EMBO/SourceData huggingface dataset:
Figure legend: "11-month-old APP/PS-1-21+/+/Lyz2-Cre+/+/Eporloxp/loxp mice  (APP/PS1-21+EPOR-MKO) or APP/PS-1-21+/+/Lyz2-Cre+/+/Epor+/+ mice  (APP/PS1-21+EPOR-C), Aβ plaques  in the cortex  and hippocampus  of mice  of 11-month-old (M) (n = 5) were detected by IHC. Data information: Unpaired t-tests were used for the comparison of two groups. Results are presented as mean ± s.d., *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001 and ****P &lt; 0.0001; ns denotes no statistical significance. IHC, Immunohistochemical staining."
NCBI gene IDs:
"APP: 351
Cre: 2777477
Epor: 13857
EPOR: 13857
Lyz2: 17105
PS-1: 5663
PS1: 5663"
Figure legend: "Both non-cognitive and cognitive behavioral  impairments of APP/PS1-21 mice  (11 m) were analyzed by nest construction assay, social interaction assay, NORT, FCT  (n = 10). Data information: Unpaired t-tests were used for the comparison of two groups. Results are presented as mean ± s.d., *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001 and ****P &lt; 0.0001; ns denotes no statistical significance. NORT,  novel object recognition test; FCT,  fear conditioning test."
NCBI gene IDs:
"APP: 351
PS1: 5663"
Figure legend: "Splenic macrophages  from APP/PS1-21 (5- or matched WT mice were detected by immunoblotting  with the indicated antibodies (n = 3) (A, Data information: Unpaired t-tests were used for the comparison of two groups. Results are presented as mean ± s.d., *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001 and ****P &lt; 0.0001; ns denotes no statistical significance."
NCBI gene IDs:
"APP: 351
PS1: 5663"
Figure legend: "Splenic macrophages  from APP/PS1-21 11-month-old) or matched WT mice  were detected by immunoblotting  with the indicated antibodies (n = 3) B). Data information: Unpaired t-tests were used for the comparison of two groups. Results are presented as mean ± s.d., *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001 and ****P &lt; 0.0001; ns denotes no statistical significance."
NCBI gene IDs:
"APP: 351
PS1: 5663"
Figure legend: "Old APP/PS1-21 mice  (11 m) and WT mice  at the same age were treated with rhEPO (10000 IU/kg/d), ARA290  (0.03 mg/kg/d) or vehicle (i.p., once a day, for 14 days). Splenic macrophages  were isolated for detection by immunoblotting  with the indicated antibodies (n = 3) (G). Data information: vehicles were PBS. For multiple groups, one-way ANOVA was used. Results are presented as mean ± s.d., *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001 and ****P &lt; 0.0001; ns denotes no statistical significance."
NCBI gene IDs:
"APP: 351
PS1: 5663"
Figure legend: "Old APP/PS1-21 mice  (11 m) and WT mice  at the same age were treated with rhEPO (10000 IU/kg/d), ARA290  (0.03 mg/kg/d) or vehicle (i.p., once a day, for 14 days). Protein levels of IDE  and NEP  were detected by immunoblotting  with indicated antibodies (n = 3) (I). Data information: vehicles were PBS. For multiple groups, one-way ANOVA was used. Results are presented as mean ± s.d., *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001 and ****P &lt; 0.0001; ns denotes no statistical significance. IDE, insulin degrading enzyme; NEP, neprilysin."
NCBI gene IDs:
"APP: 351
PS1: 5663"
Figure legend: "G-I MDM were treated with 5μM ETO for 18h and infected in the presence of ETO with HIV-1 BaL and DNA isolated 18 h post‐infection for qPCR.2LTR circles. (n = 3, mean ± s.e.m.; *P‐value ≤ 0.05, paired t‐test)."
NCBI gene IDs:
"2LTR circles: "
Figure legend: "G-I MDM were treated with 5μM ETO for 18h and infected in the presence of ETO with HIV-1 BaL and DNA isolated 18 h post‐infection for qPCR.Integrated copies of viral DNA, Alu-Gag qPCR. (n = 3, mean ± s.e.m.; ***P‐value ≤ 0.001, paired t‐test)."
NCBI gene IDs:
"viral DNA: "
Figure legend: "MDM were treated with 5μM ETO for 18h and co‐infected in the presence of ETO with VSV‐G HIV‐1 GFP and SIVmac virus‐like particles containing Vpx/Vpr (SIV VLP) or deleted for Vpx (SIV VLP del Vpx) or deleted for Vpr (SIV VLP del Vpr). Cells from a representative donor were used for immunoblotting. The percentage of infected cells was quantified by the automated cell‐imaging system Hermes WiScan and ImageJ 48h post-infection. (n = 4, mean ± s.e.m.; **P‐value ≤ 0.01; (ns) non‐significant, paired t‐test)."
NCBI gene IDs:
"Vpr: 956112
Vpx: 1490006"
Figure legend: "D-F. MDM were treated with 5μM ETO for 18h and co‐infected in the presence of ETO with HIV-1 BaL and SIVmac virus‐like particles containing Vpx/Vpr (SIV VLP). DNA was isolated 18 h post‐infection for qPCR quantification of F. Late RT products; G. 2LTR circles; H integrated viral DNA.Late viral RT products. AZT: MDM treated with 20μM AZT, a reverse-transcriptase inhibitor, were used as control. (n = 3, mean ± s.e.m.; (ns) non‐significant, paired t‐test)."
NCBI gene IDs:
"2LTR circles: 
viral DNA: 
Vpr: 956112
Vpx: 1490006"
Figure legend: "D-F. MDM were treated with 5μM ETO for 18h and co‐infected in the presence of ETO with HIV-1 BaL and SIVmac virus‐like particles containing Vpx/Vpr (SIV VLP). DNA was isolated 18 h post‐infection for qPCR quantification of F. Late RT products; G. 2LTR circles; H integrated viral DNA.2LTR circles. (n = 3, mean ± s.e.m.; (ns) non‐significant; *P‐value ≤ 0.05, paired t‐test)."
NCBI gene IDs:
"2LTR circles: 
viral DNA: 
Vpr: 956112
Vpx: 1490006"
Figure legend: "D-F. MDM were treated with 5μM ETO for 18h and co‐infected in the presence of ETO with HIV-1 BaL and SIVmac virus‐like particles containing Vpx/Vpr (SIV VLP). DNA was isolated 18 h post‐infection for qPCR quantification of F. Late RT products; G. 2LTR circles; H integrated viral DNA.Integrated copies of viral DNA, Alu-Gag qPCR. (n = 3, mean ± s.e.m.; (ns) non‐significant; **P‐value ≤ 0.01, paired t‐test)."
NCBI gene IDs:
"2LTR circles: 
viral DNA: 
Vpr: 956112
Vpx: 1490006"
Figure legend: "A-B. MDM were treated with 5μM ETO for 18h and co‐infected in the presence of ETO with VSV‐G HIV‐1 GFP and SIVmac virus‐like particles containing Vpx wild type (WT)/Vpr or Vpx Q76A mutant/Vpr (SIV VLP Q76A). (n = 3, mean ± s.e.m.; (ns) non‐significant; *P‐value ≤ 0.05; **P‐value ≤ 0.01, paired t‐test).MDM were differentiated and cultured in Human serum instead of FCS."
NCBI gene IDs:
"Vpr: 956112
Vpx: 1490006"
Figure legend: "A-B. MDM were treated with 5μM ETO for 18h and co‐infected in the presence of ETO with VSV‐G HIV‐1 GFP and SIVmac virus‐like particles containing Vpx wild type (WT)/Vpr or Vpx Q76A mutant/Vpr (SIV VLP Q76A). (n = 3, mean ± s.e.m.; (ns) non‐significant; *P‐value ≤ 0.05; **P‐value ≤ 0.01, paired t‐test).MDM were differentiated and cultured in FCS. A standard culture condition used in all experiments. See Materials and Methods."
NCBI gene IDs:
"Vpr: 956112
Vpx: 1490006"
Figure legend: "C-F. MDM we treated with 5μM ETO for 18h and co‐infected in the presence of ETO with HIV-1 BaL and SIV VLP Q76A. DNA was isolated 18 h post‐infection for qPCR quantification of D. Late RT products; E. 2LTR circles; F. integrated viral DNA.Late viral RT products. AZT: MDM treated with 20μM AZT, a reverse-transcriptase inhibitor, were used as control. (n = 3, mean ± s.e.m.; (ns) non‐significant; *P‐value ≤ 0.05, paired t‐test)."
NCBI gene IDs:
"2LTR circles: 
viral DNA: "
Figure legend: "C-F. MDM we treated with 5μM ETO for 18h and co‐infected in the presence of ETO with HIV-1 BaL and SIV VLP Q76A. DNA was isolated 18 h post‐infection for qPCR quantification of D. Late RT products; E. 2LTR circles; F. integrated viral DNA.2LTR circles. (n = 3, mean ± s.e.m.; (ns) non‐significant; *P‐value ≤ 0.05, paired t‐test)."
NCBI gene IDs:
"2LTR circles: 
viral DNA: "
Figure legend: "C-F. MDM we treated with 5μM ETO for 18h and co‐infected in the presence of ETO with HIV-1 BaL and SIV VLP Q76A. DNA was isolated 18 h post‐infection for qPCR quantification of D. Late RT products; E. 2LTR circles; F. integrated viral DNA.Integrated copies of viral DNA, Alu-Gag qPCR. (n = 3, mean ± s.e.m.; *P‐value ≤ 0.05; **P‐value ≤ 0.01, paired t‐test)."
NCBI gene IDs:
"2LTR circles: 
viral DNA: "
Figure legend: "MDM were treated with 5μM ETO for 18h, 3μg/ml cGAMP and 10ng/ml IFNβfor 18h. RNA was isolated and qPCR performed for selected genes using TaqMan assays. Expression levels of target genes were normalised to GAPDH. (n = 3, mean ± s.e.m.; *P‐value ≤ 0.05; (ns) non‐significant, paired t‐test)."
NCBI gene IDs:
"GAPDH: 2597"
Figure legend: "B atg19Δ cells containing HTB‐Atg19 were grown to mid‐log phase. Atg19 was affinity purified and subjected to mass spectrometric phosphorylation mapping. Phosphorylation sites: enlarged; lysine substitutions: gray; Atg11 binding region: green."
NCBI gene IDs:
"Atg11: 856162
Atg19: 854072
atg19: 854072"
Figure legend: "C atg19Δ cells containing GFP‐Atg19 wild‐type or mutants as indicated were grown to mid‐log phase. Processing of endogenous Ape1 was analyzed by Western blotting and quantified by calculating the ratio of cleaved versus uncleaved Ape1 normalized to the wild‐type. Atg19 expression was assessed by anti‐GFP Western blotting."
NCBI gene IDs:
"Atg19: 854072
atg19: 854072"
Figure legend: "D atg19Δ GFP‐Atg11 Atg1‐TAP cells containing myc‐Atg19 as indicated were grown to log phase. Atg11 was immunoprecipitated, and bound Atg19 was analyzed by Western blotting."
NCBI gene IDs:
"Atg1: 852695
Atg11: 856162
Atg19: 854072
atg19: 854072"
Figure legend: "E GST‐fused propeptide of Ape1, Atg19 as indicated, and a His‐tagged fragment of Atg11 (amino acids 685-1178) were purified from Escherichia coli, mixed, and propeptide‐bound proteins were isolated and analyzed by Coomassie staining. Quantification of three individual experiments is shown. Error bars represent standard deviation."
NCBI gene IDs:
"Atg19: 854072"
Figure legend: "A GFP‐Atg11 Ape1‐mRuby atg19Δ cells containing myc‐Atg19 as indicated and Cup1‐Ape1 were grown to log phase. Overexpression of Ape1 was induced by addition of 250 μM copper sulfate for 3 h, and autophagy was induced by treating cells for 1 h with rapamycin. Scale bar, 5 μm."
NCBI gene IDs:
"Ape1: 853758
Atg11: 856162
Atg19: 854072
atg19: 854072
Cup1: 856450"
Figure legend: "B Ape1‐mRuby atg19Δ cells containing GFP‐Atg19 wild‐type or GFP‐Atg19‐3A were analyzed in log phase. Scale bar, 5 μm."
NCBI gene IDs:
"Atg19: 854072
atg19: 854072"
Figure legend: "C GFP‐Atg8 Ape1‐mRuby atg19Δ cells containing myc‐Atg19 as indicated and Cup1‐Ape1 were analyzed as in (A). Scale bar, 5 μm."
NCBI gene IDs:
"Ape1: 853758
Atg19: 854072
atg19: 854072
Atg8: 852200
Cup1: 856450"
Figure legend: "B atg34Δ yeast cells containing HTB‐Atg34 were grown to mid‐log phase and treated with rapamycin. Atg34 was affinity purified and subjected to mass spectrometric phosphorylation mapping. Phosphorylation sites: enlarged; Atg11 binding region: green; lysine substitution: gray."
NCBI gene IDs:
"Atg11: 856162
Atg34: 854071
atg34: 854071"
Figure legend: "C Ams1‐GFP atg19Δatg34Δ cells containing protein A (Stag)‐tagged Atg34 as indicated were starved for 4 h. Processing of endogenous Ams1‐GFP was analyzed by Western blotting and quantified by calculating the ratio of free GFP versus uncleaved Ams1‐GFP normalized to the wild‐type. Expression of Atg34 proteins was assessed by anti‐protein A Western blotting."
NCBI gene IDs:
"Ams1: 852721
atg1: 852695
atg34: 854071"
Figure legend: "F In vitro phosphorylation of recombinant Atg19, Atg19‐3A, and Atg19‐3D using wild‐type and kinase‐dead Atg1‐D211A as described in (E)."
NCBI gene IDs:
"Atg19: 854072"
Figure legend: "A Wild‐type, hrr25‐ts, and hrr25‐ts cells containing HRR25 on a centromeric plasmid were grown to mid‐log phase at 18°C followed by 2 and 4 h of log‐phase growth at 37°C. Ape1 processing was analyzed by Western blotting."
NCBI gene IDs:
"HRR25: 855897
hrr25‐ts: 855897"
Figure legend: "B atg19Δ and atg19Δ hrr25‐ts cells containing GFP‐Atg19 as indicated were analyzed for Ape1 processing in log phase after 2 h at 37°C."
NCBI gene IDs:
"Atg19: 854072
atg19: 854072
hrr25‐ts: 855897"
Figure legend: "C GFP‐Atg11, GFP‐Atg11 hrr25‐ts, and GFP‐Atg11 atg1‐D211A cells were analyzed for GFP‐Atg11 dot formation. Quantification of at least 70 cells in three individual experiments is shown. Error bars represent standard deviation. Scale bar, 3 μm."
NCBI gene IDs:
"atg1: 852695
Atg11: 856162
hrr25‐ts: 855897"
Figure legend: "D GFP‐Atg11, GFP‐Atg11 hrr25‐ts, and GFP‐Atg11 atg19Δ cells containing BFP‐Ape1 and Cup1‐Ape1 were grown to log phase. Overexpression of Ape1 was induced by addition of 250 μM CuSO4 for 3 h. coloc.: Cells with GFP‐Atg11/BFP‐Ape1 co‐localization. n = 50 (wt), 84 (hrr25‐ts), 127 (atg19Δ). Scale bar, 3 μm."
NCBI gene IDs:
"Ape1: 853758
Atg11: 856162
atg19: 854072
Cup1: 856450
hrr25‐ts: 855897"
Figure legend: "E Hrr25 was immunoprecipitated from Hrr25‐TAP cells and as a control from a non‐tagged wild‐type strain. In vitro phosphorylation of recombinant Atg19, Atg19‐3A, Atg34, and GST using the kinase‐bound beads was performed as described in Fig E. Both Atg19 panels are from the same gel with the same exposure."
NCBI gene IDs:
"Atg19: 854072"
Figure legend: "Confocal images of tPH-CynA-KikGR (green) and PH-Crac (red) expressing wild-type Dictyostelium AX3 cells (left) and PI3K1-2- Dictyostelium cells (right) treated with 5 µM Latrunculin A."
NCBI gene IDs:
"PI3K1: "
Figure legend: "(L) Representative confocal images of tPH-CynA-KikGR in wild-type Dictyostelium AX2 or RacH− cells treated with 5 μM latrunculin A Scale bar: 5 μm. (M) Ratio of membrane to cytosol intensity of tPH-CynA-KikGR in wild-type Dictyostelium AX2 and RacH− cells. T-test was carried out by GraphPad Prism, ****P ≤ 0.0001 versus AX2 group; mean ± SEM (n = 33)."
NCBI gene IDs:
"RacH: 8617155"
Figure legend: "B Activity of each allele at 10 positive control SNPs and 1 negative control SNP in stimulated T cells. GATA1, NF-κB, and RUNX1 constructs were designed to include a binding site for the indicated transcription factors (+) or with that site disrupted (-). Fixed effects meta-analysis P value is shown: *&lt;0.05; **&lt;0.01, ***&lt;0.001, ****&lt;0.0001. Box and whisker plots represent median and IQR (box) and min-to-max (whiskers)."
NCBI gene IDs:
"GATA1: 2623
NF-κB: 4790
RUNX1: 861"
Figure legend: "D Expression-modulating effect of each SNP [log2(OR)] as measured in MPRA and validation experiments. OR were calculated using the median activity of allelic constructs and are presented with respect to the risk allele (luciferase: n=5, MPRA: n=12)."
NCBI gene IDs:
"luciferase: "
Figure legend: " B Pie chart depicting Bayesian fine-mapping results for an AS-associated locus on 2p15 (left panel). MPRA results in stimulated T cells (right panel) showing that rs6759298 has a significant expression-modulating effect (the strongest of any variant at this locus) while the other candidate SNPs have negligible effects. "
NCBI gene IDs:
"2p15: 
rs6759298: "
Figure legend: " C GWAS results (Liu et al, 2015) at a Crohn's disease and multiple sclerosis-associated locus on 6p23 (left panel). MPRA for candidate SNPs in stimulated T cells (right panel) identifying a SNP (rs34421390) with by far the greatest expression-modulating effect at this locus (blue, risk allele reduces expression; red, risk allele increases expression). Dotted horizontal line represents significance threshold (corrected for multiple-testing). "
NCBI gene IDs:
"rs34421390: "
Figure legend: "D GWAS results at a Type 1 Diabetes-associated locus on 14q32 (Onengut-Gumuscu et al, 2015; left panel). MPRA for the candidate SNPs in stimulated T cells (right panel). The construct with the largest and most significant effect contains the risk alleles for 2 SNPs (rs1988588 and rs3902659), each of which has a smaller effect when tested individually (position indicated by vertical dotted line). Dotted horizontal line represents significance threshold (corrected for multiple-testing)."
NCBI gene IDs:
"rs1988588: 
rs3902659: "
Figure legend: "C A single variant (rs6927172) has the largest and most significant expression-modulating activity in resting (left panel) and stimulated CD4 T cells (right panel) with the risk allele reducing transcription. Plots represent median and IQR (box) and min-to-max (whiskers). FDR-corrected meta-analysis P value shown."
NCBI gene IDs:
"rs6927172: "
Figure legend: " E Allele-specific NF-κB binding in CD4 T cells from rs6927172 heterozygotes, demonstrating reduced NF-κB binding to the risk allele following stimulation (n=8; one-sample t-test, two-tailed). "
NCBI gene IDs:
"rs6927172: "
Figure legend: " G Genome-wide H3K27ac ChIP-seq in stimulated CD4 T cells from major- and minor-allele homozygotes at rs6927172 (n=6). Upper panels show input-normalised H3K27ac signals plotted against enhancer rank. Super-enhancers are defined above the inflection point of the curve. Lower panels show H3K27ac reads from a major (left) and a minor (risk) allele homozygote (right) in a 9kb window around rs6927172. "
NCBI gene IDs:
"rs6927172: "
Figure legend: "I Expression of genes on 6q23 in CD4 T cells from 131 patients with active IBD, stratified by rs6927172 genotype (qPCR; one-way ANOVA). Error bars represent SD. Expression of IL20RA and IL22RAR2 not detected."
NCBI gene IDs:
"rs6927172: 
IL20RA: 53832
IL22RAR2: 116379"
Figure legend: "D Expression of genes on 6q23 in EU-containing mRNA (EU added at time of stimulation) showing that deletion of the NF-κB binding site specifically reduces transcription of TNFAIP3, but not other genes at this locus (n=6; one sample t-test). Representative data from the DH gRNA combination."
NCBI gene IDs:
"NF-κB: 4790
TNFAIP3: 7128"
Figure legend: " G Secretion of effector cytokines following deletion of the NF-κB binding site - Th1 (left panel, IFNγ), Th17 (centre panel, IL-17A) and Th2 subsets (right panel, IL-4) (n=6, paired t-test, one-tailed). "
NCBI gene IDs:
"NF-κB: 4790"
Figure legend: "F-G.  Primary root length and  Lateral root  density of 21-day-old, mock- and SA190-colonized Col-0, aba2-1 and qpyr/pyl  plants upon growth  for 16 days on ½ MS + 25% PEG. Data information: Boxplot shows data from three independent biological replicates (technical replicates n = 36) where whiskers represents minimum and maximum values, \"+\" indicates mean and horizontal line represents median. Asterisks indicate the statistical differences based on the Student's t-test (* p &lt; 0.05, *** p &lt; 0.001)."
NCBI gene IDs:
"aba2: 841665"
Figure legend: "B. Relative  gene expression  of aquaporin PIP  and TIP genes by qRT-PCR analysis normalized to tubulin  levels in 21-days old mock- and SA190-colonized roots of Arabidopsis  grown for 16 days on ½ MS with or without 25% PEG. Data information: Values represent the means of three biological experiments. Error bars indicate SE. All plots represent the mean of 3 biological replicates (biological replicates n= 3). Asterisks indicate a statistical difference based on the Student's t-test (* p &lt; 0.05; ** p &lt; 0.01; *** p &lt; 0.001)."
NCBI gene IDs:
"tubulin: 836391"
Figure legend: "C. Relative  gene expression of aquaporin PIP and TIP genes by  qRT-PCR analysis in Col-0, aba2-1 and qpyr/pyl mutants normalized to tubulin  levels in 21-days old mock- and SA190-colonized roots  of Arabidopsis  grown for 16 days on ½ MS with or without 25% PEG. Data information: Values represent the means of three biological experiments. Error bars indicate SE. All plots represent the mean of 3 biological replicates (biological replicates n= 3). Asterisks indicate a statistical difference based on the Student's t-test (* p &lt; 0.05; ** p &lt; 0.01; *** p &lt; 0.001)."
NCBI gene IDs:
"aba2: 841665
tubulin: 836391"
Figure legend: "Relative enrichment of the H3K4me3 mark at the indicated gene loci of selected PIPs and TIPs of non-colonized (Mock) and SA190-colonized (SA190) plants in Col-0 and aba2-1 mutant as determined by chromatin immunoprecipitation-qPCR  (ChIP-qPCR). The regions targeted for amplification are labelled as R1, R2 and R3. R1 encompasses 5'-UTR, R2 is close to the transcription start site (TSS) while R3 is outside the gene body. Amplification values were normalized to input and H3  and region 3 (R3) of non-colonized (Mock) Col-0 plants. The plots represent the means of 2 biological replicates. Error bars represent SE. (ns) non-significant Asterisks indicate a statistical difference based on 2-way ANOVA (*p ≤ 0.05; **p ≤ 0.01; ***p ≤ 0.001 for p value differences between the conditions when compared to Col-0 Mock using Dunnett's multiple comparison test)."
NCBI gene IDs:
"aba2: 841665"
Figure legend: "A-B. Total fresh weight  of 21 days old non-colonized- (Mock) and SA190-colonized (SA190) Col-0, tip2;1  and qpip  plants grown for 16 days under normal (½ MS) or drought stress proxy conditions (½ MS + 25% PEG). Data information: All plots represent the mean of 3 biological replicates. Error bars represent SE. Boxplot shows data from three independent biological replicates (technical replicates n = (A) 16-20, (B) 8-20 where whiskers represents minimum and maximum values, \"+\" indicates mean and horizontal line represents median. Asterisks indicate the statistical differences based on the Student's t-test (* p &lt; 0.05, *** p &lt; 0.001). Asterisks indicate a statistical difference based on the Student's t-test *** p &lt; 0.001)."
NCBI gene IDs:
"tip2;1: 820870"
Figure legend: "(B) Immunoblotting (IB) analysis of wild type (WT) and PAQR3-deficient MEFs after GS for different time as indicated."
NCBI gene IDs:
"PAQR3: 231474"
Figure legend: "(C) WT and PAQR3-deficient MEFs were treated with 80 mM chloroquine (CQ) for 2 h to induce LC3-II accumulation. Whole-cell lysates were harvested for IB analysis of LC3-II."
NCBI gene IDs:
"PAQR3: 231474"
Figure legend: "(D) Autophagosome-like structures in WT and PAQR3-deleted MEFs were detected after GS for 4 h by transmission electron microscopy. * indicates autophagosome-like structures. N, nucleus.(E) Quantitative analysis of autophagic vacuoles in transmission electron microscopy images. Thirty cells were quantified from each independent experiment，which was repeated for three times with similar results. Values are presented as mean ± SD, ***p &lt; 0.001."
NCBI gene IDs:
"PAQR3: 231474"
Figure legend: "(F) Immunofluorescence staining of LC3 in WT or PAQR3-deficient MEFs after GS for 4 h. The arrowhead indicates representative LC3-positive puncta. Scale bar: 10 μm."
NCBI gene IDs:
"PAQR3: 231474"
Figure legend: "(G, H) HeLa cells were infected by PAQR3 knockdown or overexpression lentivirus together with their respective control virus. After GS for 1 h, the cell lysates were harvested for IB."
NCBI gene IDs:
"PAQR3: 152559"
Figure legend: "(A~C) HeLa cells stably expressing GFP-DFCP1 were transfected with or without PAQR3-specific shRNA. GFP signals were observed in these cells before or after glucose starvation (GS, shown in A). The knockdown efficiency of PAQR3 is shown in B and the statistics of GFP-positive puncta per cell is illustrated in C. Values are presented as mean ± SD, *** P &lt; 0.001. Scale bar: 10 μm."
NCBI gene IDs:
"PAQR3: 152559"
Figure legend: "(D) GFP-WIPI1 was transfected into WT or PAQR3-deficient MEFs. 24 h later, the cells were incubated under GS for 4 h, followed by fluorescence observation. Scale bar: 10 μm."
NCBI gene IDs:
"PAQR3: 231474"
Figure legend: "(E) Different VPS34 complexes of WT or PAQR3 knockout HeLa cells were immunoprecipitated by ATG14L and UVRAG antibodies respectively in normal medium (NM) or GS. Then PI(3)P level was determined by a quantitative ELISA assay. The PI(3)P level was normalized to the amount of ATG14L or UVRAG used in the assay (n = 5; ***p &lt; 0.001; ns, not significant)."
NCBI gene IDs:
"PAQR3: 152559"
Figure legend: "(F) HeLa cells infected with control or PAQR3-overexpressed lentivirus were treated with GS for 4 h. PI(3)P levels were determined as in Figure 2E(n = 5; **p &lt; 0.01; ns, not significant)."
NCBI gene IDs:
"PAQR3: 152559"
Figure legend: "(G, H) PAQR3 knockout HeLa cells were transfected with plasmids of multiple PAQR3 deletion mutants. At 24 h after the transfection, the cell lysates were used to immunoprecipitate VPS34 complex by ATG14L antibody, followed by immunoblotting. The activity of ATG14L-linked VPS34 activity was detected by a quantitative ELISA assay. The PI(3)P level was normalized to the amount of ATG14L (n = 5; **p &lt; 0.01)."
NCBI gene IDs:
"PAQR3: 152559"