EMBO/SourceData huggingface dataset:
Figure legend: "Analysis of mutant APP  substrates with regards to their effects on the response of GSEC  to the imidazole-based GSM III. Aβ profiles secreted by HEK293T  cells transiently expressing WT or mutant APPC99 substrates in presence of vehicle (DMSO) or 1 µM GSM III were analysed by mass spectrometry (MS). (E) APP  mutation-driven effects on GSEC  processivity according to the Aβ(37+38)/(40+42) ratio are presented as % of the WT condition (mean ± SD). One-way ANOVA followed by Dunnett's post-hoc test with comparison to WT was used to determine statistical significance; ****P &lt; 0.0001. F(DFn, DFd): F (4, 17) = 71.68."
NCBI gene IDs:
"APP: 351"
Figure legend: "(B) Aβ profiles generated by WT or mutant PSEN1  cell lines transduced with APPC99. Dotted lines indicate the levels of Aβ  peptides (%) in WT profiles. Data presented as mean ± SD, N ≥ 3 independent experiments."
NCBI gene IDs:
"APP: 351
PSEN1: 5663"
Figure legend: "(C) Pocket filling PSEN1  V236W and Y106W-V236W substitutions lead to increased Aβ(37+38)/(40+42) ratio, indicating the activation of the sequential GSEC-mediated cleavage of  APPC99. Data presented as mean ± SD, N ≥ 3 independent experiments."
NCBI gene IDs:
"PSEN1: 5663"
Figure legend: "(D)  Aβ profile  analysis in  dose-response experiments for  GSM III revealed no modulation of the PSEN1  V236W mutant cell line. Data are presented as mean ± SD, N = 2 independent experiments. For comparison purposes, WT and V236W mutant Aβ profiles are presented in panel 6B."
NCBI gene IDs:
"PSEN1: 5663"
Figure legend: "(E) GSEC  activity  assay using purified GSEC  and an APP-based fluorogenic peptide as substrate Upper panel: In the non-cleaved state the Dpn  (2,4-dinitrophenyl) quencher group suppresses fluorescent emission from the Nma  (N-methyl-o-aminobenzoic acid) fluorophore through  Förster resonance energy transfer (FRET). Upon GSEC  cleavage, the Nma  group emits at λ = 430 nm a fluorescent signal upon excitation at λ = 355 nm. Lower panel: Specific activities for the purified WT or mutant GSECs   (bearing the indicated substitutions in PSEN1) treated with DMSO  (vehicle), 10 µM GSMIII or GSM II. Data are normalized to the WT GSEC  activity in DMSO  (vehicle). Data are shown as mean ± SD, N ≥ 3 independent experiments. Significance is shown for meaningful comparisons; two-way ANOVA with comparison to WT was used to determine statistical significance; **P &lt; 0.01, ***P &lt; 0.001, ****P &lt; 0.0001, ns: not significant."
NCBI gene IDs:
"APP: 351
PSEN1: 5663"
Figure legend: "(F) Transition state analogue inhibitor  L-685,458 (Inhibitor X) treatment of WT, V236W or Y240W mutant PSEN1  cell lines. Inhibitory profiles  and derived IC50 values (table) indicate that the PSEN1-V236W significantly increases the affinity for the inhibitor. Dotted line indicates 50% inhibition. Data presented as mean ± SD, N = 3 independent experiments."
NCBI gene IDs:
"PSEN1: 5663"
Figure legend: "A, A targeted MAPPIT screen identifies several DUBs as putative RAS interactors. A MAPPIT array containing DUB prey library was screened with HRAS G12V as bait. pSEL(+2L)-HRAS G12V was expressed in HEK293T cells together with the indicated prey. BRAF served as a positive control. Each measurement was done in triplicate. The results are expressed as a mean of normalized luciferase activity (leptin-treated cells vs leptin-untreated cells). The overall mean value + 2 s.d. served as a threshold."
NCBI gene IDs:
"BRAF: 673
HRAS: 3265
RAS: 3265"
Figure legend: "B, MAPPIT assay confirms the interaction between OTUB1 and RAS proteins. pSEL(+2L) vectors coding RAS proteins were expressed in HEK293T cells together with the indicated prey. Empty vector and two random baits, MAL and eDHFR, were used as negative controls. REM2 and EFHA1 preys that bind to the bait receptor itself was used to evaluate expression of the RAS baits. The results are expressed as a mean of normalized luciferase activity ± s.e.m (leptin-treated cells vs leptin-untreated cells), n=3."
NCBI gene IDs:
"eDHFR: 1719
RAS: 3265
MAL: 4118
EFHA1: 221154
REM2: 161253"
Figure legend: "C, NRAS Q61K mutant co-immunoprecipitates with OTUB1. At 48 hours post-transfection with Flag-tagged NRAS Q61K and HA-tagged OTUB1 expression constructs, HA-tagged OTUB1 was immunoprecipitated with anti-HA-agarose followed by immunoblotting using anti-Flag or anti-HA antibodies."
NCBI gene IDs:
"NRAS: 4893
OTUB1: 55611"
Figure legend: "D, OTUB1 interacts with wt NRAS and active NRAS mutant. Flag-tagged NRAS proteins were immunoprecipitated using anti-Flag (M2) agarose from HEK293T cells overexpressing HA-tagged OTUB1 or empty vector (V)."
NCBI gene IDs:
"NRAS: 4893
OTUB1: 55611"
Figure legend: "E, GTP binding does not affect the complex formation between NRAS and OTUB1. Recombinant Flag-tagged NRAS was incubated with lysates derived from HEK293T cells expressing HA-tagged OTUB1 in the excess of GTP-γ-S or GDP, followed by immunoblotting with the indicated antibodies."
NCBI gene IDs:
"NRAS: 4893
OTUB1: 55611"
Figure legend: "F, OTUB1 interacts with wt KRAS. Flag-tagged KRAS was immunoprecipitated using anti-Flag (M2) agarose from HEK293T cells overexpressing HA-tagged OTUB1 or empty vector (V). C, D, E, F, Immunoprecipitates, IP. Whole cell lysate, WCL."
NCBI gene IDs:
"KRAS: 3845
OTUB1: 55611"
Figure legend: "G, OTUB1 co-localizes with KRAS at the plasmamembrane. At 24 hours after co-transfection with GFP-tagged KRAS and HA-tagged OTUB1, HeLa cells were immunostained with anti-HA antibody. The outlined areas are shown at higher magnification at the top of each image. Scale bar, 10 micron."
NCBI gene IDs:
"KRAS: 3845
OTUB1: 55611"
Figure legend: "A, Suppression of OTUB1 expression increases NRAS mono- and di-ubiquitination. 6xHis-tagged ubiquitin and Flag-NRAS were introduced into HEK293T cells expressing shGFP or shRNAs against OTUB1. Ubiquitinated NRAS was purified by Co2+ metal affinity chromatography and detected by anti-Flag antibody."
NCBI gene IDs:
"GFP: 
NRAS: 4893
OTUB1: 55611"
Figure legend: "B, C, D, Catalytic activity of OTUB1 is not required to inhibit RAS ubiquitination. 6xHis-tagged ubiquitin and RAS expression constructs were introduced into HEK293T cells expressing wt HA-OTUB1, the catalytically dead mutant HA-OTUB1 C91S, or empty vector (V). Ubiquitinated RAS was purified by Co2+ metal affinity chromatography and detected by anti-Flag antibody."
NCBI gene IDs:
"RAS: 3265
OTUB1: 55611"
Figure legend: "E, OTUB1 induces membrane RAS re-localization. Confocal imaging of HeLa cells expressing the indicated constructs. For each sample, z-stacks obtained by scanning the sample from the apical to the basal layer. Step-size, 2 micron."
NCBI gene IDs:
"RAS: 3265"
Figure legend: "A, B, OTUB1 overexpression promotes serum-induced activation of endogenous wt RAS (A) or wt NRAS (B). GTP-bound RAS was pulled down from HEK293T cells expressing HA-tagged OTUB1 or empty vector (V) using recombinant RAF1 RBD conjugated to agarose beads. Input was controlled by immunoblotting using anti-panRAS or anti-Flag antibodies"
NCBI gene IDs:
"RAS: 3265
NRAS: 4893
OTUB1: 55611"
Figure legend: "C, D OTUB1 enhances serum-induced ERK1/2 phosphorylation in endogenous wt RAS (C) or wt KRAS (D). Levels of phosphorylated ERK1/2 and total ERK1/2 in HEK293T cells expressing HA-tagged OTUB1 or empty vector (V) were analyzed by Meso Scale assay. The results are expressed as a mean of pERK1/2 levels relative to total ERK1/2 ± s.e.m. n=2."
NCBI gene IDs:
"RAS: 3265
KRAS: 3845
OTUB1: 55611"
Figure legend: " . E, F, Overexpression of wt OTUB1 (E) or the catalytically dead mutant OTUB1 C91S mutant (F) promotes serum-induced MAPK activation in cell expressing wt NRAS. Whole cell lysates were analyzed by immunoblotting using the indicated antibodies. "
NCBI gene IDs:
"NRAS: 4893
OTUB1: 55611"
Figure legend: "G, H, Overexpression of OTUB1 has no effect on serum-induced MAPK activation in cell expressing mutant NRAS Q61K or KRAS G12V. Whole cell lysates were analyzed by immunoblotting using antibodies as indicated. A,B,C,D,E,F,G,H Serum-starved HEK293T cells expressing the indicated constructs were stimulated with 10% serum for the indicated time periods."
NCBI gene IDs:
"KRAS: 3845
NRAS: 4893
OTUB1: 55611"
Figure legend: "I, Immunoblot of OTUB1 overexpression in immortalized human embryonic kidney epithelial cells (HEK TEST), expressing empty vector (V), myristoylated AKT1 (myr-AKT), MEK1 D218,D222 mutant (MEKDD)."
NCBI gene IDs:
"AKT: 207
AKT1: 207
MEK1: 5604"
Figure legend: "J, K, OTUB1 cooperates with active AKT1 to promote anchorage-independent growth. Representative images of soft-agar colonies formed by HEK TEST cells expressing the indicated constructs. The number of soft agar colonies formed by cells expressing OTUB1 compared to cells expressing an empty vector. Data are presented as mean ± s.e.m. p-values were determined by two-sided t-Test, n=2."
NCBI gene IDs:
"AKT1: 207
OTUB1: 55611"
Figure legend: "B,C, OTUB1 overexpression in TCGA lung carcinomas is associated with 11q13.1 copy number alteration. Pearson correlation of OTUB1 copy number (log2 ratio) with OTUB1 mRNA levels (RNAseq normalized read counts, log2 transformed) was analyzed."
NCBI gene IDs:
"OTUB1: 55611"
Figure legend: "D,E,F, OTUB1 expression in TCGA lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (SCC) patients. Patients were stratified according to their OTUB1 mRNA levels and/or their KRAS status as described in Materials and Methods. Box whisker plots represent OTUB1 mRNA expression levels in TCGA lung carcinoma patients determined by RNAseq analysis. p-values were determined by two-sided t-Test. Total number of patients, n."
NCBI gene IDs:
"KRAS: 3845
OTUB1: 55611"
Figure legend: "G, Gain of 11q13.1 locus is an early event in lung adenocarcinoma development. TCGA lung adenocarcinoma patients with diploid or gain of the OTUB1 locus were stratified according tumor stages (T1-T4). Total numbers of patients, n. Statistical comparison of the sample distributions were compared using Chi-square test."
NCBI gene IDs:
"OTUB1: 55611"
Figure legend: "H, OTUB1 mRNA overexpression is an early event in lung adenocarcinoma development. TCGA lung adenocarcinoma patients were stratified by tumor stages (T1-T4) and OTUB1 expression levels as described in Materials and Methods. Total numbers of patients, n. Statistical comparison of the sample distributions were compared using Chi-square test."
NCBI gene IDs:
"OTUB1: 55611"
Figure legend: "I, KRAS mutation is a late event in lung adenocarcinoma progression. TCGA lung adenocarcinoma patients with different KRAS mutation status were stratified by tumor stages (T1-T4). Total numbers of patients, n. Statistical comparison of the sample distributions were compared using Chi-square test."
NCBI gene IDs:
"KRAS: 3845"
Figure legend: ", Suppression of OTUB1 expression in NSCLC cell lines by specific shRNAs against OTUB1 was confirmed by immunoblotting using antibody against OTUB1."
NCBI gene IDs:
"OTUB1: 55611"
Figure legend: "B, OTUB1 suppression decreases serum-induced ERK1/2 phosphorylation. Serum-starved A549 cells expressing shRNAs against OTUB1 or GFP were stimulated with 10% serum for the indicated time periods. Levels of phosphorylated ERK1/2 and total ERK1/2 were analyzed by Meso Scale assay. The results are expressed as a mean of pERK1/2 levels relative to total ERK1/2 ± s.e.m; p-values were determined by two-sided t-Test, n=2."
NCBI gene IDs:
"OTUB1: 55611"
Figure legend: "C, D, OTUB1 suppression impairs the anchorage-independent growth of Western blot cancer cell lines. Representative images of soft-agar colonies formed by Western blot cells expressing shRNAs against OTUB1 or GFP. The number of soft agar colonies formed by cells expressing shOTUB1 compared to cells expressing shGFP. Data are presented as mean ± s.e.m. p-values were determined by two-sided t-Test, n=3."
NCBI gene IDs:
"OTUB1: 55611"
Figure legend: "C, D, OTUB1 suppression impairs the anchorage-independent growth of lung cancer cell lines. Representative images of soft-agar colonies formed by lung cells expressing shRNAs against OTUB1 or GFP. The number of soft agar colonies formed by cells expressing shOTUB1 compared to cells expressing shGFP. Data are presented as mean ± s.e.m. p-values were determined by two-sided t-Test, n=3."
NCBI gene IDs:
"OTUB1: 55611"
Figure legend: "E, Xenograft tumor growth of A549 cells expressing shRNAs against GFP or OTUB1 subcutaneously injected into nude mice. p-value was determined by 2-way ANOVA."
NCBI gene IDs:
"OTUB1: 55611"
Figure legend: "A, OTUB1 overexpression promotes serum-induced MAPK activation in wt KRAS H1993 lung adenocarcinoma cells."
NCBI gene IDs:
"KRAS: 3845
OTUB1: 55611"
Figure legend: "B, OTUB1 overexpression does not affect serum-induced MAPK activation in mutant KRAS A549 lung adenocarcinoma cells. A,B, Serum-starved lung cells expressing Flag-OTUB1 or an empty vector (V) were stimulated with 10% serum for the indicated time periods. Whole cell lysates were analyzed by immunoblotting using antibodies against pERK1/2, ERK1/2, Flag and vinculin."
NCBI gene IDs:
"KRAS: 3845
OTUB1: 55611"
Figure legend: "C, Representative immunoblots of Flag-tagged OTUB1 overexpression in lung adenocarcinoma cell lines"
NCBI gene IDs:
"OTUB1: 55611"
Figure legend: "D, E, OTUB1 overexpression affects anchorage-independent growth of lung adenocarcinoma cell lines. Representative images of soft-agar colonies formed by the indicated cells expressing Flag-OTUB1 or empty vector (V). The number of soft agar colonies formed by OTUB1 expressing cells compared to cells expressing an empty vector. Data are presented as mean ± s.e.m. p-values were determined by two-sided t-Test, n=3."
NCBI gene IDs:
"OTUB1: 55611"
Figure legend: "F,G, Xenograft tumor growth of A549, H1993 or H1437 cells expressing Flag-OTUB1 or an empty vector (V) subcutaneously injected into nude mice. p-values were determined by 2-way ANOVA."
NCBI gene IDs:
"OTUB1: 55611"
Figure legend: "B, OTUB1 expression in lung non-small cell carcinomas with different KRAS mutation status. OTUB1 expression was assessed in TMA samples by IHC."
NCBI gene IDs:
"KRAS: 3845"
Figure legend: "E, OTUB1 levels correlates with increased levels of phosphorylated-ERK1/2 in wt KRAS lung adenocarcinomas. Association between OTUB1 and pERK1/2 expression levels was assessed in the same tumor samples by IHC."
NCBI gene IDs:
"KRAS: 3845"
Figure legend: "G, Wt KRAS lung adenocarcinoma TCGA patients with medium OTUB1 expression have poorer overall survival."
NCBI gene IDs:
"KRAS: 3845
OTUB1: 55611"
Figure legend: " H, OTUB1 expression levels are not associated with survival rate of KRAS-mutant lung adenocarcinoma TCGA patients. G,H, Patients were stratified according to their OTUB1 mRNA levels and/or their KRAS status as described in Materials and Methods. Overall survival of lung adenocarcinoma patients expressing different levels of OTUB1 mRNA as measured by Kaplan-Meier curves. p-values were determined by Log Rank Test. "
NCBI gene IDs:
"KRAS: 3845
OTUB1: 55611"
Figure legend: "(F-G) (F) NIH-3T3  cells were transiently transfected with either pEGFP or pEGFP-PPE2. After 24 hours of transfection, cells were fixed and observed under a confocal microscope. DAPI  was used to stain  the nucleus. (G) Nuclear localization  of rPPE2  was measured by calculating colocalization  coefficient. Data information: Data represent Mean ± SEM of more than 50 cells of three independent experiments. For Figure G, unpaired t-test was applied to calculate p values."
NCBI gene IDs:
"EGFP: 
PPE2: 886684"
Figure legend: "(E) Varying concentrations of rPPE2 protein were incubated with [γ-32P]-ATP  oligonucleotides of 60 bp spanning SCF  promoter.  DNA-protein  complexes were resolved on 7% native polyacrylamide  gel. In cold  competition reactions, equimolar cold/unlabeled 60 bp oligonucleotides were used (arrow represents PPE2-oligo complex). The data shown are representative of 3 independent experiments."
NCBI gene IDs:
"SCF: 17311"
Figure legend: "(E) H4K20me1 (blue) and H3K27me3 (red) accumulation across the Xi after 12 h of DOX treatment. The black line is a locally estimated scatterplot smoothing (LOESS) regression on all 10-kb windows (dots). Below each plot shown is the Xist locus (green bar) and Xist entry sites (black bars)."
NCBI gene IDs:
"Xist: 213742"
Figure legend: "(A) Genome browser tracks showing H3K27me3 (top) and H4K20me1 (bottom) accumulation at a gene silenced rapidly (Rnf12) or more slowly (Pgk1). Allele-specific tracks were overlaid (B6 in red and Cast in blue). Note strong H4K20me1 bi-allelic pre-marking at gene bodies."
NCBI gene IDs:
"Pgk1: 18655
Rnf12: 19820"
Figure legend: "(B) Representative image of IF/RNA FISH for Xist RNA and H4K20me1 in cells expressing XistFL or XistΔBC. Arrowheads point to the Xist RNA domains. Scale bar = 5 μm."
NCBI gene IDs:
"Xist: 213742"
Figure legend: "(C) Graph represents the mean % +/- StDev of Xist RNA domains enriched for H4K20me1 (left) or H3K27me3 (right) in cells expressing XistWT or XistΔBC. Shown are averages from at least 2 independent experiments; minimum of 50 Xist RNA domains were counted per experiment; only P-values corresponding to significant differences from unpaired Student's t-test comparing mutants to Xist FL are indicated as * (P-value &lt; 0.05). Data for H3K27me3 was extracted from published data (Bousard et al., 2019)."
NCBI gene IDs:
"Xist: 213742"
Figure legend: "B Body  weight of Uqcrh -/- mice and wild-type littermates at 1-2 weeks (n = 5 to 10), during the post-weaning period from 5-6 weeks of age (n = 3 to 7) and weekly from 6 to 10 weeks (n = 13 to 66), data are shown as mean ± SD. **** p &lt; 0.0001, 2-Way ANOVA, from 7.5wk of age  for Uqcrh-/- males  and  females versus sex-matched controls. Data are shown as single data points and median, or categorical data, males and  females pooled, since genotype-related effects were comparable for both sexes from different cohorts. * p &lt; 0.05, *** p &lt;0.001, Wilcoxon rank-sum test."
NCBI gene IDs:
"Uqcrh: 66576"
Figure legend: "C, D Clinical chemistry plasma concentrations of parameters related to acid-base balance (Lactate and Ammonia) and metabolic state (Glucose) n = 15 Uqcrh-/- and 16 WT pups 1-2-week-old (C); n = 15 f, 15 m  Uqcrh-/- and 15 f,15 m WT mice aged 8-9 weeks (D); sex not differentiated. Data shown as scatter dot plots with line at median. * p &lt; 0.05, ** p &lt; 0.01, **** p &lt; 0.0001, Wilcoxon rank sum test."
NCBI gene IDs:
"Uqcrh: 66576"
Figure legend: "F Measures related to  behaviour  and  neurological function, data generated by the SHIRPA (9 weeks old, F), n = 7f, 8m Uqcrh-/- and 8f, 9m WT animals. Prepulse inhibition   of the acoustic startle as a parameter associated with sensorimotor gating (10 weeks, E right panel), n = 7 f/5 m Uqcrh-/- and 8 f/ 9 m WT mice. Sex is not differentiated. Data are shown as scatter dot plots with a line representing the median. *** p &lt; 0.001, **** p &lt; 0.0001, Wilcoxon rank-sum test."
NCBI gene IDs:
"Uqcrh: 66576"
Figure legend: "G Parameters related to  heart  function generated by  Echocardiography (ECHO) and Electrocardiography  (ECG), n = 15 f, 15 m Uqcrh-/- and 15 f, 15 m WT mice, 6 weeks old."
NCBI gene IDs:
"Uqcrh: 66576"
Figure legend: "A Respiratory chain  enzyme activities from  human control (green) and patient (red)  fibroblasts. Mean activities of controls (n = 8) are set to 100% and error bars represent 1 standard deviation. Data are normalised to citrate synthase (CS) activity. B Respiratory chain enzyme activities in  heart,  brain and  liver, of wild-type and  Uqcrh-/- mice. Data are normalised to  citrate synthase  (CS) activity. Values are given as mean ± SD, n = 4 WT, 5 Uqcrh-/- (Heart), 3 WT, 3 Uqcrh-/- (Brain), 1 WT and 2 Uqcrh-/- (Liver). * p &lt; 0.05, **** p &lt; 0.0001, 2-way ANOVA (Multiple comparison). "
NCBI gene IDs:
"Uqcrh: 66576"
Figure legend: "F Immunohistochemical staining of UQCRC2 was performed on  liver,  heart and kidney derived from wild-type and Uqcrh-/- mice at 9 weeks of age. Staining of VDAC1/porin was also carried out G Graphs indicate score values of immunohistochemical staining intensity of both VDAC1/porin  and UQCRC2. Data are given as mean ± SEM. * p &lt; 0.05; n = 3, Student's t-test (unpaired samples)."
NCBI gene IDs:
"Uqcrh: 66576"
Figure legend: "A  Western blot  analysis of control (n = 2, C1-2) and patient fibroblasts  transduced with a lentiviral vector (pLVX) containing wild-type UQCRH. Expression of wild-type UQCRH was induced using various concentrations of doxycycline (dox) up to 20 ng/ml for 72 hours. B BN-PAGE analysis of control (n = 2, C1-2) and  patient fibroblasts  transduced with a lentiviral vector (pLVX) containing wild-type UQCRH. Transduced fibroblasts were either uninduced or induced with 20 ng/ml doxycycline (dox) for 72 hours. "
NCBI gene IDs:
"UQCRH: 7388"
Figure legend: "C Immunofluorescence for UQCRC2 (green), VDAC1/porin (red) and nuclei  (DAPI, blue), in control (NHDF) fibroblasts. D Immunofluorescence for  UQCRC2 (green), VDAC1/porin (red) and  nuclei  (DAPI, blue), in patient fibroblasts. E Immunofluorescence for UQCRC2 (green), VDAC1/porin (red) and  nuclei  (DAPI, blue), in control (NHDF) fibroblasts  transduced with wild-type UQCRH. F Immunofluorescence  for UQCRC2 (green), VDAC1/porin (red) and  nuclei  (DAPI, blue), in  patient fibroblasts  transduced with wild-type (WT) UQCRH. G Immunofluorescence for UQCRC2 (green), VDAC1/porin (red) and nuclei  (DAPI, blue), in control (NHDF) fibroblasts transduced with the pseudogene UQCRHL. H Immunofluorescence for UQCRC2 (green), VDAC1/porin (red) and nuclei  (DAPI, blue), in patient fibroblasts transduced with the pseudogene UQCRHL. I Graph indicates the staining intensity of  UQCRC2 in control (NHDF) fibroblasts (green) and patient fibroblasts  (red), those respective cell lines transduced (T) with wild-type UQCRH (diagonal lines) and those cell lines transduced with the pseudogene UQCRHL (vertical lines) measured using Image J, Data are given as mean ± SEM. One-way ANOVA (Kruskal-Wallis test), * p &lt; 0.05; n = 3 macroscopic field (10-14 cells for macroscopic field were measured). "
NCBI gene IDs:
"UQCRH: 7388
UQCRHL: 440567"
Figure legend: "heart tissue from wild-type (WT) and Uqcrh-/- mice  were solubilised with  digitonin and separated on native gradient gels. F BN-PAGE gel stained  with Coomassie (left) and NADH:NTB reductase activity stain  (right) showing molecular weight marker (BHM) and heart  tissue samples from wild-type (WT) and Uqcrh-/- mice. G BN-PAGE and immunoblot using the antibody to CIII  subunit UQCRC2 in heart  tissue samples from wild-type (WT) and Uqcrh-/- mice. H Further  complexome analysis of the BN-PAGE gels shown in F, shown here are average IBAQ values of subunits from complexes III, I and IV "
NCBI gene IDs:
"Uqcrh: 66576"
Figure legend: "I Profile of complex III (averaged IBAQ values) in wild-type (+/+, solid line) and Uqcrh-/- (-/-, dashed line) heart  tissue. J Profile of complexes III (red), I (yellow) and IV (green) to visualise and assess supercomplex composition and stability in wild-type (+/+, solid line) and Uqcrh-/- (-/-, dashed line) heart tissue. "
NCBI gene IDs:
"Uqcrh: 66576"
Figure legend: "Flow cytometry analysis of H-2Kb surface expression on splenocytes derived from C57BL/6 wild type (left side) or LMP7-/- (right side) mice treated with vehicle (DMSO), ONX 0914 (300 nM), PRN1126 (300 nM), ML604440 (300 nM), LU-001i (300 nM), PRN1126+ML604440 (300 nM each), or PRN1126+LU-001i (300 nM each) overnight. Unstained splenocytes were used as negative control. Pooled data from three independent experiments (n=9) are shown as the means of median fluorescent intensity ± SEM. All data were statistically compared to the DMSO treated group. **P &lt; 0.01, ***P &lt; 0.001. One-way ANOVA."
NCBI gene IDs:
"LMP7: 16913"
Figure legend: "WT and SNX10 KO Caco-2 cells were treated with indicated doses of  OMVs  for 24h. Protein expression of E-cadherin and  SNX10 was determined by immunoblots (A) and quantified by ImageJ software (B) (n = 3 independent experiments). Data information: Data are means ± SD. One-way ANOVA followed by Bonferroni post hoc test was used for statistical analyzes. *p &lt; 0.05; **p &lt; 0.01; ***p &lt; 0.001."
NCBI gene IDs:
"SNX10: 29887"