Sample Set Annotation Tool: Whole blood transcriptional profiles of patients with active tuberculosis (TB) and other inflammatory and infectious diseases-GSE22098

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Tuberculosis (TB), caused by infection with Mycobacterium tuberculosis (M. tuberculosis), is a major cause of morbidity and mortality worldwide and efforts to control TB are hampered by difficulties with diagnosis, prevention and treatment. Most people infected with M. tuberculosis remain asymptomatic, termed latent TB, with a 10% lifetime risk of developing active TB disease, but current tests cannot identify which individuals will develop disease. The immune response to M. tuberculosis is complex and incompletely characterized, hindering development of new diagnostics, therapies and vaccines. The goals of this study include: 1. Identify a transcript signature for active TB in intermediate and high burden settings, correlating with radiological extent of disease and reverting to that of healthy controls following treatment; 2. Identify a specific transcript signature that discriminated active TB from other inflammatory and infectious diseases; 3. Classify TB signature using modular and pathway analysis tools.

Hypothesis

Experimental Design

Three milliliters of whole blood was collected in Tempus tubes from 12 pediatric streptococcus, 40 pediatric staphylococcus, 31 still’s disease, 82 pediatric systemic lupus erythematosus (SLE) and 28 adult SLE patients. RNA was extracted and globin reduced. Labeled cRNA was hybridized to Illumina Human HT-12 Beadchips. Healthy controls were included to match patients’ demographic data. Genespring software was used to analyze active TB transcript signatures, comparing with healthy controls and other inflammatory and infectious diseases.

Experimental Variables

Controls

Methods

The data were analyzed 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=GSE22098

Expected Samples:

274 Samples Loaded: 274

Species

Human (Homo sapiens)

Sample Source

Whole Blood

Disease

Tuberculosis

Treatment Protocol

Growth Protocol

Extraction Protocol

Ambion Temput Isolation kit

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	Age	Ethnicity	Gender	Illness	!Sample_title
GSM549324	55	Caucasian	Male	Still	WB-Still-4639
GSM549325	22	Asian	Male	Still	WB-Still-5161
GSM549326	83	Caucasian	Male	Still	WB-Still-5163
GSM549327	42	Caucasian	Female	Still	WB-Still-5667
GSM549328	51	Caucasian	Male	Still	WB-Still-5666

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File

Samples Viewer / Editor

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	Ethnicity	Gender	Illness	!Sample Title	Healthy control
GSM549324	55	Caucasian	Male	Still	WB-Still-4639
GSM549325	22	Asian	Male	Still	WB-Still-5161
GSM549326	83	Caucasian	Male	Still	WB-Still-5163
GSM549327	42	Caucasian	Female	Still	WB-Still-5667
GSM549328	51	Caucasian	Male	Still	WB-Still-5666
GSM549329	19	Caucasian	Male	Still	WB-Still-1281
GSM549331	34	Caucasian	Male	Still	WB-Still-1102
GSM549333	38	Caucasian	Female	Still	WB-Still-1934
GSM549335	48	Hispanic	Female	Still	WB-Still-1935
GSM549336	54	Caucasian	Male	Still	WB-Still-1936
GSM549338	29	Caucasian	Female	Still	WB-Still-2166
GSM549340	37	Native American	Female	Still	WB-Still-2358
GSM549342	17	Caucasian	Male	Still	WB-Still-2362
GSM549344	64	Caucasian	Female	Still	WB-Still-5870
GSM549345	31	Caucasian	Male	Still	WB-Still-5871
GSM549346	70	Caucasian	Male	Still	WB-Still-5872
GSM549347	27	Caucasian	Male	Still	WB-Still-6038
GSM549348	63	Native American	Female	Still	WB-Still-6167
GSM549349	38	Hispanic	Female	Still	WB-Still-6168
GSM549350	44	Caucasian	Female	Still	WB-Still-6037
GSM549351	32	Hispanic	Female	Still	WB-Still-8980
GSM549352	26	Caucasian	Male	Still	WB-Still-7760
GSM549353	19	Caucasian	Male	Still	WB-Still-8560
GSM549354	48	Hispanic	Female	Still	WB-Still-6652
GSM549355	19	Caucasian	Male	Still	WB-Still-6653
GSM549356	59	Caucasian	Male	Still	WB-Still-7759
GSM549357	54	Caucasian	Male	Still	WB-Still-8059
GSM549358	36	Caucasian	Female	ASLE	WB-ASLE-5320
GSM549359	36	Caucasian	Female	ASLE	WB-ASLE-5321
GSM549360	79	Caucasian	Female	ASLE	WB-ASLE-5670
GSM549361	29	Asian	Female	ASLE	WB-ASLE-5671
GSM549362	30	Caucasian	Female	ASLE	WB-ASLE-6066
GSM549363	45	African American	Female	ASLE	WB-ASLE-6067
GSM549364	28	Hispanic	Male	ASLE	WB-ASLE-6068
GSM549365	53	Caucasian	Female	ASLE	WB-ASLE-6643
GSM549366	28	Caucasian	Female	ASLE	WB-ASLE-6644
GSM549367	28	Asian	Female	ASLE	WB-ASLE-6069
GSM549368	20	African American	Female	ASLE	WB-ASLE-6070
GSM549369	38	African American	Female	ASLE	WB-ASLE-6071
GSM549370	31	Caucasian	Male	ASLE	WB-ASLE-6641
GSM549371	46	Hispanic	Female	ASLE	WB-ASLE-6642
GSM549372	37	Caucasian	Female	ASLE	WB-ASLE-6650
GSM549373	49	Caucasian	Female	ASLE	WB-ASLE-6645
GSM549374	33	Hispanic	Female	ASLE	WB-ASLE-6646
GSM549375	50	Caucasian	Female	ASLE	WB-ASLE-6647
GSM549376	18	Caucasian	Female	ASLE	WB-ASLE-7984
GSM549377	24	Caucasian	Female	ASLE	WB-ASLE-7985
GSM549378	49	African American	Female	ASLE	WB-ASLE-7987
GSM549379	52	Caucasian	Male	ASLE	WB-ASLE-7988
GSM549380	50	Caucasian	Female	ASLE	WB-ASLE-7989
GSM549381	35	African American	Female	ASLE	WB-ASLE-7990
GSM549382	21	Hispanic	Male	ASLE	WB-ASLE-2773
GSM549383	48	Hispanic	Female	ASLE	WB-ASLE-7995
GSM549384	34	African American	Female	ASLE	WB-ASLE-8178
GSM549385	51	Caucasian	Female	ASLE	WB-ASLE-8174
GSM549386	15	Hispanic	Male	PSLE	WB-PSLE-5947
GSM549387	16	Hispanic	Female	PSLE	WB-PSLE-5953
GSM549388	13	Caucasian	Female	PSLE	WB-PSLE-5949
GSM549389	15	Hispanic	Female	PSLE	WB-PSLE-5970
GSM549390	17	Asian	Female	PSLE	WB-PSLE-5980
GSM549391	16	Caucasian	Male	PSLE	WB-PSLE-7456
GSM549392	14	Hispanic	Female	PSLE	WB-PSLE-7457
GSM549393	17	Hispanic	Female	PSLE	WB-PSLE-7458
GSM549394	17	Hispanic	Female	PSLE	WB-PSLE-7459
GSM549395	17	African American	Female	PSLE	WB-PSLE-5610
GSM549396	16	Caucasian	Female	PSLE	WB-PSLE-5611
GSM549397	15	African American	Female	PSLE	WB-PSLE-5612
GSM549398	17	Hispanic	Female	PSLE	WB-PSLE-5624
GSM549399	18	Hispanic	Female	PSLE	WB-PSLE-5626
GSM549400	14	Hispanic	Male	PSLE	WB-PSLE-5933
GSM549401	17	Hispanic	Female	PSLE	WB-PSLE-5623
GSM549402	16	Hispanic	Female	PSLE	WB-PSLE-5932
GSM549403	17	Hispanic	Female	PSLE	WB-PSLE-5944
GSM549404	14	Hispanic	Male	PSLE	WB-PSLE-5945
GSM549405	16	African American	Female	PSLE	WB-PSLE-7466
GSM549406	15	African American	Female	PSLE	WB-PSLE-7471
GSM549407	14	Hispanic	Female	PSLE	WB-PSLE-7465
GSM549408	16	Hispanic	Female	PSLE	WB-PSLE-7486
GSM549409	16	Caucasian	Female	PSLE	WB-PSLE-5608
GSM549410	17	African American	Female	PSLE	WB-PSLE-5600
GSM549411	17	Hispanic	Male	PSLE	WB-PSLE-5613
GSM549412	17	Hispanic	Female	PSLE	WB-PSLE-5614
GSM549413	17	Hispanic	Female	PSLE	WB-PSLE-5615
GSM549414	16	African American	Female	PSLE	WB-PSLE-5618
GSM549415	16	African American	Female	PSLE	WB-PSLE-5954
GSM549416	13	Hispanic	Male	PSLE	WB-PSLE-5952
GSM549417	15	Hispanic	Female	PSLE	WB-PSLE-8933
GSM549418	13	Caucasian	Female	PSLE	WB-PSLE-5627
GSM549419	29	Caucasian	Female	Still	WB-Still-9678
GSM549420	25	Caucasian	Female	Still	WB-Still-9686
GSM549421	6	Hispanic	Female	Staph	WB-Staph-1340
GSM549422	9	Caucasian	Male	Staph	WB-Staph-1342
GSM549423	6	African American	Female	Staph	WB-Staph-1343
GSM549424	11	Caucasian	Male	Staph	WB-Staph-1344
GSM549425	15	African American	Male	Staph	WB-Staph-1345
GSM549426	5	African American	Male	Staph	WB-Staph-1402
GSM549427	13	Caucasian	Male	Staph	WB-Staph-1346
GSM549428	3	Hispanic	Male	Staph	WB-Staph-1347
GSM549429	11	Caucasian	Female	Staph	WB-Staph-5825
GSM549430	17	Hispanic	Male	Staph	WB-Staph-5827
GSM549431	4	Hispanic	Female	Staph	WB-Staph-5839
GSM549432	5	African American	Male	Staph	WB-Staph-5840
GSM549433	1	Hispanic	Female	Staph	WB-Staph-1338
GSM549434	9	African American	Male	Staph	WB-Staph-1339
GSM549435	1	African American	Female	Strep	WB-Strep-5800
GSM549436	5	Hispanic	Female	Strep	WB-Strep-5808
GSM549437	6	Asian	Female	Strep	WB-Strep-5813
GSM549438	14	African American	Male	Strep	WB-Strep-5838
GSM549439	5	Hispanic	Female	Strep	WB-Strep-6549
GSM549440	7	Caucasian	Male	Strep	WB-Strep-8854
GSM549441	1	Hispanic	Male	Strep	WB-Strep-2736
GSM549442	6	Hispanic	Male	Strep	WB-Strep-9483
GSM549443	5	Caucasian	Female	Strep	WB-Strep-9484
GSM549444	16	Caucasian	Male	Strep	WB-Strep-5781
GSM549445	1	Hispanic	Female	Strep	WB-Strep-8869
GSM549446	1	Caucasian	Male	Strep	WB-Strep-5074
GSM549447	10	Caucasian	Female	Staph	WB-Staph-2707
GSM549448	3	African American	Male	Staph	WB-Staph-2388
GSM549449	2	Hispanic	Female	Staph	WB-Staph-5068
GSM549450	11	African American	Male	Staph	WB-Staph-5040
GSM549451	10	Hispanic	Female	Staph	WB-Staph-9598
GSM549452	1	African American	Male	Staph	WB-Staph-9601
GSM549453	8	Hispanic	Female	Staph	WB-Staph-9548
GSM549454	2	African American	Male	Staph	WB-Staph-9553
GSM549455	8	African American	Female	Staph	WB-Staph-9552
GSM549456	0	African American	Female	Staph	WB-Staph-9555
GSM549457	1	Caucasian	Female	Staph	WB-Staph-9556
GSM549458	7	African American	Female	Staph	WB-Staph-9569
GSM549459	9	African American	Male	Staph	WB-Staph-5064
GSM549460	11	Hispanic	Male	Staph	WB-Staph-5046
GSM549461	1	African American	Male	Staph	WB-Staph-9558
GSM549462	6	Hispanic	Female	Staph	WB-Staph-9559
GSM549463	2	African American	Female	Staph	WB-Staph-9560
GSM549464	10	African American	Female	Staph	WB-Staph-9561
GSM549465	11	African American	Male	Staph	WB-Staph-9562
GSM549466	12	Caucasian	Male	Staph	WB-Staph-2741
GSM549467	5	African American	Female	Staph	WB-Staph-9549
GSM549468	1	Hispanic	Female	Staph	WB-Staph-9557
GSM549469	15	Caucasian	Male	Staph	WB-Staph-5069
GSM549470	8	Hispanic	Female	Staph	WB-Staph-5037
GSM549471	12	African American	Female	Staph	WB-Staph-2745
GSM549472	13	Caucasian	Male	Staph	WB-Staph-9565
GSM549473	58	Caucasian	Female	Still	WB-Still-5986
GSM549474	35	Asian	Female	Still	WB-Still-5985
GSM549475	12	Hispanic	Female	PSLE	WB-PSLE-5982
GSM549476	18	Caucasian	Female	PSLE	WB-PSLE-6156
GSM549477	12	Hispanic	Female	PSLE	WB-PSLE-9870
GSM549478	13	African American	Female	PSLE	WB-PSLE-7393
GSM549479	14	Hispanic	Female	PSLE	WB-PSLE-2925
GSM549480	9	Hispanic	Female	PSLE	WB-PSLE-1914
GSM549481	18	Caucasian	Female	PSLE	WB-PSLE-2145
GSM549482	18	Hispanic	Female	PSLE	WB-PSLE-3193
GSM549483	16	Hispanic	Female	PSLE	WB-PSLE-0067
GSM549484	18	Hispanic	Female	PSLE	WB-PSLE-2526
GSM549485	14	Hispanic	Female	PSLE	WB-PSLE-2552
GSM549486	17	Caucasian	Female	PSLE	WB-PSLE-2546
GSM549487	18	Hispanic	Female	PSLE	WB-PSLE-2610
GSM549488	10	African American	Female	PSLE	WB-PSLE-8148
GSM549489	17	African American	Female	PSLE	WB-PSLE-6166
GSM549490	7	African American	Male	PSLE	WB-PSLE-8943
GSM549491	18	Hispanic	Female	PSLE	WB-PSLE-8074
GSM549492	18	African American	Female	PSLE	WB-PSLE-8152
GSM549493	15	Hispanic	Female	PSLE	WB-PSLE-0481
GSM549494	16	Hispanic	Female	PSLE	WB-PSLE-0683
GSM549495	16	Hispanic	Male	PSLE	WB-PSLE-8955
GSM549496	15	Asian	Female	PSLE	WB-PSLE-8956
GSM549497	18	African American	Female	PSLE	WB-PSLE-8965
GSM549498	18	African American	Female	PSLE	WB-PSLE-7469
GSM549499	17	Hispanic	Female	PSLE	WB-PSLE-7474
GSM549500	14	Hispanic	Female	PSLE	WB-PSLE-2408
GSM549501	15	Asian	Female	PSLE	WB-PSLE-2418
GSM549502	13	Hispanic	Male	PSLE	WB-PSLE-5583
GSM549503	19	Hispanic	Female	PSLE	WB-PSLE-5587
GSM549504	11	African American	Female	PSLE	WB-PSLE-5622
GSM549505	9	Hispanic	Male	PSLE	WB-PSLE-6298
GSM549506	11	Hispanic	Female	PSLE	WB-PSLE-8144
GSM549507	18	Asian	Female	PSLE	WB-PSLE-7384
GSM549508	11	Caucasian	Female	PSLE	WB-PSLE-5657
GSM549509	8	Caucasian	Female	PSLE	WB-PSLE-6029
GSM549510	15	Hispanic	Male	PSLE	WB-PSLE-6055
GSM549511	18	African American	Male	PSLE	WB-PSLE-6165
GSM549512	8	Hispanic	Female	PSLE	WB-PSLE-2938
GSM549513	16	Hispanic	Female	PSLE	WB-PSLE-2416
GSM549514	10	Hispanic	Female	PSLE	WB-PSLE-2919
GSM549515	12	Caucasian	Female	PSLE	WB-PSLE-9632
GSM549516	11	Caucasian	Female	PSLE	WB-PSLE-2420
GSM549517	16	Hispanic	Female	PSLE	WB-PSLE-1515
GSM549518	13	Hispanic	Male	PSLE	WB-PSLE-0581
GSM549519	17	African American	Female	PSLE	WB-PSLE-1916
GSM549520	14	African American	Female	PSLE	WB-PSLE-0582
GSM549521	13	African American	Female	PSLE	WB-PSLE-5951
GSM549522	12	Hispanic	Female	PSLE	WB-PSLE-9872
GSM549523	13	Hispanic	Female	PSLE	WB-PSLE-8411
GSM550320	28	Caucasian	Female		WB-H-2862	Still
GSM550321	28	Caucasian	Female		WB-H-2863	Still
GSM550322	24	Caucasian	Female		WB-H-6459	Still
GSM550323	33	Caucasian	Female		WB-H-6422	Still
GSM550324	38	Caucasian	Female		WB-H-2292	Still
GSM550325	29	Caucasian	Female		WB-H-2293	Still
GSM550326	25	Caucasian	Male		WB-H-2865	Still
GSM550327	35	Caucasian	Male		WB-H-6393	Still
GSM550328	27	Caucasian	Male		WB-H-5685	Still
GSM550329	38	Caucasian	Male		WB-H-2289	Still
GSM550330	49	Caucasian	Female		WB-H-2290	Still
GSM550331	27	Caucasian	Male		WB-H-2864	Still
GSM550332	35	Asian	Male		WB-H-5684	Still
GSM550333	29	Caucasian	Female		WB-H-5682	Still
GSM550334	43	Caucasian	Male		WB-H-5556	Still
GSM550335	20	Caucasian	Female		WB-H-6725	Still
GSM550336	30	Caucasian	Male		WB-H-6726	Still
GSM550337	50	Caucasian	Female		WB-H-6635	Still
GSM550338	44	Caucasian	Female		WB-H-6639	Still
GSM550339	58	Caucasian	Male		WB-H-6680	Still
GSM550340	31	Caucasian	Female		WB-H-6724	Still
GSM550341	53	Caucasian	Female		WB-H-1051	ASLE
GSM550342	45	Caucasian	Female		WB-H-1052	ASLE
GSM550343	55	Caucasian	Female		WB-H-1055	ASLE
GSM550344	43	Caucasian	Female		WB-H-1074	ASLE
GSM550345	43	Caucasian	Female		WB-H-1081	ASLE
GSM550346	42	Caucasian	Female		WB-H-7466	ASLE
GSM550347	57	Caucasian	Female		WB-H-7975	ASLE
GSM550348	51	Caucasian	Female		WB-H-4260	ASLE
GSM550349	74	Caucasian	Female		WB-H-3339	ASLE
GSM550350	43	Caucasian	Male		WB-H-4259	ASLE
GSM550351	84	Caucasian	Female		WB-H-4556	ASLE
GSM550352	37	Caucasian	Female		WB-H-7831	ASLE
GSM550353	39	Hispanic	Female		WB-H-7832	ASLE
GSM550354	35	Asian	Female		WB-H-7833	ASLE
GSM550355	45	Caucasian	Male		WB-H-7835	ASLE
GSM550356	43	Caucasian	Female		WB-H-7836	ASLE
GSM550357	43	Caucasian	Female		WB-H-7837	ASLE
GSM550358	14	Hispanic	Female		WB-H-1359	pSLE
GSM550359	15	Caucasian	Female		WB-H-1595	pSLE
GSM550360	14	Hispanic	Male		WB-H-2804-2	pSLE
GSM550361	16	Hispanic	Female		WB-H-5679-2	pSLE
GSM550362	17	Afican American	Female		WB-H-6035	pSLE
GSM550363	16	Caucasian	Female		WB-H-6411	pSLE
GSM550364	16	Hispanic	Female		WB-H-2812	pSLE
GSM550365	16	Hispanic	Male		WB-H-2806	pSLE
GSM550366	11	Afican American	Male		WB-H-2818	Strep and Staph
GSM550367	7	Hispanic	Male		WB-H-9128	Strep and Staph
GSM550368	8	Caucasian	Male		WB-H-0565	Strep and Staph
GSM550369	6	Hispanic	Female		WB-H-0545	Strep and Staph
GSM550370	10	Hispanic	Female		WB-H-2811	Strep and Staph
GSM550371	5	Hispanic	Male		WB-H-2704	Strep and Staph
GSM550372	8	Hispanic	Male		WB-H-9361	Strep and Staph
GSM550373	15	Hispanic	Female		WB-H-9363	Strep and Staph
GSM550374	18	Hispanic	Male		WB-H-9369	Strep and Staph
GSM550375	5	Hispanic	Male		WB-H-9355	Strep and Staph
GSM550376	6	Hispanic	Female		WB-H-9357	Strep and Staph
GSM550377	17	Hispanic	Male		WB-H-9371	Strep and Staph
GSM550378	4	Caucasian	Female		WB-H-9868	Strep and Staph
GSM550379	8	Hispanic	Female		WB-H-1134	Strep and Staph
GSM550380	12	Afican American	Female		WB-H-0853	Strep and Staph
GSM550381	4	Afican American	Female		WB-H-5851	Strep and Staph
GSM550382	10	Afican American	Female		WB-H-1358	Strep and Staph
GSM550383	8	Caucasian/Asian	Male		WB-H-0537	Strep and Staph
GSM550384	7	Caucasian	Male		WB-H-8550	Strep and Staph
GSM550385	5	Afican American	Male		WB-H-1946	Strep and Staph
GSM550386	5	Hispanic	Male		WB-H-1254	Strep and Staph
GSM550387	6	Afican American	Female		WB-H-2819	Strep and Staph
GSM550388	7	Caucasian	Male		WB-H-4276	Strep and Staph
GSM550389	24	Asian	Female		WB-H-5683	Still
GSM550390	16	Hispanic	Female		WB-H-5679	pSLE
GSM550391	14	Hispanic	Male		WB-H-2804	pSLE
GSM550392	14	Hispanic	Female		WB-H-1136	pSLE
GSM550393	11	Hispanic	Male		WB-H-1137	pSLE
GSM550394	9	Asian	Female		WB-H-1149	pSLE
GSM550395	10	Afican American	Female		WB-H-1358-2	pSLE
GSM550396	10	Hispanic	Female		WB-H-2811-2	pSLE
GSM550397	17	Hispanic	Female		WB-H-7254	pSLE
GSM550398	18	Caucasian	Female		WB-H-2846	pSLE
GSM550399	14	Afican American	Male		WB-H-2817	pSLE
GSM550400	18	Afican American	Female		WB-H-4637	pSLE

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SIDRA