EMBO/SourceData huggingface dataset:
Figure legend: "Panel (a) shows example TEM ultrastructure images obtained from male and female mice pancreas and the columns shows the granules size distribution. Granules size was analyzed in at least 10 images from 3 wild-type and 5 Trpml1-/- mice."
NCBI gene IDs:
"Trpml1: 94178"
Figure legend: "(b) Fixed acini were co-stained with Amylase (granules) and LAMP1 (lysosomes) and the fold overlap was calculated from 14 and 11 images obtained from 3 wild-type and 3 Trpml1-/- mice, respectively."
NCBI gene IDs:
"Trpml1: 94178"
Figure legend: "(c) Live wild-type and Trpml1-/- acini were labeled with mitotracker (green) and lysotracker (red). The panels show the merged green, red and DIC images. The large vesicles are marked by white arrows and shown at higher magnification in the inserts. The overlap between lysosomes and granules was determined by ImageJ (see methods). The results are from 14 wild-type and 30 Trpml1-/- acini each comprising 3-7 cells and obtained from 3 wild-type and 4 Trpml1-/- mice."
NCBI gene IDs:
"Trpml1: 94178"
Figure legend: "(e) Enhanced exocytosis of the lysosomal acid phosphatase by Trpml1-/-acini stimulated with 100 pM CCK. The results are the mean±s.e.m of 3 experiments with acini obtained from 3 wild-type and 3 Trpml1-/-mice."
NCBI gene IDs:
"Trpml1: 94178"
Figure legend: "(a) Isolated acini from wild-type (black) and Trpml1-/- mice (red) loaded with Fura2 were used to determine [Ca2+]i in response to stimulation with 100 µM carbachol. The traces are the mean±s.e.m. of 6 acinar clusters. Similar results were obtained in 3 experiments."
NCBI gene IDs:
"Trpml1: 94178"
Figure legend: "(b, c) Saliva was collected from wild-type (black) and Trpml1-/- mice (red) injected I.P. with 10 mg/kg pilocarpine (b) or 1 mg/kg pilocarpine and 0.6 mg/kg isoproterenol (c) over 20-40 min to stimulate fluid secretion by pilocarpine and amylase secretion by isoproterenol. Each condition used 4-5 mice from each like and the results are given as the mean±s.e.m."
NCBI gene IDs:
"Trpml1: 94178"
Figure legend: "(e, f) Isolated acini from the parotid glands of wild-type (black) or Trpml1-/- mice (red) were used to measure amylase secretion in response to 50 nM isoproterenol for the indicated times (e) and the indicated isoproterenol concentrations during 30 min stimulation (f). The results are the mean±s.e.m obtained from two mice of each line."
NCBI gene IDs:
"Trpml1: 94178"
Figure legend: "(a) shows example TEM images and (b) shows the granules size distribution in parotid glands determined from 10 images obtained from 3 wild-type mice and 14 images obtained from 4 Trpml1-/- mice."
NCBI gene IDs:
"Trpml1: 94178"
Figure legend: "(d) Acini isolated from the parotid glands of wild-type and Trpml1-/- mice were incubated with mitotracker (green) and lysotracker. The large vesicles in the secretory granules/lysosomal area are marked by white arrows. The average number of enlarged profiles is given in the columns and obtained from 3 acinar preparations of each line."
NCBI gene IDs:
"Trpml1: 94178"
Figure legend: "(e) Shown is the time course (left panel) and averaged 10 min secretion (columns) of the lysosomal marker acid phosphatase in the saliva collected from wild-type (black) and Trpml1-/- mice (red) stimulated with 1 mg/kg pilocarpine and 0.6 mg/kg isoproterenol. The mean±s.e.m is from 4 mice of each line."
NCBI gene IDs:
"Trpml1: 94178"
Figure legend: "(a, b) example traces of mEPSCs recorded from wild-type (a) and Trpml1-/-(b) micebrain slices as detailed in Methods. The lower traces in each panel show the portion of the traces marked by dotted boxes in an expanded time scale. (c) histogram distribution of the events at each mEPSC. The lower columns show the distribution of the higher amplitude mEPSCs. (d) the frequency of mEPSCs in each line. The results in (c, b) are the mean±s.e.m of 8 experiments each obtained from 4 mice of each line."
NCBI gene IDs:
"Trpml1: 94178"
Figure legend: "(e) the mean±s.e.m of the Ca2+ signal in response to depolarization with 30 mM KCl of 6 and 5 experiments with wild-type and Trpml1-/- slices, respectively."
NCBI gene IDs:
"Trpml1: 94178"
Figure legend: "(a) example TEM images of synapses in wild-type and Trpml1-/-micebraincortex. (b) the distribution of synaptic vesicle size determined in 10 and 14 images obtained from 3 wild-type and 3 Trpml1-/-mice, respectively. (c) example TEM images at low magnification of wild-type and Trpml1-/-micebraincortical slices with the dark PSD profiles marked by white arrows. (d) average number of PSD/µm2 analyzed in at least 10 images obtained from 3 mice of each line."
NCBI gene IDs:
"Trpml1: 94178"
Figure legend: "(e) Glutamate levels and secretion by cultured cerebral cortical neurons. Total glutamate measured in non-stimulated wild-type (black) and Trpml1-/- (green) neurons and neurons stimulated by depolarization with 30 mM KCl (blue and red)."
NCBI gene IDs:
"Trpml1: 94178"
Figure legend: "(f) Rescue of glutamate levels and secretion by expression of TRPML1 in cultured cerebral cortical neurons. Total glutamate measured in non-stimulated Trpml1-/- neurons (green) and Trpml1-/- neurons transfected with TRPML1 (black) and untransfected (red) and TRPML1-transfected (clue) Trpml1-/- neurons stimulated by depolarization with 30 mM KCl."
NCBI gene IDs:
"TRPML1: 94178
Trpml1: 94178"
Figure legend: "(g) averaged Co-IP of SNAP25 and VAMP2 in three brain regions of wild-type and Trpml1-/- mice. The images of all blots are given in Extended view Figure E4."
NCBI gene IDs:
"Trpml1: 94178"
Figure legend: "B-C. Wound healing assays were performed using IBIDI® chambers to evaluate the role of the AhR  on cell migration. Images of the wound  were captured using an Axio Vert.A1 inverted microscope (Carl Zeiss®) at 5x magnification. The histogram represents the mean ± s.d. Wound  closure was determined by measuring the distance between the edges of the wound  at time  0 and 15 h (n = 3 independent technical experiments for each cell lines or conditions) and compared using unpaired t-tests with the Sidak-Bonferroni method. B. Results obtained with BRAFi-sensitive or resistant SK28  cells KO for the AhR  in the absence of treatment. (n = 3 independent technical experiments for each cell lines). C. Results obtained for the migration assay  (0 to 15 h) for SK28  R cells KO or not for the AhR  after treatment or not with 10 μM CH-223191. (n = 3 independent technical experiments for each cell lines or conditions, mean ± s.d.). Statistical analysis using unpaired t-tests with the Sidak-Bonferroni method has been performed between the mean of the 3 independent experiments."
NCBI gene IDs:
"AhR: 196"
Figure legend: "D. Three-dimensional spheroid growth  of BRAFi-sensitive or resistant SK28  cells KO before or after knockout of AhR  by CRISPR/Cas9  in the absence of treatment. Images were captured four days after implantation of the spheroids  into collagen  gel. (n = 4 independent technical experiments, mean ± s.d. E. Three-dimensional spheroid growth  of BRAFi-resistant SK28  cells KO before or after knockout of AhR  by CRISPR/Cas9  after daily treatment with the specific AhR  inhibitor CH-223191 (5 μM) for one week or in the absence of treatment. Images were captured four days after implantation of the spheroids  into collagen  gel. (n = 3 independent technical experiments, mean ± s.d.). Statistical analysis using unpaired t-tests method has been performed with the Sidak-Bonferroni method, (p&lt;0.01 ##, **; p&lt;0.001 ###,***)."
NCBI gene IDs:
"CRISPR: 
AhR: 196
Cas9: 69900935"
Figure legend: "A. AhR  Protein levels in 501Mel  CTR cells and those transduced with sgRNA targeting AhR  (#1, #2) were analyzed by western blotting."
NCBI gene IDs:
"AhR: 196"
Figure legend: "D. AhR  Protein levels in SK28R WT, KO, and KO CA-AhR  cells were analyzed by western blotting."
NCBI gene IDs:
"AhR: 196"
Figure legend: "F. Three-dimensional spheroid growth  of SK28  cells KO or not for AhR  by CRISPR/Cas9  and rescued by the constitutive active form of AhR  (KO CA-AhR). Images were captured four days after spheroid implantation (n = 3 independent technical experiments, mean ± s.d.). Comparisons were performed using unpaired t-tests with the Sidak-Bonferroni method."
NCBI gene IDs:
"CRISPR: 
AhR: 196
Cas9: 69900935"
Figure legend: "C. Protein levels of the AhR, p-SRC  (Y416), SRC, p-FAK  (Y576/577), and FAK  in the SK28R cell line KO or not for AhR  by CRISPR/Cas9  or after rescue with the activated-form of the AhR  (CA-AhR)."
NCBI gene IDs:
"CRISPR: 
AhR: 196
Cas9: 69900935"
Figure legend: "(a) Kaplan-Meier survival plot of cohorts of induced Vil Apc, Vil Apc Huwe1het and Vil Apc Huwe1hom mice. Deletion of Huwe1 led to a significant reduction in survival of these animals (Vil Apc vs Vil Apc Huwe1het / Vil Apc Huwe1hom, Log Rank, p &lt; 0.001, n ≥ 10)."
NCBI gene IDs:
"Apc: 11789
Huwe1: 59026
Vil: 22349"
Figure legend: "(b) Wholemount isolation of small intestines from Vil Apc and Vil Apc Huwe1hom mice culled at clinical endpoint. Note the huge numbers of tiny macroscopic adenomas visible in the Vil Apc Huwe1hom intestine (red arrows)."
NCBI gene IDs:
"Apc: 11789
Huwe1: 59026
Vil: 22349"
Figure legend: "(c) H&amp;amp;amp;E staining of intestinal cross sections from Vil Apc and Vil Apc Huwe1hom mice demonstrating the increased adenoma burden following Huwe1 deletion. Black arrows indicate individual adenomas. Scale bars = 200 µm."
NCBI gene IDs:
"Apc: 11789
Huwe1: 59026
Vil: 22349"
Figure legend: "(d) Quantification of total tumour numbers per gut in sacrificed Vil Apc, Vil Apc Huwe1het and Vil Apc Huwe1hom mice. Deletion of Huwe1 led to a significant increase in the number of tumours per gut (Mann Whitney, n ≥ 5)."
NCBI gene IDs:
"Apc: 11789
Huwe1: 59026
Vil: 22349"
Figure legend: "(a) H&amp;amp;amp;E staining of control and Huwe1 deleted intestinal epithelium. Shortened villi in Huwe1 deficient tissue are indicated. Scale bars = 100 µm. (b) BrdU IHC of control and Huwe1 deleted intestinal epithelium. Scale bars = 100 µm. (c) PAS staining identifying Goblet cells. No gross changes were observed. Scale bars = 100 µm. (d) Lysozyme staining (Paneth cell marker) of control and Huwe1 deleted small intestine. Note the occurrence of lysozyme positive cells away from the crypt base (black arrows). Scale bars = 100 µm."
NCBI gene IDs:
"Huwe1: 59026"
Figure legend: "(e) Dual Periodic acid-Schiff / Alcian blue staining to identify Paneth cell secretory vesicles (light blue / pink - marked with black arrows) and goblet cells (dark blue / purple - marked with red arrows). Note Paneth cell secretory vesicles are restricted to crypt base in both control and Huwe1 deficient small intestines (inset - black arrows). Scale bars = 100µm."
NCBI gene IDs:
"Huwe1: 59026"
Figure legend: "(f) MMP7 staining of control and Huwe1 deleted small intestine. Note MMP7 staining is restricted to crypt base in Huwe1 deficient intestines. Scale bars = 100µm."
NCBI gene IDs:
"Huwe1: 59026"
Figure legend: "(a) HUWE1 and MYC Western blot analysis of epithelial cell extractions from control and Huwe1 deficient intestines. Levels of MYC protein are significantly increased in normal intestines lacking HUWE1 (Mann Whitney, p = 0.04, n = 3)."
NCBI gene IDs:
"Huwe1: 59026"
Figure legend: "(b) QRT-PCR analysis of Myc expression in control and Huwe1 deficient intestines."
NCBI gene IDs:
"Huwe1: 59026
Myc: 17869"
Figure legend: "(c) MYC IHC in tumours from Vil Apc and Vil Apc Huwe1hom mice. Scale bars = 50 µm."
NCBI gene IDs:
"Apc: 11789
Huwe1: 59026
Vil: 22349"
Figure legend: "(d) MYC Western blot in protein extracts from Vil Apc and Vil Apc Huwe1hom tumours. Levels of MYC protein are significantly increased in tumours lacking HUWE1 (Mann Whitney, p = 0.04, n = 3)."
NCBI gene IDs:
"Apc: 11789
HUWE1: 59026
Huwe1: 59026
Vil: 22349"
Figure legend: "(e) QRT-PCR analysis of Myc expression in tumours from Vil Apc and Vil Apc Huwe1hom mice."
NCBI gene IDs:
"Apc: 11789
Huwe1: 59026
Myc: 17869
Vil: 22349"
Figure legend: "(a) Kaplan-Meier survival plot of cohorts of induced Vil Apc Pten, Vil Apc Pten Huwe1, Vil Apc Pten Myc and Vil Apc Pten Huwe1 Myc mice. Heterozygous deletion of Myc led to a specific and significant increase in survival of Huwe1 deleted animals (Vil Apc Pten Huwe1 vs Vil Apc Pten Huwe1 Myc, Log Rank, p &lt; 0.001, n ≥ 16)."
NCBI gene IDs:
"Apc: 11789
Huwe1: 59026
Myc: 17869
Pten: 19211
Vil: 22349"
Figure legend: "(b) Quantification of total tumour numbers per gut in sacrificed Vil Apc Pten, Vil Apc Pten Huwe1, Vil Apc Pten Myc and Vil Apc Pten Huwe1 Myc mice. Heterozygous deletion of Myc did not reduce the number of tumours in Huwe1 deleted mice (Vil Apc Pten Huwe1 vs Vil Apc Pten Huwe1 Myc. Mann Whitney, n ≥ 10)."
NCBI gene IDs:
"Apc: 11789
Huwe1: 59026
Myc: 17869
Pten: 19211
Vil: 22349"
Figure legend: "(c) Kaplan-Meier survival plot of cohorts of induced AhCre-ERT Apc Pten and AhCre-ERT Apc Pten MycT58A mice. Overexpression of proteolytically stabilised MYC led to a significant reduction in survival (Log Rank, p &lt; 0.001, n = 14 vs 21)."
NCBI gene IDs:
"Cre: 
Ah: 11622
Apc: 11789
ER: 13983///13982
Myc: 17869
Pten: 19211"
Figure legend: "(d) Quantification of total tumour numbers per gut in sacrificed Apc Pten and Apc Pten MycT58A mice. Overexpression of proteolytically stabilised MYC did not increase the number of tumours in Apc Pten mice (Mann Whitney, n = 9 vs 19)."
NCBI gene IDs:
"Apc: 11789
MYC: 17869
Myc: 17869
Pten: 19211"
Figure legend: "(a) H2AX Western blot in protein extracts from control and Huwe1 deficient intestinal epithelial cells. Band intensity relative to βactin displayed under each lane (Mann-Whitney, p = 0.04, n = 3 vs 3)."
NCBI gene IDs:
"Huwe1: 59026"
Figure legend: "(b) γ-H2AX IHC showing increased positivity in Huwe1 deleted intestinal cells. Scale bars = 50 µm."
NCBI gene IDs:
"Huwe1: 59026"
Figure legend: "(c) γ-H2AX Western blot in protein extracts from control and Huwe1 deficient intestinal epithelial cells (Mann-Whitney, p = 0.04, n = 3 vs 3)."
NCBI gene IDs:
"Huwe1: 59026"
Figure legend: "(d) γ-H2AX IHC of Vil Apc and Vil Apc Huwe1hom tumours, note increased positivity in Huwe1 deficient tumours. Scale bars = 50 µm."
NCBI gene IDs:
"Apc: 11789
Huwe1: 59026
Vil: 22349"
Figure legend: "(a) Caspase 3 IHC of tumours from Lgr5 Apc and Lgr5 Apc Huwe1 mice either untreated or 6h post treatment with 7.5mg/kg cisplatin. Arrows identify caspase 3 positive cells. Scale bars = 50 µm. (b) Quantification of cisplatin treatment showing a significant increase in apoptosis in Huwe1 deficient tumour cells (Mann-Whitney, n = 3 vs 5)."
NCBI gene IDs:
"Apc: 11789
Huwe1: 59026
Lgr5: 14160"
Figure legend: "(c) Comparison of somatic mutation rate (mutations / Mb) between human tumours carrying HUWE1 mutations or not. Note the significant increase in mutational burden in HUWE1 mutated tumours (Mann-Whitney, p = 0.0002, n ≥ 15)."
NCBI gene IDs:
"HUWE1: 10075"
Figure legend: "(d) Comparison of somatic mutation rate (mutations / Mb) between human tumours carrying HUWE1 mutations or not grouped according to MLH1 status. Note that the increased mutation rate is found primarily in tumours where MLH1 is not silenced indicating increased mutation rate (and HUWE1 mutation itself) is not due to silencing of MLH1 (Mann-Whitney, p = 0.0007, n ≥ 11)."
NCBI gene IDs:
"HUWE1: 10075
MLH1: 4292"
Figure legend: "(e) Survival analysis of colorectal cancer patients treated with adjuvant chemotherapy divided by HUWE1 expression levels. Note the lowest HUWE1 expressing quartile of patients respond significantly better to chemotherapy. (f) Survival analysis of colorectal cancer patients not treated with adjuvant chemotherapy divided by HUWE1 expression levels. Note the lowest HUWE1 expressing quartile of patients do not survive significantly longer than those expressing higher levels of HUWE1 if not treated with chemotherapy."
NCBI gene IDs:
"HUWE1: 10075"
Figure legend: "(b) Kaplan-Meier survival plot of cohorts of induced Lgr5 Apc and Lgr5 Apc Huwe1 mice. Deletion of Huwe1 led to a significant reduction in survival of these animals (Log Rank, p &lt; 0.001, n ≥ 15)."
NCBI gene IDs:
"Apc: 11789
Huwe1: 59026
Lgr5: 14160"
Figure legend: "(c) Lysozyme IHC demonstrating increased lysozyme positive cell numbers in tumours from Lgr5 Apc Huwe1 mice. Scale bars = 200 µm (low magnification), 100 µm (high magnification inset). (d) OLFM4 IHC demonstrating expanded stem cell population in Lgr5 Apc Huwe1 tumours. Scale bars = 200 µm (low magnification), 100 µm (high magnification inset)."
NCBI gene IDs:
"Apc: 11789
Huwe1: 59026
Lgr5: 14160"
Figure legend: "(a) MCL1 Western blot in protein extracts from Vil Apc and Vil Apc Huwe1hom tumours. Levels of MCL1 protein are significantly increased in tumours lacking HUWE1 (Mann Whitney, p = 0.04, n = 3)."
NCBI gene IDs:
"Apc: 11789
HUWE1: 59026
Huwe1: 59026
Vil: 22349"
Figure legend: "(b) Kaplan-Meier survival plot of cohorts of induced Lgr5 Apc Huwe1 and Lgr5 Apc Huwe1 Mcl1 mice. Deletion of one copy of Mcl1 led to a significant increase in survival of these animals (Log Rank, p = 0.0052, n = 9 vs 10)."
NCBI gene IDs:
"Apc: 11789
Huwe1: 59026
Lgr5: 14160
Mcl1: 17210"
Figure legend: "(c) Ratio of adenoma / indolent lesions observed in Lgr5 Apc Huwe1 and Lgr5 Apc Huwe1 Mcl1het mice. Note the decreased ration of adenoma / indolent lesions observed upon Mcl1 deletion (Mann-Whitney, p=0.0281, n = 8 v 8)."
NCBI gene IDs:
"Apc: 11789
Huwe1: 59026
Lgr5: 14160
Mcl1: 17210"
Figure legend: "E, Overlay of normalized (at 705 nm) difference spectra plus a difference spectrum of the photosensory domain in the presence of the bacterial HO BphO"
NCBI gene IDs:
"BphO: 879778"
Figure legend: "(D) CMH2DCFDA staining of H2O2 and quantification of signal intensity in the muscle tissues of 50-day old control flies and flies with NDUFS2 or NDUFS3 knockdown (n=5 per group)."
NCBI gene IDs:
"NDUFS3: 38378
NDUFS2: 43798"
Figure legend: "(A, B) Survival curves showing effect of neuronal dSirt2 knockdown on fly lifespan under normal and CPT-treatment conditions (n=3 groups, 20-25 flies per group). (C, D) Survival curves showing effect of muscle dFoxo knockdown on fly lifespan under normal and CPT-treatment conditions (n=3 groups, 20-25 flies per group). (E, F) Survival curves showing effect of neuronal ATG1 knockdown on fly lifespan under normal and CPT-treatment conditions (n=3 groups, 20-25 flies per group)."
NCBI gene IDs:
"ATG1: 39454
Foxo: 41709
Sirt2: 42414"
Figure legend: "(A, B) Survival curves showing effect of CPT treatment on the lifespan of Mhc&gt;APP.C99 flies (**p&lt;0.01 logrank, **p&lt;0.01 Wang Allison) (A) and elav&gt;APP.BACE flies (**p&lt;0.01 logrank, **p&lt;0.01 Wang Allison) (B) (n=3 groups, 20-25 flies per group)."
NCBI gene IDs:
"APP: 351
BACE: 23621
elav: 31000
Mhc: 35007"
Figure legend: "(E) Immunofluorescence images and data quantification showing effect of CPT on the formation of ubiquitin- and 6E10-positive amyloid aggregates in the brain of elav&gt;APP.BACE flies (n=5)."
NCBI gene IDs:
"APP: 351
BACE: 23621
elav: 31000"
Figure legend: "(G) Quantification of the effect of CPT on DA neuron number in the PPL1 cluster of elav&gt;APP/BACE fly brain (n=4 sets, 5 brains per set)."
NCBI gene IDs:
"APP: 351
BACE: 23621
elav: 31000"
Figure legend: "(a) Anti-VHR and anti-actin immunoblots of lysates of HeLa cells transfected with a control luciferase siRNA or VHR siRNA and cultured for the indicated number of days."
NCBI gene IDs:
"VHR: 1845"
Figure legend: "(b) Number of cells at the start of the experiment (200,000) and on day 3 for HeLa cells transfected with a control luciferase siRNA (black bars) or with VHR siRNA (white bars)."
NCBI gene IDs:
"VHR: 1845"
Figure legend: "(c) Light microscopy of HeLa cells transfected with a control luciferase siRNA or VHR siRNA and cultured for three days."
NCBI gene IDs:
"VHR: 1845"
Figure legend: "(d) Thymidine incorporation by HeLa cells transfected with a control luciferase siRNA or with VHR siRNA. The data represent the mean ± sd. (n = 3)."
NCBI gene IDs:
"VHR: 1845"
Figure legend: "(e) β-galactosidase staining of HeLa cells transfected with a control luciferase siRNA or VHR siRNA and cultured for three days. Note the increased number of blue-staining granules in many cells. ("
NCBI gene IDs:
"VHR: 1845"
Figure legend: "(f) Telomerase activity of cells treated with the indicated concentrations of VHR siRNA. Each sample was analysed in triplicate, with RNAse added to a fourth sample."
NCBI gene IDs:
"VHR: 1845"
Figure legend: "(a) Cell-cycle distribution and cell number count of cells transfected with control or VHR siRNA and observed for 4-5 days. The cells were stained with propidium iodide for DNA content and analysed by FACS after the indicated number of days in culture."
NCBI gene IDs:
"VHR: 1845"
Figure legend: "(b) Confocal microscopy of the same HeLa cells stained for VHR (green) and BrdU (red) to indicate S-phase entry, and DNA (DAPI, blue). Control siRNA-treated cells and cells treated with VHR are shown. The bottom panels represent merges of the 3 images above"
NCBI gene IDs:
"VHR: 1845"
Figure legend: "(e) Confocal microscopy of control or VHR siRNA-transfected HeLa cells stained for VHR (green) and phospho H3 (red) to indicate M-phase entry, and DNA (DAPI, blue). The bottom panels represent merges of the images above."
NCBI gene IDs:
"VHR: 1845"
Figure legend: "(f) Immunoblots of total lysates of control siRNA transfected cells and VHR siRNA cells with the indicated antibodies. Note that VHR was downregulated by approximately 80%, wheras actin levels were unchanged."
NCBI gene IDs:
"VHR: 1845"
Figure legend: "(g) Immunoblot with anti-p21Cip1-WAF1 of total lysates of cells transfected with control siRNA (lanes 1-2), two different VHR siRNAs cells (lanes 3-6) or another control siRNA (lanes 7-8). The scale bars represent 10 μm in b and e."
NCBI gene IDs:
"VHR: 1845"
Figure legend: "(a) Proliferation of cells transfected 3 days earlier with a combination of control siRNA or VHR siRNA together with Mek, Jnk or Mek plus Jnk siRNAs. The data are calculated as percentage of control (control siRNA alone) and represent the mean ± s.d. from three independent experiments. The starting cell numbers were 150,000 or 200,000 and the control cells had increased by 5.3, 5.0 and 13-fold in the three experiments."
NCBI gene IDs:
"VHR: 1845
Mek: 5609
Jnk: 5599"
Figure legend: "(F) Representative immunoblot of LC3 and p62 in MEFs of indicated genotype. MEFs were treated with tunicamycin (5 μg/ml) or vehicle control in the presence or absence of bafilomycin A1 (400 nM), and endogenous LC3 and p62 levels were measured by immunoblotting. Data represent the ratios of LC3-II to LC3-I and p62 to actin in the absence of bafilomycin, which were normalized LRRK+/+ MEFs. Error bars represent ±SD from four independent experiments. Data information: For graph the P values was determined by a Mann-Whitney U test. ns = not significant, *P &lt; 0.05, **P &lt; 0.01."
NCBI gene IDs:
"LRRK: 66725"
Figure legend: "MEFs were transfected with mitochondrially targeted Cameleon. Free Ca2+ dynamics in the mitochondrial matrix were visualized using FRET. Mitochondrial [Ca2+] ([Ca2+]m) was continuously monitored by FRET imaging data are represented as absolute [Ca2+] in μmol. (C) Peak values of Ca2+ transients in MEFs transfected with IP3R or shRNA against IP3R, or treated with 2-AP (20 mM). Error bars represent ±SD from six independent experiments. Data information: For graph the P values was determined by a Mann-Whitney U test. ns = not significant, *P &lt; 0.05, **P &lt; 0.01"
NCBI gene IDs:
"IP3R: 16438"
Figure legend: "MEFs were transfected with mitochondrially targeted Cameleon. Free Ca2+ dynamics in the mitochondrial matrix were visualized using FRET. Mitochondrial [Ca2+] ([Ca2+]m) was continuously monitored by FRET imaging data are represented as absolute [Ca2+] in μmol. (D) Peak values of Ca2+ transients in MEFs transfected with VDAC1 or shRNA against VDAC1. Error bars represent ±SD from six independent experiments. Data information: For graph the P values was determined by a Mann-Whitney U test. ns = not significant, *P &lt; 0.05, **P &lt; 0.01"
NCBI gene IDs:
"VDAC1: 22333"