EMBO/SourceData huggingface dataset:
Figure legend: "FMR1 mRNA levels were analyzed via RT-qPCR in EBV-transformed lymphocyte cells derived from the patient's blood samples. Patient cells showed a ˜60% decrease in FMR1 mRNA compared to control cells (*P = 0.010, 0.383 ± 0.110 SD, n = 3). Treatment with translational blocker puromycin restored FMR1 mRNA levels in patient cells (*P = 0.048, 0.383 ± 0.110 SD versus 1.25 ± 0.166 SD, n = 3), suggesting that the reduction of FMR1 mRNA in these cells is primarily due to nonsense-mediated decay. RT-qPCR reactions were run in triplicate in three independent experiments. Fold changes in FMR1 expression, normalized to HRPT expression, were calculated using the ΔΔCT method, and analyzed statistically with a two-tailed t-test (GraphPad). Error bars represent mean values with SD."
NCBI gene IDs:
"HRPT: 
FMR1: 2332"
Figure legend: "A-C HEK293 (A) and SH-Sy5y (B) cells, as well as primary neurons from FMR1 KO mice (C), were transfected with vectors encoding the GFP-tagged wild-type FMRP (GFP-FMR1WT) or the GFP-tagged patient FMRP (GFP-FMR1G-insertion) under the control of a β-actin promoter. Wild-type FMRP localizes predominantly in the cytoplasm, whereas the patient FMRP forms nuclear and nucleolar aggregates that colocalize with nucleophosmin. Scale bars in (A, B) represent 10 μm. Scale bar in (C) represents 5 μm."
NCBI gene IDs:
"β-actin: 60
FMR1: 2332
FMR1: 14265"
Figure legend: "Transfected HEK293 cells expressing a GFP-tagged FMRP in which the C-terminus is truncated following the G-ins. mutation site (GFP-FMR1ΔCt). GFP-FMR1ΔCt protein is exclusively cytoplasmic, suggesting that the truncation of the C-terminus alone is not sufficient to explain the localization change observed for the patientFMRP.Transfected HEK293 cells expressing a modified version of GFP-tagged patientFMRP (GFP-FMR1G-ins. [NLSmutated]). The novel amino acid sequence in the C-terminus of patientFMRP [RKRTRRKRTWRRLQRKRRSLPNR] contains stretches of arginines and lysines predicted to function as a nuclear localization signal (based on Expasy protein motif scanner, ScanProsite). Mutating adjacent R and K residues into alanines [RARTRAARTWARLQRAARSLPNR] abolishes the nucleolar localization of the patientFMRP, strongly suggesting that the novel amino acid sequence present in the patientFMRP C-terminus is a functional nuclear localization signal (NLS)."
NCBI gene IDs:
"FMR1: 2332"
Figure legend: "Transfected HEK293 cells expressing GFP-tagged wild-type FMRP fused to the patient NLS motif (GFP-FMR1wt+NLS). Unlike the patient FMRP, GFP-FMR1wt+NLS protein is predominantly cytoplasmic and does not aggregate in the nucleus. However, treatment of HEK293 cells expressing GFP-FMR1wt+NLS with leptomycin B-an inhibitor of nuclear export-resulted in the appearance of nucleolar inclusions. This suggests that the presence of a full-length C-terminus facilitates the nuclear export of FMRP in this context.Transfected HEK293 cells expressing a modified version of GFP-tagged patient FMRP, in which the truncation of the C-terminus is reverted by restoring the open reading frame (GFP-FMR1G-ins.[Ct restored]). The patient protein is not detected in the nucleus when the C-terminus is intact; however, nucleolar retention of the protein is observed upon leptomycin B treatment of the transfected cells. In line with results from (A), this suggests that an intact C-terminus enables nuclear export of the FMR1 protein.Data information: Scale bar represents 10 μm."
NCBI gene IDs:
"FMR1: 2332"
Figure legend: "The morphology of small lateral ventral neurons (sLNvs) is sensitive to dfmr1 activity. Overexpression of wild-type dfmr1 in the sLNv neurons results in a consistent \"axonal collapse\" phenotype, where the branching of axonal termini of sLNvs is reduced. Scale bars represent 50 and 10 μm (magnified images)."
NCBI gene IDs:
"dfmr1: 37528"
Figure legend: "Overexpression of wild-type dfmr1 (UAS-dfmr1wt) using a LNv neuron-specific driver line (Pdf-Gal4) causes reduction of branching area-\"axonal collapse\"-in the sLNv axonal termini. dfmr1ΔCt and dfmr1wt+NLS overexpression phenocopies overexpression of dfmr1wt, suggesting that the truncation of the C-terminus or the presence of the patient NLS alone does not impair or alter the functional efficacy of dfmr1 in this context. However, overexpression of dfmr1ΔCt+NLS fails to cause collapse of sLNv termini, indicating a significant loss or change of Dfmrp protein function. Axonal morphology is visualized by expressing CD8-GFP under the control of the same neuronal driver. Scale bar represents 10 μm.Quantification of axonal termini branching in LNv neurons overexpressing various dfmr1 alleles. Overexpression of dfmr1wt, dfmr1ΔCt, or dfmr1wt+NLS significantly reduced axonal branching area [****P &lt; 0.0001; control 101.3 ± 29.76 SD, n = 30; UAS-dfmrwt 45.41 ± 21.69 SD, n = 29; UAS-dfmrΔCt 52.31 ± 14.67 SD, n = 32; UAS-dfmrwt+NLS 72.45 ± 21.83 SD, n = 29; UAS-dfmrΔCt+NLS 117.8 ± 36.96 SD, n = 28]. dfmr1ΔCt+NLS overexpression does not result in a significant change of axonal branching area compared to the background control [Pdf-Gal4, UAS-GFP] (P = 0.672). For quantification purposes, each branching area (n) was manually outlined, starting from the first point of defasculation of the axonal bundle. These measurements were normalized for variability in brain size across samples using LNv commissure length measurements for each brain. Two-tailed t-tests using Welch's correction were then used to compare controls with mutant phenotypes (GraphPad). Error bars represent mean values with SD. Dots visible for box plots of UAS-dfmrwt and UAS-dfmrΔCt represent samples that outlier the whiskers."
NCBI gene IDs:
"Gal4: 
dfmr: 37528
dfmr1: 37528
Dfmrp: 37528
Pdf: 43193"
Figure legend: "Overexpression of dfmr1ΔCt+NLS results in aberrant axonal termini morphology. Axonal guidance defects were frequently observed (arrowheads) and scored manually for bifurcations of the axon bundle (9/48), tangling of axons in the termini (13/48), and apparent looping of axons (7/48)."
NCBI gene IDs:
"dfmr1: 37528"
Figure legend: "A-D Subcellular localization of transgenically expressed dfmr1wt, dfmr1ΔCt, dfmr1wt+NLS, and dfmr1ΔCt+NLS proteins in LNv neurons. DfmrpΔCt+NLS shows nuclear localization (A), colocalizing with the genetically encoded nuclear marker RedStinger, while Dfmrpwt, DfmrpΔCt, and Dfmrpwt+NLS are predominantly cytoplasmic (B-D). These results suggest that an intact C-terminus can mediate the nuclear export of the Dfmrp protein. Scale bar represents 5 μm."
NCBI gene IDs:
"dfmr1: 37528
Dfmrp: 37528"
Figure legend: "(A) Kaplan-Meier  estimate of overall survival of patients diagnosed with primary melanoma stratified by  CCN4  transcript abundance, with patients at risk tabulated below graph, Original data obtained from SKCM arm of TCGA and stratified based on CCN4 mRNA expression (CCN4 high/positive &gt; 1 FPKM: blue, CCN4 low/negative &lt; 1 FPKM: red). P-value calculated using the Peto &amp; Peto modified Gehan-Wilcoxon test."
NCBI gene IDs:
"CCN4: 8840"
Figure legend: "(B-E)  B16F0 knockout created with Homology-Directed Repair approach with controls for  puromycin selection (B16F0-Ctr) created with pBabe-puro retrovirus. YUMM1.7  knockout created with double nickase approach with KO1 and KO2 indicating two different clones. Wildtype (WT: red)  B16F0 (B,C) and  YUMM1.7 (D,E) cells and CCN4  knockout variants (KO1: blue, KO2: black) were subcutaneously injected into (B,D) C57BL/6 immunocompetent and (C,E) NSG immunocompromised mice. Tumor volumes measured by caliper as a function of  time after tumor challenge, with n expressed as the number of mice with tumors over the number of mice injected."
NCBI gene IDs:
"CCN4: 22402"
Figure legend: "(B-I) Graphs summarizing the change in frequency of immune cells in the YUMM1.7 tumor microenvironment following CCN4 knockout (n=6 /group). (B) CD3+, (C) CD4+, (D) CD8+, (E) NK cells, (F) CD11c+ TAMs, (G)  TANs, (H)  DCs, and (I) MDSC. Statistical significance was assessed using a Student's t-test using six biological replicates with results annotated with *: 0.01 "
NCBI gene IDs:
"CCN4: 22402"
Figure legend: "(K) Kaplan-Meier summary of the fraction tumor free in a 2x2 factor experimental design (n = 5 / group), where Tet-on vector control (red) versus inducible mCCN4 vector (black) and in the presence (dotted lines) or absence (solid lines) of doxycycline were the two factors."
NCBI gene IDs:
"CCN4: 22402"
Figure legend: "(M) Representative flow cytometry data of the frequency of tumor-infiltrating  MDSC (GR1+ CD11c−/lo : dotted box) from the live  CD45+ CD11b+ compartment isolated from  CCN4-induced rescue (ID mCCN4 +  Dox) and CCN4 knockout (YM1.7-KO1) YUMM1.7 tumors."
NCBI gene IDs:
"CCN4: 22402"
Figure legend: "(E-H) Graphs summarizing G-MDSCs (E,G) and M-MDSCs (F,H) in the spleens of time-matched YUMM1.7-WT and CCN4 KO (KO1) tumor bearing mice  (n = 4/group) expressed as percentage of CD45+ (E,F) and total number per gram spleen (G,H). Statistical significance was assessed using a Student's t-test with results annotated with *: 0.01 tumor free mice."
NCBI gene IDs:
"CCN4: 22402"
Figure legend: "(A) Cytokine, chemokine, and growth factor expression by YUMM1.7-WT and CCN4-KO cells in vitro assayed using R&amp;D Systems' Mouse XL  Cytokine Array. Orange dots represent results for specific cytokine probes while blue dots represent positive and negative controls. Dotted lines enclose a null distribution estimated from positive and negative controls."
NCBI gene IDs:
"CCN4: 22402"
Figure legend: "(J-K) Analysis of the extracellular acidification rate (ECAR) associated with (J) glycolysis and (K) glycolytic capacity assayed by Seahorse Analyzer in WT and CCN4-KO tumors (n ≥ 12 biological replicates/group) after 36 hours ex vivo. Statistical significance was assessed using a Student's t-test with results annotated with ***: p&lt;0.001. Results of biological replicates summarized as mean ± SEM."
NCBI gene IDs:
"CCN4: 22402"
Figure legend: "(A) ELISpot  for  IFNγ  release by CD8+ T cells using parental YUMM1.7 and CCN4-KO YUMM1.7  (KO1) cells as targets and different amount of in vivo activated CD8+ T cells. Statistical significance was assessed using a Student's t-test with results annotated with ***: p&lt;0.001. Results of three biological replicates summarized as mean ± SEM. (B) ELISpot for IFNγ release by in vivo activated CD8+ T cells  with CCN4-inducible cells as targets in the presence or absence of 0.5 mg/ml doxycycline. Statistical significance was assessed using a Student's t-test with results annotated with ***: p&lt;0.001. Results of biological replicates summarized as mean ± SEM."
NCBI gene IDs:
"CCN4: 22402"
Figure legend: "(C) CD8+ T cells isolated from the  spleens of C57BL/6 mice that rejected  YUMM1.7  tumors were assayed by in vitro ELISpot using variants of the YUMM1.7 cell line as targets (WT YUMM1.7 (Ym1.7) - yellow, CCN4-KO YUMM1.7 (Ym1.7-KO1)- light green,  CCN4-KO YUMM1.7 with a blank inducible expression vector (Ym1.7-KO1-IDvector) - dark green and blue, CCN4-KO YUMM1.7 with a CCN4 inducible expression vector (Ym1.7-KO1-IDmCCN4) - purple and red). Representative images shown under indicated condition with scale bar indicating 1 mm. Variants containing the inducible expression vector were also cultured in the absence (dark green and purple) or presence of 0.5 μg/ml  doxycycline (blue and red).  CD8+ T cells expressing IFNγ  and TNFα were quantified following 24 hour co-culture (bar graph). Results shown as mean ± S.D. for three biological replicates. Statistical significance was assessed using a Student's t-test with results annotated with ***: p&lt;0.001 and n.s.: p&gt;0.05."
NCBI gene IDs:
"CCN4: 22402"
Figure legend: "(A) Average tumor volumes of mice bearing YUMM1.7-WT (squares and triangles) or CCN4-KO (KO1, circles and inverted triangles) tumors (n = 4 mice/group). Groups were treated with either  αPD1  (triangles and inverted triangles) or isotype control (squares and circles) antibodies when the tumors reached 100 mm3 (dotted line). Statistical significance at each time point was assessed using a Student's t-test with results annotated with *: 0.01 "
NCBI gene IDs:
"CCN4: 22402"
Figure legend: "CD8+ T cells  expressing PD1 within the tumor and spleen  were assayed by  flow cytometry  in mice bearing WT and CCN4-KO YUMM1.7 tumors Results representative of three biological replicates and summarized as mean ± SD. Statistical significance was assessed using a Student's t-test."
NCBI gene IDs:
"CCN4: 22402"
Figure legend: "B Identification of RabGGTβ as a binding protein of PTAR1. Anti-FLAG immunoprecipitates from control HeLa S3 cells or FLAG-PTAR1-expressing HeLa S3 cells were analyzed by SDS-PAGE and silver staining. The 35 kDa protein was identified as RabGGTβ by mass spectrometry. The asterisk denotes a degradation product of FLAG-PTAR1."
NCBI gene IDs:
"FLAG: 
PTAR1: 375743"
Figure legend: "D Biotin-geranylation of recombinant Ykt6 by GGTase-III. Bacterially produced recombinant untagged Ykt6 (left) was incubated with buffer, GGTase-III, or RabGGTase in the absence or presence of BGPP for 30 min at 37ºC. Biotin-geranylated Ykt6 was detected"
NCBI gene IDs:
"Ykt6: 10652"
Figure legend: "Geranylgeranylation of unprenyl WT Ykt6 and the site 1 or site 2 mutants by GGTase-III. WT and mutant Ykt6 proteins (5 μM each) were incubated with GGTase-III (100 nM) and 3H-GGPP (1 μM), and the amount of 3H-geranylgeranyl transferred to Ykt6 was quantified (mean ± SEM, n = 3)."
NCBI gene IDs:
"Ykt6: 10652"
Figure legend: "A Immunoblot of cell lysates from WT HAP1 cells and PTAR1 KO HAP1 cells using anti-Ykt6 antibody. Note the slight difference in the gel mobility of Ykt6 (arrows)."
NCBI gene IDs:
"PTAR1: 375743"
Figure legend: "C Prenylation status of Ykt6 in WT and PTAR1 KO cells. Recombinant Ykt6 samples and cell lysates of WT cells, PTAR1 KO cells, and PTAR1 KO cells stably expressing PTAR1 (KO + PTAR1) were separated by DOC-PAGE (upper) or SDS-PAGE (lower), and analyzed by immunoblotting with anti-Ykt6 antibody."
NCBI gene IDs:
"PTAR1: 375743"
Figure legend: "D In vitro reconstitution of Ykt6 double prenylation. Dialyzed cytosol prepared from PTAR1 KO HAP1 cells was incubated at 37ºC for the indicated times with recombinant GGTase-III (100 nM) or RabGGTase (100 nM) in the absence or presence of GGPP (10 μM). After incubation, reaction products were separated by DOC-PAGE (upper) or SDS-PAGE (lower), and analyzed by immunoblotting with anti-Ykt6 antibody."
NCBI gene IDs:
"PTAR1: 375743"
Figure legend: "A Representative confocal images of the Golgi apparatus in WT or PTAR1 KO HeLa cells. Cells were co-immunostained for GM130 (a cis-Golgi marker) and golgin-97 (a trans-Golgi marker). Images were deconvoluted using Huygens software. The lower panels show magnified images of the boxed region of the upper panels. Scale bars, 5 μm."
NCBI gene IDs:
"PTAR1: 375743"
Figure legend: "B Electron micrographs of the Golgi apparatus in WT or PTAR1 KO HAP1 cells. Arrows indicate Golgi stacks. Arrowheads indicate examples of unfused vesicles accumulated around the swollen Golgi cisternae in PTAR1 KO cells. Scale bars, 500 nm."
NCBI gene IDs:
"PTAR1: 375743"
Figure legend: "Defect in intra-Golgi trafficking in PTAR1 KO cells. (C) VSVG-GFP expressing WT and PTAR1 KO HeLa cells were cultured at 40ºC and then shifted to 32ºC. VSVG-GFP fluorescence images taken at the indicated times after the temperature shift are shown. The right panel shows quantification of VSVG-GFP fluorescence in the Golgi region after the temperature shift (mean ± SEM, n = 6)."
NCBI gene IDs:
"GFP: 
PTAR1: 375743
VSVG: 1489834"
Figure legend: "Defect in intra-Golgi trafficking in PTAR1 KO cells. (D) VSVG-GFP expressing WT HeLa cells, PTAR1 KO HeLa cells, and PTAR1 KO HeLa cells stably expressing PTAR1 (KO + PTAR1) were cultured at 40ºC and then shifted to 32ºC. At the indicated time points, cell surface proteins were biotinylated using sulfo-NHS-LC-biotin. Biotinylated VSVG-GFP was purified from cell lysates using avidin agarose and analyzed by immunoblotting with anti-GFP antibody. The right panel shows quantification of the cell surface biotinylated VSVG-GFP (means ± SEM, n = 3). Data were analyzed by one-way ANOVA with Dunnett's post-hoc test. *p &lt; 0.05, ***p &lt; 0.001."
NCBI gene IDs:
"GFP: 
PTAR1: 375743
VSVG: 1489834"
Figure legend: "E Analysis of LAMP1 glycosylation. Cell lysates of WT HeLa cells, PTAR1 KO HeLa cells, and PTAR1 KO HeLa cells stably expressing PTAR1 (KO + PTAR1) were analyzed by immunoblotting with anti-LAMP1 antibody (upper). Sialylated LAMP1 was precipitated from the cell lysates using Maackia amurensis leucoagglutinin (MAL) agarose and analyzed by immunoblotting (lower)."
NCBI gene IDs:
"PTAR1: 375743"
Figure legend: "F Defect in the Golgi SNARE assembly in PTAR1 KO cells. The Golgi SNARE complex was immunoprecipitated from NEM-treated WT HAP1 cells, PTAR1 KO HAP1 cells, and PTAR1 KO HAP1 cells stably expressing PTAR1 (KO + PTAR1) using control mouse IgG, anti-GS28 IgG, or anti-syntaxin 5 IgG. Immunoprecipitates were analyzed by immunoblotting with antibodies against syntaxin 5, GS28, GS15, and Ykt6. Syntaxin 5 has two isoforms with different translation initiation sites. Inputs were 20% (syntaxin 5, GS28, and GS15) and 2% (Ykt6). The data shown are representative of three independent experiments with similar results."
NCBI gene IDs:
"PTAR1: 375743"
Figure legend: "E‐G Relative mtDNA level (E), MitoSox fluorescence (F) and TMRM fluorescence (G) of cells stably expressing AOX or empty vector, as indicated, after 5 days of treatment with dsRNA against CG2968, as shown. Note that these cells were cultured in the presence of hygromycin to maintain the AOX‐expressing or control plasmid."
NCBI gene IDs:
"AOX: 5656847
CG2968: 31950"
Figure legend: "H Indicated parameters, following 5 days of treatment with dsRNA against CG2968, in cells grown in galactose‐containing (Gal) medium."
NCBI gene IDs:
"CG2968: 31950"
Figure legend: "D. Western blot of total protein extracts from control S2 cells and cells treated with dsRNAs against GFP or CG2968 (cV), probed for NDUFS3 (cI), ATP synthase subunit α (cV) and GAPDH (loading control)."
NCBI gene IDs:
"CG2968: 31950"
Figure legend: "(C) GFP-LC3 CHO cells were preincubated for 30 min in the presence or absence of 10 µM H89, and then they were incubated for 2 h with 1 mM dbcAMP to verify the activity of H89. Afterwards, cells were lysed with sample buffer and the samples were subjected to Western blot analysis using a rabbit anti-phosphoCREB and the corresponding HRP-labeled secondary antibody, and subsequently developed with an enhanced chemiluminescence detection kit. The band intensities were quantified with the Adobe Photoshop program (lower panel). These data are representative of two independent experiments."
NCBI gene IDs:
"LC3: 362245///64862"
Figure legend: "(A) GFP-LC3 CHO cells were preincubated with 10 µM 8-pCPT-2′-O-Me-cAMP (8-pCPT) for 30 min and then they were treated for 4 h with 10 µg/ml of α-hemolysin (Hla) or subjected to starvation conditions (Stv). Cells without any treatment were used as control. Cells were immediately analyzed by confocal microscopy. Quantification of the percentage of cells presenting LC3 puncta upon incubation under the different conditions is shown in the right panel (n = 50 cells/condition). These data are representative of two independent experiments."
NCBI gene IDs:
"LC3: 362245///64862"
Figure legend: "(B) CHO cells were cotransfected with GFP-LC3 and myc-EPAC wt (left panel) or myc-ΔEPAC (right panel). Twenty-four hours after transfection they were incubated for 2 h in starvation medium (Stv) or treated for 4 h with 10 µg/ml of α-hemolysin (Hla). Cells without any treatment were used as control (Ctr). Cells were analyzed by confocal microscopy. Images are representative of two independent experiments. (C) Quantification of the percentage of cells presenting LC3 puncta upon incubation under the different conditions (n = 20 cells/condition). These data are representative of two independent experiments"
NCBI gene IDs:
"EPAC: 
LC3: 64862///362245"
Figure legend: "(A) CHO cells were cotransfected with RFP-LC3 and GFP-Rap2b wt (left panel) or GFP-Rap2b ΔAAX (right panel). Twenty-four hours after transfection, they were incubated for 2 h in starvation medium (Stv), with 50 ng/µl of rapamycin (Rapa) in full nutrient media, or treated for 4 h with 10 µg/ml of α-hemolysin (Hla). Cells without any treatment were used as control (Ctr). Cells were analyzed by confocal microscopy. Images are representative of three independent experiments."
NCBI gene IDs:
"Rap2b: 5912"
Figure legend: "(C) CHO cells were transfected with GFP-Rap2b wt or GFP-Rap2b ΔAAX and incubated with complete medium without (Ctr) or with 10 µg/ml of α-hemolysin (Hla) for 4 h, with 50 ng/µl of rapamycin (Rapa) or subjected to starvation conditions (Stv) for 2 h in the absence or presence of bafilomycin A1. Afterwards, cells were lysed with sample buffer and the samples were subjected to Western blot analysis using a rabbit anti-LC3 and the corresponding HRP-labeled secondary antibody, and subsequently developed with an enhanced chemiluminescence detection kit. These data are representative of two independent experiments."
NCBI gene IDs:
"Rap2b: 5912"
Figure legend: "(A) HeLa cells were cotransfected with Rap2b siRNA and GFP-LC3 (right panel) or irrelevant siRNA and GFP-LC3 (left panel). Forty-eight hours after transfection, they were incubated for 2 h in starvation medium (Stv), with 50 ng/µl of rapamycin (Rapa) or treated for 4 h with 10 µg/ml of α-hemolysin (Hla). Cells without any treatment were used as control (Ctr). Cells were analyzed by confocal microscopy. Images are representative of two independent experiments."
NCBI gene IDs:
"LC3: 362245///64862
Rap2b: 5912"
Figure legend: "(C) Upper panel: The knockdown of Rap2b was determined by Western blot as indicated in Materials and Methods. Lower panel: The band intensities of two independent experiments were quantified with the Adobe Photoshop program, and normalized against tubulin. * p&lt;0.05 (paired Student's t-test)."
NCBI gene IDs:
"Rap2b: 5912"
Figure legend: "(D) HeLa cells were cotransfected with GFP-LC3 and Rap2b siRNA or an irrelevant siRNA and incubated for 4 h with complete medium in the absence (Ctr) or presence of 10 µg/ml of α-hemolysin (Hla), with 50 ng/µl of rapamycin (Rapa) or subjected to starvation conditions (Stv) for 2 h. Afterwards, cells were lysed with sample buffer and the samples were subjected to Western blot analysis using a rabbit anti-LC3 and the corresponding HRP-labeled secondary antibody, and subsequently developed with an enhanced chemiluminescence detection kit. These data are representative of two independent experiments."
NCBI gene IDs:
"LC3: 64862///362245
Rap2b: 5912"
Figure legend: "cAMP cannot inhibit the autophagy induced by the toxin in cells overexpressing the Rap2b negative mutant.(A) CHO cells were cotransfected with RFP-LC3 and GFP-Rap2b ΔAAX. Twenty-four hours after transfection they were incubated for 2 h in starvation medium (Stv) or treated for 4 h with 10 µg/ml of α-hemolysin (Hla) in the presence (right panels) or absence of 1 mM dbcAMP (left panels). Cells without any treatment were used as control (Ctr). Cells were analyzed by confocal microscopy. Images are representative of two independent experiments. (B) Quantification of the percentage of cells presenting LC3 puncta (i.e., stimulated cells) upon incubation with the different conditions. These data are representative of two independent experiments."
NCBI gene IDs:
"LC3: 362245///64862
Rap2b: 5912"
Figure legend: "CHO cells were cotransfected with GFP-LC3 and myc-EPAC wt (upper panel) or myc-ΔEPAC (lower panel). Twenty-four hours after transfection, they were infected for 4 h with the wt strain of S. aureus (wt), the mutant deficient for α-hemolysin (Hla−), or the Hla(−) mutant expressing an α-hemolysin plasmid (Hla(−)+pHla). The nucleus and the bacteria were labeled with TOPRO as indicated in Materials and Methods and immediately visualized by confocal microscopy. Images are representative of three independent experiments."
NCBI gene IDs:
"EPAC: 
LC3: 64862///362245"