EMBO/SourceData huggingface dataset:
Figure legend: " (B) Upper panel, Distribution of distance to nucleus, normalized on cell size, quantified by image (as in a) segmentation (see Material and Method, Confocal microscopy and early/late quantification) of EEA-1+ endosomes. Results are from two independent experiments for a total of 830 early endosomes in 13 shCTL/GFP cells (64 ± 6 endosomes per cell), 719 early endosomes in 10 shSTIM1/GFP cells (60 ± 6 endosomes per cell) and 820 early endosomes in 12 shSTIM1/GFP-STIM1 WT cells (68 ± 6 endosomes per cell) and analyzed by a parametric two-tailed analysis of variance (ANOVA) with Bonferroni post hoc analysis. ANOVA p≤ 0,001; Bonferroni for shCTL/GFP and shSTIM1/GFP p≤ 0,001 *** (orange) and for shSTIM1/GFP and shSTIM1/GFP-STIM1 WT p≤ 0,001 *** (green). Lower panel, Distribution of distance to nucleus, normalized on cell size, quantified by image (as in a) segmentation (see Material and Method, Confocal microscopy and early/late quantification) of EEA-1+ endosomes. Results are from two independent experiments for a total of 820 early endosomes in 12 shSTIM1/GFP-STIM1 WT cells (68 ± 6 endosomes per cell) and 400 early endosomes in 12 shSTIM1/GFP-STIM1 NN cells (33 ± 7 endosomes per cell) and analyzed a two-tailed heteroscedastic Student's t-test, p≤ 0,001 ***. "
NCBI gene IDs:
"GFP: 
STIM1: 6786"
Figure legend: " (C) Average size, normalized on cell size, quantified by image (as in a) segmentation (see Material and Method, Confocal microscopy and early/late quantification) of EEA-1+ endosomes. Results are the average ± SEM of two independent experiments for a total 830 early endosomes in 13 shCTL/GFP cells (64 ± 6 endosomes per cell), 719 early endosomes in 10 shSTIM1/GFP cells (60 ± 6 endosomes per cell), 820 early endosomes in 12 shSTIM1/GFP-STIM1 WT cells (68 ± 6 endosomes per cell) and 400 early endosomes in 12 shSTIM1/GFP-STIM1 NN cells (33 ± 7 endosomes per cell) and analyzed by a parametric two-tailed analysis of variance (ANOVA) with Bonferroni post hoc analysis. ANOVA p≤ 0,001; Bonferroni for shCTL/GFP and shSTIM1/GFP p≤ 0,001 ***, for shCTL/GFP and shSTIM1/GFP-STIM1 WT p&gt; 0.05 not significant (ns), for shSTIM1/GFP-STIM WT and shSTIM1/GFP-STIM1 NN p≤ 0,001 *** and for shSTIM1/GFP and shSTIM1/GFP-STIM1 NN p≤ 0,05 *. "
NCBI gene IDs:
"GFP: 
STIM: 6786
STIM1: 6786"
Figure legend: " (D) Average number, normalized on cell size, quantified by image (as in a) segmentation (see Material and Method, Confocal microscopy and early/late quantification) of EEA-1+ endosomes. Results are the average ± SEM of two independent experiments for a total 830 early endosomes in 13 shCTL/GFP cells (64 ± 6 endosomes per cell), 719 early endosomes in 10 shSTIM1/GFP cells (60 ± 6 endosomes per cell), 820 early endosomes in 12 shSTIM1/GFP-STIM1 WT cells (68 ± 6 endosomes per cell) and 400 early endosomes in 12 shSTIM1/GFP-STIM1 NN cells (33 ± 7 endosomes per cell) and analyzed by a parametric two-tailed analysis of variance (ANOVA) with Bonferroni post hoc analysis. ANOVA p≤ 0,001; Bonferroni for shCTL/GFP and shSTIM1/GFP p≤ 0,01 **, for shCTL/GFP and shSTIM1/GFP-STIM1 WT p&gt; 0.05 not significant (ns), for shSTIM1/GFP-STIM WT and shSTIM1/GFP-STIM1 NN p≤ 0,001 *** and for shSTIM1/GFP and shSTIM1/GFP-STIM1 NN p≤ 0,001 ***. "
NCBI gene IDs:
"GFP: 
STIM: 6786
STIM1: 6786"
Figure legend: "(A) mRNA levels of KIFC1, KIFC2 and KIFC3 in ECs. Values are normalized on GAPDH mRNA levels. Results are the average ± SD of three independent experiments and analyzed by a parametric two-tailed analysis of variance (ANOVA) with Bonferroni post hoc analysis. ANOVA p≤ 0,01; Bonferroni for KIFC1 and KIFC2 p≤ 0,01 ** and for KIFC1 and KIFC3 p≤ 0,05 *."
NCBI gene IDs:
"GAPDH: 2597
KIFC1: 3833
KIFC2: 90990
KIFC3: 3801"
Figure legend: "(B) Representative Western Blot analysis of endogenous KIFC1 and STIM1 proteins (both normalized on total tubulin levels) in ECs silenced with a control siRNA (siCTL) or one targeting KIFC1 (siKIFC1) or two control siRNAs (siCTLsiCTL) or two targeting KIFC1 and STIM1 (siKIFC1siSTIM1). Results are the average ± SD of three independent experiments and analyzed by a parametric two-tailed analysis of variance (ANOVA) with Bonferroni post hoc analysis. ANOVA p≤ 0,01; Bonferroni for siCTL and siKIFC1, KIFC1 expression p≤ 0,001 ***, STIM1 expression p&gt; 0.05 not significant (ns) and for siCTLsiCTL and siKIFC1siSTIM1, KIFC1 expression p≤ 0,01 **, STIM1 expression p≤ 0,05 *."
NCBI gene IDs:
"KIFC1: 3833
STIM1: 6786"
Figure legend: " (C) Confocal microscopy images of ECs silenced with a control siRNA (siCTL) or one targeting KIFC1 (siKIFC1) or one targeting STIM1 (siSTIM1) or two targeting both (siKIFC1siSTIM1) and stained for endogenous EEA-1 (in green) and LAMP-1 (in red) to visualize EEs and LEs, respectively, and DAPI (in blue) to highlight the nucleus. The yellow line is drawn to define cell periphery. Scale bar = 20 μm. On the right, inset panels to highlight respective perinuclear and peripheral area of the cell. Scale bar = 5 μm. "
NCBI gene IDs:
"KIFC1: 3833
STIM1: 6786"
Figure legend: " (D) Distribution of distance to nucleus, normalized on cell size, quantified by image (as in c) segmentation (see Material and Method, Confocal microscopy and early/late quantification) of EEA-1+ endosomes in siCTL and siKIFC1 ECs. Results are from three independent experiments for a total of 4091 early endosomes in 19 siCTL cells (215 ± 20 endosomes per cell) and 2275 early endosomes in 20 siKIFC1 cells (114 ± 10 endosomes per cell) and analyzed by a two-tailed heteroscedastic Student's t-test, p≤ 0,001 ***. "
NCBI gene IDs:
"KIFC1: 3833"
Figure legend: " (E) Distribution of distance to nucleus quantified by image (as in c) segmentation (see Material and Method, Confocal microscopy and early/late quantification) of EEA-1+ endosomes. Results are from three independent experiments for a total of 4091 early endosomes in 19 siCTL cells (215 ± 20 endosomes per cell), 2275 early endosomes in 20 siKIFC1 cells (114 ± 10 endosomes per cell) and 3257 early endosomes in 18 siKIFC1/siSTIM1 cells (181 ± 14 endosomes per cell). Data are analyzed by a parametric two-tailed analysis of variance (ANOVA) with Bonferroni post hoc analysis. ANOVA p≤ 0,001; Bonferroni for siCTL and siKIFC1 ECs p≤ 0,001 *** (orange) and for siKIFC1 and siSTIM1/siKIFC1 ECs p≤ 0,001 *** (green). On the right-hand side of the plot, colored bands represent the average cell diameter, significantly changing throughout the conditions. Data are analyzed by a parametric two-tailed analysis of variance (ANOVA) with Bonferroni post hoc analysis. ANOVA p≤ 0,01; Bonferroni for siCTL and siKIFC1 ECs p&gt; 0.05 not significant (orange ns) and for siKIFC1 and siSTIM1/siKIFC1 ECs p≤ 0,01 ** (green). "
NCBI gene IDs:
"KIFC1: 3833
STIM1: 6786"
Figure legend: " (C) Representative Western Blot analysis of endogenous HOOK1 or HOOK3 and total tubulin proteins in ECs, silenced with a control siRNA (siCTL) or one targeting HOOK1 (siHOOK1; on the left) or one targeting HOOK3 (siHOOK3; on the right). "
NCBI gene IDs:
"HOOK1: 51361
HOOK3: 84376"
Figure legend: " (D) Confocal microscopy images of ECs silenced with a control siRNA (siCTL) or one targeting HOOK1 (siHOOK1) or one targeting HOOK3 (siHOOK3) or two targeting both (siHOOK1siHOOK3) and stained for endogenous EEA-1 (in green) and LAMP-1 (in red) to visualize EEs and LEs, respectively, and DAPI (in blue) to highlight the nucleus. The yellow line is drawn to define cell periphery. Scale bar = 20 μm. On the right, inset panels to highlight respective perinuclear and peripheral area of the cell. Scale bar = 5 μm. "
NCBI gene IDs:
"HOOK1: 51361
HOOK3: 84376"
Figure legend: " (E) Distribution of distance to nucleus, normalized on cell size, quantified by image (as in d) segmentation (see Material and Method, Confocal microscopy and early/late quantification) of EEA-1+ endosomes. Results are from three independent experiments for a total of 1193 early endosomes in 12 siCTL cells (99 ± 9 endosomes per cell) and 1104 early endosomes in 21 siHOOK1 cells (53 ± 4 endosomes per cell) and analyzed by a two-tailed heteroscedastic Student's t-test, p≤ 0,001 ***. "
NCBI gene IDs:
"HOOK1: 51361"
Figure legend: " (F) Distribution of distance to nucleus, normalized on cell size, quantified by image (as in d) segmentation (see Material and Method, Confocal microscopy and early/late quantification) of EEA-1+ endosomes. Results are from three independent experiments for a total of 1193 early endosomes in 12 siCTL cells (99 ± 7 endosomes per cell) and 1282 early endosomes in 22 siHOOK3 cells (58 ± 5 endosomes per cell) and analyzed by a two-tailed heteroscedastic Student's t-test, p≤ 0,001 ***. "
NCBI gene IDs:
"HOOK3: 84376"
Figure legend: " (G) Distribution of distance to nucleus quantified by image (as in d) segmentation (see Material and Method, Confocal microscopy and early/late quantification) of EEA-1+ endosomes. Results are from three independent experiments for a total of 1193 early endosomes in 12 siCTL cells (99 ± 7 endosomes per cell), 1104 EEs in 21 siHOOK1 cells (53 ± 4 endosomes per cell) and 2340 EEs in 19 siHOOK1/siHOOK3 cells (123 ± 11 endosomes per cell) and analyzed by a parametric two-tailed analysis of variance (ANOVA) with Bonferroni post hoc analysis. ANOVA p≤ 0,001; Bonferroni for siCTL and siHOOK1 ECs p≤ 0,001 *** (orange) and for siHOOK1 and siHOOK1/siHOOK3 ECs p≤ 0,001 *** (green). On the right hand side of the plot, colored bands represent the average cell diameter, significantly changing throughout the conditions. Data are analyzed by a parametric two-tailed analysis of variance (ANOVA) with Bonferroni post hoc analysis. ANOVA p≤ 0,001; Bonferroni for siCTL and siHOOK1 ECs p&gt; 0.05 not significant (orange ns) and for siHOOK1 and siHOOK1/siHOOK3 ECs p≤ 0,001 *** (green). "
NCBI gene IDs:
"HOOK1: 51361
HOOK3: 84376"
Figure legend: " (A) Confocal microscopy images of ECs silenced with a control shRNA (shCTL) or one targeting STIM1 (shSTIM1), to which the pH-sensitive dye pHrodo Green was given and then cells were stained for LAMP-1 (in red) to visualize LEs and DAPI (in blue) to highlight the nucleus. Scale bar = 20 μm. (B) Relative amount of LAMP-1+ LEs positive to the pH-sensitive dye pHrodo (as in a) in shCTL and shSTIM1 ECs. Results are the average ± SEM of three independent experiments for a total of 90 cells (30 cell for experiment) and analyzed by a two-tailed heteroscedastic Student's t-test, p≤ 0,001 ***. "
NCBI gene IDs:
"STIM1: 6786"
Figure legend: " (C) Representative Western Blot analysis of endogenous Raptor, total and phospho-Thr389 S6K1 proteins (normalized on total tubulin levels) in ECs silenced with a control shRNA (shCTL) or one targeting STIM1 (siSTIM1). Numbers above each band represent respective N.O.D. average (two biological replicates) quantification. "
NCBI gene IDs:
"STIM1: 6786"
Figure legend: "(D) Representative Western Blot analysis of endogenous LC3-I and -II proteins (both normalized on total tubulin levels and represented as ratio LC3-II/LC3-I) in ECs silenced with a control shRNA (shCTL) or one targeting STIM1 (siSTIM1). Results are the average ± SD of three independent experiments and analyzed by a two-tailed heteroscedastic Student's t-test, p≤ 0,01 **."
NCBI gene IDs:
"STIM1: 6786"
Figure legend: "(A) Confocal microscopy of GFP-TRIM33-overexpressing mESCs  and differentiated cells. Scale bar = 5 µm. (B) Line scans of GFP-TRIM33  and DAPI  fluorescence imaging in each cell context at the position depicted by the white line (from left to right). These line scans were processed by plot profile using image J software. (C) FRAP  assays showing recovery time  of normalized fluorescence signals for GFP-TRIM33  puncta in mESCs. Photobleaching  occurs at t = 5s. Data are the mean ± S.D. of three biological experiments."
NCBI gene IDs:
"GFP: 
TRIM33: 51592"
Figure legend: "(F) Western blot analysis of TRIM33 interactions  with PML  in lysates of HEK293T cells co-transfected with plasmids encoding Flag-PML  and GFP-TRIM33. GFP-TRIM33  was immunoprecipitated  with anti-GFP  affinity beads and immune complexes were detected using antibodies targeting Flag  and GFP. Protein inputs were detected using antibodies against Flag  and GFP  in the same amount of cell lysates. (n = 3). Data information: All data are from three biological replicates."
NCBI gene IDs:
"Flag: 
GFP: 
PML: 5371
TRIM33: 51592"
Figure legend: "(H) Lysates from HEK293T  cells co-transfected with plasmids encoding either full length Flag-TRIM33  or the Flag-TRIM33-RBCC domain alone and full-length HA-PML  or the HA-PML-RBCC domain alone immunoprecipitated  with anti-Flag  affinity beads. Protein complexes were detected using antibodies against Flag  and HA. The protein inputs were detected using antibodies against Flag  and HA  in the same amount of cell lysates. (n = 3). Data information: All data are from three biological replicates."
NCBI gene IDs:
"Flag: 
HA: 
PML: 5371
TRIM33: 51592"
Figure legend: "(A) Representative images of immunofluorescence staining of PML  in WT and Pml  null mESCs. Scale bar = 5 µm."
NCBI gene IDs:
"Pml: 18854"
Figure legend: "(B) Representative  confocal microscopy images of mESCs  overexpressing mCherry-PML  or GFP-PML  (top). Representative confocal microscopy  images of mESCs  overexpressing mCherry-EV or GFP-EV (bottom). Scale bar = 5 µm. (C) FRAP  assays quantifying normalized fluorescence recovery of GFP-PML  signal in mESCs. Photobleaching  occurs at t = 5s. Data are the mean ± S.D. of four biological experiments."
NCBI gene IDs:
"GFP: 
mCherry: 
PML: 5371"
Figure legend: "K) Representative images of co-localization  assays with GFP-TRIM33  in mESCs Pml  null (K). Scale bar = 5 µm. L) Line scans of GFP-TRIM33 fluorescence imaging in each cell context at the position depicted by the white line (from left to right). These line scans were processed by plot profile using image J software. (M) Column graph of the numbers of GFP-TRIM33  puncta and DAPI  in mESCs."
NCBI gene IDs:
"Pml: 18854"
Figure legend: "(N) Scatter plot of the numbers of GFP-TRIM33  puncta (per cell) in WT and Pml  KO mESCs. (n = 20). (O) Scatter plot of the volume of GFP-TRIM33  puncta (per cell) in WT and Pml  KO mESCs. (n = 20). Data information: In panels (N, O, 20 individual puncta with three biological experiments were analyzed. Significant differences were determined by t-tests. (*p &lt; 0.05, ****p &lt; 0.0001). "
NCBI gene IDs:
"Pml: 18854"
Figure legend: "(P) Representative images of immunofluorescence staining  of PML  in WT and Trim33  null mESCs. Scale bar = 10 µm. (Q) Scatter plot of the numbers of PML NBs  (per cell) in WT and Trim33  KO mESCs. (n = 20). (R) Scatter plot of the proportion of PML NBs  (per cell) in WT and Trim33  KO mESCs. (n = 20). Data information: In panels Q and R), 20 individual puncta with three biological experiments were analyzed. Significant differences were determined by t-tests. (*p &lt; 0.05, ****p &lt; 0.0001). "
NCBI gene IDs:
"Trim33: 94093"
Figure legend: "G, H Luciferin  assay of NFAT  activity (G) and Nfatc1  mRNA expression  (H) in J76-NFATRE-luc  and TCR052 cells stimulated with α-human CD3  (OKT3) (1 µgml-1) in the presence of α-human CD28  (1 µgml-1) for 4 h or treated with DSF  (5 µM) for 2 h. The levels of NFAT  activity were normalized with TCR052  cells treated with DMSO  (n = 3). Data information: data are representative of 3 independent experiments, mean ± SD. **P&lt;0.01; ***P&lt;0.001; ****P&lt;0.0001; two-way analysis of variance (ANOVA) in (G, H)]."
NCBI gene IDs:
"luc: 
Nfatc1: 4772
NFAT: 4772"
Figure legend: "I Western blot  analysis of p-CD3ζ, LCK  and p-Zap70  in LCK-deficient cells were infected with the lentivirus  collected from human HEK293T  cells transfected with control plasmid (Control) (1 µg), LCK(WT) (1 µg), or LCK(C20/23S) (1 µg) with psPAX2 (1 µg) and pMD2.G (1 µg) for 48 h followed by treatment with DSF  (5 µM) for 2 h stimulated with α-human CD3  and α-human CD28  for 5 min. Data information: data are representative of I) independent experiments"
NCBI gene IDs:
"LCK: 3932"
Figure legend: "D A heatmap of upregulated genes associated with TCR and T cell activation-related genes in DSF  relative to that in DMSO. One column indicates one sample in each condition (n = 3). Data information: data are representative of 3 independent experiments"
NCBI gene IDs:
"TCR: 21577///110067///110066///21473"
Figure legend: "A. GFP-Snc1-PEM protein accumulates in atg1Δ, atg8Δ, and atg11Δ mutant cells. Lysates were prepared from wild type (WT), ypt1-1 (for comparison), atg1Δ, atg8Δ, and atg11Δ mutant cells transformed with a 2μ plasmid expressing GFP-Snc1-PEM from the TPI promoter. The level of GFP-Snc1-PEM was determined using immunoblot analysis with anti-GFP antibodies. The bands were quantified and increase in the protein level in mutant versus the WT cells is shown under the blot and adjusted to the G6PDH loading control."
NCBI gene IDs:
"PEM: 
atg1: 852695
atg11: 856162
atg8: 852200
Snc1: 851203
ypt1-1: 850505"
Figure legend: "B. GFP-Snc1-PEM protein accumulates in aberrant ER structures in atg1Δ, atg8Δ, and atg11Δ mutant cells. The ER-marker Sec61 was tagged with mCherry in strains from panel A, and the cells were examined by live-cell microscopy. Shown from left to right: DIC, GFP, mCherry, merge, % cells with intracellular GFP-Snc1-PEM (number of cells with internal GFP-Snc1-PEM / number of cells visualized), and % cells in which intra-cellular Snc1-PEM co-localizes with Sec61."
NCBI gene IDs:
"atg1: 852695
atg11: 856162
atg8: 852200"
Figure legend: "C. UPR is induced in atg1Δ, atg8Δ, and atg11Δ mutant cells. Cells from panel A were transformed with a second plasmid that expresses β-gal from a UPR promoter. UPR was determined and expressed as % of the WT response."
NCBI gene IDs:
"atg1: 852695
atg11: 856162
atg8: 852200"
Figure legend: "D-E. Unlike deletion of Atg11, deletion of other known selective Atgs required for the CVT pathway (Atg19), mitophagy (Atg32) and pexophagy (Atg36), does not result in increase of GFP-Snc1-PEM protein level (D"
NCBI gene IDs:
"Atg11: 856162
Atg19: 854072
Atg32: 854660
Atg36: 853254"
Figure legend: "D-E. Unlike deletion of Atg11, deletion of other known selective Atgs required for the CVT pathway (Atg19), mitophagy (Atg32) and pexophagy (Atg36), does not result in increase of GFP-Snc1-PEM protein level (D), intra-cellular accumulation of GFP-Snc1-PEM, (E),"
NCBI gene IDs:
"Atg11: 856162
Atg19: 854072
Atg32: 854660
Atg36: 853254"
Figure legend: "D-E. Unlike deletion of Atg11, deletion of other known selective Atgs required for the CVT pathway (Atg19), mitophagy (Atg32) and pexophagy (Atg36), does not result in increase of GFP-Snc1-PEM protein level (D), intra-cellular accumulation of GFP-Snc1-PEM, (E), and induction of the UPR response (F). Wild type (WT), atg19Δ, atg11Δ, atg32Δ, and atg36Δ mutant cells overexpressing GFP-Snc1-PEM were analyzed as described for panels A-C, respectively. E. Shown from left to right: DIC, GFP, and % cells with intracellular Snc1-PEM structures. +/- and error bars represent STDEV. Results in this figure represent at least two independent experiments."
NCBI gene IDs:
"Atg11: 856162
atg11: 856162
atg19: 854072
Atg19: 854072
atg32: 854660
Atg32: 854660
atg36: 853254
Atg36: 853254"
Figure legend: "A-C. While the level of overexpressed GFP-Snc1-PEM is increased in atg9∆ and atg2∆, but not atg18∆, mutant cells, it does not accumulate in aberrant structures and does not induce UPR. Wild type (WT), atg9∆, atg18∆, and atg2∆ mutant cells overexpressing GFP-Snc1-PEM were analyzed as described for Fig 1A-1C, respectively. The tested phenotypes: the level of GFP-Snc1-PEM protein (A),"
NCBI gene IDs:
"PEM: 
atg18: 850577
atg2: 855479
atg9: 851406"
Figure legend: "A-C. While the level of overexpressed GFP-Snc1-PEM is increased in atg9∆ and atg2∆, but not atg18∆, mutant cells, it does not accumulate in aberrant structures and does not induce UPR. Wild type (WT), atg9∆, atg18∆, and atg2∆ mutant cells overexpressing GFP-Snc1-PEM were analyzed as described for Fig 1A-1C, respectively. The tested phenotypes: the level of GFP-Snc1-PEM protein (A), accumulation of GFP-Snc1-PEM in aberrant structures (B)"
NCBI gene IDs:
"PEM: 
atg18: 850577
atg2: 855479
atg9: 851406"
Figure legend: "A-C. While the level of overexpressed GFP-Snc1-PEM is increased in atg9∆ and atg2∆, but not atg18∆, mutant cells, it does not accumulate in aberrant structures and does not induce UPR. Wild type (WT), atg9∆, atg18∆, and atg2∆ mutant cells overexpressing GFP-Snc1-PEM were analyzed as described for Fig 1A-1C, respectively. The tested phenotypes: the level of GFP-Snc1-PEM protein (A), accumulation of GFP-Snc1-PEM in aberrant structures (B), and induction of the UPR response (C,atg1∆ is shown as a positive control)."
NCBI gene IDs:
"PEM: 
atg1: 852695
atg18: 850577
atg2: 855479
atg9: 851406"
Figure legend: "D-G. Atg9 is epistatic to Atg11 in macro-ER-phagy. ATG9 was deleted in wild type and atg11∆ mutant cells and the effects of overexpression of GFP-Snc1-PEM were determined in the single and double mutants as described in Fig 1 legend. D. Deletion of ATG9 in wild type (WT) or atg11∆ mutant cells results in an increase of GFP-Snc1-PEM protein level similar to the increase in atg11∆ mutant cells."
NCBI gene IDs:
"PEM: 
Atg11: 856162
atg11: 856162
Atg9: 851406
ATG9: 851406"
Figure legend: "E. Deletion of ATG9 in wild type or atg11∆ mutant cells results in an increase of intracellular GFP-Snc1-PEM fluorescence. However, only ~20% of the atg9∆ single-, and atg9∆ atg11∆ double-mutant cells accumulate GFP-Snc1-PEM in aberrant structures, as compared with ~75% of atg11∆ mutant cells. Shown from top to bottom: DIC, GFP, % cells with aberrant intracellular GFP-Snc1-PEM structures, ratio of GFP-Snc1-PEM fluorescence inside/PM (30 cells were analyzed for each strain)."
NCBI gene IDs:
"PEM: 
atg11: 856162
ATG9: 851406
atg9: 851406"
Figure legend: "F. UPR is induced in atg11∆, but not in atg9∆ single- and atg9∆ atg11∆ double-mutant cells overexpressing GFP-Snc1-PEM."
NCBI gene IDs:
"PEM: 
atg11: 856162
atg9: 851406"
Figure legend: "G. UPR can be induced in atg9∆ single-, and atg9 atg11∆ double-mutant cells overexpressing GFP-Snc1-PEM by tunicamycin. +/- and error bars represent STDEV. Results in this figure represent at least two independent experiments."
NCBI gene IDs:
"PEM: 
atg11: 856162
atg9: 851406"
Figure legend: "A-C.ATG9 was deleted in ypt1-1, WT and sec12ts mutant cells and the effect of overexpression of GFP-Snc1-PEM was determined in single and double mutant cells. Experiments were performed as described for Fig 1A-1C, respectively. A. Snc1-PEM is increased ~3 fold in atg9∆ and sec12ts as compared to ~20 fold in ypt1-1 mutant cells. Importantly, atg9∆ is epstatic to the ypt1-1, but not to the sec12ts, mutation. Left, immuno-blot analysis, increase of the protein level in mutant versus the WT cells is shown under the blot; right, a bar graph summarizing the quantified data"
NCBI gene IDs:
"ATG9: 851406
atg9: 851406
sec12ts: 855760
ypt1-1: 850505"
Figure legend: ". Whereas deletion of ATG9 in ypt1-1 mutant cells results in three fold lower accumulation of GFP-Snc1-PEM in aberrant structures (85% to 27%), its deletion in sec12ts mutant cells results in two fold increased accumulation (~40% to ~80%). Shown from top to bottom: DIC, GFP, and % cells with intracellular Snc1-PEM structures."
NCBI gene IDs:
"ATG9: 851406
sec12ts: 855760
ypt1-1: 850505"
Figure legend: "C. Deletion of ATG9 in ypt1-1 mutant cells overexpressing Snc1-PEM results in ~3.5 lower UPR (p-value&lt;0.0005), but a slightly increased UPR in sec12ts mutant cells (p-value = 0.05)."
NCBI gene IDs:
"ATG9: 851406
sec12ts: 855760
ypt1-1: 850505"