EMBO/SourceData huggingface dataset:
Figure legend: "(J) U2OS cells were treated with siLUCIFERASE (siLUC), siRASSF1A (siR1A) or si53BP1, treated with 10 μM BrdU for 24 h prior to I-PpoI mRNA transfection. 6 h post I-PpoI treated cells were pre-extracted, fixed and stained for BrdU under non denaturing conditions to visualize ssDNA. (K) Quantification of (J). Fold change of nuclear BrdU signal relative to siLUC is shown. Error bars represent standard deviation and derive from 3 independent experiments."
NCBI gene IDs:
"I-PpoI: 
LUC: 
LUCIFERASE: 
R1A: 11186
RASSF1A: 11186
53BP1: 7158"
Figure legend: "(L) HeLa cells were transfected with I-PpoI endonuclease and stained for MST2 and γH2AX. Fluorescence intensity profiles of MST2 (green) and γH2AX (red) signals across the HeLa nuclei are shown. Position of line scan indicated by the yellow line."
NCBI gene IDs:
"I-PpoI endonuclease: "
Figure legend: "(M) Validation of the MST2 siRNA with western blot."
NCBI gene IDs:
"MST2: 6788"
Figure legend: "(N) HeLa cells treated with siLUCIFERASE (siLUC) or siMST2 and 48 h later transfected with I-PpoI mRNA. Cells were treated with 5-EU for 30 min prior to fixation and assessed for incorporation. (O) Quantification of 5-EU intensity in siLUCIFERASE (siLUC) or siMST2 treated cells transfected with I-PpoI mRNA. Middle line represents the median and the boxes 25th and 75th percentiles. The whiskers mark the smallest and largest values. 100 values were analyzed in each condition."
NCBI gene IDs:
"I-PpoI: 
LUC: 
LUCIFERASE: 
MST2: 6788"
Figure legend: "(P) HeLa cells were treated with siLUCIFERASE (siLUC) or siMST2 and 48 h post transfection cells were transfected with I-PpoI mRNA. 6 h post transfection cells were fixed and stained for RASSF1A (R1A) and γH2AX. (Q) Quantification of (P). Error bars represent standard deviation and derive from 3 independent experiments."
NCBI gene IDs:
"I-PpoI: 
LUC: 
LUCIFERASE: 
MST2: 6788"
Figure legend: "(R-W) HeLa cells treated with siLUCIFERASE (siLUC) or siMST2 and 48 h later transfected with I-PpoI mRNA. Cells were stained for ATM-pS1981 (R), KAP1-pS824 (T) and RPA (V) and quantified (S, U, W). 108 values in (S), 95 values in (U) and 100 values in (W) were analysed."
NCBI gene IDs:
"I-PpoI: 
LUC: 
LUCIFERASE: 
MST2: 6788"
Figure legend: "(C) Clonogenic survival analysis and representative images of HeLa cells treated with the indicated siRNAs followed by I‐PpoI WT or I-PpoI H98A mRNA transfections. Survival ratio I-PpoI WT/I-PpoI H98A in each siRNA condition is presented. Error bars represent standard deviation and derive from 3 independent experiments."
NCBI gene IDs:
"I-PpoI: 
I‐PpoI: "
Figure legend: "(E) 45S rDNA copy number analysis in patients' tumors compared to adjacent controls in the LUAD cohort. 67 tumor samples and 43 samples from adjacent tissue were analyzed. (F) 45S rDNA copy number analysis in the LUAD patient samples based on RASSF1A CpG promoter methylation. 67 samples were analysed."
NCBI gene IDs:
"RASSF1A: 11186"
Figure legend: "E The qRT-PCR validation of APA switching. Eight genes with lengthened and shortened 3' UTRs in HEK293T  and in MCF-7  cells were chosen. PRPF4B, CTNNBIP1, PHB  and RCL1  were selected from HEK293T cells, and rest genes are MCF-7 cells. KD (Extended/Common)/Ctr (Extended/Common) &lt;1 indicates a shorter 3' UTR in the knockdown sample, and vice versa. Data are presented as mean ± SEM of three biological replicates. *p&lt;0.05, **p&lt;0.01, the p values were obtained from unpaired two-tailed Student's t-test."
NCBI gene IDs:
"CTNNBIP1: 56998
PHB: 5245
PRPF4B: 8899
RCL1: 10171"
Figure legend: "A Higher proportion of target genes in the list of genes with shortened 3'UTRs after knockdown of YTHDC1. The p values were obtained by Fisher's exact test. *p=1.227×10-3, **p=3.725×10-4, NA: no significance."
NCBI gene IDs:
"YTHDC1: 91746"
Figure legend: "E Scatter plot of protein and mRNA ratios of  dual luciferase report assay with λN-BoxB system. λN, YTHDC1  and λN-YTHDC1  were co-transfected with a bicistronic vector. Two batches of experiments with three biological repeats were performed. Both luciferase activity  and mRNA levels were measured. To test the effect of YTHDC1 binding  on the proximal APA site, a linear model with the co-transfected genes and batch as independent variables was fitted. Data are presented as mean ± SEM of three biological replicates. ** p&lt;0.01 with t-test from linear model."
NCBI gene IDs:
"λN: 2703540
YTHDC1: 91746"
Figure legend: "F Overexpression of YTHDC1-WT and YTHDC1-Mut (W377A, W428A) revealed by Western blot."
NCBI gene IDs:
"YTHDC1: 91746"
Figure legend: "G Scatter plot of  qRT-PCR for APA validation. Mutation of the m6A binding  site of YTHDC1  loses its inhibitory effect on proximal APA sites. Extended/Common ratios of ten genes were obtained by qRT-PCR in HEK293T  cells overexpressing YTHDC1-WT and YTHDC1-Mut. The ratios were normalized to those of control cells. Data are presented as mean ± SEM of three biological replicates. *p&lt;0.05, **p&lt;0.01, ns: no significance. the p values were obtained from unpaired two-tailed Student's t-test."
NCBI gene IDs:
"YTHDC1: 91746"
Figure legend: "B Co-IP  assay using Myc-FIP1L1, Myc-PABPC1  and Myc-PABPC4  to pull down endogenous YTHDC1  in the presence of  RNase A."
NCBI gene IDs:
"Myc: 
FIP1L1: 81608
PABPC1: 26986
PABPC4: 8761"
Figure legend: "B Co-IP assays using truncated FIP1L1  proteins revealed that the proline-rich domain of FIP1L1  plays an important role in interacting  with YTHDC1."
NCBI gene IDs:
"FIP1L1: 81608"
Figure legend: "C Mutation of FIP1L1  nearly abrogates the interaction  between YTHDC1  and FIP1L1  compared with wild type."
NCBI gene IDs:
"FIP1L1: 81608"
Figure legend: "D-G Co-IP assays using different domains of YTHDC1  revealed that the N-terminus (1-344 aa) and YTH domain (364-507 aa) of YTHDC1 interact  with FIP1L1."
NCBI gene IDs:
"YTHDC1: 91746"
Figure legend: "B YTHDC1  inhibits the interaction  between Myc-FIP1L1  and FLAG-CPSF4. A substantially suppressed level of interaction  between Myc-FIP1L1  and FLAG-CPSF4  was observed when FLAG-YTHDC1  input was increased."
NCBI gene IDs:
"YTHDC1: 91746"
Figure legend: "C Knockdown of YTHDC1  enhances endogenous FIP1L1  recruitment to CPSF4, indicating that YTHDC1  plays an important role in interfering with the 3' end processing complex interaction."
NCBI gene IDs:
"YTHDC1: 91746"
Figure legend: "D YTHDC1   has little effect on the interaction  between Myc-FIP1L1  and FLAG-PAPOLA. The interaction  between Myc-FIP1L1  and FLAG-PAPOLA  was not significantly affected when FLAG-YTHDC1  was increased."
NCBI gene IDs:
"FLAG: 
YTHDC1: 91746"
Figure legend: "F The mutation of prolines in FIP1L1   abrogated the inhibitory effect of YTHDC1   on the interaction  between FIP1L1  and CPSF4."
NCBI gene IDs:
"YTHDC1: 91746"
Figure legend: "G qRT-PCR validation of APA site switching in a bicistronic dual luciferase system. FIP1L1-Mut could significantly increase the ratios of Rluc/Fluc  compared to FIP1L1-WT, indicating that YTHDC1  inhibits the use of proximal APA sites by interacting with the proline-rich domain of FIP1L1. Data are presented as mean ± SEM of three biological replicates. **p=8.77×10-4, the p values were obtained with unpaired two-tailed Student's t-test."
NCBI gene IDs:
"Fluc: 
Rluc: 
FIP1L1: 81608"
Figure legend: "E Sanger sequencing  was used to genotype eGFP-FIP1L1  and mScarlet-YTHDC1  homozygous cell lines."
NCBI gene IDs:
"eGFP: 
mScarlet: 
FIP1L1: 81608
YTHDC1: 91746"
Figure legend: "I Genome-edited eGFP-FIP1L1 HEK293T  cells expressing Dsred-YTHDC1-WT and Dsred-YTHDC1-Mut were examined by confocal microscopy. DsRed-YTHDC1-WT forms LLPS to compartmentalize FIL1L1, but DsRed-YTHDC1-Mut diffuses in the nucleus without droplet structure. Droplet structures are indicated by arrows. Scale bars: upper 8.09 µm, lower 6.64 µm. J Colocalization  of YTHDC1-WT and YTHDC1-Mut in figure I was assessed by calculating the average overlap coefficient according to Leica TCS SP8 microscope software. Data are presented as mean ± SEM of 15 cells. ****p=6.46×10-4, the p values were obtained with unpaired two-tailed Student's t-test."
NCBI gene IDs:
"Dsred: 
DsRed: 
eGFP: 
FIP1L1: 81608
YTHDC1: 91746"
Figure legend: "(A) Chromatin immunoprecipitation (ChIP) analysis of receptor binding to the ER8 element (region 1) of the nrf2 promoter. Immunoprecipitation with nonspecific IgG and PCR amplification of an adjacent region (2) served as controls. ChIP assays were also carried out to analyse binding to ER8s in the il10, ddit3 and tyrobp genes. RAR, retinoic acid receptor; VDR, vitamin D receptor."
NCBI gene IDs:
"ddit3: 1649
il10: 3586
nrf2: 4780
tyrobp: 7305"
Figure legend: "(B) Reverse transcription-PCR analysis of 1,25‐dihydroxyvitamin D3 (1,25D3)‐ or retinoic acid (RA)‐regulated expression of ddit3, il10, and tyrobp in U937, Calu‐3 and MCF‐7 cells."
NCBI gene IDs:
"ddit3: 1649
il10: 3586
tyrobp: 7305"
Figure legend: "(A) Electrophoretic mobility shift assay (EMSA) of binding of vitamin D receptors (VDRs)/retinoid X receptors (RXRs) to thep19ink4dER8, with binding to the mouseosteopontin (mop) DR3vitamin D responsive element as a control, along with a comparison of binding to ER6 and ER8 motifs (right‐hand panel)."
NCBI gene IDs:
"p19: 1032"
Figure legend: "(B) EMSA of retinoic acid receptor (RAR)/RXR binding to the p19ink4d ER8, and the rarβ DR5 retinoic acid response element, as a control."
NCBI gene IDs:
"p19: 1032"
Figure legend: "(C) Chromatin immunoprecipitation (ChIP) analysis of binding of VDRs and RARs to the p19ink4d ER8 (region 1) and RNA polymerase II (POLII) binding to the transcription start site."
NCBI gene IDs:
"p19: 1032"
Figure legend: "(D) ReChIP analysis confirms the presence of VDR/RXRs and RAR/RXRs but not of VDR/RARs on the p19ink4d ER8."
NCBI gene IDs:
"p19: 1032"
Figure legend: "(E) Cloning of p19ink4d promoter containing or lacking ER8 upstream of a luciferase reporter. 3 (1,25D3)‐ (F) and retinoic acid (RA)‐regulated (G) luciferase expression is dependent on the ER8 element in the p19ink4d promoter. Luciferase expression driven by a thymidine kinase (tk) control promoter is shown."
NCBI gene IDs:
"p19: 1032
thymidine kinase: 2703374"
Figure legend: "3 and retinoic acid induce p19ink4d expression. Expression of p19ink4d messenger RNA by reverse transcription-PCR (A) or protein by western blotting (B) was carried out on extracts of cells treated with 3 (1,25D3) or retinoic acid (RA), as indicated."
NCBI gene IDs:
"p19: 1032"
Figure legend: "(C) Treatment with 1,25D3 or RA transiently enhances co‐immunoprecipitation (IP) of p19INK4D with cyclin‐dependent kinase CDK4 in U937 cells. Similar results were obtained in SCC25 cells (not shown). A control western blot (W) of CDK4 levels in ligand‐treated cells is shown below."
NCBI gene IDs:
"p19: 1032"
Figure legend: "(D) Treatment with 1,25D3 enhances co‐immunoprecipitation of p27KIP1 with CDK4 in U937 cells. Extracts of U937 cells were probed for p27KIP1 and CDK4, and immunoprecipitated with an anti‐CDK antibody and probed for p27KIP1 co‐immunoprecipitation."
NCBI gene IDs:
"p27KIP1: 1027"
Figure legend: "(A) Short interfering RNAs (siRNA) knockdown of p19ink4d messenger RNA and protein in SCC25 cells. SiRNAs were directed against p19ink4d, scrambled p19ink4d (Scr.) or cyclophilin (cyc.) controls."
NCBI gene IDs:
"p19: 1032
cyclophilin: 835985"
Figure legend: "(B) Combined knockdown of p27KIP1 and p19INK4D in SCC25 cells analysed by western blotting for p27KIP1 (top) and p19INK4D (bottom)."
NCBI gene IDs:
"p27KIP1: 1027
p19: 1032"
Figure legend: "(C,D) Fluorescence‐activated cell sorting analysis of cell‐cycle distribution of control SCC25 cells, or cells transfected with scrambled (Scr), p19ink4d‐ or p27kip1‐directed siRNAs, individually or together (Dbl). (C) Cells were treated with vehicle or 1,25‐dihydroxyvitamin D3 (1,25D3), as indicated. (D) Cells were treated with DMSO vehicle, retinoic acid (RA) or 1,25D3, as indicated."
NCBI gene IDs:
"p27kip1: 1027
p19: 1032"
Figure legend: "(E) Loss of p19INK4D enhances lysosomal β‐galactosidase activity in SCC25 cells. (Left) Histogram of numbers of cells staining for β‐galactosidase activity in the absence (−) or presence of 1,25D3 in control cells (−) or in cells transfected with scrambled (Scr) or p19INK4D siRNAs. (Right) Bright field images of untransfected cells (−/−) or p19INK4D‐depleted cells treated with 1,25D3 (p19/D3)."
NCBI gene IDs:
"p19: 1032
p19INK4D: 1032"
Figure legend: "(F) Loss of p19INK4D induces lysosomal fusion. Analysis of lysosomal fusion (autophagosomes) in SCC25 cells treated as in (E), stained for incorporation of lysotracker red. Nuclei were counterstained with Hoechst (blue)."
NCBI gene IDs:
"p19INK4D: 1032"
Figure legend: "Media from soluble TREM2-Fc transfected HEK293T cells incubated with Aβ42 fibrils. Top left panel shows original media samples. Top right panel shows the presence of soluble TREM2 associated with Aβ42 pellet. The bottom two panels represent the same samples as the top, but probed with 6E10 RIPA lysate from TREM2 transfected HEK293T cells incubated with Aβ42 fibrils. Top left panel shows original RIPA lysate samples and top right panel shows the presence of TREM2 associated with Aβ42 pellet. The bottom two panels represent the same samples as the top, but probed with 6E10 Western blo had been cropped to facilitate the reading and originals with the supernatant fractions are available in Fig EV1. All experiments were replicated 3 independent times"
NCBI gene IDs:
"TREM2: 54209"
Figure legend: "Media from soluble TREM2-Fc and APOE3 co transfected HEK293T cells incubated with agarose beads anti-Human IgG Fc. Left panels show original media samples. Right panels show the purified soluble TREM2-Fc (bottom) and the presence of APOE3 with the purified soluble TREM2-Fc (top) Western blo had been cropped to facilitate the reading and originals with the supernatant fractions are available in Fig EV1. All experiments were replicated 3 independent times"
NCBI gene IDs:
"APOE3: 348
TREM2: 54209"
Figure legend: "Media from soluble TREM-Fc family member transfected HEK293T cells incubated with Aβ42 fibrils. Top panel shows original media sample and the presence of TREM family members associated with Aβ42 pellet. Bottom panel shows original media and Aβ42 pellet probed with 6E10"
NCBI gene IDs:
"TREM: 54209"
Figure legend: "Media from soluble TREM-Fc family members and APOE3 co transfected HEK293T cells incubated with agarose beads anti-Human IgG Fc. Top panel shows original media sample and the presence of soluble TREM family members associated with APOE3. Bottom panel shows original media and purified soluble TREM-Fc family members probed with anti-V5"
NCBI gene IDs:
"APOE3: 348
TREM: 54209"
Figure legend: "2B4 NFAT-GFP reporter cells transduced with TREM2 or AD variant R47H were incubated with various concentrations of Aβ42 oligomers for 12 hours. GFP expression was detected at 1 µM Aβ42 oligomers with TREM2 transduced cells. No GFP expression was detected with Aβ42 oligomers from control transduced cells. Results were expressed as the percentage ± GFP cells averaged of ± standard error (n = 3, * p &lt; 0.05 compared with mock, **** p&lt; 0.0001 compared with mock, # p &lt; 0.05 compared with TREM2, #### p &lt; 0.0001 compared with TREM2, Two-way ANOVA, Bonferroni multiple comparisons, see Appendix table S3 for p value)"
NCBI gene IDs:
"TREM2: 54209"
Figure legend: " B-2B4 NFAT-GFP reporter cells transduced with TREM2 or variants (R47H, R62H and T96K) were incubated with 10 µM Aβ42 oligomers for 12 hours. No GFP expression was detected with Aβ42 oligomers from control transduced cells. Results were expressed as the percentage GFP cells averaged of ± standard error (n = 3, * p &lt; 0.05 compared with TREM2, ** p &lt; 0.05 compared with TREM2, **** p&lt; 0.0001 compared with TREM2, ## p &lt; 0.01 compared with TREM2 T96K, #### p &lt; 0.0001 compared with TREM2 T96K, ANOVA, Dunnett's multiple comparisons test, see Appendix table S3 for p value "
NCBI gene IDs:
"TREM2: 54209"
Figure legend: "HEK293T cells transfected with TREM2 or AD variant incubated with 500 nM Aβ42 monomers were lysed for Aβ42 quantifications by ELISA. Expression of TREM2 increases Aβ42 level detected compared to mock control as well the AD variant. Results were averaged ± standard error (n = 9, # p &lt; 0.05 compared with TREM2, ## p&lt; 0.01 compared with TREM2, *** p&lt; 0.001 compared with mock, **** p &lt;0.0001 compared with mock, ANOVA, Tukey's Multiple Comparison Test, see Appendix table S3 for p value)"
NCBI gene IDs:
"TREM2: 54209"
Figure legend: "HEK293T cells transfected with TREM2 were incubated with Aβ42 oligomers for 16 hours. Conditioned media and cell lysate were analyzed by Western blot for TREM2 (RIPA lysate) and soluble TREM2 (media) detection. Experiment was replicated 3 independent times"
NCBI gene IDs:
"TREM2: 54209"
Figure legend: "HEK293T cells transfected with TREM2 were subjected to cell membrane biotinylation for purification. Bottom panel in D shows the presence of TREM2 in the purified product. Endogenous APP and β-tubulin were used as controls for the purification (middle and upper panels). Experiment was replicated 3 independent time"
NCBI gene IDs:
"TREM2: 54209"
Figure legend: " D Real-time PCR analysis of Ido1 and Tgfb1 transcripts in pDCs stimulated for 18 h with TGF-β, in the presence or absence (Ctrl, control) of catalytic PI3K inhibitors, normalized to the expression of Gapdh and presented relative to results in untreated cells (dotted line, 1-fold). "
NCBI gene IDs:
"Gapdh: 14433
Ido1: 15930
Tgfb1: 21803"
Figure legend: "F Real-time PCR analysis of Ido1 and Tgfb1 transcripts in pDCs transfected with p110α-, β-, δ-specific, or negative control (nc) siRNA and stimulated for 18 h with TGF-β, normalized to the expression of Gapdh and presented relative to results in unstimulated cells (dotted line, 1-fold)."
NCBI gene IDs:
"Gapdh: 14433
Ido1: 15930
p110α: 18706
Tgfb1: 21803"
Figure legend: "D Immunoblotting with anti-IDO1 and -p85 antibodies of IDO1 immunoprecipitates obtained from P1.HTR cells transfected with IDO1.WT or IDO1.Y149F. Mock-transfected P1.HTR cells were used as a control."
NCBI gene IDs:
"IDO1: 15930"
Figure legend: "A Confocal immunofluorescence microscopy images of P1.HTR cells either untransfected (Untr) or transfected with IDO1.WT (WT) or vector alone (Mock) and stained with antibodies recognizing IDO1 (green). Nuclei were stained with DAPI (blue). Scale bar, 20 µm."
NCBI gene IDs:
"IDO1: 15930"
Figure legend: "B Confocal immunofluorescence microscopy images of P1.HTR cells transfected with IDO1.WT, co-stained with antibodies recognizing IDO1 (green) and markers of intracellular organelles and structures (as indicated; red). Nuclei were stained with DAPI (blue). The merge imagine is shown for all stainings or without DAPI (no DAPI). Scale bar, 10 µm."
NCBI gene IDs:
"IDO1: 15930"
Figure legend: "C Immunoblotting analysis of EE purified from P1.IDO1.WT cells. Mock-transfected cells as in A were used as control."
NCBI gene IDs:
"IDO1: 15930"
Figure legend: "A Confocal immunofluorescence microscopy images of P1.HTR cells transfected with IDO1.WT or IDO1.Y149F and co-stained with antibodies recognizing IDO1 (green) and EEA1 (red). Nuclei were stained with DAPI (blue). The merge imagine is shown for all stainings or without DAPI (no DAPI). Scale bar, 10 µm."
NCBI gene IDs:
"IDO1: 15930"
Figure legend: "C Distribution of IDO1.WT and the IDO1.Y149F mutants in homogenates of P1.HTR cells along the isopycnic sucrose gradient as in Fig 3D. Fractions were immunoblotted using antibodies specific for IDO1."
NCBI gene IDs:
"IDO1: 15930"
Figure legend: "D The distribution of IDO1.WT and IDO1.Y149F proteins along the isopycnic sucrose gradient is shown in term of densitometric analysis in each fraction (mean ± SD of three experiments)."
NCBI gene IDs:
"IDO1: 15930"
Figure legend: "B Confocal immunofluorescence microscopy images of P1.HTR cells transfected with IDO1.WT incubated with class IA PI3K p110 isoform inhibitors (indicated) or medium alone (Ctrl) for 24 h and co-stained with antibodies recognizing IDO1 (green) and EEA1 (red). Nuclei were stained with DAPI (blue). The merge imagine is shown for all stainings or without DAPI (no DAPI). Scale bar, 10 µm."
NCBI gene IDs:
"IDO1: 15930"
Figure legend: "D Tyrosine phosphatase activity in anti-IDO1 immunoprecipitates from P1.HTR cells transfected with IDO1.WT cells and treated with PI3K catalytic inhibitors (indicated) or medium alone (ctrl). Data represent the mean ± SD (n = 3 technical replicates)."
NCBI gene IDs:
"IDO1: 15930"
Figure legend: "(C) Growth curves of strains deleted for car1, car2 or car3, and a wild-type control. Strains were grown in EMM (black), EMM with antimycin A (red), EMM with arginine (light blue) or EMM with both arginine and antimycin A (dark blue) as indicated."
NCBI gene IDs:
"car3: 
car1: 2541313
car2: 2540626"
Figure legend: "(D) Growth curves of strains deleted for car2 (top) or car3 (bottom). Strains were grown in EMM (black), EMM with antimycin A (red), EMM with arginine and antimycin A (dark blue), EMM with mix of all amino acids and antimycin A (bright blue), and EMM with antimycin A and each individual amino acid from the mix (grey)."
NCBI gene IDs:
"car3: 
car2: 2540626"
Figure legend: "(E) Growth curves of wild-type control (WT) and car2 deletion strain (Δcar2). Strains were grown in EMM media with antimycin A and with either a mix of all amino acids (+AA mix) or different combinations of lysine (K), glutamine (Q), glutamic acid (E), or arginine (R) as indicated. Dashed line: time point where wild-type strain saturates in EMM with amino-acid mix."
NCBI gene IDs:
"car2: 2540626"
Figure legend: "(C) Heat map of expression changes for transcripts repressed over 2-fold at 30 min in cells supplemented with arginine (EMM +R) relative to cells without supplementation (EMM). Values for timepoints 0 and 30 min after antimycin A addition are shown for cells grown in EMM, EMM with arginine and ssp1 deletion mutant grown in EMM. The data are normalised to EMM timepoint 0."
NCBI gene IDs:
"ssp1: 2538951"
Figure legend: "G. Loss of LRP6 by serum starvation was mediated in a caveolin-1-dependent manner. HEK293 cells were transfected with caveolin siRNA and incubated in serum-free medium for 4 h. Cells were lysed and the cell lysates were analyzed by immunoblotting."
NCBI gene IDs:
"caveolin: 857
caveolin-1: 857"
Figure legend: "B. Knockdown of LRP6 induced the phosphorylation of YAP even under nutrient-rich condition. HEK293T cells were transfected with GFP siRNA as a control and LRP6 siRNA under nutrient-rich conditions. The ratio of p-YAP/total-YAP of three independent immunoblot bands was quantified (biological replicates, right panel). Error bars indicate standard deviation of biological triplicate measurements. *P &lt; 0.05. Student's t-test was used for statistical analysis."
NCBI gene IDs:
"GFP: 
LRP6: 4040"
Figure legend: "C. Overexpression of LRP6 blocked the increase of YAP phosphorylation under serum starvation conditions. HEK293T cells were transfected with empty vector (-) or LRP6-EGFP as indicated in the figure. One day after transfection, cells were incubated in serum-free medium for 4 h. Cells were lysed and the cell lysates were analyzed by immunoblotting (left panel). The ratio of LRP6/β-actin and p-YAP/YAP of three independent immunoblots was quantified (middle and right panel, respectively). Error bars indicate standard deviation of biological triplicate measurements. *P &lt; 0.05 and ***P &lt; 0.001. Student's t-test was used for statistical analysis."
NCBI gene IDs:
"EGFP: 
LRP6: 4040"
Figure legend: "D. Knockdown of LRP6 reduced YAP reporter activity. HEK293T cells were transfected with GFP siRNA as a control, LRP6 siRNA, pRL-TK and 8XGTIIC luciferase reporter constructs. One day after transfection, luciferase activity was measured. Error bars indicate standard deviation of biological triplicate measurements. ***P &lt; 0.005. Student's t-test was used for statistical analysis."
NCBI gene IDs:
"8XGTIIC: 
GFP: 
luciferase: 
TK: 
LRP6: 4040"