Xenopus tropicalis strain:Xtr
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ABSTRACT:
PROVIDER: PRJNA302326 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:RNA-seq technology was used to identify differentially localized transcripts from Xenopus laevis and Xenopus tropicalis stage VI oocytes. Besides the discovery of a group of novel animally enriched RNAs, this study revealed a surprisingly low conservation of vegetal RNA localization between the two frog species. mRNA profiles of Xenopus laevis and Xenopus tropicalis animal and vegetal oocyte halves were generated by RNA-seq technology. For Xenopus laevis, animal and vegetal oocyte RNA preparations from two different females were generated in duplicates. For Xenopus tropicalis, animal and vegetal oocyte RNA preparations from two different females were analyzed.
2015-12-09 | E-GEOD-58420 | biostudies-arrayexpress
Project description:High-throughput sequencing of small RNAs from Xenopus tropicalis (adult liver, adult skin, oocytes stage I, II, III, IV, V, VI). total RNA, ~18-42 nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH
2009-07-10 | GSE14952 | GEO
Project description:RNA-seq technology was used to identify differentially localized transcripts from Xenopus laevis and Xenopus tropicalis stage VI oocytes. Besides the discovery of a group of novel animally enriched RNAs, this study revealed a surprisingly low conservation of vegetal RNA localization between the two frog species.
2015-12-09 | GSE58420 | GEO
Project description:High-throughput sequencing of small RNAs from Xenopus tropicalis (adult liver, adult skin, oocytes stage I, II, III, IV, V, VI). total RNA, ~18-42 nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH Illumina/Solexa sequencing of adult liver, adult skin, oocytes stage I, II, III, IV, V, VI
2009-07-09 | E-GEOD-14952 | biostudies-arrayexpress
Project description:To compare nuclear and cytoplasmic RNA from a single cell type, free of cross-contamination, we studied the oocyte of the frog Xenopus tropicalis, a giant cell with an equally giant nucleus. We isolated RNA from manually dissected nuclei and cytoplasm of mature oocytes and subjected it to deep sequencing. Cytoplasmic mRNA 10 consisted primarily of spliced exons derived from ~6700 annotated genes. Nearly all of these genes were represented in the nucleus by intronic sequences. However, unspliced nascent transcripts were not detected. Inhibition of transcription or splicing for 1M-bM-^@M-^S2 d had little or no effect on the abundance of nuclear intronic sequences, demonstrating that they are unusually stable. RTM-bM-^@M-^SPCR analysis showed that these stable intronic sequences are transcribed from the coding strand and that a given intron can be processed into more than one 15 molecule. Stable intronic sequence RNA (sisRNA) from the oocyte nucleus constitutes a new class of noncoding RNA. sisRNA is detectable by RTM-bM-^@M-^SPCR in samples of total RNA from embryos up to the mid-blastula stage, when zygotic transcription begins. Storage of sisRNA in the oocyte nucleus and its transmission to the developing embryo suggest that it may play important regulatory roles during oogenesis and/or early embryogenesis. The individual germinal vesicle (GV) samples' log2 signals were compared pairwise with those from enucleated oocytes.
2012-11-26 | E-GEOD-41530 | biostudies-arrayexpress
Project description:Transposable elements comprise a large proportion of animal genomes. Transcripts of transposable elements are a source for the synthesis of endogenous siRNAs and piRNAs. In order to determine if small RNAs mapped to expressed Tc1-like elements are present during early Xenopus tropicalis development, we used Illumina (Solexa) to sequence small RNAs from gastrula-stage embryos. We obtained about 17 million reads that mapped perfectly to the genome. Small RNAs mapped to selected transposable elements were characterized and the expression of selected small RNAs was experimentally verified during development. This is the first deep sequencing experiment for small RNAs in the Xenopus tropicalis gastrula. Analysis of small RNAs expressed in the Xenopus tropicalis gastrula.
2011-06-18 | E-GEOD-30067 | biostudies-arrayexpress
Project description:Transposable elements comprise a large proportion of animal genomes. Transcripts of transposable elements are a source for the synthesis of endogenous siRNAs and piRNAs. In order to determine if small RNAs mapped to expressed Tc1-like elements are present during early Xenopus tropicalis development, we used Illumina (Solexa) to sequence small RNAs from gastrula-stage embryos. We obtained about 17 million reads that mapped perfectly to the genome. Small RNAs mapped to selected transposable elements were characterized and the expression of selected small RNAs was experimentally verified during development. This is the first deep sequencing experiment for small RNAs in the Xenopus tropicalis gastrula.
2011-06-18 | GSE30067 | GEO
Project description:High-throughput sequencing of small RNAs from Xenopus tropicalis
| PRJNA111817 | ENA
Project description:To compare nuclear and cytoplasmic RNA from a single cell type, free of cross-contamination, we studied the oocyte of the frog Xenopus tropicalis, a giant cell with an equally giant nucleus. We isolated RNA from manually dissected nuclei and cytoplasm of mature oocytes and subjected it to deep sequencing. Cytoplasmic mRNA 10 consisted primarily of spliced exons derived from ~6700 annotated genes. Nearly all of these genes were represented in the nucleus by intronic sequences. However, unspliced nascent transcripts were not detected. Inhibition of transcription or splicing for 1–2 d had little or no effect on the abundance of nuclear intronic sequences, demonstrating that they are unusually stable. RT–PCR analysis showed that these stable intronic sequences are transcribed from the coding strand and that a given intron can be processed into more than one 15 molecule. Stable intronic sequence RNA (sisRNA) from the oocyte nucleus constitutes a new class of noncoding RNA. sisRNA is detectable by RT–PCR in samples of total RNA from embryos up to the mid-blastula stage, when zygotic transcription begins. Storage of sisRNA in the oocyte nucleus and its transmission to the developing embryo suggest that it may play important regulatory roles during oogenesis and/or early embryogenesis.
2012-11-26 | GSE41530 | GEO