EMBO/SourceData huggingface dataset:
Figure legend: "The PAF1 foci are dependent on SMC5 and SMC6B. (A) CFP-PAF1 was transfected alone or co-transfected with the RNAi construct of SMC5 (SMC5-Ri) into Col-0 protoplasts. (C) CFP-PAF1 was transfected into the protoplasts of Col-0 or smc6b, respectively. The protoplasts were treated with 20 μM BLE for 2 h before imaging. The percentage of cells with foci. The data were represented as means ± SEM (n = 3 biological replicates). For each sample, at least 32 cells were scored. The statistical significance was determined using two-way ANOVA analysis. **, P &lt; 0.01; ***, P &lt; 0.001."
NCBI gene IDs:
"CFP: 
PAF1: 844312
smc6b: 836267
SMC6B: 836267
SMC5: 831449"
Figure legend: "(G and H) eChIP-qPCR assays. (G) The SMC5-Ri construct was transfected into the protoplasts of SSDIS/CFP-PAF1 transgenic plants. (H) The 35S:CFP-PAF1 construct was transfected into the protoplasts of SSDIS/smc6b or SSDIS/Col-0 transgenic plants. The protoplasts were treated with 100 μM DEX for 4 h to induce DSBs. The eChIP assays were carried out using an anti-GFP antibody. The immunoprecipitated DNA (eChIP) and the input DNA were subjected to qPCR analysis. The ratios of eChIP and input are shown. UBQ5 serves as a negative control. The data are represented as means ± SD (n = 3 technical replicates). The statistical significance was determined using two-tailed Students' t-test. ns, not significant; ****, P &lt; 0.0001."
NCBI gene IDs:
"CFP: 
PAF1: 844312
smc6b: 836267
SMC5: 831449
UBQ5: 825398"
Figure legend: "(I and J) The UBC2 foci are dependent on VIP5. UBC2-mCherry and/or VIP5-YFP were transfected into the vip5 protoplasts. The protoplasts were treated with 20 μM BLE for 2 h before imaging. Scale bars = 2.5 μm. The data in (J) were represented as means ± SEM (n = 3 biological replicates). For each sample, at least 30 cells were scored. The statistical significance was determined using two-way ANOVA analysis. ****, P &lt; 0.0001. All experiments were repeated at least three times with similar results."
NCBI gene IDs:
"mCherry: 
YFP: 
UBC2: 814805
vip5: 842395
VIP5: 842395"
Figure legend: "(E-J) The HUB1/2 foci are dependent on UBC2. VIP5-CFP, HUB1/2-YFP, and/or UBC2-mCherry were transfected into the ubc1 ubc2-c1 protoplasts. The protoplasts were treated with 20 μM BLE for 2 h before imaging. Bars = 2.5 μm. The data in (F, G, I, and J) were represented as means ± SEM (n = 3 biological replicates). For each sample, at least 60 cells were scored. The statistical significance was determined using two-way ANOVA analysis. ns, not significant; **, P &lt; 0.01."
NCBI gene IDs:
"CFP: 
mCherry: 
YFP: 
HUB1: 819104
ubc1: 838002
UBC2: 814805
ubc2: 814805
VIP5: 842395"
Figure legend: "(I and J) eChIP-qPCR assays. (I) The SSDIS/Col-0 transgenic Arabidopsis was mock-treated or treated with 100 μM DEX for 4 h. (J) The SSDIS/Col-0 and SSDIS/ddrm4-1 transgenic Arabidopsis were treated with 100 μM DEX for 4 h. The eChIP assays were carried out using an anti-H2Bub antibody. The immunoprecipitated DNA (eChIP) and the input DNA were subjected to qPCR analysis. The ratios of eChIP and input are shown. UBQ5 serves as a negative control. The data are represented as means ± SD (n = 3 technical replicates). (I) The data are relative to the values of Mock. (J) The data are relative to the values of UBQ5 in Col-0. The statistical significance was determined using two-tailed Students' t-test. ns, not significant; *, P &lt; 0.05; **, P &lt; 0.01; ***, P &lt; 0.001; ****, P &lt; 0.0001. The experiments were repeated at least twice with similar results."
NCBI gene IDs:
"ddrm4: 844312
UBQ5: 825398"
Figure legend: "B) Histological sections of 3 IDHwt PDXs (P3, T434, P8) and 3 IDHm PDXs ((T394, E478, T186) showing a large ROI (boxed rectangle, &gt;500 pixels) within the tumor area applied for targeted quantification of selected metabolites. Left rectangle in P3 PDX was used as control contralateral brain (CB) for quantifications. Middle panel shows tissue distribution of D-2-hydroxyglutarate (D2HG) by MSI, which is exclusively detected in IDHm PDXs (D2HG in IDHwt tumours is below detection limit). Right panel shows tissue distribution of a key metabolite (m/z 778.51) presenting strong accumulation in IDHm lower grade gliomas (LGG) versus glioblastomas (GBM) independent of IDH status. An intensity-dependent color code indicates the relative amount of a specific compound (defined by m/z value) throughout the tissue section."
NCBI gene IDs:
"IDH: 15926"
Figure legend: "C) Quantification of several high mass metabolites differentially present in IDHm PDXs (IDHwt glioblastomas (GBM) in blue, IDHm GBM in orange, IDHm lower grade gliomas (LGG) in red, contralateral control brain (CB) in grey). Box plots represent log values of metabolite intensities measured within a large ROI (&gt;500 pixels). Many metabolites in this mass range (m/z 700-900) have been putatively assigned to phospholipids (Tables EV2-3). m/z represents the mass over charge ratio of ionized metabolites, as measured by the mass spectrometer. Except where otherwise indicated, statistical significance was calculated for IDHm (n=3) versus IDHwt (n=3) PDXs using T test. pv: p-values."
NCBI gene IDs:
"IDH: 15926"
Figure legend: "A) MALDI imaging of indicated metabolites in IDHwt PDX (P3), IDHm PDX (E478) and control brain (CB). Hex-P: hexose-phosphate; AMP, ADP, ATP: adenosine mono-, di- and triphosphate respectively."
NCBI gene IDs:
"IDH: 15926"
Figure legend: "B) LC-MS quantification of indicated metabolites in 6 PDXs. Relative quantities of metabolites are expressed in log scale and normalized to tissue quantity used for extract preparation. IDHwt glioblastomas (GBM) in blue, IDHm GBM in orange, IDHm lower grade gliomas (LGG) in red, contralateral control brain (CB) in grey. Sdh7-P: sedoheptulose-7-phosphate."
NCBI gene IDs:
"IDH: 15926"
Figure legend: "A) LC-MS quantification of steady-state level of glycolysis and TCA cycle metabolites in three IDH1wt and three IDH1m PDXs and contralateral control brain (CB) (n=3/ sample/ group). Metabolites showing statistically significant group differences between IDH1wt and IDH1m are indicated (pvalue: * &lt;0.05). Color code as in Fig. 1-2."
NCBI gene IDs:
"IDH1: 15926"
Figure legend: "C) In vivo flux analysis of 13C-labelled glucose injected 20 minutes prior to sacrifice in one IDH1wt PDX (P3) and one IDH1m PDX (E478) (n=3/ sample). The percentage of glucose-derived 13C label is shown in selected metabolites containing 0 to 6 13C atoms (13C0 - 13C6 as indicated by color code). Note the absence of 13C2 label of αKG and D2HG in IDHm tumours, while the label was detectable in IDHwt PDX and in contralateral brain of both tumors (lower panel)."
NCBI gene IDs:
"IDH: 15926
IDH1: 15926"
Figure legend: "A) MALDI imaging of key metabolites in IDHwt (P3) and IDHm (E478) glioma PDX, compared to control brain (CB) sections."
NCBI gene IDs:
"IDH: 15926"
Figure legend: "B) Quantification of metabolite distribution by MSI in 6 PDX with IDH1wt and IDH1m status (n=3 / group) and in contralateral control brain (CB). No significant differences between IDH groups were detected, although significant differences are found between tumors and control brain (glutamate, apsartate). Color code as in Fig. 1, NAA: N-acetylaspartic acid; NAAG: N-acetylaspartylglutamic acid."
NCBI gene IDs:
"IDH: 15926
IDH1: 15926"
Figure legend: "A) NADPH levels are reduced in IDHm compared to wildtype tumors, resulting in a reduced NADPH/NAD+ ratio (n=3/ sample). p-value from T test: *&lt;0.05. NADPH, NADP: reduced, oxydized nicotinamide adenine dinucleotide phosphate, NADH, NAD: reduced, oxydized nicotinamide adenine dinucleotide."
NCBI gene IDs:
"IDH: 15926"
Figure legend: "B) MALDI images for glutathione (GSH) and cystathionine on IDHwt (P3) and IDHm (E478) PDXs."
NCBI gene IDs:
"IDH: 15926"
Figure legend: "D) LC-MS quantification of independent samples for GSH, GSSG (oxidized GSH), GSSG/GSH ratio and cystathionine from 6 PDXs (n=3/ sample / group). Statistical significance between IDH groups calculated by T test, pv: p-value."
NCBI gene IDs:
"IDH: 15926"
Figure legend: "A) Comparative gene expression analysis of key enzymes involved in GSH and cysteine synthesis and supply in IDHwt (n=220), IDHm with 1p/19q co-deletion (n=151) or IDHm without 1p/19q co-deletion (n=226) patients based on TCGA RNA-seq data from a cohort of 597 patients. CBS: Cystathionine beta synthase, key enzyme of the transsulfuration pathway. GCLC: catalytic subunit of glutamate-cysteine ligase. SLC7A11: gene encoding xCT, the cystine-glutamate antiporter."
NCBI gene IDs:
"CBS: 875
GCLC: 2729
IDH: 3417
SLC7A11: 23657"
Figure legend: "B) Kaplan-Meier curves of CBS gene expression versus overall survival in patients with IDHwt, IDHm with or without 1p/19q co-deletion. Statistical significance for the survival analysis is shown as: pv: p-value, ns= non significant."
NCBI gene IDs:
"CBS: 875
IDH: 3417"
Figure legend: "(B) Effect of MBCD on total rates of protein degradation, measured as in (A), in wild‐type mouse fibroblasts and in fibroblasts stably RNA interfered for LAMP‐2A (LAMP‐2A(−)). The ratio of degradation in MBCD‐treated and untreated cells is shown for cells maintained with or without 10 mM 3‐methyladenine (3MA)."
NCBI gene IDs:
"LAMP‐2A: 16784"
Figure legend: "(D) The percentage of total lysosomal hLAMP‐2A present in each fraction was determined by densitometric quantification of immunoblots as the ones shown here. Values, corrected for the amount of mLAMP‐2A in each fraction, are mean+s.e. of 3-4 experiments."
NCBI gene IDs:
"LAMP‐2A: 3920"
Figure legend: "(F) Proteolysis of a pool of 3[H]labeled cytosolic proteins by intact (left) or disrupted (right) lysosomes isolated from untransfected mouse fibroblasts (none) or fibroblasts transfected with wild‐type (WT) or the indicated mutant forms of hLAMP‐2A. Values are the mean+s.e. of two experiments with triplicate samples."
NCBI gene IDs:
"LAMP‐2A: 3920"
Figure legend: "B Relative abundance of mRNA for the cyp-34A4 gene. Values are based on qRT-PCR analysis, with the relative levels for each gene normalized to the value observed in the wild-type control. ***P&lt;0.001, ANOVA with Dunnett's posthoc comparison to wild type. N=3 trials. Error bars indicate SEM."
NCBI gene IDs:
"cyp-34A4: 188350"
Figure legend: "F Quantified fluorescence as in (B) for animals exposed to the indicated RNAi vector or empty vector (EV) control, and in either a wild type (WT) or fat-1(wa9) genetic background. *P&lt;0.001, ANOVA with Dunnett's posthoc comparison to the wild-type control equivalent time point. N=20 animals per genotype and time point. Error bars indicate SEM."
NCBI gene IDs:
"fat-1: 178291"
Figure legend: "A) Gene expression of multiple cachexia-associated markers in gastrocnemius muscles of individual animals from Study 1 (n=5 for tumor-bearing groups; n=6 for tumor-free groups). Expression was determined by qRT-PCR and presented as described in the Materials and Methods (Geometric Mean ± Geometric STD). B) Androgen receptor (AR) mRNA expression in gastrocnemius muscles from Study 1. Statistics: p values provided in Appendix Table S5A-B. Dunnett's multiple comparison test. CEBPδ, n=4, insufficient sample to analyze all tumor-bearing GTx-024-treated animals."
NCBI gene IDs:
"Androgen receptor: 11835
AR: 11835
CEBPδ: 12609"
Figure legend: "C) Significance values from GSEA using combined STAT3 gene sets identified in B. Each treatment group is compared to tumor-bearing control (cachexia) transcriptomes."
NCBI gene IDs:
"STAT3: 20848"
Figure legend: "D) Heat map of DEGs within the combined STAT3 gene sets representing mean z scores calculated from normalized RNAseq count data. Tumor-free control (black checkered), GTx-024-treated tumor-free (blue checkered), tumor-bearing control (black), GTx-024-treated tumor-bearing (blue), AR-42-treated tumor-bearing (red) and Combination-treated tumor-bearing (green)."
NCBI gene IDs:
"STAT3: 20848"
Figure legend: "E) Results of GSEA using combined ATF-1 gene sets identified in B across treatment groups versus tumor-bearing control (cachexia) transcriptomes."
NCBI gene IDs:
"ATF-1: 11908"
Figure legend: "Tumor-free control (black checkered), GTx-024-treated tumor-free (blue checkered), tumor-bearing control (black), GTx-024-treated tumor-bearing (blue), AR-42-treated tumor-bearing (red) and Combination-treated tumor-bearing (green). F) Heat map of DEGs within the combined ATF-1 gene sets (mean z score). Treatment groups are as in D."
NCBI gene IDs:
"ATF-1: 11908"
Figure legend: "G) mRNA expression of mediators of IL-6 signaling upstream of STAT3. Data presented as mean±SD of per animal log-transformed fold change (log2FC) values versus tumor-free controls. Groups: Tumor-free control (n=6), tumor-free GTx-024 treated (n=5), tumor-bearing receiving vehicle (n=4), GTx-024 (n=5), AR-42 (n=5) or Combination (n=6)."
NCBI gene IDs:
"IL-6: 16193
STAT3: 20848"
Figure legend: "C) Significance values from GSEA using combined CTNNB1 gene sets. Each treatment group was compared to tumor-free control transcriptomes. *FDR &lt; 1e-5 determined, set to 1e-5 for plot."
NCBI gene IDs:
"CTNNB1: 12387"
Figure legend: "D) Enrichment plots from GSEA of the CTNNB1 gene set for each treatment group versus tumor-free control comparisons. GTx-024-treated tumor-free (blue checkered), tumor-bearing control (black), GTx-024-treated tumor-bearing (blue), AR-42-treated tumor-bearing (red) and Combination-treated tumor-bearing (green)."
NCBI gene IDs:
"CTNNB1: 12387"
Figure legend: "E) mRNA expression of WNT effectors upstream of β-catenin. Data are presented as mean±SD of log-transformed fold change (log2FC) values versus tumor-free controls. Groups: Tumor-free control (n=6), tumor-free GTx-024 treated (n=5), tumor-bearing receiving vehicle (n=4), GTx-024 (n=5), AR-42 (n=5) or Combination (n=6)."
NCBI gene IDs:
"β-catenin: 12387"
Figure legend: ", B. survival of Ssrp1fl/fl; CreERT2+/+ mice  of different  ages (weeks) after the start of tamoxifen (TMX) treatment. B.  Kaplan-Meier survival curves. Log-rank test p = 0.032 for the oldest male age group versus all other  male  groups; p = 0.013 for all females versus all males; for all other comparisons p &gt; 0.05. n = 6-10 mice."
NCBI gene IDs:
"Cre: 2777477
ERT2: 5595
Ssrp1: 20833"
Figure legend: "C. Normalized  blood cell counts in Ssrp1fl/fl; CreERT2+/+ mice treated with vehicle or tamoxifen on day 7 after start of treatment. Mean ± SD, * indicates p &lt; 0.05 (unpaired t-test). n = 3 mice."
NCBI gene IDs:
"Cre: 2777477
ERT2: 5595
Ssrp1: 20833"
Figure legend: "A, B. Effect of tamoxifen on replication in the spleen (A) and  intestine (B) of Ssrp1fl/fl; CreERT2+/+ mice.  EdU was given to  mice three days after the end of tamoxifen  treatment (1 hour before tissue collection). Organ sections were  stained  for total DNA  (Hoechst), EdU, and SSRP1. Scale bars - 100 μM. C. Quantitation of  EdU staining. Mean number of EdU positive cells per field of view +/- SD. n &gt; 5 fields of view per mouse. 3 mice were analyzed. D. Quantitation of cleaved caspase-3 staining. Mean number of positive cells per fields of view +/- SD, n &gt; 5 fields of view per mouse Two male and female mice  were analyzed. Data information: P-values for C and D were calculated using the unpaired t-test."
NCBI gene IDs:
"Cre: 2777477
ERT2: 5595
Ssrp1: 20833"
Figure legend: "D. UMAP plots with color-coded  intestinal stem cells identified by transcriptional signatures of intestinal stem cells or by expression  of Lgr5  or Gkn3 genes."
NCBI gene IDs:
"Gkn3: 68888
Lgr5: 14160"
Figure legend: "F, G. Effect of  4-OHT  administration on  intestinal organoids of different genotypes kept in the presence (undifferentiated) or absence (differentiated) of R-spondin-1. F. The  viability of organoids assessed by the resorufin  assay. Mean ± SD, n = 3 wells per mouse. P &lt; 0.05 are shown (unpaired t-test). Organoids were isolated from two  mice  of each genotype. G. IF images of  intestinal organoids from Ssrp1fl/fl; CreERT2+/+ mice kept in the presence or absence of R-Spondin-1. The  organoids  were stained  with antibodies to  LGR5 and SSRP1  and counterstained  with Hoechst (DNA)."
NCBI gene IDs:
"Cre: 2777477
ERT2: 5595
Ssrp1: 20833"
Figure legend: " B) Dyads of metaphase II chromosome spreads of control, Bub1KD, Mps1∆N and Reversine-treated oocytes (from GVBD onwards) stained with Sgo2 antibody (red), CREST serum (green) and Hoechst (blue). "
NCBI gene IDs:
"Bub1: 12236
Mps1: 17476"
Figure legend: " A) Metaphase II oocytes from mice carrying a conditional, oocyte-specific invalidation of separase (Separaseflox/flox Zp3 Cre+, or Sep-/-) and oocytes from litter mates (Separaseflox/flox, or Sep+/+) were obtained after superovulation. In vivo matured control (Sep+/+) and Sep-/- oocytes are found in oviducts at comparable numbers, enclosed by cumulus cells. Example of cumulus enclosed oocytes from the oviduct is shown below. In (A), n indicates the number of mice and a mean number of oocytes per mouse of each genotype, error bars are + s.e.m. "
NCBI gene IDs:
"Sep: 105988
separase: 105988
Separase: 105988
Zp3: 22788"
Figure legend: " D) Metaphase-to-anaphase transition of meiosis II in oocytes of the indicated genotype cultured in vitro and injected with the separase constructs as indicated, in GV. The schemes indicate the chromosome figures observed upon activation. Chromosome spreads are stained with CREST serum (green), and Rec8 antibody (red). DNA was stained with DAPI (blue). In (D) n indicates the number of oocytes with the shown phenotype (e.g., upon successful activation) and the total number of oocytes analyzed. "
NCBI gene IDs:
"separase: 105988"
Figure legend: " A) Sep+/+ or Sep-/- oocytes were matured in vitro until metaphase II. Sep-/- oocytes were injected with wild-type separase or cleavage mutant separase encoding mRNAs in metaphase II. Oocytes were either fixed in metaphase II or activated and fixed in anaphase II. Spreads were stained with Rec8 antibody (red), CREST serum (green), and DAPI (blue) to label DNA. n indicates the number of oocytes with the shown phenotype (e.g. in anaphase II, after successful activation) and the total number of oocytes analysed "
NCBI gene IDs:
"Sep: 105988
separase: 105988"
Figure legend: " B) Representative image of kinetochore individualization in Sep-/- oocytes injected with wild-type separase in metaphase II and fixed after activation, from A). Shown is staining with CREST serum (green), and DAPI (blue) to label DNA. Arrows indicate separated sister kinetochores. The scheme on the left illustrates the individualization of sister kinetochores (green arrows) at anaphase II. n indicates the number of oocytes with the shown phenotype (e.g. in anaphase II, after successful activation) and the total number of oocytes analysed Scale bars: 10 µm, except bottom panel in B), where the scale bar is 2 μm. "
NCBI gene IDs:
"Sep: 105988
separase: 105988"
Figure legend: " A) Live imaging movie of GFP-Sgo2 expressing oocytes (from GV onwards) undergoing meiosis I. The green channel to visualize GFP-Sgo2 localized to chromosomes is shown. Timepoints were taken every 10min, shown is a montage of selected frames such as indicated (hours: time after GVBD) at the metaphase-to-anaphase transition of meiosis I and in metaphase II. Each timepoint is comprised of an overlay of 11 z-sections of 3μm for GFP. The arrow heads indicate bivalents. In (A-C) n indicates the number of control non-injected and GFP-Sgo2-expressing oocytes analyzed "
NCBI gene IDs:
"GFP: 
Sgo2: 68549"
Figure legend: " C) Metaphase I (4hrs after GVBD) and II spreads after GFP-Sgo2 expression (from GV onwards). Spreads were stained with CREST serum (red), Hoechst for DNA (grey), GFP-Sgo2 was visualized by GFP fluorescence (green). Arrowheads mark separated sister kinetochores. On the right, graph showing percentage of metaphase II spreads containing bivalent chromosomes. In (A-C) n indicates the number of control non-injected and GFP -Sgo2-expressing oocytes analyzed The number of analysed oocytes in C)"
NCBI gene IDs:
"GFP: 
Sgo2: 68549"
Figure legend: " D) Chromosome spreads of oocytes expressing GFP-Sgo2 (from GV onwards) in metaphase II, and upon activation. Spreads were labeled with Rec8 antibody (shown in red, far-red secondary antibody was used), CREST serum (pseudo-colored in green), and Hoechst (blue). GFP direct fluorescence was imaged for GFP-Sgo2 detection. Below the corresponding chromosome figures are represented in the schemes. E) Quantification of Rec8 signal found around and in between CREST signals that were close to each other. Below: scheme illustrating how Rec8 signals (in red) were measured at the indicated meiotic stages. Ifluor stands for a mean fluorescence intensity of the area within the box (dotted lines). Meta: metaphase, ana: anaphase. D), the number of oocytes with the shown phenotype and the total number of oocytes analyzed. On each graph, mean is shown, error bars are +s.e.m. in C) and and ± SD in E), asterisks indicate significant difference (**** = p&lt;0,0001) according to Mann-Whitney U test. AU: arbitrary units. The number of analysed kinetochore pairs in E) is indicated."
NCBI gene IDs:
"GFP: 
Sgo2: 68549"
Figure legend: "A HEK 293 cells were transfected with mCherry-tagged Parkin and FLAG-tagged UBQLN2 for 24 h, and then were treated with 5 µg/mL Antimycin A and Oligomycin A (A/O) for 4 h and 24 h. The cells were stained with anti-FLAG (green) antibody and anti-TOM20 (gray), and then were visualized using confocal microscopy. Scale bars, 10 µm. Insets were higher magnifications of the dashed box area. Scale bars, 2.5 µm. B, C The dashed square is magnified as shown in the boxed region in A with corresponding line scan indicating Parkin and UBQLN2 co-localization on the depolarized mitochondria (the line scan indicates pixel intensity of Parkin and UBQLN2)."
NCBI gene IDs:
"FLAG: 
mCherry: 
Parkin: 5071
UBQLN2: 29978"
Figure legend: "D HEK 293 cells were transfected with mCherry-tagged Parkin and EGFP-tagged UBQLN2. 24 h after transfection, cells were treated with 1 µg/mL A/O for 4 h, and then were harvested for the isolation of mitochondria. Whole cell (Total), cytosol (Cyto) and mitochondria (Mito) were lysed and analyzed by western blotting with the indicated antibodies."
NCBI gene IDs:
"EGFP: 
mCherry: 
Parkin: 5071
UBQLN2: 29978"
Figure legend: "A Domain structure of Parkin in upper region. HEK 293 cells were transfected with HA-tagged UBQLN2 and FLAG-tagged Parkin WT or mutants (K161N, T240R, C418R, C431F and P437L) for 24 h, and then were treated with 5 µg/mL A/O for 5 h. The cells were stained with anti-HA (green) and FLAG (red) antibodies. Then the cells were visualized using confocal microscopy. Scale bars, 10 µm. Lower panel were higher magnifications of the dashed box area. Scale bars, 2.5 µm. B, C The quantification data of the Parkin or UBQLN2 with mitochondrial localization in A. At least 60 anti-HA-UBQLN2 or anti-FLAG-Parkin positive cells were counted for each sample. Data from three independent experiments were represented as means ± SD., ns, not significantly different; **, p&lt;0.01; ***, p&lt;0.001, one-way ANOVA."
NCBI gene IDs:
"FLAG: 
HA: 
Parkin: 5071
UBQLN2: 29978"
Figure legend: "B HEK 293 cells were transfected with indicated siRNA. After 48 h, the cells were re-transfected with FLAG-Parkin and mt-mKeima for 17 h. Then the cells were treated with 5 µg/mL A/O for 5 h, and visualized using confocal microscopy. Intracellular mt-mKeima signal excited at 458 nm (measuring mitochondria with a neutral pH) was shown in green color, while red color indicated the mt-mKeima fluorescence excited at 561 nm (measuring mitochondria with an acidic pH) in the same cell. Scale bars, 10 µm."
NCBI gene IDs:
"FLAG: 
Parkin: 5071"
Figure legend: "G HEK 293 cells were transfected with indicated siRNAs. After 24 h, the cells were re-transfected with FLAG tag or FLAG-tagged UBQLN2WT or ∆UBA, along with mCherry-Parkin for 24 h. The cells then were treated with or without 1 µg/mL A/O for 24 h. The cell lysates were subjected to immunoblot with indicated antibodies."
NCBI gene IDs:
"FLAG: 
mCherry: 
Parkin: 5071
UBQLN2: 29978"