Blood Transcriptional Profiles of Active TB (Separated cells)-GSE19443
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.
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.
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.
Patient group: Active PTB; Healthy controls (BCG vaccinated only) and Cell populations: Neutrophils, Monocytes, CD4+, CD8+. Ethnicity - a range of ethnic groups is represented.
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).
RNA was extracted from immune cells purified using Dynabeads (Invitrogen); cells selected were neutrophils, monocytes
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
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 |
File |
---|
All fields are editable except the "Sample ID" column. To edit a cell, click within the cell. To edit a "date" cell, click on the calendar icon. To cancel an edit, press the ESC key.
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 |
Name | ||
---|---|---|
All Samples | View | |
Splited by Cell types and Diseases | Default | View |
In order to make new Group Sets or change settings, please log in. |
Group Set | |
---|---|
All Samples | |
Splited by Cell types and Diseases |