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Transcriptional profiling of setb morphants

ABSTRACT: 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.

ORGANISM(S): Danio rerio

PROVIDER: GSE70049 | GEO | 2016/06/01

SECONDARY ACCESSION(S): PRJNA287537

REPOSITORIES: GEO

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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

Zebrafish embryos: hdac1 Morphants vs Standard control morphants

Project description:Transcriptional profiling of hdac1 morphant zebrafish embryos in comparison to standard control injected embryos. Embryos where injected at the one cell stage with either a translation blocking morpholino (Hdac1 ATG), splice blocking morpholino (Hdac1 Splice) or Hdac1 mismatch control morpholino (Hdac1 control). RNA was extracted and compared in a two-colour hybridisation to the comman reference Standard control morpholino injected embryos. Common reference experiment, hdac1 morphants vs. standard control morphants. Biological replicates: 2 (except Splice which was technical rather than biological)

2011-01-21 | E-GEOD-26708 | biostudies-arrayexpress

Zebrafish embryos: hdac1 Morphants vs Standard control morphants at 12, 18 and 27 hpf

Project description:Transcriptional profiling of hdac1 ATG morphant zebrafish embryos in comparison to standard control injected embryos. Embryos where injected at the one cell stage with either a translation blocking morpholino (Hdac1 ATG) or Standard control morpholino (StCo). RNA was extracted at 12, 18 and 27hpf from both sets of embryos and compared with a two-colour hybridisation. Timecourse experiment, hdac1 ATG morphants vs. standard control morphants. Biological replicates: 3

2011-01-21 | E-GEOD-26709 | biostudies-arrayexpress

Zebrafish embryos: hdac1 Morphants vs Standard control morphants

2011-01-21 | GSE26708 | GEO

Transcription profiling of zebrafish neuromasts to investigate the role of ERbeta2 in neuromasts development

Project description:The role of ERbeta2 in zebrafish larvae was investigated by injection of a Morpholino against ERbeta2. After 72hpf, the morphants showed a strong disruption in their sensory systems. ERbeta2 has been shown to be needed for the normal functioning of the sensory system organs, the neuromasts. The mechanisms involved in the neuromast disruption in ERbeta2 morphants was identified by microarrays gene screening. After comparison of two screening with low and high concentration of Morpholinos, genes that were present in the two microarrays screening were selected. The genes were then chosen by relevance for the mechanisms involved in the role of ERbeta2 in neuromast development. The ngn1 transcription factor, Notch3 and Notch1a showed to be up-regulated, also confirmed by in situ hybridization. The Notch signaling is known to be involved in cell fate in developing neuromasts. The overall conclusion is that ERbeta2 by interacting with the notch signaling pathways is critical for normal development of the neuromast of the lateral line in zebrafish. Experiment Overall Design: Zebrafish eggs until 4 cell stage were injected either with Morpholino blocking the translation ERbeta2 (ERbeta2 MO), either with a standard control Morpholino (coMO) at a concentration of 15uM. Two biological replicates for ERbeta2 MO, two replicates for coMO and two replicates for uninjected embryos (blank). A total of 6 samples were performed.

2008-10-26 | E-GEOD-13157 | biostudies-arrayexpress

Transcription profiling of zebrafish embryos to investigate the role of ERbeta2 in zebrafish neuromasts development - 50uM

Project description:The role of ERbeta2 in zebrafish larvae was investigated by injection of a Morpholino against ERbeta2. After 72hpf, the morphants showed a strong disruption in their sensory systems. ERbeta2 has been shown to be needed for the normal functioning of the sensory system organs, the neuromasts. The mechanisms involved in the neuromast disruption in ERbeta2 morphants was identified by microarrays gene screening. After comparison of two screening with low and hign concentration of Morpholinos, genes that were present in the two microarrays screening were selected. The genes were then chosen by relevance for the mechanisms involved in the role of ERbeta2 in neuromast development. The ngn1 transcription factor, Notch3 and Notch1a showed to be up-regulated, also confirmed by in situ hybridization. The Notch signaling is known to be involved in cell fate in developing neuromasts. The overall conclusion is that ERbeta2 by interacting with the notch signaling pathways is critical for normal development of the neuromast of the lateral line in zebrafish. Experiment Overall Design: Zebrafish eggs until 4 cell stage were injected either with Morpholino blocking the translation ERbeta2 (ERbeta2 MO), either with a standard control Morpholino (coMO) at a concentration of 50uM. Two biological replicates for ERbeta2 MO, two replicates for coMO and two replicates for uninjected embryos (blank). A total of 6 samples were performed.

2008-10-26 | E-GEOD-13158 | biostudies-arrayexpress

The role of ERbeta2 in zebrafish neuromasts development 15uM

2008-10-16 | GSE13157 | GEO

The role of ERbeta2 in zebrafish neuromasts development 50uM

Project description:The role of ERbeta2 in zebrafish larvae was investigated by injection of a Morpholino against ERbeta2. After 72hpf, the morphants showed a strong disruption in their sensory systems. ERbeta2 has been shown to be needed for the normal functioning of the sensory system organs, the neuromasts. The mechanisms involved in the neuromast disruption in ERbeta2 morphants was identified by microarrays gene screening. After comparison of two screening with low and hign concentration of Morpholinos, genes that were present in the two microarrays screening were selected. The genes were then chosen by relevance for the mechanisms involved in the role of ERbeta2 in neuromast development. The ngn1 transcription factor, Notch3 and Notch1a showed to be up-regulated, also confirmed by in situ hybridization. The Notch signaling is known to be involved in cell fate in developing neuromasts. The overall conclusion is that ERbeta2 by interacting with the notch signaling pathways is critical for normal development of the neuromast of the lateral line in zebrafish. Keywords: knock down experiment

2008-10-16 | GSE13158 | GEO

Zebrafish embryos: hdac1 Morphants vs Standard control morphants at 12, 18 and 27 hpf

2011-01-21 | GSE26709 | GEO

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

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