Sample Set Annotation Tool: The National NeuroAIDS Tissue Consortium Brain Gene Array: Two types of HIV-associated neurocognitive impairment

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Finding the differences in gene expression in three regions of the brain, basal ganglia, white matter, and frontal cortex, in normal, HIV infected, HIV infected with neurocognitive impairment, and HIV infected with both neurocognitive impairment and encephalitis patients.

Hypothesis

Experimental Design

Twenty-four human subjects in four groups were examined A) Uninfected controls; B) HIV-1 infected subjects with no substantial neurocognitive impairment (NCI); C) Infected with substantial NCI without HIV encephalitis (HIVE); D) Infected with substantial NCI and HIVE. RNA from neocortex, white matter, and neostriatum was processed with the Affymetrix® array platform.

Experimental Variables

WM: white matter

FC: frontal cortex

BG: basal ganglia

HIV

HH: HIV with HAD

HHH: HIV with HAD and HIVE

Controls

Methods

Additional Information

Expected Samples:

72 Samples Loaded: 72

Species

Human (Homo sapiens)

Sample Source

Brain

Disease

HIV, Neurological disorders

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	!Sample Title	Age	Gender	!Sample_title	tissue
GSM876838	A1_white_matter_Control	44	male	A1_white_matter_Control	White matter
GSM876839	A2_white_matter_Control	53	male	A2_white_matter_Control	White matter
GSM876840	A3_white_matter_Control	63	male	A3_white_matter_Control	White matter
GSM876841	A4_white_matter_Control	58	male	A4_white_matter_Control	White matter
GSM876842	A5_white_matter_Control	34	male	A5_white_matter_Control	White matter

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File
sampleset4000026_sampleannotations.csv Sample Set Spreadsheet

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Sample ID	!Sample Title	Age	Gender	!Sample Title	Tissue	Race	Phenotype	HIV status
GSM876838	A1_white_matter_Control	44	male	A1_white_matter_Control	White matter	White	normal (control)	normal
GSM876839	A2_white_matter_Control	53	male	A2_white_matter_Control	White matter	White	normal (control)	normal
GSM876840	A3_white_matter_Control	63	male	A3_white_matter_Control	White matter	Hispanic	normal (control)	normal
GSM876841	A4_white_matter_Control	58	male	A4_white_matter_Control	White matter	White	normal (control)	normal
GSM876842	A5_white_matter_Control	34	male	A5_white_matter_Control	White matter	White	normal (control)	normal
GSM876843	A6_white_matter_Control	48	female	A6_white_matter_Control	White matter	White	normal (control)	normal
GSM876844	B1_white_matter_HIV infected	49	male	B1_white_matter_HIV infected	White matter	White	HIV Infected	HIV infected
GSM876845	B2_white_matter_HIV infected	47	male	B2_white_matter_HIV infected	White matter	White	HIV Infected	HIV infected
GSM876846	B3_white_matter_HIV infected	44	male	B3_white_matter_HIV infected	White matter	White	HIV Infected	HIV infected
GSM876847	B4_white_matter_HIV infected	59	male	B4_white_matter_HIV infected	White matter	White	HIV Infected	HIV infected
GSM876848	B5_white_matter_HIV infected	60	male	B5_white_matter_HIV infected	White matter	White	HIV Infected	HIV infected
GSM876849	B6_white_matter_HIV infected	39	male	B6_white_matter_HIV infected	White matter	White	HIV Infected	HIV infected
GSM876850	C1_white_matter_HIV infected_w/HAD_w/o HIVE	33	male	C1_white_matter_HIV infected_w/HAD_w/o HIVE	White matter	Black	HIV Infected with neurocognitive impairment (HAD: HIV-associated dementia)	HIV infected
GSM876851	C2_white_matter_HIV infected_w/HAD_w/o HIVE	35	male	C2_white_matter_HIV infected_w/HAD_w/o HIVE	White matter	White	HIV Infected with neurocognitive impairment (HAD: HIV-associated dementia)	HIV infected
GSM876852	C3_white_matter_HIV infected_w/HAD_w/o HIVE	57	male	C3_white_matter_HIV infected_w/HAD_w/o HIVE	White matter	White	HIV Infected with neurocognitive impairment (HAD: HIV-associated dementia)	HIV infected
GSM876853	C4_white_matter_HIV infected_w/HAD_w/o HIVE	36	male	C4_white_matter_HIV infected_w/HAD_w/o HIVE	White matter	Hispanic	HIV Infected with neurocognitive impairment (HAD: HIV-associated dementia)	HIV infected
GSM876854	C5_white_matter_HIV infected_w/HAD_w/o HIVE	52	male	C5_white_matter_HIV infected_w/HAD_w/o HIVE	White matter	White	HIV Infected with neurocognitive impairment (HAD: HIV-associated dementia)	HIV infected
GSM876855	C6_white_matter_HIV infected_w/HAD_w/o HIVE	41	male	C6_white_matter_HIV infected_w/HAD_w/o HIVE	White matter	Hispanic	HIV Infected with neurocognitive impairment (HAD: HIV-associated dementia)	HIV infected
GSM876856	C7_white_matter_HIV infected_w/HAD_w/o HIVE	52	male	C7_white_matter_HIV infected_w/HAD_w/o HIVE	White matter	White	HIV Infected with neurocognitive impairment (HAD: HIV-associated dementia)	HIV infected
GSM876857	D1_white_matter_HIV infected_w/HAD_w/ HIVE	48	male	D1_white_matter_HIV infected_w/HAD_w/ HIVE	White matter	White	HIV Infected with HAD and HIV encephalitis (HIVE)	HIV infected
GSM876858	D2_white_matter_HIV infected_w/HAD_w/ HIVE	32	male	D2_white_matter_HIV infected_w/HAD_w/ HIVE	White matter	White	HIV Infected with HAD and HIV encephalitis (HIVE)	HIV infected
GSM876859	D3_white_matter_HIV infected_w/HAD_w/ HIVE	39	male	D3_white_matter_HIV infected_w/HAD_w/ HIVE	White matter	White	HIV Infected with HAD and HIV encephalitis (HIVE)	HIV infected
GSM876860	D4_white_matter_HIV infected_w/HAD_w/ HIVE	55	male	D4_white_matter_HIV infected_w/HAD_w/ HIVE	White matter	White	HIV Infected with HAD and HIV encephalitis (HIVE)	HIV infected
GSM876861	D5_white_matter_HIV infected_w/HAD_w/ HIVE	41	male	D5_white_matter_HIV infected_w/HAD_w/ HIVE	White matter	Hispanic	HIV Infected with HAD and HIV encephalitis (HIVE)	HIV infected
GSM876862	A1_Frontal_Cortex_Control	44	male	A1_Frontal_Cortex_Control	Frontal cortex	White	normal (control)	normal
GSM876863	A2_Frontal_Cortex_Control	53	male	A2_Frontal_Cortex_Control	Frontal cortex	White	normal (control)	normal
GSM876864	A3_Frontal_Cortex_Control	63	male	A3_Frontal_Cortex_Control	Frontal cortex	Hispanic	normal (control)	normal
GSM876865	A4_Frontal_Cortex_Control	58	male	A4_Frontal_Cortex_Control	Frontal cortex	White	normal (control)	normal
GSM876866	A5_Frontal_Cortex_Control	34	male	A5_Frontal_Cortex_Control	Frontal cortex	White	normal (control)	normal
GSM876867	A6_Frontal_Cortex_Control	48	female	A6_Frontal_Cortex_Control	Frontal cortex	White	normal (control)	normal
GSM876868	B1_Frontal_Cortex_HIV infected	49	male	B1_Frontal_Cortex_HIV infected	Frontal cortex	White	HIV Infected	HIV infected
GSM876869	B2_Frontal_Cortex_HIV infected	47	male	B2_Frontal_Cortex_HIV infected	Frontal cortex	White	HIV Infected	HIV infected
GSM876870	B3_Frontal_Cortex_HIV infected	44	male	B3_Frontal_Cortex_HIV infected	Frontal cortex	White	HIV Infected	HIV infected
GSM876871	B4_Frontal_Cortex_HIV infected	59	male	B4_Frontal_Cortex_HIV infected	Frontal cortex	White	HIV Infected	HIV infected
GSM876872	B5_Frontal_Cortex_HIV infected	60	male	B5_Frontal_Cortex_HIV infected	Frontal cortex	White	HIV Infected	HIV infected
GSM876873	B6_Frontal_Cortex_HIV infected	39	male	B6_Frontal_Cortex_HIV infected	Frontal cortex	White	HIV Infected	HIV infected
GSM876874	C1_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE	33	male	C1_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE	Frontal cortex	Black	HIV Infected with neurocognitive impairment (HAD: HIV-associated dementia)	HIV infected
GSM876875	C2_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE	35	male	C2_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE	Frontal cortex	White	HIV Infected with neurocognitive impairment (HAD: HIV-associated dementia)	HIV infected
GSM876876	C3_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE	57	male	C3_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE	Frontal cortex	White	HIV Infected with neurocognitive impairment (HAD: HIV-associated dementia)	HIV infected
GSM876877	C4_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE	36	male	C4_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE	Frontal cortex	Hispanic	HIV Infected with neurocognitive impairment (HAD: HIV-associated dementia)	HIV infected
GSM876878	C5_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE	52	male	C5_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE	Frontal cortex	White	HIV Infected with neurocognitive impairment (HAD: HIV-associated dementia)	HIV infected
GSM876879	C6_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE	41	male	C6_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE	Frontal cortex	Hispanic	HIV Infected with neurocognitive impairment (HAD: HIV-associated dementia)	HIV infected
GSM876880	C7_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE	52	male	C7_Frontal_Cortex_HIV infected_w/HAD_w/o HIVE	Frontal cortex	White	HIV Infected with neurocognitive impairment (HAD: HIV-associated dementia)	HIV infected
GSM876881	D1_Frontal_Cortex_HIV infected_w/HAD_w/ HIVE	48	male	D1_Frontal_Cortex_HIV infected_w/HAD_w/ HIVE	Frontal cortex	White	HIV Infected with HAD and HIV encephalitis (HIVE)	HIV infected
GSM876882	D2_Frontal_Cortex_HIV infected_w/HAD_w/ HIVE	32	male	D2_Frontal_Cortex_HIV infected_w/HAD_w/ HIVE	Frontal cortex	White	HIV Infected with HAD and HIV encephalitis (HIVE)	HIV infected
GSM876883	D3_Frontal_Cortex_HIV infected_w/HAD_w/ HIVE	39	male	D3_Frontal_Cortex_HIV infected_w/HAD_w/ HIVE	Frontal cortex	White	HIV Infected with HAD and HIV encephalitis (HIVE)	HIV infected
GSM876884	D4_Frontal_Cortex_HIV infected_w/HAD_w/ HIVE	55	male	D4_Frontal_Cortex_HIV infected_w/HAD_w/ HIVE	Frontal cortex	White	HIV Infected with HAD and HIV encephalitis (HIVE)	HIV infected
GSM876885	D5_Frontal_Cortex_HIV infected_w/HAD_w/ HIVE	41	male	D5_Frontal_Cortex_HIV infected_w/HAD_w/ HIVE	Frontal cortex	Hispanic	HIV Infected with HAD and HIV encephalitis (HIVE)	HIV infected
GSM876886	A1_basal_ganglia_Control	44	male	A1_basal_ganglia_Control	Basal ganglia	White	normal (control)	normal
GSM876887	A2_basal_ganglia_Control	53	male	A2_basal_ganglia_Control	Basal ganglia	White	normal (control)	normal
GSM876888	A3_basal_ganglia_Control	63	male	A3_basal_ganglia_Control	Basal ganglia	Hispanic	normal (control)	normal
GSM876889	A4_basal_ganglia_Control	58	male	A4_basal_ganglia_Control	Basal ganglia	White	normal (control)	normal
GSM876890	A5_basal_ganglia_Control	34	male	A5_basal_ganglia_Control	Basal ganglia	White	normal (control)	normal
GSM876891	A6_basal_ganglia_Control	48	female	A6_basal_ganglia_Control	Basal ganglia	White	normal (control)	normal
GSM876892	B1_basal_ganglia_HIV infected	49	male	B1_basal_ganglia_HIV infected	Basal ganglia	White	HIV Infected	HIV infected
GSM876893	B2_basal_ganglia_HIV infected	47	male	B2_basal_ganglia_HIV infected	Basal ganglia	White	HIV Infected	HIV infected
GSM876894	B3_basal_ganglia_HIV infected	44	male	B3_basal_ganglia_HIV infected	Basal ganglia	White	HIV Infected	HIV infected
GSM876895	B4_basal_ganglia_HIV infected	59	male	B4_basal_ganglia_HIV infected	Basal ganglia	White	HIV Infected	HIV infected
GSM876896	B5_basal_ganglia_HIV infected	60	male	B5_basal_ganglia_HIV infected	Basal ganglia	White	HIV Infected	HIV infected
GSM876897	B6_basal_ganglia_HIV infected	39	male	B6_basal_ganglia_HIV infected	Basal ganglia	White	HIV Infected	HIV infected
GSM876898	C1_basal_ganglia_HIV infected_w/HAD_w/o HIVE	33	male	C1_basal_ganglia_HIV infected_w/HAD_w/o HIVE	Basal ganglia	Black	HIV Infected with HAD	HIV infected
GSM876899	C2_basal_ganglia_HIV infected_w/HAD_w/o HIVE	35	male	C2_basal_ganglia_HIV infected_w/HAD_w/o HIVE	Basal ganglia	White	HIV Infected with HAD	HIV infected
GSM876900	C3_basal_ganglia_HIV infected_w/HAD_w/o HIVE	57	male	C3_basal_ganglia_HIV infected_w/HAD_w/o HIVE	Basal ganglia	White	HIV Infected with HAD	HIV infected
GSM876901	C4_basal_ganglia_HIV infected_w/HAD_w/o HIVE	36	male	C4_basal_ganglia_HIV infected_w/HAD_w/o HIVE	Basal ganglia	Hispanic	HIV Infected with HAD	HIV infected
GSM876902	C5_basal_ganglia_HIV infected_w/HAD_w/o HIVE	52	male	C5_basal_ganglia_HIV infected_w/HAD_w/o HIVE	Basal ganglia	White	HIV Infected with HAD	HIV infected
GSM876903	C6_basal_ganglia_HIV infected_w/HAD_w/o HIVE	41	male	C6_basal_ganglia_HIV infected_w/HAD_w/o HIVE	Basal ganglia	Hispanic	HIV Infected with HAD	HIV infected
GSM876904	C7_basal_ganglia_HIV infected_w/HAD_w/o HIVE	52	male	C7_basal_ganglia_HIV infected_w/HAD_w/o HIVE	Basal ganglia	White	HIV Infected with HAD	HIV infected
GSM876905	D1_basal_ganglia_HIV infected_w/HAD_w/ HIVE	48	male	D1_basal_ganglia_HIV infected_w/HAD_w/ HIVE	Basal ganglia	White	HIV Infected with HAD and encephalitis	HIV infected
GSM876906	D2_basal_ganglia_HIV infected_w/HAD_w/ HIVE	32	male	D2_basal_ganglia_HIV infected_w/HAD_w/ HIVE	Basal ganglia	White	HIV Infected with HAD and encephalitis	HIV infected
GSM876907	D3_basal_ganglia_HIV infected_w/HAD_w/ HIVE	39	male	D3_basal_ganglia_HIV infected_w/HAD_w/ HIVE	Basal ganglia	White	HIV Infected with HAD and encephalitis	HIV infected
GSM876908	D4_basal_ganglia_HIV infected_w/HAD_w/ HIVE	55	male	D4_basal_ganglia_HIV infected_w/HAD_w/ HIVE	Basal ganglia	White	HIV Infected with HAD and encephalitis	HIV infected
GSM876909	D5_basal_ganglia_HIV infected_w/HAD_w/ HIVE	41	male	D5_basal_ganglia_HIV infected_w/HAD_w/ HIVE	Basal ganglia	Hispanic	HIV Infected with HAD and encephalitis	HIV infected

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