Sample Set Annotation Tool: In vitro responses of fibroblasts from patients with TBK1 deficiency after TLR3 dependent and independent stimuli. GSE38652

Study Design
Assay
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Purpose

We report here two unrelated HSE patients carrying different heterozygous mutations (D50A and G159A) in TBK1, the gene encoding TANK-binding kinase 1, a kinase at the crossroads of multiple IFN-inducing signaling pathways. Both mutant TBK1 alleles are loss-of-function, but through different mechanisms: protein instability (D50A) or a loss of kinase activity (G159A). Both are also associated with an autosomal dominant (AD) trait, but by different mechanisms: haplotype-insufficiency (D50A) or negative dominance (G159A). A defect in poly(I:C)-induced TLR3 responses can be detected in fibroblasts heterozygous for G159A, but not for D50A TBK1.

Hypothesis

Experimental Design

Skin fibroblast cell lines were derived from healthy controls (n=3), patients with deficiencies for TBK1 (n=2), TLR3 (n=2), STAT1 (n=1) and cultured for 2 or 8 hours in the presence of IFNa (105 IU/ml), IL1b (20ng/ml), or poly I:C (25ug/ml) or left unstimulated for the same length of time.

Experimental Variables

Controls

Methods

Additional Information

Expected Samples:

58 Samples Loaded: 58

Species

Human (Homo sapiens)

Sample Source

Fibroblast

Disease

TBK1 deficiency, TLR3 deficiency, STAT1 deficiency

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	!Sample Title	Gender	group	concentration	stimulation
GSM946860	P1_IFNa_2h	female	AR TBK1 IFNa 2h	10^5 IU/ml	IFNa
GSM946861	TLR3_PIC_2h	male	AR TLR3 PIC 2h	25ug/ml	Poly I:C
GSM946862	TLR3_IFNa_2h	male	AR TLR3 IFNa_2h	10^5 IU/ml	IFNa
GSM946863	TLR3p_IL1b_8h	female	AR TLR3 IL1b 8h	20ng/ml	IL1b
GSM946864	C1_IL1b_8h	male	Control IL1b 8h	20ng/ml	IL1b

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sampleset4000038_sampleannotations_Group.csv Sample Set Spreadsheet
sampleset4000038_sampleannotations_Group.csv Sample Set Spreadsheet
sampleset4000038_sampleannotations_Group.csv Sample Set Spreadsheet
sampleset4000038_sampleannotations_Group.csv Sample Set Spreadsheet

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Sample ID	!Sample Title	Gender	Group	Concentration	Stimulation	Timepoints
GSM946860	P1_IFNa_2h	female	AR TBK1 IFNa 2h	10^5 IU/ml	IFNa	2h
GSM946861	TLR3_PIC_2h	male	AR TLR3 PIC 2h	25ug/ml	Poly I:C	2h
GSM946862	TLR3_IFNa_2h	male	AR TLR3 IFNa_2h	10^5 IU/ml	IFNa	2h
GSM946863	TLR3p_IL1b_8h	female	AR TLR3 IL1b 8h	20ng/ml	IL1b	8h
GSM946864	C1_IL1b_8h	male	Control IL1b 8h	20ng/ml	IL1b	8h
GSM946865	C1_PIC_2h	male	Control PIC 2h	25ug/ml	Poly I:C	2h
GSM946866	C1_IL1b_2h	male	Control IL1b 2h	20ng/ml	IL1b	2h
GSM946867	P1_IL1b_8h	female	AR TBK1 IL1b 8h	20ng/ml	IL1b	8h
GSM946868	C16_PIC_8h	male	Control PIC 8h	25ug/ml	Poly I:C	8h
GSM946869	STAT1_NS_	male	AR STAT1 NS		NS
GSM946870	STAT1_IFNa_8h	male	AR STAT1 IFNa 8h	10^5 IU/ml	IFNa	8h
GSM946871	P2_IFNa_2h	female	AR TBK1 IFNa 2h	10^5 IU/ml	IFNa	2h
GSM946872	P2_PIC_2h	female	AR TBK1 PIC 2h	25ug/ml	Poly I:C	2h
GSM946873	P1_NS_	female	AR TBK1 NS		NS
GSM946874	C8_IL1b_8h	male	Control IL1b 8h	20ng/ml	IL1b	8h
GSM946875	P1_PIC_2h	female	AR TBK1 PIC 2h	25ug/ml	Poly I:C	2h
GSM946876	STAT1_PIC_2h	male	AR STAT1 PIC 2h	25ug/ml	Poly I:C	2h
GSM946877	C1_PIC_8h	male	Control_PIC_8h	25ug/ml	Poly I:C	8h
GSM946878	C16_IFNa_2h	male	Control IFNa 2h	10^5 IU/ml	IFNa	2h
GSM946879	P1_IL1b_2h	female	AR TBK1 IL1b 2h	20ng/ml	IL1b	2h
GSM946880	C16_IL1b_8h	male	Control IL1b 8h	20ng/ml	IL1b	8h
GSM946881	STAT1_IL1b_8h	male	AR STAT1 IL1b 8h	20ng/ml	IL1b	8h
GSM946882	C8_IFNa_8h	male	Control IFNa 8h	10^5 IU/ml	IFNa	8h
GSM946883	C1_IFNa_8h	male	Control IFNa 8h	10^5 IU/ml	IFNa	8h
GSM946884	TLR3_IFNa_8h	male	AR TLR3 IFNa 8h	10^5 IU/ml	IFNa	8h
GSM946885	C16_NS_	male	Control NS		NS
GSM946886	C1_NS_	male	Control NS		NS
GSM946887	STAT1_PIC_8h	male	AR STAT1 PIC 8h	25ug/ml	Poly I:C	8h
GSM946888	TLR3_NS_	male	AR TLR3 NS		NS
GSM946889	TLR3_IL1b_8h	male	AR TLR3 IL1b 8h	20ng/ml	IL1b	8h
GSM946890	C8_NS_	male	Control NS		NS
GSM946891	P2_IL1b_2h	female	AR TBK1 IL1b 2h	20ng/ml	IL1b	2h
GSM946892	C1_IFNa_2h	male	Control IFNa 2h	10^5 IU/ml	IFNa	2h
GSM946893	C8_IL1b_2h	male	Control IL1b 2h	20ng/ml	IL1b	2h
GSM946894	C16_IL1b_2h	male	Control IL1b 2h	20ng/ml	IL1b	2h
GSM946895	C8_PIC_8h	male	Control PIC 8h	25ug/ml	Poly I:C	8h
GSM946896	TLR3_PIC_8h	male	AR TLR3 PIC 8h	25ug/ml	Poly I:C	8h
GSM946897	C16_PIC_2h	male	Control PIC 2h	25ug/ml	Poly I:C	2h
GSM946898	P2_PIC_8h	female	AR TBK1 PIC 8h	25ug/ml	Poly I:C	8h
GSM946899	P2_IL1b_8h	female	AR TBK1 IL1b 8h	20ng/ml	IL1b	8h
GSM946900	P1_PIC_8h	female	AR TBK1 PIC 8h	25ug/ml	Poly I:C	8h
GSM946901	C8_IFNa_2h	male	Control IFNa 2h	10^5 IU/ml	IFNa	2h
GSM946902	P2_NS_	female	AR TBK1 NS		NS
GSM946903	TLR3p_NS_	female	AR TLR3 NS		NS
GSM946904	TLR3p_IFNa_8h	female	AR TLR3 IFNa 8h	10^5 IU/ml	IFNa	8h
GSM946905	C8_PIC_2h	male	Control PIC 2h	25ug/ml	Poly I:C	2h
GSM946906	C16_IFNa_8h	male	Control IFNa 8h	10^5 IU/ml	IFNa	8h
GSM946907	STAT1_IL1b_2h	male	AR STAT1 IL1b 2h	20ng/ml	IL1b	2h
GSM946908	P1_IFNa_8h	female	AR TBK1 IFNa 8h	10^5 IU/ml	IFNa	8h
GSM946909	P2_IFNa_8h	female	AR TBK1 IFNa 8h	10^5 IU/ml	IFNa	8h
GSM946910	STAT1_IFNa_2h	male	AR STAT1 IFNa 2h	10^5 IU/ml	IFNa	2h
GSM946911	TLR3p_IFNa_2h	female	AR TLR3 IFNa 2h	10^5 IU/ml	IFNa	2h
GSM946912	TLR3p_PIC_8h	female	AR TLR3 PIC 8h	25ug/ml	Poly I:C	8h
GSM946913	TLR3_IL1b_2h	male	AR TLR3 IL1b 2h	20ng/ml	IL1b	2h
GSM946914	TLR3p_IL1b_2h	female	AR TLR3 IL1b 2h	20ng/ml	IL1b	2h
GSM946915	TLR3p_PIC_2h	female	AR TLR3 PIC 2h	25ug/ml	Poly I:C	2h
GSM946916	P1_IFNa_2h, rep	female	AR TBK1 IFNa 2h	10^5 IU/ml	IFNa	2h
GSM946917	TLR3_PIC_2h, rep	male	AR TLR3 PIC 2h	25ug/ml	Poly I:C	2h

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