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||Tsukuba GeneTechnology Laboratories Inc (TGL)|
Phenotypes of organisms, including cancerous states, are the results of information in the genome. The genome information for those are currently investigated using GWAS based on SNP genotyping (DNA level), as well as microarray/real time PCR for gene expression (RNA level).
Lately, since the cost of SNP analysis has declined, 10-times more SNPs than those used a decade ago are being used for genotyping, leading to find more accurate loci responsible for the phenotypes. Concerning the gene expression analysis, with the progress of RNA sequencing technique, the analysis on a specific region of a gene using microarray/real time PCR has shifted to that on all region of the genes, i.e., all transcripts of respective genes (non-targeted analysis).
Tsukuba GeneTechnology Laboratories Inc (TGL) performs SNP genotyping of various species with TGL’s partner company, and conducts GWAS analysis using the genotyped data to elucidate loci responsible for phenotypes. TGL also provides the results of CLUSTER and STRUCTURE analyses.
Regarding the gene expression analysis, TGL performs RNA sequencing in the partner company, and conducts analysis of the sequence data with TopHat2/STAR at gene and/or exon level, then with Cufflinks/Cuffdiff, and finally with R-libraries. Through the analysis, we provide Scatter plot, Ma-plot, Volcano plot, Heatmap, Cluster map, and PCA plot. In addition, we provide expressions of exons in a given gene and spreadsheet including exon sequence for determination of real-time PCR primers.
Very soon, TGL will provide an analysis which elucidate difference of two genomes. For example, alterations of genome through passage of IPS cells will be clarified.
TGL is a venture company derived from University of Tsukuba and National Institute of Agrobiological Sciences and supported by both orgnizations.
Please feel free to ask us for further details.
Not only nucleotide and amino acid sequence, phenotype data (e.g. morphology) can be used for phylogenetic analysis.
For phylogenic tree construction, distance matrix method, maximum parsimony method, maximum likelihood method, and Baysian method have widely been used. We support all of these methods.
Currently, a sequence region suitable for in situ hybridization probe is quested in the open-reading frame or 3’UTR, and determined appropriately. However, transcriptome analysis based on RNA sequencing has revealed that various levels of exon expression are generated in a given gene.
Therefore, in order to obtain a significant result in in situ hybridization, the determination of the probe region is of utmost importance. We propose the candidate regions for probe(underlined with green), based on the customer’s thought.