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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Comparison of animal-blastomeres' RNA content to vegetal-most half of vegetal blastomeres' RNA content at the 8-cell stage of Xenopus laevis embryos to identify animal-enriched transcripts

ABSTRACT: In Xenopus laevis, a number of studies identified vegetal factors that specify the germ line, endoderm and dorsal axis, but there are few studies demonstrating roles for animal-enriched maternal mRNAs. Therefore, we carried out a microarray analysis to identify novel maternal transcripts enriched in animal blastomeres. We sought to maximize differences between animal and vegetal samples. To that end, we dissected 8-cell embryos into animal blastomeres and vegetal blastomeres, and further dissected the vegetal blastomeres into vegetal-most halves (VP) and equatorial regions (discarded).

ORGANISM(S): Xenopus laevis

SUBMITTER: Sally Moody

PROVIDER: E-GEOD-48659 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Novel animal pole-enriched maternal mRNAs are preferentially expressed in neural ectoderm.

Grant Paaqua A PA Yan Bo B Johnson Michael A MA Johnson Diana L E DL Moody Sally A SA

Developmental dynamics : an official publication of the American Association of Anatomists 20131221 3

<h4>Background</h4>Many animals utilize maternal mRNAs to pre-pattern the embryo before the onset of zygotic transcription. In Xenopus laevis, vegetal factors specify the germ line, endoderm, and dorsal axis, but there are few studies demonstrating roles for animal-enriched maternal mRNAs. Therefore, we carried out a microarray analysis to identify novel maternal transcripts enriched in 8-cell-stage animal blastomeres.<h4>Results</h4>We identified 39 mRNAs isolated from 8-cell animal blastomeres ...[more]

PMID: 24155242

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Comparison of animal-blastomeres' RNA content to vegetal-most half of vegetal blastomeres' RNA content at the 8-cell stage of Xenopus laevis embryos to identify animal-enriched transcripts

Project description:In Xenopus laevis, a number of studies identified vegetal factors that specify the germ line, endoderm and dorsal axis, but there are few studies demonstrating roles for animal-enriched maternal mRNAs. Therefore, we carried out a microarray analysis to identify novel maternal transcripts enriched in animal blastomeres.

2013-12-21 | GSE48659 | GEO

The identification of differentially expressed genes between animal and vegetal blastomeres in Xenopus laevis

Project description:To identify asymmetrically localized maternal mRNAs along the animal-vegetal axis in cleavage Xenopus embryos, we isolated animal and vegetal blastomeres at 8-cell stage, extracted the maternal mRNA respectively and analyzed them by RNA-seq technology. We identified 43 maternal transcripts significantly enriched in the vegetal region (FDR<0.05) by R/Bioconductor package DESeq RNAseq of animal and vegetal blastomeres with 2 biological replicates

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The identification of differentially expressed genes between animal and vegetal blastomeres in Xenopus laevis

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2016-03-23 | E-MTAB-3321 | 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. Four kinds of sample. Two series comparison (A4.1+a4.2+b4.2 blastomeres vs B4.1 blastomeres and Animal blastomeres vs Vegetal blastomeres) were examined including dye swap analyses.

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Project description:Comparison of animal-blastomeres' RNA content to vegetal-most half of vegetal blastomeres' RNA content at the 8-cell stage of Xenopus laevis embryos to identify animal-enriched transcripts

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High Throughput Analysis Reveals Novel Maternal Germline RNAs Critical for PGC Preservation and Proper Migration

Project description:During oogenesis hundreds of RNAs are selectively localized to either the animal or vegetal cortical region. These maternal RNAs include determinants of both somatic and germline fates. Although microarray analysis has contributed to identifying localized determinants, it is not comprehensive and is limited to known transcripts. Here, we utilized high throughput RNA-sequencing analysis to comprehensively interrogate both animal and vegetal pole RNAs in the fully-grown Xenopus laevis oocyte. We identified 411 enriched RNAs at the vegetal pole, 198 of them annotated transcripts, and 27 RNAs enriched at the animal pole, 15 annotated. Of these, 90 were novel RNAs over 4-fold enriched at the vegetal pole and 6 over 10-fold at the animal pole. Unlike mRNAs, we found that microRNAs were not asymmetrically distributed. Whole mount in situ hybridization revealed all 17 selected RNAs were localized, confirming our data set. Biological function and network analysis of vegetally enriched transcripts identified protein-modifying enzymes, receptors, ligands, RNA binding proteins and 10 transcription factors or co-factors with 5 defining hubs linking 47 genes in a network. Initial functional studies of maternal vegetally-localized RNAs show, for the first time, that sox7 plays an important role in primordial germ cell (PGC) development and efnb1(ephrinB1), known to play important roles in migration/adhesion in the nervous system, is required for proper PGC migration. Based on our findings, we propose potential pathways operating at the vegetal pole that highlight where future investigations might be most fruitful.

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