RNA-seq of control and talpid2 facial prominences
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ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE52757 | GEO | 2014/06/24
SECONDARY ACCESSION(S): PRJNA229973
REPOSITORIES: GEO
Similar Datasets
Project description:We report the RNA profiles of both control and talpid2 frontonasal, maxillary, and mandibular prominences of the chick face at Hamburger and Hamilton (HH) stage 25. For more details please see: "The cellular and molecular etiology of the craniofacial defects in the avian ciliopathic mutant, talpid2." Facial prominences (frontonasal, maxillary, and mandibular) from 8 control and 8 talpid2 HH 25 embryos were harvested, pooled, and RNA-seq was preformed on samples.
2014-06-24 | E-GEOD-52757 | biostudies-arrayexpress
Project description:Growth and patterning of the face relies on several small buds of tissue, the facial prominences, which surround the primitive mouth. Beginning around E10 of mouse development the prominences undergo rapid growth and morphogenesis. By E11.5 the medial nasal prominences are in close apposition in the midline, as are the maxillary and medial nasal prominences on either side of the developing face. Subsequently, by E12.5 the nasal and maxillary prominences fuse to form a continuous shelf at the front of the face - the primary palate. Individual prominences are associated with specific developmental processes, and this is reflected by patterns of differential gene expression that give the prominences their unique identities. Thus, only the mandibular and maxillary prominences give rise to dentition while the frontonasal prominence has a unique role in olfaction, and the mandibular prominence in taste. We used microarrays to detail the differential gene expression program in each of the mandibular, maxillary, and frontonasal prominences during the key developmental timepoints of E10.0 through E12.5. Keywords: time course
2008-08-30 | GSE7759 | GEO
Project description:Growth and patterning of the face relies on several small buds of tissue, the facial prominences, which surround the primitive mouth. Beginning around E10 of mouse development the prominences undergo rapid growth and morphogenesis. By E11.5 the medial nasal prominences are in close apposition in the midline, as are the maxillary and medial nasal prominences on either side of the developing face. Subsequently, by E12.5 the nasal and maxillary prominences fuse to form a continuous shelf at the front of the face - the primary palate. Individual prominences are associated with specific developmental processes, and this is reflected by patterns of differential gene expression that give the prominences their unique identities. Thus, only the mandibular and maxillary prominences give rise to dentition while the frontonasal prominence has a unique role in olfaction, and the mandibular prominence in taste. We used microarrays to detail the differential gene expression program in each of the mandibular, maxillary, and frontonasal prominences during the key developmental timepoints of E10.0 through E12.5. Experiment Overall Design: Analysis of gene expression during growth and fusion of the facial prominences in the C57BL/6J mouse strain between embryonic (E) day 10.0 and 12.5. At the earliest timepoint, E10, only the mandibular prominence is a distinct entity that can be readily identified and dissected. The frontonasal prominence and the maxillary prominence are very small and not discrete from other components of the head such as the forebrain until E10.5. Analysis of these tissues at earlier timepoints would require laser capture and preamplification steps - techniques that were not used for the later timepoints. Thus samples were isolated from the mandibular prominence at E10.0 and from the mandibular, maxillary and frontonasal prominences of mouse embryos from E10.5 to E12.5, at 0.5 day intervals. In order to obtain sufficient sample for hybridization, each sample represents a pool of between 3 and 48 embryos depending on the timepoint. Specifically, the number of embryos were 40-48 for E10.0 (mandibular prominence only), 24-8 for E10.5, 8-9 for E11.0 and E11.5 and 3-4 for E12.0 and E12.5. Seven replicate samples were taken for each of the later five timepoints in each of the three prominences, with an additional seven samples for the mandibular E10.0 timepoint, for a total of 112 samples.
2008-10-26 | E-GEOD-7759 | biostudies-arrayexpress
Project description:The face is one of the three regions most frequently affected by congenital defects in humans. In order to understand the molecular mechanisms involved it is necessary to have a more complete picture of gene expression in the embryo. Here we use microarrays to profile expression in chicken facial prominences, post neural crest migration and prior to differentiation of mesenchymal cells. Chip-wide analysis revealed that maxillary and mandibular prominences had similar expression profiles while the frontonasal mass chips were distinct. Of the 3094 genes that were differentially expressed in one or more regions of the face, a group of 56 genes was subsequently validated with quantitative PCR and a subset examined with in situ hybridization. Microarrays trends were consistent with the QPCR data for the majority of genes (81%). On the basis of QPCR and microarray data, groups of genes that characterize each of the facial prominences can be determined. We used microarrays to detail the global programme of gene expression underlying facial morphogensis Experiment Overall Design: Chicken embryos were selected at a stage after neural crest cells have ceased migration, when facial prominences have formed and prior to ctyodifferentiation of cartilage, bone, muscle. Microdissection was used to isolate facial prominences. Embryos were dissected on ice in Hanks Buffered Salt Solution and batches of 26-32 pieces were snap frozen in liquid Nitrogen. These pooled facial prominences comprised one biological replicate. A total of three biological replicates were generated for the frontonasal mass, maxillary and mandibular prominences.
2009-11-10 | E-GEOD-18477 | biostudies-arrayexpress
Project description:The face is one of the three regions most frequently affected by congenital defects in humans. In order to understand the molecular mechanisms involved it is necessary to have a more complete picture of gene expression in the embryo. Here we use microarrays to profile expression in chicken facial prominences, post neural crest migration and prior to differentiation of mesenchymal cells. Chip-wide analysis revealed that maxillary and mandibular prominences had similar expression profiles while the frontonasal mass chips were distinct. Of the 3094 genes that were differentially expressed in one or more regions of the face, a group of 56 genes was subsequently validated with quantitative PCR and a subset examined with in situ hybridization. Microarrays trends were consistent with the QPCR data for the majority of genes (81%). On the basis of QPCR and microarray data, groups of genes that characterize each of the facial prominences can be determined. We used microarrays to detail the global programme of gene expression underlying facial morphogensis keyword: craniofacial
2009-10-30 | GSE18477 | GEO
Project description:The patterning of the facial midline involves early specification of neural crest cells to form skeletal tissues that support the upper jaw . In order to understand the molecular mechanisms involved we have taken advantage of a beak duplication model developed in the chicken embryo. Here we can induce the transformation of the side of the beak into a second midline that is easily identifiable by the formation of a supernumerary egg tooth. The phenotype is induced by implanting two microscopic beads, one soaked in retinoic acid and the other soaked in Noggin into the side of the head of the chicken embryo. Here we use microarrays to profile expression of maxillary mesenchyme 16h after placing the beads. A subset of genes were validated using in situ hybridization and QPCR. The aims of the study are to test the function of these genes using retroviral transgenesis, knockdown with morpholinos or expression of secreted proteins and their application to the embryo. Embryos were incubated at 38 degrees C until they reached Hamburger Hamilton Stage 15 or 25 somites. Four different treatments were carried out consisting of two beads simultaneously implanted into the side of the head between the eye and mandibular arch. The beads were either Noggin+retinoic acid, Tris+retinoic acid, Noggin+DMSO or the control, Tris+DMSO. Embryos were reincubated for another 16h until they reached stage 18. Embryos were dissected on ice in Hanks Buffered Salt Solution and batches of 12-15 maxillary pieces were snap frozen in liquid Nitrogen. These pooled facial prominences comprised one biological replicate. A total of three biological replicates were generated for each treatment.
2014-02-28 | E-GEOD-52227 | biostudies-arrayexpress
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.
2016-08-23 | E-MTAB-4048 | biostudies-arrayexpress
Project description:Avian beaks show extreme species-specific variability in morphology, though they develop from the same primordial structures. In both humans and birds, cranial neural crest cells are the primary source of mesenchyme for the frontonasal prominence; previous work has shown that these cells contain molecular information that regulate species-specific facial variation. To determine the molecular basis of avian craniofacial patterning, we have gene expression profiled micro-dissected cranial neural crest cells from the frontonasal prominence of three bird species (chickens, quails, and ducks) during embryonic development. These changes in gene expression were measured on a custom built, cross-species, long oligonucleotide microarray that interrogates the vast majority of transcription factor (TF) genes plus a wide variety of signaling pathways. Samples were isolated at two developmental stages, before (Hamilton Hamburger stage [HH] 20) and after (HH25) morphological distinctions between the species are evident. Keywords: cross-species comparison Frontonasal mesenchymal cells were micro-dissected two developmental stages, before (Hamilton Hamburger stage [HH] 20) and after (HH25) morphological distinctions between the species are evident. For each sample, mesenchyme from 40 embryos was pooled. For each stage-matched comparison between chicken and quail, experiments include technical replicates as well as dye-switches for a total of 12 microarrays.
2009-12-02 | E-GEOD-11027 | biostudies-arrayexpress
Project description:Avian beaks show extreme species-specific variability in morphology, though they develop from the same primordial structures. In both humans and birds, cranial neural crest cells are the primary source of mesenchyme for the frontonasal prominence; previous work has shown that these cells contain molecular information that regulate species-specific facial variation. To determine the molecular basis of avian craniofacial patterning, we have gene expression profiled micro-dissected cranial neural crest cells from the frontonasal prominence of three bird species (chickens, quails, and ducks) during embryonic development. These changes in gene expression were measured on a custom built, cross-species, long oligonucleotide microarray that interrogates the vast majority of transcription factor (TF) genes plus a wide variety of signaling pathways. Samples were isolated at two developmental stages, before (Hamburger Hamilton stage [HH] 20) and after (HH25) morphological distinctions between the species are evident. Keywords: cross-species comparison Frontonasal mesenchymal cells were micro-dissected two developmental stages, before (Hamburger Hamilton stage [HH] 20) and after (HH25) morphological distinctions between the species are evident. For each sample, mesenchyme from 40 embryos was pooled. For each stage-matched comparison between duck and chicken, experiments include technical replicates as well as dye-switches for a total of 14 microarrays.
2009-12-02 | E-GEOD-11028 | biostudies-arrayexpress
Project description:Avian beaks show extreme species-specific variability in morphology, though they develop from the same primordial structures. In both humans and birds, cranial neural crest cells are the primary source of mesenchyme for the frontonasal prominence; previous work has shown that these cells contain molecular information that regulate species-specific facial variation. To determine the molecular basis of avian craniofacial patterning, we have gene expression profiled micro-dissected cranial neural crest cells from the frontonasal prominence of three bird species (chickens, quails, and ducks) during embryonic development. These changes in gene expression were measured on a custom built, cross-species, long oligonucleotide microarray that interrogates the vast majority of transcription factor (TF) genes plus a wide variety of signaling pathways. Samples were isolated at two developmental stages, before (Hamburger Hamilton stage [HH] 20) and after (HH25) morphological distinctions between the species are evident. Keywords: cross-species comparison Frontonasal mesenchymal cells were micro-dissected two developmental stages, before (Hamburger Hamilton stage [HH] 20) and after (HH25) morphological distinctions between the species are evident. For each sample, mesenchyme from 40 embryos was pooled. For each stage-matched comparison between duck and quail, experiments include technical replicates as well as dye-switches for a total of 17 microarrays.
2009-12-02 | E-GEOD-11029 | biostudies-arrayexpress