The embryonic node functions as an instructive stem cell niche (bulk RNA-seq)
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB38460 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4173383.fastq.gz | Fastqsanger.gz | |||
| ERR4173384.fastq.gz | Fastqsanger.gz | |||
| ERR4173385.fastq.gz | Fastqsanger.gz | |||
| ERR4173386.fastq.gz | Fastqsanger.gz | |||
| ERR4173387.fastq.gz | Fastqsanger.gz |
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Project description:The embryonic node functions as an instructive stem cell niche (scRNA-seq)
| PRJEB38461 | ENA
Project description:During development, the amniote organizer, Hensen’s node, contributes cells to the developing axis in head-to-tail direction. However, some cells remain resident in the node and it has been suggested that these resident cells are stem cells. This study aimed to characterise single resident cells and their environment within the node. Using the chick as an amniote model, we generated transcriptomes of single resident cells (scRNA-seq of GFP cells that remained resident till stage-HH8 following a GFP-donor homotopic transplant into a non-GFP host) and of six node sub-regions (bulk RNA-seq of GFP-transgenic stage-HH8 node, but otherwise un-manipulated embryos). We also obtained transcriptomes of single cells with resident behaviour that would normally never enter the node, but were made to do so (scRNA-seq of cells that remained resident till HH8 following a GFP-donor heterotopic/heterochronic transplant into a non-GFP host).
2022-02-02 | E-MTAB-9115 | biostudies-arrayexpress
Project description:During development, the amniote organizer, Hensen’s node, contributes cells to the developing axis in head-to-tail direction. However, some cells remain resident in the node and it has been suggested that these resident cells are stem cells. This study aimed to characterise single resident cells and their environment within the node. Using the chick as an amniote model, we generated transcriptomes of single resident cells (scRNA-seq of GFP cells that remained resident till stage-HH8 following a GFP-donor homotopic transplant into a non-GFP host) and of six node sub-regions (bulk RNA-seq of GFP-transgenic stage-HH8 node, but otherwise un-manipulated embryos). We also obtained transcriptomes of single cells with resident behaviour that would normally never enter the node, but were made to do so (scRNA-seq of cells that remained resident till HH8 following a GFP-donor heterotopic/heterochronic transplant into a non-GFP host).
2022-02-02 | E-MTAB-9116 | biostudies-arrayexpress
Project description:scRNA-seq of Gallus gallus embryo xenografts to investigate how the embryonic node functions as an instructive stem cell niche
| PRJEB49477 | ENA
Project description:During development, the amniote organizer, Hensen’s node, contributes cells to the developing axis in head-to-tail direction. However, some cells remain resident in the node and it has been suggested that these resident cells are stem cells. This study aimed to characterise single resident cells and their environment within the node. Using the chick as an amniote model, we generated transcriptomes of single resident cells (scRNA-seq of GFP cells that remained resident till stage-HH8 following a GFP-donor homotopic transplant into a non-GFP host) and of six node sub-regions (bulk RNA-seq of GFP-transgenic stage-HH8 node, but otherwise un-manipulated embryos). We also obtained transcriptomes of single cells with resident behaviour that would normally never enter the node, but were made to do so (scRNA-seq of cells that remained resident till HH8 following a GFP-donor heterotopic/heterochronic transplant into a non-GFP host).
2022-02-02 | E-MTAB-11216 | biostudies-arrayexpress
Project description:In warm-blooded vertebrate embryos (mammals and birds), the axial tissues of the body form from a growth zone at the tail end, Hensen's node, which generates neural, mesodermal, and endodermal structures along the midline. While most cells only pass through this region, the node has been suggested to contain a small population of resident stem cells. However, it is unknown whether the rest of the node constitutes an instructive niche that specifies this self-renewal behavior. Here, we use heterotopic transplantation of groups and single cells and show that cells not destined to enter the node can become resident and self-renew. Long-term resident cells are restricted to the posterior part of the node and single-cell RNA-sequencing reveals that the majority of these resident cells preferentially express G2/M phase cell-cycle-related genes. These results provide strong evidence that the node functions as a niche to maintain self-renewal of axial progenitors.
| S-EPMC8812687 | biostudies-literature
Project description:Stromal cells (SCs) establish the compartmentalization of lymphoid tissues critical to the immune response. However, the full diversity of lymph node (LN) SCs remains undefined. Using droplet-based single-cell RNA sequencing we identified 9 peripheral LNs non-endothelial SC subsets. Included are the established subsets Ccl19hi T-zone reticular cells (TRCs), marginal reticular cells, follicular dendritic cells (FDCs) and perivascular cells. We also identified Ccl19lo TRCs, likely including cholesterol-25-hydroxylase+ cells located at the T-zone perimeter, Cxcl9+ TRCs in the T-zone and interfollicular region, CD34+ SCs in the capsule and medullary vessel adventitia, indolethylamine N-methyltransferase+ SCs in the medullary cords and Nr4a1+ SCs in several niches. These data help define how transcriptionally distinct LN SCs support niche-restricted immune functions and they provide evidence that many SCs are in an activated state.
2018-05-10 | GSE112903 | GEO
Project description:To determine pathways activated during sinoatrial node morphogenesis we conducted bulk RNA sequencing on functionally validated tissue preps of embryonic sinoatrial node and atria.
2023-03-22 | GSE227027 | GEO
Project description:Lymph node metastasis is a poor prognosis indicator in esophageal cancer. Although tumor spreading currently forms the main basis for therapy selection, the molecular mechanisms underlying the metastatic pathway remain insufficiently understood. Several studies aimed to investigate these mechanisms but focused mainly on regulatory patterns in the tumors themselves and/or the invaded lymph nodes. To date no study has yet investigated the potential changes on transcription level, which take place within the yet non-invaded niche. Here we provide a comprehensive description of these regulations in patients. In this study the transcriptomic profiles of regional lymph nodes were determined for two patient groups: patients classified as pN1 (metastasis) or pN0 (no metastasis) respectively. All investigated lymph nodes, also those from pN1 patients, were still free of metastasis. The gene expression data was obtained via microarray analysis. Top candidates were validated via PCR and immunohistochemistry. The results show that regional lymph nodes of pN1 patients differ decisively from those of pN0 patients – even before metastasis has taken place. In the pN0 group distinct immune response patterns were observed. In contrast, lymph nodes of the pN1 group exhibited a clear profile of reduced immune response and reduced proliferation, but increased apoptosis, enhanced hypoplasia and morphological conversion processes. DKK1 was the most significant gene associated with the molecular mechanisms taking place in lymph nodes of patients suffering from metastasis (pN1). We assume that the two molecular profiles observed constitute two different stages of a progressive disease. Finally we suggest that DKK1 might play an important role within the mechanisms leading to lymph node metastasis. First, samples were classified according to the principal status of the patients exhibiting (pN1 group) or non-exhibiting (pN0 group) metastasis in regional lymph nodes. The comparison of pN1 and pN0 patients should highlight the general differences in regulations that might lead to or prevent from metastasis. Second, two lymph node samples were collected from each patient, one node located close to the tumor (regional) and the second node distant to the tumor. While the distant nodes served as reference sample the regional nodes were investigated for transcriptional regulations. Key to the work presented here is that all nodes investigated were made sure to be still metastasis free, independent of the patients’ pN1/pN0 classification and of the location relative to the tumor. This should allow the identification of early changes occurring prior to metastasis homing.
2015-05-18 | E-GEOD-51021 | biostudies-arrayexpress
Project description:Specialized niche environments specify and maintain stem and progenitor cells, but little is known about the identities and functional interactions of niche components in vivo. Here, we describe a modular system for the generation of artificial hematopoietic niches in the mouse embryo. A circumscribed tissue that lacks niche function but is physiologically accessible for hematopoietic progenitor cells is functionalized by individual and combinatorial expression of four factors, the chemokines Ccl25 and Cxcl12, the cytokine Scf and the Notch ligand DLL4. The distinct phenotypes and variable numbers of hematopoietic cells in the resulting niches reveal synergistic, context-dependent and hierarchical interactions among niche effector molecules. The surprisingly simple rules determining niche outcomes enable the in vivo engineering of artificial niches conducive to the presence of distinct myeloid or T or B lymphoid lineage precursors. The dataset comprises 24 samples divided into eight sample groups each representing a different lymphoid progenitor cell type isolated from wild-type (+/-) or transgenic (-/-) thymic niches. -/-, Foxn1-deficient genotype; +/-, Foxn1 heterozygous phenotype; DP, CD4/CD8 double-poisztive thymocytes; DN3, CD4/CD8-negative stage 3 thymocytes; SP4, CD4 single-positive thymocytes; SP8, CD8 single-positive thymocytes; B IgM-, IgM surface negative B cells; B IgM+, IgM surface positive B cells; B IgM- -/-, IgM surface negative B cells from Foxn1-deficient genotype.
2012-08-24 | E-GEOD-33268 | biostudies-arrayexpress