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Mouse embryonic stem cells (mESCs) differentiation towards ventral hindbrain neuronal cell types [d4.5, d5.5 and d6.5]

ABSTRACT: mESCs treated with retinoic acid (RA) and a Shh agonist (SAG) recapitulated ventral hindbrain development and produced a population of neural progenitors with a minor presence of other cell types.

ORGANISM(S): Mus musculus

PROVIDER: GSE114640 | GEO | 2020/07/30

REPOSITORIES: GEO

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Mouse embryonic stem cells (mESCs) differentiation towards ventral hindbrain neuronal cell types [d0-d3.5]

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Mouse embryonic stem cells (mESCs) differentiation towards ventral hindbrain neuronal cell types [d4.5, d5.5 and d6.5]

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Single cell transcriptome of regional human embryonic stem cell-derived dorsal and ventral neurons from the hindbrain and spinal cord

Project description:We generated single RNA-seq data to measure transcriptional profiles of 14 hESC-derived neuronal populations, representing distinct regions along the dorsoventral and rostrocaudal axes of the developing hindbrain and human spinal cord. These cells are differentiated using a modular protocol that first induces collinear activation of region-specific HOX genes by exposure to FGF8 and Wnt signaling (Lippmann et al, 2015 PMID:25843047). By transitioning to media containing retinoic acid (RA), SB-431542, and LDN-193189, we generate dedicated posterior central nervous system progenitors with unique rostrocaudal identities. Dorsal patterning by BMP4 or ventral patterning by Sonic hedgehog agonists (smoothened agonist (SAG) and Purmorphamine (Pur)), followed by DAPT gave rise to somatosensory or locomotor neuronal cultures. In total we recovered the transcriptomes of 46,959 cells. Analysis verified expression of increasingly caudal HOX paralogs that could be correlated to hindbrain (HOX1-5; H24, H48, and H72), cervical (HOX1-8; H72 and H120), thoracic (HOX1-9; H168), and thoracolumbar (HOX1-11; H216 and H216R) spinal regions. The dataset also includes representation from major cardinal neuron types. Comparison with existing mouse and human datasets revealed the overall similarity between in vitro-derived and in vivo neurons. Moreover, we detect hundreds of transcriptional markers within region-specific neuronal phenotypes, enabling discovery of novel gene expression patterns along the human developmental axes.

2022-07-28 | GSE186697 | GEO

Cell type specific RNAseq from crosslinked and and TF-Sorted ventral neural tube cell types

Project description:In many developing tissues the spatial and temporal pattern of gene expression is organised by secreted signals functioning in a graded manner over multiple cell diameters. Cis Regulatory Elements (CREs) interpret these graded inputs to control gene expression. How this is accomplished remains poorly understood. The morphogen Sonic hedgehog (Shh) acts in a graded manner to direct neural progenitor specification in the neural tube. Here, we uncover two distinct ways in which CREs translate graded Shh signaling into differential gene expression. A common set of CREs are used to control gene activity in the majority of ventral neural progenitors. These CREs integrate cell type specific inputs to control gene expression. By contrast, the most ventral progenitors use a unique set of CREs. These are established by the pioneer factor FOXA2, paralleling the role of FOXA2 in endoderm. Moreover, FOXA2 binds a subset of the same sites in neural and endoderm cells. Together the data identify distinct cis regulatory strategies for the interpretation of morphogen signaling and raise the possibility of an evolutionarily conserved role for Foxa2-mediated cell specification across tissues.

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Single-cell RNA-seq of motor neuron progenitors differentiated from mouse embryonic stem cell line HM1 by treatment with RA and SAG

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2018-02-01 | E-MTAB-5466 | biostudies-arrayexpress

NEUROMESO

Project description:Exposure of mouse ESCs to a sequence of extrinsic signals, which recapitulates in vivo development, generates a bipotential neuromesodermal precursor (NMP) that can be directed to differentiate into either spinal cord or paraxial mesodermal tissue. To induce differentiation,mouse ES cells were plated on CellBINDSurface dishes (Corning) precoated with 0.1% gelatin (Sigma) at a density of 5x10^3 cells cm-2 in N2B27 medium. Cells were grown in N2B27 supplemented with 10ng/ml bFGF (R&D) for 3 days (D1-D3) and then were transferred into serum free media without bFGF (D3-D5). To induce ventral hindbrain identity NPCs (NH) 100nM RA (Sigma) and 500nM SAG (Calbiochem) was added from D3-D5. Spinal cord identity (NP) was induced by the addition of 5nM CHIR 99021 (Axon) from D2 to D3 followed by 100nM RA, 500nM SAG from D3-D5. To induce mesodermal differentiation the cells were treated with CHIR99021 from D2-D5.

2014-07-18 | E-MTAB-2268 | biostudies-arrayexpress

A single cell transcriptome atlas of the developing zebrafish hindbrain [scRNA-Seq]

Project description:Purpose: The goal of this study is to understand the progressive patterning of neurogenesis of the developing zebrafish hindbrain. 16hpf, 24hpf and 44hpf zebrafish hindbrains were used for single-cell RNA-sequencing with the aim to uncover hindbrain development. Methods: 40 microdissected hindbrains per each stage were dissociated at loaded into the 10x Genomics Chromium Platform, and sequenced using Illumina HiSeq 4000. Conclusions: Our study constitute a resource of hindbrain gene expression during development. We have identified transcriptional programs involved in: rhombomere segmental identity, dorso-ventral patterning, boundary and centre progenitor cells and temporal regulation of neurogenesis.

2019-12-05 | GSE141427 | GEO

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