Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential Gene expression in CCR5+ versus CCR5- OT-I T cells

ABSTRACT: OT-I T cells were exposed to CpG ODN-activated CCR5ko Lymph nodes for 6 h, stained for surface CCR5 and FACS-sorted into CCR5+ and CCR5- fractions In the study presented here freshly isolated OT1 T cells were exposed for 6h at 37oC to teased-out CpG ODN-activated CCR5ko LNs in 96-well plates and stained for surface CCR5 before sorting into CCR5+ (Hua2) and CCR5- (Hua1) fractions. High quality total RNA isolated from each cell fraction using TRIZOL and Qiagen RNEasy kit per manufacture's recommendation was subjected to microarray analysis using the Affymetrix Mouse Gene ST 1.0 array chip to discover differentially expressed genes.

ORGANISM(S): Mus musculus

SUBMITTER: David Askew

PROVIDER: E-GEOD-76820 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Differential Gene expression in CCR5+ versus CCR5- OT-I T cells

Project description:OT-I T cells were exposed to CpG ODN-activated CCR5ko Lymph nodes for 6 h, stained for surface CCR5 and FACS-sorted into CCR5+ and CCR5- fractions

2016-01-14 | GSE76820 | GEO

RNA-seq bulk of CCR6+Th-cell subsets in Crohn’s Disease, peripheral blood and intestinal lamina propria

Project description:This RNA seq experiment was designed to identify a gene signature of a CCR5-expressing subset of human intestinal Th17-cells. T helper-cells from peripheral blood of healthy donors and from the lamina propria of Crohn’s Disease patients were FACS-purified according to the expression of the chemokine receptors CCR6, CCR5 and CXCR3. Four CCR6+Th- subsets were isolated according to CXCR3 and CCR5 expression: two CXCR3- Th17 subsets (CCR5-: “cTh17” or CCR5+: “pTh17”) and two subsets of CXCR3+ Th1/17-cells (CCR5+ or CCR5-)

2023-07-27 | E-MTAB-13178 | biostudies-arrayexpress

RNA-seq of human peripheral blood B helper T-cell subsets

Project description:Human T-cells that express CXCR5 and/or CCR6 provide help to naive B-cells for IgG production. To understand the molecular pathways that are shared or unique to individual B helper T-cell subsets in human peripheral blood, CD4+IL-7R+CD25-/lo helper T-cells were purified according to the expression of CXCR5, CCR6, CXCR3, CD161 and CCR5 as follows: 1) TFH17(CD161-): CXCR5+CXCR6+CXCR3-CD161- 2) Th17: CXCR5-CCR6+CXCR3-, CD161+ or CCR5+ 3) CCR6”SP”: CXCR5-CCR6+CXCR3-CD161-CCR5- RNA-seq was performed with FACS-purified T-cell subsets from 3 healthy individuals.

2020-03-11 | E-MTAB-8862 | biostudies-arrayexpress

RNA-seq of Tfh cells from BALB/c and C57Bl/6 mice immunized with OVA-IFA or OVA-CpG

Project description:The aim of the project was the identification of the transcriptional signature of effector T cells and Tfh cells that emerge following immunization with different adjuvants. For this purpose OVA-specific TCR-transgenic cells (from DO11.10 or OT-II mice) were adoptively transferred into congenic BALB/c or C57Bl/6 mice, subsequently immunized with OVA-IFA or OVA-CpG. At day 11, the OVA-specific T effector and Tfh cells were FACS sorted from the draining lymph nodes for RNA sequencing.

2023-04-15 | E-MTAB-12086 | biostudies-arrayexpress

Single cell RNA-seq of sorted Tfh cells from C57BL/6 Foxp3-GFP mice immunized with OVA-IFA and OVA-CpG

Project description:The aim of the project was the identification of the transcriptional signature of Tfh cells that emerge following immunization with different adjuvants. For this purpose C57Bl/6 mice, bearing a Foxp3-GFP reporter system, were immunized with OVA-IFA or OVA-CpG. At day 11 post-immunization, Foxp3 negative Tfh cells were FACS-sorted from the draining lymph nodes and processed for single cell RNA sequencing.

2023-07-31 | E-MTAB-12085 | biostudies-arrayexpress

Suppression of TLR9-dependent gene expression in vivo mediated by TTAGGG motifs

Project description:Immunostimulatory CpG ODN trigger an innate immune response characterized by the rapid production of pro-inflammatory cytokines and chemokines, an effect that persists for days to weeks in vivo. Previous studies established that gene up-regulation is maximal 3 hr after CpG ODN treatment of normal mice {Klaschik et al. JLB 2009}. The immunostimulatory activity of CpG ODN is blocked by the addition of immunosuppressive ODN expressing multiple TTAGGG motifs. To clarify the mechanism underlying this suppression, changes in gene expresssion were evaluated by microarray in mice treated with 400 ìg of CpG ODN + 400 ìg of suppressive ODN. Data from 4 independent biological replicates/time point and treatment group and 6 untreated controls were used for all statistical analyses. A reference design was used. Reference cDNA vs. sample cDNA were hybridized to same array.

2011-06-01 | E-GEOD-22156 | biostudies-arrayexpress

CCR5 HIV controllers

Project description:CCR5 HIV controllers

| PRJEB48153 | ENA

Short and long-term changes in gene expression mediated by the activation of TLR9

Project description:CpG DNA binds to Toll-like receptor 9 to stimulate a strong innate immune response. Despite extensive studies of TLR9 mediated signal transduction, the scope of CpG-induced changes in gene expression is incompletely understood. In particular, the prolonged effects of CpG ODN (oligodeoxynucleotide) on gene activation have not been investigated despite evidence that a single dose of CpG ODN alters immune reactivity for several weeks. This study used gene expression analysis to monitor changes in mRNA levels for 14 days, and identified the genes, pathways, functional groups and regulatory networks triggered in vivo following CpG ODN administration. Two discrete peaks of gene activation (at 3 hr and 5 days) were observed after CpG administration. Both the regulation and function of genes activated during the second peak differed from those triggered shortly after CpG administration. Initial gene up-regulation corresponded to a period when TLR9 ligation stimulated genes functionally associated with the generation of innate and adaptive immune responses (e.g. the NF-kB and B-cell receptor pathways). The second peak reflected processes associated with cell division (e.g., cell cycle and DNA replication & repair). Whereas TNF and IFNG played central roles regulating the first peak of activation, E2F1, E2F2, BRCA1, and HRAS had major impact on the networks controlling the second peak. The complex bimodal pattern of gene expression elicited by CpG ODN administration provides novel insights into the long term effects of CpG DNA on genes associated with immunity and cell proliferation. Data from 4 independent biological replicates/time point (9 time points) and 6 untreated controls were used for all statistical analyses. A reference design was used. Reference cDNA vs. sample cDNA were hybridized to same array.

2010-05-16 | E-GEOD-16465 | biostudies-arrayexpress

People with HIV have higher percentages of circulating CCR5+ CD8+ T cells and lower percentages of CCR5+ regulatory T cells

Project description:CCR5 is the main HIV co-receptor. We aimed to (1) compare CCR5 expression on immune cells between people living with HIV (PLHIV) using combination antiretroviral therapy (cART) and HIV-uninfected controls, (2) relate CCR5 expression to viral reservoir size and (3) assess detereminants of CCR5 expression. Percentages of CCR5 positive cells (%) and CCR5 mean fluorescence intensity (MFI) assessed by flow cytometry in monocytes and lymphocyte subsets were correlated to host factors, HIV-1 cell-associated (CA)-RNA and CA-DNA, plasma inflammation markers and metabolites.

2022-08-12 | PXD031628 | Pride

IRF-5 and IRF-8 govern the response of Human Plasmacytoid Dendritic Cells following TLR9 ligation

Project description:Synthetic oligonucleotides (ODNs) containing CpG motifs stimulate human plasmacytoid dendritic cells (pDCs) to produce type-1 interferons (IFN) and pro-inflammatory cytokines. Previous studies demonstrated that interferon regulatory factors (IRFs) played a central role in mediating CpG-induced pDC activation. This work explores the inverse effects of IRF-5 and IRF-8 on CpG dependent gene expression. Results from RNA interference and microarray studies indicate that IRF-5 up-regulates TLR9-driven gene expression whereas IRF-8 down-regulates the same genes. Several findings support the conclusion that IRF-8 inhibits TLR9 dependent gene expression by directly blocking the activity of IRF-5. First, the inhibitory activity of IRF-8 is only observed when IRF-5 is present. Second, proximity ligation analysis shows that IRF-8 and IRF-5 co-localize within the cytoplasm of resting human pDC and co-translocate to the nucleus after CpG stimulation. Taken together, these findings suggest that two transcription factors with opposing functions control TLR9 signaling in human pDCs. CAL-1 cells were transfected with siRNA targeting IRF-5 (IRF-5si) and left unstimulated (n=4, technical repeats) or stimulated with K-type CpG ODN (n=4, technical repeats). CAL-1 cells were transfected with siRNA targeting IRF-8 (IRF-8si) and left unstimulated (n=4, technical repeats) or stimulated with K-type CpG ODN (n=4, technical repeats). CAL-1 cells were transfected with control siRNA (Contsi) and left unstimulated (n=4, technical repeats) or stimulated with K-type CpG ODN (n=4, technical repeats).

2016-06-01 | E-GEOD-70429 | biostudies-arrayexpress

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