Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos

ABSTRACT: Here we report on genome-wide small RNA and transcriptome profiling of blastula, gastrula and neurula-stage Xenopus tropicalis embryos using deep sequencing. By combining bioinformatic analysis of the small RNA-seq dataset with experimental validation, we identify novel microRNAs and Piwi-interacting RNAs. We show that microRNA expression is highly dynamic and spatially localized in early embryos in contrast to Piwi-interacting RNAs, and we validate a novel microRNA prediction pipeline. We go on to identify a new class of small intronic non-coding RNAs, that we name sincRNAs. On a genome-wide scale we find that genes containing sincRNA clusters are transcriptionally repressed. Our data suggest a novel mechanism of sincRNA-mediated gene silencing in vertebrates.

ORGANISM(S): Xenopus tropicalis

PROVIDER: GSE38605 | GEO | 2013/09/23

SECONDARY ACCESSION(S): PRJNA168208

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos

Project description:Here we report on genome-wide small RNA and transcriptome profiling of blastula, gastrula and neurula-stage Xenopus tropicalis embryos using deep sequencing. By combining bioinformatic analysis of the small RNA-seq dataset with experimental validation, we identify novel microRNAs and Piwi-interacting RNAs. We show that microRNA expression is highly dynamic and spatially localized in early embryos in contrast to Piwi-interacting RNAs, and we validate a novel microRNA prediction pipeline. We go on to identify a new class of small intronic non-coding RNAs, that we name sincRNAs. On a genome-wide scale we find that genes containing sincRNA clusters are transcriptionally repressed. Our data suggest a novel mechanism of sincRNA-mediated gene silencing in vertebrates. Examination of small RNAs and mRNA at 3 stages of Xenopus embryonic development.

2013-09-23 | E-GEOD-38605 | biostudies-arrayexpress

High-throughput sequencing of small RNAs from chicken embryos

Project description:We applied Illumina sequencing to identify microRNAs (miRNAs) and piwi-interacting small RNAs (piRNAs) in the pre- and post-gastrula chicken embryos, and simultaneously obtain a comprehensive expression profile of miRNAs at diverse developmental stages. Discovery and characterization of small RNA species from pre-gastrula and post-gastrula chicken embryos through deep sequencing

2011-12-15 | E-GEOD-28668 | biostudies-arrayexpress

High-throughput sequencing of small RNAs from chicken embryos

2011-12-15 | GSE28668 | GEO

Whole embryo depletion of Taf15 in gastrula and neurula stage Xenopus tropicalis embryos

Project description:We examined the role of Taf15 in in gastrula and neurula stage Xenopus tropicalis embryos.

2021-07-24 | GSE180671 | GEO

Transcription profiling of Xenopus embryos from early blastula to early neurula stages

Project description:Gene expression was analysed in normally developing Xenopus laevis embryos from early blastula to early neurula stages

2009-03-01 | E-MEXP-2059 | biostudies-arrayexpress

Interactome analysis of Aedes aegypti PIWI proteins

Project description:PIWI-interacting (pi) RNAs are a class of small RNAs that have diverse functions in mosquitoes. In order to uncover novel components involved in biogenesis or function of the piRNA pathway in Aedes aegypti mosquitoes, we performed mass spectrometry analyses on immunoprecipitated PIWI proteins and their interactors.

2021-04-28 | PXD021382 | Pride

Proteomic and Transcriptomic Analysis of Neural Cell Fate in Developing Xenopus laevis Embryos and Explants

Project description:Purpose: Study the developing neural cell fate of the D1 blastomere in the 8-cell embryo. Determine what transcripts are dependant on cell/cell signaling and which are inherit to the single cell and do not depend on the rest of the embryo. Methods: D1 blastomere was either injected with fluorescent dye or explanted away from the developing embryo. Transcript profile was taken at 7 time points: 8-cell, 16-cell, 32-cell, blastula, gastrula, early neurula, and mid/late neurula. 3 biological triplicates were taken at each time point for both the dissect and explant condition. Results: Up until blastula stage, dissect and explant transcript profiles remain fairly similar. But following this the profiles completely diverge, with the dissect tissue heading towards the neural fate while the explant samples head towards an ectoderm/epithelial fate.

2021-01-01 | GSE147621 | GEO

Development of omic biomarkers for Fathead minnow larva (Pimephales promelas) exposed to ethinyl estradiol [non-coding small RNA]

Project description:This work aimed to expand the panel of gene expression-based biomarkers to include estrogens, to identify training strategies that maximize the range of applicable concentrations, and to evaluate the potential for two classes of small non-coding RNAs (sncRNAs), microRNA (miRNA) and piwi-interacting RNA (piRNA), as biomarkers.

2021-03-12 | GSE158857 | GEO

Analysis of small RNAs in piRNA pathway mutant mouse testes

Project description:Piwi-interacting RNAs are 25-32 nt small RNAs bound to Piwi proteins. To know the steps where factors involved in the piRNA biogenesis (MILI, MIWI2, ZUC (MitoPLD), MVH) work, we sequenced small RNAs from mutant mouse testes and analyzed piRNAs.

2010-05-27 | GSE20327 | GEO

Analysis of small RNAs in piRNA pathway mutant mouse testes

2010-05-27 | E-GEOD-20327 | biostudies-arrayexpress