Single cell chromatin accessibility profiles of the chick embryonic ectoderm
Ontology highlight
ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE271424 | GEO | 2025/12/02
REPOSITORIES: GEO
Similar Datasets
Project description:The vertebrate ectoderm gives rise to a variety of cell lineages, including neural, neural crest, placodal and non-neural cell fates. How cell fates are specified at the neural plate border (the region surrounding the neural plate) is not fully understood. We therefore carried out 10x scRNAseq of the chick epiblast to investigate cell fate specification at the neural plate border. Embryos were dissected and pooled according to stage. The tissue was then dissociated and FAC sorted to remove dead cells and remaining doublets before cells were stored in MeOH. Due to the time required to dissect embryos, multiple rounds of collections were carried out, with collections from the same stage pooled prior to 10x sequencing. Libraries were sequenced using an Illumina HiSeq 4000 at the Francis Crick Institute, London. This collection was a follow up to E-MTAB-10408.
2023-08-25 | E-MTAB-11444 | biostudies-arrayexpress
Project description:Single cell chromatin accessibility profiles of the chick embryonic ectoderm
| PRJNA1131374 | ENA
Project description:The goal of the current NS23158 funding is to understand how neural fate-stabilizing (NFS) genes function in order to provide fundamental knowledge about their potential roles in neural stem cell development. Neural fate-stabilization is characterized by the expansion of the neural ectoderm shortly after it has been induced by the repression BMP signaling. During this time period a number of early-expressed NFS genes are expressed, each of which expands the neural plate in gain-of-function assays. But, we do not know how these genes are related to one another or whether they are arranged in a linear gene pathway or multi-path hierarchy. One aim of this grant is to elucidate the relationship of Six1, an early-expressed NFS gene that we cloned, to other NFS-genes. We propose to greatly enhance this analysis by utilizing DNA microarray analyses to identify unsuspected and novel target genes. What is the function of Six1 in establishing the lateral neural ectoderm, that gives rise to the placodes and how does it specifically relate to other NFS-genes? In the parent grant we proposed to study the relationship of NFS genes to one that we cloned, Six1 (Brugmann et al., 2004). Six1 expands the placodal ectoderm and holds it in an immature state. In the original grant, we proposed to study whether Six1 activates or suppresses the expression of 6 known lateral NFS genes, using PCR and in situ hybridization of animal caps and whole embryos. Herein we propose to use DNA microarray technology to reveal a much broader spectrum of potential target genes. Six1, a sine oculis transcription factor which is expressed in the early placodal ectoderm that gives rise to the cranial PNS, is a key regulator of neural placodal fate (Brugmann et al., 2004, Development). Being a newly cloned gene, we hypothesize that we will identify numerous downstream targets of Six1 by the proposed microarray analyses. This information will allow us to study their function by gain- and loss-of function studies in the whole embryo. Animal cap (AC) explants are a naïve embryonic ectoderm that is removed from embryonic signaling centers. They allow one to perform gene induction assays in the absence of confounding growth factors, and thus are ideal for identifying downstream targets of transcription factors. In this experiment we will take a gain-of-function approach to identify which genes are induced/repressed by Six1. Six1 mRNA (400pg) will be injected at the 2-cell stage, and embryos cultured until stage 8, at which time the zygotic genome begins transcription. AC explants will be cut from the embryos and cultured in Normal Amphibian�s Medium. When ACs reach stage 10.5, an early step in neural ectoderm specification, they will be cultured in 200ng/nl Noggin protein (R&D Systems) to induce the expression of neural plate genes. When ACs reach stage 16, at which time the placodes have formed, they will be snap frozen in liquid nitrogen and RNA purified according to the Qiagen Rneasy Protect kit protocols. Our preliminary experiments indicate that 8-10ug of total RNA can be recovered with high purity from ~150 ACs with this method. As controls, RNA will be purified from uninjected animal caps, also treated with Noggin, derived from sibling embryos. We will repeat the experiment 5 times (total of 10 samples). Extracted RNA will be evaluated for quality, reverse transcribed into cDNA, amplified, fragmented and then biotinylated using the NuGEN Ovation Biotin System kit.
2008-06-11 | E-GEOD-11144 | biostudies-arrayexpress
Project description:The epithelial-to-mesenchymal transition (EMT) and migration of cranial neural crest cells are critical processes that occur in the early embryo that permit proper craniofacial patterning. Disruptions in these processes not only impair development but also lead to various diseases, underscoring the need for their detailed understanding at the molecular level. The chick embryo has served historically as an excellent model for human embryonic development. While chick cranial neural crest cell EMT and migration have been characterized at the transcript level, studies at the protein level—to allow direct measurement of the active players—have not been undertaken to date. In this study, we applied mass spectrometry (MS)-based proteomics to establish a deep proteomics profile of the midbrain region during early embryonic development. We developed a proteomics method combining optimal lysis conditions and offline fractionation with nanoflow liquid chromatography coupled to high-resolution MS to analyze the tissue from this region, which identified >5,900 proteins involved in key pathways related to neural crest cell EMT and migration such as signaling, proteolysis/extracellular matrix (ECM), and transcriptional regulation. This study offers valuable insight into important developmental processes occurring in the midbrain region and demonstrates the utility of proteomics for characterization of various tissues during chick embryogenesis.
2023-10-25 | PXD042200 | Pride
Project description:The goal of the current NS23158 funding is to understand how neural fate-stabilizing (NFS) genes function in order to provide fundamental knowledge about their potential roles in neural stem cell development. Neural fate-stabilization is characterized by the expansion of the neural ectoderm shortly after it has been induced by the repression BMP signaling. During this time period a number of early-expressed NFS genes are expressed, each of which expands the neural plate in gain-of-function assays. But, we do not know how these genes are related to one another or whether they are arranged in a linear gene pathway or multi-path hierarchy. One aim of this grant is to elucidate the relationship of Six1, an early-expressed NFS gene that we cloned, to other NFS-genes. We propose to greatly enhance this analysis by utilizing DNA microarray analyses to identify unsuspected and novel target genes. What is the function of Six1 in establishing the lateral neural ectoderm, that gives rise to the placodes and how does it specifically relate to other NFS-genes? In the parent grant we proposed to study the relationship of NFS genes to one that we cloned, Six1 (Brugmann et al., 2004). Six1 expands the placodal ectoderm and holds it in an immature state. In the original grant, we proposed to study whether Six1 activates or suppresses the expression of 6 known lateral NFS genes, using PCR and in situ hybridization of animal caps and whole embryos. Herein we propose to use DNA microarray technology to reveal a much broader spectrum of potential target genes. Six1, a sine oculis transcription factor which is expressed in the early placodal ectoderm that gives rise to the cranial PNS, is a key regulator of neural placodal fate (Brugmann et al., 2004, Development). Being a newly cloned gene, we hypothesize that we will identify numerous downstream targets of Six1 by the proposed microarray analyses. This information will allow us to study their function by gain- and loss-of function studies in the whole embryo. Animal cap (AC) explants are a naïve embryonic ectoderm that is removed from embryonic signaling centers. They allow one to perform gene induction assays in the absence of confounding growth factors, and thus are ideal for identifying downstream targets of transcription factors. In this experiment we will take a gain-of-function approach to identify which genes are induced/repressed by Six1. Six1 mRNA (400pg) will be injected at the 2-cell stage, and embryos cultured until stage 8, at which time the zygotic genome begins transcription. AC explants will be cut from the embryos and cultured in Normal Amphibians Medium. When ACs reach stage 10.5, an early step in neural ectoderm specification, they will be cultured in 200ng/nl Noggin protein (R&D Systems) to induce the expression of neural plate genes. When ACs reach stage 16, at which time the placodes have formed, they will be snap frozen in liquid nitrogen and RNA purified according to the Qiagen Rneasy Protect kit protocols. Our preliminary experiments indicate that 8-10ug of total RNA can be recovered with high purity from ~150 ACs with this method. As controls, RNA will be purified from uninjected animal caps, also treated with Noggin, derived from sibling embryos. We will repeat the experiment 5 times (total of 10 samples). Extracted RNA will be evaluated for quality, reverse transcribed into cDNA, amplified, fragmented and then biotinylated using the NuGEN Ovation Biotin System kit. Keywords: neural fate, noggin, Six-1
2008-04-12 | GSE11144 | GEO
Project description:chick intermediate neural explants
| PRJEB5921 | ENA
Project description:A systematic survey of the transcriptional status of individual segments of the developing chick hindbrain (r1-5) and the adjacent region of the embryonic midbrain (m) during the HH11 stage of chick development Affymetrix Chicken GeneChip Expression Study Paralell comparison of defined regions of the neural tube during early chick development
2014-06-25 | E-GEOD-48359 | biostudies-arrayexpress
Project description:10x single cell RNAseq of chick ectoderm from stages HH5 to ss4
| PRJEB51065 | ENA
Project description:The inner ear develops from a patch of thickened cranial ectoderm adjacent to the hindbrain called the otic placode. Studies in a number of vertebrate species suggest that the initial steps in induction of the otic placode are regulated by members of the Fibroblast Growth Factor (FGF) family, and that inhibition of FGF signaling can prevent otic placode formation. To better understand the genetic pathways activated by FGF signaling during otic placode induction, we performed microarray experiments to estimate the proportion of chicken otic placode genes that can be up-regulated by the FGF pathway in a simple culture model of otic placode induction. Surprisingly, we find that FGF is only sufficient to induce about 15% of chick otic placode-specific genes in our experimental system. However, pharmacological blockade of the FGF pathway in cultured chick embryos showed that although FGF signaling was not sufficient to induce the majority of otic placode-specific genes, it was still necessary for their expression in vivo. These inhibitor experiments further suggest that the early steps in otic placode induction regulated by FGF signaling occur through the MAP kinase pathway. Although our work suggests that FGF signaling is necessary for otic placode induction, it demonstrates that other unidentified signaling pathways are required to co-operate with FGF signaling to induce the full otic placode program. 8 samples were analyzed. These contain two replicates of each of the following four catergories: Otic ectoderm, Non-Otic (lateral) ectoderm, Trigeminal Ectoderm cultured - FGF, Trigeminal Ectoderm cultured + FGF
2012-12-12 | E-GEOD-42845 | biostudies-arrayexpress
Project description:Type IV collagen is the main component of the basement membrane which gives strength to the blood-gas barrier. In avians the formation of the blood-gas barrier happens rapidly and before hatching. We have performed a microarray expression analysis in late chick lung development and found that COL4A1 and COL4A2 were among the most significantly upregulated genes during the formation of the avian blood-gas barrier. Our study showed that type IV collagen and therefore the basement membrane play fundamental roles in coordinating alveolar morphogenesis. Four developmental stages of chick lung maturation (E14, E15, E16, E18). Three biological replicates per time point.
2015-11-01 | E-GEOD-72385 | biostudies-arrayexpress