EMBO/SourceData huggingface dataset:
Figure legend: "(B) Cytosol and Golgi fractionations were isolated from the livers of PAQR3-deleted mice and their littermate controls. Equal protein amounts of cytosol and Golgi fractions were subjected to IB."
NCBI gene IDs:
"PAQR3: 231474"
Figure legend: "(F) The lysates of WT or PAQR3 knockout MEFs were used in IP and IB."
NCBI gene IDs:
"PAQR3: 231474"
Figure legend: "(G) MEFs were infected with control or PAQR3-expressing lentivirus. Then a quantitative immunodepletion assay was performed with increasing amounts of the indicated antibodies. Supernatants of MEF lysates after immunodepletion (Post-IP) were examined to determine the level of VPS34 complex proteins."
NCBI gene IDs:
"PAQR3: 231474"
Figure legend: "(E) Purified GST or GST-fused PAQR3 (1-71) (GST fused NH2-terminal 71aa of PAQR3) on glutathione agarose beads was mixed with purified His tagged proteins as indicated. After incubation at 4 °C for 3 h, the samples were washed extensively and subjected to IB."
NCBI gene IDs:
"PAQR3: 152559"
Figure legend: "(F, G) Different PAQR3 deletion constructs were co-transfected with Flag-tagged Beclin1 (F) into HEK293T cells. The cells were then subjected to IP and IB."
NCBI gene IDs:
"PAQR3: 152559"
Figure legend: "(C) WT or AMPKa1/2 double knockout MEFs were incubated under NM or GS for 4 h, followed by IB with Phos-tag gel or regular SDS-PAGE."
NCBI gene IDs:
"AMPKa1: 105787"
Figure legend: "(E) Bacterial purified His-tagged NH2-terminal 71 amino acid of PAQR3 was incubated with or without purified Flag-tagged ATG14L. Then the complexes were treated with WT AMPK or DN-AMPK (dominant negative AMPK) for the indicated time in vitro. PAQR3 phosphorylation was examined by Phos-tag gel."
NCBI gene IDs:
"ATG14L: 22863"
Figure legend: "(F) HeLa cells infected with control or ATG14L-expressing lentivirus were incubated under GS for different time as indicated. Whole cell lysates were analyzed by both Phos-tag gel and regular SDS-PAGE."
NCBI gene IDs:
"ATG14L: 22863"
Figure legend: "(G) HeLa cells were infected by lentivirus expressing control shRNA or ATG14L-specific shRNA. Then the ATG14L knockdown cells were stably re-expressed with shRNA-resistant ATG14L (rATG14L) or Beclin1 and incubated under NM or GS for 4 h. Whole cell lysates were analyzed by both Phos-tag gel and regular SDS-PAGE."
NCBI gene IDs:
"ATG14L: 22863"
Figure legend: "(A) Bacterial purified His-tagged WT or T32A NH2-terminal 71aa of PAQR3 was incubated with or without Flag-tagged ATG14L purified from HEK293T cells. Then the complexes were incubated with AMPK for the indicated time and subjected to Phos-tag gel or regular SDS-PAGE."
NCBI gene IDs:
"PAQR3: 152559"
Figure legend: "(B) PAQR3-deficient HeLa cells were transfected with WT or T32A mutants of PAQR3 plasmids. 24 h later, the cells were incubated with normal medium (NM) or glucose starvation (GS) for 4 h, followed by immunoblotting (IB) in Phos-tag gel or regular SDS-PAGE."
NCBI gene IDs:
"PAQR3: 152559"
Figure legend: "(E) WT, phosphorylation defective (T32A), or phospho-mimetic (T32E) PAQR3 were transfected in the presence or absence of constitutively active AMPK (CA-AMPK) into PAQR3-deficient HeLa cells as indicated. 24 h later, the cells without AMPK transfection were treated with GS for 4 h. 10% of the cell lysates were subjected to IB to detect PAQR3 expression level (shown in Appendix Fig S4A), the remaining cell lysates were used to immunoprecipitate VPS34 complexes by ATG14L antibody, followed by VPS34 activity measurement by a quantitative PI(3)P ELISA assay. The PI(3)P level was normalized to the amount of ATG14L (n = 5; *p &lt; 0.05; **p &lt; 0.01 as compared to the first group)."
NCBI gene IDs:
"AMPK: 
PAQR3: 152559"
Figure legend: "(F) PAQR3-deficient HeLa cells were infected with lentivirus expressing WT or T32A PAQR3. Then PAQR3 expression levels were examined by IB."
NCBI gene IDs:
"PAQR3: 152559"
Figure legend: "(G) Both WT HeLa cells and PAQR3 knockout HeLa cells infected with lentivirus expressing WT or T32A PAQR3 were treated with GS for 2 h or 4 h respectively. Cell lysates were analyzed by IB."
NCBI gene IDs:
"PAQR3: 152559"
Figure legend: "(A, B) Representative immunohistochemical images of LC3 staining in skeletal muscle (A) and liver (B) after 80 min exercise in WT and PAQR3-deleted mice. Scale bar in (A): 20 μm. Scale bar in (B): 50 μm."
NCBI gene IDs:
"PAQR3: 231474"
Figure legend: "(C, D) Immunoblotting analysis of skeletal muscle (C) and liver (D) from WT or PAQR3 knockout mice at rest or after 80 min exercise."
NCBI gene IDs:
"PAQR3: 231474"
Figure legend: "(E) Abnormal limb-clasping of PAQR3 knockout mice when suspended by its tail. Quantification scoring of the limb clasping phenotype is shown on the right (n = 7 for each group; **p &lt; 0.01)."
NCBI gene IDs:
"PAQR3: 231474"
Figure legend: "(H) The supernatants of liver lysates form WT or PAQR3 knockout mice were subjected to gel filtration analysis, followed by IB."
NCBI gene IDs:
"PAQR3: 231474"
Figure legend: "Representative images of the size of Mex3a mutant mice and control littermates at postnatal day (P)15. Scale bar, 1 cm. Genotypes were confirmed by Mex3a mRNA ISH in intestinal tissue (right panels). Scale bars, 50 μm. The offspring number (n) and observed genotype frequencies (%) resulting from heterozygous crosses are indicated below."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "Absolute weight of Mex3a KO mice and control littermates at different ages. Data is represented in a box and whiskers plot as mean (middle line) with the minimum and maximum distribution values. Each point depicts one animal (WT: P1, n = 15; P8, n = 36; P15, n = 43; P22, n = 14; Adult, n = 14; Mex3a+/-: P1, n = 24; P8, n = 90; P15, n = 90; P22, n = 37; Adult, n = 21; Mex3a-/-: P1, n = 9; P8, n = 24; P15, n = 26; P22, n = 14; Adult, n = 8) ***P = 0.0003, ****P &lt; 0.0001, two-way ANOVA test."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "Kaplan-Meier survival curves for the different Mex3a genotypes (n = 80 for each genotype) ****P &lt; 0.0001, Log-rank (Mantel-Cox) test."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "Macroscopic assessment of the gastrointestinal tract of Mex3a KO and WT mice. These images are representative of the phenotype observed in mutant animals euthanized at different postnatal days. Boxed areas depict the distal small intestinal section (ileum) used for subsequent immunohistochemical analyses."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "H&amp;E staining of a Mex3a KO and WT littermate at P19. Inserts depict high magnification of the boxed areas."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "Average crypt depth (C) of WT animals (n = 3, &gt; 40 crypts counted per animal) and Mex3a mutants (n = 6, &gt; 20 crypts counted per animal). Also shown is the average villi height (D) of WT animals (n = 3, &gt; 25 villi counted per animal) and Mex3a mutants (n = 6, &gt; 15 villi counted per animal). Data is represented as mean ± standard error between P16 and P18. *P = 0.03, ***P = 0.0006, Student`s t test."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "mRNA ISH staining for the stem cell markers (H) Lgr5, (I) Olfm4, (J) Lrig1, and (K) Hopx in ileal sections of Mex3a mutants and littermate controls at P19. Inserts depict high magnification of the boxed areas."
NCBI gene IDs:
"Hopx: 74318
Lgr5: 14160
Lrig1: 16206
Mex3a: 72640
Olfm4: 380924"
Figure legend: "qPCR analysis of the expression level of the indicated stem cell markers in freshly isolated crypt fractions from Mex3a KO and WT animals (n = 3 of each genotype). Data is represented as mean fold-change plus standard error in Mex3a KO mice relatively to WT animals (dashed line). *P = 0.0208, **P &lt; 0.01, ***P = 0.0007, Student`s t test."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "Quantification of the size (diameter length) of Mex3a KO and WT organoid-initiating structures 2 days after crypt isolation (n = 3 for each genotype, &gt; 150 structures counted in total). Data is represented in a box and whiskers plot as mean (middle line) with the minimum and maximum distribution values. Each point depicts one organoid-initiating structure. ****P &lt; 0.0001, Student`s t test. Phase contrast microscopy images of intestinal organoids generated by Mex3a-/- and WT crypts 6 days after crypt isolation. Scale bars, 100 μm."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "Representative phase contrast microscopy images of Mex3a KO and WT intestinal organoids at days 2 and 4 of culture after 10 weekly passages. Scale bars, 100 μm."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "qPCR analysis of crypt lineage marker genes in organoid cultures at day 2. Data is presented as the mean fold-change plus standard error (n = 4 for each genotype) for target gene expression in Mex3a KO intestinal organoids relative to WT (dashed line). *P &lt; 0.05, Student`s t test."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "Immunohistochemistry staining for the Paneth cell marker LYZ1 in Mex3a KO and WT intestinal organoid sections at day 2 of culture. Scale bars, 50 μm."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "qPCR analysis of crypt lineage marker genes in organoid cultures at day 4. Data is presented as the mean fold-change plus standard error (n = 4 for each genotype) for target gene expression in Mex3a KO intestinal organoids relative to WT (dashed line)."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "mRNA ISH staining for the stem cell markers Mex3a, Lgr5, Hopx and Lrig1 in Mex3a KO and WT intestinal organoid sections at day 2 of culture. Scale bars, 50 μm."
NCBI gene IDs:
"Hopx: 74318
Lgr5: 14160
Lrig1: 16206
Mex3a: 72640"
Figure legend: "Representative images of immunofluorescence staining for the proliferation marker KI67 and BrdU incorporation in Mex3a KO and WT animals. Mice were injected at P17 and sacrificed at P20 (n = 3 for each genotype). Scale bars, 50 μm."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "Hierarchical clustering of samples (n = 3 for each genotype) and heatmap of differentially expressed genes between the Mex3a-/- and WT mice. The red colour represents over-expression, while the blue colour under-expression."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "GSEA pre-ranked analysis comparing the Mex3a-/- transcriptional profile against (E) the Mex3ahigh"
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "GSEA pre-ranked analysis comparing the Mex3a-/- transcriptional profile against the Lgr5high and (G) the Wnt signalling pathway gene signatures."
NCBI gene IDs:
"Lgr5: 14160
Mex3a: 72640"
Figure legend: "qPCR analysis of selected genes in a cohort of independent mice. Data is presented as the mean fold-change of target gene expression in 2 biological replicates (Mex3a-/- Vs WT #1 and Mex3a-/- Vs WT #2) of Mex3a KO intestinal crypts relative to the respective WT controls (dashed line)."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "Immunohistochemistry staining for PPARγ in Mex3a KO and WT mice ileum. Inserts depict high magnification of the boxed areas. Scale bars, 50 μm."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "Pparg mRNA ISH in ileal sections of Mex3a mutants and littermate controls at P18. Inserts depict high magnification of the boxed areas. Scale bars, 50 μm."
NCBI gene IDs:
"Mex3a: 72640
Pparg: 19016"
Figure legend: "qPCR analysis of PPARγ transcriptional targets in organoid cultures at day 4. Data is presented as the mean fold-change plus standard error (n = 3 for each genotype) for target gene expression in Mex3a KO intestinal organoids relative to WT (dashed line)."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "Representative phase contrast microscopy images of Mex3a KO and WT intestinal organoids after 5 days of treatment with 50 μM Pioglitazone or vehicle (DMSO). Scale bars, 100 μm."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "qPCR analysis of Lgr5, Pcna and Angptl4 expression in organoid cultures after 5 days of treatment with 50 μM Pioglitazone. Data is presented as the mean fold-change plus standard error (n = 4 for each genotype) for target gene expression in Pioglitazone-treated organoids relative to the DMSO vehicle (dashed line). * P = 0.02, Student`s t test."
NCBI gene IDs:
"Angptl4: 57875
Lgr5: 14160
Pcna: 18538"
Figure legend: "Representative phase contrast microscopy images of Mex3a KO and WT intestinal organoids at day 1 after passaging Pioglitazone- or vehicle (DMSO)-treated organoids. Scale bars, 100 μm."
NCBI gene IDs:
"Mex3a: 72640"
Figure legend: "Transposon screen validation of UBX5. ubx5∆ restores the growth of tdp1wss1. Cells were grown in YEPD and spotted on a medium supplemented with 1 mM auxin (for tdp1-degron degradation) and 5 μg/mL Camptothecin (CPT). Plates were incubated for 2 days at 30°C."
NCBI gene IDs:
"tdp1: 852525
UBX5: 851930
ubx5: 851930
wss1: 856536"
Figure legend: "Ubx5 levels are decreased in tdp1wss1. (E) HA-Ubx5 protein levels at steady state are compared by immunoblotting in different mutants. Mutant strains carrying the additional ubx5∆ mutation were complemented with a plasmid expressing HA-tagged Ubx5 from the endogenous pUBX5 promoter. 1mM auxin was added where indicated for 6 h to degrade tdp1-degron, when present. Pgk1 was used as a loading control."
NCBI gene IDs:
"HA: 
tdp1: 852525
ubx5: 851930
Ubx5: 851930
UBX5: 851930
wss1: 856536"
Figure legend: "The UBX∆ mutant of Ubx5 is sufficient to suppress FA and HU sensitivities of wss1∆. ubx5∆wss1∆ mutants were complemented with plasmids encoding HA-Ubx5-WT or HA-Ubx5 mutants overexpressed from the pGAL promoter; cells were grown in SC-trp and either treated with 40 mM FA for 15 min or spotted directly on 20 mM HU. Plates were prepared either with glucose (no HA-Ubx5 expression) or galactose (HA-Ubx5 expression) as the source of sugar. Plates were incubated for 2.5 days at 30°C. o/e, overexpression."
NCBI gene IDs:
"HA: 
GAL: 855828
Ubx5: 851930
ubx5: 851930
wss1: 856536"
Figure legend: "(B) The ubx5∆ mutation rescues growth defects caused by Flp-nick galactose-induction in the tdp1∆ wss1∆ top1∆ mutant. Indicated strains were grown in YEP-2% raffinose prior to plating on YEP-2% glucose or YEP-2% galactose plates. Plates were incubated for 3 days at 30°C."
NCBI gene IDs:
"tdp1: 852525
top1: 854156
ubx5: 851930
wss1: 856536"
Figure legend: "(E) Ubx5 occupancy at the Flp-bound FRT site. Levels of Ubx5-TAP were monitored by ChIP and qPCR following formaldehyde crosslinking in cells grown as described in (C). The graph shows enrichment of qPCR signals over the unrelated intergenic region. Data are presented as means ± SDs for n = 5 independent biological replicates. p-values for +200 bp were defined by 2-way ANOVA using Tukey's multiple comparisons test (n.s., non-significant; *p &lt; 0.05; ** p &lt; 0.01; **** p &lt; 0.0001). In addition to the indicated mutations, all strains are bar1∆ Ubx5-TAP. No FRT strain and raffinose (raf) samples were used as negative controls."
NCBI gene IDs:
"TAP: 
bar1: 854797
Ubx5: 851930"
Figure legend: "Cdc48 occupancy at the Flp-bound FRT site. Levels of Cdc48-TAP were monitored by ChIP and qPCR following formaldehyde crosslinking in asynchronous cells before and after Flp-cc induction with galactose. The graph shows enrichment of qPCR signal over the unrelated intergenic region. Data are presented as means ± SDs of 3 to 4 independent biological replicates. p-values for +200 bp were defined by 2‑way ANOVA using Tukey's multiple comparisons test (n.s., non-significant; **** p &lt; 0.0001). In addition to the indicated mutations, all strains are Cdc48-TAP. No FRT strain was used as a negative control."
NCBI gene IDs:
"TAP: 
Cdc48: 851431"
Figure legend: "Ubiquitination of the FRT locus. Asynchronous cultures were grown in 2% raffinose (raf) or additionally supplemented with 3% galactose (gal) to induce flp-H305L expression. Cells were also collected during glucose repression of flp-H305L expression at time points 30 min (glu 30') and 120 min (glu 120'). Ubiquitin antibody was used for ChIP-qPCR analysis following formaldehyde crosslinking. Data are shown as the mean ± SDs of three to six independent replicates. p-values for +200 bp were defined by 2‑way ANOVA using Tukey's multiple comparisons test (n.s., non-significant; *p &lt; 0.05; *** p &lt; 0.001; **** p &lt; 0.0001). In addition to all indicated mutations, all strains are bar1∆ Ddi1-TAP."
NCBI gene IDs:
"TAP: 
bar1: 854797
Ddi1: 856886"
Figure legend: "ubx5∆ restores wss1∆ resistance to HU and FA but not upon additional deletion of DDI1. Strains were grown in YEPD and either treated with 40 mM FA for 15 min or directly spotted on plates containing 100 mM of HU or 5 μg/mL CPT. Plates were incubated for 2 days at 30°C."
NCBI gene IDs:
"DDI1: 856886
ubx5: 851930
wss1: 856536"
Figure legend: "Endogenous HA-Ddi1 levels are still elevated upon additional ubx5∆ mutation. Levels in total cell extracts were compared by immunoblotting. For quantification, anti-HA signal was normalized to Pgk1 and then normalized to WT (see (D)). Quantification of HA-Ddi1 levels shown in (C). The anti-HA signal was compared to Pgk1 and normalized to WT. Quantifications of 5 biological replicates are presented as means ± SDs. Significance was defined by ordinary one-way ANOVA using Dunnett's multiple comparisons test and WT as a control (*p &lt; 0.05; ** p &lt; 0.01)."
NCBI gene IDs:
"ubx5: 851930"
Figure legend: "Catalytic activity of the protease Ddi1 is essential for survival of the ubx5∆ wss1∆ yeast mutant. Mutants carrying wild-type (WT) Ddi1, D220A catalytic mutant or ddi1∆ in combination with ubx5∆, wss1∆ or double ubx5∆ wss1∆ were grown in YEPD. Cells were treated with 40 mM formaldehyde (FA) for 15 min or directly spotted on plates supplemented with 100 mM hydroxyurea (HU). Plates were incubated for 2 days at 30°C."
NCBI gene IDs:
"ddi1: 856886
Ddi1: 856886
ubx5: 851930
wss1: 856536"
Figure legend: "Ubx5 loss restores HU-induced Rpb1 degradation in wss1∆ and requires Ddi1. Rpb1 levels were defined in cells growing in the presence of 200 mM HU and 100 μg/mL cycloheximide (CHX) at the indicated time points. Rpb1 and Pgk1 levels in total cell extracts were probed by immunoblotting and quantified using fluorescent secondary antibodies. See (B) for quantifications. Images show immunoblotting using chemiluminescence."
NCBI gene IDs:
"Ddi1: 856886
Ubx5: 851930
wss1: 856536"
Figure legend: " A. Expression heat map of netrin-3 and netrin-1. Receptors of netrin-1 and putative receptors of netrin-3: DCC, UNC5-A, -B, -C, -D, Neogenin, APP, CD146 are presented. The color legend (right-hand side) describes all tumor types included in the heat map. Asterisks indicate the two main pathologies in which netrin-3 expression is detectable. C. Percentage of cell lines positive for netrin-1 and/or -3 expression. Co-occurrence of expression was calculated using Fisher's exact test. P-value is indicated in the table. "
NCBI gene IDs:
"APP: 351
DCC: 1630
CD146: 4162
Neogenin: 4756
netrin-1: 9423
netrin-3: 4917
UNC5-A: 90249"
Figure legend: " B. Analysis of netrin-1 and -3 expression in tumor cell lines and ranked according to netrin-1 expression "
NCBI gene IDs:
"netrin-1: 9423"
Figure legend: " A. Quantification of netrin-3 gene expression by q-RT-PCR in a panel of 181 human NB stages 1, 2, 3, 4 and 4S. Number of cases is indicated on the graph. Error bars indicate s.e.m. Statistical treatment of the data was performed using a two-sided Student t-test. "
NCBI gene IDs:
"netrin-3: 4917"
Figure legend: " B. Quantification of netrin-3 gene expression by q-RT-PCR in a panel of 181 human neuroblastoma patients, defined as low- and high-risk NB. The number of cases is indicated on the graph. Error bars indicate s.e.m. Statistical treatment of the data was performed using a two-sided Student t-test. "
NCBI gene IDs:
"netrin-3: 4917"
Figure legend: " C. Netrin-3 high expression is a marker of poor prognosis in NB. 280 months overall Kaplan-Meier survival curves in a panel of 181 patients of all NB stages. The cohort was dichotomized base on netrin-3 median expression (in green and red). Statistical treatment of the data: Mantel-Cox; p value is indicated below the graph. "
NCBI gene IDs:
"netrin-3: 4917
Netrin-3: 4917"
Figure legend: " D. Netrin-3 high expression is a marker of poor prognosis in aggressive NB. 280 months overall Kaplan-Meier survival curves in a panel of 54 stage 4 patients. The cohort was dichotomized base on netrin-3 expression, as presented in panel C. Statistical treatment of the data: Mantel-Cox; p-value is indicated below the graph. E. Confirmation in 498 RNA-seq NB patients that netrin-3 high expression is a marker of poor prognosis in NB. 6,000 days overall Kaplan-Meier survival curves. The cohort was dichotomized based on netrin-3 median expression (in green and red). Statistical treatment of the data: Mantel-Cox; p-value is indicated below the graph."
NCBI gene IDs:
"netrin-3: 4917
Netrin-3: 4917"
Figure legend: " A. Gene Set Enrichment Analysis (GSEA) in high netrin-3 NB patients. The cohort was dichotomized with the n=50 lowest vs 50 highest: amplification the MYCN pathway (p=0.039; fdqr=0.025). "
NCBI gene IDs:
"MYCN: 4613
netrin-3: 4917"
Figure legend: " B. Netrin-3 expression is higher in MYCN amplified NB patients. The cohort was dichotomized based on mycn amplification and sorted for netrin-3 expression. Statistical treatment of the data: Welsh test; p-value is indicated on the graph. Error bars indicate s.e.m (boxes= 25th to 75th percentile; central band= mean; whiskers = min to max)."
NCBI gene IDs:
"MYCN: 4613
mycn: 4613
netrin-3: 4917
Netrin-3: 4917"
Figure legend: " C. Q-RT-PCR analysis of netrin-3 gene expression in IMR32 (n=5) and IGRN91 (n=5) NB cell lines after MYCN silencing by siRNA (U-test). Error bars indicate s.e.m. "
NCBI gene IDs:
"MYCN: 4613
netrin-3: 4917"
Figure legend: " D. ChIP-seq analysis of MYCN binding, active enhancer epigenetic marks H3K27ac, H3K4me1, and active promoter epigenetic mark H3K4me3, on netrin-3 locus (red line). An enrichment of MYCN, associated with active enhancer marks, was detected in three different neuroblastoma cell lines NB-1643, COGN415 and LAN5. "
NCBI gene IDs:
"MYCN: 4613
netrin-3: 4917"
Figure legend: " E. Quantitative analysis showing the size of IGRN91 primary tumors implanted on CAM and silenced or not for netrin-3 (n=11 siScr, n=9 siNetrin-3; U-test). Error bars indicate s.e.m. F. Quantitative analysis showing the size of IMR32 primary tumors silenced or not for netrin-3 (n=5 siScr, n=7 siNetrin-3; U-test). Error bars indicate s.e.m. "
NCBI gene IDs:
"netrin-3: 4917
Netrin-3: 4917"
Figure legend: " A. Deep analysis of netrin-3 gene expression in lung cancer cell lines (n=76; RNA-Seq). "
NCBI gene IDs:
"netrin-3: 4917"
Figure legend: " B. Q-RT-PCR analysis of netrin-1 and -3 expression, in lung cancer cell Lines (Error bars indicate SD, n=3). "
NCBI gene IDs:
"netrin-1: 9423"
Figure legend: "  C. Representative netrin-3 and -1 mRNA detection, using RNAscope on SCLC paraffin embedded tumor sections. Negative control DAPB, positive control PPiB. Each brown dot is a unique molecule of mRNA of each targeted gene (n=10, scale bars 20µm). D. Quantification of netrin-3 and -1 expression in human SCLC paraffin embedded tumor sections (High≥ 50% marked cells; Low≤ 5%).  "
NCBI gene IDs:
"DAPB: 
netrin-3: 4917
PPiB: 5479"
Figure legend: " A. ChIP-seq analysis of NeuroD1 and ASCL-1 binding on the netrin-3 gene promoter. A major binding site was detected (red and blue peaks for NeuroD1 and ASCL1 respectively). Input controls are shown below (black). "
NCBI gene IDs:
"netrin-3: 4917"
Figure legend: " B. ChIP-seq analysis of NeuroD1 and ASCL-1 chromatin enrichment, which was associated with broad H3K27ac-enriched regions at the netrin-3 locus (red line), indicating a transcriptionally active region in SCLC cell lines. (rep= experimental replicates). "
NCBI gene IDs:
"netrin-3: 4917"
Figure legend: " C. Q-RT-PCR analysis of netrin-3 gene expression in NCI-H82 (n=6) and NCI-H69 (n=4) SCLC cell lines after Neurod-1 and ASCL-1 silencing by siRNAs (U-test). Error bars indicate s.e.m. "
NCBI gene IDs:
"ASCL-1: 429
Neurod-1: 4760
netrin-3: 4917"