Sample Set Annotation Tool: Blood Transcriptional Profiles of Active TB (Separated cells)-GSE19443

Study Design
Assay
Sample Info
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Analysis

Purpose

We aimed to characterise the transcriptional response during TB and identify if cell subsets drove changes in whole blood cellular composition. The aim of the experiment was to define transcriptional signatures in neutrophils, monocytes, CD4+ and CD8+ cells from blood of active TB patients and healthy controls to distinguish the signature of active TB patients from each other and from healthy controls. This will help in the diagnosis of active tuberculosis, which normally relies on culture of the bacilli, which can take up to 6 weeks, sometimes the bacilli cannot be obtained from sputum thus requiring invasive techniques obtaining bronchoalveolar lavage (BAL). In some cases the bacill cannot be grown from sputum or BAL.

Hypothesis

This dataset aims to dissect the whole blood transcriptional signature by determining if elements of the whole blood signature are still present in purified cell subpopulations.

Experimental Design

Whole blood collected in EDTA tubes from patients with active TB disease and healthy controls. Blood was then processed or separated sequentially into neutrophil, monocyte, CD4+ or CD8+ populations and then processed. 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 or bronchoalvelolar lavage fluid. Healthy controls - these were volunteers without exposure to TB who were negative by both tuberculin skin test (<15mm if BCG vaccinated, <6mm if unvaccinated); who were also negative by IGRA (as described above). This dataset: PTB, n = 7 patients (whole blood, neutrophils, monocytes, CD4+ or CD8+). BCG+, n = 4 patients (whole blood, neutrophils, monocytes, CD4+ or CD8+). Experimental variables : Patient group: Active PTB; Healthy controls (BCG vaccinated only) and Cell populations: Neutrophils, Monocytes, CD4+, CD8+. Ethnicity - a range of ethnic groups is represented.

Experimental Variables

Patient group: Active PTB; Healthy controls (BCG vaccinated only) and Cell populations: Neutrophils, Monocytes, CD4+, CD8+. Ethnicity - a range of ethnic groups is represented.

Controls

Healthy controls - these were volunteers without exposure to TB who were negative by both tuberculin skin test (<6mm unvaccinated); who were also negative by IGRA (as described above).

Methods

RNA was extracted from immune cells purified using Dynabeads (Invitrogen); cells selected were neutrophils, monocytes

Additional Information

Berry MP, Graham CM, McNab FW, Xu Z et al. An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature2010 Aug 19;466(7309):973-7. PMID: 20725040

Expected Samples:

44 Samples Loaded: 44

Species

Human (Homo sapiens)

Sample Source

Neutrophils , CD8 T cells , CD4 T cells , Monocytes

Disease

Tuberculosis

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	Age	Bal Culture	Bal Smear	Ethnicity	Exposure Latent
GSM484551	40	no_growth_6_weeks	nil	White	n.a
GSM484552	40	no_growth_6_weeks	nil	White	n.a
GSM484553	40	no_growth_6_weeks	nil	White	n.a
GSM484554	40	no_growth_6_weeks	nil	White	n.a
GSM484555	26	n.a	n.a	Asian other	n.a

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Sample ID	Age	Bal Culture	Bal Smear	Ethnicity	Exposure Latent	Gender	Illness	Index Case Disease Site	Isolate Sensitivity	Sputum Culture	Sputum Smear	Tst	!Sample Title	Region of birth	Geographical region	Modal x-ray grade	Bcg vaccinated	Smear of index case
GSM484551	40	no_growth_6_weeks	nil	White	n.a	Male	PTB	True	Fully_sensitive	tuberculosis	nil	n.a	Neutrophil-Active TB	non_UK_Born	London	Minimal	Yes	True
GSM484552	40	no_growth_6_weeks	nil	White	n.a	Male	PTB	True	Fully_sensitive	tuberculosis	nil	n.a	Monocyte-Active TB	non_UK_Born	London	Minimal	Yes	True
GSM484553	40	no_growth_6_weeks	nil	White	n.a	Male	PTB	True	Fully_sensitive	tuberculosis	nil	n.a	CD4-Active TB	non_UK_Born	London	Minimal	Yes	True
GSM484554	40	no_growth_6_weeks	nil	White	n.a	Male	PTB	True	Fully_sensitive	tuberculosis	nil	n.a	CD8-Active TB	non_UK_Born	London	Minimal	Yes	True
GSM484555	26	n.a	n.a	Asian other	n.a	Male	PTB	n.a	Resistant Isoniazid + Ethambu	tuberculosis	+	n.a	Neutrophil-Active TB	non_UK_Born	London	Advanced	Not_Known	n.a
GSM484556	26	n.a	n.a	Asian other	n.a	Male	PTB	n.a	Resistant Isoniazid + Ethambu	tuberculosis	+	n.a	Monocyte-Active TB	non_UK_Born	London	Advanced	Not_Known	n.a
GSM484557	26	n.a	n.a	Asian other	n.a	Male	PTB	n.a	Resistant Isoniazid + Ethambu	tuberculosis	+	n.a	CD4-Active TB	non_UK_Born	London	Advanced	Not_Known	n.a
GSM484558	26	n.a	n.a	Asian other	n.a	Male	PTB	n.a	Resistant Isoniazid + Ethambu	tuberculosis	+	n.a	CD8-Active TB	non_UK_Born	London	Advanced	Not_Known	n.a
GSM484559	33	n.a	n.a	White	n.a	Male	PTB	n.a	Resistant Streptomycin, Ethio	tuberculosis	+++	21	Neutrophil-Active TB	non_UK_Born	London	Moderate	Yes	n.a
GSM484560	33	n.a	n.a	White	n.a	Male	PTB	n.a	Resistant Streptomycin, Ethio	tuberculosis	+++	21	Monocyte-Active TB	non_UK_Born	London	Moderate	Yes	n.a
GSM484561	33	n.a	n.a	White	n.a	Male	PTB	n.a	Resistant Streptomycin, Ethio	tuberculosis	+++	21	CD4-Active TB	non_UK_Born	London	Moderate	Yes	n.a
GSM484562	33	n.a	n.a	White	n.a	Male	PTB	n.a	Resistant Streptomycin, Ethio	tuberculosis	+++	21	CD8-Active TB	non_UK_Born	London	Moderate	Yes	n.a
GSM484563	18	tuberculosis	nil	South Asian	n.a	Female	PTB	unknown	Fully_sensitive	tuberculosis	nil	20	Neutrophil-Active TB	UK_Born	London	Advanced	Yes	n.a
GSM484564	18	tuberculosis	nil	South Asian	n.a	Female	PTB	unknown	Fully_sensitive	tuberculosis	nil	20	Monocyte-Active TB	UK_Born	London	Advanced	Yes	n.a
GSM484565	18	tuberculosis	nil	South Asian	n.a	Female	PTB	unknown	Fully_sensitive	tuberculosis	nil	20	CD4-Active TB	UK_Born	London	Advanced	Yes	n.a
GSM484566	18	tuberculosis	nil	South Asian	n.a	Female	PTB	unknown	Fully_sensitive	tuberculosis	nil	20	CD8-Active TB	UK_Born	London	Advanced	Yes	n.a
GSM484567	28	n.a	n.a	White	n.a	Male	Control (BCG+)	n.a	n.a	n.a	n.a	9	Neutrophil-Healthy	non_UK_Born	London	True	Yes	n.a
GSM484568	28	n.a	n.a	White	n.a	Male	Control (BCG+)	n.a	n.a	n.a	n.a	9	Monocyte-Healthy	non_UK_Born	London	True	Yes	n.a
GSM484569	28	n.a	n.a	White	n.a	Male	Control (BCG+)	n.a	n.a	n.a	n.a	9	CD4-Healthy	non_UK_Born	London	True	Yes	n.a
GSM484570	28	n.a	n.a	White	n.a	Male	Control (BCG+)	n.a	n.a	n.a	n.a	9	CD8-Healthy	non_UK_Born	London	True	Yes	n.a
GSM484571	22	n.a	n.a	South Asian	n.a	Male	PTB	n.a	Fully_sensitive	tuberculosis	nil	15	Neutrophil-Active TB	non_UK_Born	London	Moderate	Yes	n.a
GSM484572	22	n.a	n.a	South Asian	n.a	Male	PTB	n.a	Fully_sensitive	tuberculosis	nil	15	Monocyte-Active TB	non_UK_Born	London	Moderate	Yes	n.a
GSM484573	22	n.a	n.a	South Asian	n.a	Male	PTB	n.a	Fully_sensitive	tuberculosis	nil	15	CD4-Active TB	non_UK_Born	London	Moderate	Yes	n.a
GSM484574	22	n.a	n.a	South Asian	n.a	Male	PTB	n.a	Fully_sensitive	tuberculosis	nil	15	CD8-Active TB	non_UK_Born	London	Moderate	Yes	n.a
GSM484575	21	n.a	n.a	White	n.a	Male	Control (BCG+)	n.a	n.a	n.a	n.a	9	Neutrophil-Healthy	UK_Born	London	True	Yes	n.a
GSM484576	21	n.a	n.a	White	n.a	Male	Control (BCG+)	n.a	n.a	n.a	n.a	9	Monocyte-Healthy	UK_Born	London	True	Yes	n.a
GSM484577	21	n.a	n.a	White	n.a	Male	Control (BCG+)	n.a	n.a	n.a	n.a	9	CD4-Healthy	UK_Born	London	True	Yes	n.a
GSM484578	21	n.a	n.a	White	n.a	Male	Control (BCG+)	n.a	n.a	n.a	n.a	9	CD8-Healthy	UK_Born	London	True	Yes	n.a
GSM484579	32	tuberculosis	nil	Black	n.a	Male	PTB	n.a	Fully_sensitive	tuberculosis	nil	23	Neutrophil-Active TB	non_UK_Born	London	Moderate	Yes	n.a
GSM484580	32	tuberculosis	nil	Black	n.a	Male	PTB	n.a	Fully_sensitive	tuberculosis	nil	23	Monocyte-Active TB	non_UK_Born	London	Moderate	Yes	n.a
GSM484581	32	tuberculosis	nil	Black	n.a	Male	PTB	n.a	Fully_sensitive	tuberculosis	nil	23	CD4-Active TB	non_UK_Born	London	Moderate	Yes	n.a
GSM484582	32	tuberculosis	nil	Black	n.a	Male	PTB	n.a	Fully_sensitive	tuberculosis	nil	23	CD8-Active TB	non_UK_Born	London	Moderate	Yes	n.a
GSM484583	55	tuberculosis	nil	South Asian	n.a	Female	PTB	n.a	Fully_sensitive	n.a	n.a	n.a	Neutrophil-Active TB	non_UK_Born	London	Advanced	Yes	n.a
GSM484584	55	tuberculosis	nil	South Asian	n.a	Female	PTB	n.a	Fully_sensitive	n.a	n.a	n.a	Monocyte-Active TB	non_UK_Born	London	Advanced	Yes	n.a
GSM484585	55	tuberculosis	nil	South Asian	n.a	Female	PTB	n.a	Fully_sensitive	n.a	n.a	n.a	CD4-Active TB	non_UK_Born	London	Advanced	Yes	n.a
GSM484586	55	tuberculosis	nil	South Asian	n.a	Female	PTB	n.a	Fully_sensitive	n.a	n.a	n.a	CD8-Active TB	non_UK_Born	London	Advanced	Yes	n.a
GSM484587	49	n.a	n.a	South Asian	n.a	Female	Control (BCG+)	n.a	n.a	n.a	n.a	0	Neutrophil-Healthy	non_UK_Born	London	True	Yes	n.a
GSM484588	49	n.a	n.a	South Asian	n.a	Female	Control (BCG+)	n.a	n.a	n.a	n.a	0	Monocyte-Healthy	non_UK_Born	London	True	Yes	n.a
GSM484589	49	n.a	n.a	South Asian	n.a	Female	Control (BCG+)	n.a	n.a	n.a	n.a	0	CD4-Healthy	non_UK_Born	London	True	Yes	n.a
GSM484590	49	n.a	n.a	South Asian	n.a	Female	Control (BCG+)	n.a	n.a	n.a	n.a	0	CD8-Healthy	non_UK_Born	London	True	Yes	n.a
GSM484591	41	n.a	n.a	South Asian	n.a	Female	Control (BCG+)	n.a	n.a	n.a	n.a	10	Neutrophil-Healthy	non_UK_Born	London	True	Yes	n.a
GSM484592	41	n.a	n.a	South Asian	n.a	Female	Control (BCG+)	n.a	n.a	n.a	n.a	10	Monocyte-Healthy	non_UK_Born	London	True	Yes	n.a
GSM484593	41	n.a	n.a	South Asian	n.a	Female	Control (BCG+)	n.a	n.a	n.a	n.a	10	CD4-Healthy	non_UK_Born	London	True	Yes	n.a
GSM484594	41	n.a	n.a	South Asian	n.a	Female	Control (BCG+)	n.a	n.a	n.a	n.a	10	CD8-Healthy	non_UK_Born	London	True	Yes	n.a

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