Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression changes in Itpr triple conditional knockout T cell progenitors

ABSTRACT: Calicum plays critical roles in developing T cells, promoting survival, proliferation, and differentiation at multiple stages of maturation. Calcium release from intracellular stores due to T cell receptor and pre-T cell receptor signaling is thought to require the inositol triphosphate receptors (Itpr), however the requirement for these receptors has not been investigated. We used microarrays to examine gene expression differences between control and Itpr deficient T cell progenitors. We used microarrays to identify changes in the transcriptional programme of developing T cells prior to acquisition of a mature T cell receptor and identified several developmentally important genes altered in the absence of Itpr. Thymocyte progenitors at DN4 or ISP were harvested for RNA extraction from three independent control Itpr1/Itpr2/Itpr3 triple homozygous floxed (CTL) or Tie2-Cre Itpr1/Itpr2/Itrp3 triple homozygous floxed (KO) thymii, pooled, and hybridized on Affymetrix microarrarys. To obtain a homogenous population of thymocyte progenitors, we FACS purified cells and collect RNA from only DN4 or ISP T cells. ISP T cells were defined as CD4- CD8+ CD24+ CD3-. DN4 T cells were defined as CD45+ CD24+ CD3- CD4- CD8- CD25- CD44- CD19- B220- gdTCR- Ter119- Mac1- Gr1-. Thymocytes were harvested from neonatal mice, ranging from 7 to 10 days of age and lacked any signs of malignancy or disease.

ORGANISM(S): Mus musculus

SUBMITTER: Sylvia Evans

PROVIDER: E-GEOD-57997 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

New role for the (pro)renin receptor in T cell development

Project description:The (pro)renin receptor (PRR) was originally thought to be important in regulating blood pressure via the renin-angiotensin system (RAS), however it is emerging that PRR is instead generally essential for cellular development via its involvement in Wnt signalling. Here, we have specifically deleted PRR from T cells, which require Wnt for their development. T cell-specific PRR-knockout (cKO) mice (ATP6AP2flox/y;Lck-CRE) had a significant decrease in thymic cellularity, corresponding with a 100-fold decrease in the number of CD4+ and CD8+ thymocytes, and a large increase in double negative (DN) precursors. Further characterisation of DN T cell progenitors revealed that deletion of PRR impaired T cell development at multiple stages; including transition from DN3(CD25+CD44-) - DN4(CD25-CD44-), DN4-CD4+ CD8+ double positive (DP), DP-intermediate single positive (CD3-CD8+ ISP) cells. We performed gene expression analysis on sorted DN3 T cells, which indicated that PRR cKO T cells have perturbations in key cellular pathways essential at the DN3 stage, such as RNA processing and translation. Our study identifies a new role for PRR in multiple facets of T cell development, and gives further support to the notion that PRR is generally essential for cellular development.

2015-07-01 | E-MTAB-3568 | biostudies-arrayexpress

Whole Genome Expression Array in Human T-cell Acute Lymphoblastic Leukemia

Project description:Childhood T-ALL samples were compared with thymocyte subsets we compared key molecules of wnt signaling pathway in our cohort RNA was isolated from the bone marrow samples of childhood T-ALL patients at the time of diagnosis with a blast count over 90% and hybridized to Affymetrix GeneChip HU-133 Plus.2 .Thymic subsets were sorted by FACS and labeled as DN(CD3,CD4,CD8 neg), DP3poz tot(CD3,CD4,CD8poz), DP3neg(CD3neg,CD4,CD8poz), ISP(Immature single positive), SP4(Single positive CD4), SP8 (Single positive CD8).

2013-04-19 | E-GEOD-46170 | biostudies-arrayexpress

scRNAseq in Pten enhancer wild-type or deleted thymocytes, enriched for immature thymocyte stages (CD4-CD3-)

Project description:Single cell suspensions of total thymocytes were obtained from Pten enhancer (PE) wild-type or knockout mice. This single-cell suspension was enriched in CD4-CD3- immature thymocyte progenitor cells. CD4-CD3- enriched thymocytes were then mixed 1:1 with single-cell suspensions from total unenriched thymocytes and subsequntly loaded in a 10x Chromium instrument for single-cell RNAseq analyses. Our results revealed Pten levels are signifcantly decreased in CD4-CD8- double negative (DN) thymocytes, CD8+ intermediate single positive (ISP) thymocytes and CD4+CD8+ double positive (DP) thymocytes in PE knockout mice, compared to PE wild-type mice.

2020-12-17 | GSE156070 | GEO

Transcription profiling of mouse double negative thymocytes

Project description:In order to understand the molecular mechanisms of DN thymocyte development, it may be also of use to clarify how these developmental processes are regulated in terms of their entire gene expression, to which cell differentiation is ultimately ascribed. In the current study, we approached this issue by investigating gene expression profiles in discrete subsets of DN thymocytes under development, in which DN2, DN3, and DN4 thymocytes were sorted and subjected to expression profiling analysis with high-density oligonucleotide microarrays. Experiment Overall Design: The DN2, DN3, and DN4 populations were FACS-sorted from DN thymocytes harvested from four C57BL/6 mice and analyzed by AffymetrixÂ® Mouse Genome 430 2.0 ArrayÂ® for gene expression. Four independent experiments were performed using 16 mice.

2008-06-15 | E-GEOD-7784 | biostudies-arrayexpress

Gene expression in DN4 thymocytes from mice with an inducible deletion of Ikaros

Project description:The aim of the experiment was to visualize genes under the control of Ikaros during early T cell development. We used mice carrying floxed Ikaros alleles that were crossed with the Rosa26-CreERT2 mice, and which were injected with tamoxifen for 4 days. DN4 thymocytes were sorted from 4 mice (5-6 week-old) which are positive or not for the Rosa26-CreERT2 transgene. DN4 cells were sorted from 2 Ikf/f Rosa26-CreERT2+ mice and 2 Ikf/f mice, which were all treated with tamoxifen for 4 days. Loss of Ikaros was confirmed in sorted cells from the Ikf/f Rosa26-CreERT2+ mice by western blot. Gene expression profiles were determined on total RNA from sorted cells with Affymetrix Mouse Gene arrays.

2013-04-17 | E-GEOD-46093 | biostudies-arrayexpress

Alternative splicing controlled by heterogeneous nuclear ribonucleoprotein L (hnRNP L) regulates development, proliferation and migration of thymic pre-T cells

Project description:The regulation of post-transcriptional modifications of pre-mRNA by alternative splicing is important for cellular function, development and immunity The receptor tyrosine phosphatase CD45, which is expressed on all hematopoietic cells, is known for its role in the development and activation of T cells. To investigate the role of hnRNP L further, we have generated conditional hnRNP L knockout mice carrying floxed alleles and the T-cell specific Lck-Cre recombinase transgene. The Lck-Cre transgene is active in DN3, DN4 as well as in DP and SP cells. We found that deletion of hnRNP L results in a decreased thymic cellularity caused by a partial block at the transition stage between DN4 and DP cells. In addition, hnRNP L-/- thymocytes express aberrant levels of the CD45RA splice isoform and show high levels of phosphorylated Lck at the activator tyrosine Y394 but lacking phosphorylation of the inhibitory tyrosine Y505. This is indicative of an increased basal Lck activation and correlated with a higher proliferation rate of DN4 cells in hnRNP L-/- mice. Deletion of hnRNP L also blocked egress of SP cells to peripheral lymphoid organs and the migration of SP thymocytes in response to the chemokines CCL21 and SDF-1a. Since we found that actin polymerization was also compromised in hnRNP L-/- SP cells, we propose that a defect in the signal transduction cascade downstream of the chemokine receptors CCR7 and CXCR4 caused by the absence of hnRNP L is responsible for this phenotype. Our results indicate that hnRNPL regulates pre-T cell development and migration by regulating CD45 pre-mRNA splicing and chemokine receptor signaling. RNA-seq from Thymocytes from WT mice compared to KO (hnRNP L) mice

2012-04-23 | E-GEOD-33306 | biostudies-arrayexpress

The critical role of chondroitin sulfate proteoglycan interactions with receptor PTPσ in the inhibition of neural repair after stroke

Project description:We used RNAseq to compare transcriptome of peri-infarct cortex in stroke mice that received vehicle or ISP treatment (which blocks the PTPsigma receptor signaling) at 14 days post stroke. The purpose of this project is to identify genes that are differentially expressed in control stroke mice and ISP treated stroke mice that might mediated the behavioral improvement in ISP treated stroke mice.

2021-03-16 | GSE168934 | GEO

Gene expression in DN4 thymocytes from mice with an inducible deletion of Ikaros

2013-04-17 | GSE46093 | GEO

Overexpression of LMO2 causes aberrant human T-cell development in vivo by three potentially distinct cellular mechanisms

Project description:LMO2 overexpressing transgenic mouse models suggest an accumulation of immature T-cell progenitors in the thymus as main pre-leukemic event. The effects of LMO2 overexpression on human T-cell development in vivo, however, are unknown. Here we report studies of a humanized mouse model transplanted with LMO2 transduced human hematopoietic stem and progenitor cells. The effects of LMO2 overexpression were confined to the T-cell lineage although initially multipotent cells were transduced. Three effects of LMO2 on human T-cell development were observed: 1) a block at the DN/ISP stage, 2) an accumulation of CD4+CD8+ double positive CD3- cells and 3) an altered CD8/CD4 ratio with enhanced peripheral T lymphocytes

2016-03-26 | GSE79625 | GEO

The major diversification of Vγ1.1+ and Vγ2+ thymocytes in mice occurs after commitment to the γδ T-cell lineage

Project description:Adult murine gammadelta thymocytes can be divided into two major subsets based on their expression of TCRVgamma1.1 or TCRVgamma2, respectively. gammadelta thymocytes mature through distinct stages characterized by CD24 and CD73 in the following order: immature uncommitted (CD24+CD73-), immature committed (CD24+CD73+) and mature (CD24-CD73+). In this dataset we have sorted gammadelta thymocytes into 6 distinct populations based on subset and developmental stage and analyzed their gene expression. These data were used to identify 3400 differentially expressed genes during gammadelta thymocyte development and to show that the two major adult gammadelta T cells follow a similar path through early development and mainly diversify after commitment to the gammadelta T cell lineage.

2016-07-28 | GSE75920 | 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