Bos taurus
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR184141_1.fastq.gz | Fastqsanger.gz | |||
| DRR184141_2.fastq.gz | Fastqsanger.gz | |||
| DRR184142_1.fastq.gz | Fastqsanger.gz | |||
| DRR184142_2.fastq.gz | Fastqsanger.gz | |||
| DRR184143_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptome profiling of inner cell mass and trophectoderm in blastocyst in the bos taurus
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Project description:Lineage specification and X chromosome dosage compensation are two crucial biological processes that occur during preimplantation embryonic development. While these processes have been studied extensively in mice and humans, they are less understood in other species. This study aims to provide fundamental insights into bovine preimplantation development using single-cell RNA-sequencing. The study analyzes the transcriptomes of 286 individual cells and reveals that bovine trophectoderm/inner cell mass transcriptomes diverge at the early blastocyst stage, after cavitation but before blastocyst expansion. The study also identifies transcriptomic markers and provides the timing of lineage specification events in the bovine embryo. Moreover, the study confirms the occurrence of X chromosome dosage compensation from morula to middle blastocyst and reveals that this compensation results from downregulation of X-linked genes in female embryonic cells. The transcriptional atlas generated by this study is expected to be widely useful in improving our understanding of mammalian early embryo development.
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Project description:Blastocysts consist of cells that form the inner cell mass and the trophectoderm. The full transcriptome of bovine blastocyst embryos was examined in this study. Total RNA was isolated from three independent batches of blastocysts. Using Poly(A) capture mRNA was isolated and cDNA libraries prepared using Illumina TruSeq RNA sample Prep Kit. The libraries were sequenced using Illumina HiSeq 4000. This dataset should serve as a baseline for understanding bovine pluripotency and trophoblast stem cells providing a snapshot for functional interpretation of preimplantation embryo development.
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Project description:Gene expression profile of in vitro produced bovine blastocyst with and without Thyroid hormone supplementation
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Project description:Genes and signaling pathways involved in pluripotency have been studied extensively in mouse and human pre-implantation embryos and embryonic stem (ES) cells. The unsuccessful attempts to generate ES cell lines from other species including cattle suggests that other genes and pathways are involved in maintaining pluripotency in these species. To investigate which genes are involved in bovine pluripotency, expression profiles were generated from morula, blastocyst, trophectoderm and inner cell mass (ICM) samples using microarray analysis. As MAPK inhibition can increase the NANOG/GATA6 ratio in the inner cell mass, additionally blastocysts were cultured in the presence of a MAPK inhibitor and changes in gene expression in the inner cell mass were analyzed. Between morula and blastocyst 3,774 genes were differentially expressed and the largest differences were found in blastocyst up-regulated genes. Gene ontology (GO) analysis shows lipid metabolic process as the term most enriched with genes expressed at higher levels in blastocysts. Genes with higher expression levels in morulae were enriched in the RNA processing GO term. Of the 497 differentially expressed genes comparing ICM and TE the expression of NANOG, SOX2 and POU5F1 was indeed increased in the ICM confirming their evolutionary preserved role in pluripotency. Several genes implicated to be involved in differentiation or fate determination were also expressed at higher levels in the ICM. Genes expressed at higher levels in the ICM were enriched in the RNA splicing and regulation of gene expression GO term. Although NANOG expression was elevated upon MAPK inhibition, SOX2 and POU5F1 expression showed little increase. Expression of other genes in the MAPK pathway including DUSP4 and SPRY4, or influenced by MAPK inhibition such as IFNT, was affected. The data obtained from the microarray studies provide further insight in gene expression during bovine embryonic development. They show an expression profile in pluripotent cells that indicates a pluripotent but epiblast-like state. These data indicate that MAPK inhibition alone is not sufficient to maintain a pluripotent character in bovine cells. Microarrays used were bovine whole genome gene expression microarrays V2 (Agilent Technologies) representing 43,653 Bos taurus 60-mer oligos in a 4x44K layout. RNA samples from morula, blastocyst and dissected inner cell mass (ICM) and trophectoderm (TE) were compared in a common reference experiment design using 8 dual channel microarrays with each sample hybridized against an identical sample consisting of a pool of blastocysts total RNA. Within each group of two microarrays for each stage/tissue type, sample versus common reference hybridizations were performed in balanced dye-swap.
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