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MicroRNA-Seq of Gallus gallus embryo tissues: Undetermined Presomitic Mesoderm (PSM), Determined PSM, and Limb bud

ABSTRACT: microRNA-Seq of Gallus gallus embryo tissues: Undetermined Presomitic Mesoderm (PSM), Determined PSM, and Limb bud

PROVIDER: PRJEB33661 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3450210.fastq.gz	Fastqsanger.gz
	ERR3450211.fastq.gz	Fastqsanger.gz
	ERR3450212.fastq.gz	Fastqsanger.gz
	ERR3450205.fastq.gz	Fastqsanger.gz
	ERR3450206.fastq.gz	Fastqsanger.gz

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microRNA-Seq of Gallus gallus embryo tissues: Undetermined Presomitic Mesoderm (PSM), Determined PSM, and Limb bud

Project description:This analysis aims at finding the microRNAs present in three chick embryo undifferentiated tissues (pools of tissues): Undetermined Presomitic Mesoderm (PSM-U), Determined Presomitic Mesoderm (PSM-D) and Distal limb bud (Limb).

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Transcriptomic landscape of developing Presomitic mesoderm (PSM)

Project description:Stem cell-derived tissues have wide potential for modelling developmental and pathological processes as well as cell-based therapy. However, it has proven difficult to generate several key cell types in vitro, including skeletal muscle. In vertebrates, skeletal muscles derive during embryogenesis from the presomitic mesoderm (PSM). Using PSM development as a guide to establish conditions for the differentiation of monolayer cultures of embryonic stem (ES) cells into PSM-like cells without the introduction of transgenes or cell sorting. We generated a high resolution transcriptome expression landscape along the PSM of the mouse embryo, by microdissecting consecutive fragment of the PSM along the antero-posterior axis of the embryo. We took advantage of the observation that during development of embryo, the antero-posterior spatial position of the tissue is directly correlated to its differentiation (time) stage, thus generating an expression time-course of presomitic mesoderm development.

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The Presomitic Mesoderm (PSM) CREB family transcriptome

Project description:Dynamic gene expression in the PSM of vertebrates is critical for the spatial and temporal patterning of somites. Using microarray analysis, we explored in detail, genes that are differentially regulated upon removal of CREB family function from the mouse PSM. Mouse PSM from R26R^AC/AC (Control) and R26R^AC/AC;T-Cre (Mutant) were harvested for RNA extraction. Nine PSM's from control and mutant genotypes were combined to generate three biological replicates (three PSM's/replicate). Samples were then applied to microarray analysis to identify differentially expressed genes between controls and mutants.

2013-04-27 | E-GEOD-46426 | biostudies-arrayexpress

Transcriptomic landscape of developing Presomitic Mesoderm (PSM) from Tailbud to somite in E9.5 mouse embryo and in in vitro differentiated Paraxial mesoderm derived from mouse embryonic stem cells (mESCs).

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Gene expression analysis of mouse E9.5 presomitic mesoderm wt vs TCre/+;Taf10flox/flox

Project description:Presomitic mesoderm (PSM) were microdissected from E9.5 mouse embryos (WT and TCre/+;Taf10flox/flox). 3 PSM (17-19 somites stage) were pooled per microarray, in triplicates, per genotypes

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Subcellular proteomics of murine presomitic mesoderm

Project description:We studied the effects of different stimuli on on the subcellular proteome of primary murine presomitic mesoderm tissue (PSM) in two separate experiments. In the first experiment, tissue was treated ex vivo with either fructose-6-phosphate, fructose-1,6-bisphosphate, or control treatment before subcellular fractionation using a subcellular protein fractionation kit (Thermo Fisher Scientific 78840). In the second experiment, PSMs from transgenic and control mice were extracted and subcellularly fractionated as above. Samples were multiplexed using TMT and analyzed on LC-MS/MS.

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RNA-seq of mouse embryonic stem cells differentiated to EpiSCs and further to presomitic mesoderm (PSM) via Wnt activation (CHIR99021) to study the influence of FGF signaling on PSM induction

Project description:Presomitic mesoderm (PSM) cells are the precursors of the somites, which flank both sides of the neural tube and give rise to the musculo-skeletal system shaping the vertebrate body. WNT and FGF signalling control the formation of both the PSM and the somites, and show a graded distribution with highest levels in the posterior PSM. We have employed reporter for the PSM control gene Tbx6 to investigate the differentiation of mouse ESCs from the naĂŻve state to PSM state. Feeder-free ESCs were seeded and grown on fibronectin (3-5 ng/ml)-coated plates in ESC medium containing LIF, PD0325901 and CHIR99021 (2i medium) to bring them to a naive state of pluripotency. Following this, the cells were brought to an EpiSC state by treating them with Activin A and FGF2. The EpiSC-like cells were then differentiated to PSM using CHIR99021 either alone or along with FGF ligands, FGF2 or FGF8 (Low concentration: 10 ng/ml or High concentration: 250ng/ml).

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Self-Renewing Presomitic Mesoderm Progenitor Lines Reprogrammed from human urine cells [Reprogramming scRNA-seq]

Project description:Vertebrae formation is the defining feature of all vertebrates1,2. Yet, each vertebrate species appears to have a unique timing mechanism for forming somites along the vertebral column3-5. Human vertebrate formation remains poorly studied due to technical and ethical limitations. Here we report the generation of self-renewing stem cells with characteristic presomitic mesoderm (PSM) features by reprogramming epithelial cells isolated from human urine. These induced expandable presomitic mesoderm progenitor cells (UiPSM) proliferated extensively for more than 30 passages in chemically defined conditions, robustly producing 1040 UiPSM cells. UiPSM established presomitic mesodermal transcription profile, not detected pluripotency, ectoderm and endoderm related genes. UiPSM developed into presomitic mesodermal lineage cells, such as skeletal muscle cells(skm), osteoblast and chrondroblast cells in vivo and vitro, when transplanted UiPSM derived human skm cells in muscle injury model, the skm cells can survive in vivo and contribute to muscle regeneration up to one month. Thus, UiPSM is a powerful system to study human somite development and provide strategies for regenerative medicine in musculoskeletal system

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