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Validation of gene expression from rice locus (self-hybridization)

ABSTRACT: Transcription from 23K TIGR–loci were confirmed by full–length cDNA mapping, but other 33K TIGR–loci were not confirmed. However, it was not natural to think that full–length cDNA libraries was included almost rice genes, because the transcription of 3K CDS–ANE were confirmed by other transcriptome resources in TIGR OSA1. So, for detection of gene expression from FL–locus and TIGR–locus, we designed about 82K 60mer oligo probes based on TIGR Pseudomolecules release 2. However, TIGR–locus was revised according to revised Pseudomolecules and other additional transcriptome resources. Therefore designed 82K probes were re-mapped on TIGR4 ,and 63455 probes were mapped on 43090 locus Keywords: tissue type comparison

ORGANISM(S): Oryza sativa

PROVIDER: GSE7366 | GEO | 2007/11/28

SECONDARY ACCESSION(S): PRJNA100441

REPOSITORIES: GEO

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Project description:Whole-transcriptome gene-expression analyses are commonly performed in species that have a sequenced genome and for which microarrays are commercially available. To do such analyses in species with no or limited genome data, i.e. non-model organisms, necessary transcriptomics resources, i.e. an annotated transcriptome and a validated gene-expression microarray, must first be developed. The aim of the present study was to establish an advanced approach for developing transcriptomics resources for non-model organisms by combining next-generation sequencing (NGS) and microarray technology. We applied our approach to the non-biting midge Chironomus riparius, an ecologically relevant species that is widely used in sediment ecotoxicity testing. We sampled extensively covering all C. riparius developmental stages as well as toxicant exposed larvae and obtained from a normalized cDNA library 1.5 M NGS reads totalling 501 Mbp. Using the NGS data we developed transcriptomics resources in several steps. First, we designed 844 k probes directly on the NGS reads, as well as 76 k probes targeting expressed sequence tags of related species. These probes were tested for their affinity to C. riparius DNA and mRNA, by performing two biological experiments with a 1 M probe-selection microarray that contained the entire probe-library. Subsequently, the 1.5 M NGS reads were assembled into 23,709 isotigs and 135,082 singletons, which were associated to ~55 k, respectively, ~61 k gene ontology terms and which corresponded together to 22,593 unique protein accessions. An algorithm was developed that took the assembly and the probe affinities to DNA and mRNA into account, what resulted in 59 k highly-reliable probes that targeted uniquely 95% of the isotigs and 18% of the singletons. Concluding, our approach allowed the development of high-quality transcriptomics resources for C. riparius, and is applicable to any non-model organism. It is expected, that these resources will advance ecotoxicity testing with C. riparius as whole-transcriptome gene-expression analysis are now possible with this species.

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Validation of gene expression from rice locus (self-hybridization)

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