EMBO/SourceData huggingface dataset:
Figure legend: "(D-G) BMDM were transduced with a retroviral vector expressing CALHM6-eGFP. BMDM (3x105) were plated on coverslips and pre-treated with IFN-γ and LPS for 6 h. (D) Freshly isolated primary CD3-NK1.1+ cells isolated from mouse spleens were added for 0, 10, 20, or 40 min on top of plated BMDMs that were generated from bone marrow cells transduced with a retroviral vector expressing CALHM6-eGFP. The interacting cells were then fixed and stained with phalloidin to identify actin and DAPI to identify nucleus. Synaptic interaction between BMDM and NK cell is indicated by white arrowheads; entire collapsed imaging Z-stack is shown. (E) Images were blinded and CALHM6-eGFP polarisation towards CD3-NK1.1+ cells manually scored only in Z-slices where BMDM-NK interaction was identified (p-value calculated by two-way ANOVA of polarisation and time points). Numbers on top of each bar indicate number of synapses scored for that time point. (F) IgG2a-opsonised sRBC labelled with PHK26 were added on top of plated CALHM-eGFP-expressing BMDM. One single Z-slice containing BMDM-sRBC interaction plane is shown. Synaptic interaction between BMDM and sRBC cell is indicated by white arrowheads (G) Quantified results of experiment in F. Numbers on top of each bar indicate number of synapses scored for that time point. Longer time points were not possible to score for opsonised sRBC because of the speed of the phagocytosis as sRBC were quickly internalised. Images taken with 60x objective (p-value calculated by two-way ANOVA of polarisation and time points)."
NCBI gene IDs:
"eGFP: 
CALHM6: 215900"
Figure legend: "(B) WT or Calhm6-/- BMDM stimulated with IFN-γ (10 ng/ml) for 24 h were lysed with 1% Triton X100-containing buffer with cOmplete protease inhibitor cocktail and treated with increasing concentrations of DTT. The samples, without boiling, were resolved by SDS-PAGE gel (one representative experiment of two is shown, n = 4 mice). Lack of DTT influences solubilisation of GADPH monomer, and its detection for immunoblotting."
NCBI gene IDs:
"Calhm6: 215900"
Figure legend: "(G) Current-voltage (I-V) relations for WT-mCALHM6, E119R-mCALHM6 and control (ASO) in 2-mM Ba2+ bath solution (pooled individual whole-cell patches, WT-mCALHM6 n = 13, E119R-mCALHM6 n = 4, control = 4, SEM error bars)."
NCBI gene IDs:
"CALHM6: 215900"
Figure legend: "(A) Fura-2 fluorescence ratio (F340/380) recorded in N2a cells expressing human CALHM1 (hCALHM1), mouse CALHM6 (mCALHM6) or control (vector) in response to removal and subsequent add-back of extracellular Ca2+. Traces representative of four independent experiments for each, normalized to baseline ratio. Right: Resting F340/380 ratio in N2a cells expressing hCALHM1, mCALHM6 or vector in 2 mM Ca2+ (the error bars represent SEM)."
NCBI gene IDs:
"CALHM1: 255022
CALHM6: 215900"
Figure legend: "(E) Steady-state ATP release from activated macrophages: BMDMs were plated at 150,000 cells/well in a 48-well plate, and incubated for 3 h with Poly(I:C) (50 μg/ml), LPS (100 ng/ml) and ATPase inhibitor ARL67156 (1 mM) in culture medium. Control cells were incubated with 1 mM ARL67156 only. ATP release (nM) measured using Sigma ATP Bioluminescent Assay: WT without stimulation: 9.12 ± 0.76; WT with stimulation: 22.16 ± 1.83; Calhm6-/- cells without stimulation: 8.76 ± 0.55; KO cells with stimulation: 12.19 ± .75. (pooled results from three independent experiments, WT mice = 3, Calhm6-/- mice = 3, Two-tailed unpaired Student's T test, error bars represent SEM)."
NCBI gene IDs:
"Calhm6: 215900"
Figure legend: "(H) The expression  level of AURKB  in PANC-1  cells transfected with control or ROR1   siRNA and in ROR1high or ROR1low cells from  S2-VP10 and PDO#1 xenografts  (n = 3). Data information: Data are presented as mean ± s.e.m., two-sided t-test. *, p &lt; 0.05; n.s., not significant."
NCBI gene IDs:
"AURKB: 9212
ROR1: 4919"
Figure legend: "(I) Western blot  analysis of ROR1, AURKB, and β-actin in  S2-VP10 and S2-013  cells transfected with control or ROR1   siRNA."
NCBI gene IDs:
"ROR1: 4919"
Figure legend: "(K)  Organoid  formation assay  of ROR1high or ROR1low cells derived from S2-VP10 EGFP  (control) or S2-VP10 AURKB-EGFP xenografts  (n = 3, biological replicates). Representative images and the number of organoids   are shown. Data information: Scale bars, 1 mm (K). Data are presented as mean ± s.e.m., two-sided t-test. *, p &lt; 0.05; n.s., not significant."
NCBI gene IDs:
"EGFP: 
AURKB: 9212"
Figure legend: "(L) Western blot  analysis of ROR1, AKT, phospho-AKT  (Ser473), and β-actin in S2-VP10  and S2-013 cells transfected with control or ROR1   siRNA."
NCBI gene IDs:
"ROR1: 4919"
Figure legend: "(N) Western blot  analysis of ROR1, c-Myc, phospho-RB  (Ser780), E2F1, and  β-actin in  S2-VP10 and S2-013  cells transfected with control or ROR1  siRNA."
NCBI gene IDs:
"ROR1: 4919"
Figure legend: "(A)-(C) Representative images of ROR1, mCherry, and aSMA staining  in the  primary tumor  (pancreas) (A) and metastatic lesions  in the lung  (B) and mesenteric lymph node (C) after orthotopic transplantation of S2-VP10-mCherry  cells into the pancreas  of BRJ mice. Data information: Scale bars, 100 µm"
NCBI gene IDs:
"mCherry: "
Figure legend: "(A), H3K4me1,  K3K4me3, H3K27ac, and open chromatin  profiles  around the ROR1  gene by  CUT&amp;RUN and ATAC-sequencing in cultured S2-VP10 cells (A) The ROR1  promoter (blue-shaded boxes) and enhancer elements (green-shaded box) of ROR1  are indicated."
NCBI gene IDs:
"ROR1: 4919"
Figure legend: "(E) YAP  occupancy at the ROR1  enhancer as determined by ChIP-qPCR. The known YAP  targets, CTGF  and CYR61  promoters, were tested as positive controls, and ROR1   intron 1 and AFM   promoter were tested as negative controls (n = 4, biological replicates)."
NCBI gene IDs:
"AFM: 173
CYR61: 3491
CTGF: 1490
ROR1: 4919"
Figure legend: "(G)  Western blot  analysis of YAP, TAZ, ROR1, and β-actin in S2-VP10  cells transfected with control or YAP1/WWTR1  siRNA."
NCBI gene IDs:
"WWTR1: 25937
YAP1: 10413"
Figure legend: "(I) Relative expression  of ROR1  and YAP   target genes (CTGF  and CYR61) in S2-VP10  cells treated with DMSO  or verteporfin  (VP) (n = 3, biological replicates). mRNA levels are normalized to that of RPS18."
NCBI gene IDs:
"CYR61: 3491
CTGF: 1490
ROR1: 4919
RPS18: 6222"
Figure legend: "(O), Treatment of PDO#1 and S2-VP10 organoids  with DMSO  or JQ1  (n = 3, biological replicates). Relative expression  of ROR1  (O), mRNA levels are normalized to that of RPS18. Data information: Data are presented as mean ± s.e.m., *, p &lt; 0.05. ; two-sided t-test (O)"
NCBI gene IDs:
"ROR1: 4919
RPS18: 6222"
Figure legend: "E, F Co‐immunoprecipitation of endogenous TBC1D5 and ATG9A with myc‐VPS29(E) transiently overexpressed in 293T cells or with HA‐Flag‐VPS35 (F) transiently overexpressed in 293T cells, treated with DMSO or KU0063794 (6 h)."
NCBI gene IDs:
"VPS29: 51699"
Figure legend: "I Magnified still images extracted from Supplementary Movie S2. mCherry‐TBC1D5 co‐localizes with GFP‐ATG9 upon autophagy induction by mTOR inhibitor, KU0063794."
NCBI gene IDs:
"GFP: "
Figure legend: "A Lysates of U2OS cells stably expressing control shRNA or shRNA targeting VPS29 or TBC1D5. Cells were treated with DMSO or KU0063794 (6 h), lysed in RIPA buffer (1% SDS) and lysates were subjected to SDS-PAGE."
NCBI gene IDs:
"TBC1D5: 9779
VPS29: 51699"
Figure legend: "B U2OS cells stably expressing mCherry‐ATG9 were depleted of VPS29 and TBC1D5 using shRNAs, treated with DMSO or KU0063794 (6 h), fixed with 2% PFA, and immunostained with anti‐LAMP1 antibody."
NCBI gene IDs:
"TBC1D5: 9779
VPS29: 51699"
Figure legend: "E Quantification of ATG9 and LAMP1 co−localization in cells stably depleted for TBC1D5 (shRNA#1) or VPS29 (shRNA#2), transiently transfected with myc−TBC1D5 plasmid resistant to TBC1D5 shRNA#1. Cells were treated with KU0063794 (6 h), 20 h post−transfection, fixed, and immunostained with anti−LAMP1 and anti−myc antibodies."
NCBI gene IDs:
"TBC1D5: 9779"
Figure legend: "F Control shRNA and U2OS cell lysates depleted for TBC1D5 (shRNA#1), transfected with empty plasmid or with shRNA‐resistant myc‐TBC1D5."
NCBI gene IDs:
"TBC1D5: 9779"
Figure legend: "G Immunofluorescence of TBC1D5 (shRNA#1) cells transiently transfected with shRNA‐resistant myc‐TBC1D5, treated with KU0063794 (6 h). 20 h post‐transfection cells were treated, subsequently fixed, and immunostained with anti‐myc and anti‐LAMP1 antibodies."
NCBI gene IDs:
"TBC1D5: 9779"
Figure legend: "B Control cells and TBC1D5 (shRNA#1) U2OS cell lysates subjected to SDS-PAGE, subsequently blotted with endogenous antibodies for AP2 subunits AP2A1 and AP2M1."
NCBI gene IDs:
"TBC1D5: 9779"
Figure legend: "C Immunofluorescent staining of AP2A1 in U2OS shRNA control, or shRNA#1 TBC1D5 cells treated with KU0063974 or DMSO (6 h)."
NCBI gene IDs:
"TBC1D5: 9779"
Figure legend: "A U2OS cells stably expressing HA‐Flag‐ATG9A transfected with siRNA targeting AP2A1 (40 nM), or siRNA AllStar control (40 nM) were treated with KU0063794 or DMSO (6 h) 4 days post‐transfection, fixed, and stained with anti‐HA antibody."
NCBI gene IDs:
"AP2A1: 160"
Figure legend: "C Lysates of U2OS cells transfected with siRNA targeting AP2A1, or siRNA control AllStars analyzed by SDS-PAGE."
NCBI gene IDs:
"AP2A1: 160"
Figure legend: "D U2OS cells stably expressing mCherry−ATG9 were transiently transfected with GFP−Dynamin 2 or GFP−Dynamin 2 (K44A), 20 h post−transfection cells were fixed and with anti−TBC1D5 antibody. ATG9A and Dynamin 2co−localization is indicated by arrows."
NCBI gene IDs:
"Dynamin 2: 1785"
Figure legend: "Immunofluorescence and reporter expression in spheroids derived from single WT and Hdac3-/- naïve mESCs. DNA counterstain is Hoechst. Dashed white lines indicate the embryonic Gata6::mCherry negative part. Scale bar: 10 μm."
NCBI gene IDs:
"Hdac3: 15183"
Figure legend: "Nanog&gt;GFP and Gata6::mCherry fluorescence intensities of WT and Hdac3-/- Fraction of Gata6::mCherry positive cells in indicated genotypes and conditions after 4d Jak(i) blocks LIF, LDN19 BMP4 and PD03 FGF signaling. Average and SD of at least two independent clones."
NCBI gene IDs:
"Hdac3: 15183"
Figure legend: "Scatter plots of log2 fold change (FC) gene expression changes (∆mRNA) between naïve Hdac3-/- or Dax1-/- mutants and WT mESCs (left), between Nanog>GFP-expressing Hdac3-/- or Dax1-/- mutants and WT cells (middle), and between Gata6::mCherry-expressing Hdac3-/- or Dax1-/- mutants and Nanog>GFP-expressing WT cells (right). Cluster 5 genes are colored and selected PrE TFs labeled."
NCBI gene IDs:
"GFP: 
mCherry: 
Gata6: 14465
Hdac3: 15183
Nanog: 71950
Dax1: 11614"
Figure legend: "Expression of PrE markers relative to Dax1-/- cells (B), and fraction of Gata6::mCherry positive cells after 3d in SLRA (C) in indicated genotypes. Average and SD of three independent clones."
NCBI gene IDs:
"mCherry: 
Gata6: 14465
Dax1: 11614"
Figure legend: "Genome-browser view of the Gata6 locus showing accessibility and chromatin mark changes in indicated mutants, and of ChIPseq signals of indicated TFs and H3K27ac in E6.5 VE and EPI. The grey area indicates enh-45."
NCBI gene IDs:
"Gata6: 14465"
Figure legend: "Confocal microscopy of YFP-ATG8e-labeled autophagic bodies in root cells of Col-0/YFP-ATG8e and VISP1OE/YFP-ATG8e plants. 7-day-old seedlings were inoculated in liquid ½MS medium with 1 µM ConA for 12 h in dark. Scale bar = 20 μm.   Puncta numbers of YFP-ATG8e-labeled autophagic bodies per 10 cells in panel A. Data points represent means of three biological repeats. Error bars indicate SD. ***p &lt; 0.001 (Student's t-test).   "
NCBI gene IDs:
"YFP: 
ATG8e: 819125"
Figure legend: "Long-term symptoms of Col-0, VISP1OE1, VISP1OE2, rdr6-15, and sgs3-1 plants inoculated with CMV-2blm at 50 dpi. Scale bar = 2 cm."
NCBI gene IDs:
"rdr6: 824112
sgs3: 832422"
Figure legend: "Northern blotting analyzing accumulation of genomic RNAs (gRNAs) in systemically leaves of Col-0, OE1 (VISP1OE1), OE2 (VISP1OE2), rdr6-15, and sgs3-1 plants infected by CMV-2blm at 14 dpi. Methylene blue-stained rRNA were used as loading controls.   Northern blotting analyzing accumulation of RNA3-derived   vsiRNAs in the same samples as shown in panel D."
NCBI gene IDs:
"rdr6: 824112
sgs3: 832422"
Figure legend: "Long-term systemic symptoms of Col-0, visp1-1, visp1-2, rdr6-15, and sgs3-1 plants inoculated with CMV-2blm at 50 dpi. Scale bar = 2 cm."
NCBI gene IDs:
"rdr6: 824112
sgs3: 832422"
Figure legend: "Confocal analysis of effect of VISP1-Flag VISP1mARM-Flag, and VISP1mUIM-Flag on RDR6-YN and SGS3-YC formed bodies in N. benthamiana leaves at 60 hpi. EV: empty vector. Scale bar = 20 μm.   Numbers of RDR6-YN and SGS3-YC formed bodies per 10 cells in E were used for quantification. Data points represent means of three biological repeats. Error bars indicate SD. Letters indicate significant differences (ANOVA, P &lt; 0.05).   "
NCBI gene IDs:
"Flag: "
Figure legend: "Western blotting detecting accumulation of the endogenous SGS3 protein in leaves of 2-week-old Col-0, VISP1OE, visp1, and sgs3-1 Arabidopsis plants with anti-SGS3 antibodies.   Western blotting detecting accumulation of the endogenous SGS3 protein in leaves of 2-week-old Col-0, VISP1OE, VISP1mUIM/OE, and VISP1mARM/OE Arabidopsis plants.   Western blotting detecting accumulation of the endogenous SGS3 protein in 2-week-old VISP1-overexpressing Col-0, atg5-1, and atg7-1 mutants.   "
NCBI gene IDs:
"atg5: 831594
atg7: 834630
sgs3: 832422"
Figure legend: "Developmental phenotypes of rosette leaves of 5-week-old Col-0, visp1-1, visp1-2, VISP1OE1, VISP1OE2, and sgs3-1 seedlings. Arrowheads indicate the 8th and 9th rosette leaves from the top leaves. Scale bar = 2 cm.   The length/width ratios of the 8th and 9th rosette leaves of the seedlings shown in A. Every dot represents data from the length/width ratio of one leave (n = 20). Letters indicate significant   differences (ANOVA, P &lt; 0.05)."
NCBI gene IDs:
"sgs3: 832422"
Figure legend: "Northern blotting detecting accumulation of TAS1-TasiR255, TAS2-TasiR1511, TAS3-TasiR5′D8, miR173, and miR390 in leaves of Arabidopsis plants shown in panel A. Values represent relative accumulation (RA) of siRNAs and values in Col-0 plants were set as 1. rRNA served as loading controls."
NCBI gene IDs:
"miR173: 
miR390: 
TAS1: 
TasiR1511: 
TasiR255: 
TasiR5′D8: 
TAS2: 3768418
TAS3: 3768766"
Figure legend: "(E) Mrp17 variants rescue ∆mrp17 strain growth defect on respiratory media: the indicated variants or empty vector (EV) were introduced in WT yeast and then the genomic MRP17 was disrupted by knock out, the resulting mutants were serially diluted 10× and spotted on media containing glucose or glycerol as a sole carbon source."
NCBI gene IDs:
"MRP17: 853867
Mrp17: 853867
mrp17: 853867"
Figure legend: "(A) The in vitro import of Mrp17-DHFRmut is sensitive to the elimination of outer mitochondrial membrane proteins by trypsinization (left), more so than the model import substrate Atp1 (right). Mitochondria were incubated with the indicated concentrations of trypsin and the import assay was performed as described in the legend for Fig. 2. Proteinase K (PK) was not added to the sample without mitochondria. (B) In vitro translocation of Mrp17-DHFRmut into mitochondria isolated from WT and ∆tom20 yeast showing reduced translocation in ∆tom20 background."
NCBI gene IDs:
"tom20: 852973"
Figure legend: "(G),(H) Import of Mrp17-DHFRmut and control proteins Atp1 and Aac1 into WT, tim17-ts (G) and tim22-ts (H) mitochondria. Import was performed at indicated temperatures, proteinase K was added to all samples except the loading control in the first lane of each autoradiograph (20% of protein amount used for each import reaction). The full autoradiograph for Aac1 with molecular weight markers is shown in Appendix Figure S6D."
NCBI gene IDs:
"tim17: 853298
tim22: 851309"
Figure legend: "(b) Coimmuno-precipitation (IP) of Fbxo7-HA and Flag-Parkin in whole-cell lysates from U2OS cells over-expressing both proteins. IB, immunoblot. Molecular mass markers are in kilodaltons."
NCBI gene IDs:
"Fbxo7: 25793
Parkin: 5071"
Figure legend: "(c) Coimmunoprecipitation of endogenous Fbxo7 with Flag-Parkin in HEK293T cells transfected with Flag-Parkin or a control protein (EGFP)."
NCBI gene IDs:
"Parkin: O60260///5071"
Figure legend: "(d) Flag immunoprecipitation was repeated in U2OS cells transfected with Flag-Parkin and either full-length (1-522) T7-Fbxo7 or an N-terminal truncation lacking the Ubl domain (89-522)."
NCBI gene IDs:
"Fbxo7: 25793"
Figure legend: "(e) As in d, using lysates from U2OS cells expressing Flag-Parkin and T7-Fbxo7, either full length (1-522) or a C-terminal deletion of the proline-rich region (1-398). * indicates IgG heavy chain."
NCBI gene IDs:
"Fbxo7: 25793"
Figure legend: "(f) In vitro-translated Flag-Parkin was incubated with bacterially expressed GST or GST fused to the Fbxo7 Ubl domain (1-88) immobilized on glutathione beads. Bead-bound proteins and inputs were analyzed by immunoblotting with anti-Parkin antibodies."
NCBI gene IDs:
"Fbxo7: 25793
Parkin: 5071"
Figure legend: "(g) The disease-causing mutation T22M interferes with Fbxo7's interaction with Parkin. Coimmunoprecipitation was performed as in b using lysates from U2OS cells expressing Flag-Parkin and WT or T22M Fbxo7-HA."
NCBI gene IDs:
"Fbxo7: 25793
Parkin: 5071"
Figure legend: "(h) Coimmunoprecipitation of Flag-Parkin and Fbxo7 in the mitochondrial and cytosolic fractions of HEK293T cells overexpressing both proteins. CxVα and GAPDH are markers for mitochondria and cytoplasm, respectively. All western blots are representative of experiments performed at least three times. Full-length blots are presented in Supplementary Figure 9."
NCBI gene IDs:
"Fbxo7: 25793
Parkin: 5071"
Figure legend: "(b) Fbxo7 levels are increased in Flag-Parkin complexes immunoprecipitated (IP) from the mitochondrial fraction of HEK293T cells transfected with Flag-Parkin and untagged Fbxo7 following 1 or 3 h treatment with CCCP (10 µM)."
NCBI gene IDs:
"Parkin: 5071"
Figure legend: "(c) Parkin localization at the mitochondria was assessed by immunocytochemistry in SH-SY5Y cells transfected with Flag-Parkin plus scrambled (scr) or Fbxo7 siRNA, following 1 or 3 h treatment with CCCP (10 μM). Cells were scored visually for the colocalization of Flag-Parkin with HtrA2, a mitochondrial marker. Images are displayed for cells transfected as indicated, following 0 or 3 h CCCP treatment. For corresponding images at 1 h treatment, see Supplementary Figure 2c. Nuclei (blue) were stained with DAPI. Scale bars, 10 μm."
NCBI gene IDs:
"Fbxo7: 25793
Parkin: 5071"
Figure legend: "(d) Loss of Flag-Parkin translocation upon Fbxo7 silencing is rescued by WT and R378G Fbxo7, but not by T22M Fbxo7, by R498X Fbxo7 or by Fbxo7 in which the mitochondrial targeting sequence is mutated (mt-MTS). For c,d, histograms indicate the percentage of cells in which Parkin localized to the mitochondria. Data are presented as mean of three experiments ± s.e.m. *P 0.05, **P 0.01 compared to cells transfected with Flag-Parkin plus Fbxo7 siRNA."
NCBI gene IDs:
"Fbxo7: 25793
Parkin: 5071"
Figure legend: "(e) T7-tagged WT Fbxo7 localizes to both cytosolic (C) and mitochondrial (M) fractions of transfected HEK293T cells, but MTS mutant (mt-MTS) Fbxo7 localizes only to the cytosolic fraction. CxVα and PDHE1α are mitochondrial markers; GAPDH is a cytosolic marker. All western blots are representative of experiments performed at least three times. Full-length blots are presented in Supplementary Figure 9."
NCBI gene IDs:
"Fbxo7: 25793"
Figure legend: "(a,b) Overexpression of Fbxo7 by da-GAL4 (da&gt;Fbxo7) suppresses climbing (a) and flight (b) defects of parkin mutants."
NCBI gene IDs:
"GAL4: 
da: 34413
Fbxo7: 38443
parkin: 40336"
Figure legend: "(c) Overexpression of Fbxo7 also suppresses dopaminergic (DA) neurodegeneration parkin mutants."
NCBI gene IDs:
"Fbxo7: 38443
parkin: 40336"
Figure legend: "(d-f) Top and middle panels, toluidine blue-stained sections of adult thorax. Bottom panels, transmission electron micrographs of muscle. Fbxo7 overexpression suppresses muscle degeneration and mitochondrial disruption in parkin mutants. Scale bars: 200 μm (top), 20 μm (middle), 2 μm (bottom). Images are representative of three animals per genotype."
NCBI gene IDs:
"Fbxo7: 38443
parkin: 40336"
Figure legend: "(g,h) Overexpression of Fbxo7 pathogenic mutants, mt-MTS or isoform 2 by da-GAL4 fails to rescue climbing (g) and flight (h) deficits in parkin mutants. Control genotype is park25/+; da-GAL4/+. All transgenic lines are site-directed integration except WT(4), which is random integration line 4 (see Supplementary Fig. 3 and Online Methods). Histograms indicate mean ± s.e.m. One-way ANOVA with Bonferroni correction (***P 0.001, **P 0.01). For climbing and flight assays, at least 50 flies were assessed; number of flies is shown for each bar."
NCBI gene IDs:
"GAL4: 
da: 34413
Fbxo7: 38443
parkin: 40336"
Figure legend: "(a) Coimmunoprecipitation (IP) of PINK1-Myc and Flag-Fbxo7 in whole-cell lysates from U2OS cells overexpressing both proteins. IB, immunoblot."
NCBI gene IDs:
"Fbxo7: 25793
PINK1: 65018"
Figure legend: "(b) Coimmunoprecipitation of PINK1-Myc with full-length and two N-terminally deleted Flag-Fbxo7 forms. PINK1-Myc is detected at low levels in complex with Flag-Fbxo7(89-522) but not with Flag-Fbxo7(129-522)."
NCBI gene IDs:
"Fbxo7: 25793
PINK1: 65018"
Figure legend: "(c) As in b, using lysates from U2OS cells expressing PINK1-Myc, and Flag-Fbxo7 containing either N- or C-terminal truncations."
NCBI gene IDs:
"Fbxo7: 25793
PINK1: 65018"
Figure legend: "(d) In vitro coprecipitation experiments were performed using in vitro-translated (IVT) PINK1-Myc and either GST or GST fusions of Fbxo7(1-398) or Fbxo7(129-398) immobilized on glutathione beads."
NCBI gene IDs:
"PINK1: 65018"
Figure legend: "(e) Competitive binding assays using immobilized GST-Fbxo7(1-398) incubated with IVT Flag-Parkin and/or full length (top panel) or N-terminally truncated (bottom panel) PINK1-Myc. Input and bead-bound proteins were analyzed by immunoblotting as indicated."
NCBI gene IDs:
"Fbxo7: 25793
PINK1: 65018"
Figure legend: "(f) As in e, immobilized GST-ΔN-PINK1 (top panel), GST-Parkin (middle panel) and immobilized GST alone (bottom panel) were incubated with combinations of IVT Flag-Parkin, T7-ΔN-PINK1 and Fbxo7-HA as indicated. Input and bead-bound proteins were analyzed by immunoblotting with the indicated antibodies. All western blots were performed a minimum of three times. Full-length blots are presented in Supplementary Figure 9."
NCBI gene IDs:
"Parkin: 5071
PINK1: 65018"
Figure legend: "(a) PINK1 localization at the mitochondria was assessed by immunocytochemistry in SH-SY5Y cells transfected with PINK1-HA plus scrambled (scr) or Fbxo7 siRNA following 1 or 3 h treatment with CCCP (10 μM). Cells were scored visually for the colocalization of PINK1-HA with complex Vβ subunit (CxVβ), a mitochondrial marker. Nuclei (blue) are stained with DAPI. Histograms indicate the percentage of cells in which PINK1-HA accumulated at the mitochondria. Data are presented as mean ± s.e.m.; *P 0.05. Representative images are displayed for cells transfected as indicated, following 0 or 3 h CCCP treatment. For corresponding images at 0 h and 1 h treatment, see Supplementary Figure 5a. Scale bars, 10 μm."
NCBI gene IDs:
"Fbxo7: 25793
PINK1: 65018"
Figure legend: "(b) Fbxo7 accumulation in the mitochondrial fraction following treatment with CCCP (10 μM) is impaired in SH-SY5Y cells transfected with PINK1 siRNA compared to scrambled siRNA (scr). IB, immunoblot. Full-length blots are presented in Supplementary Figure 9."
NCBI gene IDs:
"PINK1: 65018"
Figure legend: "(c-f) Overexpression of Fbxo7 does not rescue climbing (c,e) or flight (d,f) defects in PINK1 male mutants (PINK1B9) or PINK1:parkin double mutants (PINK1B9;park25, daG4). Control genotypes are PINK1B9/+; da-GAL4/+ (c,d) and da-GAL4/+ (e,f). Histograms indicate mean ± s.e.m. One-way ANOVA with Bonferroni correction (***P 0.001). For climbing and flight assays, at least 50 flies were assessed; number of flies is shown for each bar for c-f."
NCBI gene IDs:
"GAL4: 
da: 34413
Fbxo7: 25793
parkin: 50873
PINK1: 65018"