Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential gene expression in WT and AMPK deficient CD4 T cells

ABSTRACT: The purpose of the study was to compare transcriptome profiling in WT and AMPK deficient CD4 T cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE210183 | GEO | 2023/04/10

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Expression data from AMPK deficient MLL-AF9 leukemia initiating cells and whole leukemia cells

Project description:Deletion of AMPK significantly extended the onset of leukemogenesis and depleted leukemia initiating cells (LICs). To identify how AMPK regulates LICs, we performed gene expression profiling of LICs isolated from AMPK wild type leukemic mice or AMPK-deficient leukemic mice. 4 groups were analyzed; 1) Whole leukemia (GFP+) from AMPK WT ( AMPKfl/fl) mice, 2) Whole leukemia (GFP+) from AMPK-deficient ( AMPK?/?l) mice, 3) LICs=L-GMP (GFP+,lin-,c-kit+, CD16/32+,CD34+) cells from AMPK WT ( AMPKfl/fl) mice, 4) LICs=L-GMP (GFP+,lin-,c-kit+, CD16/32+,CD34+) cells from AMPK-deficient ( AMPK?/?l) mice.

2015-01-01 | E-GEOD-64602 | biostudies-arrayexpress

Expression data from AMPK deficient MLL-AF9 leukemia initiating cells and whole leukemia cells

2015-01-01 | GSE64602 | GEO

RNAseq of naive CD4 T cells deficient for Elp3 activated for 18h against WT control

Project description:CD4 T cell deficient for the Elp3 gene have a delayed cell cycle entry. We explored by RNAseq by which molecular pathway the absence of Elp3 delayed the cell cycle entry. Naive T cell from CD4-cre Elp3 fl/fl mice and WT littermate were purified and activated in vitro with CD3 and CD28 antibodies for 18h.

2020-07-31 | E-MTAB-9057 | biostudies-arrayexpress

Expression data from WT and BFAR-deficient naïve CD4+ T cells stimulated in Th9 differentiation condition for 3 days

Project description:We conducted gene expression profile analysis by using WT and BFAR-deficient naive CD4+ T cells.Gene ontology (GO) analysis revealed the most prominent biological processes altered in naive CD4+ T cells cultured in Th9 condition were associated with immune system process.

2021-04-11 | GSE153133 | GEO

Creld1-deficient CD4+ T cells

Project description:Creld1-deficient CD4+ T cells

| PRJNA641830 | ENA

Gene expression analysis of WT Th17 versus STAT4 deficient Th17 cells from EAE mice

Project description:The purpose of this study is to compare transcriptional profiles of WT and STAT4-deficient Th17 cultured cells from mice with experimental autoimmune encephalomyelitis (EAE) using RNA sequencing. WT and STAT4 deficient splenocytes from EAE immunized mice were cultured with MOG peptide under Th17 conditions for three days, and then total RNA was extracted from CD4 T cells for sequencing. Differential gene expression was determined using the DESeq2 algorithm. These data reveal a previously unrecognized role for STAT4 in Th17 gene expression and function.

2023-03-30 | GSE227049 | GEO

RNA sequencing analysis of gene expression profiles in WT and Etv5-deficient TFH cells

Project description:Purpose: The aim of this study is compare the gene expression profiles between wild-type (WT) and Etv5-deficient follicular helper T (TFH) cells to identify the molecular mechanism of how ETV5 promotes the TFH cell differentiation. Methods: TFH cells (CD4+CD44+CXCR5+PD-1+) from the spleen of WT and Etv5f/f;Cd4-Cre mice immunized with OVA in alum for 7 days were sorted by a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using TRIzol (GeneAll) according to the manufacturer’s instruction. The library for RNA sequencing was generated using the Truseq stranded mRNA library prep kit (Illumina), and sequencing was performed with Novaseq 6000 (Illumina). Results: Reads were mapped to the mouse reference genome (mm10) with Tophat (v2.0.13), and the aligned results were analyzed with Cuffdiff (v2.2.0) for differentially expressed genes (DEGs). A total of 92 genes were differentially expressed in Etv5-deficient TFH cells (46 genes upregulated and 46 genes downregulated) when compare with WT TFH cells (fold change > 2 and P-value < 0.05). Conclusions: Our study presents the first comparative gene expression analysis of TFH cells from control and T cell-specific Etv5-deficient mice. Since ETV5 usually acts as a transcription activator, we focused on the downregulated genes in Etv5-deficient TFH cells. Through this study, we identified the candidate genes that are targeted by ETV5 for TFH cell differentiation.

2023-11-08 | GSE247030 | GEO

RNAseq profiling of miR-132/212-deficient CD4+ T cells activated in vitro and in vivo.

Project description:Transcriptomic profiling of miR-132/212-deficient and WT CD4 T cells isolated from spleens of L donovani infected mice (d28) to determine the effects of miR-132/212 on CD4 T cell activation in vivo. This was combined by transcriptomic analysis of early stage in vitro activated WT and miR-132/212-deficient CD4 T cells to identify direct miR-132/212 targets in CD4 T cells.

2019-03-22 | GSE125268 | GEO

RNA Sequencing Analysis of T Cell Receptor Alpha and Beta Chain in Thymic WT versus CIC-deficient CD4+ SP Non-Treg and Treg Cells.

Project description:Purpose : The goal of this study is to compare the repertoire of T cell receptor (TCR) alpha and beta chain between WT and CIC-deficient thymic CD4+ single positive (SP) T cells, in both non-Treg and Treg populations, to confirm the effect of CIC deficiency on T cell development in the aspect of TCR repertoire. Methods : Treg (CD4+CD8-CD25+GFP+) and non-Treg (CD4+CD8-GFP-) cells from Foxp3-GFP;Cicf/f and Foxp3-GFP;Cicf/f;Vav1-Cre mice were sorted by MoFlo-XDP (Beckman Coulter). Total RNA was extracted using RiboEX (GeneAll) according to the manufacturer's instructions. RNA was then amplified using a commercially available multiplex primer mix covering the TCR alpha and beta chains in two separate PCR reactions. Reverse transcription and subsequent PCR amplification (RT-PCR1) were performed using the Qiagen OneStep RT PCR mix (Qiagen). The cDNA was selected and unused primers were removed by SPRIselect bead selection (Beckman Coulter) followed by a second round of amplification performed with a pair of primers specific for communal sites engineered onto the 5ʹ end of the C- and V- primers used during RT-PCR1. After library preparation, paired-end sequencing was performed using the Illumina Miseq v3 600-cycle Reagent Kit (Illumina). Results : We observed increased frequency of TCRs with long CDR3 length in CIC-deficient non-Treg and Treg cells. We also found significant alterations in the TCR repertoire of TCR beta chain in CIC-deficient Treg cells compared to WT cells, including altered frequency of V and J chain usage. Conclusions : Our study represents the first comparative analysis of TCR repertoire of thymic CD4 SP cells from WT and hematopoietic lineage cell-specific Cic deficient mice. We concluded that CIC deficiency leads to alterations in TCR repertoire of thymic Treg cells.

2021-05-07 | GSE173996 | GEO

Population gene expression of anti-viral CD4 T cells in Bcl6 and Blimp1 deficient conditions

Project description:Population gene expression of effector CD4+ T cells WT, Bcl6-deficient , Blimp1-deficient or Bcl6 Blimp1-deficient was determined by RNAseq after LCMV Armstrong infection

2021-11-05 | GSE149597 | 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