EMBO/SourceData huggingface dataset:
Figure legend: "C Motif analysis of recovered UPF1-associated transcripts analyzed by RIP-Seq Transcripts are divided into tertiles by hnRNP L and PTBP1 binding motif density and 3'UTR length. Data are represented and analyzed as in (A). Dotted line represents the median RIP-Seq efficiency of the class of transcripts with the shortest 3'UTR and low PTBP1/hnRNP L motif density. D CDF plots of selected transcript classes from (C) analyzed as in (B). Data information: **P ≤ 0.01, ***P ≤ 0.001, ****P ≤ 0.0001."
NCBI gene IDs:
"UTR: 
hnRNP L: 3191
PTBP1: 5725
UPF1: 5976"
Figure legend: "C qPCR of selected transcripts in SU-DHL-4 cells under conditions of non-targeting RNAi or hnRNP L knockdown with or without 50 μg/mL cycloheximide treatment (for 4 hours; n ≥ 3). Significance of hnRNP L KD + DMSO and NT + CHX were compared to NT + DMSO, and hnRNP L KD + CHX was compared to hnRNP L KD + DMSO. Bars represent the mean ± SD. For clarity, only a single star was used to indicate significance; in all cases P ≤ 0.05 in two-tailed Student's t-tests."
NCBI gene IDs:
"hnRNP L: 3191"
Figure legend: "E Half-life determination from RT-qPCR detection of reporter constructs in HeLa Tet-off cells transfected with non-targeting or UPF1 siRNAs. For plots comparing non-targeting with UPF1 knockdown, significance is compared to the non-targeting condition using the the sum-of-squares F test. The fourth plot compares the non-targeting decay curves of the three reporters, and significance is compared to the decay of the fusion transcript. Points represent the mean ± SD from qRT-PCR at each time point of at least 3 independent experiments."
NCBI gene IDs:
"UPF1: 5976"
Figure legend: "A qPCR of selected transcripts in SU-DHL-4 cells under conditions of BCL2 knockdown, hnRNP L knockdown, or non-targeting control siRNA Nucleofection (n ≥ 4 independent experiments). Bars indicate mean ± SD. Significance was determined compared to NT using two-tailed Student's t-tests. Data information: *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001, ****P ≤ 0.0001."
NCBI gene IDs:
"BCL2: 596
hnRNP L: 3191"
Figure legend: "C qPCR of selected transcripts in SU-DHL-6 cells under conditions of hnRNP L knockdown or non-targeting control (n = 5 independent experiments). Bars indicate mean ± SD. Significance of hnRNP L KD was determined compared to NT using two-tailed Student's t-tests. Data information: *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001."
NCBI gene IDs:
"hnRNP L: 3191"
Figure legend: "A. Immunofluorescence microscopy of control, parental and patient fibroblasts labeled for LAMP-1. Patient fibroblasts (VPS41S285P/R662* and VPS41c.1423-2A&gt;G/R662*) show more LAMP-1 puncta, which are distributed throughout the cell. (A') Quantification shows a significant increase in the number of LAMP-1 positive compartments for both patients. &gt;15 Cells per condition were quantified (n=3). Scale bars, 10µm."
NCBI gene IDs:
"VPS41: 27072"
Figure legend: "D. HeLaVPS41KO cells transfected with VPS41WT-APEX2-V5, VPS41S285P-APEX2-V5 or VPS41R662*-APEX2-V5 constructs labeled for LAMP-1 and V5 immunofluorescence microscopy. All VPS41 variants co-localize with LAMP-1, indicating that VPS41S285P and VPS41R662* are recruited to late endosomes/lysosomes. Scale bars 10µm; zoom of squared area, 1µm."
NCBI gene IDs:
"V5: 
APEX2: 606508
VPS41: 27072"
Figure legend: "H. VPS41WT/WT, VPS41WT/R662* and VPS41S285P/R662* primary fibroblasts incubated with Dextran-568 for 0.5, 2, 5, 8 and 24 hours. Colocalization of Dextran-568 and SiR-Lysosome Cathepsin D (SiR-Lyso) reveals a delay in lysosomal delivery in maternal (VPS41WT/R662*) and patient (VPS41S285P/R662*) cells at 2 hours of Dextran uptake. After 5 hours, maternal cells show similar to control colocalization levels. Patient cells show only after 24 hours colocalization levels similar to control, indicating a delay rather than a block in late endosome - lysosome fusion. &gt;10 Cells per cell line were quantified."
NCBI gene IDs:
"VPS41: 27072"
Figure legend: "A. Western blot of LC3 expression levels in control and patient fibroblasts. In steady state (0 hours) conditions, patient fibroblasts have a higher ratio of lipidated LC3 (LC3II):LC3I than control cells. Induction of autophagy by nutrient starvation (2 hours incubation with minimal EBSS medium) results in a raise in LC3II:LC3I ratio in both control and patient cells, but in VPS41S285P/R662* fibroblasts this increase is only modest (quantified in A') (n=2)."
NCBI gene IDs:
"VPS41: 27072"
Figure legend: "E. Immunofluorescence of HeLaWT and HeLaVPS41KO cells transfected with LC3GFP/RFP tandem construct. The increased percentage of GFP/RFP-positive compartments in HeLaVPS41KO cells indicate a block in autophagic flux (quantified in E'). &gt;12 Cells per cell line were quantified. Scale bars 10µm; zoom, 1µm."
NCBI gene IDs:
"VPS41: 27072"
Figure legend: "A. Immunofluorescence of control, parental and patient fibroblasts labeled for LAMP-1 and mTOR. In steady state conditions (0 hours) VPS41S285P/R662* fibroblasts show less colocalization between mTOR and LAMP-1. VPS41WT/WT, VPS41WT/S285P and VPS41WT/R662* show an appropriate mTOR response upon nutrient deprivation (2 hours) or restimulation (2 hours starvation followed by 15 minutes restimulation) (Appendix Fig S5A). &gt;10 Cells per cell line were quantified (A'). Quantifications are performed relative to colocalization under steady state conditions per cell line (n=3). Scale bars, 10µm; zoom, 1µm."
NCBI gene IDs:
"VPS41: 27072"
Figure legend: "D. Rescue experiments of HeLaVPS41KO cells. Expression of VPS41WT-APEX2-V5, VPS41S285P-APEX2-V5 or VPS41R662*-APEX2-V5. Reintroduction of VPS41WT rescues TFE3 localization, whereas expression of mutant VPS41 has no effect (quantified in D'). &gt;83 Cells per condition were quantified (n=3). Scale bars, 10µm."
NCBI gene IDs:
"V5: 
APEX2: 606508
VPS41: 27072"
Figure legend: "B. Western blot on cellular or secreted secretogranin II (SgII) of PC12 cells VPS41KO, or VPS41KO transduced with HA-VPS41WT or HA-VPS41S285P lentivirus. Cells were washed and incubated for 30 minutes in Tyrode's solution containing 2.5 mM K+ (basal) or 90 mM K+ (stimulated). No difference in secreted sgII levels was observed between VPS41WT and VPS41S285P."
NCBI gene IDs:
"HA: 
VPS41: 27072"
Figure legend: "C. Graph representing the percentage of animals with 6 normal dopaminergic neurons in the anterior region of Pdat-1::GFP; Pdat-1:: α-syn (strain UA44) animals with heterozygous expression of hVPS41 variants. Heterozygous expression of hVPS41WT with either variant (strains UA389 or UA390) significantly rescues neurons from α-synuclein-induced degeneration at day 7 whereas compound heterozygous expression (strain UA391) fails to rescue neurodegeneration. At day 10, none of the heterozygous backgrounds significantly rescues α-synuclein-induced neurodegeneration. n=30 Adult worms for each of 3 independent experiments for the α-synuclein (α-syn) strain (total of 90 worms) and n=90 for each independent transgenic strain (30 worms/trial x 3 independent transgenic lines = 270 worms) for each of 3 independent experiments. D. Representative images of DA neurons from C. elegans expressing Pdat-1::GFP; Pdat-1:: α-syn, with or without hVPS41 variants, as described in (C). Intact DA neurons are indicated with arrowheads and missing neurons are indicated with arrows. Scale bar 20µm. "
NCBI gene IDs:
"α-syn: 
α-synuclein: 
dat-1: 
VPS41: 27072"
Figure legend: "(E) Representative adult midgut from control esgReDDM at day 14 after temperature shift in variable demand. ECs renewed are marked positively by persistent RFP labelling (red-only cells). (F and G) Few ECs had been renewed in 'Low' midguts after 14 (F) and 21 (G) days of tracing. Data information: Scale bars, 50µm."
NCBI gene IDs:
"esg: 34903"
Figure legend: "(H-J) Age-synchronized posterior midguts of control (esgReDDM&gt;, H) and p35 overexpression in stem and progenitor cells (esgReDDM&gt;p35, p35 I and J) at 7 days after temperature shift. Arrows in (H, I) point to newly differentiated ECs. In (J), tumour mass is found in the anterior midgut. Data information: Scale bars, 50µm."
NCBI gene IDs:
"p35: 34385
esg: 34903"
Figure legend: "(K), Quantification of mitosis PH3+ cells in posterior midgut (pmg) (control: gut scored n=13 and esg&gt;p35, p35: n=22]). Student t-test (**** = P &lt; 0.0001). Data information: In the boxplots, the box extends from the 25th to 75th percentiles and whiskers show all points, min to max."
NCBI gene IDs:
"p35: 34385
esg: 34903"
Figure legend: "(L), Diap1 is monitored by the GFP.4.3. (green) reporter (Djiane et al., 2013; Zhang et al., 2008). Diap1-GFP is detected in a subset of adult midgut esg+ cells that are negative for the mitotic marker PH3 (red, inset) and for EE marker Prospero (Pros, grey in inset). Diap1-GFP is not detected in mature EC (large nuclei cells, DAPI in blue). Data information: Scale bars, 50µm."
NCBI gene IDs:
"esg: 34903"
Figure legend: "(C) Control GBE-Su(H)ReDDM&gt; and (D) GBE-Su(H)ReDDM&gt;p35, p35 midguts after 7 days of tracing. Data information: Scale bars, 100µm"
NCBI gene IDs:
"p35: 34385"
Figure legend: "(F-J) Adult midguts of (F) control kluReDDM&gt; (G) kluReDDM&gt;Debcl-RNAi, (H) kluReDDM&gt;Drice-RNAi, (I) kluReDDM&gt;Diap1-RNAi, (J) kluReDDM&gt;Diap1 midguts after 7 days of tracing. The arrows point to examples of PH3+ labelled ISCs. Data information: Scale bars, 100µm"
NCBI gene IDs:
"Debcl: 53585
Diap1: 39753
Drice: 43514
klu: 39228"
Figure legend: "(N) Quantification of klu+ cells and renewed ECs in kluReDDM&gt;Diap1 posterior midguts (n=8) relative to 'Low' control in K and L, respectively. Data information: ox and whisker plot showing min to max values and the box is extending from the 25th to 75th percentiles. The line in the middle of the box is plotted at the median. P values (*, P&lt;0.0261; **, P&lt;0.005; ***, P&lt;0.0021) calculated by one-way ANOVA with Bonferroni correction."
NCBI gene IDs:
"Diap1: 39753
klu: 39228"
Figure legend: "(A-E) Confocal images of representative midguts of the indicated genotypes using kluReDDM for tracing and age- and EB-specific transgene expression at day 7 after temperature shift. ISC mitosis was monitored by using PH3 labelling (white) in all guts. (B-E) Accumulation and loss of klu+ cells by loss (B and E) and gain (C and D) of N and EGFR signalling. In (C), the accumulation of EC-committed EBs (klu+ cells) in midguts with constitutively activated EGFR (kluReDDM> EGFRact) is accompanied with a non-autonomous increase in ISC mitosis. Inset in (C) shows labelling with Dl (blue), revealing symmetric ISC mitoses Data information: Scale bar, 100µm for all images."
NCBI gene IDs:
"klu: 39228"
Figure legend: "Confocal images of representative midguts of the indicated genotypes Rescue of the loss of EBs induced by gain of Notch (H-RNAi) by expressing Debcl-RNAi. Data information: Scale bar, 100µm for all images."
NCBI gene IDs:
"Debcl: 53585"
Figure legend: "Confocal images of representative midguts of the indicated genotypes escue of the loss of EBs induced by loss of EGFR (EGFRDN) by expressing Debcl-RNAi. (J and K) Impact of gain of expression (J) and loss by RNAi expression (K) of lz using kluReDDM White arrowheads point to examples of mitosis labelled by PH3+. (L and M) Impact of gain of expression (L) or loss by RNAi expression (M) of klu (M) using kluReDDM. Data information: Scale bar, 100µm for all images."
NCBI gene IDs:
"Debcl: 53585
klu: 39228
lz: 31883"
Figure legend: "(N-R) Images of representative midguts of esgReDDM at day 7 after temperature shift of the indicated genotypes. PH3 labelling (white) detected rare mitoses in the mutant genotypes. Data information: Scale bar, 100µm for all images."
NCBI gene IDs:
"esg: 34903"
Figure legend: "(D) Quantification of the number of Diap1-GFP+. Note that in p35-expressing midguts reared in 'Low', GFP levels are not increased, consistent with the p35 protein suppressing apoptosis downstream of Diap1. Data information (n= 17, 13, 12, 10, 21, 24). P values were calculated using one-way ANOVA Bonferroni corrected (****, P &lt; 0,0001)."
NCBI gene IDs:
"p35: 34385"
Figure legend: "F: Co-IP of clathrin with Venus-tagged HURPWT and HURP∆MUT constructs in asynchronous and mitotic HeLa cells."
NCBI gene IDs:
"Venus: 
HURP: 9787"
Figure legend: "G Co-IP of clathrin with Venus-tagged HURPWT, HURP∆MUT and HURPS839A constructs in mitotic HeLa cells."
NCBI gene IDs:
"Venus: 
HURP: 9787"
Figure legend: "H: Representative images of HURPWT, HURP∆MUT and HURPS839A in the different mitotic stages."
NCBI gene IDs:
"HURP: 9787"
Figure legend: "I-J: RNAi rescue experiments (n=2), which included the knockdown of endogenous HURP and re-expressing either RNAi resistant HURPWT, HURP∆MUT and HURPS839A. In order to assess mitotic behaviour of the cells, the time required of control, HURP knockdown, HURPWT, HURP∆MUT and HURPS839A HeLa cells to progress through mitosis (NEBD-anaphase) was established using time-lapse microscopy. Every circle represents one analysed cell. The number of cells analysed is indicated as n in I. Mann-Whitney test was performed to assess significant differences in the median time required for mitotic progression (*: p-value≤0.05, ***: p-value: ≤0.001, ****: p-value ≤0.0001; ns: non-significant)"
NCBI gene IDs:
"HURP: 9787"
Figure legend: "F  Immunoblot  analysis of ectopic HIF2α protein levels in 293T  cells with gradually increased amount of ectopic USP33. 0.5 µg of HA-tagged  HIF2α plasmids together with the increased amounts of GFP-tagged  USP33  plasmids (0, 0.1, 0.2 or 0.3 μg) were introduced into  293T  cells. Forty-eight hours post transfection, levels of ectopic  HIF2α-HA and GFP-USP33 were analyzed by  immunoblot analysis. Concomitantly increased levels of ectopic  HIF2α and USP33 expression  indicated the positive regulation of HIF2α protein by  USP33. G Immunoblot  analysis of ectopic  HIF2α protein levels in 293T cells expressing ectopic wild type (WT) USP33 or the catalytically dead (CD)  USP33. HA-tagged  HIF2α plasmids (0.5 µg) were introduced into 293T  cells alone or together with  GFP-tagged WT or CD USP33  plasmids (0.2 µg). Levels of ectopic HIF2α-HA and GFP-USP33 were analyzed 48 hours post transfection. Expression  of the wild type USP33 but not the catalytically dead USP33 increased the ectopic  HIF2α  protein levels."
NCBI gene IDs:
"GFP: 
HA: 
HIF2α: 2034
USP33: 23032"
Figure legend: "G Co-immunoprecipitation to detect the interaction between HIF2α  and the wild-type (WT) or the catalytically dead (CD) USP33. Ectopic HA-tagged HIF2α  were expressed in 293T  cells with GFP-tagged wild-type or catalytically dead USP33. Cell lysates were subjected to immunoprecipitation  with anti-HA antibodies. Co-immunoprecipitated products immunoblotted with the indicated antibodies. The catalytically dead USP33  relative to the wild type USP33   showed a stronger affinity to HIF2α."
NCBI gene IDs:
"GFP: 
HA: 
HIF2α: 2034
USP33: 23032"
Figure legend: "G Co-immunoprecipitation to determine the  serine phosphorylation sites in human HIF2α responsible for its binding to USP33. Ectopic  GFP-tagged  USP33 along with HA-tagged wild type  HIF2α or HIF2α mutants with indicated  serine to  alanine point mutations were expressed in 293T cells. Cell lysates were subjected to  immunoprecipitation  with anti-HA agaroses Co-immunoprecipitated products were immunoblotted with the indicated antibodies. The S484A mutation largely attenuated the  interaction of HIF2α with  USP33, indicating that the  serine  484 site in HIF2α was the most important  phosphorylation site for the interaction  between  HIF2α and  USP33."
NCBI gene IDs:
"GFP: 
HA: 
HIF2α: 2034
USP33: 23032"
Figure legend: "B Representative images of   tumorsphere formation of T387  GSCs expressing USP33-targeting shRNA (shUSP33) or non-targeting shRNA (shNT). Twenty-four hours after  lentiviral infection, T387 GSCs expressing shUSP33 or shNT were planted in 96 well plates at the density of 2,000 cells per well and cultured for 48 hours under normoxia (20%  O2) or  hypoxia (5%  O2). Disruption of USP33 inhibited GSC tumorsphere  formation in normoxia  and dramatically suppressed  GSC tumorsphere  formation in hypoxia. Scale bar, 200 μm."
NCBI gene IDs:
"USP33: 23032"
Figure legend: "E Cell titer  assays showing cell growth  of T387 GSCs expressing shUSP33 or shNT in normoxia or  hypoxia. GSCs were transduced with shNT or shUSP33  through lentiviral infection for 24 hours, and then split into 96 well plates at the concentration of 2,000 cells per well. Cell titer  was determined by the Glo luminescent cell viability assay  kit (Promega) at the indicated time points. Disruption of USP33 inhibited GSC growth in normoxia and hypoxia. The experiment has been repeated three times. The presented curves were based on three technical replicates. *, p &lt; 0.05; **, p &lt; 0.01; ***, p &lt; 0.001 (mean ± s.e.m.; two tailed unpaired t-test)."
NCBI gene IDs:
"USP33: 23032"
Figure legend: "F Representative  immunofluorescent staining of the apoptotic marker cleaved  caspase 3 in T387  GSCs  expressing shUSP33 or shNT in normoxia or hypoxia. GSCs  were attached to hESC-Qualified Matrix (Corning) in 6-well plates at the concentration of 50,000 cells per well. Forty-eight hours post infection with shUSP33 or shNT  lentiviruses, cells were  stained for cleaved caspase 3 (green) and nuclei  (blue). Scale bar, 80 μm."
NCBI gene IDs:
"USP33: 23032"
Figure legend: "C, Representative images of autonomous fluorescent signals of  4HRE-d2GFP in xenografts derived from or shUSP33- or shNT- expressing T387 GSCs  transduced with 4HRE-d2GFP. Scale bar, 200 μm."
NCBI gene IDs:
"d2GFP: 
USP33: 23032
4HRE: 7422"
Figure legend: "E, Representative images of autonomous fluorescent signals of 4HRE-d2GFP (green) and  immunofluorescent staining of the  stem cell  marker SOX2 (red) in xenografts  derived from T387  GSCs transduced with 4HRE-d2GFP. More GFP signals were detected in the  SOX2+ cells compared with the SOX2- cells, suggesting a stronger  hypoxia response in GSCs relative to NSTCs. Scale bar, 200 μm."
NCBI gene IDs:
"d2GFP: 
SOX2: 6657
4HRE: 7422"
Figure legend: "G, Representative images of immunofluorescent staining  of the apoptotic marker cleaved caspase 3  (red) and autonomous fluorescent signals of 4HRE-d2GFP (green) in xenografts  derived from T387 GSCs transduced with 4HRE-d2GFP. The  GFP+ population had much less apoptosis   relative to the GFP- population, suggesting that hypoxia  response inhibited  cell apoptosis. Scale bar, 200 μm."
NCBI gene IDs:
"d2GFP: 
GFP: 
4HRE: 7422"
Figure legend: "B Kaplan-Meier survival curves of mice bearing GBMs  derived from T387 GSCs  expressing shUSP33 or shNT from (A). Disruption of USP33  extended the survival  of mice bearing GSC-derived GBM tumors. (n= 5  mice for each group; shUSP33#42 vs shNT, p = 0.0185; shUSP33#45 vs shNT, p = 0.0027; two-tailed log-rank test)."
NCBI gene IDs:
"USP33: 23032"
Figure legend: "E, F  Immunofluorescent  analysis (E) and statistical quantifications (F) of the cell proliferation marker Ki67  in xenografts  derived from T387 GSCs expressing shUSP33 or shNT. Disruption of USP33 in  GSCs reduced cell proliferation  in GBM xenografts. Scale bar, 80 μm. (n = 5 tumors for each group; ***, p &lt; 0.001; mean ± s.e.m.; two tailed unpaired t-test)."
NCBI gene IDs:
"USP33: 23032"
Figure legend: "(B) Representative fluorescent images (red) showing that mouse primary cortical neurons were transduced with shRNA-control or shATIC #6 at DIV 3 and then transfected with MYC-LRRK2-WT and DsRed at a plasmid ratio of 10:1 at DIV 5. Neuronal viability was analyzed at 72-hour post-transfection with non-viable neurons exhibiting no obvious neurite process (arrow). Scale bars, 100 μm. (C) Quantification of neuronal viability. Bars indicate the viability (n &gt; 100) for each transfection condition expressed as a percent of control neurons (DsRed with pcDNA3.1 empty vector). Data represent the mean ± SEM from three independent experiments with n &gt; 100 cells quantified in each experiment. **p &lt; 0.01, ***p &lt; 0.001 by one-way ANOVA followed by a Tukey's post hoc test."
NCBI gene IDs:
"DsRed: 
MYC: 
ATIC: 108147
LRRK2: 120892"
Figure legend: "(D and E) Endogenous LRRK2 levels in ATIC overexpression cells. SH-SY5Y cells were transfected with V5-ATIC or empty vector. After 48 hours, LRRK2 expression levels were analyzed by Western blot. Images were quantified by ImageJ software. Data are mean ± SEM, n=3 independent experiments. ***p &lt; 0.001 by Student's t tests."
NCBI gene IDs:
"V5: 
ATIC: 471"
Figure legend: "(H and I) Endogenous LRRK2 levels in ATIC KO cells upon LV-flag-ATIC expressing. SH-SY5Y WT or ATIC KO cells were infected with lentiviruses carrying Flag-ATIC or empty vector. After 48 hours, LRRK2 expression levels were analyzed by Western blot. Images were quantified by ImageJ software. Data are the means ± SEM, n=3 independent experiments. ***p &lt; 0.001 by one-way ANOVA followed by a Tukey's post hoc test."
NCBI gene IDs:
"flag: 
Flag: 
ATIC: 471"
Figure legend: "(A and B) Overexpressed LRRK2 levels in HEK 293T cells upon AICAr treatment. HEK293 cells were transfected with MYC-LRRK2 and treated with or without 1mM AICAr for 48 hours. LRRK2 levels were analyzed by Western blot."
NCBI gene IDs:
"MYC: 
LRRK2: 120892"
Figure legend: "(S) Representative fluorescent images (green) showing that mouse primary cortical neurons were co-transfected with MYC-LRRK2 WT or G2019S (GS), and eGFP at a plasmid ratio of 10:1 at DIV 5, and treated with or without 1mM AICAr. Neuronal viability was analyzed at 48-hour post-transfection with non-viable neurons exhibiting no obvious neurite process (arrow). Scale bars, 100 μm. (T) Quantification of neuronal viability. Bars indicate the viability (n &gt; 100) for each transfection condition expressed as a percent of control neurons (eGFP with pcDNA3.1 empty vector). Data represent the mean ± SEM from three independent experiments with n &gt; 100 cells quantified in each experiment. *p &lt; 0.05, ***p &lt; 0.001, ****p &lt; 0.0001 by one-way ANOVA followed by a Tukey's post hoc test."
NCBI gene IDs:
"eGFP: 
MYC: 
LRRK2: 120892"
Figure legend: "(C) LRRK2 and GBA mRNA levels upon AICAr treatment. SH-SY5Y cells were treated with or without 2mM AICAr for 24 hours. Total RNA was extracted. LRRK2 and GBA mRNA levels were analyzed by real-time PCR. Data are mean ± SEM, n=4 independent experiments. **p &lt; 0.01 by Student's t tests. ns: not statistically significant. (D) LRRK2 mRNA level upon AICAr treatment in the presence of actinomycin D. SH-SY5Y cells were treated with or without 2mM AICAr for 24 hours and in the presence of 10μg/ml actinomycin D. Total RNA was extracted. LRRK2 mRNA levels were analyzed by real-time PCR. Data are mean ± SEM, n=4 independent experiments. **p &lt; 0.01, ****p &lt; 0.0001 by two-way ANOVA followed by Sidak's multiple comparison test."
NCBI gene IDs:
"GBA: 106627981
LRRK2: 120892"
Figure legend: "(E and F) LRRK2 expression levels from native LRRK2 cDNA and synthesized LRRK2 cDNA with synonymous codons upon AICAr treatment. HEK 293T cells were transfected with Flag-LRRK2 with native cDNA or with synthesized cDNA, and treated with or without 1mM AICAr for 48 hours. LRRK2 expression levels were analyzed by Western blot. Images were quantified by ImageJ software. Data are mean ± SEM, n=3 independent experiments. ***p &lt; 0.001 by Student's t tests."
NCBI gene IDs:
"Flag: 
LRRK2: 
LRRK2: 120892"
Figure legend: "(I and J) The specific region (2221-3927bp) of the synthesized Flag-LRRK2 cDNA was replaced with the native sequence and the response of this chimeric LRRK2 cDNA expression to AICAr treatment was analyzed by Western blot. Images were quantified by ImageJ software. Data are mean ± SEM, n=3 independent experiments. ****p &lt; 0.0001 by Student's t tests."
NCBI gene IDs:
"Flag: 
LRRK2: "
Figure legend: "(B LRRK2 protein levels in AUF1 knockout (KO) cells upon AICAr treatment. SH-SY5Y WT and AUF1 KO cells were treated with or without 1mM AICAr for 48 hours. LRRK2 expression levels were analyzed by Western blot."
NCBI gene IDs:
"AUF1: 3184"