EMBO/SourceData huggingface dataset:
Figure legend: "(D) Immunoblotting analysis of coimmunoprecipitated TFEB-FLAG-S211A with Rag heterodimers. IP, immunoprecipitation."
NCBI gene IDs:
"TFEB: 7942"
Figure legend: "(A) ARPE-19 cells were infected with adenovirus expressing TFEB-FLAG-WT. 16 h later, cells were incubated with 250 nM Torin-1 for 1 h or starved in serum- and amino acid-free medium for 3 h. Cells were then fixed, permeabilized with 0.2% saponin, and double stained with antibodies against TFEB (used to detect recombinant TFEB) and Lamp1."
NCBI gene IDs:
"TFEB: 7942"
Figure legend: "(B) ARPE-19 cells were infected with adenovirus expressing TFEB-FLAG-S211A. 12 h later, cells were starved in serum- and amino acid-free medium for 4 h (starvation) or kept in complete medium (control). Cells were then fixed, permeabilized with 0.2% Triton X-100, and stained with antibodies against FLAG (used to detect TFEB-S211A)."
NCBI gene IDs:
"TFEB: 7942"
Figure legend: "(A and B) ARPE-19 cells were transfected with either active or inactive RagB/D heterodimers and infected with adenovirus expressing TFEB-FLAG-WT (A) or TFEB-FLAG-S211A (B). After 12 h, cells were double stained with antibodies against FLAG and GST (used to detect TFEB or Rag proteins, respectively). (C) Quantification of TFEB-WT nuclear localization from A. (D) Quantification of TFEB-S211A lysosomal localization from B."
NCBI gene IDs:
"TFEB: 7942"
Figure legend: "(A) Summary of the nuclear and lysosomal distribution of several TFEB amino acid and deletion mutants in ARPE-19 cells treated with either DMSO or Torin-1."
NCBI gene IDs:
"TFEB: 7942"
Figure legend: "(B) ARPE-19 cells were nucleofected with the indicated Rag- and TFEB-expressing plasmids. After 12 h, cell lysates were immunoprecipitated with the anti-FLAG antibody and analyzed by immunoblotting with antibodies against FLAG and GST (used to detect TFEB and Rag proteins, respectively)."
NCBI gene IDs:
"TFEB: 7942"
Figure legend: "(C) FLAG-tagged TFEB-WT or TFEB deletion mutants were immunoprecipitated with the anti-FLAG antibody and analyzed by immunoblotting with antibodies against FLAG, 14-3-3 binding motif, or 14-3-3."
NCBI gene IDs:
"TFEB: 7942"
Figure legend: "(D) Immunofluorescence confocal microscopy showing the subcellular distribution of TFEB-WT and TFEB-S3A/R4A mutant upon incubation with DMSO (vehicle) or 250 nM Torin-1 for 1 h. Cells were fixed, permeabilized with 0.2% Triton X-100, and stained with antibodies against FLAG (used to detect TFEB)."
NCBI gene IDs:
"TFEB: 7942"
Figure legend: "(E) ARPE-19 cells expressing either TFEB-S211A or TFEB-S211A-Δ30 were double stained with antibodies against TFEB and Lamp1. Regions within the dotted boxes are magnified in the insets."
NCBI gene IDs:
"TFEB: 7942"
Figure legend: "(A) ARPE-19 cells coexpressing active RagB/D heterodimer and the indicated TFEB plasmids were fixed, permeabilized with 0.2% saponin, and stained with antibodies against GST (used to detect Rag proteins). Regions within the dotted boxes are magnified in the insets. Bars, 10 µm."
NCBI gene IDs:
"TFEB: 7942"
Figure legend: "(B) ARPE-19 cells were cotransfected with active RagB/D heterodimers and the indicated TFEB constructs. After 18 h, cell lysates were immunoprecipitated with the anti-HA antibody (used to immunoprecipitate Rag proteins) and immunoblotted with antibodies against GFP and GST (used to detect TFEB-GFP and Rag proteins, respectively). The white line indicates that intervening lanes have been spliced out."
NCBI gene IDs:
"TFEB: 7942"
Figure legend: "(C) Immunofluorescence confocal microscopy showing the subcellular distribution of TFEB-(1-30)-GFP in ARPE-19 cells coexpressing active RagB/D heterodimers (antibodies against GST were used to detect Rags). Bar, 4 µm."
NCBI gene IDs:
"TFEB: 7942"
Figure legend: "(D) Relative RT-PCR analysis of the mRNA expression of autophagy (ATG9B and UVRAG) and lysosomal (MCOLN1) genes in ARPE-19 cells infected with the indicated adenovirus for 48 h. The values are expressed as a ratio to RNA from cells infected with control adenovirus (Ad.-Null). Values are means ± SD of two independent experiments. ***, P &lt; 0.001; **, P &lt; 0.01."
NCBI gene IDs:
"ATG9B: 285973
MCOLN1: 57192
UVRAG: 7405"
Figure legend: "(G) ARPE-19 cells expressing active (RagBGTP/RagDGDP) or inactive (RagBGDP/RagDGTP) Rag heterodimers were immunoprecipitated with the anti-FLAG antibody and immunoblotted with antibodies against FLAG and GST (used to detect MITF and Rag proteins, respectively)."
NCBI gene IDs:
"RagB: 10325
RagD: 58528"
Figure legend: "(H) HEK-293T cells expressing active (RagBGTP/RagDGDP) or inactive (RagBGDP/RagDGTP) Rag heterodimers were pulled down using glutathione-Sepharose beads and immunoblotted with antibodies against GST and MITF (used to detect Rag proteins and endogenous MITF, respectively). IP, immunoprecipitation."
NCBI gene IDs:
"RagB: 10325
RagD: 58528"
Figure legend: "(G) Left, Ki67 staining  of PDI+/+ and PDI-/- hESCs. Scale bar, 25 µm. Right, statistical analysis of Ki67-positive cells. n = 3 independent experiments. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"PDI: 5034"
Figure legend: "(C) Immunostaining  of PDI  and calreticulin  (CRT) in PDI+/+ and PDI-/- hMSCs, CRT  was used as ER  marker. Scale bar, 25 µm."
NCBI gene IDs:
"PDI: 5034"
Figure legend: "(D) Western blotting  analysis of PDI  family members expression  in PDI+/+ and PDI-/- hMSCs  at early-passage  (P3) and   late-passage   (P8). GAPDH  was used as the loading control."
NCBI gene IDs:
"PDI: 5034"
Figure legend: "(G) Left, Ki67 staining  of PDI+/+ and PDI-/- hMSCs  at P8. Scale bar, 20 µm. Right, statistical analysis of Ki67-positive cells. n = 3 biological repeats. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"PDI: 5034"
Figure legend: "(H) Left, SA-β-gal staining  of PDI+/+ and PDI-/- hMSCs  at P8. Scale bar, 200 µm. Right, statistical analysis of SA-β-gal-positive cells. n = 3 biological repeats. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"PDI: 5034"
Figure legend: "(K) Left, western blotting showing the P16 expression  in PDI+/+ and PDI-/- hMSCs  at P8. GAPDH  was used as the loading control. Right, statistical analysis of relative P16 protein expression  levels. n = 3 independent experiments. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"PDI: 5034"
Figure legend: "(M) Left, Immunostaining  of 53BP1  and γH2AX  in PDI+/+ and PDI-/- hMSCs  at P8. White arrowheads indicate 53BP1  and γH2AX  double positive cells. Right, statistical analysis of 53BP1  and γH2AX  double positive cells. Scale bar, 10 µm. n = 3 biological repeats. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"PDI: 5034"
Figure legend: "(P) Left, Ki67 staining  of PDI-/- hMSCs  transduced with lentiviruses  expressing Luc  or PDI. Scale bar, 10 µm. Right, statistical analysis of Ki67-positive cells. n = 3 biological repeats. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"Luc: 
PDI: 5034"
Figure legend: "(Q) Left, SA-β-gal staining  of PDI-/- hMSCs  transduced with lentiviruses  expressing Luc  or PDI. Scale bar, 200 µm. Right, statistical analysis of SA-β-gal-positive cells. n = 3 biological repeats. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"Luc: 
PDI: 5034"
Figure legend: "(A) Oxidative  folding of Myc-tagged J-Chain (JcM). PDI+/+ and PDI-/- hMSCs  were transfected with JcM  for 48 hr, then were pulsed with DTT  and chased at indicated time  after DTT  removal. The lysates were analyzed using non-reducing SDS-15% PAGE and α-Myc western blotting. The mobility of reduced JcM  monomers (Red), oxidized  monomers (Oxi), homodimers (Dim), and high-molecular-weight (HMW) species are indicated."
NCBI gene IDs:
"JcM: 3512
PDI: 5034"
Figure legend: "(D) Time-dependent changes of H2O2  levels in the ER  of PDI+/+ and PDI-/- hMSCs  at P8. Left, the fluorescence intensity ratio of HyPer-ER  at 535 nm with excitation at 488 and 405 nm were firstly monitored at resting state for 5 min, followed by addition of 0.5 mM DTT  (yellow bar) for another 15 min. Right, statistical analysis of the fluorescence intensity ratio at 488/405 nm excitation of HyPer-ER  probe at 15 min post DTT  addition. n = 3 independent experiments. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"PDI: 5034"
Figure legend: "(E) Analysis of the H2O2  levels in PDI+/+ and PDI-/- hMSCs at P8 using Amplex Red assays. n = 3 biological repeats. (F) Analysis of the cellular total ROS  levels in PDI+/+ and PDI-/- hMSCs  at P8 using H2DCFDA  probe. n = 3 biological repeats. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"PDI: 5034"
Figure legend: "(M) Confocal  imaging of PDI+/+ and PDI-/- hMSCs  expressing Hyper7-nucleus  at steady state and upon addition of 2 mM DTT. The fluorescence intensity ratio at 488/405 nm obtained from individual cells was calculated at indicated times  with a representative false color image. Scale bar, 10 μm."
NCBI gene IDs:
"PDI: 5034"
Figure legend: "(C, D) Density plot showing that upregulated (C) or downregulated (D) genes in the LP hMSCs  (PDI+/+, LP   vs. PDI+/+, EP) that were restored after PDI  deletion (PDI-/-, LP   vs. PDI+/+, LP). Comparisons were performed with two-sided Wilcoxon signed-rank test."
NCBI gene IDs:
"PDI: 5034"
Figure legend: "(K) Conjoint analysis showing the secretion levels of PDI  and those in (I) and various SASPs from multiple senescence inducers and in plasma  proteome from 3,087 healthy individuals RS, replicative senescence (PDI+/+, LP   vs. PDI+/+, EP). ATV, atazanavir  treatment; RAS, inducible RAS  overexpression; IR, X-irradiation. The color keys that change from dark blue to dark purple represent the fold change of gene and protein, change from white to red represent the change in protein levels per unit increase in the covariate in plasma  proteomic."
NCBI gene IDs:
"RAS: 
PDI: 5034"
Figure legend: "(A) qPCR  analysis of SERPINE1  expression in PDI+/+ and PDI-/- hMSCs  at EP   and LP. n = 3 independent experiments. Data information: In (A, data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"PDI: 5034
SERPINE1: 5054"
Figure legend: "(B) Western blotting analysis of SERPINE1  protein in PDI+/+ and PDI-/- hMSCs  at EP   and LP. GAPDH  was used as the loading control of cell lysates. Ponceau  was used as the loading control of conditional medium."
NCBI gene IDs:
"PDI: 5034"
Figure legend: "(F) Left, Ki67 staining  in PDI-/- hMSCs  transduced with sgNTC or  SERPINE1-targeting activation sgRNAs. Scale bar, 20 μm. Right, statistical analysis of Ki67-positive cells. n = 3 independent experiments. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"PDI: 5034
SERPINE1: 5054"
Figure legend: "(G) Left, SA-β-gal staining  in PDI-/- hMSCs  transduced with sgNTC or SERPINE1-targeting activation sgRNAs. Scale bar, 200 μm. Right, statistical analysis of SA-β-gal-positive cells. n = 3 biological repeats. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"PDI: 5034
SERPINE1: 5054"
Figure legend: "(H) qPCR  analysis of the SERPINE1  mRNA expression in PDI+/+ and PDI-/- hMSCs  treated with the indicated concentration H2O2  for 4 days. n = 3 independent experiments. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"PDI: 5034
SERPINE1: 5054"
Figure legend: "(J) H2O2  levels in PDI-/- hMSCs  transduced with lentiviruses  expressing Luc  or PDI   were determined by the fluorescence ratio of HyPer-ER  at 488/405 nm excitation after the addition of 0.5 mM DTT  for 15 min. n = 3 biological repeats. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"Luc: 
PDI: 5034"
Figure legend: "(K) H2O2  levels in PDI-/- hMSCs  transduced with lentiviruses  expressing Luc  or PDI   were determined by the fluorescence ratio of HyPer7-nucleus  at 500/400 nm excitation after the addition of 2 mM DTT  for 20 min. n = 3 independent experiments. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"Luc: 
PDI: 5034"
Figure legend: "(A) Western blotting of PDI expression  in replicative senescent (RS) hMSCs, Hutchinson-Gilford Progeria Syndrome (HGPS) hMSCs, WS hMSCs  and human  primary hMSCs  from an old individual transduced with sgNTC or PDI-targeting sgRNA. GAPDH  was used as the loading control."
NCBI gene IDs:
"PDI: 5034"
Figure legend: "(B) Single clonal formation assay  in RS hMSCs, HGPS hMSCs, WS hMSCs  and human  primary hMSCs  from an old individual transduced with sgNTC or PDI-targeting sgRNA. n = 3 biological repeats. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"PDI: 5034"
Figure legend: "(C) SA-β-gal staining  in RS hMSCs, HGPS hMSCs, WS hMSCs  and human  primary hMSCs  from an old individual transduced with sgNTC or PDI-targeting sgRNA. n = 3 biological repeats. Scale bar, 200 µm. Data information: data are presented as mean ± SEM, two-tailed Student's t-test."
NCBI gene IDs:
"PDI: 5034"
Figure legend: "C. Flag-tagged WT and mutant WDTC1proteins were transiently expressed in 293T cells. Flag-WDTC1 complexes were immunoprecipitated with anti-FLAG and their associated proteins were detected by immunoblotting as indicated; EV, empty vector control."
NCBI gene IDs:
"WDTC1: 23038"
Figure legend: "E. 293T cells were transfected with HA-ubiquitin along with various combinations of plasmid and siRNA as indicated. Transfected cells were lysed under denaturing conditions to obtain whole cell extracts (WCE) and immunoprecipitated with anti-FLAG. WDTC1 ubiquitylation was evaluated by immunoblotting as indicated."
NCBI gene IDs:
"WDTC1: 23038"
Figure legend: "F. 293T cells transiently expressing Flag-WDTC1 were transfected with scramble (scrm) siRNA or siRNAs against DDB1, CUL4A and CUL4B. Flag-WDTC1 levels and knockdown efficiency were assessed by immunoblotting as indicated."
NCBI gene IDs:
"DDB1: 1642"
Figure legend: "A. Schematic of WDTC1 knockdown-rescue lentiviral vector (top). 3T3-L1preadipocytes were lentivirally transduced to generate stable cells expressing a non-specific (NS) shRNA control, shWDTC1 targeting endogenous Wdtc1mRNA, or cells simultaneously expressing shWDTC1 and shRNA-resistant WDTC1; bottom, confirmation of knockdown and WDTC1 ectopic expression."
NCBI gene IDs:
"WDTC1: 23038
Wdtc1: Q8N5D0///230796"
Figure legend: "B. Chromatin enriched nuclear extracts from 293T cells cotransfected with Flag-WDTC1 and HA tagged core histones were immunoprecipitated (IP) with anti-FLAG and immunoblotted (IB) as indicated. The probable H2AK119ub1 band detected in the nuclear extract is indicated by an asterisk."
NCBI gene IDs:
"WDTC1: 23038"
Figure legend: "D. Affinity purified Flag-WDTC1 wildtype and mutant ΔH complexes from 293T cells were the source of E3 ligase in in vitro ubiquitylation assays. Copurification of CRL4 E3 ligase proteins was confirmed by immunoblotting and Coomassie Blue staining (left panel). In vitro ubiquitylation assays of recombinant H2A were performed in the presence of indicated proteins. Reaction products were resolved by SDS-PAGE, and ubiquitylatedH2A was detected by anti-H2AK119ub1 (right panel)."
NCBI gene IDs:
"H2A: 
WDTC1: 23038"
Figure legend: "A Representative photographs of fly eyes expressing (CGG)90-EGFP under a GMR-GAL4 driver, with various belle disruptions."
NCBI gene IDs:
"EGFP: 
belle: 45826
GAL4: 855828"
Figure legend: "B Quantitation of GMR-GAL4, (CGG)90-EGFP eye phenotypes with belle disruptions (Mann-Whitney U test with Bonferonni corrections for multiple comparisons; n=35-77/genotype). Data Information: For all panels, * P≤0.05, ** P≤0.01, *** P≤0.001, **** P≤0.0001 for the specified statistical test. All data in all panels are presented as mean ± SD (compiled from ≥3 replicates)."
NCBI gene IDs:
"EGFP: 
belle: 45826
GAL4: 855828"
Figure legend: "Longevity assays of (CGG)90-EGFP; Tub5-GS (Log-rank Mantel-Cox test with Bonferroni corrections for multiple comparisons; n=110-219/genotype) flies with belle knockdown. Data Information: For all panels, * P≤0.05, ** P≤0.01, *** P≤0.001, **** P≤0.0001 for the specified statistical test. All data in all panels are presented as mean ± SD (compiled from ≥3 replicates)."
NCBI gene IDs:
"EGFP: 
Tub5: 
belle: 45826"
Figure legend: "Longevity assays of (CGG)90-EGFP; ElaV-GS (n=147-299/genotype) flies with belle knockdown. Data Information: For all panels, * P≤0.05, ** P≤0.01, *** P≤0.001, **** P≤0.0001 for the specified statistical test. All data in all panels are presented as mean ± SD (compiled from ≥3 replicates)."
NCBI gene IDs:
"EGFP: 
belle: 45826
ElaV: 31000"
Figure legend: "G Abundance of (CGG)90-EGFP mRNA normalized to RPL32 mRNA, following belle knockdown, determined by qRT-PCR (n=8/genotype)."
NCBI gene IDs:
"EGFP: 
belle: 45826
RPL32: 43573"
Figure legend: "H Western blot of AUG-driven EGFP in EGFP; Tub5-GS flies with and without belle knockdown."
NCBI gene IDs:
"EGFP: 
Tub5: 
belle: 45826"
Figure legend: "A Dose-response curves showing the effects of two independent anti-DDX3X siRNAs on the expression of AUG-NL-3xF (top) and (CGG)100 +1 NL-3xF (bottom) reporters. Plasmid-based reporters were transfected into HeLa cells 24 hours after knockdown, and reporter expression was quantified by luminescence. Nanoluciferase (NL) luminescence has been normalized to luminescence from firefly luciferase (FF), which was co-transfected, in order to control for transfection variability. Asterisks refer to comparisons between anti-DDX3X siRNAs and siRNAs against EGFP (siEGFP; two-way ANOVA with Dunnett's multiple comparisons test; n=12/condition). Data Information: For all panels, * P≤0.05, ** P≤0.01, *** P≤0.001, **** P≤0.0001 for the specified statistical test. All panels depict data as means ± SD (compiled from ≥3 replicates)."
NCBI gene IDs:
"EGFP: 
FF: 
luciferase: 
Nanoluciferase: 
NL: 
DDX3X: 1654"
Figure legend: "(CGG)n +1 NL-3xF expression (normalized to FF) with and without DDX3X knockdown across a range of CGG repeat sizes. Black asterisks refer to comparisons between siDDX3X- and siEGFP-treated cells; orange asterisks refer to comparisons between siDDX3X-treated cells expressing AUG-NL-3xF and those expressing a different reporter (two-way ANOVA with Tukey's multiple comparisons test; n=17-30/condition). Data Information: For all panels, * P≤0.05, ** P≤0.01, *** P≤0.001, **** P≤0.0001 for the specified statistical test. All panels depict data as means ± SD (compiled from ≥3 replicates)."
NCBI gene IDs:
"EGFP: 
FF: 
NL: 
DDX3X: 1654"
Figure legend: "(CGG)n +2 NL-3xF expression (normalized to FF) with and without DDX3X knockdown across a range of CGG repeat sizes. Black asterisks refer to comparisons between siDDX3X- and siEGFP-treated cells; orange asterisks refer to comparisons between siDDX3X-treated cells expressing AUG-NL-3xF and those expressing a different reporter (two-way ANOVA with Tukey's multiple comparisons test; n=17-30/condition). Data Information: For all panels, * P≤0.05, ** P≤0.01, *** P≤0.001, **** P≤0.0001 for the specified statistical test. All panels depict data as means ± SD (compiled from ≥3 replicates)."
NCBI gene IDs:
"EGFP: 
FF: 
NL: 
DDX3X: 1654"
Figure legend: "Western blots of FMRpolyG-NL-3xF products with and without DDX3X knockdown across a range of repeat sizes."
NCBI gene IDs:
"DDX3X: 1654"
Figure legend: "Western blots of FMRpolyA-NL-3xF products with and without DDX3X knockdown across a range of repeat sizes."
NCBI gene IDs:
"NL: 
DDX3X: 1654"
Figure legend: "A Expression of in vitro transcribed AUG, +1 (CGG)100, and +2 (CGG)100 NL-3xF RNAs following DDX3X knockdown in HeLa cells, expressed as NL luminescence normalized to FF luminescence. (Student's t test with Bonferroni corrections for multiple comparisons; n=21/condition). Data Information: For all panels, ns=non-significant, *** P≤0.001, **** P≤0.0001 for the specified statistical test. All panels depict data as means ± SD, unless indicated otherwise (compiled from ≥3 replicates)."
NCBI gene IDs:
"FF: 
NL: 
DDX3X: 1654"
Figure legend: "B Abundance of reporter mRNAs following DDX3X knockdown and plasmid-reporter transfection, determined by qRT-PCR. (n=7/condition.) This panel depicts data as means ± SEM."
NCBI gene IDs:
"DDX3X: 1654"
Figure legend: "C Expression of AUG-NL-3xF and +1 (CGG)100 NL-3xF in in vitro translation extracts, collected from HeLa cells treated with siRNAs against EGFP or DDX3X (two-way ANOVA with Tukey's multiple comparisons test; n=4/condition). Data Information: For all panels, ns=non-significant, *** P≤0.001, **** P≤0.0001 for the specified statistical test. All panels depict data as means ± SD, unless indicated otherwise (compiled from ≥3 replicates)."
NCBI gene IDs:
"EGFP: 
NL: 
DDX3X: 1654"
Figure legend: "D Enrichment of HSPA1A and +1 (CGG)100 NL-3xF mRNA following anti-DDX3X RIP, relative to incubation with isotype control IgG. MALAT RNA, in contrast, is not enriched (Student's t test, n=3)."
NCBI gene IDs:
"NL: 
DDX3X: 1654
HSPA1A: 3303
MALAT: 378938"
Figure legend: "E Expression of +1 and +2 (CGG)100 NL-3xF plasmid reporters with and without an AUG inserted 5' to the CGG repeat, with and without DDX3X knockdown. Black asterisks refer to comparisons between siDDX3X- and siEGFP-treated cells; orange asterisks refer to comparisons between siDDX3X-treated cells expressing either +1 or +2 (CGG)100 NL-3xF and those expressing the respective AUG-driven variant (two-way ANOVA with Tukey's multiple comparisons test; n=11-12/condition). Data Information: For all panels, ns=non-significant, *** P≤0.001, **** P≤0.0001 for the specified statistical test. All panels depict data as means ± SD, unless indicated otherwise (compiled from ≥3 replicates)."
NCBI gene IDs:
"EGFP: 
NL: 
DDX3X: 1654"
Figure legend: "F Expression of NL-3xF plasmids with initiator AUG codons mutated to near-AUG codons, with and without DDX3X knockdown (two-way ANOVA with Dunnett's multiple comparisons test; n=18-24/condition). Black asterisks refer to comparisons between siEGFP-treated and siDDX3X-treated cells; orange asterisks refer to comparisons between siDDX3X-treated cells expressing AUG-NL-3xF and those expressing a different reporter; white asterisks refer to comparisons between siDDX3X-treated cells expressing +1 (CGG)100 NL-3xF and those expressing a different reporter. Data Information: For all panels, ns=non-significant, *** P≤0.001, **** P≤0.0001 for the specified statistical test. All panels depict data as means ± SD, unless indicated otherwise (compiled from ≥3 replicates)."
NCBI gene IDs:
"EGFP: 
NL: 
DDX3X: 1654"
Figure legend: "G Expression of in vitro transcribed near-AUG reporter RNAs in in vitro translation extracts, collected from HeLa cells treated with siRNAs against EGFP or DDX3X. (n=4/group)."
NCBI gene IDs:
"EGFP: 
DDX3X: 1654"
Figure legend: "A Representative photographs of GMR-GAL4; (CGG)90-EGFP fly eyes expressing manipulations of eIF4B and eIF4H. (B) Quantitation of GMR-GAL4, (CGG)90-EGFP eye phenotypes with eIF4B/H manipulations (Mann-Whitney U test with Bonferroni corrections for multiple comparisons; n=26-55/genotype). Data Information: For all panels, ns=non-significant, * P≤0.05, ** P≤0.01, **** P≤0.0001 for the specified statistical test. All panels present data as means ± SD (compiled from ≥3 replicates)."
NCBI gene IDs:
"EGFP: 
eIF4B: 3355041
eIF4H: 49809
GAL4: 855828"
Figure legend: "C, D Expression of plasmid-based AUG-NL and +1 (CGG)100 NL-3xF reporters (C), or co-transfected AUG-FF reporters (D), following knockdown of EIF4B or EIF4H. Black asterisks refer to comparisons between siEGFP- and siEIF4B/H-treated cells; pink and blue asterisks refer to comparisons between siEIF4B- (pink) or siEIF4H- (blue) treated cells expressing AUG-NL-3xF and those expressing +1 (CGG)100 (two-way ANOVA with Tukey's multiple comparisons test, n=9/condition)."
NCBI gene IDs:
"EGFP: 
FF: 
NL: 
EIF4B: 1975
EIF4H: 7458"