Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data of thymospheres

ABSTRACT: Evidence suggests that a stem cell-driven differentiation hierarchy maintains the dynamic thymic epithelial cell (TEC) network that governs T lymphocyte development. The identification of TEC stem/progenitor cells has been a major focus in the field and several candidates with contrasting phenotypes have been described. a Foxn1neg EpCAMneg cell population was shown to generate so-called thymospheres. We used Affymetrix mouse 1ST arrays to analyze their gene expression profile.

ORGANISM(S): Mus musculus

PROVIDER: GSE99024 | GEO | 2017/05/18

SECONDARY ACCESSION(S): PRJNA387023

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Next-generation sequencing of cTEC and mTEC isolated from non-pregnant and pregnant females lacking the expression of Klf4 (KO) or not (LOX)

Project description:Stress-induced thymic involution is defined by profound damage to thymic epithelial cells (TECs), resulting in an acute and transient reduction of thymopoietic capacity. During pregnancy, thymic involution is not associated with TEC loss but rather with TEC quality modifications. Study of the mechanisms of TEC maintenance during pregnancy may be of critical importance for identifying new players for thymic regeneration in other models of thymic involution. We report a strong enrichment for motifs recognized by KLF4 based on genes differentially expressed in TECs of pregnant females. Therefore, we studied the impact of Klf4 deletion in TECs during pregnancy by analyzing thymus composition and TEC transcriptome. Conditional Klf4 deletion in homeostatic conditions does not injure thymic integrity. However, pregnant females lacking Klf4 show a disrupted thymus with substantial loss of thymic epithelial cells. Klf4 maintains cTEC number during pregnancy by maintaining cell survival and inhibiting the transition to a mesenchymal state. Our study reveals Klf4 as a protective factor for TECs during pregnancy-associated thymic involution and represents a potential study subject for other models of stress-induced thymic involution.

2022-09-30 | GSE210885 | GEO

Characterization of Fetal Specific Transcriptional Programs in Thymic Epithelial Cells Identifies Myc as a Critical Determinant of Thymus Size [single cell RNA-Seq]

Project description:The thymus is the site of T cell development. Although much is known about the development and differentiation of the T lymphocyte compartment, less is known about the thymic epithelial cell (TEC) populations fostering their development. Here we use next generation sequencing approaches to identify transcriptional programs unique to TEC at specific stages of mouse life. This strategy identified Myc as a regulator of the fetal program, driving the rapid expansion in thymic size during fetal life.

2019-10-30 | GSE131339 | GEO

Characterization of Fetal Specific Transcriptional Programs in Thymic Epithelial Cells Identifies Myc as a Critical Determinant of Thymus Size [bulk RNA-Seq]

2019-10-30 | GSE129192 | GEO

Chromatin accessiblity in mouse thymic epithelial cells to determine active regulatory elements.

Project description:The thymus is the site of T cell development. Although much is known about the development and differentiation of the T lymphocyte compartment, less is known about the thymic epithelial cell (TEC). Foxn1 is critical for the development and function of the thymus. Here, we used ATAC-Seq to identify regions of accessible chromatin in TEC and keratinocytes of the skin to identify candidate active regulatory elements critical for tissue specific expression of Foxn1.

2019-05-29 | GSE131595 | GEO

Thymic epithelial cell alterations and defective thymopoiesis lead to central and peripheral tolerance perturbation in MHCII deficiency

Project description:Major Histocompatibility Complex (MHC) class II (MHCII) deficiency, also known as Bare Lymphocyte Syndrome (BLS), is a rare combined immunodeficiency due to mutations in genes regulating expression of MHCII molecules. MHCII deficiency results in impaired cellular and humoral immune responses, leading to severe infections and autoimmunity. The contribution of thymic epithelial cell (TEC) defects to the pathogenesis of this primary immunodeficiency has not been well characterized to date, in particular in regard to immune dysregulation. To this aim, we have performed an in-depth cellular and molecular characterization of TEC alterations in this disease. We observed an overall perturbation of thymic structure and function in both MHCII-/- mice and patients. Transcriptomic and proteomic profiling of murine TEC revealed several alterations. In particular, in MHCII-/- mice, impaired cross-talk and mTEC maturation resulted in altered promiscuous gene expression and leaky central tolerance. Furthermore, we observed peripheral tolerance impairment, likely due to defective Treg cell generation and/or function and B cell tolerance breakdown. Overall, our findings reveal disease-specific TEC defects resulting in perturbation of central tolerance and limiting the potential effect of hematopoietic stem cell transplantation in MHCII deficiency.

2022-01-28 | GSE166463 | GEO

Dynamic changes of nonepithelial thymic stroma during thymus organogenesis

Project description:The thymic stroma provides the microenvironment for T cell lineage commitment, development, maturation, and repertoire selection. While the thymic epithelial cell (TEC) compartment is relatively well characterised, a comparably detailed analysis of the non-TEC stromal compartment including the endothelial cells and fibroblasts is currently lacking. Here, we probe the composition of thymic mesenchymal cells and their dynamic change during thymus organogenesis. Using a single cell transcriptomic approach, we identify previously unappreciated heterogeneity within the non-TEC stromal compartment and demonstrate dynamic shifts within non-TEC stromal cell populations over thymic development. We then use a compound heterozygous model (Tbx1+/-Crkl+/-) for 22q11.2DS syndrome to show that significant reductions of multiple mesenchymal subpopulations associated with functional defects and accelerated aging are associated with the thymic hypoplasia observed in this condition. Thus, we provided a comprehensive picture of non-TEC thymic stromal development and their functional defects in a disease model of thymic hypoplasia.

2022-05-13 | GSE163520 | GEO

RNA-seq profiling of thymic epithelial cells from Mcl1 knockout and wildtype mice

Project description:T cell differentiation is governed by interactions with thymic epithelial cells (TECs) and defects in this process undermine immune function and tolerance. To uncover new strategies to restore thymic function and adaptive immunity in immunodeficiency, we sought to determine the molecular mechanisms that control life and death decisions in TEC. We created a mouse model which specifically deleted the pro-survival gene Mcl1 in TEC. We found that while BCL-2 and BCL-XL were dispensable for TEC homeostasis, MCL-1 deficiency impacted on TEC as early as E15.5, resulting in early thymic atrophy and T cell lymphopenia, with near complete loss of thymic tissue by 2 months of age. MCL-1 was not necessary for TEC differentiation but was continually required for the survival of medullary TEC, including autoimmune regulator (AIRE) expressing TECs and the maintenance of overall thymic architecture. To understand the molecular mechanisms in more detail, RNA-seq profiling was undertaken of cortical and medullary thymic epithelial cells (cTECs and mTECs) from wildtype and knockout mice.

2017-09-25 | GSE102227 | GEO

Gene expression analysis of FOXN1+ thymic endoderm cells derived from the in vitro differentiation of human embryonic stem cells

Project description:The goal of this study was to document the gene expression profile of FOXN1+ thymic endoderm cells derived from the in vitro differentiation of human pluripotent stem cells. Thymic epithelial cells (TECs) play a critical role in T-cell maturation and tolerance induction. The generation of TECs from in vitro differentiation of human pluripotent stem cells (PSCs) would provide a platform for studying the mechanisms of this interaction and have implications for immune reconstitution. To facilitate analysis of PSC-derived TECs, we generated human embryonic stem cell (hESC) reporter lines in which sequences encoding GFP were targeted to FOXN1, a gene required for TEC development. Using this FOXN1GFP/w line as a read out, we developed a reproducible protocol for generating FOXN1-GFP+ thymic endoderm cells. Transcriptional profiling and flow cytometry identified Integrin-β4 (ITGB4, CD104) and HLA-DR as markers that could be used in combination with EpCAM to selectively purify FOXN1+ TEC progenitors from differentiating cultures of unmanipulated PSCs. Human FOXN1+ TEC progenitors generated from PSCs will facilitate the study of thymus biology and are a valuable resource for future applications in regenerative medicine Human embryonic stem cells were differentiated for 30 days using the protocol described by Soh et al, 2014. The hESCs used in this protocol had been genetically modified by targeting sequences encoding GFP to the FOXN1 locus, thus enabling FOXN1 expressing cells to be identified on the basis of GFP expression. At differentiation day 30, differentiating cells were separated into three fractions using FACS. These fractions were the FOXN1+(GFP+)EpCAM+, FOXN1-(GFP-)EpCAM+, FOXN1-(GFP-)EpCAM-.

2014-05-01 | E-GEOD-56373 | biostudies-arrayexpress

Activation of Inflammation and Metabolic Networks in Age-related Thymic Involution.

Project description:Genetic modeling of thymic involution has demonstrated the importance of individual inflammatory pathways affecting the thymic microenvironment, particularly thymic epithelial cells (TEC). We studied the pathogenic processes in chronological aging of the murine thymus. We used microarrays to elucidate the global gene expression and to identify a leading edge subset of age-associated genes in TEC. Analyses of the TEC transcriptome demonstrated altered expression associated with inflammatory and fatty acid metabolism.

2016-05-06 | GSE81163 | GEO

Thymic resilience and T cell output require Liver X Receptors

Project description:The thymus is a primary lymphoid organ necessary for optimal T cell development. Here we show that liver X receptors, which are a class of nuclear receptors and transcription factors with diverse functions in metabolism and immunity, critically contribute to thymic integrity and function. LXRαβ-deficient mice develop a fatty, rapidly-involuting thymus, and acquire a shrunken and prematurely senescent peripheral T cell repertoire. The functions of LXRαβ are cell specific and the resulting phenotypes mutually independent. Whereas macrophages require LXRαβ for reverse cholesterol transport and lipid removal, thymic epithelial cells (TEC) and thymocytes respectively utilize LXRαβ for self-renewal and negative selection. Consequently, TEC-derived LXRαβ protect against premature involution in homeostasis and orchestrate thymic regeneration following stress, while thymocyte-derived LXRαβ limit cell disposal during negative selection and confer heightened sensitivity to experimental autoimmune encephalomyelitis. These results identify three distinct but complementary mechanisms by which LXRαβ govern T lymphocyte education.

2020-01-29 | GSE144342 | GEO

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