Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Discovery of genes involved in facial midline specification

ABSTRACT: 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.

ORGANISM(S): Gallus gallus

PROVIDER: GSE52227 | GEO | 2014/02/28

SECONDARY ACCESSION(S): PRJNA227186

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Discovery of genes involved in facial midline specification

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

Interactome of Human Embryo Implantation: Identification of Gene Expression Pathways, Regulation, and Integrated Regulatory Networks.

Project description:Possible interactions between endometrium and implanting embryo in humans

2011-12-16 | E-MEXP-3111 | biostudies-arrayexpress

Proteomic analysis of liver tissues in chicken embryo

Project description:To investigate the mechanisms of the defense system during chicken embryo development, protein profiling of liver tissues in chicken embryo at was conducted. TMT was used to analyze the liver tissues proteomes with significantly different activity of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) in chicken embryo.

2021-04-01 | PXD025137 | iProX

Comparative transcription profiling of mouse, chicken and zebrafish in the presomitic mesoderms to identify cyclic genes of the segmentation clock

Project description:4 microarray time series was generated to identify cyclic genes of the segmentation clock in the mouse (2 time series), the chicken and the zebrafish. The right posterior half presomitic mesoderms (PSM) from 20 mouse embryos, 18 chicken embryos and 21 zebrafish embryos were dissected while the contralateral side of the embryo containing the left PSM was immediately fixed to be analyzed by in situ hybridization using a Lfng (fot mosue and chicken) or hes7 (zebrafish) probe to order the samples along the segmentation clock oscillation cycle. Probes were produced from RNA extracted from each of the dissected posterior half PSMs using a two-step amplification protocol and were hybridized to Affymetrix GeneChip MOE430A, MOE430 2.0, Affymetrix GeneChip chicken genome array, or Affymetrix GeneChip zebrafish array.

2011-06-10 | E-MTAB-406 | biostudies-arrayexpress

Xenopus laevis

Project description:Single cell RNA-seq of regenerating hindlimbs that were implanted with FGF10-soaked beads

| PRJDB12234 | ENA

Chromatin profiling of Drosophila CNS subpopulations identifies active transcriptional enhancers

Project description:Transcriptional analysis of Drosophila CNS midline cells provides a useful system for studying transcriptional regulation at the genomic level due to a well-characterized set of midline-expressed genes and in vivo-validated enhancers. To investigate how access to regulatory information is controlled during midline cell development, we performed FAIRE-seq on FACS-purified midline cells. We find that regions of the genome with a strong midline FAIRE peak and weak whole-embryo FAIRE peak (“midline-enriched”) often correspond to midline enhancers near a midline-expressed gene and provides a useful predictive tool. Analysis of a large collection of midline enhancers revealed that those with a midline-enriched peak were located near midline-expressed genes, as were about half of the midline enhancers that overlapped a midline FAIRE peak that was not statistically "midline-enriched". There is a substantial fraction of midline enhancers that do not have a midline FAIRE peak and these tend to reside in chromatin regions that are not transcriptionally active and thus, unlikely to drive midline activity in vivo. This study emphasizes the utility of combining chromatin analysis of purified cell populations with gene expression and enhancer datasets to determine an experimentally useful chromatin profile that identifies biologically relevant enhancers and genes.

2016-10-18 | GSE83463 | GEO

Microarray analysis in senescent chicken embryo fibroblast

Project description:Transcriptional profiling of healthy chicken embryo fibroblast (CEF, P4) cells comparing senescent chicken embryo fibroblast (CEF, P18) cells. Goal was to identify differentially expressed genes comparing between healthy (P4) and senescent (P18) CEF cells.

2011-05-12 | GSE29258 | GEO

Differential gene expression in immortal DF-1 chicken embryo fibroblast cell line

Project description:Transcriptional profiling of chicken embryo fibroblast (CEF) cells comparing CEF derived immortal chicken embryo fibroblast cell line (DF-1). Goal was to determine differentially expressed genes of CEF which were changed responding DF-1.

2011-05-12 | GSE29257 | GEO

Deep Sequencing Analysis of miRNAs Expression in leg muscle of Xinghua Chicken

Project description:Purpose:We have used RNA-seq to examine of differentially expressed miRNAs in chicken leg muscle of three different development stages (11 embryo ages, 16 embryo ages, and 1 day old post hatch chick).The aims of this study are characterization of miRNAs differentially expressed in different developmental stage of chicken embryo, using RNA sequence sample. Methods: On this study we used two embryonic stage and one post hatch chick leg muscle of Xinghua chicken breed. Total RNA from E11 day embryo, E16 day embryo and 1 day post hatch chick was isolated by TRIzol following the manufacturer’s protocol (Invitrogen, CA, USA). Each stages were designed two samples, and the total samples were six (three group × two sample/group) and RNA samples of six individuals were pooled with equal amounts, and then were subjected to Illumina deep sequencing. Results: After eliminating adaptor and low-quality reads, a total of 5,302,700, 6,556,747, 5,359,793, 4,213,112, 7,112,885 and 7,469,939 clean reads were obtained in group E11 (E11.1-E11.2), group E16 (E16.1-E16.2) and group P1 (P1.1–P1.2) libraries, respectively. The clean reads were aligned to the chicken genome databases, miRBase, Rfam, RepBase and mRNA. Conclusions:To assess miRNA expression during chicken embryo skeletal muscle development, we sequenced and analyzed leg muscle at 11 day embryo age, 16 day embryo age, and 1 days post hatch.

2017-06-22 | GSE100321 | GEO

Transcriptional Profiling of Host Gene Expression in Chicken Embryo Lung Cells Infected with Laryngotracheitis Virus

Project description:Transcriptional profiling of chicken embryo lung cells infected infectious laryngotracheitis virus (ILTV) comparing control uninfected lung cells. Goal was to determine the changes of host gene expression by ILTV infection and host-virus interaction. Two-condition experiment, uninfected chicken embryo lung cells vs. infected chicken embryo lung cells. Biological replicates: 1 control uninfected sample, 1 infected experimental sample at each 1dpi, 3dpi, 5dpi, and 7 dpi.

2010-03-10 | E-GEOD-20630 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data