Sample Set Annotation Tool: Blood Transcriptional Profiles of TB in South Africa-GSE19442

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

The aim of this study was to compare the transcriptional response to TB in regions of different incidence / prevalence.

Hypothesis

Experimental Design

Whole blood collected in tempus tubes from patients with different spectra of TB disease. All patients were sampled prior to the initiation of any antimycobacterial therapy. Active Pulmonary TB: PTB - All patients confirmed by isolation of Mycobacterium Tuberculosis on culture of sputum. Latent TB: LTB - All patients were screened at a tuberculosis clinic. All were positive by Interferon-Gamma Release assay(IGRA); specifically Quantiferon Gold In-Tube Assay (Cellestis, Australia). Latent patients had no clinical, or microbiological evidence of active infection and were asymptomatic. Experimental Variables: Patient group: Active PTB; Latent TB. There are no healthy controls in this dataset as it was being used for validation only. Controls: Latent TB individuals are used as a control for PTB in this dataset since there are few to no unexposed adult controls in Cape Town.

Experimental Variables

Controls

Methods

The data were analysed using BeadStudio version 1.5.1.3 using the average chip normalization method.

Additional Information

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19442

Expected Samples:

51 Samples Loaded: 51

Species

Human (Homo sapiens)

Sample Source

Whole Blood

Disease

Tuberculosis

Treatment Protocol

Growth Protocol

Extraction Protocol

RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	Age	Ethnicity	Gender	Illness	Sputum Culture
GSM484500	22	Black	Male	PTB	M.tuberculosis
GSM484501	21	Black	Female	PTB	M.tuberculosis
GSM484502	27	Black	Male	PTB	M.tuberculosis
GSM484503	25	Black	Male	PTB	M.tuberculosis
GSM484504	33	Black	Female	LATENT TB	n.a

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Samples Viewer / Editor

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Sample ID	Age	Ethnicity	Gender	Illness	Sputum Culture	Sputum Smear	Tst	!Sample Title	Region of birth	Geographical region	Bcg vaccinated
GSM484500	22	Black	Male	PTB	M.tuberculosis	3+	n.a	PTB_SA_val001	non_UK_born	South Africa	No
GSM484501	21	Black	Female	PTB	M.tuberculosis	1+	n.a	PTB_SA_val002	non_UK_born	South Africa	Yes
GSM484502	27	Black	Male	PTB	M.tuberculosis	3+	n.a	PTB_SA_val003	non_UK_born	South Africa	No
GSM484503	25	Black	Male	PTB	M.tuberculosis	Negative	n.a	PTB_SA_val004	non_UK_born	South Africa	Yes
GSM484504	33	Black	Female	LATENT TB	n.a	n.a	15	LTB_SA_val021	non_UK_born	South Africa	No
GSM484505	19	Black	Female	LATENT TB	n.a	n.a	14	LTB_SA_val022	non_UK_born	South Africa	No
GSM484506	21	Black	Male	LATENT TB	n.a	n.a	15	LTB_SA_val023	non_UK_born	South Africa	No
GSM484507	20	Black	Female	LATENT TB	n.a	n.a	22	LTB_SA_val024	non_UK_born	South Africa	Not Known
GSM484508	24	Black	Female	LATENT TB	n.a	n.a	5	LTB_SA_val025	non_UK_born	South Africa	Not Known
GSM484509	22	Black	Female	LATENT TB	n.a	n.a	20	LTB_SA_val026	non_UK_born	South Africa	Not Known
GSM484510	24	Black	Male	LATENT TB	n.a	n.a	7	LTB_SA_val027	non_UK_born	South Africa	No
GSM484511	18	Black	Female	LATENT TB	n.a	n.a	0	LTB_SA_val028	non_UK_born	South Africa	No
GSM484512	18	Black	Female	LATENT TB	n.a	n.a	15	LTB_SA_val029	non_UK_born	South Africa	No
GSM484513	24	Black	Female	LATENT TB	n.a	n.a	0	LTB_SA_val030	non_UK_born	South Africa	Not Known
GSM484514	22	Black	Male	LATENT TB	n.a	n.a	0	LTB_SA_val031	non_UK_born	South Africa	Not Known
GSM484515	25	Black	Male	PTB	M.tuberculosis	3+	n.a	PTB_SA_val005	non_UK_born	South Africa	Yes
GSM484516	47	Black	Male	PTB	M.tuberculosis	2+	n.a	PTB_SA_val006	non_UK_born	South Africa	No
GSM484517	32	Black	Female	PTB	M.tuberculosis	1+	n.a	PTB_SA_val007	non_UK_born	South Africa	Yes
GSM484518	40	Black	Male	PTB	M.tuberculosis	1+	n.a	PTB_SA_val008	non_UK_born	South Africa	No
GSM484519	46	Black	Female	PTB	M.tuberculosis	3+	n.a	PTB_SA_val009	non_UK_born	South Africa	Yes
GSM484520	18	Black	Male	LATENT TB	n.a	n.a	0	LTB_SA_val032	non_UK_born	South Africa	No
GSM484521	18	Black	Male	LATENT TB	n.a	n.a	4	LTB_SA_val033	non_UK_born	South Africa	No
GSM484522	18	Black	Female	LATENT TB	n.a	n.a	0	LTB_SA_val034	non_UK_born	South Africa	No
GSM484523	20	Black	Female	LATENT TB	n.a	n.a	11	LTB_SA_val035	non_UK_born	South Africa	No
GSM484524	42	Black	Male	PTB	M.tuberculosis	1+	n.a	PTB_SA_val010	non_UK_born	South Africa	No
GSM484525	48	Black	Female	PTB	M.tuberculosis	2+	n.a	PTB_SA_val011	non_UK_born	South Africa	No
GSM484526	27	Black	Male	PTB	M.tuberculosis	2+	n.a	PTB_SA_val012	non_UK_born	South Africa	No
GSM484527	45	Black	Male	PTB	M.tuberculosis	Scanty Positive	n.a	PTB_SA_val013	non_UK_born	South Africa	No
GSM484528	21	Black	Male	LATENT TB	n.a	n.a	14	LTB_SA_val037	non_UK_born	South Africa	No
GSM484529	24	Black	Female	LATENT TB	n.a	n.a	20	LTB_SA_val038	non_UK_born	South Africa	No
GSM484530	21	Black	Male	LATENT TB	n.a	n.a	10	LTB_SA_val039	non_UK_born	South Africa	No
GSM484531	27	Black	Female	LATENT TB	n.a	n.a	14	LTB_SA_val040	non_UK_born	South Africa	No
GSM484532	24	Black	Male	LATENT TB	n.a	n.a	0	LTB_SA_val041	non_UK_born	South Africa	No
GSM484533	23	Black	Male	PTB	M.tuberculosis	1+	n.a	PTB_SA_val014	non_UK_born	South Africa	No
GSM484534	24	Black	Female	PTB	M.tuberculosis	3+	n.a	PTB_SA_val015	non_UK_born	South Africa	Yes
GSM484535	38	Black	Male	PTB	M.tuberculosis	3+	n.a	PTB_SA_val016	non_UK_born	South Africa	No
GSM484536	27	Black	Male	PTB	M.tuberculosis	2+	n.a	PTB_SA_val017	non_UK_born	South Africa	No
GSM484537	18	Black	Female	LATENT TB	n.a	n.a	12	LTB_SA_val043	non_UK_born	South Africa	No
GSM484538	20	Black	Female	LATENT TB	n.a	n.a	24	LTB_SA_val044	non_UK_born	South Africa	No
GSM484539	24	Black	Female	LATENT TB	n.a	n.a	15	LTB_SA_val045	non_UK_born	South Africa	Yes
GSM484540	22	Black	Male	LATENT TB	n.a	n.a	10	LTB_SA_val046	non_UK_born	South Africa	Yes
GSM484541	26	Black	Male	LATENT TB	n.a	n.a	15	LTB_SA_val047	non_UK_born	South Africa	Yes
GSM484542	24	Black	Male	LATENT TB	n.a	n.a	10	LTB_SA_val048	non_UK_born	South Africa	Yes
GSM484543	31	Black	Male	PTB	M.tuberculosis	1+	n.a	PTB_SA_val018	non_UK_born	South Africa	No
GSM484544	41	Black	Male	PTB	M.tuberculosis	3+	n.a	PTB_SA_val019	non_UK_born	South Africa	No
GSM484545	42	Black	Male	PTB	M.tuberculosis	2+	n.a	PTB_SA_val020	non_UK_born	South Africa	No
GSM484546	21	Black	Female	LATENT TB	n.a	n.a	20	LTB_SA_val036	non_UK_born	South Africa	No
GSM484547	23	Black	Female	LATENT TB	n.a	n.a	18	LTB_SA_val042	non_UK_born	South Africa	No
GSM484548	19	Black	Female	LATENT TB	n.a	n.a	12	LTB_SA_val049	non_UK_born	South Africa	No
GSM484549	20	Black	Female	LATENT TB	n.a	n.a	14	LTB_SA_val050	non_UK_born	South Africa	No
GSM484550	23	Black	Female	LATENT TB	n.a	n.a	15	LTB_SA_val051	non_UK_born	South Africa	No

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SIDRA