Sample Set Annotation Tool: Whole Blood Transcriptional Response to Early Acute HIV

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

The objective of this study is to: 1) Characterize the transcriptional signature of early acute HIV infection. 2) Eucidate the evolution of the signature in both anti-retroviral treated and untreated populations over a 24 week time course. 3) Correlate clinical and disease related parameters to heterogenaity in the transcriptional signature to identify pathways explaining clinical heterogeneity 4) Compare the acute signature of HIV infection to other acute viral signatures.

Hypothesis

Experimental Design

58 acute HIV patients were recruited from locations in Africa (n=43) and the United States (n=15). These patients were allocated into training (n=18), test (n=10) and validation sets (n=30). Patient samples were collected at study enrollment (confirmed acute) for all patients and at weeks 1,2,4,12,and 24 for training and test set constituents. 13 of 15 US patients initiated anti-retroviral therapy after after enrollment and before the week 1 visit. The remaining 2 US patients and 43 African patients were not placed on therapy through the 24 week time course. Matched uninfected controls patients were also recruited from each site (n= 55). In total 232 samples were collected.

Experimental Variables

Controls

Methods

Additional Information

Expected Samples:

185 Samples Loaded: 185

Species

Human (Homo sapiens)

Sample Source

Whole Blood

Disease

HIV

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	Age	Ethnicity	Gender	Illness	!Sample_title
GSM728352	56	US	Male	HIV	700010040E
GSM728353	56	US	Male	HIV	700010040W4
GSM728354	56	US	Male	HIV	700010040W12
GSM728355	56	US	Male	HIV	700010040W24
GSM728356	23	US	Male	HIV	700010077E

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File

Samples Viewer / Editor

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Sample ID	Age	Ethnicity	Gender	Illness	!Sample Title	Race	Treatment	Viral load	Cd4 count	Dataset	Feibig stage	Calculated viral set point	Week
GSM728352	56	US	Male	HIV	700010040E	White	NO	298026	929	Training Set	5	13183	E
GSM728353	56	US	Male	HIV	700010040W4	White	NO	89156	ND	Training Set	ND	13183	W04
GSM728354	56	US	Male	HIV	700010040W12	White	NO	17587	1017	Training Set	ND	13183	W12
GSM728355	56	US	Male	HIV	700010040W24	White	NO	29453	986	Training Set	ND	13183	W24
GSM728356	23	US	Male	HIV	700010077E	African American	NO	144145	806	Training Set	5	3631	E
GSM728357	23	US	Male	HIV	700010077W1	African American	NO	37560	ND	Training Set	ND	3631	W01
GSM728358	23	US	Male	HIV	700010077W12	African American	NO	3073	914	Training Set	ND	3631	W12
GSM728359	23	US	Male	HIV	700010077W24	African American	NO	1680	664	Training Set	ND	3631	W24
GSM728360	26	US	Male	Healthy	700010163H8	African American	NA	ND	ND	Training Set	NA	NA	W08
GSM728361	47	US	Female	Healthy	701010084HE	White	NA	ND	1674	Training Set	NA	NA	E
GSM728362	45	US	Male	HIV	700010081W4	White	YES	50	621	Training Set	ND	NA	W04
GSM728363	45	US	Male	HIV	700010081E	White	NO	3746	805	Training Set	5	NA	E
GSM728364	45	US	Male	HIV	700010081W1	White	YES	104	ND	Training Set	ND	NA	W01
GSM728365	45	US	Male	HIV	700010081W2	White	YES	50	ND	Training Set	ND	NA	W02
GSM728366	45	US	Male	HIV	700010081W12	White	YES	50	680	Training Set	ND	NA	W12
GSM728367	45	US	Male	HIV	700010081W24	White	YES	50	589	Training Set	ND	NA	W24
GSM728368	56	US	Male	HIV	700010106E	White	NO	ND	227	Training Set	1-2	NA	E
GSM728369	56	US	Male	HIV	700010106W1	White	YES	14538865	ND	Training Set	ND	NA	W01
GSM728370	56	US	Male	HIV	700010106W2	White	YES	265006	ND	Training Set	ND	NA	W02
GSM728371	56	US	Male	HIV	700010106W4	White	YES	26468	ND	Training Set	ND	NA	W04
GSM728372	56	US	Male	HIV	700010106W12	White	YES	50	688	Training Set	ND	NA	W12
GSM728373	56	US	Male	HIV	700010106W24	White	YES	107	621	Training Set	ND	NA	W24
GSM728374	24	US	Male	HIV	700010150E	White	NO	589437	389	Training Set	5	NA	E
GSM728375	24	US	Male	HIV	700010150W1	White	YES	36405	ND	Training Set	ND	NA	W01
GSM728376	24	US	Male	HIV	700010150W2	White	YES	30424	526	Training Set	ND	NA	W02
GSM728377	24	US	Male	HIV	700010150W4	White	YES	17099	ND	Training Set	ND	NA	W04
GSM728378	24	US	Male	HIV	700010150W12	White	YES	127	641	Training Set	ND	NA	W12
GSM728379	24	US	Male	HIV	700010150W24	White	YES	50	529	Training Set	ND	NA	W24
GSM728380	49	US	Male	HIV	700010224E	White	NO	605652	13	Training Set	4	NA	E
GSM728381	49	US	Male	HIV	700010224W2	White	YES	3505	74	Training Set	ND	NA	W02
GSM728382	49	US	Male	HIV	700010224W4	White	YES	1461	92	Training Set	ND	NA	W04
GSM728383	49	US	Male	HIV	700010224W1	White	YES	28183	ND	Training Set	ND	NA	W01
GSM728384	49	US	Male	HIV	700010224W12	White	YES	96	166	Training Set	ND	NA	W12
GSM728385	49	US	Male	HIV	700010224W24	White	YES	50	200	Training Set	ND	NA	W24
GSM728386	20	US	Male	HIV	700010238E	African American	YES	596908	587	Training Set	5-6	NA	E
GSM728387	20	US	Male	HIV	700010238W1	African American	YES	3546	ND	Training Set	ND	NA	W01
GSM728388	20	US	Male	HIV	700010238W2	African American	YES	985	804	Training Set	ND	NA	W02
GSM728389	20	US	Male	HIV	700010238W12	African American	YES	50	618	Training Set	ND	NA	W12
GSM728391	20	US	Male	HIV	700010238W24	African American	YES	50	791	Training Set	ND	NA	W24
GSM728392	25	US	Male	HIV	700010246E	White	NO	4395721	1012	Training Set	4	NA	E
GSM728393	25	US	Male	HIV	700010246W1	White	YES	32107	ND	Training Set	ND	NA	W01
GSM728394	25	US	Male	HIV	700010246W2	White	YES	4325	973	Training Set	ND	NA	W02
GSM728395	25	US	Male	HIV	700010246W4	White	YES	638	ND	Training Set	ND	NA	W04
GSM728396	25	US	Male	HIV	700010246W12	White	YES	50	1015	Training Set	ND	NA	W12
GSM728397	25	US	Male	HIV	700010246W24	White	YES	50	851	Training Set	ND	NA	W24
GSM728398	25	US	Male	HIV	701010027E	White	NO	194744	542	Training Set	5	NA	E
GSM728399	25	US	Male	HIV	701010027W2	White	YES	1515	ND	Training Set	ND	NA	W02
GSM728400	25	US	Male	HIV	701010027W4	White	YES	1836	ND	Training Set	ND	NA	W04
GSM728401	25	US	Male	HIV	701010027W12	White	YES	50	ND	Training Set	ND	NA	W12
GSM728402	25	US	Male	HIV	701010027W24	White	YES	50	532	Training Set	ND	NA	W24
GSM728403	36	US	Female	HIV	701010043E	African American	NO	5532	717	Training Set	5	NA	E
GSM728404	36	US	Female	HIV	701010043W2	African American	YES	1250	ND	Training Set	ND	NA	W02
GSM728405	36	US	Female	HIV	701010043W4	African American	YES	380	ND	Training Set	ND	NA	W04
GSM728406	36	US	Female	HIV	701010043W12	African American	YES	50	ND	Training Set	ND	NA	W12
GSM728407	36	US	Female	HIV	701010043W24	African American	YES	50	917	Training Set	ND	NA	W24
GSM728408	38	US	Male	HIV	701010068E	White	NO	3714389	109	Training Set	4	NA	E
GSM728409	38	US	Male	HIV	701010068W1	White	YES	70536	ND	Training Set	ND	NA	W01
GSM728410	38	US	Male	HIV	701010068W2	White	YES	21081	ND	Training Set	ND	NA	W02
GSM728411	38	US	Male	HIV	701010068W4	White	YES	6487	ND	Training Set	ND	NA	W04
GSM728412	38	US	Male	HIV	701010068W8	White	YES	331	ND	Training Set	ND	NA	W08
GSM728413	38	US	Male	HIV	701010068W24	White	YES	99	363	Training Set	ND	NA	W24
GSM728414	24	African	Male	HIV	702010047E	African Ngoni	NO	331625	547	Training Set	4	131826	E
GSM728415	24	African	Male	HIV	702010047W1	African Ngoni	NO	750000	ND	Training Set	ND	131826	W01
GSM728416	24	African	Male	HIV	702010047W2	African Ngoni	NO	578440	ND	Training Set	ND	131826	W02
GSM728417	24	African	Male	HIV	702010047W4	African Ngoni	NO	225327	ND	Training Set	ND	131826	W04
GSM728418	24	African	Male	HIV	702010047W12	African Ngoni	NO	152130	ND	Training Set	ND	131826	W12
GSM728419	24	African	Male	HIV	702010047W24	African Ngoni	NO	145905	ND	Training Set	ND	131826	W24
GSM728420	25	African	Male	HIV	703010010W1	African Tumbuka	NO	287756	ND	Training Set	ND	158489	W01
GSM728421	25	African	Male	HIV	703010010W2	African Tumbuka	NO	489476	224	Training Set	ND	158489	W02
GSM728422	25	African	Male	HIV	703010010E	African Tumbuka	NO	408727	202	Training Set	3	158489	E
GSM728423	25	African	Male	HIV	703010010W4	African Tumbuka	NO	214173	ND	Training Set	ND	158489	W04
GSM728424	25	African	Male	HIV	703010010W24	African Tumbuka	NO	61105	ND	Training Set	ND	158489	W24
GSM728425	25	African	Male	HIV	703010010W12	African Tumbuka	NO	155723	ND	Training Set	ND	158489	W12
GSM728426	28	African	Male	HIV	703010054E	African Tumbuka	NO	13936	593	Training Set	5	12589	E
GSM728427	28	African	Male	HIV	703010054W1	African Tumbuka	NO	9241	ND	Training Set	ND	12589	W01
GSM728428	28	African	Male	HIV	703010054W4	African Tumbuka	NO	38141	ND	Training Set	ND	12589	W04
GSM728429	28	African	Male	HIV	703010054W12	African Tumbuka	NO	1090	1086	Training Set	ND	12589	W12
GSM728430	28	African	Male	HIV	703010054W24	African Tumbuka	NO	20282	ND	Training Set	ND	12589	W24
GSM728431	28	African	Male	HIV	703010054W2	African Tumbuka	NO	13158	936	Training Set	ND	12589	W02
GSM728432	20	African	Male	HIV	703010131E	African Lomwe	NO	437369	247	Training Set	3	23988	E
GSM728433	20	African	Male	HIV	703010131W1	African Lomwe	NO	9366	ND	Training Set	ND	23988	W01
GSM728434	20	African	Male	HIV	703010131W2	African Lomwe	NO	7764	ND	Training Set	ND	23988	W02
GSM728435	20	African	Male	HIV	703010131W4	African Lomwe	NO	53169	ND	Training Set	ND	23988	W04
GSM728436	20	African	Male	HIV	703010131W12	African Lomwe	NO	15424	395	Training Set	ND	23988	W12
GSM728437	20	African	Male	HIV	703010131W24	African Lomwe	NO	50709	310	Training Set	ND	23988	W24
GSM728439	18	African	Female	HIV	703010159E	African Chewa	NO	73453	606	Training Set	1-2	9120	E
GSM728440	18	African	Female	HIV	703010159W1	African Chewa	NO	587457	ND	Training Set	ND	9120	W01
GSM728441	18	African	Female	HIV	703010159W2	African Chewa	NO	570786	ND	Training Set	ND	9120	W02
GSM728442	18	African	Female	HIV	703010159W4	African Chewa	NO	13566	ND	Training Set	ND	9120	W04
GSM728443	18	African	Female	HIV	703010159W12	African Chewa	NO	71474	463	Training Set	ND	9120	W12
GSM728444	18	African	Female	HIV	703010159W24	African Chewa	NO	4926	413	Training Set	ND	9120	W24
GSM728445	38	African	Male	HIV	704010042E	African Black	NO	133000	263	Training Set	5	123027	E
GSM728446	38	African	Male	HIV	704010042W1	African Black	NO	84800	ND	Training Set	ND	123027	W01
GSM728447	38	African	Male	HIV	704010042W2	African Black	NO	201000	ND	Training Set	ND	123027	W02
GSM728448	38	African	Male	HIV	704010042W4	African Black	NO	340000	ND	Training Set	ND	123027	W04
GSM728449	38	African	Male	HIV	704010042W12	African Black	NO	29600	ND	Training Set	ND	123027	W12
GSM728450	38	African	Male	HIV	704010042W24	African Black	NO	102000	357	Training Set	ND	123027	W24
GSM728451	25	African	Female	HIV	704010083E	African Black	NO	750000	496	Training Set	3	218776	E
GSM728452	25	African	Female	HIV	704010083W1	African Black	NO	735000	571	Training Set	ND	218776	W01
GSM728453	25	African	Female	HIV	704010083W2	African Black	NO	708000	ND	Training Set	ND	218776	W02
GSM728454	25	African	Female	HIV	704010083W12	African Black	NO	517000	ND	Training Set	ND	218776	W12
GSM728455	25	African	Female	HIV	704010083W4	African Black	NO	125000	438	Training Set	ND	218776	W04
GSM728456	25	African	Female	HIV	704010083W24	African Black	NO	293000	471	Training Set	ND	218776	W24
GSM728457	34	African	Male	Healthy	705010031H8	African Black	NA	NA	ND	Training Set	NA	NA	W08
GSM728458	21	African	Female	Healthy	704010091H8	African Black	NA	NA	ND	Training Set	NA	NA	W08
GSM728459	26	US	Male	Healthy	701010120HE	African American	NA	NA	813	Training Set	NA	NA	E
GSM728460	48	African	Female	Healthy	703010062HE	African Chewa	NA	NA	550	Training Set	NA	NA	E
GSM728461	45	African	Male	Healthy	703010036H8	African Ngoni	NA	NA	ND	Training Set	NA	NA	W08
GSM728462	25	African	Male	Healthy	703010115HE	African Lomwe	NA	NA	ND	Training Set	NA	NA	E
GSM728463	27	African	Female	Healthy	706010033H8	African Black	NA	NA	ND	Training Set	NA	NA	W08
GSM728464	24	African	Female	Healthy	706010041HE	African Black	NA	NA	ND	Training Set	NA	NA	E
GSM728465	19	African	Male	Healthy	706010057HE	African Black	NA	NA	1125	Training Set	NA	NA	E
GSM728466	27	African	Male	Healthy	706010065HE	African Black	NA	NA	1140	Training Set	NA	NA	E
GSM728467	29	African	Male	Healthy	703010049HE	African Chewa	NA	NA	729	Training Set	NA	NA	E
GSM728468	25	African	Female	Healthy	703010144H8	African Chewa	NA	NA	1155	Training Set	NA	NA	W08
GSM728469	31	African	Female	Healthy	703010178H8	African Chewa	NA	NA	868	Training Set	NA	NA	W08
GSM728470	46	US	Male	Healthy	700010382HE	African American	NA	NA	1251	Training Set	NA	NA	E
GSM728471	25	US	Male	HIV	701010027W1	White	YES	3687	ND	Training Set	ND	NA	W01
GSM728472	66	US	Male	HIV	701010092E	African American	NO	207143	155	Test Set	5-6	ND	E
GSM728473	66	US	Male	HIV	701010092W2	African American	YES	5554	223	Test Set	ND	ND	W02
GSM728474	66	US	Male	HIV	701010092W4	African American	YES	261	ND	Test Set	ND	ND	W04
GSM728475	66	US	Male	HIV	701010092W12	African American	YES	50	175	Test Set	ND	ND	W12
GSM728476	66	US	Male	HIV	701010092W24	African American	YES	50	143	Test Set	ND	ND	W24
GSM728477	31	US	Male	Healthy	700010357E	White	NA	NA	ND	Test Set	ND	ND	E
GSM728478	50	US	Male	HIV	701010137E	White	NO	225873	798	Test Set	5	ND	E
GSM728479	50	US	Male	HIV	701010137W1	White	YES	9481	ND	Test Set	ND	ND	W01
GSM728480	50	US	Male	HIV	701010137W2	White	YES	1695	820	Test Set	ND	ND	W02
GSM728481	50	US	Male	HIV	701010137W12	White	YES	224	832	Test Set	ND	ND	W12
GSM728482	50	US	Male	HIV	701010137W24	White	YES	50	638	Test Set	ND	ND	W24
GSM728483	35	US	Male	HIV	701010145E	White	NO	76509	675	Test Set	5	ND	E
GSM728484	35	US	Male	HIV	701010145W1	White	YES	2010	ND	Test Set	ND	ND	W01
GSM728485	35	US	Male	HIV	701010145W2	White	YES	962	807	Test Set	ND	ND	W02
GSM728486	35	US	Male	HIV	701010145W4	White	YES	131	ND	Test Set	ND	ND	W04
GSM728487	35	US	Male	HIV	701010145W12	White	YES	50	835	Test Set	ND	ND	W12
GSM728488	35	US	Male	HIV	701010145W24	White	YES	50	686	Test Set	ND	ND	W24
GSM728489	37	US	Male	HIV	701010172E	White	NO	101007	487	Test Set	5	ND	E
GSM728490	37	US	Male	HIV	701010172W1	White	YES	8354	ND	Test Set	ND	ND	W01
GSM728491	37	US	Male	HIV	701010172W2	White	YES	912	1410	Test Set	ND	ND	W02
GSM728492	37	US	Male	HIV	701010172W4	White	YES	50	1227	Test Set	ND	ND	W04
GSM728493	21	African	Male	HIV	702010157E	African Lomwe	NO	750000	382	Test Set	4	45709	E
GSM728494	21	African	Male	HIV	702010157W1	African Lomwe	NO	236831	ND	Test Set	ND	45709	W01
GSM728495	21	African	Male	HIV	702010157W12	African Lomwe	NO	167761	ND	Test Set	ND	45709	W12
GSM728496	21	African	Male	HIV	702010176E	African Ngoni	NO	750000	ND	Test Set	5	147911	E
GSM728497	21	African	Male	HIV	702010176W2	African Ngoni	NO	743732	ND	Test Set	ND	147911	W02
GSM728498	21	African	Male	HIV	702010176W4	African Ngoni	NO	208341	337	Test Set	ND	147911	W04
GSM728499	21	African	Male	HIV	702010176W12	African Ngoni	NO	135944	ND	Test Set	ND	147911	W12
GSM728500	24	African	Male	HIV	703010200E	African Chewa	NO	128677	111	Test Set	4	154882	E
GSM728501	24	African	Male	HIV	703010200W2	African Chewa	NO	125291	ND	Test Set	ND	154882	W02
GSM728502	24	African	Male	HIV	703010200W4	African Chewa	NO	109551	ND	Test Set	ND	154882	W04
GSM728503	24	African	Male	HIV	703010200W1	African Chewa	NO	514236	ND	Test Set	ND	154882	W01
GSM728504	24	African	Male	HIV	703010200W12	African Chewa	NO	62167	192	Test Set	ND	154882	W12
GSM728505	24	African	Male	HIV	703010200W24	African Chewa	NO	216057	247	Test Set	ND	154882	W24
GSM728506	29	African	Male	HIV	704010152E	White	NO	106000	609	Test Set	5-6	6607	E
GSM728507	29	African	Male	HIV	704010152W4	White	NO	16300	903	Test Set	ND	6607	W04
GSM728508	29	African	Male	HIV	704010152W12	White	NO	32900	ND	Test Set	ND	6607	W12
GSM728509	21	US	Male	Healthy	700010365E	African American	NA	NA	ND	Test Set	ND	ND	E
GSM728510	22	US	Female	Healthy	700010451E	White	NA	NA	ND	Test Set	ND	ND	E
GSM728511	27	African	Male	HIV	706010164E	African black	NO	23600	700	Test Set	4	Unstable	E
GSM728512	27	African	Male	HIV	706010164W1	African black	NO	98200	ND	Test Set	ND	Unstable	W01
GSM728513	27	African	Male	HIV	706010164W4	African black	NO	537000	ND	Test Set	ND	Unstable	W04
GSM728514	27	African	Male	HIV	706010164W12	African black	NO	10200	669	Test Set	ND	Unstable	W12
GSM728515	27	African	Male	HIV	706010164W24	African black	NO	127000	449	Test Set	ND	Unstable	W24
GSM728516	19	African	Male	HIV	706010170E	African black	NO	77500	198	Test Set	5-6	93100	E
GSM728517	19	African	Male	HIV	706010170W4	African black	NO	134000	179	Test Set	ND	93100	W04
GSM728518	19	African	Male	HIV	706010170W12	African black	NO	63000	236	Test Set	ND	93100	W12
GSM728519	19	African	Male	HIV	706010170W24	African black	NO	90100	159	Test Set	ND	93100	W24
GSM728520	29	US	Female	Healthy	700010488E	White	NA	NA	ND	Test Set	ND	ND	E
GSM728521	26	US	Female	Healthy	700010496W1	White	NA	NA	ND	Test Set	ND	ND	W01
GSM728522	27	US	Female	Healthy	700010530E	White	NA	NA	ND	Test Set	ND	ND	E
GSM728523	28	African	Male	Healthy	706010188E	African black	NA	NA	475	Test Set	ND	ND	E
GSM728524	29	African	Male	Healthy	706010196W8	African black	NA	NA	ND	Test Set	ND	ND	W08
GSM728525	22	African	Female	Healthy	706010208W8	African black	NA	NA	ND	Test Set	ND	ND	W08
GSM728526	22	African	Female	Healthy	706010214E	African black	NA	NA	781	Test Set	ND	ND	E
GSM728527	42	US	Male	Healthy	701010161E	White	NA	NA	ND	Test Set	ND	ND	E
GSM728528	26	African	Male	Healthy	702010012W8	African Chewa	NA	NA	ND	Test Set	ND	ND	W08
GSM728529	40	African	Male	Healthy	702010039E	African Lomwe	NA	NA	879	Test Set	ND	ND	E
GSM728530	21	African	Male	Healthy	702010064E	African Lomwe	NA	NA	927	Test Set	ND	ND	E
GSM728531	30	African	Male	Healthy	702010104E	African Ngoni	NA	NA	994	Test Set	ND	ND	E
GSM728532	24	African	Male	Healthy	702010129E	African Lomwe	NA	NA	650	Test Set	ND	ND	E
GSM728533	35	African	Male	Healthy	702010165E	African Tonga	NA	NA	ND	Test Set	ND	ND	E
GSM728534	28	African	Male	Healthy	702010182W8	African Yao	NA	NA	ND	Test Set	ND	ND	W08
GSM728535	21	African	Female	Healthy	704010146W8	African black	NA	NA	ND	Test Set	ND	ND	W08
GSM728536	36	African	Female	Healthy	704010187W8	African black	NA	NA	ND	Test Set	ND	ND	W08
GSM728537	25	African	Female	Healthy	704010195W8	African black	NA	NA	ND	Test Set	ND	ND	W08
GSM728538	37	African	Male	Healthy	704010249E	African black	NA	NA	ND	Test Set	ND	ND	E

Group Sets View in Gene Expression Browser

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Module Analysis

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SIDRA