GEO DataSets

(Submitter supplied) Analyzed the effects of HIV-1 (MN) and HIV-2 (ROD) infection on the expression of host factors in PBMC at the RNA level using the Agilent Whole Human Genome Oligo Microarray.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

9 Samples

Download data: TXT

(Submitter supplied) We analyzed transcriptomic data from infected and uninfected T-cells to identify pseudogenes and their parent genes showing differential expression in HIV-1 infection

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

2 Samples

Download data: DIFF

(Submitter supplied) We used Affymetix HG Focus GeneChip to measure the expression levels of HIV seronegative and seropositive individuals in human PBMCs in vivo. GSM39104 -GSM39115 are HIV seronegative samples; GSM39116-GSM39137 are HIV seropositive but drug naive samples; GSM39138-GSM39147 are HIV seropositive samples used to test serostatus biomarker; GSM39148-GSM39170 are HIV seropositive individuals whose CD4 cells decrease over time; GSM39171-GSM39187 are HIV seropositive individuals whose CD4 cells increase over time; GSM39188-GSM39190 are HIV seropositive samples used to test CD4 cell increase/decrease over time. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1449

Platform:

GPL201

87 Samples

Download data: CEL

Analysis of peripheral blood mononuclear cells from HIV-1 seropositive and seronegative individuals. Results used to identify a 10-gene signature used for determining HIV-1 serostatus, and a 6-gene signature to identify seropositive individuals exhibiting changes in CD4+ T cell counts.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 disease state, 4 other, 3 protocol sets

Platform:

GPL201

Series:

GSE2171

87 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL14907 GPL6947

24 Samples

Download data

(Submitter supplied) Host cells respond to exogenous infectious agents such as viruses, including HIV-1. Studies have evaluated the changes associated with virus infection at the transcriptional and translational levels of the cellular genes involved in specific pathways. While this approach is useful, in our view it provides only a partial view of genome-wide changes. Recently, technological advances in the expression profiling at the microRNA (miRNA) and mRNA levels have made it possible to evaluate the changes in the components of multiple pathways. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

12 Samples

Download data: TXT

(Submitter supplied) Host cells respond to exogenous infectious agents such as viruses, including HIV-1. Studies have evaluated the changes associated with virus infection at the transcriptional and translational levels of the cellular genes involved in specific pathways. While this approach is useful, in our view it provides only a partial view of genome-wide changes. Recently, technological advances in the expression profiling at the microRNA (miRNA) and mRNA levels have made it possible to evaluate the changes in the components of multiple pathways. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL14907

12 Samples

Download data: XLS

(Submitter supplied) A significant percentage of HIV-infected individuals experience a sharp decline in CD4+ T cell counts and progress to AIDS quickly after primary infection. Identification of biomarkers distinguishing rapid progressors (RPs) versus chronic progressors (CPs) is critical for early clinical intervention and could provide novel strategies to facilitate vaccine design and immune therapy. mRNA and miRNA expression profiles in the peripheral blood mononuclear cells (PBMCs) of RPs and CPs were investigated at 111±22 days (Mean±SD) of HIV infection. more...

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL16683

50 Samples

Download data: TXT

(Submitter supplied) A significant percentage of HIV-infected individuals experience a sharp decline in CD4+ T cell counts and progress to AIDS quickly after primary infection. Identification of biomarkers distinguishing rapid progressors (RPs) versus chronic progressors (CPs) is critical for early clinical intervention and could provide novel strategies to facilitate vaccine design and immune therapy. mRNA and miRNA expression profiles in the peripheral blood mononuclear cells (PBMCs) of RPs and CPs were investigated at 111±22 days (Mean±SD) of HIV infection. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16025

13 Samples

Download data: PAIR

(Submitter supplied) HIV infection of CD4 T cells induces a range of host transcriptional changes in mRNAs as well as microRNAs that may coordinate changes in mRNAs.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10999

26 Samples

Download data: TXT

(Submitter supplied) HIV-1 Vpr protein is a multifunctional protein which perturbs human transcriptome and interacts with a number of cellular proteins. In this study, we have attempted to explore the efffects of Vpr on human transcriptome and have identified several genes which are involved in innate immune responses. We used the microarray analysis to elucidate the differnetail expression pattern of differnet genes in human dendritic cells infected with HIV-1 Vpr. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

4 Samples

Download data: CEL

(Submitter supplied) To systematically investigate early host transcriptional response to HIV-1 infection, including polyadenylated and non-polyadenylated transcripts, we separately sequenced Total RNAs (Total RNA-seq) from HIV-1-infected SupT1 cells, a human CD4+ T cell line. We show many non-polyadenylated RNAs were also differentially expressed upon HIV-1 infection, as expected only detected by Total RNA-seq. Interestingly, we identified 8 times more differentially expressed genes at 12 hour post-infection by Total RNA-seq than by mRNA-seq, mostly protein-coding genes.

Organism:

Homo sapiens; Human immunodeficiency virus 1

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18160 GPL11154

16 Samples

Download data: TXT

(Submitter supplied) In this study, we have investigated the relationship between genome-wide DNA methylation pattern and HIV infection using the methylated DNA immunoprecipitation - microarray method. A pair of monozygotic twins was recruited: one of the twins was infected with HIV while the other was not. The immunoprecipitated CpG-methylated DNA from HIV positive subject (test) and from HIV negative subject (input control) were labelled with Cy5 and Cy3 respectively

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL16284

1 Sample

Download data: PAIR

(Submitter supplied) Throughout HIV-1 replication cycle, a complex interplay of host-pathogen interactions takes place in the infected cell, leading to production of new virions. The virus modulates the host cellular machinery in order to support its life cycle, while controlling intracellular defense. We have investigated the dynamic host response to HIV-1 infection by systematically measuring transcriptome, proteome and phosphoproteome expression changes in infected and uninfected SupT1 CD4+ T cells at 5 time-points throughout the HIV-1 replication cycle. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: FA, GTF, TXT

(Submitter supplied) Transcriptomic analyses from early human immunodeficiency virus (HIV) infection have the potential to reveal how HIV causes widespread and lasting damage to biological functions, especially in the immune system. Previous studies have been hampered by difficulties in obtaining early specimens. We studied 29 HIV infected subjects 1 month from presentation and 46 contemporaneous uninfected controls. We used RNA-seq to examine circulating immune cells to describe in detail the profound gene dysregulation observed in early HIV infection. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

74 Samples

Download data: CSV

(Submitter supplied) We performed a 3' RACE of a novel HIV RNA TAR-gag in order to determine the sequence of the RNA at the 3' end. Our data had shown that TAR-gag was potentially a noncoding RNA and our hypothesis was that TAR-gag ended somewhere prior to the end of the gag region of the HIV genome. The 3' RACE experiment showed that TAR-gag actually consists of four different RNA clusters, the longest of which ends at 615 bases from the transcription start site; this is in the middle of the p17 region of the gag gene. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: WIG

(Submitter supplied) This data corresponds to the microRNA expression profiles for the exact same samples from GSE180273.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

24 Samples

Download data: XLSX

(Submitter supplied) It has been proposed that macrophages could serve as long-lived compartments for HIV-1 infection under in vivo situations because these cells are resistant to the virus-mediated cytopathic effect, produce progeny virus over extended periods of time and are localized in tissues that are often less accessible by treatment. Comprehensive experimental studies are thus needed to characterize the HIV-1-induced modulation of host genes in these myeloid lineage cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

24 Samples

Download data: XLSX

(Submitter supplied) During HIV-1 infection, there is a massive perturbation of host gene expression, but as yet, genome-wide studies have not identified host genes affecting HIV-1 replication in lymphatic tissue, the primary site of virus-host interactions. In this study, we isolated RNA from the inguinal lymph nodes of 22 HIV-1-infected individuals and utilized a microarray approach to identify host genes critically important for viral replication in lymphatic tissue by examining gene expression associated with viral load. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

42 Samples

Download data: CEL

(Submitter supplied) BACKGROUND: Understanding individual patient host response to viruses is key to designing optimal personalized therapy. Unsurprisingly, in-vivo human experimentation to understand individualized dynamic response of the transcriptome to viruses are rarely studied because of the obvious limitations stemming from ethical considerations of the clinical risk. OBJECTIVE: In this rhinovirus study, we first hypothesized that ex-vivo human cells response to virus can serve as a proxy for otherwise controversial in-vivo human experimentation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

8 Samples

Download data: CEL