ectopic expression on  C-circle  levels in ATRX-mutated and ATRX-wt cell lines. Error bars represent the mean ± SEM from n = 2 experiments, n.s. = non-significant, *p &lt; 0.05, Mann-Whitney test."
NCBI gene IDs:
"ATRX: 546"
Figure legend: "(E) C-circle assay showing rescue of ATRX  ectopic expression by TOP3A  overexpression in U2OS osteosarcoma  cells Error bars represent the mean ± SEM from n = 2 experiments, n.s. = non-significant, *p &lt; 0.05, Mann-Whitney test. Western blot and quantification of TOP3A  expression is shown for U2OS  cells overexpressing TOP3A."
NCBI gene IDs:
"ATRX: 546
TOP3A: 7156"
Figure legend: "(B) Representative images of telomeric  DNA (green) and PML  protein (red) colocalizations  (APBs) in osteosarcoma  and in vitro-immortalized ATRX-mutated or ATRX-wt cell lines according to TOP3A  KD. Scale bars are 5 μm. (C) Quantification of APB  frequency in osteosarcoma  and in vitro-immortalized ATRX-mutated or ATRX-wt cell lines according to TOP3A  KD; Error bars represent the mean ± SEM from n = 3 experiments, n = 150 cells scored per treatment, n.s., non-significant; Mann-Whitney test. (D) Effect of TOP3A  KD on Telomere  Dysfunction-Induced Foci (TIFs) in osteosarcoma  and in vitro-immortalized cell lines; Error bars represent the mean ± SEM from n = 3 experiments, n = 150 cells scored per treatment, *p &lt; 0.05, **p &lt; 0.005; Mann-Whitney test."
NCBI gene IDs:
"ATRX: 546
TOP3A: 7156"
Figure legend: "(E) Distributions of TeSLA  fragments in osteosarcoma  and in vitro-immortalized ATRX-mutated or ATRX-wt cell lines according to TOP3A  KD (left panel; each dot represents a TeSLA  fragment), and representative TeSLA Southern Blot image for NY  (right panel)."
NCBI gene IDs:
"ATRX: 546
TOP3A: 7156"
Figure legend: "(A) FISH-IF  of telomeres  (in red) and BLM  (in green) in TOP3A-depleted cells BLM  foci at telomeres  are indicated by white arrows. Error bars represent the mean ± SEM from n = 3 experiments, n = 150 cells scored per treatment, n.s. = non-significant, **p &lt; 0.01, Mann-Whitney test. Scale bars are 5 μm."
NCBI gene IDs:
"TOP3A: 7156"
Figure legend: "(B) ATSA assay assessing ALT-mediated telomeric DNA synthesis (telomere  in red, EdU  in purple) in PML  (in green) according to TOP3A  KD. EdU  signal at APB  (telomere/PML) are indicated by white arrows. Approximately 150 cells were divided into five groups (0,1-2, 3-4, 5-6n and ≥7) based on the number of EdU+APBs. Scale bars are 5 μm."
NCBI gene IDs:
"TOP3A: 7156"
Figure legend: "Expression of USP28 (left) and TP63 (right) in human lung squamous cell carcinomas (SCC, n=498), adenocarcinomas (ADC, n=513) and normal non-transformed tissue (normal SCC=338, normal ADC=348). Xena UCSC software. In box plots, the centre line reflects the median, the cross represents the mean and the upper and lower box limits indicates the first and third quartile. Whiskers extend 1.5x the IQR and outliers are marked as dots."
NCBI gene IDs:
"TP63: 8626
USP28: 57646"
Figure legend: "Correlation of mRNA expression of USP28 and TP63 in lung SCC (left, n=498), ADC (right, n=513) and normal, non-transformed tissue (normal SCC=338, normal ADC=348). R: Spearmans correlation coefficient; m=Slope. Xena UCSC software."
NCBI gene IDs:
"TP63: 8626
USP28: 57646"
Figure legend: "Kaplan-Meier estimator of NSCLC patients stratified by USP28 (left, n=1145) and TP63 (right, n=1926) expression. p-values were calculated using log-rank test. HR: hazard ratio. Kmplot software."
NCBI gene IDs:
"TP63: 8626
USP28: 57646"
Figure legend: "Kaplan-Meier estimator of lung SCC patients stratified by USP28 expression (n=271). The p-value was calculated using a logrank test. HR: hazard ratio. Kmplot software."
NCBI gene IDs:
"USP28: 57646"
Figure legend: "Co-immunoprecipitation of exogenous HA-USP28 and FLAG-ΔNp63 in HEK293 cells. Either HA-USP28 or FLAG-ΔNp63 were precipitated and blotted against FLAG-ΔNp63 or HA-USP28. The input corresponds to 10% of the total protein amount used for the IP (ACTIN as loading control)."
NCBI gene IDs:
"FLAG: 
HA: 
ΔNp63: 8626
USP28: 57646"
Figure legend: "Ni-NTA His-ubiquitin pulldown in control transfected or HA-USP28 overexpressing HEK293 cells, followed by immunoblot against exogenous ΔNp63. The input corresponds to 10% of the total protein amount used for the pull down. Relative ubiquitination of the representative immunoblot was calculated using undefined for normalization."
NCBI gene IDs:
"HA: 
USP28: 57646"
Figure legend: "Ni-NTA His-ubiquitin pulldown K48 or K63 in control and HA-USP28 overexpressing HEK293 cells, followed by immunoblot against exogenous ΔNp63. The input corresponds to 10% of the total protein amount used for the pulldown. Relative ubiquitination of the representative immunoblot was calculated using VINCULIN for normalization."
NCBI gene IDs:
"HA: 
USP28: 57646"
Figure legend: "Ni-NTA His-ubiquitin pulldown in control, FLAG-USP28 or FLAG-USP28 C171A transfected HEK293 cells, followed by immunoblot against exogenous ΔNp63. The input corresponds to 10% of the total protein amount used for the pulldown. Relative ubiquitination of the representative immunoblot was calculated using ACTIN for normalization."
NCBI gene IDs:
"FLAG: 
USP28: 57646"
Figure legend: "CHX chase assay (100ug/ml) of control, FLAG-USP28 or FLAG-USP28 C171A transfected HEK293 cells for indicated time points. Representative immunoblot analysis of FLAG (USP28) and ∆Np63 as well quantification of relative protein abundance (ACTIN as loading control)."
NCBI gene IDs:
"FLAG: 
USP28: 57646"
Figure legend: "Inducible depletion of USP28 in A-431 upon treatment with doxycycline (1µg/ml) for 96h, western blot (left, VINCULIN as loading control) and qPCR analysis of USP28 and ∆Np63 expression relative to ACTIN (right) was performed."
NCBI gene IDs:
"ACTIN: 
∆Np63: 8626
USP28: 57646"
Figure legend: "Tandem ubiquitin binding entity (TUBE) pulldown of endogenous ubiquitylated ∆Np63 in A-431 cells upon DOX depletion of USP28. Relative ubiquitination of the representative immunoblot was calculated using ACTIN for normalization."
NCBI gene IDs:
"USP28: 57646"
Figure legend: "Cycloheximide (CHX) chase assay (100µg/ml) of control or inducible sh-USP28 A-431 cell line (EtOH or 1µg/ml dox) for indicated time points. Representative immunoblot (left, VINCULIN as loading control) of USP28 and ∆Np63 and quantification of relative protein abundance (right)."
NCBI gene IDs:
"USP28: 57646"
Figure legend: "Doxycycline induced murine USP28 overexpression (EtOH or 1ug/ml dox for 96 hours) in A-431 cells followed by immunoblot (VINCULIN as loading control) and qPCR analysis of USP28 and ∆Np63. For qPCR, human USP28 and murine USP28 (mUSP28) primers were used. Relative mRNA was calculated using ∆∆Ct analysis for human USP28 and ∆Ct for mUSP28 (ACTIN as housekeeping)."
NCBI gene IDs:
"ACTIN: 
∆Np63: 8626
USP28: 57646
USP28: 235323"
Figure legend: "TUBE pulldown of endogenous ubiquitylated ∆Np63 in A-431 cells upon overexpression of mUSP28 for 96 hours (EtOH or 1µg/ml dox). Relative ubiquitination of the representative immunoblot was calculated using ACTIN for normalization."
NCBI gene IDs:
"USP28: 235323"
Figure legend: "CHX chase assay (100µg/ml) of control or inducible mUSP28 overexpressing A-431 cell line (EtOH or 1µg/ml dox) for indicated time points. Representative immunoblot analysis of USP28 and ∆Np63 as well quantification of relative protein abundance (VINCULIN as loading control)."
NCBI gene IDs:
"USP28: 235323"
Figure legend: "Immunoblot of control (sh-NTC) and two independent shRNA targeting USP28 (sh-USP28#1 and #2) for ∆Np63 and USP28 protein abundance in LUDLU-1adh (VINCULIN as loading control), followed by qPCR analysis of USP28 and ∆Np63 expression relative to ACTIN."
NCBI gene IDs:
"ACTIN: 
∆Np63: 8626
USP28: 57646"
Figure legend: "Doxycycline induced mUSP28 overexpression (EtOH or 1µg/ml dox for 96 hours) in LUDLU-1adh cells followed by immunoblot (VINCULIN as loading control) and qPCR analysis of USP28, mUSP28 and ∆Np63. Relative mRNA was calculated using ∆∆Ct analysis for human USP28 and ∆Ct for mUSP28 (ACTIN as housekeeping for the analysis)."
NCBI gene IDs:
"ACTIN: 
∆Np63: 8626
USP28: 235323
USP28: 57646"
Figure legend: "Correlation of gene expression changes upon constitutive transduction of A-431 cells with either shRNA targeting USP28 (sh-USP28#1) or ∆Np63 (sh-∆Np63#2) relative to non-targeting control (sh-NTC). The diagonal line reflects a regression build on a linear model. R: Pearsons correlation coefficient, m: slope of the linear regression model"
NCBI gene IDs:
"∆Np63: 8626
USP28: 57646"
Figure legend: "Gene set enrichment analysis (GSEA) of a gene set of significantly down-regulated genes in sh-∆Np63#2 transfected A-431 cells (\"Down-regulated sh-∆NP63\", Appendix Table S1). The gene set was analysed in sh-∆Np63#2 (left) and sh-USP28#1-depleted (right) A-431 cells. (N)ES: (normalised) enrichment score"
NCBI gene IDs:
"∆Np63: 8626
∆NP63: 8626
USP28: 57646"
Figure legend: "Gene set enrichment analysis (GSEA) of a gene set of significantly down-regulated genes in sh-USP28#1 transfected A-431 cells (\"Down-regulated sh-USP28\", Appendix Table S1). The gene set was analysed in shUSP28#1 (left) and sh-∆Np63#-depleted (right) A-431 cells. (N)ES: (normalised) enrichment score"
NCBI gene IDs:
"∆Np63: 8626
USP28: 57646"
Figure legend: "Immunoblot of endogenous ΔNp63 and USP28 in A-431 cells stably transduced with constitutive shRNA-non-targeting control (NTC) or against USP28 and transiently transfected with exogenous ΔNp63. ACTIN served as loading control. Representative western blot from three independent experiments."
NCBI gene IDs:
"ΔNp63: 8626
USP28: 57646"
Figure legend: "Cell growth of A-431 cells stably transduced with constitutive shRNA-non-targeting control (NTC) or against USP28 and transiently transfected with exogenous ΔNp63. Total cell number was measured and assessed at indicated time points. Quantitative graph is represented as mean ± SD of three experiments (n=3). p-values were calculated using two-tailed t-test statistical analysis. *p-value &lt; 0.05, **p-value &lt; 0.01"
NCBI gene IDs:
"ΔNp63: 8626
USP28: 57646"
Figure legend: "Relative expression of SCC marker genes KRT5, 14 and 19 in A-431 cells stably transduced with constitutive shRNA-non-targeting control (NTC), two independent shRNA-ΔNp63, two independent shRNA-USP28 or ΔNp63 in shRNA-USP28#1, normalised to ACTIN. Quantitative graph is represented as mean ± SD of three experiments (n=3)."
NCBI gene IDs:
"ACTIN: 
KRT5: 3852
ΔNp63: 8626
USP28: 57646"
Figure legend: "Relative expression of epithelial marker genes KRT10 and GPCR5A in A-431 cells stably transduced with constitutive shRNA-non-targeting control (NTC), two independent shRNA-ΔNp63 and shRNA-USP28#1, normalised to ACTIN. Quantitative graph is represented as mean ± SD of three experiments (n=3)."
NCBI gene IDs:
"ACTIN: 
GPCR5A: 9052
KRT10: 3858
ΔNp63: 8626
USP28: 57646"
Figure legend: "Genomic signature of primary human lung SCC samples comprising USP28, ∆Np63, KRT5, KRT14, KRT19, DSG3, MKI67, PCNA and GPRC5A. Samples were sorted dependent on relative USP28 expression (high to low). n=553. Xena UCSC software."
NCBI gene IDs:
"DSG3: 1830
GPRC5A: 9052
KRT14: 3861
KRT19: 3880
KRT5: 3852
MKI67: 4288
PCNA: 5111
∆Np63: 8626
USP28: 57646"
Figure legend: "GSEA of consensus squamous cancer marker genes (se Appendix Table S2) in A-431 cells stably transduced with sh-∆Np63#2 or sh-NTC. (N)ES: (normalised) enrichment score GSEA of consensus squamous cancer marker genes in A-431 cells stably transduced with sh-USP28#1 or sh-NTC. (N)ES: (normalised) enrichment score"
NCBI gene IDs:
"∆Np63: 8626
USP28: 57646"
Figure legend: "Correlation of mRNA expression of consensus squamous cancer marker genes and TP63 in lung SCC and non-transformed lung tissue (Normal). R: Spearmans correlation coefficient. n=836. Gepia software. Correlation of mRNA expression of consensus squamous cancer marker genes and USP28 in lung SCC and non-transformed lung tissue (Normal). R: Spearmans correlation coefficient. N=836. Gepia software."
NCBI gene IDs:
"TP63: 8626
USP28: 57646"
Figure legend: "Representative qPCR of SCC and ADC marker expression in two independent KP lung tumour clones, resulting in KPADC and KPSCC; (ACTIN served as loading control). Quantitative graph is represented as mean ± SD of three experiments (n=3)."
NCBI gene IDs:
"ACTIN: "
Figure legend: "Representative haematoxylin and eosin (H&amp;E) images of tumour bearing animals 8 weeks post intratracheal transplantation of 2 × 105 cells/animal. KPSCC sh-NTC (n=3); KPSCC sh-USP28 (n=3), Scale bar = 5000µm"
NCBI gene IDs:
"USP28: 235323"
Figure legend: "Quantification of % tumour area (top, normalised to total lung area) and lung tumour numbers (bottom) on KPSCC sh-NTC (n=6) and KPSCC sh-USP28 (n=6) animals."
NCBI gene IDs:
"USP28: 57646"
Figure legend: "Representative IHC staining for ADC (TTF-1) and SCC (KRT5 and ∆Np63) marker expression as well as Usp28 and GFP abundance in KPSCC sh-NTC (n=3) and KPSCC sh-USP28 (n=3) lung tumours. Scale bar =50 µm"
NCBI gene IDs:
"USP28: 235323"
Figure legend: "Analysis of occurring TP63 genetic alterations in lung squamous (LUSC), cervical (CESC), oesophagus (ESCA), head and neck (HNSC) and pancreatic (PAAD) tumours. Cbioportal."
NCBI gene IDs:
"TP63: 8626"
Figure legend: "Expression of TP63 (left) and USP28 (right) in human Lung (n=498), Cervix (n=254), Oesophagus (n=96) and HNSC (n=522) SCC tumours and normal non-transformed tissue (nLung=338 nCervix=3, nOesophagus=11 and nHNSC=44). In box plots, the centre line reflects the median, the cross represents the mean and the upper and lower box limits indicates the first and third quartile. Whiskers extend 1.5x the IQR. p-values were calculated using two-tailed t-test statistical analysis. Xena UCSC software."
NCBI gene IDs:
"TP63: 8626
USP28: 57646"
Figure legend: "Correlation of mRNA expression of KRT14 / KRT7 and TP63 in ADC and SCC tumours for Lung (nADC=513 and nSCC=498), Cervix (nADC=47 and nSCC=254) and Oesophagus (nADC=89 and nSCC=96). Blue dots: ADC; Red dots: SCC; R= Spearmans correlation coefficient; m: Slope. Xena UCSC."
NCBI gene IDs:
"KRT14: 3861
KRT7: 3855
TP63: 8626"
Figure legend: "Immunoblot of control (sh-NTC) and two independent shRNA targeting USP28 (sh-USP28#1 and #2) for ∆Np63, KRT14 and USP28 protein abundance in H1299, LUDLU-1adh, HELA, SiHa, Ca Ski, PANC-1 and BXPC-3 (ACTIN as loading control)."
NCBI gene IDs:
"USP28: 57646"
Figure legend: "Cells were seeded at equal cell density and counted after five days, Brigth field images of control or sh-USP28#2 infected H1299, LUDLU-1adh, Hela, CaSKI, PANC-1 and BXPC-3 cells before quantification. Scale bar = 30µm Relative number of H1299, LUDLU-1adh, Hela, CaSKI, SiHa, PANC-1 and BXPC-3 sh-USP28#2 cells compared with sh-NTC control cells. p-values were calculated using two-tailed t-test statistical analysis. SiHa* = Notably, the human SCC cell line SiHa was negative for ΔNp63."
NCBI gene IDs:
"USP28: 57646"
Figure legend: "(D) Control and  EXT1-/- XG1  cells were exposed to SARS-CoV-2  pseudovirus or SARS-CoV-2 pseudovirus pre-treated with 250 IU/mL UF  heparin for 30 min at 37°C. After incubation for 4h at 4°C, cells were lysed and binding  was measured by  ELISA. Data information: Data show the mean values and error bars are the SEM. Statistical analysis was performed using two-way ANOVA with Dunnett's multiple-comparison test. *P≤0.05, **P≤0.01 (n=3)."
NCBI gene IDs:
"EXT1: 2131"
Figure legend: "(A) Namalwa cells ectopically expressing either Syndecan 1 or 4 were exposed to either SARS-CoV-2  pseudovirus alone or SARS-Cov-2  pseudovirus pre-treated with UF heparin  (250 IU/mL) or LMWH enoxaparin (250 IU/mL) for 30 min at 37°C. Binding was measured after 4 hours at 4°C by ELISA. (B) SARS-CoV-2 isolate (hCoV-19/Italy) was pre-incubated with LMWH  enoxaparin (250 IU/mL) for 30 min at 37°C. Namalwa  cells expressing Syndecan 1 and 4 were exposed to either SARS-CoV-2 isolate (100 TCID/mL) or SARS-CoV-2 isolate (100 TCID/mL) pre-treated with LMWH LMWH enoxaparin (250 IU/mL) for 4 hours at 4°C and binding was determined by  quantitative real-time PCR. Data show the mean values and error bars are the SEM. Statistical analysis was performed using (A) 2way-ANOVA with Dunnett's multiple-comparison test. *P≤0.05, **P≤0.01 (n = 7), (B) 2way-ANOVA with Sidak's multiple-comparison test. *P≤0.05, **P≤0.01, ***P≤0.001, ****P≤0.0001 (n = 3 measured in triplicate)."
NCBI gene IDs:
"Syndecan 1: 6382"
Figure legend: "(B) SARS-CoV-2 isolate (hCoV-19/Italy) was pre-treated for 30 min at 37°C with either LMWH enoxaparin (250 IU/mL) or one of the following neutralizing antibodies (COVA1-18, 1-21 and 2-15), a non-neutralizing antibody (COVA1-27) or a human IgG1 isotype control, all at the concentration of 1 pg/mL. SARS-CoV-2 isolate alone or with blocks was added at a concentration of 100 TICD/mL. Detection of virus  binding to Syndecan 1 expressing  Namalwa was measured by  quantitative real-time PCR. Data information: Data show the mean values and error bars are the SEM. Statistical analysis was performed using ordinary one-way with Tukey's multiple-comparison test. *P≤0.05, **P≤0.01 (n=2 measured in duplicates)."
NCBI gene IDs:
"Syndecan 1: 6382"
Figure legend: "(B) ACE2, Syndecan 1  and Syndecan 4 cell surface expression on nasal epithelial cells, compared to polarized epithelial Calu-3 was confirmed by quantitative real-time PCR. (C, D) Nasal epithelial cells were exposed to SARS-CoV-2  isolate (hCoV-19/Italy, 100 TCID/mL) either directly or after pre-treatment with antibodies against ACE2 cell surface receptors (1 hour at 37°C )or after pre-treatment with LMWH enoxaparin (250 IU/mL) for 30 min at 37°C. Detection of viral binding  after 4 hours at 4°C (C) and persistently-infected cells lysed after 24 hours at 37°C (D) was determined by quantitative real-time PCR. Data information: Data show the mean values and error bars are the SEM. Statistical analysis was performed using (C, D) ordinary on-way ANOVA with Tukey's multiple-comparison test. *P≤0.05, **P≤0.01, ***P≤0.001, ****P≤0.0001 (C) (n=3), (D) (n=3 in duplicates)."
NCBI gene IDs:
"ACE2: 59272
Syndecan 1: 6382
Syndecan 4: 6385"
Figure legend: "B. Bimolecular fluorescence complementation between subunits of the Dsl complex and the COPI coat. The BiFC pair β'-COPVN•Dsl3pVC yielded fluorescent foci that showed dramatically reduced fluorescence intensity in the COPI binding-deficient dsl1-5xWA mutant. Schematic yeast cell representations depict the typical BiFC foci localization patterns. Scale bar 10 μm."
NCBI gene IDs:
"dsl1: 855463"
Figure legend: "C. Quantification of the β'-COPVN•Dsl3pVC BiFC signals in wild type cells and in COPI binding-deficient dsl1-5xWA and dsl1-Δlasso mutants (as shown exemplarily in (B)). Mean values + SEM of at least three independent experiments (n=3-8) are displayed. Statistical analysis was carried out by comparing the number of cells with BiFC signals over integrated thresholds to those without signals (*=p&lt;0,05). dsl1 mutant strains show a significant decrease in brightness, spot number and spot size in comparison with their corresponding DSL1 wild type strains (two-sample t-test). The dsl1-5xWA mutation also led to comparable signal reduction in cells carrying the VNI152L variant in the β'-COPVN I152L•Dsl3pVC combination."
NCBI gene IDs:
"dsl1: 855463
DSL1: 855463"
Figure legend: "F. Growth effects of Venus fragment tags in dsl1 mutant cells. Serial tenfold dilutions of liquid cell cultures were spotted on agar plates and incubated at 30 °C for two days. The images in the second row show that β'COPVN producing cells expressing the dsl1-5xWA mutation could not grow. The complementation of β'COPVN by its cognate interaction partners Dsl1pVC and Dsl3pVC, but not by non-cognate BiFC partners (Sec24pVC, Sec16pVC or VCRer1p), suppressed these growth defects. Spot assays of exemplary BiFC partners are depicted. Asterisk: Dsl1pVC carrying the dsl1-5xWA defect was expressed from a plasmid. See Fig EV1, EV2 and Appendix Fig S1 for full data display."
NCBI gene IDs:
"dsl1: 855463"