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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Thymic T-cell progenitor development is supported by membrane bound Kit ligand provided by a combined vascular endothelial and epithelial niche.

ABSTRACT: Gene expression analysis of purified KitL-tomato+ and KitL-tomato- thymic vascular endothelial cells, cortical and medullary thymic epithelial cells from 5 weeks old male kitL-tomato reporter mice Differentially expressed genes analysis of thymic stromal cells

ORGANISM(S): Mus musculus

SUBMITTER: Supat Thongjuea

PROVIDER: E-GEOD-62741 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A dynamic niche provides Kit ligand in a stage-specific manner to the earliest thymocyte progenitors.

Buono Mario M Facchini Raffaella R Matsuoka Sahoko S Thongjuea Supat S Waithe Dominique D Luis Tiago C TC Giustacchini Alice A Besmer Peter P Mead Adam J AJ Jacobsen Sten Eirik W SE Nerlov Claus C

Nature cell biology 20160118 2

Thymic T cell development is initiated from bone-marrow-derived multi potent thymus-seeding progenitors. During the early stages of thymocyte differentiation, progenitors become T cell restricted. However, the cellular environments supporting these critical initial stages of T cell development within the thymic cortex are not known. Here we use the dependence of early, c-Kit-expressing thymic progenitors on Kit ligand (KitL) to show that CD4(-)CD8(-)c-Kit(+)CD25(-) DN1-stage progenitors associat ...[more]

PMID: 26780297

Similar Datasets

Thymic T-cell progenitor development is supported by membrane bound Kit ligand provided by a combined vascular endothelial and epithelial niche.

Project description:Gene expression analysis of purified KitL-tomato+ and KitL-tomato- thymic vascular endothelial cells, cortical and medullary thymic epithelial cells from 5 weeks old male kitL-tomato reporter mice

2016-01-18 | GSE62741 | GEO

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

Project description:We assessed Smart-Seq, a new single-cell RNA-Seq library preparation method, on a variety of mouse and human RNA samples or cells. We generated RNA-Seq libraries for dilution series of MAQC reference RNA and mouse brain RNA to assess technical reproducibility, and for a variety of individual cells including putative circulating tumour cells.

2012-07-22 | E-GEOD-38495 | biostudies-arrayexpress

Bi-directional signaling by membrane-bound KitL induces proliferation and co-ordinates thymic endothelial cell and thymocyte expansion

Project description:The ligand for the c-Kit receptor, KitL, exists as a membrane-associated (mKitL) and a soluble form (sKitL). KitL functions outside c-Kit activation have not been identified. We show that co-culture of c-Kit– and mKitL–expressing NIH3T3 cells results in signaling through mKitL: c-Kit–bound mKitL recruits calcium-modulating cyclophilin ligand (CAML) to selectively activate Akt, leading to CREB phosphorylation, mTOR pathway activation, and increased cell proliferation. Activation of mKitL in thymic vascular endothelial cells (VECs) induces mKitL- and Akt-dependent proliferation, and genetic ablation of mKitL in thymic VECs blocks their c-Kit responsiveness and proliferation during neonatal thymic expansion. Therefore, mKitL–c-Kit form a bi-directional signaling complex that acts in the developing thymus to coordinate thymic VEC and early thymic progenitor (ETP) expansion by simultaneously promoting ETP survival and VEC proliferation. This mechanism may be relevant to both normal tissues and malignant tumors that depend on KitL–c-Kit signaling for their proliferation.

2018-11-21 | PXD011061 | Pride

Lympho-myeloid contribution of an immune-restricted progenitor emerging prior to definitive hematopoietic stem cells

Project description:An immune-restricted lymphomyeloid-primed progenitor with the capacity to contribute to both myeloid and lymphoid lineages in the developing embryo emerges prior to definitive HSCs. Examination of fetal sorted lymphoid primed progentors and adult progenitors The fastq files are not provided at this time due to further analyses.

2013-11-26 | E-GEOD-50896 | biostudies-arrayexpress

Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo

Project description:Gene expression analysis of purified hematopoietic stem and progenitor cells isolated from low to intermediate risk MDS patients and age-matched normal healthy controls. Analysis of lineage associated genes and PCA clustering of populations

2014-05-23 | E-GEOD-55689 | biostudies-arrayexpress

Identification and quantification of allele specific proteins and homeolog expression bias in an allopolyploid non-model crop by integrating transcriptomics and proteomics.

Project description:The fate of doubled genes, from allopolyploid or autopolyploid origin, is controlled at multiple levels within the central dogma: gene loss or silencing, neo- and/or sub functionalization, inter genomic transfer, allele dominance/co-dominance, differences in transcription/translation efficiency, post translational modifications… These regulatory processes through evolution have caused a plethora of genotype x environment interactions displayed in the modern day phenotypes. The study of non-model crops is challenging but solutions are emerging. More and more, one gets insight into the tolerance mechanisms of a specific genotype. By integrating transcriptomics into our proteomic data, we studied the genetic diversity of an allopolyploid ABB banana, a tolerant genotype, and compared it to two different sensitive AAA genotypes. The root growth of the ABB cultivar was 60 % higher under mild osmotic stress. 234,000 spectra were aligned and quantified, resulting in 2,753 identified root proteins. 383 gene loci displayed genotype specific differential expression whereof 252 showed at least one Single Amino Acid Polymorphism (SAAP). The homeoallelic contribution was assessed using transcriptome read alignment, thus revealing each allele contribution at the RNA level. This provides insight in the structure and the organization of the triploid genome. In the ABB cultivar, allele expressions are supposed to follow a 1/3 and 2/3 pattern. We found that many genes deviated from this expectation and we show that 32 gene loci even displayed a 100% read preference for the allele that was unique for the ABB tolerant genotype , suggesting that the presence of unique alleles and homoelog expression bias is correlated to the observed phenotype.

2018-01-29 | PXD006375 | Pride

Opposing roles for the lncRNA Haunt and its genomic locus in regulating HOXA gene activation during embryonic stem cell differentiation

Project description:Long noncoding RNAs (lncRNAs) have been implicated in controlling various aspects of embryonic stem cell (ESC) biology, although the functions of specific lncRNAs, and the molecular mechanisms through which they act, remain unclear. Here, we demonstrate discrete and opposing roles for the lncRNA transcript Haunt and its genomic locus in regulating the HOXA gene cluster during ESC differentiation. Reducing or enhancing Haunt expression, with minimal disruption of the Haunt locus, led to up- or down-regulation of HOXA genes, respectively. In contrast, increasingly large genomic deletions within the Haunt locus attenuated HOXA activation. The Haunt DNA locus contains potential enhancers of HOXA activation, whereas Haunt RNA acts to prevent aberrant HOXA expression. This work reveals a multi-faceted model of lncRNA-mediated transcriptional regulation of the HOXA cluster, with distinct roles for a lncRNA transcript and its genomic locus, while illustrating the power of rapid CRISPR/Cas9-based genome editing for assigning lncRNA functions. All RNA-seq(s) were designed to reveal the differentially expressed genes among different stages of ESCs differentiation, or differentially expressed genes between wild-type or Haunt or HOXA mutant cells during RA-induced differentiation. All ChIRP-Seq were used to reveal the DNA or RNA targets of Haunt before or after RA treatment.

2015-04-20 | E-GEOD-58514 | biostudies-arrayexpress

Deep Biosphere - Beatrix 326 BH2 (270712)

Project description:This project aims to investigate the metabolic pathways expressed by the active microbial community occurring at the deep continental subsurface. Subsurface chemoLithoautotrophic Microbial Ecosystems (SLiMEs) under oligotrophic conditions are supported by H2; however, the overall ecological trophic structures of these communities are poorly understood. Some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa appear to support inverted trophic pyramids wherein methanogens contributing <5% of the total DNA apparently produce CH4 that supports the rest of the community. Here we show the active metabolic relationships of one such trophic structure by combining metatranscriptomic assemblies, metaproteomic and stable isotopic data, and thermodynamic modeling. Four autotrophic β-proteobacteria genera that are capable of oxidizing sulfur by denitrification dominate. They co-occur with sulfate reducers, anaerobic methane oxidizers and methanogens, which each comprises <5% of the total community. Defining trophic levels of microbial chemolithoautotrophs by the number of transfers from the initial abiotic H2-driven CO2 fixation, we propose a top-down cascade influence of the metabolic consumers that enhances the fitness of the metabolic producers to explain the inverted biomass pyramid of a multitrophic SLiME. Symbiotic partnerships are pivotal in the deep biosphere on and potentially beyond the Earth.

2018-10-27 | PXD004634 | Pride

Host plant shift and acaricide resistance effects on gene expression in the two-spotted spider mite, T. urticae

Project description:The goal of our microarray experiments was twofold: 1) Compare the gene expression profile of acaricide resistant spider mite strains (MAR-AB and MR-VP) with that of a susceptible spider mite strain (London); 2) Study gene expression changes in spider mites from the London strain upon transfer from bean, a suitable host, to tomato, a less favorable host. These gene expression changes upon host change were measured for three timepoints (2 hour on tomato (Tomato-2h), 12 hour on tomato (Tomato-12h) and 5 generations on tomato (Tomato-5G)). 23 samples were analyzed: 6 biological replicates for MR-VP, 5 biological replicates for MAR-AB and four biological replicates each for Tomato-2h, Tomato-12h and Tomato-5G

2012-12-04 | E-GEOD-39869 | biostudies-arrayexpress

Affinity and Dose of TCR Engagement Yield Proportional Enhancer and Gene Activity in CD4+ T Cells

Project description:Affinity and dose of T cell receptor (TCR) interaction with antigens govern the magnitude of CD4+ T cell responses, but questions remain regarding the quantitative translation of TCR engagement into downstream signals. We find that while the response of CD4+ T cells to antigenic stimulation is bimodal, activated cells exhibit analog responses proportional to signal strength. Gene expression output reflects TCR signal strength, providing a signature of T cell activation. Expression changes rely on a pre-established enhancer landscape and quantitative acetylation at AP-1 binding sites. Finally, we show that graded expression of activation genes depends on ERK pathway activation, suggesting that an ERK-AP-1 axis translates TCR signal strength into proportional activation of enhancers and genes essential for T cell function. CD4+ T cells from transgenic AND mice were sequenced under the conditions indicated. Replicates are included for each type of data (RNA-Seq, ChIP-Seq), and are numbered accordingly. The No Peptide condition serves as the untreated control for the peptide-treated samples, and inputs are provided for ChIP-Sequencing samples.

2016-06-01 | E-GEOD-69545 | biostudies-arrayexpress

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