Sample Set Annotation Tool: Differential Gene Expression in HIV-Infected Individuals Following ART

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

A paired analysis of peripheral blood mononuclear cells (PBMCs) isolated before and after antiretroviral therapy (ART) from a robust number of HIV-infected patients (N=36).

Results identify a total of 4,157 DEGs following ART in HIV-infected participants and the transition from a period of active virus replication before ART to one of viral suppression

Hypothesis

Experimental Design

This study evaluated PBMC gene expression in cells from 36 (4 dropped from analysis) recently HIV-infected individuals to identify differentially expressed genes following 48 weeks of ART

Experimental Variables

Controls

Methods

Additional Information

Expected Samples:

72 Samples Loaded: 72

Species

Human (Homo sapiens)

Sample Source

PBMC

Disease

HIV

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

Please log in in order to upload files.

Samples Preview

Sample ID	Age	Ethnicity	!Sample_title	batch	sdf file
GSM1080991	31 years	White	Pt1_before_drug	1	4307579061.sdf
GSM1080992	36 years	White	Pt2_before_drug	1	4307579072.sdf
GSM1080993	39 years	American Indian	Pt3_before_drug	1	4307579061.sdf
GSM1080994	38 years	White	Pt4_before_drug	1	4307579061.sdf
GSM1080995	52 years	White	Pt5_before_drug	1	4307579061.sdf

Please log in in order to upload files.

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	!Sample Title	Batch	Sdf file	Treatment	Subject	Drug regimen	Reanalysis	Analysis	Cd4+ t cell count, cells/ul	Cd4+ t cell count measurement	Sex
GSM1080991	31 years	White	Pt1_before_drug	1	4307579061.sdf	baseline	Pt1	NNRTI	re-analysis of GSM477695	Patient included in analysis	463.00	baseline	Male
GSM1080992	36 years	White	Pt2_before_drug	1	4307579072.sdf	baseline	Pt2	NNRTI	re-analysis of GSM477696	Patient included in analysis	449.00	baseline	Male
GSM1080993	39 years	American Indian	Pt3_before_drug	1	4307579061.sdf	baseline	Pt3	NNRTI	re-analysis of GSM477697	Patient included in analysis	226.00	baseline	Male
GSM1080994	38 years	White	Pt4_before_drug	1	4307579061.sdf	baseline	Pt4	NNRTI	re-analysis of GSM477698	Patient included in analysis	310.50	baseline	Male
GSM1080995	52 years	White	Pt5_before_drug	1	4307579061.sdf	baseline	Pt5	NNRTI	re-analysis of GSM477699	Patient included in analysis	388.00	baseline	Male
GSM1080996	42 years	White	Pt6_before_drug	1	4307579072.sdf	baseline	Pt6	NNRTI	re-analysis of GSM477700	Patient included in analysis	413.67	baseline	Male
GSM1080997	24 years	African American	Pt7_before_drug	1	4307579072.sdf	baseline	Pt7	NNRTI	re-analysis of GSM477701	Patient included in analysis	232.00	baseline	Male
GSM1080998	38 years	White	Pt8_before_drug	1	4307579062.sdf	baseline	Pt8	NNRTI	re-analysis of GSM477702	Patient included in analysis	285.00	baseline	Male
GSM1080999	28 years	White	Pt9_before_drug	1	4307579061.sdf	baseline	Pt9	NNRTI	re-analysis of GSM477703	Patient included in analysis	413.50	baseline	Male
GSM1081000	33 years	Asian	Pt10_before_drug	1	4307579060.sdf	baseline	Pt10	NNRTI	re-analysis of GSM477704	Patient included in analysis	282.67	baseline	Male
GSM1081001	28 years	White	Pt11_before_drug	1	4307579060.sdf	baseline	Pt11	NNRTI	re-analysis of GSM477705	Patient included in analysis	383.00	baseline	Male
GSM1081002	19 years	White	Pt12_before_drug	1	4307579060.sdf	baseline	Pt12	NNRTI	re-analysis of GSM477706	Patient included in analysis	226.00	baseline	Male
GSM1081003	29 years	White	Pt13_before_drug	2	4463361135.sdf	baseline	Pt13	PI	re-analysis of GSM477707	Patient dropped from analysis	404.57	baseline	Male
GSM1081004	50 years	White	Pt14_before_drug	2	4463361135.sdf	baseline	Pt14	PI	re-analysis of GSM477708	Patient dropped from analysis	425.33	baseline	Male
GSM1081005	58 years	White	Pt15_before_drug	2	4463361239.sdf	baseline	Pt15	PI	re-analysis of GSM477709	Patient dropped from analysis	454.33	baseline	Male
GSM1081006	50 years	White	Pt16_before_drug	2	4463361135.sdf	baseline	Pt16	PI	re-analysis of GSM477710	Patient dropped from analysis	414.33	baseline	Male
GSM1081007	33 years	White	Pt17_before_drug	2	4463361177.sdf	baseline	Pt17	PI	re-analysis of GSM477711	Patient included in analysis	221.50	baseline	Male
GSM1081008	24 years	American Indian	Pt18_before_drug	2	4463361239.sdf	baseline	Pt18	PI	re-analysis of GSM477712	Patient included in analysis	362.00	baseline	Male
GSM1081009	39 years	White	Pt19_before_drug	2	4463361156.sdf	baseline	Pt19	PI	re-analysis of GSM477713	Patient included in analysis	200.67	baseline	Male
GSM1081010	34 years	African American	Pt20_before_drug	2	4463361239.sdf	baseline	Pt20	PI	re-analysis of GSM477714	Patient included in analysis	315.75	baseline	Male
GSM1081011	40 years	Asian	Pt21_before_drug	2	4463361177.sdf	baseline	Pt21	PI	re-analysis of GSM477715	Patient included in analysis	224.00	baseline	Male
GSM1081012	37 years	Asian	Pt22_before_drug	2	4463361156.sdf	baseline	Pt22	PI	re-analysis of GSM477716	Patient included in analysis	210.00	baseline	Male
GSM1081013	54 years	White	Pt23_before_drug	2	4463361177.sdf	baseline	Pt23	PI	re-analysis of GSM477717	Patient included in analysis	272.50	baseline	Male
GSM1081014	27 years	White	Pt24_before_drug	2	4463361177.sdf	baseline	Pt24	PI	re-analysis of GSM477718	Patient included in analysis	398.00	baseline	Male
GSM1081015	34 years	White	Pt25_before_drug	2	4531933134.sdf	baseline	Pt25	Switchers	New analysis	Patient included in analysis	401.50	baseline	Male
GSM1081016	43 years	White	Pt26_before_drug	2	4531933134.sdf	baseline	Pt26	Switchers	New analysis	Patient included in analysis	233.00	baseline	Male
GSM1081017	49 years	White	Pt27_before_drug	2	4531933135.sdf	baseline	Pt27	Switchers	New analysis	Patient included in analysis	368.00	baseline	Male
GSM1081018	36 years	White	Pt28_before_drug	2	4531933139.sdf	baseline	Pt28	Switchers	New analysis	Patient included in analysis	445.00	baseline	Male
GSM1081019	42 years	Asian	Pt29_before_drug	2	4531933139.sdf	baseline	Pt29	Switchers	New analysis	Patient included in analysis	578.00	baseline	Male
GSM1081020	45 years	White	Pt30_before_drug	2	4531933137.sdf	baseline	Pt30	Switchers	New analysis	Patient included in analysis	500.50	baseline	Male
GSM1081021	42 years	White	Pt31_before_drug	2	4531933134.sdf	baseline	Pt31	Switchers	New analysis	Patient included in analysis	491.50	baseline	Male
GSM1081022	47 years	White	Pt32_before_drug	2	4531933139.sdf	baseline	Pt32	Switchers	New analysis	Patient included in analysis	418.50	baseline	Male
GSM1081023	27 years	White	Pt33_before_drug	2	4531933137.sdf	baseline	Pt33	Switchers	New analysis	Patient included in analysis	305.00	baseline	Male
GSM1081024	29 years	White	Pt34_before_drug	2	4531933134.sdf	baseline	Pt34	Switchers	New analysis	Patient included in analysis	461.50	baseline	Male
GSM1081025	38 years	White	Pt35_before_drug	2	4531933137.sdf	baseline	Pt35	Switchers	New analysis	Patient included in analysis	233.50	baseline	Male
GSM1081026	34 years	White	Pt36_before_drug	2	4531933135.sdf	baseline	Pt36	Switchers	New analysis	Patient included in analysis	316.00	baseline	Male
GSM1081027	31 years	White	Pt1_after_drug	1	4307579062.sdf	antiretroviral therapy	Pt1	NNRTI	New analysis	Patient included in analysis	539.00	after 48 weeks	Male
GSM1081028	36 years	White	Pt2_after_drug	1	4307579062.sdf	antiretroviral therapy	Pt2	NNRTI	New analysis	Patient included in analysis	548.00	after 48 weeks	Male
GSM1081029	39 years	American Indian	Pt3_after_drug	1	4307579072.sdf	antiretroviral therapy	Pt3	NNRTI	New analysis	Patient included in analysis	471.00	after 48 weeks	Male
GSM1081030	38 years	White	Pt4_after_drug	1	4307579062.sdf	antiretroviral therapy	Pt4	NNRTI	New analysis	Patient included in analysis	663.00	after 48 weeks	Male
GSM1081031	52 years	White	Pt5_after_drug	1	4307579060.sdf	antiretroviral therapy	Pt5	NNRTI	New analysis	Patient included in analysis	320.00	after 48 weeks	Male
GSM1081032	42 years	White	Pt6_after_drug	1	4307579072.sdf	antiretroviral therapy	Pt6	NNRTI	New analysis	Patient included in analysis	504.00	after 48 weeks	Male
GSM1081033	24 years	African American	Pt7_after_drug	1	4307579060.sdf	antiretroviral therapy	Pt7	NNRTI	New analysis	Patient included in analysis	988.00	after 48 weeks	Male
GSM1081034	38 years	White	Pt8_after_drug	1	4307579072.sdf	antiretroviral therapy	Pt8	NNRTI	New analysis	Patient included in analysis	564.00	after 48 weeks	Male
GSM1081035	28 years	White	Pt9_after_drug	1	4307579060.sdf	antiretroviral therapy	Pt9	NNRTI	New analysis	Patient included in analysis	776.00	after 48 weeks	Male
GSM1081036	33 years	Asian	Pt10_after_drug	1	4307579061.sdf	antiretroviral therapy	Pt10	NNRTI	New analysis	Patient included in analysis	302.00	after 48 weeks	Male
GSM1081037	28 years	White	Pt11_after_drug	1	4307579062.sdf	antiretroviral therapy	Pt11	NNRTI	New analysis	Patient included in analysis	434.00	after 48 weeks	Male
GSM1081038	19 years	White	Pt12_after_drug	1	4307579062.sdf	antiretroviral therapy	Pt12	NNRTI	New analysis	Patient included in analysis	656.00	after 48 weeks	Male
GSM1081039	29 years	White	Pt13_after_drug	2	4463361156.sdf	antiretroviral therapy	Pt13	PI	New analysis	Patient dropped from analysis	492.00	after 48 weeks	Male
GSM1081040	50 years	White	Pt14_after_drug	2	4463361156.sdf	antiretroviral therapy	Pt14	PI	New analysis	Patient dropped from analysis	404.00	after 48 weeks	Male
GSM1081041	58 years	White	Pt15_after_drug	2	4463361177.sdf	antiretroviral therapy	Pt15	PI	New analysis	Patient dropped from analysis	544.00	after 48 weeks	Male
GSM1081042	50 years	White	Pt16_after_drug	2	4463361156.sdf	antiretroviral therapy	Pt16	PI	New analysis	Patient dropped from analysis	539.00	after 48 weeks	Male
GSM1081043	33 years	White	Pt17_after_drug	2	4463361135.sdf	antiretroviral therapy	Pt17	PI	New analysis	Patient included in analysis	791.00	after 48 weeks	Male
GSM1081044	24 years	American Indian	Pt18_after_drug	2	4463361156.sdf	antiretroviral therapy	Pt18	PI	New analysis	Patient included in analysis	476.00	after 48 weeks	Male
GSM1081045	39 years	White	Pt19_after_drug	2	4463361239.sdf	antiretroviral therapy	Pt19	PI	New analysis	Patient included in analysis	484.00	after 48 weeks	Male
GSM1081046	34 years	African American	Pt20_after_drug	2	4463361177.sdf	antiretroviral therapy	Pt20	PI	New analysis	Patient included in analysis	434.00	after 48 weeks	Male
GSM1081047	40 years	Asian	Pt21_after_drug	2	4463361135.sdf	antiretroviral therapy	Pt21	PI	New analysis	Patient included in analysis	678.00	after 48 weeks	Male
GSM1081048	37 years	Asian	Pt22_after_drug	2	4463361239.sdf	antiretroviral therapy	Pt22	PI	New analysis	Patient included in analysis	502.00	after 48 weeks	Male
GSM1081049	54 years	White	Pt23_after_drug	2	4463361135.sdf	antiretroviral therapy	Pt23	PI	New analysis	Patient included in analysis	806.00	after 48 weeks	Male
GSM1081050	27 years	White	Pt24_after_drug	2	4463361239.sdf	antiretroviral therapy	Pt24	PI	New analysis	Patient included in analysis	1078.00	after 48 weeks	Male
GSM1081051	34 years	White	Pt25_after_drug	2	4531933135.sdf	antiretroviral therapy	Pt25	Switchers	New analysis	Patient included in analysis	409.00	after 48 weeks	Male
GSM1081052	43 years	White	Pt26_after_drug	2	4531933137.sdf	antiretroviral therapy	Pt26	Switchers	New analysis	Patient included in analysis	257.00	after 48 weeks	Male
GSM1081053	49 years	White	Pt27_after_drug	2	4531933134.sdf	antiretroviral therapy	Pt27	Switchers	New analysis	Patient included in analysis	432.00	after 48 weeks	Male
GSM1081054	36 years	White	Pt28_after_drug	2	4531933135.sdf	antiretroviral therapy	Pt28	Switchers	New analysis	Patient included in analysis	577.00	after 48 weeks	Male
GSM1081055	42 years	Asian	Pt29_after_drug	2	4531933137.sdf	antiretroviral therapy	Pt29	Switchers	New analysis	Patient included in analysis	634.00	after 48 weeks	Male
GSM1081056	45 years	White	Pt30_after_drug	2	4531933139.sdf	antiretroviral therapy	Pt30	Switchers	New analysis	Patient included in analysis	680.00	after 48 weeks	Male
GSM1081057	42 years	White	Pt31_after_drug	2	4531933139.sdf	antiretroviral therapy	Pt31	Switchers	New analysis	Patient included in analysis	692.00	after 48 weeks	Male
GSM1081058	47 years	White	Pt32_after_drug	2	4531933134.sdf	antiretroviral therapy	Pt32	Switchers	New analysis	Patient included in analysis	639.00	after 48 weeks	Male
GSM1081059	27 years	White	Pt33_after_drug	2	4531933139.sdf	antiretroviral therapy	Pt33	Switchers	New analysis	Patient included in analysis	552.00	after 48 weeks	Male
GSM1081060	29 years	White	Pt34_after_drug	2	4531933135.sdf	antiretroviral therapy	Pt34	Switchers	New analysis	Patient included in analysis	710.00	after 48 weeks	Male
GSM1081061	38 years	White	Pt35_after_drug	2	4531933135.sdf	antiretroviral therapy	Pt35	Switchers	New analysis	Patient included in analysis	456.00	after 48 weeks	Male
GSM1081062	34 years	White	Pt36_after_drug	2	4531933137.sdf	antiretroviral therapy	Pt36	Switchers	New analysis	Patient included in analysis	676.00	after 48 weeks	Male

Group Sets View in Gene Expression Browser

Name
All Samples	Default	View
In order to make new Group Sets or change settings, please log in.

Module Analysis

Group Set
All Samples

SIDRA