EMBO/SourceData huggingface dataset:
Figure legend: "(A) The indicated cells stably expressing YFP-LC3 and mCherry-Parkin were treated with valinomycin for 3 hr followed by immunofluorescence microscopy with anti-Cytochrome c antibody. Confocal images were acquired as z-stacks comprising 6 sequential sections with 0.8 μm z-intervals. Scale bars, 10 μm."
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(B) TBC1D15−/− cells prepared as in (A) were subjected to immunoelectron microscopy with anti-GFP antibody. White arrowheads indicate YFP-LC3-labeled tubules. High magnification image is shown in the lower panel. Scale bars, 500 nm."
NCBI gene IDs:
"TBC1D15: 64786"
Figure legend: "(C) The indicated cells prepared as in (A) were subjected to immunostaining with anti-Tubulin antibody. YFP-LC3 and Tubulin staining are merged in the right panels. Magnified images are shown for TBC1D15−/− cells. Scale bars, 10 μm."
NCBI gene IDs:
"TBC1D15: 64786"
Figure legend: "(A and B) YFP-Parkin stably expressing cells were treated with valinomycin for indicated times. Total cell lysates were subjected to immunoblotting. I and II denote cytosolic and lipidated LC3B, respectively. An asterisk indicates ubiquitinated TOMM20. (C) Indicated protein amounts as in (B) were quantified. The amount of protein without valinomycin treatment was set to 100%. The error bars represent ±SD from three independent experiments."
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(D) YFP-Parkin stably expressing WT HCT116 cells were treated with or without valinomycin for 40 hr. Total cell lysates were analyzed by immunoblotting."
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(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."
NCBI gene IDs:
"DRP1: 10059
MFF: 56947"
Figure legend: "(D) WT, FIS1−/−, and TBC1D15−/− cells stably expressing YFP-LC3 were grown in starvation media. Z-stacks of confocal images are shown. Scale bars, 20 μm. (E) The number of YFP-LC3 dots in cells under growth or starvation conditions was quantified. The error bars represent ±SD from three independent replicates. Over 50 cells were counted in each well."
NCBI gene IDs:
"FIS1: 51024
TBC1D15: 64786"
Figure legend: "(A) TBC1D15−/− cells and those stably expressing HA-TBC1D15 WT and HA-TBC1D15 (Δ221-250), and FIS1−/− cells stably expressing HA-TBC1D15 WT were subjected to immunostaining with anti-TOMM20 and anti-HA antibodies. Scale bars, 10 μm."
NCBI gene IDs:
"FIS1: 51024
TBC1D15: 64786"
Figure legend: "(B) HA-TBC1D15 WT or HA-TBC1D15 (Δ221-250) with or without Fis1 was transiently overexpressed (OE) in HeLa cells. Cells were subjected to immunostaining with anti-HA and anti-Fis1 antibodies. Scale bars, 20 μm."
NCBI gene IDs:
"Fis1: 51024
TBC1D15: 64786"
Figure legend: "(C) YFP-TBC1D17 together with pcDNA vector or Fis1 was transiently overexpressed (OE) in HeLa cells. Cells were subjected to immunostaining with anti-Fis1 and anti-Cytochrome c antibodies. Scale bars, 20 μm."
NCBI gene IDs:
"Fis1: 51024"
Figure legend: "(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."
NCBI gene IDs:
"Fis1: 51024
TBC1D15: 64786
TBC1D17: 79735"
Figure legend: "(E) YFP, YFP-TBC1D15, or YFP-TBC1D17 was co-overexpressed with HA-TBC1D15 (upper panel) or HA-TBC1D17 (lower panel) 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-GFP and anti-HA antibodies."
NCBI gene IDs:
"TBC1D15: 64786
TBC1D17: 79735"
Figure legend: "(F) HA-TBC1D15 (Δ221-250) together with Fis1 and YFP-TBC1D15 WT or YFP-TBC1D17 WT were transiently overexpressed (OE) in HeLa cells. Cells were subjected to immunostaining with anti-HA and anti-Fis1 antibodies. Images of HA and Fis1 staining were merged in the right panels. Scale bars, 20 μm."
NCBI gene IDs:
"Fis1: 51024
TBC1D15: 64786"
Figure legend: "(B) YFP-TBC1D15 overexpressed in HEK293 cells was subjected to binding assays with GST-fused proteins (GABA, L1, and L2 represent GABARAP, GABARAPL1, and GABARAPL2, respectively). 5% input and bound fractions were analyzed by immunoblotting with anti-GFP antibody (upper panel). Coomassie brilliant blue (CBB) staining shows GST-fusion proteins in bound fractions (lower panel). (C) Binding assay carried out as in (B) with GST-GABARAPL1 WT (GST-WT) or its Y49A/L50A mutant (GST-YL). Immunoblotting with anti-GFP antibody (upper panel) and CBB staining (lower panel) are shown."
NCBI gene IDs:
"GABARAPL1: 23710"
Figure legend: "(E-H) The indicated YFP-tagged TBC1D15 full-length, truncated, or point-mutant protein or YFP-Fis1 overexpressed in HEK293 cells were subjected to binding assays with recombinant GST-GABARAPL1. 5% input and bound fractions were analyzed by immunoblotting with anti-GFP antibody (upper panel) and CBB staining (lower panel)."
NCBI gene IDs:
"Fis1: 51024
TBC1D15: 64786"
Figure legend: "(J) LC3-LC3 and mCherry-Parkin stably expressing TBC1D15−/− cells in the presence of HA-tagged TBC1D15 WT or F280A mutant were treated with valinomycin for 3 hr. Cells were subjected to immunofluorescence microscopy with anti-HA antibody. Scale bars, 10 μm. (K) The YFP-LC3 morphology of cells in (J) was quantified. The error bars represent ±SD from three independent replicates. Over 50 cells were counted in each well."
NCBI gene IDs:
"Parkin: 5071
TBC1D15: 64786"
Figure legend: "(A) Total cell lysates from HCT116 treated with control (NTC) or RAB7A siRNA were analyzed by immunoblotting."
NCBI gene IDs:
"RAB7A: 7879"
Figure legend: "(B) The indicated cells stably expressing YFP-LC3 (green) and mCherry-Parkin were treated with control (NTC) or Rab7_#5 siRNA. After 3 hr valinomycin treatment, cells were analyzed by immunofluorescence microscopy with anti-TOMM20 antibody (red). Z-stacks of confocal images are shown. Magnified images are also shown. Scale bars, 10 μm. (C) YFP-LC3 morphologies of cells in (B) were quantified. Percentages of cells harboring diffuse, punctuate or accumulated/tubulated YFP-LC3 are shown. Data and error bars were obtained from at least 50 cells in each of three independent replicates."
NCBI gene IDs:
"Parkin: 5071
Rab7: 7879"
Figure legend: "(D) The indicated cells stably expressing YFP-LC3 (green), mCherry-Parkin, and 2HA-Rab7 (Red) were treated with or without valinomycin for 3 hr and analyzed by immunofluorescence microscopy with anti-HA antibody. Magnified images are also shown. Scale bars, 10 μm."
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(E) YFP-LC3 and mCherry-Parkin stably expressing TBC1D15−/− cells in the presence of HA-tagged TBC1D15 WT or the D397A mutant were treated with valinomycin for 3 hr. Cells were subjected to immunofluorescence microscopy with anti-HA antibody. Scale bars, 10 μm. (F) The YFP-LC3 morphology of cells in (E) was quantified. The error bars represent ±SD from three independent replicates. Over 50 cells were counted in each replicate."
NCBI gene IDs:
"Parkin: 5071
TBC1D15: 64786"
Figure legend: "D. EMSA showing a differential binding of WT Oct4 and Oct6 POU domains as well as mutated Oct4151M and Oct6151S POU domains on MORE (OctOct) element. The free DNA and DNA bound by monomer or dimer are indicated."
NCBI gene IDs:
"Oct6: 5453
Oct4: 18999"
Figure legend: "E. EMSA showing binding of WT Oct4 and Oct6 POU domains as well as mutated Oct4151M and Oct6151S POU domains to SoxOct element in the absence or presence of the Sox2 HMG. The free DNA and DNA bound by monomers or dimer are indicated. Quantifications of cooperativity measurements are shown in Fig. EV3C."
NCBI gene IDs:
"Oct6: 18991
Oct4: 18999"
Figure legend: "F. Bar plot based on single tube EMSAs using cy5-SoxOct and FAM-MORE DNA elements showing the difference in DNA-binding of WT Oct4, WT Oct6, Oct4151M and Oct6151S POU domains. The mean log2 ratio of cy5 (heterodimer) and FAM (homodimer) band intensities are depicted with standard deviation (n=9). Individual data points are shown as gray jitter plots. Tukey multiple comparisons of means was performed to assess significance (*** p &lt; 0.001, ** p &lt; 0.01, * p &lt; 0.05, p &gt; 0.05 n.s.). Compare to Fig. EV1D and EV3D."
NCBI gene IDs:
"Oct6: 18991
Oct4: 18999"
Figure legend: "D. GFP-positive colonies of mouse iPSCs generated by Oct4 mutants in combination with Sox2, Klf4, and c-Myc. Colonies were imaged 16 days after second viral infection, using a fluorescence microscope. Scale bars: 250 μm; objective 10x."
NCBI gene IDs:
"Klf4: 16600
c-Myc: 17869
Oct4: 18999
Sox2: 20674"
Figure legend: "B. Oct4-GFP-positive colonies of two O6SKM iPSC lines, expanded from single colonies of pluripotent cells that were generated by the contribution of the synthetic Oct6 molecule (Oct67K,22T,LinkO4,151S). Scale bars: 250 μm."
NCBI gene IDs:
"Oct6: 18991"
Figure legend: "C. Genotyping of two O6SKM iPSC lines. Two stable lines of iPSCs generated with the Oct6, Sox2, Klf4, and c-Myc retroviral set are positive for these four transgenes but negative for the Oct4 transgene. OSKM iPSCs and OG2-MEFs were used as PCR controls."
NCBI gene IDs:
"Klf4: 16600
c-Myc: 17869
Oct6: 18991
Oct4: 18999
Sox2: 20674"
Figure legend: "F. Bisulfite sequencing of genomic Oct4, Nanog, and Col1a1 promoter regions of O6SKM iPSCs, OSKM iPSCs, and OG2-MEFs. White and black circles represent unmethylated and methylated CpG sites, respectively."
NCBI gene IDs:
"Col1a1: 12842
Nanog: 71950
Oct4: 18999"
Figure legend: "B) Baseline QT interval (top), baseline RR interval (middle), and baseline QT interval corrected with the Bazett's formula (bottom). Bar graphs are divided by isogenic pairs (LQT1R594Q and JLNSR594Q, left; LQT2corr, LQT2N996I, hESCWT, and hESC-LQT2N996I, middle; LQT1corr and LQT1R190Q, right) and in each graph the unrelated WT is shown as a comparison. N: 17-53. * = p&lt;0.05. The colour of the symbol indicates comparisons and relative statistical significance."
NCBI gene IDs:
"JLNS: 3753
LQT2: 3757
LQT1: 3784"
Figure legend: "A) Representative MEA trace (left) showing the effect of increasing concentrations of LUF7346 on FP contour, measured in LQT2N996I-CMs. Average data (right) showing the effect of LUF7346 on QT interval duration relative to baseline in CMs derived from all the hiPSC lines used in this study. * = p&lt;0.05 vs baseline. Colour in the heatmap defines the magnitude of QT shortening (blue) after treatment with increasing concentrations of LUF7346. N: 7-14."
NCBI gene IDs:
"LQT2: 3757"
Figure legend: "B) Representative AP from LQT2corr-, LQT2N996I-, LQT1corr-, and LQT1R190Q-CMs paced at 1 Hz, under baseline conditions (black) and after application of increasing concentrations of LUF7346 (colour-code is shown)."
NCBI gene IDs:
"LQT2: 3757
LQT1: 3784"
Figure legend: "C) Effect of LUF7346 on APD90, APD70, and APD50, measured in LQT2corr- (blue), LQT2N996I- (green), LQT1corr- (purple), LQT1R190Q- (dark blue) paced at 1 Hz; * = p&lt;0.05 vs baseline. The colour of the asterisk indicates comparisons and respective statistical significance. ° = p&lt;0.05 vs the genetically-matched corrected control. # = p&lt;0.05 LQT1corr vs LQT2corr. N: 12-15."
NCBI gene IDs:
"LQT2: 3757
LQT1: 3784"
Figure legend: "D) Effect of LUF7346 on APA and Ediast, measured in LQT2corr- (blue), LQT2N996I- (green), LQT1corr- (purple), and LQT1R190Q-CMs (dark blue) paced at 1 Hz. N: 12-15."
NCBI gene IDs:
"LQT2: 3757
LQT1: 3784"
Figure legend: "A) Representative MEA trace (left) showing the effect of 100 nM AST and increasing concentrations of LUF7346 in the presence of AST on FP contour, measured in LQT1R594Q-CMs. Average data (right) of the effect of AST and LUF7346 in the presence of AST on QT interval duration compared to baseline in CMs derived from all the hiPSC lines used in this study. * = p&lt;0.05 vs respective baseline. ° = p&lt;0.05 vs AST. Colour in the heatmap defines the magnitude of QT prolongation (red) and QT shortening (blue), respectively, after treatment with AST and with increasing concentrations of LUF7346 in the presence of AST. N: 5-10."
NCBI gene IDs:
"LQT1: 3784"
Figure legend: "B) Representative AP from WT-, LQT1R594Q- and JLNSR594Q-CMs, paced at 1 Hz, under baseline conditions (black), after application of 100 nM AST (red), and after addition of increasing concentrations of LUF7346 in the presence of AST (colour-code is shown)."
NCBI gene IDs:
"JLNS: 3753
LQT1: 3784"
Figure legend: "C) Effect of AST and LUF7346 in the presence of AST on APD90, APD70, and APD50 in WT- (grey), LQT1R594Q- (red) and JLNSR594Q-CMs (black) paced at 1 Hz. * = p&lt;0.05 vs respective baseline; ° = p&lt;0.05 vs AST. N: 11-16."
NCBI gene IDs:
"JLNS: 3753
LQT1: 3784"
Figure legend: "D) Effect of AST and LUF7346 in the presence of AST on APA and Ediast in WT- (grey), LQT1R594Q- (red) and JLNSR594Q-CMs (black) paced at 1 Hz. N: 11-16."
NCBI gene IDs:
"JLNS: 3753
LQT1: 3784"
Figure legend: "A: Representative AP traces measured in JLNSR594Q-CMs paced at 1 Hz, under baseline conditions (black) and after application of either AST alone (red), AST+LUF7346 3 µM (green) and AST+LUF7346 5 µM (blue)."
NCBI gene IDs:
"JLNS: 3753"
Figure legend: "(A) Detection of VgpA in supernatants from indicated strains by immunoblotting (IB) with anti-VgpA antisera."
NCBI gene IDs:
"VgpA: "
Figure legend: "(B) T3SS2 translocation of VgpA into Caco-2 cells using CyaA-based assay; VopV is a known T3SS2 effector. Error bars represent mean ± standard deviation (n=3 biologically independent experiments)."
NCBI gene IDs:
"CyaA: 
T3SS2: "
Figure legend: "(C) Localization of translocated VgpA (upper panel) and VgpAL10A (lower panel) during infection."
NCBI gene IDs:
"VgpA: "
Figure legend: " (D) Localization of VgpA (upper panel) or in VgpAL10A (lower panel) in HeLa cells after transfection. EBP2 was detected with anti-EBP2 antibody (red), VgpA and VgpAL10A were detected with anti-VgpA sera (green) and nuclei were stained with DAPI (blue). White arrows indicate co-localization of EBP2 and VgpA (upper panel). VgpAL10A localizes primarily to the nucleoplasm (white arrow, lower panel)."
NCBI gene IDs:
"VgpA: "
Figure legend: " (B) Fluorescence micrographs of Caco-2 cells transfected with siRNA targeting EBP2 (siEBP2) or control siRNA (siNC) and subsequently infected with vopZ'ΔvscN1. Cells were stained with anti-BrdU antibody (green) and DAPI (blue). "
NCBI gene IDs:
"vopZ: 
vscN1: 
EBP2: 10969"
Figure legend: " (D) The percentage of BrdU+ cells was analyzed as above for cells treated with siNC or siEBP2. Error bars represent mean ± standard deviation (n=3 biologically independent experiments). Two-way ANOVA was used for statistical analysis. *P&lt;0.05 (when compared to siNC-transfected cells that are infected with vopZ'ΔvscN1). "
NCBI gene IDs:
"vopZ: 
vscN1: 
EBP2: 10969"
Figure legend: " (E) Immunoblot of EBP2 and Actin in Caco-2 cells transfected with siEBP2 or siNC. "
NCBI gene IDs:
"EBP2: 10969"
Figure legend: " (A) Localization of c-Myc in uninfected Caco-2 cells (first row), Caco-2 cells infected with V. parahaemolyticus vopZ'ΔvscN1 (wild type VgpA, second row), Caco-2 cells infected with vopZ'ΔvscN1vgpA' (third row), Caco-2 cells infected with vopZ'ΔvscN1vgpA':pvgpA (fourth row) and Caco-2 cells infected with vopZ'ΔvscN1vgpA':pvgpAL10A (fifth row). Fixed cells were stained with DAPI (blue), and anti-EBP2 (red), and anti c-Myc (green) antibodies. White arrows are examples indicating the co-localization of EBP2 and c-Myc. "
NCBI gene IDs:
"VgpA: 
vgpA: 
vopZ: 
vscN1: "
Figure legend: " (B) Amounts of rRNA in uninfected or infected Caco-2 cells transfected with control (siNC) or EBP2-targeting (siEBP2) siRNAs. *P&lt;0.05 (when compared to the siNC-transfected cells that are infected with vopZ'ΔvscN1). "
NCBI gene IDs:
"vopZ: 
vscN1: 
EBP2: 10969"
Figure legend: " (C) Amounts of RNA polymerase I (POLR1A) were from uninfected Caco-2 cells or cells infected with indicated strains. *P&lt;0.05 (when compared to the uninfected Caco-2 cells). "
NCBI gene IDs:
"POLR1A: 25885"
Figure legend: " (A) VgpA (upper panel: animals infected with WT) and VgpAL10A (lower panel: animals infected with vgpAL10A) localization in intestinal epithelial cells of infected animals. Arrows in upper panel indicate VgpA localized as punctae in the nucleus; the arrow in the lower panel indicates VgpAL10A localized diffusively in the nucleoplasm. "
NCBI gene IDs:
"VgpA: 
vgpA: "
Figure legend: " (B) VgpA and VgpAL10A interactions with EBP2 in intestinal epithelial cells isolated from infant rabbits infected with WT or vgpAL10A V. parahaemolyticus. Inputs represent proteins detected in intestinal epithelial cells of uninfected rabbits or rabbits infected with the indicated strains. Outputs represent eluates from protein A/G beads cross-linked with anti-EBP2 (IP: anti-EBP2) or anti-VgpA (IP: anti-VgpA) antibodies and analyzed with anti-VgpA and anti-EBP2 antibodies. "
NCBI gene IDs:
"vgpA: "
Figure legend: " (D) Eighteen hours after infant rabbits were infected with WT (middle panel) or vgpAL10A (lower panel) V. parahaemolyticus, fixed sections from the small intestine were stained with antibodies to c-Myc (green), EBP2 (red), and DAPI (blue). Uninfected rabbits were processed similarly and were included as a control (upper panel). White arrows indicate co-localization of c-Myc and EBP2 (middle panel). "
NCBI gene IDs:
"vgpA: "
Figure legend: "(B) Boxplots summarizing the expression of INHBB, TGFB1 and TGFB3 ligands of the TGFβ/Activin pathway in the different groups of MB (blue WNT, red SHH, yellow Group 3 and green Group 4) and in fetal and adult cerebellum (grey) in the dataset of \"Data ref: Cavalli et al, 2017\". Wilcoxon rank-sum tests were performed to determine p-values for panel B. p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001, ****p &lt; 0.0001."
NCBI gene IDs:
"INHBB: 3625
TGFB1: 7040
TGFB3: 7043"
Figure legend: "(D) RT-qPCR were performed on RNA extracted from non-Group 3 (blue) and Group 3 (yellow) MB cell lines to compare expression levels of INHBB (left) and TGFB3 (right). The p-values were determined by unpaired t-test. *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001, ****p &lt; 0.0001. Bars represent the mean ± SD. Number of replicates is n≥3."
NCBI gene IDs:
"INHBB: 3625
TGFB3: 7043"
Figure legend: "(D) RT-qPCR were performed on total RNA extracted from 1603MED cells 48 hours after transfection with siRNA targeting INHBB. Relative INHBB expression was assessed. siCTRL condition was set at 1. The p-values were determined by unpaired t-test. *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001. Bars represent the mean ± SD. Number of replicates is n≥3."
NCBI gene IDs:
"INHBB: 3625"
Figure legend: "The level of phosphorylated Smad2 (P-Smad2) and total Smad2 (Smad2) was assessed by immunoblotting and β-actin was used as a loading control. Lower bar graphs show WB quantification of P-Smad2 (P-S2) normalized to β-actin. (E) 1603MED cells were transfected with the indicated control siRNA (siCTRL, blue) or targeting INHBB (siINHBB, red). Lysates were prepared 48 hours after transfection. Lower bar graphs represent the quantification of the relative level of P-Smad2 (P-S2) to β-actin. The p-values were determined by unpaired t-test. *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001. Bars represent the mean ± SD. Number of replicates is n≥3."
NCBI gene IDs:
"INHBB: 3625"
Figure legend: "(F) Growth curve of 1603MED cells after transfection with either siCTRL (blue) or siINHBB (red). The p-values were determined by unpaired t-test. *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001."
NCBI gene IDs:
"INHBB: 3625"
Figure legend: "(A) Ranking of top genes whose expression is correlated with INHBB in Group 3 MB patient samples. Spearman's rank correlation coefficient ρ and p-value are indicated. The p-values were determined by Spearman rank correlation test *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001."
NCBI gene IDs:
"INHBB: 3625"
Figure legend: "(C) Scatter plot of INHBB and PMEPA1 gene expression levels in all MB groups. Colored dots represent each patient samples and colors represent the MB groups (WNT in blue, SHH in red, Group 3 in yellow and Group 4 in green). The p-values were determined by Spearman rank correlation test *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001."
NCBI gene IDs:
"INHBB: 3625
PMEPA1: 56937"
Figure legend: "Immunoblot analysis of PMEPA1 levels in 1603MED (G) cells 48 hours after transfection with either siCTRL (blue) or siPMEPA1 (red). Bar graphs on the right represent the quantification of the relative level of PMEPA1 protein level normalized to β-actin. The p-values were determined by unpaired t-test *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001. Bars represent the mean ± SD. Number of replicates is n≥3."
NCBI gene IDs:
"PMEPA1: 56937"
Figure legend: "Growth curves of 1603MED (H) cells after transfection with either siCTRL (blue) or siPMEPA1 (red). The p-values were determined by two-way ANOVA *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001."
NCBI gene IDs:
"PMEPA1: 56937"
Figure legend: "Immunoblot analysis of PMEPA1 levels in D283 (I) cells 48 hours after transfection with either siCTRL (blue) or siPMEPA1 (red). Bar graphs on the right represent the quantification of the relative level of PMEPA1 protein level normalized to β-actin. The p-values were determined by unpaired t-test *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001. Bars represent the mean ± SD. Number of replicates is n≥3."
NCBI gene IDs:
"PMEPA1: 56937"
Figure legend: "Growth curves of D283 (J) cells after transfection with either siCTRL (blue) or siPMEPA1 (red). The p-values were determined by two-way ANOVA *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001."
NCBI gene IDs:
"PMEPA1: 56937"
Figure legend: "(B) Expression of INHBB in Group 3 MB cell lines and PDXs relative to HDMB03 (set at 1) by RT-qPCR. Bars represent the mean ± SD. Number of replicates is n≥3."
NCBI gene IDs:
"INHBB: 3625"
Figure legend: "(D) Boxplots representing the expression level of INHBB, PMEPA1, MYC and NRL in the different MB subtypes, as defined in Cavalli et al. (Cavalli et al., 2017). Only p-values corresponding to comparisons between Group 3 subtypes are indicated. Patient samples are colored by subtypes as indicated. (E) Scatter plot of INHBB and PMEPA1, expression levels in Group 3 patient samples. Colored dots represent each patient sample and colors represent the group 3 MB subtypes (α in yellow, β in brown and δ in orange). Wilcoxon rank-sum tests were performed for panel D. Spearman's rank correlation coefficient ρ and p-value are indicated on panel E. *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001 and ****p &lt; 0.0001. Bars represent the mean ± SD. Number of replicates is n≥3."
NCBI gene IDs:
"INHBB: 3625
MYC: 4609
NRL: 4901
PMEPA1: 56937"
Figure legend: "RT-PCR assays towards viral RNA extracted by different pcMNPs-based methods.RT-PCR assays amplifying (A) the ORF1ab region and (B) the N gene in pseudoviral RNA extracted by a manual protocol."
NCBI gene IDs:
"N gene: 43740575
ORF1ab: 43740578"
Figure legend: "RT-PCR assays amplifying the ORF1ab region in pseudoviral RNA extracted by automated protocol, and (B) RT-PCR assays amplifying the N gene in pseudoviral RNA extracted by an automated protocol."
NCBI gene IDs:
"N gene: 43740575
ORF1ab: 43740578"
Figure legend: "RT-PCR assays amplifying the N gene in pseudoviral RNA following the Conventional RT-PCR protocol, and (B) corresponding calibration curve."
NCBI gene IDs:
"N gene: 43740575"