EMBO/SourceData huggingface dataset:
Figure legend: "Model predictions of IFNα-induced dynamics of occupied GAS bindings sites (OccGASbs) and of occupied ISRE binding sites (OccISREbs) in Huh7.5 cells without prestimulation and in cells prestimulated for 24 hours with 28 pM and 280 pM IFNα that were subsequently stimulated with 1400 pM IFNα. Model predictions were performed using the prediction profile likelihood method. Lines with shading represent model predictions with 68% confidence intervals. For experimental validation, growth factor-depleted Huh7.5 cells were prestimulated with 0 pM, 28 pM and 280 pM IFNα. After 24 hours cells were stimulated with 1400 pM IFNα and IFNα-induced expression of target genes was measured by qRT-PCR. RNA levels were normalized to the geometric mean of reference genes GAPDH, HPRT and TBP, averaged and displayed as fold change, represented by filled circles with errors representing standard error of the mean calculated from biological replicates (N=3). Except for gene-specific parameters (mRNA synthesis and degradation rates, time-delay parameter and Hill coefficient), qRT-PCR data were used for model validation but not for model calibration."
NCBI gene IDs:
"GAPDH: 
GAS: 
HPRT: 
ISRE: 
TBP: "
Figure legend: "Knockdown of USP18 results in sustained signaling. USP18 knockdown efficiency determined by quantitative immunoblotting of cytoplasmic lysates of Huh7.5 transfected with USP18 siRNA relative to parental Huh7.5 cells and Huh7.5 cells transfected with non-targeting siRNA. Cells were stimulated with 1400 pM IFNα for 24 hours. Error bars represent 1σ confidence intervals estimated from biological replicates (N=6 to N=10) (left). Model fit and experimental data of Huh7.5 cells transfected with control siRNA or USP18 siRNA are shown. Cells were transfected with USP18 siRNA or control siRNA 1 day prior to growth factor-depletion. Next, cells were prestimulated with 1400 pM IFNα (yellow background) and stimulated with 1400 pM IFNα at 24 hours or untreated (white background). IFNα-induced phosphorylation of STAT1 and STAT2 and induction of USP18 and tSTAT1, comprising both phosphorylated and unphosphorylated STAT1 protein, are displayed. Experimental data were obtained by quantitative immunoblotting using chemiluminescence and CCD camera device (ImageQuant). For model purposes data in control siRNA and untransfected Huh7.5 are combined to one condition. Data from multiple time courses scaled together is displayed as filled circles with errors representing 1σ confidence interval estimated from biological replicates (N=2 to N=10) using a combined scaling and error model. Lines represent model trajectories."
NCBI gene IDs:
"USP18: 11274"
Figure legend: "Overexpression of Huh7.5 is not sufficient to explain negative memory. Induced expression of USP18 after treatment of Huh7.5-TetON-USP18 and Huh7.5-TetON-control cells with doxycycline for 24 hours in comparison with parental Huh7.5 cells treated with 1400 pM IFNα for 24 hours. Analysis was performed by quantitative immunoblotting. Error bars represent 1σ confidence intervals estimated from biological replicates (N=3 to N=5) (left). Model fits and experimental data of Huh7.5-TetON-USP18 treated with doxycycline for 24 hours and stimulated with 1400 pM IFNα or parental Huh7.5 cells prestimulated with 0 or 1400 pM IFNα and stimulated with 1400 pM IFNα after 24 hours are shown. The dynamics of IFNα-induced phosphorylation of STAT1 and STAT2 and induction of USP18 are depicted. Experimental data was obtained by quantitative immunoblotting using chemiluminescence and CCD camera device (ImageQuant). For modeling purposes data from Huh7.5-TetON empty vector control and untransduced Huh7.5 are combined to one condition. Data is displayed as filled circles with errors representing 1σ confidence-interval estimated from biological replicates (N=3 to N=4) using a combined scaling and error model. Line represents model trajectories."
NCBI gene IDs:
"USP18: 11274"
Figure legend: "(C) ELISA of IL-1β in the supernatants of wild type (WT), NLRP3 knockout (KO) #1 or AIM2 KO#1 THP-1 cells left untreated (UT), or pretreated with LPS (500 ng/ml, 3 hrs) followed by ATP (5 mM, 6 hrs) stimulation, or stimulated with poly (dA:dT) (1mg/ml, 6 hrs), or infected with ZIKV (MOI=1, 36 hrs)."
NCBI gene IDs:
"AIM2: 9447
NLRP3: 114548"
Figure legend: "(D) ELISA of IL-1β in the supernatants of two clones of NLRP3 KO THP-1 cells with or without ZIKV infection (MOI=1) at the indicated time points."
NCBI gene IDs:
"NLRP3: 114548"
Figure legend: "(E) ELISA of IL-1β in the supernatants of PBMCs from two donors transfected with control (ctrl) siRNA or NLRP3 siRNA followed by ZIKV infection (MOI=1) for 36 hrs."
NCBI gene IDs:
"NLRP3: 114548"
Figure legend: "(F) ELISA of IL-1β in the supernatant of WT, NLRP3 KO or AIM2 KO THP-1 cells with ZIKV (MR766 or GZ01) (MOI=1) or DENV-2 (MOI=1) infection for 36 hrs."
NCBI gene IDs:
"AIM2: 9447
NLRP3: 114548"
Figure legend: "(I) Immunoblot analysis of supernatants and cell extracts of 293T cells transfected with plasmids expressing NLRP3, ASC, pro-caspase-1 and pro-IL-1β together with NS1."
NCBI gene IDs:
"NS1: 
caspase-1: 834
IL-1β: 3553
NLRP3: 114548
ASC: 29108"
Figure legend: "(J) Immunoblot analysis of protein extracts of Flag-tagged NS1-inducible THP-1 cells treated with increasing doses of doxycycline (Dox) for 24 hrs."
NCBI gene IDs:
"Flag: 
NS1: "
Figure legend: "(K) ELISA of IL-1β in the supernatants of Flag-NS1-inducible THP-1 cells left unprimed then treated with ATP (5 mM, 6 hrs) or poly (I:C) (2 mg/ml, 6 hrs), or pre-treated with LPS (500 ng/ml, 3 hrs) followed by ATP (5 mM, 6 hrs) or poly (I:C) (2 mg/ml, 6 hrs) stimulation."
NCBI gene IDs:
"Flag: 
NS1: "
Figure legend: "(L) Immunoblot analysis of supernatants (Sup) and cell extracts (Lys) of Flag-NS1-inducible THP-1 cells pre-treated with LPS (500 ng/ml, 3 hrs) followed by ATP (5 mM, 6 hrs) or poly (I:C) (2 mg/ml, 6 hrs) stimulation."
NCBI gene IDs:
"Flag: 
NS1: "
Figure legend: "(B) Relative qRT-PCR analysis of ZIKV RNA in wild type (WT) or NLRP3 knockout (KO) THP-1 cells infected with ZIKV (MOI=1) for the indicated time points."
NCBI gene IDs:
"NLRP3: 114548"
Figure legend: "(C) Immunoblot analysis of extracts of WT or Nlrp3-/- BMDMs by the indicated antibodies."
NCBI gene IDs:
"Nlrp3: 114548"
Figure legend: "(D) Relative qRT-PCR analysis of ZIKV RNA in WT or Nlrp3-/- BMDMs infected with ZIKV (MOI=1) for the indicated time points."
NCBI gene IDs:
"Nlrp3: 114548"
Figure legend: "(E) Plaque titration of ZIKV in supernatants of WT or Nlrp3-/- BMDMs infected with ZIKV (MOI=1) for the indicated time points."
NCBI gene IDs:
"Nlrp3: 114548"
Figure legend: "(F) Immunoblot analysis of extracts of WT or caspase-1 KO THP-1 cells by the indicated antibodies."
NCBI gene IDs:
"caspase-1: 834"
Figure legend: "(G) Relative qRT-PCR analysis of ZIKV RNA in WT or caspase-1 KO THP-1 cells infected with ZIKV (MOI=1) for the indicated time points."
NCBI gene IDs:
"caspase-1: 834"
Figure legend: "(H) Relative qRT-PCR analysis of ZIKV RNA in NS-1-inducible THP-1 cells treated with or without doxycycline (Dox), then left untreated or treated with Ac-YVAD-cmk (20 μΜ) for 3 hrs followed by ZIKV infection (MOI=1) for the indicated time points."
NCBI gene IDs:
"NS-1: "
Figure legend: "(I) Relative qRT-PCR analysis of NLRP3 knockdown efficiency in PBMCs from two donors."
NCBI gene IDs:
"NLRP3: 114548"
Figure legend: "(J) Relative qRT-PCR analysis of ZIKV RNA in PBMCs transfected with control siRNA or NLRP3 siRNA then infected with ZIKV (MOI=1) for 36 hrs."
NCBI gene IDs:
"NLRP3: 114548"
Figure legend: "(A) Co-immunoprecipitation and immunoblot analysis of extracts of 293T cells transfected with HA-NS1 together with Flag-NLRP3, Flag-ASC, Flag-caspase-1 and Flag-IL-1β. WCL, whole cell lysates."
NCBI gene IDs:
"Flag: 
HA: 
NS1: 
caspase-1: 834
IL-1β: 3553
NLRP3: 114548
ASC: 29108"
Figure legend: "(B) Co-immunoprecipitation and immunoblot analysis of extracts of NS1-inducible THP-1 cells, which expressed Flag-tagged NS1, treated with or without doxycycline (Dox) (100 ng/ml)."
NCBI gene IDs:
"NS1: "
Figure legend: "(D) Immunoblot analysis of extracts of 293T cells transfected with Flag-caspase-1 together with increasing amount of HA-NS1. Below, caspase-1 mRNA RT-PCR; RPL13A mRNA RT-PCR serves as a loading control."
NCBI gene IDs:
"RPL13A: 
Flag: 
HA: 
NS1: 
caspase-1: 834"
Figure legend: "(E) Immunoblot analysis of extracts of 293T cells transfected with Flag-caspase-1 together with increasing amount of HA-DENV-2-NS1."
NCBI gene IDs:
"Flag: 
HA: 
NS1: 
caspase-1: 834"
Figure legend: "(F) Immunoblot analysis of extracts of 293T cells transfected with Flag-caspase-1 together with empty vector or HA-NS1 followed by cycloheximide (CHX) treatment (100 μg/ml) for the indicated time points."
NCBI gene IDs:
"Flag: 
HA: 
NS1: 
caspase-1: 834"
Figure legend: "(G) Immunoblot analysis of extracts of 293T cells transfected with Flag-caspase-1 together with empty vector or HA-NS1 then treated with MG132 (10 mM), Lactacystin (5 μM), Carfilzomib (100 mM) or CQ (50 mM) for 6 hrs."
NCBI gene IDs:
"Flag: 
HA: 
NS1: 
caspase-1: 834"
Figure legend: "(H) Co-immunoprecipitation and immunoblot analysis of extracts of Flag-NS1-inducible THP-1 cells treated with or without Dox (100 ng/ml)."
NCBI gene IDs:
"Flag: 
NS1: "
Figure legend: "(I) Co-immunoprecipitation and immunoblot analysis of extracts of 293T cells transfected with plasmids expressing Flag-caspase-1 and indicated HA-tagged WT ubiquitin or mutants (K6-, K11-, K27-, K29-, K33-, K48- and K63-Only), together with empty vector or Myc-NS1, followed by MG132 (10 mM) treatment for 6 hrs."
NCBI gene IDs:
"Flag: 
HA: 
Myc: 
NS1: 
ubiquitin: 
caspase-1: 834"
Figure legend: "(A) Immunoblot analysis of extracts of wild type (WT) and USP8 knockout (KO) 293T cells transfected with Flag-caspase-1 together with empty vector or Myc-NS1."
NCBI gene IDs:
"Flag: 
Myc: 
NS1: 
caspase-1: 834
USP8: 9101"
Figure legend: "(B) Immunoblot analysis of extracts of transfected with Flag-caspase-1 together with empty vector or Myc-USP8 then treated with or without MG132 (10 mM) for 6 hrs."
NCBI gene IDs:
"Flag: 
Myc: 
caspase-1: 834
USP8: 9101"
Figure legend: "(C) Co-immunoprecipitation and immunoblot analysis of extracts of Flag-NS1-inducible THP-1 cells treated with or without Dox (100 ng/ml) then transfected with or without poly (I:C) (2 mg/ml, 6 hrs)."
NCBI gene IDs:
"Flag: 
NS1: "
Figure legend: "(D) Co-immunoprecipitation and immunoblot analysis of extracts of 293T cells transfected with Flag-caspase-1 and Myc-USP8 together with HA-NS1 followed by MG132 treatment (10 mM) for 6 hrs."
NCBI gene IDs:
"Flag: 
HA: 
Myc: 
NS1: 
caspase-1: 834
USP8: 9101"
Figure legend: "(F) Co-immunoprecipitation and immunoblot analysis of extracts of WT and USP8 KO THP-1 cells infected with ZIKV (MOI=1) for 24 hrs."
NCBI gene IDs:
"USP8: 9101"
Figure legend: "(G) Co-immunoprecipitation and immunoblot analysis of extracts of 293T cells transfected with plasmids expressing Flag-caspase-1 and indicated HA-tagged WT ubiquitin (Ub) or mutants (K6-, K11-, K27-, K29-, K33-, K48- and K63-Only), together with empty vector or Myc-USP8, followed by MG132 (10 mM) treatment for 6 hrs."
NCBI gene IDs:
"Flag: 
HA: 
Myc: 
Ub: 
ubiquitin: 
caspase-1: 834
USP8: 9101"
Figure legend: "(H) Immunoblot analysis of extracts of WT or USP8 KO 293T cells transfected with Flag-caspase-1, HA-K11-Ub together with empty vector or Myc-NS1, followed by two-step immunoprecipitation with anti-Flag beads and immunoblot analysis with anti-HA."
NCBI gene IDs:
"Flag: 
HA: 
Myc: 
NS1: 
Ub: 
caspase-1: 834
USP8: 9101"
Figure legend: "(I) Co-immunoprecipitation and immunoblot analysis of extracts of USP8 KO 293T cells transfected with Flag-caspase-1 and HA-K11-Ub together with WT or inactive mutant C786A of USP8."
NCBI gene IDs:
"Flag: 
HA: 
Ub: 
caspase-1: 834
USP8: 9101"
Figure legend: "(A) Immunoblot analysis of extracts of 293T cells transfected with empty vector or HA-NS1 together with Flag-caspae-1 wild type (WT) and mutants (K37R, K44R or K134R). Lower panel shows the intensity analysis of the bands from the three independent experiments."
NCBI gene IDs:
"Flag: 
HA: 
NS1: 
caspae-1: 834"
Figure legend: "(B) Co-immunoprecipitation and immunoblot analysis of extracts of 293T cells transfected with HA-K11-ubiquitin (Ub) together with Flag-caspase-1 (WT, K37R, K44R, K134R)."
NCBI gene IDs:
"Flag: 
HA: 
Ub: 
ubiquitin: 
caspase-1: 834"
Figure legend: "(C) Co-immunoprecipitation and immunoblot analysis of extracts of 293T cells transfected with Flag-caspase-1 (WT or K134R) and HA-K11-Ub, together with empty vector or Myc-NS1. Lower panel shows the intensity analysis of the bands from the three independent experiments."
NCBI gene IDs:
"Flag: 
HA: 
Myc: 
NS1: 
Ub: 
caspase-1: 834"
Figure legend: "(D) Co-immunoprecipitation and immunoblot analysis of extracts of 293T cells transfected with Flag-caspase-1 (WT or K134R) and HA-K11-Ub, together with empty vector or Myc-USP8. Lower panel shows the intensity analysis of the bands from the three independent experiments."
NCBI gene IDs:
"Flag: 
HA: 
Myc: 
Ub: 
caspase-1: 834
USP8: 9101"
Figure legend: "(A) Relative qRT-PCR analysis of IFNB, IFIT2 and IFIT1 mRNA levels in wild type (WT) or caspase-1 knockout (KO) THP-1 cells infected with ZIKV (MOI=1) for the indicated time points."
NCBI gene IDs:
"caspase-1: 834
IFIT1: 3434
IFIT2: 3433
IFNB: 3456"
Figure legend: "(B) Relative qRT-PCR analysis of IFNB mRNA levels in THP-1 cells left untreated or treated with LPS (500 ng/ml, 3 hrs) and ATP (5 mM, 6 hrs), followed by ZIKV infection (MOI=1) for the indicated time points."
NCBI gene IDs:
"IFNB: 3456"
Figure legend: "(C) Relative qRT-PCR analysis of IFNB mRNA levels in wild type (WT) or NLRP3 knockout (KO) THP-1 cells infected with ZIKV (MOI=1) for the indicated time points."
NCBI gene IDs:
"IFNB: 3456
NLRP3: 114548"
Figure legend: "(D) Relative qRT-PCR analysis of IFNB , IFIT2 and IFIT1 mRNA levels in Flag-NS1-inducible THP-1 cells treated with or without Dox then left untreated or treated with YVAD (20 μM) for 3 hrs, followed by ZIKV infection (MOI=1) for the indicated time points."
NCBI gene IDs:
"Flag: 
NS1: 
IFIT1: 3434
IFIT2: 3433
IFNB: 3456"
Figure legend: "(E) Relative qRT-PCR analysis of IFNB mRNA in PBMCs transfected with control siRNA or NLRP3 siRNA then infected with ZIKV (MOI=1) for 36 hrs."
NCBI gene IDs:
"IFNB: 3456
NLRP3: 114548"
Figure legend: "(F) Relative qRT-PCR analysis of IFNB mRNA in PBMCs treated with DMSO or Ac-YVAD-cmk (20μM) for 3hrs followed by ZIKV infection (MOI=1) for 36 hrs."
NCBI gene IDs:
"IFNB: 3456"
Figure legend: "(H) ELISA of IL-1β production in brain of WT or Nlrp3-/- 1-day-old neonatal mice (n=3 per group) intracerebrally injected with 1×105 plaque-forming units (PFU) of ZIKV for 5 days."
NCBI gene IDs:
"Nlrp3: 114548"
Figure legend: "(I) Relative qRT-PCR analysis of IFNB mRNA levels in brain tissues of WT or Nlrp3-/- neonatal mice with or without ZIKV infection"
NCBI gene IDs:
"IFNB: 15977
Nlrp3: 114548"
Figure legend: "(J) ELISA of IFN-β production in brains of WT or Nlrp3-/- neonatal mice"
NCBI gene IDs:
"Nlrp3: 114548"
Figure legend: "(K) Relative qRT-PCR analysis of ZIKV RNA levels in brain tissues of WT or Nlrp3-/- neonatal mice with or without ZIKV infection"
NCBI gene IDs:
"Nlrp3: 114548"
Figure legend: "(L) Plaque titration of ZIKV in brain tissues of WT or Nlrp3-/- neonatal mice"
NCBI gene IDs:
"Nlrp3: 114548"
Figure legend: "(M) Body weight gain of WT and Nlrp3-/- neonatal mice (n=4 per group) inoculated with ZIKV (1×105 PFUs)."
NCBI gene IDs:
"Nlrp3: 114548"
Figure legend: "(A) Relative qRT-PCR analysis of ZIKV RNA levels in wild type (WT) or cGAS knockout (KO) THP-1 cells after ZIKV infection (MOI=1) for indicated time points."
NCBI gene IDs:
"cGAS: 115004"
Figure legend: "(B) Relative qRT-PCR analysis of IFNΒ, IFIT2 and IFIT1 mRNA levels in WT or cGAS KO THP-1 cells after ZIKV infection (MOI=1) for indicated time points."
NCBI gene IDs:
"cGAS: 115004
IFIT1: 3434
IFIT2: 3433
IFNΒ: 3456"
Figure legend: "(C) Relative qRT-PCR analysis of ZIKV RNA and IFNB mRNA levels in PBMCs transduced with Cas9 and small guide RNA targeting GFP, cGAS or NLRP3 and infected with ZIKV (MOI=1) for 36 hrs."
NCBI gene IDs:
"Cas9: 
GFP: 
cGAS: 115004
IFNB: 3456
NLRP3: 114548"
Figure legend: "(D) Relative qRT-PCR analysis of ZIKV RNA and IFNΒ mRNA levels in WT or cGAS KO THP-1 cells treated with or without YVAD (20 μM), followed by ZIKV infection (MOI=1) for indicated times points."
NCBI gene IDs:
"cGAS: 115004
IFNΒ: 3456"
Figure legend: "(E) Immunoblot analysis of extracts of Flag-cGAS-overexpressed THP-1 cells treated with or without YVAD (20 μM) then infected with ZIKV (MOI=5) for 24 hrs or infected with HSV-1 (MOI=1) for 24 hrs."
NCBI gene IDs:
"Flag: 
cGAS: 214763"
Figure legend: "Immunoblot analysis of WT, NLRP3 KO (F) THP-1 cells infected with ZIKV (MOI=1) for the indicated time points."
NCBI gene IDs:
"NLRP3: 114548"
Figure legend: "Immunoblot analysis of WT, caspase-1 KO (G) THP-1 cells infected with ZIKV (MOI=1) for the indicated time points."
NCBI gene IDs:
"caspase-1: 834"
Figure legend: "(H) Immunoblot analysis of extracts of WT or Nlrp3-/- BMDMs infected with ZIKV (MOI=1) for the indicated time points."
NCBI gene IDs:
"Nlrp3: 114548"
Figure legend: "(I) Immunoblot analysis of PBMCs from Donor#1 transfected with control siRNA or NLRP3 siRNA followed by ZIKV infection (MOI=1) for the indicated time points."
NCBI gene IDs:
"NLRP3: 114548"
Figure legend: "(J) Immunoblot analysis of extracts of 293T cells transfected with Myc-cGAS (tagged on C-terminal), GFP-ASC, Flag-caspase-1, together with empty vector or HA-NS1."
NCBI gene IDs:
"Flag: 
GFP: 
HA: 
Myc: 
NS1: 
caspase-1: 834
cGAS: 214763
ASC: 29108"
Figure legend: "(K) Relative qRT-PCR analysis of ZIKV RNA and IFNB mRNA levels in WT, cGAS KO THP-1 cells as well as cGAS KO THP-1 cells reconstituted with WT or D140A/D157A mutant of cGAS, followed by ZIKV infection (MOI=1) for 24 hrs."
NCBI gene IDs:
"cGAS: 115004
IFNB: 3456"
Figure legend: "B Heat map showing p53‐dependent regulation of \"EMT\"‐ and \"stemness\"‐related genes in KNCtumor cells. Fold change relative to control cells is displayed in a green red color scheme for selected genes with FClog2 1.0 or FClog2 &gt; −1.0."
NCBI gene IDs:
"p53: 22059"
Figure legend: "C Statistical analysis of wound healing assay performed in primary KNCtumor cells following p53 depletion. Time‐lapse analyzer software was used to quantify the wound closure rate. Means ± SD are shown from one out of three independent experiments."
NCBI gene IDs:
"p53: 22059"
Figure legend: "D Western blot analysis revealing protein expression levels upon p53 depletion in KNCtumor cells."
NCBI gene IDs:
"p53: 22059"
Figure legend: "E X‐fold mRNA expression of EMT‐related marker genes after p53 depletion in KNCtumor cells. Means ± SD from at least three independent experiments are shown. Asterisks display significance (*P 0.05)."
NCBI gene IDs:
"p53: 22059"
Figure legend: "A Kaplan-Meier curves showing survival of KNC, KPNC, and KPΔNC mice under the control of p48‐Cre pancreas‐specific promoters (P 0.0001 for KPNC or KPΔNC cohorts versus KNC, log‐rank test, for pairwise combination)."
NCBI gene IDs:
"Cre: 
p48: 16391"
Figure legend: "B Relative mRNA expression of NFATc1‐ and EMT‐related marker genes on administration of CsA (1 μM) in KPNC cells. Data represents means ± SD from at least three independent experiments. Asterisks show significance (*P 0.05)."
NCBI gene IDs:
"NFATc1: 18018"
Figure legend: "C Western blot analysis revealing protein expression levels in KPNC cells from the indicated proteins following transfection of siRNA control or siRNA toward NFATc1, respectively."
NCBI gene IDs:
"NFATc1: 18018"
Figure legend: "A Sox2 mRNA expression of pancreatic lysates from KNC, KPNC, and KPC mice, analyzed by real‐time PCR in three independent experiments (means ± SD)."
NCBI gene IDs:
"Sox2: 20674"
Figure legend: "E, F NFATc1 and Sox2 protein expression after (E) NFATc1 depletion or (F) upon CsA (1 μM, 24 h) treatment in Panc1 cells."
NCBI gene IDs:
"NFATc1: 4772"
Figure legend: "G Sox2 and E‐cadherin mRNA expression after NFATc1 depletion in L3.6 cells."
NCBI gene IDs:
"E‐cadherin: 999
NFATc1: 4772
Sox2: 6657"
Figure legend: "I, J ChIP assays show NFATc1 binding to Sox2 enhancer and promoter in KNC tumor cells (I)"
NCBI gene IDs:
"Sox2: 20674"
Figure legend: "I, J ChIP assays show RNA polymerase II binding to Sox2 promoter upon CsA (1 μM, 24 h) treatment in L3.6 cells (J)."
NCBI gene IDs:
"Sox2: 6657"
Figure legend: "L ChIP experiments show NFATc1 binding along with H3K27 acetylation (H3K27ac) mark at the selected Snai1 enhancer region and RNA polymerase II binding at Snai1 promoter in the presence or absence of Sox2 in KPNC tumor cells. Representative results from at least three independent experiments are shown (means ± SD; P 0.05)."
NCBI gene IDs:
"Snai1: 20613
Sox2: 20674"
Figure legend: "M Relative mRNA expression levels of EMT‐related marker genes upon Sox2 depletion in KPNC tumor cells (P 0.05)."
NCBI gene IDs:
"Sox2: 20674"
Figure legend: "N Zeb1 and Snail mRNA levels in L3.6 cells after shRNA‐mediated depletion of Sox2 and transient overexpression of NFATc1 shows that loss of Sox2 significantly rescues NFATc1‐mediated induction of EMT genes (*P 0.05)."
NCBI gene IDs:
"NFATc1: 4772
Snail: 6615
Sox2: 6657
Zeb1: 6935"
Figure legend: "B Relative mRNA expression of NFATc1 and Sox2 in L3.6 cells as well as in KPNCmicetumor cells (adherent versus spheres). Graph represents data from three independent experiments (means ± SD). Asterisks display significance (*P 0.05)."
NCBI gene IDs:
"NFATc1: 18018
Sox2: 20674"
Figure legend: "C Cell sorting was performed to collect CD44 high and low populations in KPNC spheres (left panel), which were analyzed for NFATc1 and Sox2 mRNA expression (right panel)."
NCBI gene IDs:
"NFATc1: 18018
Sox2: 20674"
Figure legend: "D Sox2 mRNA expression upon CsA (1 μM) treatment in L3.6 cells (adherent versus spheres) (*P 0.05)."
NCBI gene IDs:
"Sox2: 6657"
Figure legend: "E Bright‐field light microscopy images as well as quantification of KPNC spheres after transient NFATc1 depletion."
NCBI gene IDs:
"NFATc1: 18018"
Figure legend: "A Expression analysis of indicated miRNAs upon adenoviral re‐expression of p53 in KPΔNC tumor cells, detected by real‐time PCR (P 0.05)."
NCBI gene IDs:
"p53: 22059"
Figure legend: "B Protein expression of EMT marker genes after adenoviral re‐expression of GFP‐tagged p53 in KPΔNC tumor cells."
NCBI gene IDs:
"p53: 22059"
Figure legend: "C, D Protein (C) expression levels of EMT and stemness marker genes upon miRNA‐34a and miRNA‐200c overexpression using specific mimics in KPNC tumor cells. Representative results from at least three independent experiments are shown (means ± SD; P 0.05)."
NCBI gene IDs:
"miRNA‐200c: 723944
miRNA‐34a: 723848"
Figure legend: "C, D mRNA (D) expression levels of EMT and stemness marker genes upon miRNA‐34a and miRNA‐200c overexpression using specific mimics in KPNC tumor cells. Representative results from at least three independent experiments are shown (means ± SD; P 0.05)."
NCBI gene IDs:
"miRNA‐200c: 723944
miRNA‐34a: 723848"
Figure legend: "E Western blot analysis of EMT marker expression in KNC cells following depletion of miR‐200c."
NCBI gene IDs:
"miR‐200c: 723944"
Figure legend: "F ChIP experiments showing NFATc1 binding along with H3K27 acetylation mark at the selected Snai1 enhancer region as well as Sox2 and RNA polymerase II binding at Snai1 promoter after miR‐200c overexpression in KPNC tumor cells. Means ± SD are shown from one out of three independent experiments."
NCBI gene IDs:
"miR‐200c: 723944
Snai1: 20613"
Figure legend: "G ChIP analysis in KP∆NC tumor cells after adenoviral GFP‐tagged p53 overexpression. NFATc1 and H3K27ac binding are illustrated on Snai1 enhancer, and Sox2 and RNA polymerase II binding are demonstrated on Snai1 promoter. Means ± SD are shown from one out of three independent experiments."
NCBI gene IDs:
"Snai1: 20613
p53: 22059"
Figure legend: "H Quantification of KP∆NC tumour cell-derived spheres after adenoviralGFP‐tagged p53 overexpression."
NCBI gene IDs:
"p53: 22059"