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Comparative analysis of gene expression profiles between Nodal-overexpressing embryos with control embryos

ABSTRACT: A comprehensive search for downstream genes is necessary for understanding of functions of Nodal signaling in embryos of the ascidian Ciona intestinalis. The level of mRNA expression in Nodal-overexpressing embryos was compared with that in normal embryos at the late gastrula stage by a microarray analysis. Overexpression of Ci-nodal elevated the level of expression of 115 genes more than two-fold. These candidate target genes include those encoding transcription factors, proteins involved in cell-cell communication, and extracellular matrix components. Many of these genes were expressed in the neural plate at the late gastrula stage. Overexpression of nodal also affected the expression of genes involved in the planar cell polarity pathway and Wnt/Ca2+ pathway (prickle, Rho-like2, and PLC2), and delta1-protocadherin-like. Keywords: ascidian, Ciona intestinalis, Nodal, embryogenesis, gene expression profile

ORGANISM(S): Ciona intestinalis

PROVIDER: GSE14567 | GEO | 2010/01/26

SECONDARY ACCESSION(S): PRJNA111573

REPOSITORIES: GEO

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Comparative analysis of gene expression profiles between Nodal-overexpressing embryos with control embryos

Project description:A comprehensive search for downstream genes is necessary for understanding of functions of Nodal signaling in embryos of the ascidian Ciona intestinalis. The level of mRNA expression in Nodal-overexpressing embryos was compared with that in normal embryos at the late gastrula stage by a microarray analysis. Overexpression of Ci-nodal elevated the level of expression of 115 genes more than two-fold. These candidate target genes include those encoding transcription factors, proteins involved in cell-cell communication, and extracellular matrix components. Many of these genes were expressed in the neural plate at the late gastrula stage. Overexpression of nodal also affected the expression of genes involved in the planar cell polarity pathway and Wnt/Ca2+ pathway (prickle, Rho-like2, and PLC2), and delta1-protocadherin-like. Keywords: ascidian, Ciona intestinalis, Nodal, embryogenesis, gene expression profile two samples Dye Swap design with 2 arrays

2010-05-15 | E-GEOD-14567 | biostudies-arrayexpress

Ciona intestinalis (ascidian): control vs. TBT exposed

Project description:Transcriptional profiling of Ciona intestinalis comparing ethanol exposed asidian (control) with TBT exposed ascidian.

2010-07-20 | GSE22995 | GEO

Ciona intestinalis (ascidian): control vs. TBT exposed

Project description:Transcriptional profiling of Ciona intestinalis comparing ethanol exposed asidian (control) with TBT exposed ascidian. Two conditions experiment comparing ethanol exposed asidian (control) with TBT exposed ascidian.

2010-07-20 | E-GEOD-22995 | biostudies-arrayexpress

small RNA sequencing of two developmental stages of Ciona intestinalis

Project description:We report the comprehensive sequencing of small RNA libraries created from different developmental stages (larva and gastrula) of the basal chordate, Ciona intestinalis. These libraries were used for the identification of microRNAs in this organism. Sequencing of small RNA libraries from 2 stages of Ciona intestinalis.

2010-03-27 | E-GEOD-21078 | biostudies-arrayexpress

Comparative analysis of gene expression profiles between four kinds of blastomere at 8-cell stage embryos.

Project description:The establishment of body axes and specification of early embryonic cells depend on maternally supplied transcripts and/or proteins, several of which are localized at specific regions of fertilized eggs and early embryos. The ascidian is known to exhibit a mosaic mode of development, and this mode is largely dependent on localized maternal factors. Using blastomere isolation, microarray and whole-mount in situ hybridization, the present study of Ciona intestinalis demonstrates that maternal transcripts of a total of 17 genes are localized at the posterior-most region of fertilized eggs and early embryos. Ten of them are newly identified in the present study, while the remaining seven genes have already been characterized in the previous studies. In addition, maternal transcripts of two genes, in addition to 14 genes encoded by the mitochondrial genome, showed a mitochondria-like distribution. Despite the present comprehensive approach, we could not identify maternal transcripts that are clearly localized to the animal-pole side, the vegetal-pole side, the anterior-side or other specific regions of the early embryo. Therefore, we concluded that the posterior-most localization and mitochondria-like distribution appear to be major specialized patterns of maternal transcripts in the early Ciona embryos.

2009-04-17 | GSE15637 | GEO

Comparative analysis of gene expression profiles between four kinds of blastomere at 8-cell stage embryos.

2010-06-19 | E-GEOD-15637 | biostudies-arrayexpress

small RNA sequencing of two developmental stages of Ciona intestinalis

2010-03-27 | GSE21078 | GEO

ciHMX overexpression in Ciona intestinalis embryos

Project description:ciHMX overexpression in Ciona intestinalis embryos

| PRJNA591870 | ENA

ciHMX overexpression in Ciona intestinalis embryos

Project description:We recently showed HMX is expressed in bipolar tail neurons (BTN) in early embryos of Ciona intestinalis. In order to assess the function of the homeobox transcription factor in this cell fate, we used an overexpression strategy. ciHMX was overexpressed in the epidermis, followed by RNAseq of experimental and control embryos. We then looked for differential expression of BTN fate markers, testing if HMX is able to regulate BTN fate determination.

2021-11-26 | GSE141046 | GEO

Comparisons of transcriptome of Ciona intestinalis between eggs and 32-cell stage embryos to identify rapidly degrading maternal mRNA

Project description:A genome decoded chordate Ciona intestinalis is one of the suitable animal for analyzing genetic controls in early embryogenesis and zygotically expressed genes are especially intensely studied. However maternally expressed genes are less studied than zygotic ones because of their huge numbers. These microarray experiments were carried out to screen rapidly degrading mRNA to identify crucial maternal mRNAs for Ciona embryogenesis in relatively a short period before their degradation. Two samples (unfertilized eggs vs 32-cell stage embryos), two biological replicates, dye Swap design

2010-12-04 | E-GEOD-25817 | biostudies-arrayexpress

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