An atlas of small non-coding RNAs in Human Preimplantation Development [Small-Seq]
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PROVIDER: PRJNA1050220 | ENA |
REPOSITORIES: ENA
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Project description:An atlas of small non-coding RNAs in Human Preimplantation Development
| PRJNA1050210 | ENA
Project description:An atlas of small non-coding RNAs in Human Preimplantation Development [RNA-seq]
| PRJNA1049378 | ENA
Project description:An atlas of small non-coding RNAs in Human Preimplantation Development (Mouse embryo RNA-seq)
| PRJNA1138744 | ENA
Project description:Our current understanding of the molecular circuitries that govern early embryogenesis remains limited, particularly in the human. Small non-coding RNAs (sncRNAs) regulate gene expression transcriptionally and post-transcriptionally, however, the expression of specific biotypes and their dynamics during preimplantation development remains to be determined. Using Small-seq, we identified the abundance of and dynamic expression of piRNA, rRNA, snoRNA, tRNA, and miRNA in human embryos from day 3 to 7. Among the biotypes, both miRNA and snoRNA displayed distinct associations with developmental time and lineage formation, many of which were found to target key gene expression programs in pluripotency and lineage establishment. We observed an enrichment of the chromosome 19 miRNA cluster (C19MC) in the trophectoderm (TE), and the chromosome 14 miRNA cluster (C14MC) and MEG8-related snoRNAs in the inner cell mass (ICM). Additionally, isomiR analyses suggested miRNAs are modified differentially during blastulation. Finally, six novel miRNAs and their embryo gene targets we identified. Our analyses provide the first comprehensive measure of sncRNA biotypes and their corresponding dynamics throughout human preimplantation development, providing an extensive resource. Elucidating the functional roles of sncRNAs during preimplantation development will provide insight into the establishment of the blastocyst and exit from pluripotency. Further, better understanding the miRNA regulatory programs in human embryogenesis will inform strategies to improve embryo development and outcomes of assisted reproductive technologies. We anticipate broad usage of our data as a resource for studies aimed at understanding embryogenesis, optimising stem cell-based models, assisted reproductive technology, and stem cell biology.
2024-09-06 | GSE249708 | GEO
Project description:Our current understanding of the molecular circuitries that govern early embryogenesis remains limited, particularly in the human. Small non-coding RNAs (sncRNAs) regulate gene expression transcriptionally and post-transcriptionally, however, the expression of specific biotypes and their dynamics during preimplantation development remains to be determined. Using Small-seq, we identified the abundance of and dynamic expression of piRNA, rRNA, snoRNA, tRNA, and miRNA in human embryos from day 3 to 7. Among the biotypes, both miRNA and snoRNA displayed distinct associations with developmental time and lineage formation, many of which were found to target key gene expression programs in pluripotency and lineage establishment. We observed an enrichment of the chromosome 19 miRNA cluster (C19MC) in the trophectoderm (TE), and the chromosome 14 miRNA cluster (C14MC) and MEG8-related snoRNAs in the inner cell mass (ICM). Additionally, isomiR analyses suggested miRNAs are modified differentially during blastulation. Finally, six novel miRNAs and their embryo gene targets we identified. Our analyses provide the first comprehensive measure of sncRNA biotypes and their corresponding dynamics throughout human preimplantation development, providing an extensive resource. Elucidating the functional roles of sncRNAs during preimplantation development will provide insight into the establishment of the blastocyst and exit from pluripotency. Further, better understanding the miRNA regulatory programs in human embryogenesis will inform strategies to improve embryo development and outcomes of assisted reproductive technologies. We anticipate broad usage of our data as a resource for studies aimed at understanding embryogenesis, optimising stem cell-based models, assisted reproductive technology, and stem cell biology.
2024-09-06 | GSE249493 | GEO
Project description:Our current understanding of the molecular circuitries that govern early embryogenesis remains limited, particularly in the human. Small non-coding RNAs (sncRNAs) regulate gene expression transcriptionally and post-transcriptionally, however, the expression of specific biotypes and their dynamics during preimplantation development remains to be determined. Using Small-seq, we identified the abundance of and dynamic expression of piRNA, rRNA, snoRNA, tRNA, and miRNA in human embryos from day 3 to 7. Among the biotypes, both miRNA and snoRNA displayed distinct associations with developmental time and lineage formation, many of which were found to target key gene expression programs in pluripotency and lineage establishment. We observed an enrichment of the chromosome 19 miRNA cluster (C19MC) in the trophectoderm (TE), and the chromosome 14 miRNA cluster (C14MC) and MEG8-related snoRNAs in the inner cell mass (ICM). Additionally, isomiR analyses suggested miRNAs are modified differentially during blastulation. Finally, six novel miRNAs and their embryo gene targets we identified. Our analyses provide the first comprehensive measure of sncRNA biotypes and their corresponding dynamics throughout human preimplantation development, providing an extensive resource. Elucidating the functional roles of sncRNAs during preimplantation development will provide insight into the establishment of the blastocyst and exit from pluripotency. Further, better understanding the miRNA regulatory programs in human embryogenesis will inform strategies to improve embryo development and outcomes of assisted reproductive technologies. We anticipate broad usage of our data as a resource for studies aimed at understanding embryogenesis, optimising stem cell-based models, assisted reproductive technology, and stem cell biology.
2024-09-06 | GSE272793 | GEO
Project description:Small RNAs, including microRNAs (miRNAs), phased secondary small interfering RNAs (phasiRNA), and heterochromatic small interfering RNAs (hc-siRNA) are an essential component of gene regulation. To establish a broad potato small RNA atlas, we constructed an expression atlas of leaves, flowers, roots, and tubers of Desiree and Eva, which are commercially important potato (Solanum tuberosum) cultivars. All small RNAs identified were observed to be conserved between both cultivars, supporting the hypothesis that small RNAs have a low evolutionary rate and are mostly conserved between lineages. However, we also found that a few miRNAs showed differential accumulation between the two potato cultivars, and that hc-siRNAs have a tissue specific expression. We further identified dozens of reproductive and non-reproductive phasiRNAs originating from coding and noncoding regions that appeared to exhibit tissue-specific expression. Together, this study provides an extensive small RNA profiling of different potato tissues that might be used as a resource for future investigations.
2022-11-11 | GSE213986 | GEO
Project description:Small non-coding RNA organ expression atlas
| PRJNA686442 | ENA
Project description:An atlas of small RNAs from potato
| PRJNA883416 | ENA
Project description:The human transcriptome consists of various RNA biotypes including multiple types of non-coding RNAs (ncRNAs). Current ncRNA compendia remain incomplete partially because they are almost exclusively derived from the interrogation of small- and polyadenylated RNAs. Here, we present a more comprehensive atlas of the human transcriptome that is derived from matching polyA-, total-, and small-RNA profiles of a heterogenous collection of nearly 300 human tissues and cell lines. We report thousands of novel RNA species across all major RNA biotypes, including a hitherto poorly-cataloged class of non-polyadenylated single-exon long non-coding RNAs. In addition, we exploit intron abundance estimates from total RNA-sequencing to predict the regulatory potential of various non-coding RNAs. Our study represents a substantial expansion of the current catalogue of human ncRNAs and their regulatory interactions. All data and results are accessible through the R2 webtool and serve as a basis to further explore RNA biology and function.
2021-04-15 | GSE138734 | GEO