EMBO/SourceData huggingface dataset:
Figure legend: "(K) qRT-PCR detection of MMP transcripts including Mmp9, Mmp10, and Mmp12  in shCtrl and shGalectin-9 THP-1  cells stimulated with AG (1 μg/ml) for 24 h in absence or presence of ERK inhibitor PD98059 (10 μM). Data information: Data are means + SD averaged from 3 independent experiments performed with technical triplicates and each symbol represents the mean of technical triplicates. Two-way ANOVA followed by Dunnett's post hoc test were used for statistical analysis. ns, not significant; *, p&lt;0.05; ***, p&lt;0.001 ****, p&lt;0.0001."
NCBI gene IDs:
"Galectin-9: 3965
Mmp10: 4319
Mmp12: 4321
Mmp9: 4318"
Figure legend: "(F) Immunoblots of cell lysates of peritoneal macrophages isolated from WT or Galectin-9 KO mice stimulated with AG (1 μg/ml) in absence or presence of  TAK1 inhibitor 5Z-7-OZ (1 μM) for indicated  times. Data are representative of n=3 independent experiments."
NCBI gene IDs:
"Galectin-9: 16859"
Figure legend: "(B, WT or Galectin-9 KO mice were intraperitoneally treated with AG for 3 d in the absence or presence of the MMP inhibitor marimastat (10 mg/kg) given  intraperitoneally prior to AG  stimulation.  Lung sections  stained with H&amp;E Data information: Data are representative of n=3 independent experiments."
NCBI gene IDs:
"Galectin-9: 16859"
Figure legend: "(D, WT or Galectin-9 KO mice were intranasally infected with  H37Rv for 4 weeks in absence or presence of intranasally administrated AG aptamers (1 μg) once at a 1 week-interval. Lung sections stained with H&amp;E Data information: Data are representative of n=3 independent experiments."
NCBI gene IDs:
"Galectin-9: 16859"
Figure legend: "Cells were infected at the indicated multiplicity of infection (MOI) and analyzed after 20h. A. TMPRSS2 increases fusion and cell mortality. Right panel: Areas of GFP+ cells and PI+ cells"
NCBI gene IDs:
"TMPRSS2: 7113"
Figure legend: "Cells were infected at the indicated multiplicity of infection (MOI) and analyzed after 20h. B. IFITM1, but not IFITM2 and 3, inhibits SARS-CoV-2-induced syncytia formation. Right panels: Area of GFP+ cells"
NCBI gene IDs:
"IFITM1: 8519
IFITM2: 10581"
Figure legend: "Cells were infected at the indicated multiplicity of infection (MOI) and analyzed after 20h. D. IFITM1 decreases the number of infected cells. Right panel: Fraction of cells positive for S, normalized to control cells (transduced with pQCXIP-empty vector )."
NCBI gene IDs:
"IFITM1: 8519"
Figure legend: "D. TMPRSS2 accelerates fusion. Cells were monitored by video microscopy and the GFP area was quantified over time. Left panel: one representative experiment. Results are mean±sd from 3 fields per condition. Right panel: Mean±sd from 7 independent experiments (at 12h post transfection)."
NCBI gene IDs:
"TMPRSS2: 7113"
Figure legend: "E. Impact of TMPRSS2 and IFITMs on the kinetics of fusion by S-expressing 293T cells. One representative out of three independent experiment is shown."
NCBI gene IDs:
"TMPRSS2: 7113"
Figure legend: "A. S-expressing cells (Donor cells), ACE2-expressing cells (Acceptor cells) were co-transfected with TMPRSS2, IFITM or control plasmids. Cell fusion was quantified by measuring the GFP+ area after 18h. The indicated combinations were tested. The impact of IFITMs was measured in absence of TMPRSS2 (left panel), in presence of TMPRSS2 in donor (middle panel) or acceptor cells (right panel). Data are mean±sd of 4 independent experiments. Statistical analysis: One-Way ANOVA, ns: non-significant, ∗∗p &lt; 0.01, ∗∗∗∗p &lt; 0.0001."
NCBI gene IDs:
"TMPRSS2: 7113"
Figure legend: "Impact of TMPRSS2 on IFITMs levels. B. TMPRSS2 does not decrease IFITM amounts measured by flow cytometry. 293T cells were transfected with the indicated IFITM plasmids, with or without TMPRSS2, and analyzed 18h later."
NCBI gene IDs:
"TMPRSS2: 7113"
Figure legend: "C. Impact of TMPRSS2 on S and ACE2, measured by Western Blot. 293T cells were transfected with or without IFITM1, TMPRSS2, S or ACE2 plasmids, and analyzed 18h later."
NCBI gene IDs:
"ACE2: 59272
IFITM1: 8519
TMPRSS2: 7113"
Figure legend: "Impact of TMPRSS2 on S levels. D. TMPRSS2 decreases S surface levels, measured by flow cytometry. 293T cells were transfected with S plasmid, with or without TMPRSS2, and analyzed 18h later. Murine polyclonal anti-S antibodies, one serum from a convalescent COVID-19 patient (sera n°111), and two monoclonal antibodies (anti-S1 and anti-S2) were tested. Data are representative of three independent experiments."
NCBI gene IDs:
"TMPRSS2: 7113"
Figure legend: "I) Quantification of Northern Blot  results. Normalised to GAPDH, n=3, error bars are standard error of the mean. Asterix indicates p-value (*, p&lt;0.05, based on unpaired, 2-tailed t-test)."
NCBI gene IDs:
"GAPDH: "
Figure legend: "G. IncuCyte live-imaging analysis of WT and Casp11-/- BMDM viability  after infection with  M. catarrhalis as in D, or transfection with LPS. Data information: Data are pooled from two (G) independent experiments mean and s.e.m. in G)."
NCBI gene IDs:
"Casp11: 12363"
Figure legend: "A. Immunoblot  analysis of caspase-1 (Casp-1),  caspase-11 (Casp-11) and  gasdermin D (GSDMD) in WT, Nlrp3-/-, Casp11-/- and Aim2-/- BMDMs  left untreated (Med.) or 5 h after transfection with 5 µg of LOS  from M. catarrhalis (O35E) or 5 µg of LPS  from  E. coli. Data information: Data are from three independent experiments (A,"
NCBI gene IDs:
"Aim2: 383619
Casp11: 12363
Nlrp3: 216799"
Figure legend: "F. Transcript abundance for genes encoding GTPases in WT and Ifnar1-/- BMDMs  infected with M. catarrhalis  as in C. Transcript abundance is provided in counts per million (CPM). Data information: Data are pooled from three independent experiments"
NCBI gene IDs:
"Ifnar1: 15975"
Figure legend: "G.  qRT-PCR analysis of genes encoding the family of guanylate binding proteins (GBP1-11) in WT and Ifnar1-/- BMDMs  left untreated (Med.) or following treated as in C. Data information: Each symbol represents an independent biological replicate G). NS, no statistical significance; ** P&lt;0.01; *** P&lt;0.001; **** P&lt;0.0001 (one-way ANOVA with Dunnett's multiple-comparisons test G)). Data are from one experiment representative of four (G) independent experiments (mean and s.e.m. in G)."
NCBI gene IDs:
"GBP1: 14468
Ifnar1: 15975"
Figure legend: "F. Recovery of M. catarrhalis (as colony-forming units (CFU) from primary WT, Gbpchr3-KO and Ifnar1-/- lung fibroblasts  4, 8 and 12 h after infection  with M. catarrhalis (Ne11, MOI 100). Data information: Each symbol represents an independent biological replicate F). NS, no statistical significance; * P&lt;0.05; ** P&lt;0.01; *** P&lt;0.001; **** P&lt;0.0001 (one-way ANOVA with Dunnett's multiple-comparisons test Data are from three independent experiments F; mean and s.e.m."
NCBI gene IDs:
"Gbp: 229900///55932///14468///229898///14469
Ifnar1: 15975"
Figure legend: "G. Quantitation of intracellular bacteria by Transmission electron microscopy (TEM) in WT, Gbpchr3-KO and Ifnar1-/- BMDMs  infected with M. catarrhalis (Ne11, MOI 50) for 12 h. Each symbol represents an independent experiment (E and F). Data information: A total of 100 BMDMs  were analysed to quantify the intracellular  bacterial burden  using electron microscopy  (G). Data are from one experiment representative of two (G) independent experiments mean and s.e.m."
NCBI gene IDs:
"Gbp: 229900///55932///14468///229898///14469
Ifnar1: 15975"
Figure legend: "A. Immunoblot  analysis of caspase-1  (Casp-1), caspase-11 (Casp-11) and gasdermin D (GSDMD) in WT, Gbp1-/-, Gbp2-/-, Gbp3-/-, Gbp5-/-, Gbp7-/-, Gbp4/8/9-/-, Gbp11­­-/- and Casp11-/- BMDMs  left untreated (Med.) or assessed 10 h after infection with M. catarrhalis (Ne11, MOI 100), or 5 h after transfection with 5 µg LPS  from E. coli."
NCBI gene IDs:
"Casp11: 12363
Gbp11: 634650
Gbp2: 14469
Gbp1: 14468
Gbp3: 55932
Gbp4: 17472
Gbp5: 229898
Gbp7: 229900"
Figure legend: "A, B. Bacterial burden  and concentration of IL-18 in the spleen  of WT mice  (n=10) and Casp11-/- mice  (n=10) after M. catarrhalis infection. C, D. Bacterial burden and concentration of  IL-18 in the spleen  of WT mice  (n=10) and Nlrp3-/- mice  (n=11) after  M. catarrhalis infection. E, F.  Bacterial burden  and concentration of  IL-18 in the spleen  of WT mice  (n=10) and Gbp1-/- mice  (n=9) after  M. catarrhalis infection. G, H. Bacterial burden and concentration of IL-18 in the spleen  of WT mice  (n=10) and Gbp2-/- mice  (n=8) after M. catarrhalis infection. I, J.  Bacterial burden and concentration of  IL-18 in the spleen  of WT mice  (n=10) and Gbp3-/- mice  (n=8) after  M. catarrhalis infection. K, L. Bacterial burden and concentration of IL-18 in the spleen  of WT mice  (n=5) and Gbp5-/- mice  (n=8) after M. catarrhalis infection. Data information: A mix of male  and female mice  6-8 weeks old were used in each experiment and were injected i.p. with 2×107 CFU  of M. catarrhalis and analysed after 6 h. Each symbol represents an individual mouse  (A-L). Each panel represents data from a single experiment (mean and s.e.m. in A-L). Each experiment was performed at least two times. * P&lt;0.05; ** P&lt;0.01; *** P&lt;0.001 (two-tailed t-test (A-L))."
NCBI gene IDs:
"Casp11: 12363
Gbp2: 14469
Gbp1: 14468
Gbp3: 55932
Gbp5: 229898
Nlrp3: 216799"
Figure legend: "(A) Vero GFP-split cells were transfected with variant S proteins and imaged 18h post-transfection. Left Panel: Fusion was quantified by GFP area/ number of nuclei and normalized to D614G for each of the transfected variant S proteins. Right Panel: Representative images of Vero GFP-split cells 18h post-transfection, GFP (Green) and Hoechst (Blue). Top and bottom are the same images with and without Hoechst channel. Scale bars: 200 µm."
NCBI gene IDs:
"S proteins: 43740568"
Figure legend: "(D) Caco2 GFP-split cells were transfected with variant S proteins and imaged 18h post-transfection. Left Panel: Fusion was quantified by GFP area/ number of nuclei and normalized to D614G for each of the transfected variant S proteins. Right Panel: Representative images of Caco2 GFP-split cells 18h post-transfection, GFP (Green) and Hoechst (Blue). Top and bottom are the same images with and without Hoechst channel. Scale bars: 200 µm"
NCBI gene IDs:
"S proteins: 43740568"
Figure legend: "Representative H&amp;E (top) and immunofluorescent (IF) images (bottom) of control and Lats1/2 dKO airways at indicated time points post tamoxifen treatment. Tomato (for Scgb1a1 lineage, red), CC10 (for secretory cell, white), Acetylated tubulin (Act-Tub, for ciliated cell, green), and DAPI (blue). Scale bar, 100μm. Statistical quantification of Scgb1a1 lineage-labeled tdTomato+CC10+ secretory cells in (B)."
NCBI gene IDs:
"Lats1: 16798"
Figure legend: "Representative IF images of control and Lats1/2 dKO airways at indicated time points post tamoxifen treatment. Tomato (for Scgb1a1 lineage, red), CC10 (green), AQP5 (for AT1 cell, white), and DAPI (blue). Scale bar, 100μm. Quantification of Scgb1a1 lineage-labeled tdTomato+AQP5+ AT1 cells in (D). Data are presented as mean ± SEM (n=5 mice for each group)."
NCBI gene IDs:
"Lats1: 16798"
Figure legend: "Representative IF images of control and Lats1/2 dKO airways at indicated time points post tamoxifen treatment. Tomato (for Scgb1a1 lineage, red), CLDN4 (for DATPs, white), CC10 (G, green), AGER (H, for AT1 cell, green), and DAPI (blue). Quantification of Scgb1a1 lineage-labeled tdTomato+CLDN4+ DATPs in (G and H). Data are presented as mean ± SEM (n=5 mice for each genotype)."
NCBI gene IDs:
"Lats1: 16798"
Figure legend: "Representative H&amp;E and IF images of control, Lats1/2 dKO, and Raptor;Lats1/2 tKO airways at day 21 post tamoxifen treatment. Tomato (for Scgb1a1 lineage, red), CC10 (green, upper), AGER (green, lower), and DAPI (blue). Scale bar, 100μm."
NCBI gene IDs:
"Lats1: 16798
Raptor: 74370"
Figure legend: "Measurement of L-amino acid or essential amino acids (leucine, isoleucine, valine) contents in Scgb1a1 lineage-labeled tdTomato+ organoids derived from control, Lats1/2 dKO or Raptor;Lats1/2 tKO mice. Data are presented as mean ± SEM (n=3 technical replicates for each genotype). *p&lt;0.05, **p&lt;0.001 (Student's t-test)."
NCBI gene IDs:
"Lats1: 16798
Raptor: 74370
Scgb1a1: 22287"
Figure legend: "Western blot images for the expression of YAP, ATF4, and LAT1/Slc7a5 in control or YAP5SA overexpressed C22 airway epithelial cell line. Knockdown of ATF4 was induced by using lentiviral-mediated inducible scramble shRNA (shScramble, control) or shATF4."
NCBI gene IDs:
"ATF4: 11911
YAP5SA: 22601"
Figure legend: "Representative H&amp;E images and IF images showing the expression of secretory cell marker CC10, DATP cell marker CLDN4, and AT1 cell marker CAV1 in organoids derived from Lats1/2 dKO secretory cells with shscramble, shAtf4, or shSlc7a5. CC10 (green), CLDN4 (white), CAV1 (white) and DAPI (blue). Quantification of Scgb1a1+ lineage-labeled tdTomato+CC10+ secretory cells (red), tdTomato+CLDN4+ DATP cells (green), and tdTomato+CAV1+ AT1 cells (blue) in (E). Representative H&amp;E images and IF images showing the expression of secretory cell marker CC10, DATP cell marker CLDN4, or AT1 cell marker CAV1 in organoids derived from Scgb1a1 lineage-labeled secretory cells with or without hydroxytamoxifen-induced ATF4 overexpression. CC10 (green), CLDN4 (white), CAV1 (white), and DAPI (blue). Quantification of Scgb1a1 lineage-labeled tdTomato+CC10+ secretory cells (red), tdTomato+CLDN4+ DATP cells (green), and tdTomato+CAV1+ AT1 cells (blue) in (G)."
NCBI gene IDs:
"Atf4: 11911
ATF4: 11911
Lats1: 16798
Slc7a5: 20539"
Figure legend: "(B) Gpr56 transcript levels in isolated microglia from Gpr56 S4 mice."
NCBI gene IDs:
"Gpr56: 14766"
Figure legend: "(D) Representative images of Nissl staining of Gpr56 null and Gpr56 S4 E16.5 neocortex. Arrows indicate cortical ectopias that are shown in insets. (E) Quantification of ectopia size per section. (F) The distribution of ectopia from rostral to caudal cortex."
NCBI gene IDs:
"Gpr56: 14766"
Figure legend: "(G). Myelin basic protein (MBP) staining of corpus callosum in P28 controls, Gpr56 null and Gpr56 S4 mice."
NCBI gene IDs:
"Gpr56: 14766"
Figure legend: "(I) Gpr56 transcript levels in WT microglia at P5 and P14."
NCBI gene IDs:
"Gpr56: 14766"
Figure legend: "K) Representative images of vGlut2/Homer1 staining in the dLGN of control, Gpr56 null, and Gpr56 S4 brains at P10. Arrows pointing to the enlarged synapse in the insets. L) Relative vGlut2/Homer1 synapse density in dLGN. N=10 (Ctrl), N=6 (Gpr56 null), N=3 (Gpr56 S4)."
NCBI gene IDs:
"Gpr56: 14766"
Figure legend: "(N) Representative images and surface rendered microglia (green) in which CTB+(red) RGC inputs were engulfed. (O) Quantification of the percentage of engulfed RGC inputs in controls, Gpr56 null and Gpr56 S4 microglia."
NCBI gene IDs:
"Gpr56: 14766"
Figure legend: "(A) Gpr56 is deleted in CKO microglia. RNAscope shows Gpr56 transcripts co-localize with microglia (arrow) in controls, but not in CKO, and is absent in all cell types in the global Gpr56 KO (Gpr56 null). Arrowhead indicates non-microglia cells expressing Gpr56. RNAscope was performed in the prefrontal cortex of P30 mice. Scale bar, 20 µm. (B) Quantification of Gpr56 fluorescence signals in (A). N = 20-50 cells for each. "
NCBI gene IDs:
"Gpr56: 14766"
Figure legend: "(G) Baf A1 sensitivity assay for NDST3  KO cells after the NDST3 restoration. The NDST3  KO cells with stable expression of Flag-NDST3 or Flag-EGFP (control) were treated with 25 nM  Baf A1 for 72 h, and cell survival was measured using  calcein AM staining. The cell survival  was calculated as the fluorescence intensity of the treated cells relative to the untreated cells (n = 4 independent cultures, ****P &lt; 0.0001). Data information: Error bars represent ± standard deviation. Scale bar, 200 μm. "
NCBI gene IDs:
"EGFP: 
Flag: 
NDST3: 9348"
Figure legend: "(C) Lysosomal pH  values in WT and NDST3  KO RPE1  cells calculated from the fluorescence ratio of LysoSensor Yellow/Blue dextran staining against the pH calibration curve in (B) (n = 3 independent cultures, *P = 0.0242). (D) Lysosomal  pH values measured for WT and NDST3 KO  RPE1 cells after the treatment with Baf A1  (100 nM, 1h) (n = 3 independent cultures, *P = 0.0305). Data information: Error bars represent ± standard deviation. Scale bar, 10 μm."
NCBI gene IDs:
"NDST3: 9348"
Figure legend: "(F) Magic Red assay for Cat B proteolytic activity. WT and NDST3 KO RPE1 cells were treated with vehicle (VEH) or Baf A1 (100 nM, 1 h) and then stained with MR-(RR)2 to measure the Cathepsin B activity (n = 48 cells in the VEH-treated WT group, n = 37 cells in the VEH-treated NDST3 KO group, n = 64 cells in the Baf A1-treated WT group, n = 42 cells in the Baf A1-treated NDST3  KO group, ****P &lt; 0.0001)."
NCBI gene IDs:
"NDST3: 9348"
Figure legend: "(G) Alexa Fluor (AF) 488-dextran degradation assay. WT and NDST3 KO  RPE1 cells were loaded with AF488-dextran in culture medium and observed for fluorescence. The AF488  fluorescence signals without a chase period, with a 4-h chase period, and with the 4-h chase period in the presence of Baf A1 (100 nM, 1h) were recorded as fluorescence of uptake, chase, and chase with Baf A1, respectively. The AF488 intensity per cell was quantified and calculated into  degradation percentage according to the equation in Materials and Methods (n = 62 cells in the VEH-treated WT group, n = 36 cells in the VEH-treated  NDST3  KO group, n = 65 cells in the Baf A1-treated WT group, n = 78 cells in the Baf A1-treated NDST3 KO group, ****P &lt; 0.0001)."
NCBI gene IDs:
"NDST3: 9348"
Figure legend: "(J) The LC3  turnover assay after a 48-h Baf A1 treatment. WT and NDST3 KO  RPE1 cells were cultured with 25 nM Baf A1 for 48 h and analyzed for the LC3B-II  fold change as in (I) (n = 6 independent experiments, **P = 0.0014). Data information: Error bars represent ± standard deviation. Scale bar, 10 μm. "
NCBI gene IDs:
"NDST3: 9348"
Figure legend: "(A) To examine the levels of the V-ATPase V1-V0 holoenzyme in WT and NDST3 KO RPE1  cells, cytosolic and membrane fractions were analyzed by immunoblotting  using antibodies against the V-ATPase subunits V1A (ATP6V1A), V1C1 (ATP6V1C1), and V0D (ATP6V0D). LAMP1 and vinculin were used as loading controls for membrane proteins and cytosolic  proteins, respectively. (B) Quantification of the levels of ATP6V0D relative to LAMP1 in the  membrane fraction from (A) (n = 3 independent experiments, P = 0.7786). Data information: Error bars represent ± standard deviation."
NCBI gene IDs:
"NDST3: 9348"
Figure legend: "The assembly of V-ATPase V1-V0 holoenzymes in WT RPE1 cells over-expressing the  α-tubulin deacetylase HDAC6 or EGFP  as a control. Representative  immunoblots for ATP6V0D, ATP6V1A, ATP6V1C1, LAMP1 and GAPDH are shown in (H)."
NCBI gene IDs:
"EGFP: 
HDAC6: 10013"
Figure legend: "(M-O) Loss of  NDST3 enhances microtubule acetylation and the colocalization of the  lysosomes with V-ATPase V1 subunits. WT and NDST3  KO PRE1 cells stably expressing  LAMP1-GFP were fixed and analyzed by  immunofluorescence staining with antibodies against ATP6V1C1 and Ac-α-tubulin. The relative levels of Ac-α-tubulin (N) (n = 75 cells in the WT group, n = 79 cells in the  NDST3 KO group, ****P &lt; 0.0001) and the colocalization of LAMP1-GFP  with  ATP6V1C1 (O) (n = 75 cells in the WT group, n = 79 cells in the NDST3 KO group, ****P &lt; 0.0001) are quantified."
NCBI gene IDs:
"NDST3: 9348"
Figure legend: "(C) In vitro enzymatic assay quantitating the effect of NDST3 on α-tubulin acetylation. Flag-NDST3 was expressed in HEK 293 cells and immunoprecipitated by anti-Flag beads. Flag-EGFP was used as a control. The immunoprecipitated  protein was incubated with purified tubulin heterodimers in vitro, with or without 1 mM NAD+, 400 nM TSA, or 5 mM nicotinamide (NAM) for 2 h at room temperature. The reaction products were examined by  immunoblotting against  Ac-α-tubulin or total α-tubulin (n = 3 independent experiments, *P = 0.0185, **P &lt; 0.01, ****P &lt; 0.0001). (D) The same in vitro enzymatic assay as in (C), except that the purified  tubulin  was polymerized in the presence of 20 μM Taxol  and 1 mM GTP (n = 3 independent experiments, **P &lt; 0.01, ***P = 0.0001). Data information: Error bars represent ± standard deviation. ns means non-significant. "
NCBI gene IDs:
"Flag: 
NDST3: 9348"
Figure legend: "(A, B) NDST3 protein levels relative to β-tubulin in B lymphocytes derived from healthy controls and C9orf72-linked ALS patients, as examined by immunoblotting  (n = 3 biologically independent samples, **P = 0.0026). Data information: Error bars represent ± standard deviation."
NCBI gene IDs:
"C9orf72: 203228"
Figure legend: "(C-F) The protein levels of NDST3 relative to GAPDH (D) (**P = 0.0013), Ac-α-tubulin relative to total α-tubulin (E) (*P = 0.0379), and total α-tubulin relative to GAPDH (F) (P = 0.5700), as examined by immunoblotting, in spinal cord tissues from healthy controls and C9orf72-linked ALS patients (n = 4 biologically independent samples in the control group and n = 5 biologically independent samples in the  ALS patient group). Data information: Error bars represent ± standard deviation."
NCBI gene IDs:
"C9orf72: 203228"
Figure legend: "(G-I) Immunoblotting assays showing down-regulation of NDST3 in C9orf72 shRNA (shC9orf72)-treated RPE1  cells, as compared to control shRNA (shCTRL)-treated cells. Quantification of C9orf72  and  NDST3 expression relative to  GAPDH is shown in (H) (n = 4 independent experiments, ***P = 0.0004) and (I) (n = 4 independent experiments, ***P = 0.0001), respectively. (J-L) Immunoblotting assays showing up-regulation of NDST3 in  RPE1 cells over-expressing Flag-C9orf72 compared to those expressing Flag-EGFP as control. Quantification of C9orf72  and NDST3 expression  relative to GAPDH is shown in (K) (n = 3 independent experiments, **P = 0.0011) and (L) (n = 3 independent experiments, **P = 0.0033), respectively. Data information: Error bars represent ± standard deviation."
NCBI gene IDs:
"EGFP: 
Flag: 
C9orf72: 203228"
Figure legend: "(M, N) Baf A1 sensitivity assay for WT,  NDST3 KO, and Noco-treated NDST3 KO  RPE1 cells expressing proline-arginine poly-dipeptide (PR82). 24 h after the transfection of  PR82, WT and NDST3  KO cells were treated with vehicle or 10 μg/mL Noco overnight. The cell survival measured using calcein AM staining at 48 h post-transfection was quantified as the percentage of the fluorescence intensity for treated cells relative to that of untreated cells (n = 3 independent cultures, *P = 0.0369, ***P = 0.0007). Scale bar, 200 μm. Data information: Error bars represent ± standard deviation."
NCBI gene IDs:
"NDST3: 9348"
Figure legend: "(D) LCL1.11 cells were transfected with siRNA specific for Atg12 or GFP, and Atg12 mRNA levels were determined 24 h later by qPCR. The relative amount of Atg12 mRNA was reduced approximately fourfold."
NCBI gene IDs:
"GFP: 
Atg12: 9140"
Figure legend: "(E) At 24 h after siRNA transfection, NeoR and NucNeoR were expressed in these cells and antigen presentation was assessed 36 h later. In cells transfected with Atg12 siRNA, but not in mock‐transfected cells or cells transfected with GFP siRNA, antigen presentation of both NeoR and NucNeoR was greatly reduced."
NCBI gene IDs:
"GFP: 
Atg12: 9140"
Figure legend: "(D) YFP-LC3 and mCherry-Parkin stably expressing TBC1D15−/− cells in the absence or presence of HA-tagged TBC1D15 WT or Δ221-250 mutant were treated with valinomycin for 3 hr. Cells were subjected to immunofluorescence microscopy with anti-HA antibody. Scale bars, 10 μm. (E) The YFP-LC3 morphology of cells in (D) was quantified. The error bars represent ±SD from three independent replicates. Over 50 cells were counted in each well."
NCBI gene IDs:
"TBC1D15: 64786"
Figure legend: "(F and G) YFP-LC3 and mCherry-Parkin stably expressing WT (F) and TBC1D15−/− (G) cells were treated with valinomycin for 3 hr and then subjected to immunoelectron microscopy with anti-GFP antibody. The square in panel a shows enlarged areas in panel b Scale bars, 500 nm."
NCBI gene IDs:
"TBC1D15: 64786"