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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of chicken Sex-dimorphic gene expression and ineffective dosage compensation of Z-linked genes in gastrulating embryos

ABSTRACT: Sex determination is still poorly understood in birds and no key determinants have so far been identified. In contrast to most other species, dosage compensation of bird sex chromosomal genes appears rather ineffective. By comparing microarrays of microdissected primitive streak from single chicken embryos, we identified a large number of genes differentially expressed between male and female embryos at a very early stage (Hamburger and Hamilton stage 4), long before any sexual differentiation occurs. Most of these genes are located on the Z chromosome, which indicates that dosage compensation is ineffective in early chicken embryos. Gene ontology analyses using an enhanced annotation tool for Affymetrix probesets of the chicken genome shows that among the male-biased genes found on the Z chromosome, more than 20 genes have a role in sex differentiation. Experiment Overall Design: Primitive streak tissues were dissected out of individual Hamburger and Hamilton (HH) stage 4 chicken embryos and extracted for total RNA. Total RNA was amplified 2-cycles, biotin-labeled and hybridized to Affymetrix chicken GeneChip. Gene expression profiles of female and male samples were analyzed for sex-dimorphic expression.

ORGANISM(S): Gallus gallus

SUBMITTER: Sachin Mathur

PROVIDER: E-GEOD-16064 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Sex-dimorphic gene expression and ineffective dosage compensation of Z-linked genes in gastrulating chicken embryos

Project description:Sex determination is still poorly understood in birds and no key determinants have so far been identified. In contrast to most other species, dosage compensation of bird sex chromosomal genes appears rather ineffective. By comparing microarrays of microdissected primitive streak from single chicken embryos, we identified a large number of genes differentially expressed between male and female embryos at a very early stage (Hamburger and Hamilton stage 4), long before any sexual differentiation occurs. Most of these genes are located on the Z chromosome, which indicates that dosage compensation is ineffective in early chicken embryos. Gene ontology analyses using an enhanced annotation tool for Affymetrix probesets of the chicken genome shows that among the male-biased genes found on the Z chromosome, more than 20 genes have a role in sex differentiation.

2009-05-13 | GSE16064 | GEO

Transcriptional profiling by array of chick embryonic tissues: gastrulation, neural tube/notochord and limb development.

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

Single-cell sequencing of stage 4 chicken embryos

Project description:Abstract from Vermillion et al: During vertebrate development, progenitor cells give rise to tissues and organs through a complex choreography that commences at gastrulation. A hallmark event of gastrulation is the formation of the primitive streak, a linear assembly of cells along the anterior-posterior (AP) axis of the developing organism. To examine the primitive streak at a single-cell resolution, we measured the transcriptomes of individual chick cells from the streak or the surrounding tissue (the rest of the area pellucida) in Hamburger-Hamilton stage 4 embryos. The single-cell transcriptomes were then ordered by the statistical method Wave-Crest to deduce both the relative position along the AP axis and the prospective lineage of single cells. The ordered transcriptomes reveal intricate patterns of gene expression along the primitive streak.

2018-04-18 | GSE89910 | GEO

Expression Profile of Chicken Primitive Streak (HH4) Tissues

Project description:In birds and mammals, all mesoderm cells are generated from the primitive streak. Nascent mesoderm cells contain unique dorso-ventral (D/V) identities depending on their relative ingression position along the streak. Molecular mechanisms controlling this initial phase of mesoderm diversification are not well-understood. Using chick model, we generated high-quality transcriptomic datasets of different streak regions and analyzed their molecular heterogeneity. Streak tissues were dissected from stage-matched HH4 chick embryos and were further divided into four equal pieces along its anterio-posterior length (termed “A”, “B”, “C” and “D”, with “A” representing most anterior and therefore most dorsal and “D” most posterior and therefore most ventral). Each of the four regions was represented by three independent samples (n=3), with each sample containing 5-7 μg total RNA derived from 85-93 pooled pieces. 5 μg of RNA from each sample were used to screen Affymetrix Chicken Genome Array without an amplification step.

2010-07-29 | E-GEOD-22230 | biostudies-arrayexpress

Chicken neural crest and neural plate

Project description:Neural cest cells are a transient stem cell-like population appearing during vertebrate embryonic development. Generation of the cranial neural crest is known to require a balanced combination of FGF and BMP levels. However, it is poorly understood how the functions of such growth factors are controlled in the extracellular spaces. Here we identifiy the extracelluar matrix protein anosmin (Gga.14976.1.S1_at, clone ChEST132d10) as a novel molecule synthesized locally in the cranial neural crest of chicken embryos. Cranial neural folds (NF) and ventral neural plates (NP) were dissected from Hamburger & Hamilton stage 8 (HH8) embryos (80 to 14 embryos, n=4), and total RNA was analyzed using a GeneChip chicken genome arrays (Affymetrix)

2012-05-31 | E-GEOD-38381 | biostudies-arrayexpress

scRNA-Seq analysis of differentiation to primitive streak fate of mouse embryonic stem cells

Project description:scRNA-Seq analysis of differentiation to primitive streak fate of mouse embryonic stem cells

2022-01-20 | E-MTAB-10243 | biostudies-arrayexpress

Gallus gallus

Project description:Sex-dimorphic gene expression and ineffective dosage compensation of Z-linked genes in gastrulating chicken embryos

| PRJNA115485 | ENA

Gallus gallus Control Versus SU5402, LY294002 or U0126 Treated Preingression Epiblast from Gastrula Stage Embryos

Project description:Transcriptional profiling of the preingression epiblast versus lateral epiblast, of preingression epiblast from control embryos treated with the DMSO carrier vehicle (0.5%) versus embryos treated with SU5402, U0126 or LY294002. Embryos were stages 5-6 at time of tissue isolation. The preingression epiblast (E2 region) is the region of epiblast just lateral to the primitive streak. Lateral epiblast is the E3 region. Two condition experiment. Samples for each condition isolated from at least 30 embryos. The experiments used isolated preingression epiblast, which is defined as the region of epiblast adjacent to the primitive streak that will ingress through the primitive streak. Preingression epiblast was isolated by microdissection using tungsten needles from control embryos or embryos treated with SU5402, U0126 or LY294002.

2011-02-20 | E-GEOD-27403 | biostudies-arrayexpress

Chicken versus Quail

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

Duck versus Chicken

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

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