EMBO/SourceData huggingface dataset:
Figure legend: "A ZetaView nanoparticle tracking analysis of particle numbers and sizes of CD63+ extracellular vesicles  (EVs) isolated from the supernatants of HCC827 lung epithelial  cancer cells, which were transfected with GLK  wild-type or GLK  kinase-dead (K45E) mutant. EVs  were isolated sequentially using ExoQuick kits and then ExoQuick ULTRA columns. Data information: Data shown are representative results of two (A) independent experiments."
NCBI gene IDs:
"GLK: 8491"
Figure legend: "B Immunoblotting  of ACE2  and CD63  proteins in exosomes  isolated from GLK  wild-type- or GLK  (K45E) kinase-dead-overexpressing HCC827  cells. Exosomes  were isolated sequentially using ExoQuick kits and then ExoQuick ULTRA columns. Arrowhead denotes glycosylated ACE2  proteins; asterisk denotes non-glycosylated ACE2  proteins. Data information: Data shown are representative results of three (B, independent experiments."
NCBI gene IDs:
"GLK: 8491"
Figure legend: "D Confocal microscopy analysis of Flag-tagged ACE2  proteins (red) in recipient cells after incubation with exosomes  for 72 h. Exosomes  were isolated sequentially from the supernatants of Flag-ACE2-overexpressing or GFP-GLK  plus Flag-ACE2-coexpressing HCC827  cells using ExoQuick kits and then ExoQuick ULTRA columns. Arrows denote Flag-tagged ACE2  proteins. Original magnification, ×630; scale bars, 10 μm. Data information: Data shown are representative results of three D, independent experiments."
NCBI gene IDs:
"Flag: 
GFP: 
ACE2: 59272
GLK: 8491"
Figure legend: "D Immunoblotting  analyses of the endogenous ACE2, ACE1, CD147, and tubulin  proteins, as well as the transfected Flag-GLK  proteins in HCC827 lung epithelial cells, which were transfected with either GLK  wild-type or kinase-dead (K45E) mutant. Arrowhead denotes glycosylated ACE2  proteins; asterisk denotes non-glycosylated ACE2  proteins. Data information: Data shown are representative results of three D, independent experiments."
NCBI gene IDs:
"GLK: 8491"
Figure legend: "E Immunoblotting  of Flag-tagged ACE2  (anti-Flag), Myc-tagged GLK  (anti-GLK), and tubulin  proteins from HEK293T  cells co-transfected with Flag-ACE2  plus increasing amounts of Myc-GLK  plasmids. Data information: Data shown are representative results of three E, independent experiments."
NCBI gene IDs:
"Flag: 
Myc: 
ACE2: 59272
GLK: 8491"
Figure legend: "F Immunoblotting  of ACE2, GLK, and tubulin  proteins in the lung  tissues of wild-type or GLK-deficient mice. Arrowhead denotes glycosylated ACE2  proteins; asterisk denotes non-glycosylated ACE2  proteins. Data information: Data shown are representative results of three F, independent experiments."
NCBI gene IDs:
"GLK: 225028"
Figure legend: "G Cycloheximide pulse-chase experiments in HEK293T  cells. Immunoblotting  of Flag-tagged ACE2  (anti-Flag), Myc-tagged GLK  (anti-GLK), and tubulin  proteins from HEK293T  cells co-transfected with Flag-ACE2  and Myc-GLK. Transfected cells were treated with 100 μg/ml cycloheximide  (CHX) for up to 24 h. Data information: Data shown are representative results of three G, independent experiments."
NCBI gene IDs:
"Flag: 
Myc: 
ACE2: 59272
GLK: 8491"
Figure legend: "H Flag-tagged ACE2  proteins were immunoprecipitated from lysates of HEK293T  cells co-transfected with Flag-ACE2  and Myc-GLK, followed by immunoblotting with anti-Lsy48-linked ubiquitination  or anti-Flag  antibody. Cells were treated with 25 μM MG132  for 2 h before being harvested. NS, normal serum. Data information: Data shown are representative results of three H, independent experiments."
NCBI gene IDs:
"Flag: 
Myc: 
ACE2: 59272
GLK: 8491"
Figure legend: "I, J Cell entry eﬃciencies of SARS-CoV-2 pseudovirus (I) or VSV-G  pseudovirus (J) into GLK  wild-type- or GLK  (K45E)-overexpressing HCC827 epithelial cells were measured by luciferase activity and presented as relative light units (RLU) at 24 h post infection. n = 3 (biological replicates). Data information: In (I, J), data are presented as means ± SEM. **, P value &lt; 0.01 (ANOVA test); §§, P value &lt; 0.01 (Dunnett's test). Data shown are representative results of three I, J) independent experiments."
NCBI gene IDs:
"GLK: 8491"
Figure legend: "A Immunoblotting  analyses of ACE2  and Flag-tagged GLK  in HCC827  cells transfected with ether Flag-GLK  or Flag-GLK  (K45E) kinase-dead mutant. For immunoblotting  of phosphorylated ACE2, Phos-tagged  SDS-PAGE gel (Phos-tagTM) was used, followed by immunoblotting  with anti-ACE2  antibody. Asterisk denotes unglycosylated ACE2  proteins. Data information: Data shown are representative results of three (A independent experiments."
NCBI gene IDs:
"Flag: 
GLK: 8491"
Figure legend: "C  Mass spectrometry analysis of GLK-phosphorylated ACE2  proteins after in vitro kinase assays. ACE2  Ser776 and Ser783 residues were phosphorylated  by GLK  wild-type but not GLK  (K45E) kinase-dead mutant."
NCBI gene IDs:
"GLK: 8491"
Figure legend: "F Immunoblotting  analyses of Myc-tagged GLK, Flag-tagged ACE2, and tubulin  proteins in HEK293T  cells co-transfected with Flag-ACE2   wild-type or individual ACE2   (S776/783A, S776A, or S783A) mutants plus either empty vector or Myc-GLK. Data information: Data shown are representative results of three F, independent experiments."
NCBI gene IDs:
"Flag: 
Myc: 
ACE2: 59272
GLK: 8491"
Figure legend: "G Immunoblotting  analyses of Flag-tagged ACE2   and tubulin  proteins in HEK293T  cells transfected with Flag-ACE2   wild-type or individual phosphomimetic ACE2   (S776/783E, S776E, or S783E) mutants. Data information: Data shown are representative results of three G, independent experiments."
NCBI gene IDs:
"Flag: 
ACE2: 59272"
Figure legend: "H Flag-tagged ACE2   proteins were immunoprecipitated  from lysates of HEK293T  cells transfected with Flag-ACE2   wild-type or a phospho-mimetic ACE2   (S776/783E) mutant, followed by immunoblotting  with anti-Lsy48-linked ubiquitination  or anti-Flag  antibody. Cells were treated with 25 μM MG132  for 2 h before being harvested. Data information: Data shown are representative results of three H) independent experiments."
NCBI gene IDs:
"Flag: 
ACE2: 59272"
Figure legend: "B Immunoblotting of Myc-tagged ACE2  (anti-ACE2), Flag-tagged UBR4  (anti-Flag), and tubulin  proteins from HEK293T  cells co-transfected with Myc-ACE2  and Flag-UBR4. Arrowhead denotes Myc-tagged ACE2  proteins; asterisk denotes endogenous ACE2  proteins. Data information: Data shown are representative results of three B, independent experiments."
NCBI gene IDs:
"Flag: 
Myc: 
ACE2: 59272
UBR4: 23352"
Figure legend: "C Immunoblotting  of Flag-tagged ACE2  (anti-Flag), Myc-tagged UBR4  (anti-Myc), and tubulin  proteins from HEK293T  cells co-transfected with Flag-ACE2  and Myc-UBR4. The co-transfected cells were treated with 25 μM MG132  for 2 h before being harvested. Data information: Data shown are representative results of three C, independent experiments."
NCBI gene IDs:
"Flag: 
Myc: 
ACE2: 59272
UBR4: 23352"
Figure legend: "D Flag-tagged ACE2  proteins were immunoprecipitated  from lysates of HEK293T  cells co-transfected with Flag-ACE2  and Myc-UBR4, followed by immunoblotting  with anti-Lsy48-linked ubiquitination, anti-Myc, or anti-Flag  antibody. Cells were treated with 25 μM MG132  for 2 h before being harvested. Data information: Data shown are representative results of three D, independent experiments."
NCBI gene IDs:
"Flag: 
Myc: 
ACE2: 59272
UBR4: 23352"
Figure legend: "F Mass spectrometry analysis of the ACE2  peptides containing ubiquitination  residues from Flag-ACE2-transfected HEK293T  cells treated with 25 μM MG132  for 2 h."
NCBI gene IDs:
"Flag: 
ACE2: 59272"
Figure legend: "G Immunoblotting  analyses of Flag-tagged ACE2, Myc-tagged UBR4, and tubulin  proteins in HEK293T  cells co-transfected with Flag-ACE2  wild-type or individual (K26R, K94R, K112R, or K114R) mutants plus either empty vector or Myc-UBR4. Data information: Data shown are representative results of three G, independent experiments."
NCBI gene IDs:
"Flag: 
Myc: 
ACE2: 59272
UBR4: 23352"
Figure legend: "H Flag-tagged ACE2  proteins were immunoprecipitated  from lysates of HEK293T  cells co-transfected with Flag-ACE2  wild-type or Flag-ACE2  (K26/112/114R) mutant plus Myc-UBR4  plasmids, followed by immunoblotting  with anti-Lsy48-linked ubiquitination  or anti-Flag  antibody. Cells were treated with 25 μM MG132  for 2 h before being harvested. Data information: Data shown are representative results of three H) independent experiments."
NCBI gene IDs:
"Flag: 
Myc: 
ACE2: 59272
UBR4: 23352"
Figure legend: "Wild-type and hACE2 KI mice  were intranasally infected with  SARS-CoV-2 pseudovirus. Infection  eﬃciencies of SARS-CoV-2 pseudovirus into mouse  tissues were measured by IVIS  and presented as luminescence counts at 4 days post infection  (B). Data information: WT, wild-type mice; KI, hACE2 knockin mice."
NCBI gene IDs:
"ACE2: 59272"
Figure legend: "Wild-type and hACE2 KI mice  were intranasally infected with SARS-CoV-2 pseudovirus. Immunoblotting  of ACE2, GLK, and tubulin  proteins in the lung  tissues of infected or non-infected mice  (C). Data information: Arrowhead denotes glycosylated ACE2  proteins; asterisk denotes non-glycosylated ACE2  proteins. WT, wild-type mice; KI, hACE2 knockin mice."
NCBI gene IDs:
"ACE2: 59272"
Figure legend: "Wild-type and hACE2  KI mice  were intranasally infected with SARS-CoV-2 pseudovirus. Representative immunohistochemistry  of the SARS-CoV-2 spike  protein (in red) and GLK  protein (in green) in the lung  tissues of the infected hACE2 KI and wild-type mice  (D). Scale bars, 20 μm (D). Data information: WT, wild-type mice; KI, hACE2 knockin mice."
NCBI gene IDs:
"ACE2: 59272"
Figure legend: "Wild-type and hACE2 KI mice  were intranasally infected with SARS-CoV-2  pseudovirus. Immunoblotting  of CD9  and mouse/human ACE2  in the exosomes  isolated from the BALFs  (E) of the infected mice. Data information: Arrowhead denotes glycosylated ACE2  proteins; asterisk denotes non-glycosylated ACE2  proteins. WT, wild-type mice; KI, hACE2 knockin mice."
NCBI gene IDs:
"ACE2: 59272"
Figure legend: "Wild-type and hACE2 KI mice  were intranasally infected with  SARS-CoV-2 pseudovirus. Exosomes  were isolated sequentially using ExoQuick kits and then ExoQuick ULTRA columns. The hACE2-containing exosomes  in the lung  tissues of wild-type and hACE2 KI mice  were determined by in situ proximity ligation assays (PLA) of close proximity (&lt;40 nm) between hACE2  and the exosome  marker CD9  using anti-human ACE2  antibody plus anti-CD9  antibody (F). Scale bars, 20 μm (F). Data information: WT, wild-type mice; KI, hACE2 knockin mice."
NCBI gene IDs:
"ACE2: 59272"
Figure legend: "Human ACE2  transgenic (EF1α-hACE2 Tg) mice  were intranasally infected with 2x105 pfu of live  SARS-CoV-2. The survival rates  of in EF1α-hACE2 Tg mice  challenged with/without SARS-CoV-2 were monitored (H). Data information: Tg, transgenic mice."
NCBI gene IDs:
"ACE2: 59272
EF1α: 1915"
Figure legend: "Human ACE2  transgenic (EF1α-hACE2 Tg) mice  were intranasally infected with 2x105 pfu of live SARS-CoV-2. The lung  tissues of infected mice  at day 3 days post infection were collected and then analyzed by immunohistochemistry  (IHC) and PLA  assays. Representative IHC  data of hACE2 (in red) and GLK  (in green) in the lung  tissues of the infected wild-type and EF1α-hACE2 Tg mice  were shown (I). Cell nuclei  were stained  with DAPI. Original magnification, ×630. Scale bars, 10 μm. Data information: WT, wild-type mice; Tg, transgenic mice."
NCBI gene IDs:
"ACE2: 59272
EF1α: 1915"
Figure legend: "Human ACE2  transgenic (EF1α-hACE2 Tg) mice  were intranasally infected with 2x105 pfu of live SARS-CoV-2. The hACE2-containing exosomes  in the lung  tissues of infected wild-type and EF1α-hACE2 Tg mice  were determined by PLA  (J). Original magnification, ×630. Scale bars, 10 μm. Data information: WT, wild-type mice; Tg, transgenic mice."
NCBI gene IDs:
"ACE2: 59272
EF1α: 1915"
Figure legend: "K, Adoptive transfer of ACE2-containing exosomes  facilitates SARS-CoV-2 pseudovirus infection. Serum exosomes  (exo) isolated from wild-type (WT) mice  and hACE2 KI/activated GLK   transgenic (PolII-GLK   E351K Tg) mice  were adoptively transferred into wild-type recipient mice  every 3 days for 12 days, followed by SARS-CoV-2 pseudovirus infection. Infection  eﬃciencies into mouse  tissues were measured by IVIS  and presented as luminescence counts at 3 days post infection  (K). Data information: WT, wild-type mice; KI, hACE2 knockin mice. Tg, transgenic mice."
NCBI gene IDs:
"ACE2: 59272
GLK: 8491"
Figure legend: "L Adoptive transfer of ACE2-containing exosomes  facilitates  SARS-CoV-2 pseudovirus infection. Serum exosomes  (exo) isolated from wild-type (WT) mice  and hACE2  KI/activated GLK   transgenic (PolII-GLK   E351K Tg) mice  were adoptively transferred into wild-type recipient mice  every 3 days for 12 days, followed by SARS-CoV-2 pseudovirus infection. hACE2-containing exosomes  in the lung  tissues of exosome-recipient wild-type mice  were determined by PLA  using anti-human ACE2  antibody plus anti-CD9   antibody (L). Scale bars, 10 μm (L). Data information: WT, wild-type mice; KI, hACE2 knockin mice. Tg, transgenic mice."
NCBI gene IDs:
"ACE2: 59272
GLK: 8491"
Figure legend: "(b) in N2 wild type (black diamonds) and ung-1 mutants (red squares), (c) following the depletion of EXO-3 (red triangles), APN-1 (blue circles) or control RNAi (L4440, black diamonds) in the N2 wild-type background, and (d) in msh-2(ok2410) (orange triangles), msh-6(pk2504) (green circles) and mlh-1(ok1917) (grey squares) mutants."
NCBI gene IDs:
"APN-1: 174291
mlh-1: 176783
msh-2: 171938
msh-6: 171914
ung-1: 176633"
Figure legend: "(e) Western blottings showing expression of MSH-6 protein in the wild type strain grown on E. coli expressing control (N2) or the indicated RNAi, as well as in msh-6(pk2504) and msh-2(ok2410) mutants (top panel), and expression of MSH-2::GFP fusion protein in transgenic worms grown on E. coli expressing RNAi for MSH-2, MSH-6 or empty vector control as indicated (lower panel). Actin was used as the loading control."
NCBI gene IDs:
"MSH-2: 171938
msh-2: 171938
msh-6: 171914"
Figure legend: "(f) F1 survival after depletion of MSH-2 and MSH-6 in the mlh-1(ok1917) mutant. (g,h) F1 survival after depletion of the AP endonucleases EXO-3 and APN-1 in (g) the msh-6(pk2504) or (h) msh-2(ok2410) mutant background. Kruskal-Wallis one-way analysis on ranks (P=0.963 and P=0.985 in h and g, respectively). Mann-Whitney rank-sum test failed to identify a difference in median survival after depleting EXO-3 in the msh-6 mutant (g, P=0.929). (i) F1 survival following depletion of the indicated genes in exo-3(tm4374) mutants. (j) F1 survival in msh-6(pk2504), exo-3(tm4374) and exo-3;msh-6 double mutants. (k) F1 survival in exo-3(tm4374), mlh-1(ok1917) and exo-3;mlh-1 double mutants. All survival curves (b-d,f-k) show the mean±s.d. for each data point from three independent experiments."
NCBI gene IDs:
"APN-1: 174291
exo-3: 173069
EXO-3: 173069
mlh-1: 176783
MSH-2: 171938
msh-2: 171938
MSH-6: 171914
msh-6: 171914"
Figure legend: "(c) Quantification of the fraction (%) of 5-FU-treated embryos that contain RPA-1-positive foci in N2, mlh-1(ok1917) and exo-1(tm1842) mutants fed control (L4440) or RNAi targeting APN-1 (apn-1)."
NCBI gene IDs:
"APN-1: 174291
apn-1: 174291
exo-1: 176765
mlh-1: 176783"
Figure legend: "(d) Immunofluorescence showing CHK-1 phosphorylation at Ser139 in response to 5-FU in N2 but not in msh-6(pk2504) mutants or in N2 after apn-1(RNAi) (scale bars, 5 μm). (e) Quantification of the fraction (%) of 5-FU-treated embryos with phospho-CHK-1 foci."
NCBI gene IDs:
"apn-1: 174291
msh-6: 171914"
Figure legend: "(f) Western blottings showing H1X.101 levels in N2 and msh-6 mutants, treated (+) or not (−) with 5-FU. Actin was used as loading control. (g) Quantification of H1X.101 levels relative to actin in control versus 5-FU-treated worms. (b,c,e,g) Bar graphs show the mean±s.d. from three independent experiments."
NCBI gene IDs:
"msh-6: 171914"
Figure legend: "(d) F1 survival measured after depletion of BEC-1 (red triangles) and ATG-7 (blue squares) as compared with worms fed control RNAi (black diamonds). The survival curve shows the mean±s.d. for each data point from three independent experiments."
NCBI gene IDs:
"ATG-7: 834630
BEC-1: 177345"
Figure legend: "(f) Immunofluorescence showing anti-VPS-34 staining in N2 and atl-1(tm853) embryos in the absence or presence of 5-FU (scale bar, 5 μm)."
NCBI gene IDs:
"atl-1: 179352"
Figure legend: "(h) Induction of autophagy (% GFP-positive embryos) in control (GFP::LGG-1) and atm-1(gk186) mutants (atm-1; GFP::LGG-1). (e,g,h) Bar graphs represent mean±s.d. from three independent experiments."
NCBI gene IDs:
"atm-1: 3565793"
Figure legend: "(c) F1 survival after control (black diamonds) or bec-1 RNAi (red squares) in N2 and msh-6(pk2504) mutants. The survival curve shows the mean±s.d. for each data point from three independent experiments."
NCBI gene IDs:
"bec-1: 177345
msh-6: 171914"
Figure legend: "(c) N2 or msh-6(pk2504) embryos were continuously monitored under differential interference contrast microscopy (scale bars, 5 μm) from the three-cell stage until completion of the four-cell stage. Magnified images of representative nuclei are shown. (d) The fraction of embryos with visible, enlarged nucleoli (arrows) after 5-FU treatment was scored. Bar graphs represent mean±s.d. from three independent experiments."
NCBI gene IDs:
"msh-6: 171914"
Figure legend: "e) Western blots showing absence of LC3-II accumulation in U2OS cells transfected with siRNA against MSH-2. The same blot probed with anti-MSH-2 antibodies confirm efficient knockdown. (f) Quantification of LC3-II levels in cells transfected with control or MSH-2 siRNA with or without FU treatment for 24 h."
NCBI gene IDs:
"MSH-2: 4436"
Figure legend: "(g) Immunofluorescence showing reduced accumulation of LC3 puncta in U2OS cells transfected with siRNA against MSH-2. (h) Quantification of LC3-positive puncta in cells treated as in g."
NCBI gene IDs:
"MSH-2: 4436"
Figure legend: "(i) Quantification of normalized RPS3 protein level (black bars) or RPS3 mRNA level (white bars) in U2OS cells after 48 h 5-FU treatment. RPS3 mRNA levels were determined by quantitative real-time reverse transcriptase-PCR."
NCBI gene IDs:
"RPS3: 6188"
Figure legend: "Quantitative RT-PCR showing the mRNA expression levels of IL-1β, IL-18, ASC, CASP1 and NLRP3 in MDMs treated with P22077 (2.5 µM) and/or LPS (1 μg/mL; 4 hrs.), as indicated. Bars represent the mean fold increase from an untreated (UT) control"
NCBI gene IDs:
"ASC: 51008
CASP1: 834
IL-18: 3606
IL-1β: 3553
NLRP3: 114548"
Figure legend: "Western blots of supernatants and cell lysates from THP-1 cells engineered by CRISPR/Cas9 to induce USP7 and/or USP47 KOs. Deficiency of both USP7 and USP47 was induced by doxycycline (Doxy) treatment (1 µg/mL; 3 days), as indicated. All cells were differentiated with PMA and either unprimed or LPS-primed (1 μg/mL, 4 hrs.) and treated with nigericin (10 μM, 45 mins.), as indicated. Bands in the figure represent: Pro-IL-1β (31 kDa); mature IL-1β (mIL-1β, 17 kDa); pro-caspase-1 (pro-Casp-1; 45 kDa); mature caspase-1 (mCasp-1; 20 kDa); USP7 and USP47. β-actin is shown as a loading control. Blots are representative of at least 3 independent experiments."
NCBI gene IDs:
"Cas9: 
CRISPR: 
USP47: 55031
USP7: 7874"
Figure legend: "Western blot analysis of MsrB2 and LC3 I/II in Meg-01 cell after shMsrB2 transfection (72 hrs). Cells were then treated with H2O2 (1 mM for 1 hr) alone or with NAC (100 μM for 30 min). GAPDH was used as the loading control. Quantification and analysis of individual groups. GAPDH served as the loading control. (shMsrB2 vs. shCon; *p=0.024, shMsrB2/H2O2 vs. shCon/H2O2; *p=0.0295, shMsrB2/H2O2/NAC vs. shCon/H2O2/NAC **p=0.0100, n=3)"
NCBI gene IDs:
"MsrB2: 22921"
Figure legend: "Western blot analysis of MsrB2, pp53(S15) and LC3 I/II in Meg-01 cell after 25 mM HG treatment for 24 hrs. GAPDH was used as the loading control. Quantification analysis on individual groups. GAPDH served as the loading control. (MsrB2: shCon/HG vs. shCon; **p=0.0017, shMsrB2/HG vs. shCon/HG; *p=0.0189, pp53: shMsrB2/HG vs. shCon/HG; *p=0.0317, LC3II: shCon/HG vs. shCon; *p=0.0215, shMsrB2/HG vs. shCon/HG; *p=0.0158, n=3) The nonparametric t test was performed for comparisons of 2 groups. Analysis was performed with Prism software (GraphPad Software, Inc, La Jolla, CA). A difference of P&lt;0.05 was considered significant."
NCBI gene IDs:
"MsrB2: 22921"
Figure legend: "Levels of reactive oxygen species (ROS) quantified in the platelets using the fluorescent dye DCFH-DA. (ROS; *p=0.0139, MsrB2 fl/fl n=5, MsrB2 -/- n=6)"
NCBI gene IDs:
"MsrB2: 76467"
Figure legend: "C. Representative image and quantification of mitochondrial apoptosis, measured in freshly isolated platelets from the MsrB2 knockouts and age matched floxed mice. Results are expressed as % apoptotic cells. (TMRE; *p=0.0118, MsrB2 fl/fl n=5, MsrB2 -/- n=5)"
NCBI gene IDs:
"MsrB2: 76467"
Figure legend: "MsrB2 ubiquitination assay after transient transfection of MsrB2-GFP (1µg) with RFP empty vector (E.V.) or RFP-Parkin (3µg) in HEK293. After transfection (48hrs), an IP was performed using GFP-Trap bead, followed by Western blot analysis using UB and MsrB2 and Parkin antibodies. The nonparametric t test was performed for comparisons of 2 groups. Analysis was performed with Prism software (GraphPad Software, Inc, La Jolla, CA). A difference of P&lt;0.05 was considered significant."
NCBI gene IDs:
"GFP: 
RFP: 
MsrB2: 22921
Parkin: 5071"
Figure legend: "F. Multiplex in situ RNA hybridization  of ACE2 and SARS-CoV-2 of mock-infected and  infected 2D ileum organoids at 12 hpi  and 24 hpi. White arrows point at SARS-CoV-2-infected cells. A representative image is shown."
NCBI gene IDs:
"ACE2: 59272"
Figure legend: "A. Human ileum-derived organoids were seeded in 2D on iBIDi chamber slides. 12 and 24 hpi cells were fixed and the amount of SARS-CoV-2 infected cells (red) and the induction of ISG15 (white) was analyzed by single molecule RNA FISH. Nuclei were visualized with DAPI  (blue). White arrows indicate SARS-CoV-2 positive cells. N=3 biological samples. Representative  image is shown. Scale bar=100 um."
NCBI gene IDs:
"ISG15: 9636"
Figure legend: "D.  T84 IRF3 knock-out cells were infected with SARS-CoV-2 or  human astrovirus 1 at an MOI=3. 24 hpi, cells were incubated in the presence or absence of 2000 IU/mL of  IFNβ1. 12 h post-treatment RNA was harvested and the induction of ISG15 was analyzed by q-RT-PCR and normalized to the housekeeping gene TBP. N=3 biological replicates. Error bar indicates standard deviation. Statistics were determined by unpaired t-test."
NCBI gene IDs:
"IRF3: 3661
ISG15: 9636
TBP: 6908"
Figure legend: "E. T84 IRF3 knock-out cells were infected with SARS-CoV-2 or  human astrovirus 1  at an MOI=3. 24 hpi, cells were fixed and stained for either the SARS-CoV-2 N protein or for human astrovirus 1 (HAstV1) capsid protein. N=3 biological replicates. Representative image is shown. Scale bar=100 um."
NCBI gene IDs:
"IRF3: 3661"
Figure legend: "G. T84 MX-1 mcherry were  infected with SARS-CoV-2 at an MOI=3 or MOI=1. 24 hpi cells were incubated in the presence or absence of 2000 IU/mL of IFNβ1. 12 h post-treatment cells were fixed and stained  for SARS-CoV-2 N protein. The number of MX-1 positive, SARS-CoV-2  positive and double positive cells was quantified. N=3 biological replicates were performed. Error bar indicates standard deviation."
NCBI gene IDs:
"mcherry: 
MX-1: 4599"
Figure legend: "Immunoblot analysis of LC3B and GABARAP lipidation in wild-type (WT) and ATG16L1-KO HEK293A cells, with or without stimulation for 2h as indicated. BafA1 stands for Bafilomycin A1. Gamma-Tubulin (γ-Tubulin) is loading control. Densitometry analysis of lipidated LC3B (LC3B-II) to γ-tubulin (normalized to untreated WT cells) from immunoblots in (A). Data information: All data presented as mean + SEM, from n = 3 independent experiments. P-value determined using two-way ANOVA followed by Tukey's multiple comparisons test; ns= not significant."
NCBI gene IDs:
"ATG16L1: 55054"