EMBO/SourceData huggingface dataset:
Figure legend: "RT-PCR analysis of splicing efficiencies of the indicated pre‐mRNAs in wt and cay1∆ cells. The prp1‐1 strain carries a thermosensitive allele of the splicing factor Prp1 and was used as a positive control for splicing impairment. prp1‐1 cells were grown at 36°C for 4 h before harvesting. Amplification products corresponding to unspliced and spliced mRNAs are indicated by asterisks and gene names, respectively. rap1T indicates amplification products obtained with oligonucleotides spanning rap1+ exon 3 and thereby amplifying both spliced and unspliced mRNA. Intronless act1+ was used as a loading control. Numbers at the bottom of each panel are ratios between spliced and unspliced forms (s/u) and spliced and act1+ (s/act1). Values are expressed as fold increase over wt."
NCBI gene IDs:
"act1: 
rap1: 2540115
cay1: 2540353
prp1‐1: 14217622"
Figure legend: "Western blot analysis of Rap1-YFP protein levels in the indicated strains upon nmt1 promoter shutoff by thiamine addition. Membranes were probed with antibodies against GFP and Act1 (loading control).Quantification of Rap1-YFP protein levels in experiments as in (C). Rap1-YFP levels are expressed as fold increase over time 0 after normalization through Act1. Data points and error bars are averages and s.d. from at least four independent experiments. Statistical significance was assayed using the unpaired, two-tailed Student's t-test. *P 0.05, **P 0.01 for cay1+ versus cay1∆ samples."
NCBI gene IDs:
"nmt1: 2539108"
Figure legend: "Telomere length analysis of ApaI‐digested DNA from cay1∆trt1∆ cells harvested at increasing generation doublings (gen)."
NCBI gene IDs:
"cay1: 2540353
trt1: 2540601"
Figure legend: "Northern blot analysis of ARIA, ARRET, Tf2 retrotransposons, and 18S rRNA (loading control) in the indicated strains."
NCBI gene IDs:
"18S: 
ARIA: 
ARRET: 
Tf2: "
Figure legend: "qRT-PCR quantification of TERRA levels expressed as fold increase over wt after normalization through act1+ mRNA. Bars and error bars are averages and s.d. from 3 independent experiments. Statistical significance was assayed using the unpaired, two‐tailed Student's t‐test. **P 0.01 relative to wt."
NCBI gene IDs:
"act1: 
TERRA: "
Figure legend: "Serial dilutions of the indicated strains were spotted on complete medium and grown at 30°C or 20°C. Otrt1∆ and Otrt1∆cay1∆ are strains with circularized chromosomes lacking telomeric sequence (Supplementary Fig S7)."
NCBI gene IDs:
"cay1: 2540353
trt1: 2540601"
Figure legend: "Representative images of wt and cay1∆ cells grown for 24 h at 30°C or 20°C. Scale bar, 20 μm."
NCBI gene IDs:
"cay1: 2540353"
Figure legend: "Top: Examples of DAPI‐stained wt and cay1∆ cells grown in complete medium for 24 h at 30°C or 20°C. The white arrowhead indicates a chromosome bridge. Scale bar, 10 μm. Bottom: Quantification of chromosome bridges. Bars and error bars are averages and s.d. from three independent experiments and at least 200 cells were scored per sample in each experiment. Statistical significance was assayed using the unpaired, two‐tailed Student's t‐test. ***P 0.001 relative to 30°C."
NCBI gene IDs:
"cay1: 2540353"
Figure legend: "RT-PCR analysis of pre‐mRNA splicing efficiencies of rap1+ and poz1+ pre‐mRNAs in cay1+ and cay1Δ cells expressing Cay1‐YFP or Rap1‐YFP. Amplification products corresponding to unspliced and spliced mRNAs are indicated by asterisks and gene names, respectively. rap1T indicates amplification products obtained with oligonucleotides spanning rap1 exon 3 and thereby amplifying both spliced and unspliced mRNA. Intronless act1+ was used as a loading control. Numbers at the bottom of each panel are ratios between spliced and unspliced forms (s/u) and spliced and act1+ (s/act1). Values are expressed as fold increase over wt."
NCBI gene IDs:
"act1: 
poz1: 2542244
rap1: 2540115
Rap1: 2540115
cay1: 2540353
Cay1: 2540353"
Figure legend: "Western blot analysis of total proteins from early generation cay1+ and cay1Δ cells expressing Cay1‐YFP, Rap1‐YFP, and Taz1‐YFP using antibodies against Rap1, Taz1, and Act1 (loading control). Numbers at the bottom are ratios between Rap1 proteins (endogenous plus ectopic) and Act1 (Rap1/Act1). Values are expressed as fold increase over wt."
NCBI gene IDs:
"Rap1: 2540115
cay1: 2540353
Cay1: 2540353
Taz1: 2542313"
Figure legend: "Left: Representative YFPfluorescence microscopy and DIC images of cay1∆ strains expressing Cay1‐YFP. Scale bar, 10 μm. Right: Representative YFP and RFP fluorescence images of Cay1‐YFP‐ and Pot1‐RFP‐expressing cells. Arrows point to YFP and RFP foci within the same nucleus demonstrating lack of co‐localization. Scale bar, 5 μm."
NCBI gene IDs:
"cay1: 2540353"
Figure legend: "Representative YFPfluorescence microscopy and DIC images of cay1+ and cay1∆ strains expressing Rap1‐YFP. Scale bar, 5 μm."
NCBI gene IDs:
"cay1: 2540353"
Figure legend: "Northern blot analysis of ARIA, ARRET, and 18S rRNA (loading control) at early generations after expression of YFP‐tagged proteins. Numbers at the bottom are ratios between ARRET and 18S rRNA signals, expressed as fold increase over wt."
NCBI gene IDs:
"18S: 
ARIA: 
ARRET: "
Figure legend: "Serial dilutions of early generation cay1+ and cay1∆ cells expressing Cay1‐YFP and Rap1‐YFP were spotted on complete medium and grown at 30°C and 20°C."
NCBI gene IDs:
"Rap1: 2540115
cay1: 2540353
Cay1: 2540353"
Figure legend: "Northern blot analysis of Tf2 retrotransposons, U6 snRNA, and act1+ mRNA (loading control) in wt, cay1Δ, and prp1‐1 cells. prp1‐1 cells were grown at 36°C for 4 h before harvesting. Black arrowhead indicates unprocessed Tf2 transcripts. The asterisk indicates unspliced U6. Numbers at the bottom are the ratios between Tf2 and act1+ signals (Tf2/Act1) and expressed as fold increase over wt."
NCBI gene IDs:
"act1: 
Act1: 
Tf2: 
U6: 
cay1: 2540353
prp1‐1: 14217622"
Figure legend: "Northern blot analysis as in (A) in mpn1+ and mpn1∆ strains carrying a stably integrated extra copy of the snu6+ gene or empty vector control plasmids (ev)."
NCBI gene IDs:
"snu6: 3361572
mpn1: 2542061"
Figure legend: "To monitor the progression of the CLL-like population, blood was collected from the animals every four weeks up to an age of 60 weeks and analyzed by flow cytometry. The diagram displays the percentage of CLL-like cells in relation to all lymphocytesover a period of 60 weeks. Shown are mean values with ±SD. Significant differences between groups were determined by one-way ANOVA with Kruskal-Wallis test (no normal distribution) and corrected for multiple comparison with Dunn's test, **p&lt;0.01, ***p&lt;0.001. Summarized data from more than 40 independent experiments for individual time points, comprising n=4-75 animals per time pointand genotype. X = no surviving TCL1 x Siglecg-/-animals at the ageof 60 weeks. + indicates that in these groups only 4 animals were used for the analysis and therefore no calculation of significance was possible."
NCBI gene IDs:
"Siglecg: 243958"
Figure legend: "The percentage of B220low CD5+ leukocytes in the liver at different time points is illustrated. Besides representative dot plots show the selection of B220low CD5+ cells in the liver. Cells were pre-gated on single cells, living cells and CD45+ leukocytes. Shown are mean values with ±SD. Significant differences between groups were tested by ordinary one-way ANOVA with Šídák's post-hoc test. Data are from at least 10 independent experiments for individual time points, comprising n=5-12 animals per time point and genotype. X = no surviving TCL1 x Siglecg-/- animals at the age of 60 weeks. *p&lt;0.05, **p&lt;0.01, ****p&lt;0.0001."
NCBI gene IDs:
"Siglecg: 243958"
Figure legend: "The survival of TCL1 x Siglecg-/- mice compared to TCL1 mice is illustrated with the Kaplan-Meier survival curve. (n=81 for TCL1, n=101 for TCL1 x Siglecg-/-). The groups were compared for significant differences via log-rank test."
NCBI gene IDs:
"Siglecg: 243958"
Figure legend: "To monitor the progression of the CLL-like population, blood was collected from the animals every four weeks up to an age of 48 weeks and analysed by flow cytometry. Genotypes of the mice are: controls (Siglecg-R26ki/ki), Siglec-G overexpressing mice (Siglecg-R26ki/ki mb1cre), transgenic TCL1 controls (TCL1 x Siglecg-R26ki/ki) and transgenic TCL1 Siglec-G overexpressing mice (TCL1 x Siglecg-R26ki/ki mb1cre). Representative FACSplots show examples of stainingsof B220lowCD5+B cells (CLL-like cells) and the selected gate for B)"
NCBI gene IDs:
"cre: 2777477
R26: 14910
mb1: 14999
Siglecg: 243958
Siglec-G: 243958"
Figure legend: "To monitor the progression of the CLL-like population, blood was collected from the animals every four weeks up to an age of 48 weeks and analysed by flow cytometry. Genotypes of the mice are: controls (Siglecg-R26ki/ki), Siglec-G overexpressing mice (Siglecg-R26ki/ki mb1cre), transgenic TCL1 controls (TCL1 x Siglecg-R26ki/ki) and transgenic TCL1 Siglec-G overexpressing mice (TCL1 x Siglecg-R26ki/ki mb1cre). The diagram displays the percentage of B220lowCD5+cells in respect to lymphocytesover a time periodof 48 weeks. Shown are mean values with ±SD. Significant differences between groups were determined by one-way ANOVA with Kruskal-Wallis test (no normal distribution) and corrected for multiple comparison with Dunn's test. All time pointswere tested separately. *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001. Summarized data from more than 20 independent experiments with n=5-20 animals per time pointand genotype are shown."
NCBI gene IDs:
"cre: 2777477
R26: 14910
mb1: 14999
Siglecg: 243958
Siglec-G: 243958"
Figure legend: "(C) Absolute cell numbers of B220low CD5+ lymphocytes at 36 and 48 weeks of age in the spleen are shown as mean values with ±SD. Significant differences between groups were tested by one-way ANOVA with Kruskal-Wallis test and corrected for multiple comparison with Dunn's test. The different time points were tested separately. n=8-13 animals per time point and genotype. (D) Representative dot plots show selection and percentages of B220low CD5+ B cells in the spleen pre-gated on single cells, living cells and lymphocytes. Data are from at least 10 independent experiments for individual time points. *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001. n=48 for TCL1 x Siglecg-R26ki/ki, n= 52 for TCL1 x Siglecg-R26ki/ki mb1cre"
NCBI gene IDs:
"cre: 2777477
R26: 14910
mb1: 14999
Siglecg: 243958"
Figure legend: "(E)The percentage of B220low CD5+ lymphocytes in the liver at 36 and 48 weeks of age is illustrated. Shown are mean values with ±SD. Significant differences between groups were tested by ordinary one-way ANOVA with Šídák's post-hoc test. n=7-14 animals per time point and genotype. (F) Representative dot plots for the selection of B220low CD5+ cells in the liver. Cells were pre-gated on single cells, living cells and CD45+ leukocytes. Data are from at least 10 independent experiments for individual time points. *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001. n=48 for TCL1 x Siglecg-R26ki/ki, n= 52 for TCL1 x Siglecg-R26ki/ki mb1cre"
NCBI gene IDs:
"cre: 2777477
R26: 14910
mb1: 14999
Siglecg: 243958"
Figure legend: "(G) The differences in survival are shown as Kaplan-Meier plots and log-rank test n=59 for TCL1 x Siglecg-R26ki/ki , n=57 for TCL1 x Siglecg-R26ki/ki mb1cre)."
NCBI gene IDs:
"cre: 2777477
R26: 14910
mb1: 14999
Siglecg: 243958"
Figure legend: "TCL1 and TCL1 x Siglecg-/- B cells were analyzed by intracellular staining with phopho-specific antibodies (or total protein detecting antibody Bcl2)."
NCBI gene IDs:
"Siglecg: 243958"
Figure legend: "TCL1 x Siglecg-R26ki/ki or TCL1 x Siglecg-R26ki/ki mb1-cre B cells were analyzed by intracellular staining with phopho-specific antibodies (or total protein detecting antibody Bcl2)."
NCBI gene IDs:
"cre: 2777477
R26: 14910
mb1: 14999
Siglecg: 243958"
Figure legend: "The transcript expression (normalized counts from bulk mRNA sequencing) of SIGLEC10 is given from five healthy donors, discriminating naïve CD5- (five donors), mature CD5+ 86 donors) and CD27+ memory B cell (eight donors) subsets, from CLL tumor cells (n=9) and from five paired normal residual B (NRB) cells (n=5)."
NCBI gene IDs:
"SIGLEC10: 89790"
Figure legend: "(A) MCF-7 cells were co-transfected with either MIR-CNT (control plasmid) or MIR376A and GFP-LC3 plasmid, and GFP-LC3 dot formation was analyzed. White arrows indicate clusters of the GFP-LC3 dots in cells. (B) Quantification of the experiments in A. MIR376A overexpression, but not MIR-CNT expression, blocked starvation (STV)-induced autophagy (mean ± S.D. of independent experiments, n = 4, ***p&lt;0,01). NON STV, non-starved"
NCBI gene IDs:
"MIR376A: 494325"
Figure legend: "(C) Overexpression of MIR376A resulted in a decrease in the autophagic activity of MCF-7 cells. Starvation-induced conversion of LC3-I to LC3-II in MCF-7 cells was analyzed. Tests were performed in the presence or absence of E64d (10 µg/ml) and Pepstatin A (10 µg/ml) (E+P). LC3-II/LC3-I densitometric ratios were marked. ACTB was used as a loading control."
NCBI gene IDs:
"MIR376A: 494325"
Figure legend: "(D) MIR376A blocked starvation induced SQSTM1 degradation in MCF-7 cells. ACTB was used as a loading control. SQSTM1/ACTIN densitometric ratios were marked."
NCBI gene IDs:
"MIR376A: 494325"
Figure legend: "(A) MIR376A blocked GFP-LC3 dot formation under starvation condition."
NCBI gene IDs:
"MIR376A: 494325"
Figure legend: "(A) MIR376A blocked GFP-LC3 dot formation under starvation condition. (B) Quantitative analysis of experiments in A (mean ± S.D. of independent experiments, n = 3, ***p&lt;0,01)."
NCBI gene IDs:
"MIR376A: 494325"
Figure legend: "(C) Overexpression of MIR376A resulted in decreased autophagic flux in Huh-7 cells. Starvation-induced conversion of LC3-I to LC3-II was analyzed. Tests were performed in the presence or absence of E64d (10 µg/ml) and Pepstatin A (10 µg/ml) (E+P). LC3-II/LC3-I densitometric ratios were marked. ACTB was used as a loading control."
NCBI gene IDs:
"MIR376A: 494325"
Figure legend: "(C and D) qPCR analysis of ATG4C and BECN1 mRNA expression in control miRNA (MIR-CONT) or MIR376A overexpressing cells under non-starved (NON STV) or starved (STV) condition (mean ± S.D. of independent experiments, n = 3, *p&lt;0,05)."
NCBI gene IDs:
"ATG4C: 84938
BECN1: 8678
MIR376A: 494325"
Figure legend: "(E and F) Immunoblots showing ATG4C and BECN1 protein levels following control miRNA (MIR-CONT) or MIR376A overexpression. ACTB was used as a loading control. ATG4C/ACTB or BECN1/ACTB densitometric ratios were marked."
NCBI gene IDs:
"MIR376A: 494325"
Figure legend: "(A and B) qPCR analysis of ATG4C and BECN1 mRNA levels in MCF-7 cells transfected with control antagomirs (CNT-Ant) or antagomir-376a (Ant-376a) (mean ± S.D. of independent experiments, n = 3, **p&lt;0,03 for ATG4C, and n = 3, **p&lt;0,03 for BECN1). Results were expressed as fold changes against GAPDH mRNA levels."
NCBI gene IDs:
"ATG4C: 84938
BECN1: 8678
GAPDH: 2597
mir-376a: 494325"
Figure legend: "(C and D) ATG4C and BECN1 protein levels were increased following antagomir-376a (Ant-376a) transfection. ATG4C/ACTB or BECN1/ACTB densitometric ratios were marked."
NCBI gene IDs:
"mir-376a: 494325"
Figure legend: "(C and D) Normalized luciferase activity measuremets of lysates from 293T cells that were co-transfected with either MIR-CNT or MIR376A plasmids together with the wild-type or mutant luciferase constructs (mean ± S.D. of independent experiments, n = 3 for ATG4C tests, *p&lt;0,05 and n = 5 for BECN1 tests, ***p&lt;0,01)."
NCBI gene IDs:
"ATG4C: 84938
BECN1: 8678
MIR376A: 494325"
Figure legend: "(A) Blockage of endogenous MIR376A by Ant-376a, but not CNT-Ant further stimulated starvation (STV)-activated LC3-I to LC3-II conversion in MCF-7 cells. ACTB was used as a loading control. LC3-II/LC3-I densitometric ratios were marked."
NCBI gene IDs:
"MIR376A: 494325"
Figure legend: " MIR376A and MIR376B level changes in response to starvation stress. (A and B) TaqMan quantitative PCR (qPCR) analysis of endogenous MIR376A (A) and MIR376B (B) levels under control (CNT, no starvation) or starvation (STV, 1 to 8 hours) conditions. TaqMan qPCR data was normalized using U6 small nuclear 1 (RNU6-1) (U6) mRNA levels (mean ± S.D. of independent experiments, n = 5 for both A and B, ***p&lt;0,01).  "
NCBI gene IDs:
"MIR376A: 494325
MIR376B: 574435
RNU6-1: 26827
U6: 26827"
Figure legend: "(b) HeLa cells transfected for 24 h with control vector, or wild-type or different deletion mutants (residues 2-77, 2-275 and 232-607) of Flag-Atg16L1 were immunoprecipitated with anti-Flag antibody (Atg16L1) and immunoblotted with anti-clathrin, anti-Flag and anti-Atg5 antibodies. Clathrin interacts with the N terminus of Atg16L1, in a similar manner to Atg12-Atg5. Total lysates were run alongside as controls for protein input. FL, full-length."
NCBI gene IDs:
"Atg16L1: 55054"
Figure legend: "(a) HeLa cells transfected for 5 days with two rounds of control, epsin 1 (eps.), clathrin heavy chain (cla.), AP2 or AP1 siRNA were either left untreated or treated for 4 h with bafilomycin A1 (+/- BafA1), after which they were lysed for western blot analysis with anti-LC3 and anti-tubulin antibodies. Note that LC3-I is often very faint compared with LC3-II in HeLa cells under the protein extraction conditions we use. However, this is not a problem because it is advisable to relate LC3-II to tubulin/actin."
NCBI gene IDs:
"clathrin heavy chain: 1213
epsin 1: 29924"
Figure legend: "(b) Ratio of LC3-II to tubulin on knockdown (KD) of control, epsin, clathrin heavy chain, AP2 or AP1, with or without bafilomycin A1, quantified from three independent experiments (two for epsin) and represented in the graph. Asterisk, P 0.01; two asterisks, P 0.001; three asterisks, P 0.0001."
NCBI gene IDs:
"clathrin heavy chain: 1213
epsin: 29924"
Figure legend: "(c) HeLa cells stably expressing GFP-mRFP-LC3 (ref. 17) were transfected for 5 days with two rounds of control or clathrin heavy chain siRNA, during which they were either left untreated (UT) or treated with bafilomycin A1 (BafA1) for the last 15 h. Cells were then fixed and analysed on a Cellomics ArrayScan system. Quantification of autophagic vacuoles (AV) or autolysosomes (AL) per cell in the different conditions is shown in the graph. Asterisk, P 0.01; n.s., not significant. n = 2,000 cells."
NCBI gene IDs:
"clathrin heavy chain: 1213"
Figure legend: "(d) HeLa cells transfected for 4 days with control, clathrin heavy chain, AP1 or AP2 siRNA were grown in Hanks balanced salt solution (HBSS) for 6 h, after which the cells were fixed and immunostained for endogenous LC3. The percentages of HeLa cells with more than 50 LC3 vesicles (marked with arrows) are quantified in the graph. End., endogenous. Three asterisks, P 0.0001. n = 500 cells. All error bars represent s.e.m. Scale bars, 10 μm. Uncropped images of blots are shown in Supplementary Information, Fig. S9."
NCBI gene IDs:
"clathrin heavy chain: 1213"
Figure legend: "(a-d) HeLa cells transfected for 72 h with control, epsin 1, clathrin heavy chain, AP2 or AP1 siRNA were treated with HBSS (to induce autophagy) for 6 h, after which they were fixed and immunostained for endogenous Atg16L1. Representative cells for the control and epsin 1 siRNA are in a, and percentages of HeLa cells with Atg16L1vesicles are quantified in b (for epsin 1), c (for clathrin) and d (for AP1 and AP2). Three asterisks, P 0.0001. Scale bars, 10 μm. (Note that we used single siRNAs for all experiments and the effects were confirmed with two independent sequences for clathrin heavy chain). n = 600 cells."
NCBI gene IDs:
"clathrin heavy chain: 1213
epsin 1: 29924"
Figure legend: "(e, f) HeLa cells transfected for 24 h with Flag-tagged wild-type Atg16L1 or the Atg16L1 deletion mutants 2-275 Atg16L1 or 232-607 Atg16L1 were fixed and immunostained with anti-Flag antibody (e); the proportions of cells with Flag-Atg16L1 vesicles are represented in f. Representative images of Atg16L1 vesicles with the different mutant constructs are shown in e. The large boxes in each panel are higher magnifications of regions in the smaller boxes. Three asterisks, P 0.0001; n.s., not significant. n = 100 cells."
NCBI gene IDs:
"Atg16L1: 55054"
Figure legend: "(g-i) HeLa cells transfected with control, epsin 1, clathrin heavy chain, AP2 or AP1 siRNA, as above, were transfected with GFP-Atg16L1 and tomato LC3 for a further 24 h, after which the cells were fixed. g shows representative cells for control, epsin 1 and clathrin siRNA. The percentage of GFP-Atg16L1 (green) that co-localized (yellow, marked by arrows) with tomato LC3 vesicles (red) is quantified as shown in the graph in h (control, epsin 1 and clathrin siRNA) and i (control, AP2 and AP1 siRNA). Three asterisks, P 0.0001. n = 21 cells. Scale bars, 10 μm. All error bars represent s.e.m."
NCBI gene IDs:
"Atg16L1: 55054
clathrin heavy chain: 1213
epsin 1: 29924
LC3: 440738///81631///84557"
Figure legend: "(a) HeLa cells transfected for 24 h with GFP-Atg16L1 were fixed to reveal the Atg16L1 vesicles (green). Scale bar, 10 μm."
NCBI gene IDs:
"Atg16L1: 55054"
Figure legend: "(b) HeLa cells transiently transfected for 20 h with GFP-Atg16L1 and mRFP-GPi were cultured in starvation medium for a further 2 h. TIRF image with GFP-Atg16L1 (green) and mRFP-GPi (red) is shown. Arrows indicate co-localization between Atg16L1 and GPi. The percentage co-localization of GFP-Atg16L1 with mRFP-GPi is shown in the graph. n = 2 cells. Scale bar, 5 μm."
NCBI gene IDs:
"Atg16L1: 55054
GPi: 2821"
Figure legend: "(c) HeLa cells transfected for 24 h with GFP-Atg16L1 were either left untreated or treated with 50 μM dynasore (Sigma) for 4 h and processed for immunogold electron microscopy with anti-GFP antibodies (15-nm gold particles) and anti-clathrin antibodies (10-nm gold particles). Co-localization can be seen in the boxed areas. Quantification of clathrin-coated structures (CCS) that were associated with Atg16L1 per 1,000 μm2 is shown in the graph. Three asterisks, P 0.0001. Scale bar, 100 nm. All error bars represent s.e.m."
NCBI gene IDs:
"Atg16L1: 55054"
Figure legend: "(a) HeLa cells transfected for 24 h with GFP-Atg16L1 (green) and CFP-LC3 (blue) were incubated with Alexa Fluor-555-conjugated cholera toxin subunit B (red) for 15 min at 4 °C (allowing toxin to bind to the plasma membrane). Then cells were incubated at 37 °C (allowing internalization of cholera toxin) for 10 min and fixed for confocal analysis. Vesicles positive for both Atg16L1 and cholera toxin are yellow (also see high-magnification images at the right). Note that the small Atg16L1 vesicles co-localizing with cholera toxin are negative for LC3 (as marked with yellow arrows), and the Atg16L1 vesicles co-localizing with both cholera toxin and LC3 (marked with blue arrows) are shown in the magnified panels at the right. Scale bar, 10 μm."
NCBI gene IDs:
"Atg16L1: 55054
LC3: Q9GZQ8///Q9BXW4///Q9H492///440738///81631///84557"
Figure legend: "(b) HeLa cells transfected for 24 h with GFP-Atg16L1 (green) were incubated with Alexa Fluor-555-conjugated cholera toxin subunit B (red) as in a, after which they were fixed, immunostained for endogenous (end.) EEA1 (blue) and analysed by confocal microscopy. Vesicles positive for Atg16L1 and cholera toxin B are yellow (white arrows) and vesicles positive for both EEA1 and cholera toxin are purple (blue arrows) and are shown in the high-magnification images in the middle. The graph shows percentage co-localization. Cho. tox., cholera toxin. n = 20 cells. Scale bar, 10 μm."
NCBI gene IDs:
"Atg16L1: 55054"
Figure legend: "(a) HeLa cells transfected for 24 h with Flag-tagged wild-type Atg16L1 or the Atg16L1 deletion mutants 2-275 or 232-607 Atg16L1, together with GFP-Atg5 and CFP-LC3, were fixed and immunostained with anti-Flag antibody before confocal analysis. Co-localization of wild-type or 2-275 Atg16L1 (red) with GFP-Atg5 (green) is marked by arrows in the insets. Scale bars, 10 μm."
NCBI gene IDs:
"Atg16L1: 55054
Atg5: 9474
LC3: 440738///81631///84557"