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RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development.

GSE37452 Xenopus tropicalis Expression profiling by high throughput sequencing 40 samples Submitted 2012/05/04 Platform GPL15472
Summary
We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. In total, we obtained over 900 million reads and the deep coverage allowed us to examine the transcriptome in detail. First, we found that ~150 genes are transcribed before embryonic genome activation when transcription is generally thought to be repressed. Second, we discovered thousands of novel splice junctions, the majority of which modify existing gene structures. Third, we curated a confident set of 6686 non-coding transcripts in 3859 genomic loci. Many of these non-coding RNAs are also developmentally regulated, which suggests that they may play important roles during embryogenesis. Finally, we found hundreds of contigs that cannot be aligned to the reference genome, which indicates that the current genome (XenTro3) is still unfinished. Our results will aid in the full assembly and annotation of the Xenopus tropicalis genome.
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Direct links to NCBI, no account and no request form: the whole study as GSE37452_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 40 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA160141 and SRA study SRP012375. Searching any of these in the dataset finder brings you back here.

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