Use of serial analysis of gene expression (SAGE) technology

Yamamoto, Mikio; Wakatsuki, Toru; Hada, Akiyuki; Ryo, Akihide

doi:10.1016/s0022-1759(01)00305-2

Cited by 155 publications

(97 citation statements)

References 62 publications

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“…The total tag number of our HCC SAGE library was smaller than that of normal liver. However, it was reported that the relative tag frequencies were not influenced by total tag size when the total tag counts were >10,000 and individual tag frequencies were >20 (34). Libraries of our size can represent highly expressed genes because biological variability seems to be greater than binomial sampling variability (28).…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of hepatitis B virus-associated small hepatocellular carcinoma by serial analysis of gene expression

Kim

Lee²,

Park³

et al. 2009

Int J Oncol

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Abstract. Serial analysis of gene expression (SAGE) is a sequence-based tool that enables quantitative study of comprehensive gene expression profiles. In this study, we generated a SAGE library of hepatitis B virus (HBV)-associated small hepatocellular carcinoma (HCC) and compared it with libraries of normal liver and other organs in order to identify genes which are specifically expressed in HBV-associated small HCC. A total of 18,107 SAGE tags were obtained from the HCC SAGE library. Among the 7,405 unique tags, 240 were significantly overexpressed in HCC compared to normal liver. Seventeen genes were unequivocally matched to SAGE tags which were up-regulated 15-fold or higher in HCC compared to normal liver: four genes (fatty acid desaturase 2, ·-L-2-fucosidase, testis-specific protein Y-encoded-like 2 and Gon-4-like) were significantly overexpressed in the HCC SAGE library compared to any other SAGE libraries of human normal tissues. The significance of these genes with respect to carcinogenesis and early diagnosis of HCC needs to be elucidated in further studies.

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Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of hepatitis B virus-associated small hepatocellular carcinoma by serial analysis of gene expression

Kim

Lee²,

Park³

et al. 2009

Int J Oncol

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“…Due to the use of oligo dT primers for reverse transcription, this method can only be used for the identification of mRNAs. [14,15] During the last few years, new, fast technologies for deep sequencing called next-generation sequencing (NGS) have come into focus. With this technology, whole genomes and transcriptomes can be sequenced in a short time.…”

Section: Available Methods For the Quantification Of Gene Expression mentioning

confidence: 99%

The physiological way: Monitoring RNA expression changes as new approach to combat illegal growth promoter application

Riedmaier

Pfaffl

Meyer

2012

Drug Testing and Analysis

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The use of growth-promoting agents in food-producing animals is forbidden in the European Union (EU). Therefore a strict control programme has been developed, detecting residues of all known growth-promoting agents using chromatographical methods in combination with mass spectrometry or immunoassays. New designed xenobiotic substances or hormone cocktails are difficult to identify with these methods and therefore the development of new sensitive test methods is important.A promising indirect approach is the detection of physiological effects of the administered growth promoters on the molecular level using 'omic' technologies. The analysis of the transcriptome on mRNA and miRNA level and thereby identifying biomarkers for the use of anabolic agents is one possible strategy for developing a new screening method. This paper describes the technologies available for gene expression profiling and summarizes the efforts made in the analysis of the transcriptome in order to identify potential gene expression biomarkers for the use of growth promoters in cattle.

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“…Total RNA was extracted from rice leaves 24 h after inoculation with M. grisea by an SDS-phenol extraction protocol (Datson et al, 1999;Munasinghe et al, 2001;Yamamoto et al, 2001). mRNAs containing polyA were isolated using Oligotex-dT column (Qiagen Inc.) as recommended by the manufacturer.…”

Section: Methodsmentioning

confidence: 99%

Gene Expression Profiling in Rice Infected with Rice Blast Fungus using SAGE

Kim¹,

Kim²,

Kim³

et al. 2008

The Plant Pathology Journal

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Rice blast disease, caused by the pathogenic fungus Magnaporthe grisea, is a serious issue in rice (Oryza sativa L.) growing regions of the world. Transcript profiling in rice inoculated with the fungus has been investigated using the transcriptomics technology, serial analysis of gene expression (SAGE). Short sequence tags containing sufficient information which are ten base-pairs representing the unique transcripts were identified by SAGE technology. We identified a total of 910 tag sequences via the GenBank database, and the resulting genes were shown to be up-regulated in all functional categories under the fungal biotic stress. Compared to the compatible interaction, the stress and defense genes in the incompatible interaction appear to be more up-regulated. Particularly, thaumatin-like gene (TLP) was investigated in determining the gene and protein expression level utilizing Northern and Western blotting analyses, resulting in an increase in both the gene and the protein expression level which arose earlier in the incompatible interaction than in the compatible interaction.Keywords : abiotic stress, Magnaporthe grisea, Oryza sativa, pathogenesis-related gene, rice blast, SAGE One of the most devastating diseases in rice, called rice blast, is caused by Magnaporthe grisea (Hamer and Talbot, 1998;Kim et al., 2001). The rice blast disease is a very serious and recurrent issue in rice-growing regions of the world (Talbot, 2003). The infection usually occurs on rice plant leaves where the fungal spores of M. grisea land and attach themselves using the fungal unique adhesive structure called an appressorium (Hamer et al., 1988) to penetrate rice leaf surface by building high turgor pressure (De Jong et al., 1997). Every year, the rice blast infection has the potential to affect the amount of harvested rice by which about sixty million people can be fed (Zeifler et al., 1994), generating significant economical and humanitarian issues in rice-growing areas. It has also been reported that some strains of the fungal M. grisea not only kill rice, but also attack other major cereals and grasses (Valent and Chumley, 1991).In an effort to remedy this agricultural crisis, finding the genes that are able to defend against the fungal biotic stress would be of great value. It is an obvious interest to determine which genes would be involved in the regulation and with what gene expression level in response to M. grisea infection. Transcriptomics can be used to determine the gene expression level of the messenger RNA (mRNA) in a given cell population. Transcriptomics is the study of the transcriptome, which is the set of all mRNA or transcripts produced in a population of cells. The transcriptome varies under stress conditions because all mRNA transcripts in a cell are a reflection of the genes that are being actively expressed under any stress conditions. Two technologies can be useful tools for transcriptomics. One of the technologies is microarray analysis, which utilizes labeled cDNAs hybridized to an array of DNA element...

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Use of serial analysis of gene expression (SAGE) technology

Cited by 155 publications

References 62 publications

Transcriptome analysis of hepatitis B virus-associated small hepatocellular carcinoma by serial analysis of gene expression

Transcriptome analysis of hepatitis B virus-associated small hepatocellular carcinoma by serial analysis of gene expression

The physiological way: Monitoring RNA expression changes as new approach to combat illegal growth promoter application

Gene Expression Profiling in Rice Infected with Rice Blast Fungus using SAGE

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