Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Molecular dissection of the migrating posterior lateral line primordium during early development in zebrafish

ABSTRACT: The posterior lateral line system in zebrafish involves cell migration, proliferation and differentiation into mechanosensory cells. During development, a group of cranial placodal cells delaminate and become a coherent, migratory primordium that traverses the length of the fish to form this sensory system. As they migrate, the primordium deposits groups of cells called neuromasts, the specialized organs that contain the mechanosensory hair cells. The lateral line hair cells of fish are related to inner ear hair cells; therefore the primordium provides both a model for studying collective directional cell migration and the differentiation of sensory cells from multipotent progenitor cells. Through the combination of transgenic fish, Fluorescence Activated Cell Sorting and microarray analysis we identified a repertoire of key genes expressed in the migrating primordium and in differentiated neuromasts. We validated the specific expression in the primordium of a subset of the identified sequences by quantitative RT-PCR, and by in situ hybridization. We also show that interfering with the function of f11r and cd9b induces defects in its migratory behavior. Finally, pathway construction revealed functional relationships among the genes enriched in the migrating cell population. Our results demonstrate that this is a robust approach to globally analyze specific expression and we predict that many of the genes identified in this study will show critical functions in developmental and tumor progression process relating to posterior lateral line development.

ORGANISM(S): Danio rerio

PROVIDER: GSE25617 | GEO | 2010/12/15

SECONDARY ACCESSION(S): PRJNA133961

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Molecular dissection of the migrating posterior lateral line primordium during early development in zebrafish

Project description:The posterior lateral line system in zebrafish involves cell migration, proliferation and differentiation into mechanosensory cells. During development, a group of cranial placodal cells delaminate and become a coherent, migratory primordium that traverses the length of the fish to form this sensory system. As they migrate, the primordium deposits groups of cells called neuromasts, the specialized organs that contain the mechanosensory hair cells. The lateral line hair cells of fish are related to inner ear hair cells; therefore the primordium provides both a model for studying collective directional cell migration and the differentiation of sensory cells from multipotent progenitor cells. Through the combination of transgenic fish, Fluorescence Activated Cell Sorting and microarray analysis we identified a repertoire of key genes expressed in the migrating primordium and in differentiated neuromasts. We validated the specific expression in the primordium of a subset of the identified sequences by quantitative RT-PCR, and by in situ hybridization. We also show that interfering with the function of f11r and cd9b induces defects in its migratory behavior. Finally, pathway construction revealed functional relationships among the genes enriched in the migrating cell population. Our results demonstrate that this is a robust approach to globally analyze specific expression and we predict that many of the genes identified in this study will show critical functions in developmental and tumor progression process relating to posterior lateral line development. The experiment was performed in two developmental stages, 36 and 48 hours post-fertilization. Two-condition experiment, GFP- (negative control) and GFP+ cells. Two biological repeats by stage, each by quadruplicate including a dye swap.

2010-12-15 | E-GEOD-25617 | biostudies-arrayexpress

Transcriptional profiling of setb morphants

Project description:We have characterised the zebrafish ortholog, setb, and investigated its role in embryogenesis. Phylogenetic analysis showed that zebrafish Setb has an amino acid sequence identity of approximately 96% with the mammalian orthologs. Whole mount immunofluorescence analysis revealed that Setb is expressed mainly in the eye, the lateral line neuromasts and the olfactory pit. Knockdown of setb using antisense morpholino oligonucleotides resulted in increased apoptosis, reduced cell proliferation and severe morphological defects. The morphant phenotypes were partially rescued when setb MO1 was co-injected with human set mRNA. In vivo labelling of hair cells in the lateral line of setb morphants with the vital fluorescent dye FM1-43 showed a significant decreased number of functional neuromasts. Gene expression analysis of setb morphants, employing DNA microarrays revealed a role of Setb in neurogenesis and the mechanosensory lateral line system. 48hpf control morpholino- and setb MO1-injected embryos in triplicates

2016-06-01 | E-GEOD-70049 | biostudies-arrayexpress

Insights into electrosensory organ development, physiology and evolution from a lateral line organ-enriched transcriptome

Project description:The anamniote lateral line system, comprising mechanosensory neuromasts and electrosensory ampullary organs, is a useful model for investigating the developmental and evolutionary diversification of different organs and cell types. Zebrafish neuromast development is increasingly well understood, but neither zebrafish nor Xenopus is electroreceptive and our molecular understanding of ampullary organ development is rudimentary. We have used RNA-seq to generate a lateral line-enriched gene-set from late-larval paddlefish (Polyodon spathula). Validation of a subset reveals expression in developing ampullary organs of transcription factor genes critical for hair cell development, and genes essential for glutamate release at hair cell ribbon synapses, suggesting close developmental, physiological and evolutionary links between non-teleost electroreceptors and hair cells. We identify an ampullary organ-specific proneural transcription factor, and candidates for the voltage-sensing L-type Cav channel and rectifying Kv channel predicted from skate (cartilaginous fish) ampullary organ electrophysiology. Overall, our results illuminate ampullary organ development, physiology and evolution.

2017-03-27 | GSE92470 | GEO

Transcriptional profiling of setb morphants

2016-06-01 | GSE70049 | GEO

Adaptive cell invasion maintains organ homeostasis

Project description:Mammalian inner ear and fish lateral line sensory hair cells depend on fluid motion to transduce environmental signals and elicit a response. In mammals, actively maintained ionic homeostasis of the cochlear and vestibular fluid (endolymph) is essential for hair cell function and numerous mammalian hearing and vestibular disorders arise from disrupted endolymph ion homeostasis. Lateral line hair cells, however, are openly exposed to the aqueous environment with fluctuating ionic composition. How sensory transduction in the lateral line is maintained during environmental changes of ionic composition is not fully understood. Using lineage labeling, in vivo time lapse imaging and scRNA-seq, we discovered highly motile skin-derived cells that invade mature mechanosensory organs of the zebrafish lateral line and differentiate into Neuromast-associated (Nm) ionocytes. Furthermore, the invasive behavior is adaptive as it is triggered by drastic fluctuations in environmental stimuli. Our findings challenge the notion of an entirely placodally-derived lateral line and identify Nm ionocytes as likely regulators of mechanosensory hair cell function possibly by modulating the ionic microenvironment. The discovery of lateral line ionocytes provides an experimentally accessible in vivo system to study cell invasion and migration, as well as the physiological adaptation of vertebrate organs to changing environmental conditions.

2021-03-11 | GSE168695 | GEO

Danio rerio

Project description:Molecular dissection of the migrating posterior lateral line primordium during early development in zebrafish

| PRJNA133961 | ENA

Single-cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes

Project description:A major cause of human deafness and vestibular dysfunction is permanent loss of the mechanosensory hair cells of the inner ear. In non-mammalian vertebrates such as zebrafish, regeneration of missing hair cells can occur throughout life. While a comparative approach has the potential to reveal the basis of such differential regenerative ability, the degree to which the inner ears of fish and mammals share common hair and supporting cell types remains unresolved. Here we perform single-cell RNA sequencing of the zebrafish inner ear at embryonic through adult stages to catalog the diversity of hair and non-sensory supporting cells. We identify a putative progenitor population for hair and supporting cells, as well as distinct hair and supporting cell types in the maculae versus cristae. The hair and supporting cell types differ from those described for the lateral line, a distributed mechanosensory organ in zebrafish in which most studies of hair cell regeneration have been conducted. In the maculae, we identify two subtypes of hair cells that share gene expression with mammalian striolar or extrastriolar hair cells. In situ hybridization reveals that these hair cell subtypes occupy distinct spatial domains within the two major macular organs, the utricle and saccule, consistent with the reported distinct electrophysiological properties of hair cells within these domains. These findings suggest that primitive specialization of spatially distinct striolar and extrastriolar hair cells likely arose in the last common ancestor of fish and mammals. The similarities of inner ear cell type composition between fish and mammals also support using zebrafish as a relevant model for understanding inner ear-specific hair cell function and regeneration.

2023-01-04 | GSE211728 | GEO

Gene expression analysis of hair cell regeneration in the zebrafish lateral line

Project description:Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However, non-mammalian animals (e.g. birds, amphibian and fish) regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates, we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA-Seq analyses on regenerating support cells purified by fluorescence activated cell sorting (FACS). The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration, because these cells can be acutely killed by exposure to neomycin, after which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. Tg(sqET20) larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 days post fertilization (dpf) Tg(sqET20) larvae at 1, 3 and 5 hours post neomycin treatment, as well as from a non-treated control. Transgenic zebrafish Tg(sqET20) larvae at 5 days post fertilization were exposed to neomycin, dissociated, and FACS sorted into GFP positive and GFP negative populations at 1, 3, and 5 hours following treatment, along with a mock treated 1 hr control. The experiment was performed in triplicate, for a total of 24 samples.

2014-03-26 | E-GEOD-56176 | biostudies-arrayexpress

Gene expression analysis of hair cell regeneration in the zebrafish lateral line

2014-03-26 | GSE56176 | GEO

Epithelial planar bipolarity emerges from Notch- mediated asymmetric inhibition of Emx2

Project description:This dataset consists of single-cell RNA-seq (mcSCRBseq) data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral-line neuromast hair cells were isolated by fluorescence activated cell sorting (FACS) from the dissociated trunks of wild type and Emx2-mutant Tg[myo6b:actb1-EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair-cell progenitors (UHCPs).

2020-03-05 | GSE143663 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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