EMBO/SourceData huggingface dataset:
Figure legend: "G: Cal27 and JHU029 cells were transfected with either siELDR or siILF3 and after 48hr cell lysates were subjected to Western blot analysis for phospho-RB and total RB using specific antibodies. The membrane was reprobed with an antibody against Actin as internal control. Bottom panels show quantitation. n = 3 biological replicates. Data are represented as the mean ± SD"
NCBI gene IDs:
"ELDR: 102725541
ILF3: 3609"
Figure legend: "H: Control or ELDR knockdown synchronized Cal27 and JHU029 cells were harvested, fixed and stained with propidium iodide. DNA content was analyzed by flow cytometry. Results are represented cell population in G1, S, and G2/M phases of the cell cycle. Right panels show percentage of cell population in different phases of cell cycle. n = 4 biological replicates. Data are represented as the mean ± SD,"
NCBI gene IDs:
"ELDR: 102725541"
Figure legend: "A: Cal27 and JHU029 cells were transfected with control or ELDR siRNA and relative expression of miR-7 was analyzed by qRT-PCR. U47 was used as an internal control. n = 3 biological replicates. Data are represented as the mean ± SD,"
NCBI gene IDs:
"U47: 
ELDR: 102725541
miR-7: 407044"
Figure legend: "B: Cal27 and JHU029 cells were transfected with control or ELDR plasmid and relative expression of miR-7 was analyzed by qRT-PCR. U47 was used as an internal control. n = 3 biological replicates. Data are represented as the mean ± SD,"
NCBI gene IDs:
"U47: 
ELDR: 102725541
miR-7: 407044"
Figure legend: "C: Cal27 and JHU029 cells were transfected with control or mimic miR-7 and relative expression of ELDR was analyzed by qRT-PCR. 18S rRNA was used as an internal control. n = 2 biological replicates; n= 3 technical replicates. Data are represented as the mean ± SD,"
NCBI gene IDs:
"18S rRNA: 
ELDR: 102725541
miR-7: 407044"
Figure legend: "D: Cal27 and JHU029 cells were transfected with miR-7 mimic, ELDR plasmid or both miR-7 and ELDR plasmid. Cell lysates were analyzed by Western blot analysis for EGFR expression using specific antibody. The membrane was reprobed with an antibody against Actin as an internal control. Representative bands were cropped from same gel. Right panels show quantitative representation of Western blot band intensities. n = 3 biological replicates. Data are represented as the mean ± SD,"
NCBI gene IDs:
"ELDR: 102725541
miR-7: 407044"
Figure legend: "E: Relative expression of miR-7 in Cal27 and JHU029 cells compared to NOK cell line analyzed by qRT-PCR. U47 was used as an internal control. n = 3 biological replicates and 3 technical replicates. Data are represented as the mean ± SD,"
NCBI gene IDs:
"U47: 
miR-7: 407044"
Figure legend: "A: Body weight was measured in control and siELDR treated mice. n=5 animal per group"
NCBI gene IDs:
"ELDR: 102725541"
Figure legend: "C: Tumors were measured using a slide caliper and tumor volumes were calculated. Arrow indicates starting point siELDR treatment. n=5 animal per group and tumor volume presented as the mean ± SD"
NCBI gene IDs:
"ELDR: 72735"
Figure legend: "D: ELDR knockdown was examined by analyzing expression of ELDR in treated tumors compared to the control tumors. 18S rRNA gene was used as internal control. n=5 animal per group and 3 technical replicates from each tumor."
NCBI gene IDs:
"18S rRNA: 
ELDR: 72735"
Figure legend: "E: Control or siELDR treated tumor lysates were subjected to Western blot analysis for EGFR and Cyclin E1expression using specific antibodies and representative bands are shown. The blot was reprobed with an antibody against Actin for normalization. Right panels show quantitation. n= 3 biological replicates from each tumor"
NCBI gene IDs:
"ELDR: 72735"
Figure legend: "F: OSCC-PDX tissue was implanted subcutaneously into the flank of NSG mice. When the tumor volume reached >70 mm3, mice were divided into two groups. 10µg of siELDR or control oligoes were injected intratumorally as described above. Body weight was measured in control and siELDR treated mice. n=5 animal per group"
NCBI gene IDs:
"ELDR: 72735"
Figure legend: "I: ELDR knockdown was examined by analyzing expression of ELDR in treated OSCC-PDX tumors compared to the control tumors. 18S gene was used as internal control. n=5 animal per group and 3 technical replicates presented as the mean ± SD"
NCBI gene IDs:
"18S: 
ELDR: 72735"
Figure legend: "D-F. Volcano plots showing RNA-seq data in mouse islets    (20% vs 5% O2  for 24 hours; n = 3 mice/group; D), human islets    (20% [n = 2 biological replicates from donor 1 sample] vs 2% [n = 3 biological replicates from donor 1 sample] O2  for 24 hours; E), and MIN6  cells (20% vs 5% O2  for 6 hours; n = 3 biological replicates; F). Atf3, Bhlhe40, and other reported hypoxia-inducible transcriptional repressor genes (Cavadas et al., 2017) are shown (red, significantly upregulated genes)."
NCBI gene IDs:
"Atf3: 11910
Bhlhe40: 20893"
Figure legend: "D-F. The effect of oxidative stress, endoplasmic reticulum stress, and energy stress on BHLHE40  expression. qRT-PCR analysis of Bhlhe40  in MIN6  cells incubated with 10μM H2O2  (n = 3 biological replicates; D), 2μM thapsigargin  (Thap) or 5 μg/ml tunicamycin (Tun) (n = 7 biological replicates; E), or 2mM metformin  (Met) for 24 hours (n = 3 biological replicates; F). Data information: Data are mean ± SEM; *p &lt; 0.05, **p &lt; 0.01, and ***p &lt; 0.001 by unpaired two-tailed Student's t test."
NCBI gene IDs:
"Bhlhe40: 20893
BHLHE40: 20893"
Figure legend: "H-K. BHLHE40  expression  in islets  from diabetic mice. BHLHE40   expression  was analyzed in ob/ob mouse islets   by qRT-PCR (n = 4 biological replicates; H) and  Western blotting  (I) and in db/db mouse islets   by Western blotting (J). Subcellular localization  of BHLHE40  in ob/ob mice islets   by immunohistochemical  analysis (K). Data information: Data are mean ± SEM; *p &lt; 0.05, **p &lt; 0.01, and ***p &lt; 0.001 by unpaired two-tailed Student's t test. β-actin was used as a loading control. Scale bar, 100 μm."
NCBI gene IDs:
"BHLHE40: 20893"
Figure legend: "A. Glucose-stimulated insulin  secretion in MIN6  cells expressing short hairpin RNA against a non-targeting Ctrl or Bhlhe40   knockdown (B40  KD) were cultured under 20% or 5% O2  for 24 hours (n = 8 biological replicates). B. Glucose-stimulated insulin  secretion in MIN6  cells infected with retroviruses  generated with pMx-Ctrl (Ctrl) or pMx-Bhlhe40  (B40  OE; n = 4 biological replicates). Data information: Data are mean ± SEM; *p &lt; 0.05, **p &lt; 0.01, and ***p &lt; 0.001 by unpaired two-tailed Student's t test. Ctrl, control; n.s., not significant."
NCBI gene IDs:
"B40: 20893
Bhlhe40: 20893"
Figure legend: "D. KCl-stimulated insulin  secretion in Ctrl and B40   OE MIN6  cells (n = 3 biological replicates). Data information: Data are mean ± SEM; *p &lt; 0.05, **p &lt; 0.01, and ***p &lt; 0.001 by unpaired two-tailed Student's t test. Ctrl, control; n.s., not significant."
NCBI gene IDs:
"B40: 20893"
Figure legend: "G. Cellular ATP  content in Ctrl and B40   KD MIN6  cells cultured under 20% or 5% O2  for 24 hours (n = 3 biological replicates). Data information: Data are mean ± SEM; *p &lt; 0.05, **p &lt; 0.01, and ***p &lt; 0.001 by unpaired two-tailed Student's t test. Ctrl, control; n.s., not significant."
NCBI gene IDs:
"B40: 20893"
Figure legend: "I-K. Mitochondrial DNA (mtDNA) content (n = 4 biological replicates; I), mitochondrial  mass (n = 4 biological replicates; J), and mitochondrial membrane potential (n = 4 biological replicates; K) in Ctrl and B40   KD MIN6  cells cultured under 20% or 5% O2  for 24 hours. Data information: Data are mean ± SEM; *p &lt; 0.05, **p &lt; 0.01, and ***p &lt; 0.001 by unpaired two-tailed Student's t test. Ctrl, control; n.s., not significant."
NCBI gene IDs:
"B40: 20893"
Figure legend: "B, Expression of DEGs shown in A was confirmed by qRT-PCR in Ctrl and B40   OE MIN6  cells (n = 3 biological replicates; B) Data information: Data are mean ± SEM; *p &lt; 0.05, **p &lt; 0.01 and ***p &lt; 0.001 by unpaired two-tailed Student's t test."
NCBI gene IDs:
"B40: 20893"
Figure legend: "D. qRT-PCR of MAFA  target genes in Ctrl and B40  KD MIN6  cells cultured under 20% or 5% O2  for 24 hours (n = 3 biological replicates). Data information: Data are mean ± SEM; *p &lt; 0.05, **p &lt; 0.01 and ***p &lt; 0.001 by unpaired two-tailed Student's t test."
NCBI gene IDs:
"B40: 20893"
Figure legend: "G. Western blot of oxidative phosphorylation complex proteins and TOM20  protein in Ctrl and B40  KD MIN6  cells cultured under 20% or 5% O2  for 24 hours, and quantification of the band intensities (n = 3 biological replicates). Data information: Data are mean ± SEM; *p &lt; 0.05, **p &lt; 0.01 and ***p &lt; 0.001 by unpaired two-tailed Student's t test. β-actin  was used as a loading control. Ctrl, control."
NCBI gene IDs:
"B40: 20893"
Figure legend: "C. Luciferase reporter assay  was performed with MIN6  cells transfected with BHLHE40   expression plasmids, pRL-SV40 plasmid, and pGL3-Mafa  plasmids (wildtype [black] and E-box mutated [red] sites; n = 4 biological replicates). D. Luciferase reporter activity  in MIN6  cells cultured under 20% or 5% O2  for 24 hours (n = 3 biological replicates). Data information: Data are mean ± SEM; *p &lt; 0.05 **p &lt; 0.01, and ***p &lt; 0.001 by unpaired two-tailed Student's t test. Ctrl, control; n.s., not significant."
NCBI gene IDs:
"BHLHE40: 20893
Mafa: 378435"
Figure legend: "H-J. Proteins sampled from Ctrl and B40  OE MIN6  cells with FLAG-Pdx1   expression (H) or from MIN6  cells with FLAG-Pdx1   expression pre-cultured under 20% or 5% O2  for 24 hours (I) were  immuno-precipitated  by IgG or anti-FLAG  antibody, after which qRT-PCR  was performed for the indicated regions (n = 9 biological replicates for H and n = 6 biological replicates for I). FLAG  (PDX1) expression in I was confirmed by Western blotting (J). Data information: Data are mean ± SEM; *p &lt; 0.05 **p &lt; 0.01, and ***p &lt; 0.001 by unpaired two-tailed Student's t test. Ctrl, control; n.s., not significant."
NCBI gene IDs:
"B40: 20893"
Figure legend: "C, D.  Glucose tolerance test  of Ctrl:ob/ob  and βB40KO:ob/ob mice  (n = 9 mice  and n = 8 mice, respectively; 6 weeks old) (C) and AUC (D). Data information: Data are mean ± SEM; *p &lt; 0.05 **p &lt; 0.01, and ***p &lt; 0.001 by unpaired two-tailed Student's t test."
NCBI gene IDs:
"B40: 20893"
Figure legend: "E. Glucose-stimulated insulin  secretion in Ctrl:ob/ob  and βB40KO:ob/ob mice  (n = 9 mice  and n = 6 mice, respectively; 8 weeks old). F. Glucose-stimulated insulin  secretion in isolated islets   from Ctrl and βB40KO mice  after culture under 5% O2  for 24 hours (n = 8 biological replicates). Data information: Data are mean ± SEM; *p &lt; 0.05 **p &lt; 0.01, and ***p &lt; 0.001 by unpaired two-tailed Student's t test."
NCBI gene IDs:
"B40: 20893"
Figure legend: "I, J. Representative images of  pancreatic islets stained  for insulin  and glucagon  in Ctrl:ob/ob  and βB40KO:ob/ob mice  (12 weeks old) (I). The ratios of total islet  area to whole pancreas  area (%) are shown (n = 3 biological replicates; J). Data information: Data are mean ± SEM; *p &lt; 0.05 **p &lt; 0.01, and ***p &lt; 0.001 by unpaired two-tailed Student's t test. Scale bar, 10 μm."
NCBI gene IDs:
"B40: 20893"
Figure legend: "K, L. Representative images of pancreatic islets stained  for insulin, MAFA, and BHLHE40  in Ctrl:ob/ob  and βB40KO:ob/ob mice  (12 weeks old) (K). Fluorescence intensities of nuclear  and cytosolic MAFA  in K were quantified (n = 30 cells; L). Data information: Data are mean ± SEM; *p &lt; 0.05 **p &lt; 0.01, and ***p &lt; 0.001 by unpaired two-tailed Student's t test. Scale bar, 10 μm."
NCBI gene IDs:
"B40: 20893"
Figure legend: "M. qRT-PCR  of Mafa  and its target genes in Ctrl:ob/ob  and βB40KO:ob/ob mice  (n = 4 mice). Data information: Data are mean ± SEM; *p &lt; 0.05 **p &lt; 0.01, and ***p &lt; 0.001 by unpaired two-tailed Student's t test."
NCBI gene IDs:
"B40: 20893
Mafa: 378435"
Figure legend: "A) Transmission electron microscopy (TEM) of MoDCs infected with P. gingivalis for 2, 12 and 24 hours (left, middle and right panels). The sections show the intra-and extra-cellular contents of Cont. (un-infected), Pg381, Mfa1+Pg and FimA+Pg infected MoDCs for the different time points"
NCBI gene IDs:
"Mfa1: 2551415
FimA: 2551422"
Figure legend: "A) DC-SIGN mRNA expression in P. gingivalis-infected MoDCs at 0.1, 1 and 10 MOIs. The figure shows the gene expression after 12 hours of Pg381 and mutant strains infections. The target gene (DC-SIGN) was normalized using the endogenous control GAPDH (ΔCt) and fold regulations were calculated using 2-(ΔΔCt) method. The statistical analysis was performed using the t-test, which accounts for the clustering of infected and un-infected controls within 3 different experiments (* p&lt;0.001)."
NCBI gene IDs:
"DC-SIGN: 30835
GAPDH: 2597"
Figure legend: "B) Immuno-electron microscopy of un-infected MoDCs (Cont.) (upper panel), MoDCs infected with Pg381 (middle panel) and Mfa1+Pg mutants (lower panel). Gold particles (marked with red rings) for positive DC-SIGN were detected in the cell membrane and cytoplasm of cells infected with Mfa1+Pg strains. Minimal positive staining for DC-SIGN was detected in the membranes of MoDCs infected with Pg381, while no cytoplasmic gold labeling was detected in these cells."
NCBI gene IDs:
"Mfa1: 2551415"
Figure legend: "C) Flow cytometry analysis of surface DC-SIGN in human MoDCs after infection with Pg381, Mfa1+Pg and FimA+Pg. The analysis of the intensity used Kruskal-Wallis test analysis of different groups and Dunn's test for multiple comparisons 3 different experiments (* p&lt;0.01)."
NCBI gene IDs:
"Mfa1: 2551415
FimA: 2551422"
Figure legend: "The effect of rapamycin on Mfa1+Pg, Pg381 and FimA+Pg survival within MoDCs are shown in figures B, C and D respectively. A three-factor repeated measures ANOVA using mixed models was used to test the effect of strain and rapamycin treatment over time on OD reading. The survival curves for the strains are showed in blue, while the effect of rapamycin treatments are in red. Bacterial survivals in the absence of MoDCs with and without rapamycin are plotted in grey and black, respectively. Statistical analysis showed that the strain by rapamycin treatment overtime interaction indicates the pattern of means in each strain (Mfa1+Pg, Pg381 and FimA+Pg) between treated (rapamycin) and untreated were significantly different overtime (p-value &lt;0.=001)."
NCBI gene IDs:
"Mfa1: 2551415
FimA: 2551422"
Figure legend: "A) Epifluorescence microscopy images of MoDCs infected with Pg381, Mfa1+Pg, FimA+Pg and MFB strains after 12 hours. LC3-II was detected in red-fluorescent (Texas red) dye and the bacterial strains were pre-labeled with CFSE (green). Co-localization of P. gingivalis and LC3-II showed in the right panels."
NCBI gene IDs:
"Mfa1: 2551415
FimA: 2551422"
Figure legend: "A) Immuno-fluorescence images of LC3-II and P. gingivalis within MoDCs pre-treated with GP120 (DC-SIGN blocker) after 12 hours of infection. LC3-II was detected in red-fluorescent dye and the bacterial strains were pre-labeled with green CFSE."
NCBI gene IDs:
"DC-SIGN: 30835"
Figure legend: "C) Flow cytometry of MoDCs treated with siRNA for DC-SIGN (si-DC-SIGN) after 12 hours. Left panels show the decrease of DC-SIGN in Cont. (un-infected), Pg381 and Mfa1+Pg-infected MoDCs."
NCBI gene IDs:
"DC-SIGN: 30835
Mfa1: 2551415"
Figure legend: "D) Epifluorescence microscopy images of MoDCs (si-DC-SIGN) infected with Pg381 and Mfa1+Pg. LC3-II was detected in red-fluorescent dye and the bacterial strains were pre-labeled with green CFSE."
NCBI gene IDs:
"DC-SIGN: 30835
Mfa1: 2551415"
Figure legend: "E) The figure shows the CFU counts of the P. gingivalis strains with MoDCs that lack DC-SIGN (si-DC-SIGN). The analysis of readings used One-way ANOVA analysis of different groups and Tukey's test for multiple comparisons (* p&lt;0.001)."
NCBI gene IDs:
"DC-SIGN: 30835"
Figure legend: "A) Scanning electron microscopy (SEM) of MoDCs of the early interaction of MoDCs with Pg381 and Mfa1+Pg (upper panel 10000x and lower panel 25000x). B) SEM for MoDCs interacting with Pg381 (green stains for bacteria are computer generated)."
NCBI gene IDs:
"Mfa1: 2551415"
Figure legend: "C) Transmission electron microscopy (TEM) of autophagosome like structures within MoDCs infected with Pg381, Mfa1+Pg and FimA+Pg for 12 hours (upper, middle and lower panels, respectively). The right and left sections show the different magnifications of randomly selected sections. Pg381 and FimA+Pg strains are mostly enclosed in the characteristics double-membrane intracellular vesicles (Orange arrows). Contrary, Mfa1+Pg escaped these autophagic (double-membrane) vesicles and enclosed within single membrane structures or freely occupy the cytoplasm (Green arrows)."
NCBI gene IDs:
"Mfa1: 2551415
FimA: 2551422"
Figure legend: "(D) Validation by western blot  of changes in specific phosphorylation  events on kinases. Left, Immunoblots  of cortical  lysates of CTL and micTNFα-KO at ZT6 for: (top) phosphorylated GSK3α/β (pGSK3α at Ser21 and pGSK3β at Ser9) and total GSK3α; and (bottom) phosphorylated MAPK  (pMAPK, MAPK3  at Thr203/Tyr205 and MAPK1  at Thr183/Tyr185) and total MAPK. Right, Ratio between phosphorylated  and total kinase normalized to CTL at ZT18 and ZT6. n=5 mice  per group. ***p=0.000009 (GSK3α), multiple t-test with Benjamini-Hochberg correction."
NCBI gene IDs:
"TNFα: 21926"
Figure legend: "(E) Kinases with altered activity between CTL and micTNF-KOs predicted by robust  kinase activity inference (RoKAI) at ZT18 and ZT6. Graph shows the z-score value of each kinase assigned by RoKAI. Kinases above and below the dotted line represent prediction of up- and downregulated activity in micTNFα-KO, respectively. Kinases are color-coded according to kinase group as described in (C)."
NCBI gene IDs:
"TNF: 21926
TNFα: 21926"
Figure legend: "(F Validation by  western blot  of altered activity of predicted kinases between CTL and micTNF-KOs. (F) Left, Immunoblots  of cortical  lysates of CTL and micTNFα-KO at ZT6 using antibodies specific to target phosphorylation  motifs of MAPK/CDK  (PXS*P, S*PX(K/R)) and PKC  ((K/R)XS*X(K/R)). Dashed boxes indicate quantified signal. Right, Ratio between phosphorylated  substrates and loading control normalized to CTL at ZT18 and ZT6. (F, n=5 mice  per group. *p=0.022 (MAPK/CDK phospho  sub), *p=0.014 (PKC phospho  sub) multiple t-test with Benjamini-Hochberg correction."
NCBI gene IDs:
"TNF: 21926
TNFα: 21926"
Figure legend: "G) Validation by  western blot  of altered activity of predicted kinases between CTL and micTNF-KOs. (G) Left, Immunoblots  show signal of phosphorylated  threonine in MARKs  activation loop. Right, Ratio between phosphorylated MARK  activation loop and loading control normalized to CTL at ZT18 and ZT6. G) n=5 mice  per group. **p=0.0091 (MARK), multiple t-test with Benjamini-Hochberg correction."
NCBI gene IDs:
"TNF: 21926"
Figure legend: "C pcDNA3-based constructs expressing MAVS-Region III-dimer, trimer and tetramer were transfected into HEK293T cells respectively. ISG54 induction were measured thirty-six hours after transfection by quantitative PCR (qPCR)."
NCBI gene IDs:
"MAVS: 
ISG54: 3433"
Figure legend: "F pcDNA3-FLAG-TRAF3IP3 (full-length and truncated forms) and pcDNA3-HA-MAVS were transfected into HEK293T cells, which were harvested thirty-six hours post transfection. Co-IP experiments were performed with anti-HA antibody, followed by immunoblotting."
NCBI gene IDs:
"FLAG: 
HA: 
MAVS: 57506
TRAF3IP3: 80342"
Figure legend: "G Human cells, including THP1, HeLa, HEK293, HEK293T as well as Traf3ip3-/- HEK293T, were lysed and subjected to immunoblotting to examine TRAF3IP3 expression."
NCBI gene IDs:
"Traf3ip3: 80342"
Figure legend: "A Three pairs of small interfering RNA against TRAF3IP3 were transfected into HEK293T cells respectively and immunoblotting were then employed to examine the knockdown efficiency. A pair of scrambled RNA oligoes was transfected and signified as con."
NCBI gene IDs:
"TRAF3IP3: 80342"
Figure legend: "B Three pairs of si-TRAF3IP3 together with IFNβ-luciferase reporter were transfected into HEK 293T cells. Twenty-four hours after transfection, the cells were infected with (SeV) or without (mock) Sendai virus, which were harvested six hours post infection to measure the luciferase activity."
NCBI gene IDs:
"luciferase: 
IFNβ: 3456
TRAF3IP3: 80342"
Figure legend: "C Si-TRAF3IP3 (oligo #1) were transfected into HEK 293 cells, which were then treated with mock, VSV, SeV, poly(I:C) or HSV-1. After various treatments, IFNB inductions were measured by qPCR."
NCBI gene IDs:
"IFNB: 3456
TRAF3IP3: 80342"
Figure legend: "D Immunoblotting to detect TRAF3IP3 in wild type and Traf3ip3-/- HEK293T cells."
NCBI gene IDs:
"Traf3ip3: 80342"
Figure legend: "E Wild type and Traf3ip3-/- HEK293T cells were treated with or without VSV, SeV or poly (I:C) as indicated for twelve hours. IFNB induction was measured by qPCR."
NCBI gene IDs:
"IFNB: 3456
Traf3ip3: 80342"
Figure legend: "F Wild type and Traf3ip3-/- HEK293T cells were infected with GFP-VSV. Fluorescent images were taken to examine GFP-VSV proliferation at eight hours post infection (left). Scale bar represents 10 micrometers. GFP-VSV titers were quantitated by plaque assay (right)."
NCBI gene IDs:
"GFP: 
Traf3ip3: 80342"
Figure legend: "G Various expression constructs were transfected into WT and Traf3ip3-/- HEK293T cells. Thirty-six hours after transfection, IFNB induction was measured by qPCR."
NCBI gene IDs:
"IFNB: 3456
Traf3ip3: 80342"
Figure legend: "H Mavs-/- HEK293T cells were transfected with empty vector, pcDNA-FLAG-MAVS, pcDNA-FLAG-MAVS-(Region III only), or pcDNA-FLAG-MAVS-(ΔRegion III), together with pcDNA3-FLAG-TRAF3IP3 or not as indicated. Twenty-four hours after transfection, cells were infected with SeV for twelve hours. IFNB induction was measured by qPCR."
NCBI gene IDs:
"FLAG: 
IFNB: 3456
Mavs: 57506
MAVS: 57506
TRAF3IP3: 80342"
Figure legend: "A The experiment was performed as described in Fig 2C. Instead of IFNB, ISG54 and IL6 inductions were measured by qPCR."
NCBI gene IDs:
"ISG54: 3433
IFNB: 3456
IL6: 3569"
Figure legend: "B HEK293 cells were transfected with si-TRAF3IP3 oligos and then treated with various stimuli. Following subcellular fractionation, S5 fractions were obtained and subjected to native PAGE for detecting IRF3 dimer by immunoblotting. The whole cell lysates were also subjected to SDS-PAGE for anti- IRF3 and tubulin immunoblotting."
NCBI gene IDs:
"TRAF3IP3: 80342"
Figure legend: "C The experiment was performed as described in Fig 2E. ISG54 and IL6 induction was measured by qPCR."
NCBI gene IDs:
"ISG54: 3433
IL6: 3569"
Figure legend: "D Wild type and Traf3ip3-/- HEK293T cells were infected with or without VSV. At indicated time points, Cells were collected and analyzed by immunoblotting. Following subcellular fractionation, S5 fractions were subjected to native PAGE to examine IRF3 dimer, and P5 fractions contained mitochondria were subjected to SDD-AGE to examine MAVS aggregation. The mitochondrial outer membrane protein Prohibitin was immunoblotted as an internal control."
NCBI gene IDs:
"Traf3ip3: 80342"
Figure legend: "A pcDNA-FLAG-TRADD and pcDNA-FLAG-TRAF3IP3 were transfected into HEK293T cells at increasing amount respectively. ISG54 and IL6 induction were measured thirty-six hours post-transfection by qPCR. Expression levels were shown in Fig EV4B. All data are presented as the mean values based on three independent experiments, and error bars indicate s.d. P values were determined by unpaired two-tailed Student's t-test. *P&lt;0.05, **P&lt;0.01 and ***P&lt;0.001 NS indicates no statistically significant difference."
NCBI gene IDs:
"FLAG: 
ISG54: 3433
IL6: 3569
TRADD: 8717
TRAF3IP3: 80342"
Figure legend: "B HEK293T cells were transfected with pcDNA3-HA-TRAF3IP3, in combination with pcDNA3-FLAG- RIG-I, MAVS, TBK1, IRF3, TRAF2, TRAF3, TRAF5, or TRAF6 as indicated. Thirty-six hours after transfection, cells were collected and anti-HA immunoprecipitations were performed. IP products were subjected to immunoblotting."
NCBI gene IDs:
"FLAG: 
HA: 
RIG-I: 23586
IRF3: 3661
MAVS: 57506
TBK1: 29110
TRAF2: 7186
TRAF3: 7187
TRAF3IP3: 80342
TRAF5: 7188
TRAF6: 7189"