Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

37 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of RNA-Seq and Microarray in Transcriptome Profiling During T Cell Activation

ABSTRACT: Samples in this study probe the gene expression kinetics in human CCR6+ Th17 memory T cells activated under Th17 condition. Human CCR6+ Th17 memory T cells were purified from PBMC and gene expression was studied over a time course of 3 days after activation under Th17 condition. RNA from these samples was also profiled using RNA-Seq to compare different transcriptome profiling technologies. PBMCs were purified from whole blood from a healthy donor. CD4+ cells were isolated by negative selection, followed by CCR6+ purification by positive selection. Two replicates of 6 time points were taken following stimulation in Th17 polarizing conditions. This submission represents microarray component of study.

ORGANISM(S): Homo sapiens

SUBMITTER: Anton Bittner

PROVIDER: E-GEOD-48978 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells.

Zhao Shanrong S Fung-Leung Wai-Ping WP Bittner Anton A Ngo Karen K Liu Xuejun X

PloS one 20140116 1

To demonstrate the benefits of RNA-Seq over microarray in transcriptome profiling, both RNA-Seq and microarray analyses were performed on RNA samples from a human T cell activation experiment. In contrast to other reports, our analyses focused on the difference, rather than similarity, between RNA-Seq and microarray technologies in transcriptome profiling. A comparison of data sets derived from RNA-Seq and Affymetrix platforms using the same set of samples showed a high correlation between gene ...[more]

PMID: 24454679

Similar Datasets

Transcriptional profiles of CCR7lo effector memory human T cell subsets

Project description:The aim of this study was to identify differentially-expressed genes in CCR4hi/CXCR3- and CCR4lo CXCR3+ CCR6+ human Th17 cell subsets Human CD45RO+ memory T cells isolated from the peripheral blood of healthy adult donors were sorted into 4 predominant CCR7lo CD25- effector memory subsets: (1) Th1 - CCR6- CCR4lo CXCR3+; (2) Th2 - CCR6- CCR4hi CXCR3+; (3) Th17 - CCR6+ CCR4hi CXCR3-; (4) Th17.1 - CCR6+ CCR4lo CXCR3-. Sorted cells were cultured in media and activated via anti-CD3/anti-CD28 beads for 36 hours. All subsets were then harvested and used for RNA extraction and microarray experiments. Th1 vs Th2; Th1 vs Th17; Th1 vs Th17.1; Th2 vs Th17; Th2 vs Th17.1; Th17 vs Th17.1

2013-12-17 | E-GEOD-49703 | biostudies-arrayexpress

Time course expression measured by microarray of fresh CD4+ response to activation from healthy individuals

Project description:Variation in individuals' adaptive immune response is believed to influence susceptibility to complex diseases in humans. The genetic basis of such variation is poorly understood. We measured gene expression from resting and activated CD4+ T cells derived from the peripheral blood of healthy individuals. We activated the primary T cells with anti-CD3/CD28 beads alone or with IFNb or Th17 polarizing cytokines. We collected peripheral blood from each human donor. We isolated peripheral blood mononuclear cells by Ficoll, and negatively selected for CD4+ T cells using RosettaSep. We then either left cells unstimulated or stimulated them with beads conjugated with anti-CD3 and anti-CD28 either without additional cytokines, or with IFNb, or with Th17 cocktail. Cells were harvest at up to 8 time points (0hr, 45min, 2hr, 4hr, 10hr, 24hr, 48hr and 72hr), lysed and RNA isolated to be profiled on microarray.

2014-08-28 | E-GEOD-60234 | biostudies-arrayexpress

Expression data for effector T cells

Project description:In this study, we examined differential gene expression in naïve human CD4+ T cells, as well as in effector Th1, Th17-negative and Th17-enriched CD4- T cell subsets. We observed a marked enrichment for increased gene expression in effector CD4+ T cells compared to naive CD4+ among immune-mediated disease oci genes. Within effector T cells, expression of disease-associated genes was increased in Th17-enriched compared to Th17-negative cells. We used microarray to examine the gene expresssion profile and level of human naïve, Th1 and effector T cell subsets. Human PBMCs were isolated and sorted to naïve, CD161-CCR6- and CD161+CCR6+ memory T cells. Naïve T cells were differentiatied to Th1 cells, and CD161-CCR6- and CD161+CCR6+ memory T cells were in vitro expanded for Th17-negative and Th17-enriched effector T cells. The gene profile was compared among naive, Th1, Th17-negative, and Th17-enriched cell subsets.

2012-05-12 | E-GEOD-32901 | biostudies-arrayexpress

Comparison of RNA-Seq and Microarray in Transcriptome Profiling During T Cell Activation

Project description:Samples in this study probe the gene expression kinetics in human CCR6+ Th17 memory T cells activated under Th17 condition. Human CCR6+ Th17 memory T cells were purified from PBMC and gene expression was studied over a time course of 3 days after activation under Th17 condition. RNA from these samples was also profiled using RNA-Seq to compare different transcriptome profiling technologies.

2014-03-11 | GSE48978 | GEO

Transcription profiling of mouse spleen CD4+ CD44Low CD62LHigh cells stimulated with anti-CD3 or anti-CD28 in the presence or absence of hTGFb-1 and mouse IL-6

Project description:Mouse spleen CD4+CD44LowCD62LHigh cells were stimulated with 2ug/ml anti-CD3(eBioscience), 2ug/ml anti-CD28 (eBioscience) in the presence (Th17 condition) or absence (Th0 condition) of hTGFb-1 (1ng/ml eBioscience), mouse IL-6(10ng/ml eBioscience). Cells were collected after 24 hourÕs culture using RNAeasy columns (Qiagen) for total RNA isolation. Isolated total RNA from Th0 and Th17 conditioned cells were submitted for the microarray gene transcription comparison analysis using Affymetrix Mouse 430A 2.0 array chips.

2008-12-21 | E-TABM-583 | biostudies-arrayexpress

CD49f defines a subset of dysfunctional regulatory T cells circulating in the human peripheral blood

Project description:The therapeutic use of regulatory T cells (Tregs) in patients with autoimmune disorders has been hampered by the biological variability of memory Treg populations in the peripheral blood. In this study, we reveal through a combination of quantitative proteomic, multiparametric flow cytometry, RNA-seq data analysis and functional assays, that CD49f is heterogeneously expressed among human Tregs and impacts their immunomodulatory function. High expression of CD49f defines a subset of dysfunctional Tregs in the human blood characterized by a Th17-like phenotype and impaired suppressive capacity. CD49f is similarly distributed between naïve and memory Tregs and impacts the expression of CD39, CTLA-4, FoxP3 and CCR6 specifically in the memory compartment. Accumulation of CD49f high memory Tregs in the blood of ulcerative colitis patients correlates with disease severity. Our results highlight important considerations for Treg immunotherapy design in patients with inflammatory bowel disease which could possibly extend to other autoimmune disorders.

2021-08-06 | PXD022095 | Pride

Transcriptional profiling of Th1, Th2, Th9, and Th17 T cell clones

Project description:We next sought to identify the transcriptional program that differentiates IL-9+Th2 cells from “conventional” Th2 cells. To this end, we selected representative Th1, Th17, Th2, and IL-9+Th2 clones (Figure 5A) and determined their transcriptome in the resting state and at different time points after activation using RNAseq. Peripheral Blood Mononuclear Cells (PBMC) were isolated by Ficoll-Plaque Plus (GE Healthcare, UK) density gradient centrifugation. Human CD4+ T cells were isolated from PBMC by EasySep positive selection kit (Stemcell Technologies) according to manufacturer’s instruction. Positively selected CD4+ T cells were washed with PBS and stained for subsequent Th cell subset sorting. Memory Th cell subsets were sorted to over 90% purity according to their expression of chemokine receptors from CD45RA-CD25-CD8-CD3+ cells: Th1(CXCR3+CCR8-CCR6-CCR4-), Th2 (CXCR3-CCR8-CCR6-CCR4+), Th17 (CXCR3-CCR8-CCR6+CCR4+), Th9 (CXCR3-CCR8+CCR6-CCR4+). Single cell Th subset clones were directly sorted into 96well plate according to their expression of chemokine receptors (see above). Single cell clones were expanded and maintained by periodic restimulation with PHA (phytohaemaglutinine, 1 µg/ml, Sigma-Chemicals) and irradiated allogenic feeder cells (5x104/well) in culture medium. T cells were polyclonally activated using beads coated with antibodies against CD3, CD2, and CD28 (T cell/bead = 2:1, human T cell activation/expansion Kit, Miltenyi). Cell cultures were sampled before activation (time 0h) and 2, 4, 6, 9, 12, 24, and 48 hours after activation.

2017-11-10 | E-MTAB-5739 | biostudies-arrayexpress

ATAC-seq of isolated primary human CD8+ T cells treated with KDACi with polyclonal stimulation for 6 days

Project description:Lysine deacetylase inhibitors (KDACi) show immunomodulatory properties, promoting differntiation of an IL7RhiPD1lo memory precursor (MPEC) phenotype on polyclonal stimulation in vitro and enhancing functional memory responses during infection or immunisation in vivo. We isolated (MACS positive selection) primary human CD8+ T cells from healthy blood donors and treated them for 6 days with low dose sodium valproate (5mM, d0) with concurrent stimulation with anti-CD2/3/28 microbeads, then undertook bulk ATACseq of lysed cells.

2024-09-01 | E-MTAB-13367 | biostudies-arrayexpress

RNA-seq of isolated primary human CD8+ T cells treated with KDACi with polyclonal stimulation for 6 days

Project description:Lysine deacetylase inhibitors (KDACi) show immunomodulatory properties, promoting differentiation of an IL7RhiPD1lo memory precursor (MPEC) phenotype on polyclonal stimulation in vitro and enhancing functional memory responses during infection or immunisation in vivo. We isolated (MACS positive selection) primary human CD8+ T cells from healthy blood donors and treated them for 6 days with low dose sodium valproate (5mM, d0) with concurrent stimulation with anti-CD2/3/28 microbeads, then undertook bulk RNAseq of lysed cells.

2024-09-01 | E-MTAB-13366 | biostudies-arrayexpress

Interleukin-23-induced transcription factor Blimp1 promotes pathogenicity of T helper 17 cells

Project description:Interleukin-23 (IL-23) is a pro-inflammatory cytokine required for the pathogenicity of T helper 17 (Th17) cells but the molecular mechanisms governing this process remain unclear. We identified the transcription factor Blimp-1 (Prdm1) as a key IL-23-induced factor that drove the inflammatory function of Th17 cells. In contrast to thymic deletion of Blimp-1, which causes T cell development defects and spontaneous autoimmunity, peripheral deletion of this transcription factor resulted in reduced Th17 activation and reduced severity of autoimmune encephalomyelitis. Furthermore, genome wide occupancy and overexpression studies in Th17 cells revealed that Blimp-1 co-localized with transcription factors RORÎ³t, STAT-3 and p300 at the Il23r, Il17a/f and Csf2 cytokine loci to enhance their expression. Blimp-1 also directly bound to and repressed cytokine loci Il2 and Bcl6. Taken together, our results demonstrate that Blimp-1 is an essential transcription factor downstream of IL-23 that acts in concert with RORÎ³t to activate the Th17 inflammatory program. Genome-wide binding analysis of Blimp1 from in vitro generated T effector and regulatory cells

2016-06-15 | E-GEOD-75724 | 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