Sequencing and de novo analysis of Oviductus Ranae initial growth transcriptome using Illumina RNA-Seq Technology
Ontology highlight
ABSTRACT:
ORGANISM(S): Rana chensinensis
SUBMITTER: Yu Zhao
PROVIDER: E-MTAB-936 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:To obtain an overview of the Oviductus Ranae gene expression profile during hibernation, a cDNA sample was prepared from Oviductus Ranae and sequenced using the Illumina sequencing platform.
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Project description:We report the use of RNA-seq data to assemble transcriptional units of adult Anopheles funestus female mosquitoes. We also analyzed expression levels and protein divergence and discovered SNPs.
2010-12-01 | GSE21977 | GEO
Project description:Anopheles funestus is one of the primary vectors of human malaria, which causes a million deaths each year in sub-Saharan Africa. Few scientific resources are available to facilitate studies of this mosquito species and relatively little is known about its basic biology and evolution, making development and implementation of novel disease control efforts more difficult. The An. funestus genome has not been sequenced, so in order to facilitate genome-scale experimental biology, we have sequenced the adult female transcriptome of An. funestus from a newly founded colony in Burkina Faso, West Africa, using the Illumina GAIIx next generation sequencing platform.We assembled short Illumina reads de novo using a novel approach involving iterative de novo assemblies and "target-based" contig clustering. We then selected a conservative set of 15,527 contigs through comparisons to four Dipteran transcriptomes as well as multiple functional and conserved protein domain databases. Comparison to the Anopheles gambiae immune system identified 339 contigs as putative immune genes, thus identifying a large portion of the immune system that can form the basis for subsequent studies of this important malaria vector. We identified 5,434 1:1 orthologues between An. funestus and An. gambiae and found that among these 1:1 orthologues, the protein sequence of those with putative immune function were significantly more diverged than the transcriptome as a whole. Short read alignments to the contig set revealed almost 367,000 genetic polymorphisms segregating in the An. funestus colony and demonstrated the utility of the assembled transcriptome for use in RNA-seq based measurements of gene expression.We developed a pipeline that makes de novo transcriptome sequencing possible in virtually any organism at a very reasonable cost ($6,300 in sequencing costs in our case). We anticipate that our approach could be used to develop genomic resources in a diversity of systems for which full genome sequence is currently unavailable. Our An. funestus contig set and analytical results provide a valuable resource for future studies in this non-model, but epidemiologically critical, vector insect.
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Project description:BackgroundRNA-Seq data is inherently nonuniform for different transcripts because of differences in gene expression. This makes it challenging to decide how much data should be generated from each sample. How much should one spend to recover the less expressed transcripts? The sequencing technology used is another consideration, as there are inevitably always biases against certain sequences. To investigate these effects, we first looked at high-depth libraries from a set of well-annotated organisms to ascertain the impact of sequencing depth on de novo assembly. We then looked at libraries sequenced from the Universal Human Reference RNA (UHRR) to compare the performance of Illumina HiSeq and MGI DNBseq™ technologies.ResultsOn the issue of sequencing depth, the amount of exomic sequence assembled plateaued using data sets of approximately 2 to 8 Gbp. However, the amount of genomic sequence assembled did not plateau for many of the analyzed organisms. Most of the unannotated genomic sequences are single-exon transcripts whose biological significance will be questionable for some users. On the issue of sequencing technology, both of the analyzed platforms recovered a similar number of full-length transcripts. The missing "gap" regions in the HiSeq assemblies were often attributed to higher GC contents, but this may be an artefact of library preparation and not of sequencing technology.ConclusionsIncreasing sequencing depth beyond modest data sets of less than 10 Gbp recovers a plethora of single-exon transcripts undocumented in genome annotations. DNBseq™ is a viable alternative to HiSeq for de novo RNA-Seq assembly.
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Project description:The Mongolian gerbil (Meriones unguiculatus) is a member of the rodent family that displays several features not found in mice or rats, including sensory specializations and social patterns more similar to those in humans. These features have made gerbils a valuable animal for research studies of auditory and visual processing, brain development, learning and memory, and neurological disorders. Here, we report the whole gerbil annotated genome sequence, and identify important similarities and differences to the human and mouse genomes. We further analyze the chromosomal structure of eight genes with high relevance for controlling neural signaling and demonstrate a high degree of homology between these genes in mouse and gerbil. This homology increases the likelihood that individual genes can be rapidly identified in gerbil and used for genetic manipulations. The availability of the gerbil genome provides a foundation for advancing our knowledge towards understanding evolution, behavior and neural function in mammals. ACCESSION NUMBER: The Whole Genome Shotgun sequence data from this project has been deposited at DDBJ/ENA/GenBank under the accession NHTI00000000. The version described in this paper is version NHTI01000000. The fragment reads, and mate pair reads have been deposited in the Sequence Read Archive under BioSample accession SAMN06897401.
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Project description:PURPOSE Diseases that involve choroidal or retinal endothelial vascular cells are leading causes of vision loss: age-related macular degeneration, retinal ischemic vasculopathies and non-infectious posterior uveitis. Proteins differentially expressed by these endothelial cell populations are potential drug targets. We used deep proteomics to define the molecular phenotype of human choroidal and retinal endothelial cells at the protein level. METHODS Choroidal and retinal endothelial cells were separately isolated from 5 human eye pairs by selection on CD31. Total protein was extracted and digested, and peptide fractions were analysed by reverse-phase liquid chromatography tandem mass spectrometry. Peptide sequences were assigned to fragment ion spectra and proteins were inferred using public protein databases. Protein abundance was determined by spectral counting. Protein expression in choroidal versus retinal endothelial cells was compared using edgeR package in R, and annotation enrichment analysis was performed. RESULTS Human choroidal or retinal endothelial cells expressed 5042 non-redundant proteins. Setting the false discovery rate at 5%, 498 proteins (14.4%) of 3454 quantifiable proteins with minimum mean spectral counts of 2.5 were differentially expressed between cell populations. Choroidal and retinal endothelial cells were enriched in angiogenic proteins, and retinal endothelial cells were also enriched in immunologic proteins. CONCLUSIONS This work demonstrates the protein heterogeneity of human choroidal and retinal vascular endothelial cells and provides multiple candidates for further study as novel treatments or drug targets for posterior eye diseases.
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Project description:Sequencing and de novo analysis of Oviductus Ranae initial growth transcriptome using Illumina RNA-Seq Technology
| PRJEB2903 | ENA