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

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

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. 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

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

Controls

Methods

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

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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File
sampleset4000046_sampleannotations.csv Sample Set Spreadsheet

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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	Conditions	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	PTB_LON_test005_sep_Neut_002	Neut_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	PTB_LON_test005_sep_Mono_003	Mono_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	PTB_LON_test005_sep_CD4_004	CD4_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	PTB_LON_test005_sep_CD8_005	CD8_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	PTB_LON_test028_sep_Neut_022	Neut_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	PTB_LON_test028_sep_Mono_023	Mono_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	PTB_LON_test028_sep_CD4_024	CD4_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	PTB_LON_test028_sep_CD8_025	CD8_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	PTB_LON_test007_sep_Neut_007	Neut_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	PTB_LON_test007_sep_Mono_008	Mono_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	PTB_LON_test007_sep_CD4_009	CD4_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	PTB_LON_test007_sep_CD8_010	CD8_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	PTB_LON_test023_sep_Neut_012	Neut_TB	UK_Born	London	Advanced	Yes	n.a
GSM484564	18	tuberculosis	nil	South Asian	n.a	Female	PTB	unknown	Fully_sensitive	tuberculosis	nil	20	PTB_LON_test023_sep_Mono_013	Mono_TB	UK_Born	London	Advanced	Yes	n.a
GSM484565	18	tuberculosis	nil	South Asian	n.a	Female	PTB	unknown	Fully_sensitive	tuberculosis	nil	20	PTB_LON_test023_sep_CD4_014	CD4_TB	UK_Born	London	Advanced	Yes	n.a
GSM484566	18	tuberculosis	nil	South Asian	n.a	Female	PTB	unknown	Fully_sensitive	tuberculosis	nil	20	PTB_LON_test023_sep_CD8_015	CD8_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	CON_LON_test035_sep_Neut_032	Neut_H	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	CON_LON_test035_sep_Mono_033	Mono_H	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	CON_LON_test035_sep_CD4_034	CD4_H	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	CON_LON_test035_sep_CD8_035	CD8_H	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	PTB_LON_test027_sep_Neut_017	Neut_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	PTB_LON_test027_sep_Mono_018	Mono_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	PTB_LON_test027_sep_CD4_019	CD4_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	PTB_LON_test027_sep_CD8_020	CD8_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	CON_LON_test036_sep_Neut_037	Neut_H	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	CON_LON_test036_sep_Mono_038	Mono_H	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	CON_LON_test036_sep_CD4_039	CD4_H	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	CON_LON_test036_sep_CD8_040	CD8_H	UK_Born	London	True	Yes	n.a
GSM484579	32	tuberculosis	nil	Black	n.a	Male	PTB	n.a	Fully_sensitive	tuberculosis	nil	23	PTB_LON_test032_sep_Neut_027	Neut_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	PTB_LON_test032_sep_Mono_028	Mono_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	PTB_LON_test032_sep_CD4_029	CD4_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	PTB_LON_test032_sep_CD8_030	CD8_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	PTB_LON_test049_sep_Neut_052	Neut_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	PTB_LON_test049_sep_Mono_053	Mono_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	PTB_LON_test049_sep_CD4_054	CD4_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	PTB_LON_test049_sep_CD8_055	CD8_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	CON_LON_test037_sep_Neut_042	Neut_H	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	CON_LON_test037_sep_Mono_043	Mono_H	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	CON_LON_test037_sep_CD4_044	CD4_H	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	CON_LON_test037_sep_CD8_045	CD8_H	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	CON_LON_test038_sep_Neut_047	Neut_H	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	CON_LON_test038_sep_Mono_048	Mono_H	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	CON_LON_test038_sep_CD4_049	CD4_H	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	CON_LON_test038_sep_CD8_050	CD8_H	non_UK_Born	London	True	Yes	n.a

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