Project description:Candida tropicalis clinical isolate #12584 was exposed to auerobasidin A (50ng/ml), Randomly 30 adaptors (T12-T41) were selected. These adaptors as well as the parent were sequenced.
Project description:Candida tropicalis clinical isolate #12584 was spread on YPD plate supplemented with 40ng/ml of aureobasidin A. Randomly 18 adaptors were selected. Eight adaptors obtained tolerance. We sequenced the tolerant adaptors.
Project description:Candida tropicalis is an opportunistic pathogen which causes candidiasis in immune-compromised individuals. It is one of the members of the non-albicans group of Candida that are known to be azole resistant and is frequently seen in individuals being treated for cancers, HIV-infection and bone-marrow transplant. Although the genome of C. tropicalis was sequenced in the year 2009, the genome annotation has not been supported by experimental validation. In the present study, we have carried out in-depth proteomic profiling of C. tropicalis using high-resolution Fourier transform mass spectrometry and mapped ~44% of the computationally predicted protein-coding genes with peptide level evidence. In addition to identifying 2,740 proteins in the cell lysate of this yeast, we also analysed the proteome of the conditioned media of C. tropicalis culture and identified several unique secreted proteins among a total of 780 proteins. By subjecting the mass spectrometry data derived from cell lysate and conditioned media to proteogenomic analysis, we identified 86 novel genes, 12 novel exons and corrected 49 computationally predicted gene models. To our knowledge, this is the first high-throughput proteomic study to refine the genome annotation of C. tropicalis.
Project description:We collected small RNA sequencing data from brain and heart of an adult Xenopus tropicalis individual to investigate the conservation of site-specific miRNA editing events identified in mammals.
Project description: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. Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole
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.
Project description:RNA was isolated from Xenopus tropicalis rax mutants and wild type siblings. This was used to generate mutant and wild type RNA libraries for solexa sequencing. The sequencing data will be compared to isolate changes that may be caused by loss of rax activity. The RNA samples were extracted with Trizol, then were DNAse treated following the Invitrogen DNAse I protocol and re-precipitated with ethanol. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Project description:We collected small RNA sequencing data from brain and heart of an adult Xenopus tropicalis individual to investigate the conservation of site-specific miRNA editing events identified in mammals. Sequencing of 2 small RNA sequencing libraries