EMBO/SourceData huggingface dataset:
Figure legend: "A. WB  analysis of the impacts of S53A 2FLAG-eIF4E  (2Flag-S53A) relative to WT 2FLAG-eIF4E  (2Flag-eIF4E) on SF production. CCND1  served as positive controls, and β-actin or HSP90  as loading controls. Both 2FLAG-eIF4E  (2Flag-eIF4E) and endogenous eIF4E  (endog-eIF4E) are shown. Each β-actin or HSP90 blot  corresponds to the above western blots. S53A eIF4E  protein levels are indistinguishable from eIF4E. Experiments were carried out using three separate clones for eIF4E, S53A and Vector controls, and one representative experiment is shown. (Right) Western blots  were quantified by FIJI, intensities normalized to Vector control and plotted using PRISM. The mean, standard deviation, and p-values are shown. Student t-test: * p&lt;0.05, **p&lt;0.01, ***p&lt;0.001."
NCBI gene IDs:
"FLAG: 
Flag: 
eIF4E: 13684
eIF4E: 1977"
Figure legend: "B. Polysomal  loading analysis was measured to assess the relevance of  eIF4E's capacity to increase translation efficiency on SF protein production. Top panel shows the polysomal  profile (at 254 nm) demonstrating that 2FLAG-eIF4E  overexpression did not alter the profile relative to Vector controls, consistent with previous studies Polysomes  were isolated by size exclusion chromatography (SEC) and thus the heaviest polysomes  elute first and monosomes   last. (Middle and Bottom panels) RNAs were monitored on heavy, light or monosome polysomes  using  RT-qPCR  and presented as a fraction for the given RNA. Known translation targets of eIF4E, MYC  and VEGF  was shifted to higher polysomes  in eIF4E  overexpressing cells as well as SF-encoding RNAs with altered polysomes  (middle) or those that were unchanged by eIF4E  including the negative control ACTB  are in the bottom panel Experiments were carried out in biological duplicates using different clones. Means are shown and p-values calculated using ANOVA (PRISM) . Data information: ANOVA test, * p&lt;0.05, **p&lt;0.01, ***p&lt;0.001"
NCBI gene IDs:
"FLAG: 
ACTB: 60
eIF4E: 13684
eIF4E: 1977
MYC: 4609
VEGF: 7422"
Figure legend: "B.  Western blot  analysis of untreated (Ctrl) and Ribavirin  treated (Rib) Vector and eIF4E NOMO-1 cell lines. Myc, and Mcl1  served as positive controls, and β-actin as a loading control. Each β-actin blot  corresponds to the above WBs. Experiments were carried out at least three independent times, and one representative experiment is shown. Ribavirin  dose was 10uM which is clinically achievable"
NCBI gene IDs:
"eIF4E: 13684"
Figure legend: "E. Total levels of UsnRNA in NOMO-1 Vector and eIF4E  cells monitored by RT-qPCR. Data were normalized to Vector control and shown as a fold change. The mean and standard deviation, as well as p-values (using Student t-test) were derived from three biological replicates each carried out in triplicate for all panels."
NCBI gene IDs:
"eIF4E: 13684"
Figure legend: "C. Validation of splicing targets identified by rMATs in U2OS (upper panel) and  NOMO-1 (lower panel) cell lines. RT-qPCR analysis using specific primers for each splicing event normalized to the corresponding total levels of that given transcript Data were normalized to Vector control to calculate fold change. The mean and standard deviation, as well as p-values were derived from three biological replicates. P-values were calculated between eIF4E  overexpressing and Vector cells (when the asterisk is over eIF4E), and eIF4E  cells treated with Ribavirin  vs eIF4E  overexpressing untreated cells (for the asterisk over Ribavirin). Data information: Student t-test, * p&lt;0.05, **p&lt;0.01, ***p&lt;0.001"
NCBI gene IDs:
"eIF4E: 13684"
Figure legend: "D. eIF4E    associates with both pre-mRNA splicing  substrates and their spliced products. The enrichment of mRNAs for splicing  targets in eIF4E-RIPs  versus input mRNAs from the nuclear  fractions of 2FLAG-eIF4E U2OS  cells monitored by RT-qPCR  using primers for the specific splice event (S for \"spliced\"), pre-mRNA specific primers to the relevant intron or intron-exon boundary (NS for \"unspliced\"), and primers specific to common regions present in all spliced and not-spliced mRNAs (All). Data were normalized to input samples and presented as a fold change. The mean, standard deviation and p-values (Student t-test) were derived from three independent experiments (each carried out in triplicate). Data information: Student t-test, * p&lt;0.05, **p&lt;0.01, ***p&lt;0.001"
NCBI gene IDs:
"FLAG: 
eIF4E: 13684"
Figure legend: "(A-C) Representative western blots of Pum1, Pum2, Fmrp, Ago2, Rbfox3, Cnot1, and Mov10 in (A) cerebellum, (B) hippocampus, and (C) cortex in both male (left panel) and female (right panel) WT, Pum1+/-, and Pum1-/- mice. All the experiments were conducted with equal numbers of 10-week-old male and female mice per genotype, for a total of at least 6 mice per genotype Graphs below show quantification for each protein by brain region, sex, and genotype. All data were normalized to Gapdh protein levels. P values were calculated by two-tailed Student's t test. *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001. P1 indicates Pum1."
NCBI gene IDs:
"Pum1: 80912"
Figure legend: "(D) Heatmap showing 166 microRNAs from cerebella of Pum1-/- male and female mice that were dysregulated (fold change -3 to +3) relative to wild-type cerebellum. (E) Heatmap showing mRNA quantification by qPCR for 49 targets co-bound by a minimum of eight dysregulated miRNAs (&gt;25% change) from panel D. Statistical significance and magnitude of dysregulation are illustrated for both male and female"
NCBI gene IDs:
"Pum1: 80912"
Figure legend: "(A, B) IP against PUM1 from Subject 1 (S1, R1147W) (A) and Subject 2 (S2, T1035S) (B) compared to their respective age-, sex-, and cell type- matched healthy controls confirm the interactions between PUM1 (used here as a positive control), and PUM2, FMRP, AGO2, CNOT1, and MOV10. Input (1%) was used as a loading control and IP against IgG was used as a negative control. GAPDH was used here as loading control, see Methods for quantification."
NCBI gene IDs:
"PUM1: 9698"
Figure legend: "(B) Representative western blots (left panel) and relative quantifications (right panel) of PUM1 and its interactors (AGO2, CNOT1, FMRP, and MOV10) in R1147W patient-derived cell lines after Myc-PUM1-WT expression."
NCBI gene IDs:
"Myc: 
PUM1: 9698"
Figure legend: "(C) mRNA quantification of the top 15 shared target genes from panel A in R1147W patient-derived cell lines after Myc-PUM1-WT expression."
NCBI gene IDs:
"Myc: 
PUM1: 9698"
Figure legend: "(A) SARS-CoV-2 genomic view showing the distribution of normalized 22nt small RNA reads from Caco-2 and A549-ACE2 cells at 24 and 48 hpi. The most abundant small RNAs are marked by the red and blue boxes. For all the experiments shown n=2."
NCBI gene IDs:
"ACE2: 59272"
Figure legend: "(C) Percentage of conservation along the nucleotide positions in the ORF7a among 4,055,609 sequenced SARS-CoV-2 genomes. The first 70 nt are shown in red and shows a higher percentage of conservation compared to the rest of the sequence of ORF7a. Boxplot shows the distribution of conservation percentage for each nucleotide either in the first 70 nt or 71-366 nt of ORF7a among 4,055,609 sequenced SARS-CoV-2 genomes. Box plots display median (line), first and third quartiles (box), and 5th /95th percentile value (whiskers). Each dot represents the outliers. Two-tailed P values were calculated using the student's t-test."
NCBI gene IDs:
"ORF7a: 43740573"
Figure legend: "(A) Log2 fold changes of the levels of hsa-miR-let-7a, CoV2-miR-O7a.1 and COV2-miR-O7a.2 in DICER1 knockdown SARS-CoV-2-infected A549-ACE2 cells compared to control cells analyzed by stem-loop RT-qPCR. Results from three independent replicates are shown."
NCBI gene IDs:
"CoV2-miR-O7a.1: 
COV2-miR-O7a.2: 
ACE2: 59272
DICER1: 23405
hsa-miR-let-7a: 406881"
Figure legend: "(B) In vitro kinetics of DICER1 mediated cleavage of pre-CoV2-miR-O7a stem-loop precursor, pre-CoV2-miR-O7a with mutations that prevent the formation of stem-loop structure and pre-hsa-miR21. Folded conformations for the three precursor molecules are shown. Fold change in the production of mature CoV2-miR-O7a.2 is shown in presence of DICER1 compared to control reaction (no DICER1) as measure by stem-loop RT-qPCR. Bars and error bars represent the average and standard deviation from three independent experiments."
NCBI gene IDs:
"CoV2-miR-O7a: 
CoV2-miR-O7a.2: 
DICER1: 23405
hsa-miR21: 406991"
Figure legend: "(C) Expression levels of the virus-derived miRNAs as a percentage of the viral genome. Absolute quantification of virus-derived miRNAs and viral genome from infected A549-ACE2 cells was performed using two spike-in (see methods). Line represents the average and individual dots represent data from two independent experiments."
NCBI gene IDs:
"ACE2: 59272"
Figure legend: "(D) copy number per cell of hsa-miR-let-7a, CoV2-miR-O7a.1 and CoV2-miR-O7a.2 in infected A549-ACE2 cells quantified using a synthetic small RNA spike-in standard curve by stem-loop RT-qPCR. Levels of hsa-miR-let-7a were normalized for the percentage of infected cells. Bars and error bars represent the average and standard deviation from at least three independent experiments."
NCBI gene IDs:
"CoV2-miR-O7a.1: 
CoV2-miR-O7a.2: 
ACE2: 59272
hsa-miR-let-7a: 406881"
Figure legend: "(E) Loading of hsa-miR-let-7a, CoV2-miR-O7a.1 and COV2-miR-O7a.2 into AGOs as measured by stem-loop RT-qPCR and analyzed as a percentage of input from the immunoprecipitates (IPs) of either pan-AGO IP or control IgG IP from infected A549-ACE2 cells. Levels of miRNA were normalized for the percentage of infected cells."
NCBI gene IDs:
"CoV2-miR-O7a.1: 
COV2-miR-O7a.2: 
ACE2: 59272
hsa-miR-let-7a: 406881"
Figure legend: "(B) Relative firefly luciferase normalized to Renilla luciferase of pmirGLO Dual-Luciferase miRNA Target Expression Vector with either CoV2-miR-O7a.2 target site or CoV2-miR-O7a.2 site with mutations in seed region at 24 h on co-transfection with CoV2-miR-O7a.2 or control miRNA mimics. Activity on transfecting control miRNA mimic was considered 100 %. Bars and error bars represent the average and standard deviation from three independent experiments."
NCBI gene IDs:
"Renilla luciferase: 
CoV2-miR-O7a.2: 
firefly luciferase: "
Figure legend: "(D) Kinetics of BATF2 and LAMP3 mRNA levels in non-induced and interferon IFN-α-induced (for 8, 16, and 24 h) A549-ACE2 cells transfected with either control or CoV2-miR-O7a.2 mimics. Normalized read abundances in transcript per million (TPM) are shown for two individual experiments (n=2)."
NCBI gene IDs:
"CoV2-miR-O7a.2: 
ACE2: 59272
BATF2: 116071
LAMP3: 27074"
Figure legend: "(E) Genomic view of the human BATF2 gene showing normalized RNA-seq reads from non-induced and IFN-α-induced (for 8 h) A549-ACE2 cells transfected with either control, CoV2-miR-O7a.1 or CoV2-miR-O7a.2 mimics. The complementary site of CoV2-miR-O7a to BATF2 3´UTR is shown."
NCBI gene IDs:
"CoV2-miR-O7a: 
CoV2-miR-O7a.1: 
CoV2-miR-O7a.2: 
ACE2: 59272
BATF2: 116071"
Figure legend: "(A, B) Volcano plots showing the log2 fold change and corresponding significance levels of ISGs upon 8 hours of IFN-α treatment in A549-ACE2 cells transfected with CoV2-miR-O7a.1 (A) or CoV2-miR-O7a.2 (B) compared to control mimic. Significantly downregulated genes are marked in red, and upregulated genes in blue. The orange horizontal line indicates two-tailed P = 0.05. n=2, dashed lines represent +1 and -1 log2 fold change."
NCBI gene IDs:
"CoV2-miR-O7a.1: 
CoV2-miR-O7a.2: 
ACE2: 59272"
Figure legend: "(C) Log2 fold change of ISGs at 8, 16, 24 hours of IFN-α treatment and categorized based on CoV2-miR-O7a.2 target sites 8mer, 7mer-m8, 7mer-A1, and no seed as shown in the schematic. The mean and standard error of the mean is shown. Number of ISGs with 8mer site n=8, 7mer-m8 n= 32, 7mer-A1 n=26 and no seed n= 92. The two-tailed p values were calculated using the Mann-Whitney-Wilcoxon test. ISGs were calculated as all the upregulated genes (≥ 3-fold; padj &lt; 0.05) in two replicates of IFN-induced versus non-induced conditions in all time points."
NCBI gene IDs:
"CoV2-miR-O7a.2: "
Figure legend: "(A) Heat map showing log2 fold change of expression of ISGs in A549-ACE2 cells across 8, 16 and 24 h time points upon IFN-α treatment compared to non-treated controls. The common upregulated genes (≥ 3-fold; padj &lt; 0.05) in IFN-induced versus non-induced conditions at all time points were categorized as ISGs."
NCBI gene IDs:
"ACE2: 59272"
Figure legend: "(A) Expression levels of CoV2-miR-O7a.1, CoV2-miR-O7a.2 and a 22 nt region from the ORF6 of the viral genome that does not produce detectable levels of small RNAs (Control ORF6) analyzed by stem-loop RT-qPCR from nasopharyngeal swabs of patients tested positive for COVID-19 or another seasonal human coronavirus (HCoV). Relative expression to hsa-miR-let-7a is shown. Ct values in parenthesis refer to the Ct value for the detection of viral genome in patient swab samples."
NCBI gene IDs:
"CoV2-miR-O7a.1: 
CoV2-miR-O7a.2: 
hsa-miR-let-7a: 406881
ORF6: 43740572"
Figure legend: "a, MEFs of RagA+/+, RagAGTP/+ and RagAGTP/GTP genotypes were deprived of amino acids for 1 h and re-stimulated for 10 min. Whole-cell protein lysates were immunoblotted for indicated proteins."
NCBI gene IDs:
"RagA: 68441"
Figure legend: "b, Total RNA was extracted from RagA+/+ (n = 3), RagAGTP/+ (n = 3) and RagAGTP/GTP (n = 2) MEFs and RagA mRNA expression determined by quantitative PCR (mean ± s.e.m.)."
NCBI gene IDs:
"RagA: 68441"
Figure legend: "c, Weights of RagA+/+ (n = 24), RagAGTP/+ (n = 52) and RagAGTP/GTP (n = 22) mice at birth (data are scatter dots, mean)."
NCBI gene IDs:
"GTP: 68441
RagA: 68441"
Figure legend: "d, Representative photographs of RagA+/+, RagAGTP/+ and RagAGTP/GTP neonates. Scale bar, 1 cm."
NCBI gene IDs:
"GTP: 68441
RagA: 68441"
Figure legend: "e, Early suppression of mTORC1 signalling after birth was determined by immunoblotting of protein extracts from liver and heart of RagA+/+ (+/+), RagAGTP/+ (G/+) and RagAGTP/GTP (G/G) neonates immediately after Caesarean section (0 h) or after 1 h of fasting (1 h fast)."
NCBI gene IDs:
"GTP: 68441
RagA: 68441"
Figure legend: "f, Liver and heart extracts from RagA+/+, RagAGTP/+ and RagAGTP/GTP neonates fasted for 10 h were analysed by immunoblotting for the indicated proteins."
NCBI gene IDs:
"GTP: 68441
RagA: 68441"
Figure legend: "a, Glycaemia drop in RagA+/+, RagAGTP/+ and RagAGTP/GTP and recovery in fasted RagA+/+ and RagAGTP/+ but not in RagAGTP/GTP neonates (+/+: n = 5, 18, 4, 5, 9, 8; G/+: n = 10, 26, 10, 13, 26, 21; G/G: n = 7, 20, 9, 10, 16, 11, for 0, 1, 2, 3, 6 and 10 h, respectively; mean ± s.e.m.)."
NCBI gene IDs:
"GTP: 68441
RagA: 68441"
Figure legend: "b, Rapamycin significantly increases glycaemia in RagAGTP/GTP fasted for 6 and 10 h (mean ± s.e.m.). NS, not significant."
NCBI gene IDs:
"GTP: 68441
RagA: 68441"
Figure legend: "c, Extension of survival by glucose injections in fasted RagAGTP/GTP neonates (untreated: n = 10; glucose: n = 5)."
NCBI gene IDs:
"GTP: 68441
RagA: 68441"
Figure legend: "e, Left: representative electron microscopy images showing abundant glycogen content in RagA+/+ and RagAGTP/GTP hepatocytes before fasting (0 h, upper panels) and more pronounced glycogen depletion after 10 h of fasting (lower panels) in RagAGTP/GTP neonates. Right: quantification of hepatic glycogen content (+/+: n = 5, 3, 4, 4; G/+: n = 11, 7, 14, 15; G/G: n = 6, 4, 4, 6; for 0, 3, 6 and 10 h, respectively; mean ± s.e.m.; AU, arbitrary units)."
NCBI gene IDs:
"GTP: 68441
RagA: 68441"
Figure legend: ". f, Partial rescue of hepatic glycogen content in RagAGTP/GTP neonates fasted for 10 h and treated with rapamycin (rapa) (mean ± s.e.m.)."
NCBI gene IDs:
"GTP: 68441
RagA: 68441"
Figure legend: "g, Quantification of neonatal plasma amounts of branched-chain (BCAA) and essential amino acids at birth (left), after 10 h fasting (middle) and after 10 h fasting with rapamycin treatment (right) (n for +/+, G/+ and G/G, respectively: n = 4, 5 and 4 for 0 h; n = 4, 4 and 3 for 10 h; n = 2, 5 and 3 for rapamycin; mean ± s.d.). Values are expressed relative to RagA+/+ amounts at each time point."
NCBI gene IDs:
"RagA: 68441"
Figure legend: "h, Extension of survival by injection of a combination of gluconeogenic amino acids (a.a.) in fasted RagAGTP/GTP neonates (untreated: n = 10; amino acids: n = 8). *P  0.05; **P  0.01; ns, P &gt; 0.0"
NCBI gene IDs:
"GTP: 68441
RagA: 68441"
Figure legend: "a, Top: representative micrographs of autophagosomes and autophagolysosomes in hepatocytes from RagA+/+ neonates fasted for 1 h. Typical autophagosome with a double limiting membrane (arrows); autophagosome and several autolysosomes (arrowheads). Scale bars, 5 µm. Bottom: frequency of the two types of organelle (early: autophagosomes; late: autophagolysosomes) detected in cell profiles of hepatocytes and skeletal myocytes from RagA+/+ and RagAGTP/GTPneonates."
NCBI gene IDs:
"GTP: 68441
RagA: 68441"
Figure legend: "e, Recombinant LC3B-GFP was expressed in RagA+/+ and RagAGTP/GTPMEFs and LC3B localization, in the presence and absence of amino acids, monitored by fluorescence microscopy. LC3B-GFP (green fluorescent protein) clustering, indicative of autophagy, was observed in amino acid-starved RagA+/+ but not RagAGTP/GTPMEFs. Scale bar, 10 µm."
NCBI gene IDs:
"GTP: 68441
RagA: 68441"
Figure legend: "f, Localization of recombinant TFEB-GFP was determined in MEFs as in e. Nuclear (active) TFEB was observed in RagA+/+ MEFs upon amino-acid withdrawal."
NCBI gene IDs:
"RagA: 68441"
Figure legend: "a) AMPKa1/a2 double knockout (DKO) and wild-type (WT) MEFs were deprived of glucose for 1 h and re-stimulated for 10 min. Wholecell extracts were immunoblotted for the indicated proteins."
NCBI gene IDs:
"AMPKa1: 5562
a2: 108079"
Figure legend: "c, RagA+/+ and RagAGTP/GTP immortalized MEFs were deprived of glucose or amino acids and surviving cells quantified in triplicate after 48 h. Cell number is indicated relative to cell number at the start of the treatment; mean ± s.d.; ***P  0.005"
NCBI gene IDs:
"GTP: 68441
RagA: 68441"
Figure legend: "d, mTOR localization as detected by immunofluorescence. In HEK-293T cells, glucose deprivation causes mTOR to localize to diffuse small puncta throughout the cytoplasm. Re-addition of glucose leads to mTOR shuttling to the lysosomal surface, co-localizing with the lysosomal protein Lamp2. HEK-293T-RagBGTP cells show mTOR localized at the lysosomal surface, regardless of glucose concentrations. Scale bars, 10 μm."
NCBI gene IDs:
"RagBGTP: 10325"
Figure legend: "f, RagA+/+ and RagAGTP/GTP primary MEFs were cultured for 1 h in media with the glucose and amino-acid concentrations measured in neonates at birth (0 h) or after fasting for 1 h (1 h) and whole-cell protein extracts were analysed by immunoblotting."
NCBI gene IDs:
"GTP: 68441
RagA: 68441"
Figure legend: "A,B) Real-time qPCR analysis of ANG-2 levels in retina and RPE/choroid complexes of JR5558 and C57Bl/6J (C57) mice. A) Relative expression levels of ANG-2 were significantly increased in the RPE/choroid complexes of JR5558mice in comparison to C57, at 50 and 62 days old (P = 0.022 at D50 and P = 0.042 and at D62). B) By contrast, retina levels of ANG-2 were not significantly different between C57 and JR5558mice, indicating neovascularization is driven locally by ANG-2. SEM is shown as error bar with n = 4 animals per group. *Denotes statistical significance of JR5558mice compared to wild type C57bl6 using unpaired T-test for each time point analyzed separately."
NCBI gene IDs:
"ANG-2: 11601"
Figure legend: "(C) Western blot detection of p62 and LC3 in H1299 cells cotransfected with the indicated shRNA and the indicated plasmid and cultured in normal medium or after H2O2 (500μM) treatment. CHK2 NTm, a shRNA nontargetable mutant CHK2 rescue plasmid."
NCBI gene IDs:
"CHK2: 11200"
Figure legend: "(D) Autophagic flux is shown by representative confocal microscopic images of 293 cells stably-expressing GFP-mCherry-LC3 transfected with the indicated shRNA following HBSS starvation and H2O2 (500μM) treatment for 3h. Scale bar, 10 μm."
NCBI gene IDs:
"GFP: 
mCherry: 
LC3: 440738///81631///84557"
Figure legend: "(C) In vitro kinase assays to test the ability of recombinant CHK2 to phosphorylate recombinant GST-Beclin 1-WT, S9093A (AA), S90A and S93A protein. Reactions were analyzed by SDS-PAGE followed by autoradiography. The asterisks in the blot indicate the phosphorylation of Beclin 1 mutants."
NCBI gene IDs:
"Beclin 1: "
Figure legend: "(B) Immunoprecipitation of Bcl-2 with Flag-Beclin 1 WT, AA mutant and DD mutant in HCT116 cells in normal medium or after H2O2 (500μM) treatment for 1h."
NCBI gene IDs:
"Beclin 1: "
Figure legend: "(C-D) Autophagy levels were determined in Beclin 1-depleted H1299 cells with reconstituted expression of Beclin 1 WT, AA mutant or DD mutant in normal medium or after H2O2 (500μM) treatment for 3h in the presence (C) or absence (D) of CHK2."
NCBI gene IDs:
"Beclin 1: 8678
CHK2: 11200"
Figure legend: "(E) Representative electron microscopic image of an autophagosome (arrow, left panel, AP) and an autolysosome (arrow, right panel, AL) in H1299 Beclin 1 WT cells treated with H2O2 (500μM) for 6 hr. Scale bars, 500 nm. Electron microscopic quantification of autophagosomes (AP) and autolysosomes (AL) in H1299 cells with the indicated plasmids cultured for 6 hr in normal or H2O2 (500μM) treatment. All quantitative data are presented as mean ± s.e.m. from 3 independent experiments; *P &lt; 0.001 compared to Beclin 1 WT; #P &lt; 0.001 compared to Beclin 1 WT treated with H2O2; &amp;P &lt; 0.001 compared to Beclin 1 WT treated with H2O2 in the absence of CHK2."
NCBI gene IDs:
"Beclin 1: 8678
CHK2: 11200"
Figure legend: "H1299 cells transfected with the indicated plasmids in normal medium or after 12h glucose starvation (C) Representative FACS analysis of apoptosis. Results from three independent experiments are presented as a histogram. Data are presented as mean ± s.e.m. from 3 independent experiments; *P &lt; 0.05 compared to Beclin 1 S9093A (AA) treated with H2O2 or hypoxia (Mann-Whitney test)."
NCBI gene IDs:
"Beclin 1: "
Figure legend: "H1299 cells transfected with the indicated plasmids in normal medium or 48h hypoxia stimulation (D). Representative FACS analysis of apoptosis. Results from three independent experiments are presented as a histogram. Data are presented as mean ± s.e.m. from 3 independent experiments; *P &lt; 0.05 compared to Beclin 1 S9093A (AA) treated with H2O2 or hypoxia (Mann-Whitney test)."
NCBI gene IDs:
"Beclin 1: "
Figure legend: "(E) CHK2+/+ and CHK2-/- mice were subjected to MCAO for 1 hr and reperfusion for 12 h. Contralateral (C) and ipsilateral (I) tissues of the mouse brain were coronally sectioned and stained with 2 % TTC."
NCBI gene IDs:
"CHK2: 50883"
Figure legend: "(G-J) Immunoblots for p62, p-Beclin 1 Ser90, p-Beclin 1 Ser93 and Beclin 1 in the cortical extracts from ischemia and reperfusion-treated CHK2+/+ and CHK2-/- mice. Quantification of p62, p-Beclin 1 Ser90 and p-Beclin 1 Ser93 protein levels (n = 3 mice). Data are presented as mean ± s.e.m.; *P &lt; 0.05, **P &lt; 0.01 (Student's t-test)."
NCBI gene IDs:
"CHK2: 50883"
Figure legend: "(A) Mitochondrial extracts from 143B cells, COX1∆ and COX2∆ mutant cybrids and their respective isogenic controls (CON-1 and CON-2) were analyzed by SDS-PAGE and immunoblotting with the indicated antibodies. The graphs (right) show densitometric quantifications of the signals normalized to CII subunit SDHA. The mean of three independent controls (CON) was set to 100 and all measurements were referenced to that value. The values represent mean ± SD (n=3-8). Mann-Whitney U test was applied for statistical analyses. Variations between controls and mutants: α, p&lt;0.05; β, p&lt;0.01; γ, p&lt;0.001. Specific variations between COX1∆ and COX2∆ mutants: ∗p&lt;0.05; ∗∗p&lt;0.01."
NCBI gene IDs:
"COX1: 4512
COX2: 4513"