RNAseq analysis of developing chick somites
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ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE61678 | GEO | 2019/12/01
REPOSITORIES: GEO
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Project description:Microarray analysis of chick embryo tissues: Hamburger Hamilton (HH) stage 3+/4 and HH6 Hensenâs node, HH 3+/4 posterior primitive streak, notochord with ventral neural tube at HH10-11, dorsal neural tube at HH10-11 and anterior and posterior thirds of the wing bud at stages HH20-21 and HH24.
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Project description:Formation of blood vessels requires the concerted regulation of an unknown number of genes in a spatial-, time- and dosage-dependent manner. We investigated vascular development in vivo by determining global gene regulation throughout the formation of the chick chorio-allantoic membrane (CAM). Our study provides a comprehensive molecular map of vascular maturation during developmental angiogenesis and might thus be a valuable resource to streamline further research of candidates susceptible to mediate pathological angiogenesis. Experiment Overall Design: The developmental stage of the embryos was determined after isolation of the CAM according to Hamburger & Hamilton (HH) (1992). CAMs were isolated from embryos at developmental day E5 (HH26), E7 (HH30), E10 (HH>35) and E14 (HH40), (n=3 embryos/day). mRNA was isolated and hybridized to Affymetrix chicken GeneChips using the Affymetrix standard protocol. We compared one embryo at a lower HH stage to three embryos at a more advanced HH stage and repeated the comparison with two more embryos. Overall, we compared expression between E7 and E5, E10 and E5, E14 and E5, E10 and E7 and E14 and E10.
2009-11-20 | E-GEOD-11636 | biostudies-arrayexpress
Project description:Somites are transient embryonic structures consisting of hundreds of cells that bud off from the anterior tip of the presomitic mesoderm (PSM) on each side of the neural tube. They give rise to the vertebrae and associated skeletal muscles, nerves, and blood vessels. To characterise the transcriptional changes that orchestrate mouse somitogenesis, we have generated coupled RNA-seq and ATAC-seq profiles of individual somites, across embryonic development. We collected the three most posterior pairs of somites, which correspond to those most recently segmented, from embryos containing 8, 18, 21, 25, 27 and 35 pairs of somites. The three somites are labelled I, II and III from the most posterior to the most anterior. From each pair, one somite was used for RNA-seq and the other one for ATAC-seq.
2023-01-24 | E-MTAB-12539 | biostudies-arrayexpress
Project description:Somites are transient embryonic structures consisting of hundreds of cells that bud off from the anterior tip of the presomitic mesoderm on each side of the neural tube. They give rise to the vertebrae and associated skeletal muscles, nerves, and blood vessels. To characterise the transcriptional changes that orchestrate mouse somitogenesis, we have generated coupled RNA-seq and ATAC-seq profiles of individual somites, across embryonic development. We collected the three most posterior pairs of somites, which correspond to those most recently segmented, from embryos containing 8, 18, 21, 25, 27 and 35 pairs of somites. The three somites are labelled I, II and III from the most posterior to the most anterior. From each pair, one somite was used for RNA-seq and the other one for ATAC-seq.
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Project description:The spinal cord is generated progressively as cells leave the caudal region of the elongating body axis such that the temporal steps of neural differentiation become spatially separated along the head to tail axis. At key stages, it is therefore possible to isolate near-adjacent cell populations from the same embryo in distinct differentiation states. Cells in the caudal lateral epiblast adjacent to the primitive streak (also known as the stem zone, SZ, in the chick) express both early neural and mesodermal genes. Other cells in the stem zone will gastrulate to form the paraxial mesoderm or remain in the epiblast cell sheet and become neural progenitors. These latter cells form a new region called the preneural tube (PNT), which is flanked by unsegmented presomitic mesoderm and represents an early neural progenitor state that can be induced by FGF signalling to revert back to a multi-potent SZ state. Rostral to this, the closed caudal neural tube (CNT) is flanked by somites and is an early site of co-expression of genes characteristic of neural progenitors, and of ventral patterning genes (Diez del Corral et al., 2003). The CNT contains the first few neurons and exposure to FGF cannot revert this tissue to a multi-potent SZ state (Diez del Corral et al., 2002). The transition from the PNT to the CNT thus involves commitment to a neural fate that this is regulated by a switch from FGF to retinoid signalling. More advanced neuroepithelium is then located in more rostral neural tube (RNT), in which neuronal differentiation is ongoing and dorsoventral pattern is refined. This experiment uses the Affymetrix GeneChip chicken genome microarray to compare the transcriptomes of microdissections of these spatially distinct cell populations from the elongating neural axis of HH stage 10 chick embryos. Dissections were carried out in L15 medium at 4°C and explants pooled in TRIzol reagent (Gibco) for RNA extraction. Notochord was removed by controlled trypsin digestion that aimed to keep the neural ventral midline. For the microarrays, at least five tissue samples for each region were pooled to make each of three biological replicates for each (n>15 for each region).
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Project description:Pbx homeodomain proteins have been implicated in the regulation of gene expression during muscle development. Whether Pbx proteins are required broadly for the regulation of muscle gene expression or are required for the expression of a specific subset of muscle gene expression is not known. We employed microarrays to determine the requirements for Pbx proteins during zebrafish development. Experiment Overall Design: Total RNA samples from control and pbx2-MO;pbx4-MO embryos were collected at two developmental stages: 10 somites and 18 somites. Their expression profiles were analyzed using Affymetrix zebrafish genome arrays, and the differentially hybridized genes were determined to be significant according to a FDR<0.05.
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