EMBO/SourceData huggingface dataset:
Figure legend: "(A) Acyl-RAC assay  of HEK293T  cells transfected with Flag-cGAS  24 h after transfection with the indicated shRNA. (B) Quantification of palmitoylation  levels of Flag-cGAS  in (A). Data information:"
NCBI gene IDs:
"Flag: 
cGAS: 115004"
Figure legend: "(D) HEK293T  cells were transfected with HA-cGAS  (WT or C474S mutant) (200 ng), Flag-STING  (200 ng) and Myc-ZDHHC18  (200 ng) expression plasmids for 24 h before  luciferase reporter assays. Data information: Data are representative of at least two independent experiments. Mean ± SEM from triplicates of technical replicates, unpaired t test; **, P˂0.005; ***, P˂0.001 (D"
NCBI gene IDs:
"Flag: 
HA: 
Myc: 
cGAS: 115004
STING: 340061
ZDHHC18: 84243"
Figure legend: "(H) Immunoprecipitation  (with an anti-Flag  antibody) and immunoblot  analysis of HEK293T  cells transfected with plasmids encoding HA-cGAS  and Flag-ZDHHC18  truncations or GFP  for 24 h. Data information: WCL: whole-cell lysate; IP: immunoprecipitation; FL: full length"
NCBI gene IDs:
"Flag: 
GFP: 
HA: 
cGAS: 115004
ZDHHC18: 84243"
Figure legend: "(J) Immunoprecipitation  (with an anti-Flag  antibody) and immunoblot  analysis of HEK293T  cells transfected with plasmids encoding HA-ZDHHC18  and Flag-cGAS truncates or GFP  for 24 h. Data information: WCL: whole-cell lysate"
NCBI gene IDs:
"Flag: 
GFP: 
HA: 
cGAS: 115004
ZDHHC18: 84243"
Figure legend: "(H)  Confocal microscopy of BMDMs  (Zdhhc18+/+ or Zdhhc18−/−) transfected with FITC-conjugated ISD  for 6 h (left). Scale bar: 20 μm."
NCBI gene IDs:
"Zdhhc18: 503610"
Figure legend: "(D) Immunoprecipitation  (with an anti-Flag  antibody) and immunoblot  analysis of HEK293T  cells transfected with plasmids encoding Flag-cGAS, HA-cGAS, and Myc-ZDHHC18  (WT or CS mutant) for 24 h. Data information: WCL: whole-cell lysate; IP: immunoprecipitation; Data are representative of at least two independent experiments."
NCBI gene IDs:
"Flag: 
HA: 
Myc: 
cGAS: 115004
ZDHHC18: 84243"
Figure legend: "(H) Immunoprecipitation  (with an anti-Flag  antibody) and immunoblot  analysis of HEK293T  cells transfected with Flag-cGAS  and HA-cGAS   (WT, C405S, C409S and C474S) expression plasmids. Data information: WCL: whole-cell lysate; IP: immunoprecipitation  Data are representative of at least two independent experiments."
NCBI gene IDs:
"Flag: 
cGAS: 115004"
Figure legend: "(A) HEK293T  cells (5×105) were transfected with HA-cGAS  (200 ng), Flag-STING  (200 ng) and Myc-ZDHHC18  (WT or CS mutant) expression plasmids (0, 50, 100, or 200 ng) for 24 h before  luciferase reporter assays were conducted. Data information: ZDHHC18(CS): a catalytic mutant with a cysteine-to-serine  substitution in the DHHC motif of ZDHHC18  All data are representative of at least two independent experiments. Mean ± SEM from triplicates of technical replicates, unpaired t test; ns, not significant; **, P˂0.01; ***, P˂0.001 (A"
NCBI gene IDs:
"Flag: 
HA: 
Myc: 
cGAS: 115004
STING: 340061
ZDHHC18: 84243"
Figure legend: "(B) HEK293T  cells (1×106) were transfected with HA-cGAS  (500 ng), Flag-STING  (500 ng) and Myc-ZDHHC18  (500 ng) expression plasmids for 24 h. TBK1 phosphorylation  was detected by immunoblotting. Data information: ZDHHC18(CS): a catalytic mutant with a cysteine-to-serine  substitution in the DHHC motif of ZDHHC18"
NCBI gene IDs:
"Flag: 
HA: 
Myc: 
cGAS: 115004
STING: 340061
ZDHHC18: 84243"
Figure legend: "(C and D) HEK293T  cells were transfected with the indicated plasmids, and the amount of cGAMP  in the lysates was quantified by  LC-MS/MS. Data information: ZDHHC18(CS): a catalytic mutant with a cysteine-to-serine  substitution in the DHHC motif of ZDHHC18; LC-MS/MS: liquid chromatography-tandem mass spectrometry;"
NCBI gene IDs:
"ZDHHC18: 84243"
Figure legend: "L929  cells stably transfected with control shRNA or ZDHHC18   shRNA The knockdown efficiency of ZDHHC18   is shown by RT-qPCR  (E) results. Data information: NC: negative control. All data are representative of at least two independent experiments. Mean ± SEM from triplicates of technical replicates, unpaired t test; ns, not significant; **, P˂0.01; ***, P˂0.001"
NCBI gene IDs:
"ZDHHC18: 503610"
Figure legend: "L929  cells stably transfected with control shRNA or ZDHHC18  shRNA efficiency of ZDHHC18  is shown by  western blotting (F) results. Data information: NC: negative control."
NCBI gene IDs:
"ZDHHC18: 503610"
Figure legend: "L929  cells stably transfected with control shRNA or ZDHHC18  shRNA were transfected with HT-DNA (2 μg/mL) for the indicated times  before RT-qPCR  analysis of Ifna4  (G), expression. Data information:  HT-DNA: herring testis DNA; NC: negative control. All data are representative of at least two independent experiments. Mean ± SEM from triplicates of technical replicates, unpaired t test; ns, not significant; **, P˂0.01; ***, P˂0.001"
NCBI gene IDs:
"Ifna4: 15967
ZDHHC18: 503610"
Figure legend: "L929  cells stably transfected with control shRNA or ZDHHC18  shRNA were transfected with HT-DNA (2 μg/mL) for the indicated times  before RT-qPCR analysis of IFNb1  (H), and Cxcl10  (I) expression. Data information: HT-DNA: herring testis DNA; NC: negative control. All data are representative of at least two independent experiments. Mean ± SEM from triplicates of technical replicates, unpaired t test; ns, not significant; **, P˂0.01; ***, P˂0.001"
NCBI gene IDs:
"Cxcl10: 15945
IFNb1: 15977
ZDHHC18: 503610"
Figure legend: "(J) L929  cells stably transfected with control shRNA or ZDHHC18  shRNA were transfected with HT-DNA  (2 μg/mL) for the indicated times   before immunoblotting  analysis with the indicated antibodies. Data information: HT-DNA: herring testis DNA; NC: negative control."
NCBI gene IDs:
"ZDHHC18: 503610"
Figure legend: "(A) Survival  analysis of Zdhhc18+/+ and Zdhhc18-/- mice  (n = 8 each, 6-8 weeks old) intranasally injected with VACV  (5 × 107 PFU per mouse) and monitored daily for survival  for 13 days using  Kaplan-Meier curves and a log-rank (Mantel-Cox) test. ***, P˂0.001."
NCBI gene IDs:
"Zdhhc18: 503610"
Figure legend: "(B) Representative photomicrographs  of H&amp;E-stained liver  and kidney  tissue sections from mice  (Zdhhc18+/+ or Zdhhc18-/-) intravenously injected with HSV-1-FS (5 × 107 PFU per mouse) or not after 2 days. Scale bars: 100 μm (liver), 200 μm (kidney). Data information: PFU: plaque-forming units; H&amp;E: hematoxylin-eosin. Data are representative of at least two independent experiments."
NCBI gene IDs:
"Zdhhc18: 503610"
Figure legend: "(C BMDMs  (Zdhhc18+/+ or Zdhhc18-/-) were infected with  HSV-1  (MOI=2) for 8 h, and viral titers in the supernatants were quantified by plaque assay. Data information: Data are representative of at least two independent experiments."
NCBI gene IDs:
"Zdhhc18: 503610"
Figure legend: "D) BMDMs  (Zdhhc18+/+ or Zdhhc18-/-) were infected with HSV-1 (MOI=2) for 8 h, and  viral titers in the supernatants were quantified by plaque assay. Data information: Data are representative of at least two independent experiments. Mean ± SEM from triplicates of technical replicates, unpaired t test; Ns: no significance; *, P˂0.05; **, P˂0.01; ****, P˂0.0001 (D"
NCBI gene IDs:
"Zdhhc18: 503610"
Figure legend: "F) Microscopy of BMDMs  (Zdhhc18+/+ or Zdhhc18-/-) infected with GFP-HSV-1 (MOI=1) for 10 h. Scale bar: 200 μm. Data information: Data are representative of at least two independent experiments."
NCBI gene IDs:
"Zdhhc18: 503610"
Figure legend: "(G) MEFs (Zdhhc18+/+ or Zdhhc18-/-) were infected with VACV  (1:200) for the indicated times  before immunoblot  analysis."
NCBI gene IDs:
"Zdhhc18: 503610"
Figure legend: "(H and I) MEFs  (Zdhhc18+/+ or Zdhhc18-/-) were infected with VACV  (1:200) for the indicated times before RT-qPCR analysis of Cxcl10  (H) and Ifnb1  (I) expression. Data information: Data are representative of at least two independent experiments. Mean ± SEM from triplicates of technical replicates, unpaired t test; Ns: no significance; *, P˂0.05; **, P˂0.01; ****, P˂0.0001"
NCBI gene IDs:
"Cxcl10: 15945
Ifnb1: 15977
Zdhhc18: 503610"
Figure legend: "(J) PBMCs  from healthy people were transfected with scrambled siRNA or ZDHHC18  siRNA (cocktail) for 48 h and then infected with VACV  (1:200) for the indicated times before RT-qPCR analysis of IFNB1 expression. Data information: Data are representative of at least two independent experiments. Mean ± SEM from triplicates of technical replicates, unpaired t test; Ns: no significance; *, P˂0.05; **, P˂0.01; ****, P˂0.0001"
NCBI gene IDs:
"IFNB1: 3456
ZDHHC18: 84243"
Figure legend: "A. qPCR analysis of Ahr expression in B cell subsets purified from C57Bl/6 mice. Ahr expression was normalized to Hprt1. n = 3-5 independent experiments; mean ± SD."
NCBI gene IDs:
"Hprt1: 
Ahr: 11622"
Figure legend: "B. qPCR analysis of Ahr expression in splenic CD19+ cells isolated from C57Bl/6 mice and cultured for 4h as indicated. Ahr expression was normalized to Hprt1. Ahr expression among groups was normalized to Medium. n = 4 independent experiments; mean ± SEM; one-way ANOVA, Dunnett's multiple comparison test."
NCBI gene IDs:
"Hprt1: 
Ahr: 11622"
Figure legend: "C. qPCR analysis of Ahr expression in splenic CD19+ cells isolated from C57Bl/6 mice and cultured for 4h with 20 ng/ml IL-4 and/or 10 μg/ml α-IgM. Ahr expression was normalized to Hprt1. Ahr expression among groups was normalized to Medium. n = 3 independent experiments; mean ± SEM; one-way ANOVA, Tukey's multiple comparison test."
NCBI gene IDs:
"Hprt1: 
Ahr: 11622"
Figure legend: "F. qPCR analysis of Ahr expression in purified splenic B cell subsets isolated from C57Bl/6 mice and cultured as indicated for 4h. Ahr expression was normalized to Hprt1. n = 2 independent experiments; mean ± range."
NCBI gene IDs:
"Hprt1: 
Ahr: 11622"
Figure legend: "G. qPCR analysis of Ahr expression in splenic CD19+ cells isolated from C57Bl/6 mice and cultured for the indicated time points with 20 ng/ml IL-4 and/or 10 μg/ml α-IgM. Ahr expression was normalized to Hprt1. Ahr expression among groups was normalized to Medium. n = 5 independent experiments; mean ± SEM; one-way ANOVA, Dunnett's multiple comparison test."
NCBI gene IDs:
"Hprt1: 
Ahr: 11622"
Figure legend: "B. qPCR analysis of Cyp1a1 expression in splenic CD19+ cells isolated from C57Bl/6 mice and cultured for 24h as indicated. Cyp1a1 expression was normalized to Hprt1. Cyp1a1 expression among groups was normalized to Medium DMSO. n = 2 independent experiments; mean ± range."
NCBI gene IDs:
"Hprt1: 
Cyp1a1: 13076"
Figure legend: "C. Flow cytometry analysis of Cyp1a1 expression, reported by eYFP, in splenic CD19+ cells isolated from Cyp1a1Cre R26R eYFP mice and cultured for 72h as indicated. Representative data of n = 3 independent experiments."
NCBI gene IDs:
"Cre: "
Figure legend: "D. qPCR analysis of Cyp1a1 expression in purified splenic B cell subsets isolated from C57Bl/6 mice and cultured as indicated for 24h. Cyp1a1 expression was normalized to Hprt1. n = 2 independent experiments; mean ± range."
NCBI gene IDs:
"Hprt1: 
Cyp1a1: 13076"
Figure legend: "A. Flow cytometry analysis of CTV dilution in splenic CD19+ cells sorted from non-immune Ahrfl/+mb1Cre+ (Ahr+/- B cells, solid grey) and Ahrfl/-mb1Cre+ (Ahr-/- B cells, black) mice stimulated for 72h as indicated. Treatment of Ahr+/- CD19+ cells with CH223191 is indicated in red. Representative data of n = 4-5 independent experiments.B-D. Flow cytometry analysis of expansion index (B), % of divided cells (C) and replication index (D) of splenic CD19+ cells sorted from non-immune Ahrfl/+mb1Cre+ (black) and Ahrfl/-mb1Cre+ (white) mice stimulated for 72h as indicated. Treatment of Ahr+/- CD19+ cells with CH223191 is indicated in red. n = 4-5 independent experiments; mean ± SEM; 2-way ANOVA, Sidak's multiple comparison test."
NCBI gene IDs:
"Cre: 
Ahr: 11622
mb1: 12518"
Figure legend: "E. Flow cytometry analysis of cell cycle distribution of splenic CD19+ cells purified from non-immune Ahrfl/+mb1Cre+ (black) and Ahrfl/-mb1Cre+ (white) mice stimulated for 48h with 5 µg/ml α-IgM. Data representative of n = 2 independent experiments; lines indicate mean; 2-way ANOVA, Sidak's multiple comparison test."
NCBI gene IDs:
"Cre: 
Ahr: 11622
mb1: 12518"
Figure legend: "A, B. Flow cytometry analysis of distribution of CD45.1+ and CD45.2+ cells in indicated cell subsets purified from bone marrow (A) and lymph node (B) of sub lethally-irradiated Rag1-/- mice 8 weeks after reconstitution with equal numbers of bone marrow cells from Ahr+/+ (CD45.1+) and Ahr-/- (CD45.2+) mice. Dashed lines indicate 50% level. Representative data of n = 2 independent experiments; two-tailed paired t test."
NCBI gene IDs:
"Ahr: 11622
Rag1: 19373"
Figure legend: "E. Flow cytometry analysis of distribution of Ahr+/+ CD45.1+CD45.2+ (black) and Ahr-/- CD45.2+ (white) cells harvested from host mice. Indicated distribution is quantified relative to transferred cells. X symbols indicate SRBC-mock-treated control. Dashed line indicates 50% threshold. Representative data of n = 3 independent experiments; two-tailed paired t test."
NCBI gene IDs:
"Ahr: 11622"
Figure legend: "F, G. Flow cytometry analysis of distribution (F) and cell numbers (G) of IgG1+ and IgG1- HEL3x-binding Ahr+/+ CD45.1+CD45.2+ (black) and Ahr-/- CD45.2+ (white) cells harvested from host mice. Representative data of n = 2 independent experiments; two-tailed paired t test."
NCBI gene IDs:
"Ahr: 11622"
Figure legend: "A, B. Tables showing top 20 down-regulated (A) genes in Ahr-/- B cells as compared to Ahr+/+ cells, after analysis by RNA sequencing. B cells were activated with 10 µg/ml α-IgM + 20 ng/ml IL-4 for 8h; 250 nM FICZ was added to the culture during the last 4h. The average read counts are directly proportional to the extent of expression of a given gene in Ahr+/+ or Ahr-/- cells. Data from n = 3 mice per group. Average read counts for the housekeeping gene Hprt1 in both Ahr+/+ and Ahr-/- B cells are indicated below the table in figure 6A."
NCBI gene IDs:
"Hprt1: 
Ahr: 11622"
Figure legend: "A, B. Tables showing top up-regulated (B) genes in Ahr-/- B cells as compared to Ahr+/+ cells, after analysis by RNA sequencing. B cells were activated with 10 µg/ml α-IgM + 20 ng/ml IL-4 for 8h; 250 nM FICZ was added to the culture during the last 4h. The average read counts are directly proportional to the extent of expression of a given gene in Ahr+/+ or Ahr-/- cells. Data from n = 3 mice per group. Average read counts for the housekeeping gene Hprt1 in both Ahr+/+ and Ahr-/- B cells are indicated below the table in figure 6A."
NCBI gene IDs:
"Hprt1: 
Ahr: 11622"
Figure legend: "C. qPCR analysis of Ccno expression in splenic CD19+ cells isolated from non-immune Ahrfl/+mb1Cre+ (Ahr+/- B cells, black) and Ahrfl/-mb1Cre+ (Ahr-/- B cells, white) mice, stimulated with 10 µg/ml anti-IgM for the indicated time points. Ccno expression was normalized to Hprt1. n = 3 independent experiments; mean ± SEM; two-way ANOVA, Sidak's multiple comparison test."
NCBI gene IDs:
"Cre: 
Ahr: 11622
Ccno: 218630
mb1: 12518"
Figure legend: "D. qPCR analysis of Ccno expression in splenic CD19+ cells isolated from C57Bl/6 mice and cultured for 8h with 20 ng/ml IL-4 and/or 10 μg/ml α-IgM. Ccno expression was normalized to Hprt1. n = 3 independent experiments; mean ± SEM; one-way ANOVA, Tukey's multiple comparison test."
NCBI gene IDs:
"Hprt1: 
Ccno: 218630"
Figure legend: "E. qPCR analysis of Ccno expression in splenic CD19+ cells isolated from C57Bl/6 mice and cultured for the indicated time points with 20 ng/ml IL-4 and/or 10 μg/ml α-IgM in presence or absence of 250 nM FICZ or 1 μM 3-MC. Ccno expression was normalized to Hprt1. n = 3 independent experiments; mean ± SEM; one-way ANOVA, Tukey's multiple comparison test."
NCBI gene IDs:
"Hprt1: 
Ccno: 218630"
Figure legend: "F. Chromatin Immunoprecipitation (ChIP) analysis of AhR interaction with the Ccno promoter and an irrelevant region (-3.3 Kb from Ccno transcription starting site) in Ahr+/+ (black) and Ahr-/- (white) B cells 5h after activation with 10 µg/ml α-IgM + 20 ng/ml IL-4. 250 nM FICZ was added in the last hour of culture. Representative data of n = 2 independent experiments; mean ± SEM; two-way ANOVA, Sidak's multiple comparison test."
NCBI gene IDs:
"Ahr: 11622
Ccno: 218630"
Figure legend: "D: Co-immunoprecipitation  of TMBIM5 and LETM1  protein in tandem in the left 3 panels. The input represents the mitochondrial  crudely isolated from HEK293  cells and was used as input for the co-IP, LETM1  was immunoprecipitated  (left panel, IP: LETM1) using a LETM1  monoclonal antibody and Protein G magnetic beads (ProtG). ProtG   beads alone were used as a negative control for binding, immunoprecipitates  were immunoblotted  (IB) for the indicated proteins to demonstrate interaction. 10% of the input was used for immunoblotting. Prohibitin  (PHB) was used as a control to illustrate no nonspecific binding  of inner mitochondrial membrane proteins complexes. The middle and right panel of the coIPs  illustrates the converse experiment, in the middle in  TMBIM5WT and right TMBIMKO, using TMBIM5  as bait (right panel, IP: TMBIM5). The last two right panels show blots  from BN-PAGE conducted in TMBIM5WT and KO."
NCBI gene IDs:
"TMBIM: 27069
TMBIM5: 27069"
Figure legend: "E: Isolated mitochondria  from three independent replicates of HEK293 TMBIM5WT and TMBIM5KO1 and KO2 were analyzed by immunoblotting  using the indicated antibodies, HSP60  and TOM40  served as mitochondrial  loading controls. F: Densitometric  analysis of the bands in (E) normalized to loading control, bar graph of three individual experiments (biological replicates), mean ± SD, One-way ANOVA with Bonferroni's multiple comparisons test performed against TMBIM5WT *p&lt;0.05, **p&lt;0.008, Two-way ANOVA with Bonferroni's multiple comparisons test performed for the OPA1  statistics against TMBIM5WT, ***p=0.0009, ****p&lt;0.0001."
NCBI gene IDs:
"TMBIM5: 27069"
Figure legend: "(E) WB analysis of NEDD4L, EZH2  and EZH1 expression in the EZH2-specific siRNA (siEZH2)- or negative control siRNA (siNC)-transfected NHEKs with  IMQ stimulation. Data information: Data are shown as the mean ± s.e.m., and are representative of three independent experiments Scale bar, 200 μm (100×) or 50 μm (400×)."
NCBI gene IDs:
"EZH2: 2146"
Figure legend: "NEDD4L was knocked out by the CRISPR Cas9 method in NHEKs. WT and NEDD4L KO NHEKs were  infected with lentivirus overexpressing NEDD4L-WT or NEDD4L-C943S mutants. cell signaling pathway activation  induced by IL-6 were detected by WB analyses Data information: Data are shown as the mean ± s.e.m., and are representative of three independent experiments"
NCBI gene IDs:
"Cas9: 57852564
NEDD4L: 23327"
Figure legend: "(G, H) Primary keratinocytes were separated from the WT and Nedd4l KO mice. (G) WB analysis of the protein expression in IL-6-induced cell signaling pathway activation. (H) WB analysis  of the proteins in the  IL-6 signaling pathway. Data information: Data are shown as the mean ± s.e.m., and are representative of three independent experiments"
NCBI gene IDs:
"Nedd4l: 83814"
Figure legend: "Six- to eight-weeks old WT and Nedd4l  cKO mice were treated with IMQ for 6 consecutive days and at the beginning of the treatment, the mice were injected  intra-epidermally with 10 μg anti-GP130 antibody or with same dosage of isotype on every other day. Representative images of Ki67 staining in back tissues are on the left. The number of Ki67-positive cells per HPF is shown on the right. Data information: Data are shown as mean ± s.e.m., and are representative of two independent experiments. Scale bar, 200 μm (100×) or 50 μm (400×). Significant differences were tested using a two-tailed Student's t test C, control, n=5, IMQ, n=6. * P＜0.05, ** P＜0.01, *** P＜0.001. NS, no significance."
NCBI gene IDs:
"Nedd4l: 83814"
Figure legend: "Six- to eight-weeks old WT and Nedd4l  cKO mice were treated with IMQ for 6 consecutive days and at the beginning of the treatment, the mice were injected intra-epidermally with 10 μg anti-GP130 antibody or with same dosage of isotype on every other day. Keratinocyte proliferation associated genes in the skin tissues  are detected using real-time PCR analysis. Data information: Data are shown as mean ± s.e.m., and are representative of two independent experiments. Scale bar, 200 μm (100×) or 50 μm (400×). Significant differences were tested using a two-tailed Student's t test D, control, n=3, IMQ, n=6. * P＜0.05, ** P＜0.01, *** P＜0.001. NS, no significance."
NCBI gene IDs:
"Nedd4l: 83814"
Figure legend: "(F) Full length Flag-GP130,  GP130-aa 616-918, GP130-aa 616-889, GP130-aa 616-764, GP130-aa 616-734 were transfected with Myc-NEDD4L into  HEK293T cells, and whole cell lysates were co-IP with ANTI-FLAG M2 magnetic beads, followed by WB with anti-Flag or anti-Myc antibodies."
NCBI gene IDs:
"Flag: 
GP130: 3572
NEDD4L: 83814"
Figure legend: "(C) WT or  NEDD4L KO NHEK  cells was infected with  lentivirus that overexpress NEDD4L-WT, NEDD4L WW domain truncated mutant (NEDD4L-ΔWW) or its enzymatic activity mutant (NEDD4L-C943S), the cells were followed by denaturation-IP with anti-GP130 antibody and WB analysis with anti-Ub antibodies."
NCBI gene IDs:
"NEDD4L: 23327"
Figure legend: "(E) WB analysis of the polyubiquitination of GP130 in HEK293T cells co-transfected with full length Myc-NEDD4L, HA-Ub and Flag-GP130 or its lysine mutants (K-R) in the intracellular domain, followed by denaturation-IP with ANTI-FLAG M2 magnetic beads and WB analysis with anti-HA antibodies."
NCBI gene IDs:
"Flag: 
HA: 
Myc: 
GP130: 3572
NEDD4L: 83814
Ub: 10537///7316///7314"
Figure legend: "(a) Expression of ATG16L1 in a set of different tissues as detected by RT-PCR (IEC, intestinal epithelial cells). The corresponding β-actin control (with a 518-bp amplicon size) is given below."
NCBI gene IDs:
"ATG16L1: 55054"
Figure legend: "b) Amounts of ATG16L1 in colonic mucosal biopsy specimens. Proteins (15 μg) from rectal mucosal biopsies of Crohn disease patients and normal controls (N) were separated by denaturing SDS-PAGE, transferred onto polyvinylidine fluoride (PVDF) membranes and probed for the presence of ATG16L1 using a specific primary antibody and horseradish peroxidase-coupled secondary antibody. The abundant 68.2-kDa band corresponds to the predicted molecular weight of the isoform encoded by GenBank AY398617 (UniProt accession number Q676U5). This major protein form was used for three-dimensional modeling of the ATG16L1 protein (Fig. 2). The 48.5-kDa band corresponds to GenBank EF079890, which contains exon 9 (harboring rs2241880) in the same reading frame as the major form."
NCBI gene IDs:
"ATG16L1: 55054"
Figure legend: "(c-i) Representative immunohistochemistry results (out of six normal controls and six individuals with Crohn disease) from colonic mucosal tissue samples from normal controls for genotype AA (c) and GG (f) and individuals with Crohn disease for genotype AA (d) and GG (g) are shown to demonstrate the cellular localization of the ATG16L1 protein. Cellular expression patterns in mononuclear cells (h) and intestinal epithelial cells (i) of a Crohn disease sample (rs2241880AA) are shown at higher magnification. e shows a Crohn disease sample without the primary antibody, used as a control. Bar represents 10 μm in c-g."
NCBI gene IDs:
"rs2241880: 55054"
Figure legend: "The 32 β-strands forming an eight-bladed β-propeller are numbered as in Supplementary Note. The location of the variant amino acid T300A in strand β3, corresponding to rs2241880, is marked in yellow."
NCBI gene IDs:
"rs2241880: 55054"
Figure legend: "Immunoblot (IB) analyses of the levels of β-catenin and RAS in DLD1, WT-HCT116, MT-HCT116, HepG2, and SW48 cells transfected with Myc-axin for 36 hr"
NCBI gene IDs:
"Myc: 
axin: 8313///8312"
Figure legend: "Effects of β-catenin knock-down on polyubiquitination-dependent degradation of RAS. IB analyses of MT-HCT116 cells transfected with control or two independent β-catenin siRNAs for 48 hr"
NCBI gene IDs:
"β-catenin: 1499"
Figure legend: "Polyubiquitination assays of MT-HCT116 cells cotransfected with two independent β-catenin siRNAs and HA-ubiquitin (Ub) for 72 hr in the presence of the proteasomal inhibitor MG132, and WCLs were immunoprecipitated with an anti-pan-RAS antibody"
NCBI gene IDs:
"Ub: 
ubiquitin: 
β-catenin: 1499"