Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of culture/microexpansion in various conditions on virus-specific CD8+ T cells

ABSTRACT: To investigate the conditions for the optimal expansion ot T cell therapeutic products, we used a microexpansion platform to screen various cytokine cocktails (no cytokines, IL-4 + IL-7, IL-15, IL-15 + IL-4, IL-15 + IL-6, and IL-15 + IL-7). We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different donors under 6 different culture/microexpansion conditions

ORGANISM(S): Homo sapiens

PROVIDER: GSE223140 | GEO | 2023/01/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Effect of culture/microexpansion in various conditions on virus-specific CD4+ T cells

Project description:To investigate the conditions for the optimal expansion ot T cell therapeutic products, we used a microexpansion platform to screen various cytokine cocktails (no cytokines, IL-4 + IL-7, IL-15, IL-15 + IL-4, IL-15 + IL-6, and IL-15 + IL-7). We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different donors under 6 different culture/microexpansion conditions

2023-01-19 | GSE223139 | GEO

Vaccine Infection T cell Comparison

Project description:Protection from pathogens relies on both humoral (antibody-mediated) and cellular (T cell-mediated) responses. While infections robustly elicit both of these types of immunity, currently approved vaccine adjuvants largely fail to induce significant T cell responses. However, recent work by our lab and others suggests that the mechanisms governing vaccine-elicited T cells (Tvac) may be substantially different than those governing infection-elicited T cells (Tinf). We have recently demonstrated that optimal subunit vaccine-elicited T cell responses rely on different cytokine signals (IL-27 and 15) and metabolic function (oxidative phosphorylation vs. aerobic glycolysis) leading to phenotypically and functionally different outcomes (memory vs. effector). Our goal was to investigate the transcriptional programming that promotes Tvac formation. Using a bulk RNAsequencing approach we compared WT Tvac at day 3 post immunization to Tvac where IL-27 or IL-15 signaling was absent, to Tinf at day 4 post infectious challenge, or to naive OT-1 T cells.

2023-07-14 | GSE237415 | GEO

Gene expression profiling of HUVEC under basal (resting) conditions

Project description:To understand the biological variability that exists between different individuals, the resting (untreated) transcriptome from 15 different individuals was examined. Transcripts expressed in a bimodal manor across the 15 biological replicates were identified for further examination. In the study presented here, HUVEC isolates from 15 different individuals were cultured until passage 4 in fully supplemented growth conditions. RNA was extracted and hybridised onto CodeLink microarrays. The expression profiles in the untreated condition were examined along side a subset of the same biological replicates treated with a cocktail of inflammatory mediators (10ng/ml TNF-α, Il-1β, Il-8) for a period of 24 hours prior to RNA extraction (also submitted).

2011-07-19 | E-GEOD-23068 | biostudies-arrayexpress

Transcriptional profiles from Dickeya dadantii 3937 in various growth conditions

Project description:We have analysed the global gene expression of the plant pathogen Dickeya dadantii 3937 when grown in vitro under different growth and stress conditions. A multi-factorial design with 32 different experimental conditions was constructed, with two biological replicates for each condition. Cells were grown to exponential phase or stationary phases in four different growth media: M63 supplemented with 0.2% sucrose as carbon source, with or without 0.2% (w/v) polygalacturonate (PGA) and with or without 0.1% Saintpaulia leaf extracts (1 g leaves in 1 L M63). Cells grown in these four media were subjected to different stresses: (i) acid stress, by an incubation of 15 min in the presence of 30 mM malic acid; (ii) oxidative stress, by an incubation of 15 min in the presence of 100 _M H2O2 or (iii) osmotic stress, by an incubation of 15 min in the presence of 300 mM NaCl. The micro-arrays used in this study were custom designed and produced by Roche NimbleGen, Inc. (Madison, WI) based on the annotated sequence of D. dadantii, available at Genbank accession number nM-! CP002038, which comprises 4597 CDS. The 4plex expression micro-arrays consist of 60-mer oligonucleotides, triplicated in three blocks on the array (5 oligonucleotides per CDS).

2015-04-16 | E-MTAB-541 | biostudies-arrayexpress

Gene expression profile of CD8+ T cell subtypes

Project description:OT-I naïve T cells, central memory T cells, effector memory T cells and skin infiltrating T cells were sorted out from mice at different timepoints post infection OT-I cells from 15-20 mice were pooled together for each microarray dataset

2017-02-21 | GSE79805 | GEO

Impact of gamma chain cytokines on the differentiation of recently antigen-activated CD8 T cells

Project description:Analysis of how different gamma chain family cytokines influence CD8 T cell differentiation. Naïve CD8 T cells were isolated from the spleens OT-I Thy1.1 TCR Tg mice. Whole splenocytes from wild-type C57BL/6 mice were used as stimulator cells. Purified naïve wild-type OT-I (1×106/well) were stimulated with OVA peptide (SIINFEKL) pulsed (5 µg/ml) and irradiated (2,000 rads) syngeneic splenocytes (6×106/well) in 24-well plates. Forty-eight hours later, activated OT-I T cells were harvested and viable cells were enriched over a Ficoll-paque gradient and washed with cRPMI prior to being reseeded in cRPMI (5×105 cells/ml) and treated with the media supplemented with various γc cytokines (IL-2, IL-4, IL-7, IL-15 and IL-21). Experimental samples were treated with 100 ng/ml of their respective gamma chain cytokine and incubated at 37ºC for 24 hours. RNA was isolated using either the RNeasy Mini kit, or a combination of TRIzol reagent and the Direct-zol RNA miniprep kit, all following manufacturer protocols. Two biological replicates for mRNA analysis were prepped using the RNeasy kit. The third replicate was prepped using the Trizol/Direct-zol approach. The quality and quantity of RNA samples was further analyzed on the Bioanalyzer. Labeled target cDNA was prepared from total RNA samples using the Ambion MessageAmp Premier protocol (3’IVT assay). Each sample target was hybridized to a Mouse 430 2.0 GeneChip array. Image processing and expression analysis were performed using Affymetrix GeneChip Command Console (AGCC) v. 3.1.1 and Affymetrix Expression Console v.1.1 software, respectively. Data from all biological replicates and conditions was imported into the Affymetrix Expression Console and normalized (RMA). RNA processing and microarray hybridization were performed by the Oregon Health & Science University Gene Microarray Shared Resource core facility in Portland, Oregon.

2014-06-06 | E-GEOD-58262 | biostudies-arrayexpress

Gene expression profile of Vibrio cholerae N16961 grown in various conditions of culture

Project description:To investigate the effect of conditions of culture on gene expression in Vibrio cholerae N16961 We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 conditions of culture in biological duplicate

2023-02-20 | GSE214813 | GEO

Hybridoma cell-culture and glycan profile dataset at various bioreactor conditions.

Project description: Not available

| S-EPMC5071535 | biostudies-literature

iTRAQ-based proteomic profiling of Vibrio parahaemolyticus under various culture conditions.

Project description: Not available

| S-EPMC4518887 | biostudies-literature

Effect of IL-6 on antigen-specific CD8+ T cell activation in vitro

Project description:Interleukin 6 (IL-6) is a pleiotropic cytokine with diverse roles in homeostasis, inflammation, and cancer. Here we performed transcriptional profiling of OT-I CD8+ T cells activated in the presence or absence of IL-6. In this study, splenocytes from wild type C57BL/6J mice were incubated with SIINFEKL peptide for two days to activate OT-I CD8+ T cells. SIINFEKL was then withdrawn, T cells were rested in medium with IL-2 for three days, and CD8+ T cells were restimulated with anti-CD3 + anti-CD28 antibodies and purified by FACS for RNA sequencing analysis on day 7. Throughout this culture period, some cells were treated with anti-IL6R antibody (clone MR16-1, 5 ug/ml), isotype control antibody (5 ug/ml), recombinant IL-6 (10 ng/ml), or recombinant hyper-IL-6 (IL-6 linked to IL6R; 20 ng/ml). Experimental conditions were run in triplicate, for a total of 15 samples. Conclusion: Neutralization of endogenous IL-6 signaling (with anti-IL6R antibody) enhances effector differentiation of CD8+ T cells, while addition of exogenous IL-6 or hyper-IL-6 suppresses effector differentiation.

2022-11-04 | GSE151157 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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