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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Single cell gene expression of early E8.5 pioneer neural crest cells and paraxial mesoderm

ABSTRACT: Laser capture microdissection (LCM) was used to isolate cells from the principal critical micro-regions, whose development, differentiation and signaling interactions are responsible for the construction of the mammalian face. At E8.5, as migrating neural crest cells begin to exit the neural fold/epidermal ectoderm boundary, we examined the facial mesenchyme, composed of neural crest and paraxial mesoderm cells, as well as cells from adjacent neuroepithelium We performed single cell studies to better define the gene expression states of the early E8.5 pioneer neural crest cells and paraxial mesoderm, and present microarray data detailing expression patterns within these embryonic cell populations. Mouse emrbyos were harvested at developmental stage E8.5 and single cells were captured from the neuroepithilium, neural crest, and paraxial mesoderm. RNA was extracted, labelled, and quantified using the Mouse ST-l microarray.

ORGANISM(S): Mus musculus

SUBMITTER: Rebekah Karns

PROVIDER: E-GEOD-55964 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Single cell gene expression of early E8.5 pioneer neural crest cells and paraxial mesoderm

Project description:Laser capture microdissection (LCM) was used to isolate cells from the principal critical micro-regions, whose development, differentiation and signaling interactions are responsible for the construction of the mammalian face. At E8.5, as migrating neural crest cells begin to exit the neural fold/epidermal ectoderm boundary, we examined the facial mesenchyme, composed of neural crest and paraxial mesoderm cells, as well as cells from adjacent neuroepithelium. For these 11 samples, we used a single cell isolation and cDNA generation protocol followed by a standard Affymetrix labeling protocol to better define the gene expression states of the early E8.5 pioneer neural crest and paraxial mesoderm cells. Using a combination of statistical and expression level filtering criteria, we have identified expression patterns present within these embryonic cell populations. The genes identified through this study are highly enriched for known critical genes as well as many genes not previously known to be cell type specific at this stage.

2014-03-18 | GSE55964 | GEO

A gene expression atlas of early craniofacial development

Project description:We present a gene expression atlas of early mouse craniofacial development. Laser capture microdissection (LCM) was used to isolate cells from the principal critical micro-regions, whose development, differentiation and signaling interactions are responsible for the construction of the mammalian face We examined the facial mesenchyme and adjacent neuroepithelium at E8.5, at E9.5 we obtain cells from the facial mesenchyme, olfactory placode/epidermal ectoderm, underlying neuroepithileium, and emerging mandibular and maxillary arches. AT E10.5 we sampled the medial and lateral prominences, olfactory pit, multiple regions of the underlying neuroepithelium the mandibular and maxillary arches, and Rathke's pouch. Mouse emrbyos were harvested at developmental stage E8.5 , E9.5, and E10.5 and cells were captured from microregions responsible for the construction of the mammalian face. RNA was extracted, labelled, and quantified using the Mouse ST-l microarray.

2014-03-18 | E-GEOD-55965 | biostudies-arrayexpress

Mus musculus

Project description:Single cell gene expression of early E8.5 pioneer neural crest cells and paraxial mesoderm

| PRJNA241447 | ENA

Single cell RNA-sequencing of E8.5 stage embryonic neural tissue from mouse

Project description:We describe a so far uncharacterized, embryonic and self-renewing Neural Plate Border Stem Cell (NBSC) population with the capacity to differentiate into central nervous and neural crest lineages. NBSCs can be obtained by neural transcription factor-mediated reprogramming (BRN2, SOX2, KLF4, and ZIC3) of human adult dermal fibroblasts and peripheral blood cells (induced Neural Plate Border Stem Cells, iNBSCs) or by directed differentiation from human induced pluripotent stem cells (NBSCs). Moreover, human (i)NBSCs share molecular and functional features with primary Neural Plate Border Stem Cells (pNBSCs) isolated from neural folds of E8.5 mouse embryos. Here we provide single cell RNA-sequencing data of neural tissue derived from two E8.5 mouse embryos. After manual isolation and enzymatic separation E8.5 neural tissue was single cell sorted and RNA sequencing was performed following the Smart-seq2 protocol. In sum, cultured pNBSCs and E8.5 neural tube cells share a similar regional identity and expression signature suggesting that pNBSCs might correspond to an endogenous progenitor in this area of the developing brain.

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A superseries of gene expression in early craniofacial development in mouse embryos at stages E8.5, E9,5, and E10.5.

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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miR-302 is a temporal regulator of neural crest development [Mouse RNA-seq]

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Differentiation analysis of Mouse Posterior Neural tube

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Sall4 regulates posterior trunk mesoderm development by promoting mesodermal gene expression and repressing neural genes in the mesoderm

Project description:The trunk axial skeleton develops from paraxial mesoderm cells. Our recent study demonstrated that conditional knockout of the stem cell factor Sall4 in mice by TCre caused tail truncation and a disorganized axial skeleton posterior to the lumbar level. Based on this phenotype, we hypothesized that, in addition to the previously reported role of Sall4 in neuromesodermal progenitors, Sall4 is involved in the development of the paraxial mesoderm tissue. ATAC-seq in TCre; Sall4 mutant posterior trunk mesoderm shows that Sall4 knockout reduces chromatin accessibility. We found that Sall4- dependent open chromatin status drives activation and repression of WNT signaling activators and repressors, respectively, to promote WNT signaling. Moreover, footprinting analysis of ATAC-seq data suggests that Sall4-dependent chromatin accessibility facilitates CTCF binding, which contributes to the repression of neural genes within the mesoderm. This study unveils multiple mechanisms by which Sall4 regulates paraxial mesoderm development by directing activation of mesodermal genes and repression of neural genes.

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