Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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ScRNA-seq of Gallus gallus embryo xenografts to investigate how the embryonic node functions as an instructive stem cell niche

ABSTRACT: 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).

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Gallus gallus

SUBMITTER: Claudio Stern

PROVIDER: E-MTAB-11216 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:"The main goal of the project is to develop a new generation of bioinformatics resources for the integrative analysis of multiple types of omics data. These resources include both novel statistical methodologies as well as user-friendly software implementations. STATegra methods address many aspects of the omics data integration problem such as the design of multiomics experiments, integrative transcriptional and regulatory networks, integrative variable selection, data fusion, integration of public domain data, and integrative pathway analysis. To support method development STATegra uses a model biological system, namely the differentiation process of mouse pre-B-cells. The STATegra consortium generated data focused on a critical step in the differentiation of B lymphocytes, which are key components of the adaptive immune system. Transcription factors of the Ikaros family are central to the normal differentiation of B cell progenitors and their expression increases in response to developmental stage-specific signals to terminate the proliferation of B cell progenitors and to initiate their differentiation. In particular, a novel biological system that models the transition from the pre-BI stage to the pre-BII subsequent stage, where B cell progenitors undergo growth arrest and differentiation, was used. The approach involves a pre-B cell line, B3 , and an inducible version of the Ikaros transcription factor, Ikaros-ERt2. Ikaros factors act to down-regulate genes that drive proliferation and to simultaneously up-regulate the expression of genes that promote the differentiation of B cell progenitors. Hence, in the B3 system, before induction of Ikaros, cells proliferate and their gene expression pattern is similar to proliferating B cell progenitors in vivo. Following Ikaros induction, B3 cells undergo gene expression changes that resemble those that occur in vivo during the transition from cycling to resting pre-B cells, followed by a marked reduction in cellular proliferation and by G1 arrest. On this system the consortium has created a high-quality data collection consisting of a replicated time course using seven different omics platforms: RNA-seq, miRNA-seq, ChIP-seq, DNase-seq, Methyl-seq, proteomics and metabolomics, which is used to assess and to validate STATegra methods."

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ScRNA-seq of Gallus gallus embryo xenografts to investigate how the embryonic node functions as an instructive stem cell niche

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