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

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

PROVIDER: PRJNA448752 | ENA |

REPOSITORIES: ENA

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

Project description: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.

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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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Generation of caudal-type serotonin neurons and hindbrain fate organoids from hPSCs

Project description:Serotonin (5-HT) neurons, the major components of the raphe nuclei, arise from ventral hindbrain progenitors. Based on the anatomical location and axonal projection, 5-HT neurons are coarsely divided into rostral and caudal groups. Here, we propose a novel strategy to generate hindbrain 5-HT neurons from human pluripotent stem cells (hPSCs), which involves the formation of ventral-type neural progenitor cells (NPCs) and stimulation of the hindbrain 5-HT neural development. A caudalizing agent, retinoid acid (RA), was used to direct the cells into the hindbrain cell fate. Approximately 30-40% of hPSCs successfully developed into 5-HT-expressing neurons using our protocol, with the majority acquiring a caudal rhombomere identity (r5-8). We further modified our monolayer differentiation system to generate 5-HT neuron-enriched hindbrain-like organoids. We have also suggested downstream applications of our 5-HT monolayer and organoid cultures to study neuronal response to gut microbiota. Our methodology could become a powerful tool for future studies related to 5-HT neurotransmission.

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

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Transcriptomic analysis of dorso-ventral cell-types of Arabidopsis shoot apical meristem

Project description:Dorso-ventral (DV) patterning at the Shoot Apical meristem (SAM) is essential for organogenesis in Arabidopsis. Dorsal and ventral gene expressed domains are separated by boundaries from where the new organ initiation starts. Here by using cell-types specific transcriptomics approach, we have identified doral, ventral and boundary specific genes in SAM.

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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.

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2015-07-21 | E-GEOD-60066 | biostudies-arrayexpress

Comparison of gene expression pattern between Wild-type and Setd2 knockout mESCs [Affymetrix]

Project description:SETD2/HYPB has been known as a histone H3K36 specific methyltransferase. However, its roles in physiology such as development and cellular function remain unclear. In this study, using mESCs as cellular model, we show that Setd2 mainly regulates differentiation of murine embryonic stem cells (mESCs) towards primitive endoderm. This study aimed at exploring how did Setd2 regulate primitive endoderm. differentiation. We used microarrays to detail the global programme of gene expression controled by setd2, which is required for endoderm differentiation. Wild type and Setd2 knockout mESCs were selected for RNA extraction and hybridization on Affymetrix GeneChip® mouse genome 430 2.0 arrays. We sought to obtain some deregulated genes, which were required for primitive endoderm differentiation. For comparison, three biological repeats of each were performed.

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Distinct transcriptomic, proteomic and epigenetic stress-responses in dorsal and ventral hippocampus

Project description:The hippocampus - one of the most studied brain regions – is a key target of the stress response and vulnerable to the detrimental effects of stress. Although its intrinsic organization is highly conserved throughout its long dorsal-ventral axis, the dorsal hippocampus is linked to spatial navigation and memory formation, whereas the ventral hippocampus is linked to emotional regulation. Here, we provide the first combined transcriptomic and proteomic profiling that reveals striking differences between dorsal and ventral hippocampus. Using various acute stress challenges we demonstrate that both regions display very distinct molecular responses, and that the ventral hippocampus is particularly responsive to the effects of stress. We demonstrate that separately analyzing dorsal and ventral hippocampus greatly increases the ability to detect region-specific stress effects, and we identify an epigenetic network, which is specifically sensitive to acute stress in the ventral hippocampus.

2019-10-03 | PXD006781 | Pride

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