Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Digital RNA-Seq for transcriptome analysis in splenic human CD4-positive T cells of mock-infected humanized mice and GFP-positive and GFP-negative CD4-positive cells of HIV1-GFP-infected humanized mice

ABSTRACT: Digital RNA-Seq for transcriptome analysis in splenic human CD4-positive T cells of mock-infected humanized mice and GFP-positive and GFP-negative CD4-positive cells of HIV1-GFP-infected humanized mice

PROVIDER: PRJNA566138 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10136800_1.fastq.gz	Fastqsanger.gz
	SRR10136800_2.fastq.gz	Fastqsanger.gz
	SRR10136801_1.fastq.gz	Fastqsanger.gz
	SRR10136801_2.fastq.gz	Fastqsanger.gz
	SRR10136802_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 74

Similar Datasets

Linker-mediated PCR for global integration site analysis in splenic human CD4-positive T cells of HIV1-GFP-infected humanized mice

Project description:To comprehensively compare the HIV-1 integration sites between viral producing cells (GFP+ cells) and non-producing cells (GFP- cells), linker-mediated PCR is performed by using the samples obtained from HIV1-GFP-infected humanized mice. Additionally, to reactivate latently infected cells, viral non-producing cells (GFP- cells) were stimulated with PMA and ionomycin ex vivo. Then, the viral integration sites in potential latently infected cells (GFP-_GFP+ cells) and the cells with dead/inactivated proviruses (GFP-_GFP- cells) were analyzed by linker-mediated PCR.

2020-07-16 | GSE137962 | GEO

Digital RNA-Seq for transcriptome analysis in splenic human CD4-positive T cells of mock-infected humanized mice and GFP-positive and GFP-negative CD4-positive cells of HIV1-GFP-infected humanized mice

Project description:Transcriptome analysis of digital RNA-sequencing (dRNA-Seq) data reveals the differentially expressed genes between GFP-positive and GFP-negative cells.

2020-07-16 | GSE137644 | GEO

Linker-mediated PCR for global integration site analysis in splenic human CD4-positive T cells of HIV1-GFP-infected humanized mice

Project description:Linker-mediated PCR for global integration site analysis in splenic human CD4-positive T cells of HIV1-GFP-infected humanized mice

| PRJNA574039 | ENA

mRNA expression levels in splenic human CD4-positive T cells of mock-infected, HIV-1-infected and pegIFN-treated humanized mice

Project description:Through RNA sequencing and reactome analyses, we report that type I interferon response is elicited in the spleen of HIV-1-infected humanized mice when compared to mock-infected humanized mice.

2017-10-13 | GSE94776 | GEO

mRNA expression levels in splenic human CD4-positive T cells of mock-infected, HIV-1-infected and pegIFN-treated humanized mice

Project description:mRNA expression levels in splenic human CD4-positive T cells of mock-infected, HIV-1-infected and pegIFN-treated humanized mice

| PRJNA374028 | ENA

RNA-seq of CD4+T cells derived from spleens of SIVcpz and HIV-1 infected humanized BLT-mice

Project description:There are many DEGs between SIVcpz and HIV-1 infected humanized BLT-mice.

2020-04-06 | GSE97518 | GEO

mRNA expression levels in splenic human mononuclear cells of mock- and HIV-1-infected humanized mice

Project description:Through RNA sequencing and gene ontology analyses, we report that immune activation is elicited in the spleen of 4 HIV-1-infected humanized mice when compared to 4 mock-infected humanized mice.

2017-04-28 | GSE92262 | GEO

Affymetrix gene expression AID-GFP-positive vs AID-GFP-negative

Project description:Affymetrix gene expression AID-GFP-positive vs AID-GFP-negative

2009-08-15 | GSE13611 | GEO

Analysis of bacterial and macrophage transcripts in ISRE-positive and negative infected macrophages

Project description:To identify bacterial transcripts that may be associated with type I IFN production in Salmonella enterica subsp typhimurium (SL1344) infected macrophages we transformed macrophages with an ISRE-GFP reporter construct and sorted separate populations of GFP positive and GFP negative infected macrophages. We then did whole transcriptome profiling, collecting both host and bacterial transcripts, for differential expression analysis

2015-09-07 | GSE65531 | GEO

Single cell transcriptomic analysis of acute and early ART-treated HIV-1-infected CD4+T cells from a reservoir-marking humanized mouse model

Project description:Human immunodeficiency virus (HIV-1) infects and depletes CD4+ T helper cells and can persist within these cells in a latent state during treatment with effective antiretroviral therapy (ART). A latent viral reservoir represents a major barrier to a cure for HIV-1 infection. A longstanding obstacle to understanding the reservoir has been the inability to identify and characterize latent cells without activating them and disrupting their resting state. To address this challenge, we have developed an HIV-1-induced lineage tracing (HILT) humanized mouse model that irreversibly marks HIV-infected cells. The system employs a genetically encoded Cre-lox switch transduced into hematopoietic stem cells which are transplanted into immunodeficient mice. Infection of CD4+ T cells in HILT mice with a Cre-expressing HIV clone irreversibly marks infected cells by switching dsRedExpress2 to EGFP expression, a phenotype that is maintained in cell harboring proviruses that are transcriptionally silent during ART. Single cell RNA sequencing (scRNAseq) of infected T cells in the presence or absence of ART reveals HIV infection in diverse CD4+ T cell transcriptional lineages indicating that infected cells with active or suppressed transcription exist in many different T cell lineages. We examined genetic pathways that are more frequently altered in infected cells when compared with uninfected bystander cells. A comparison of pathways that are regulated in opposite directions in acute versus early ART-treated (persistent) infection identified EIF2α-, sirtuin-, and ILK-signaling pathways which contain known transcriptional regulators of HIV transcription. Lastly, we find that resveratrol, a drug that impact sirtuin pathways can influence latency establishment in an acute infection setting.

2024-12-31 | GSE236107 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data