Affymetrix生物芯片解决方案概述.doc

Affymetrix生物芯片解决方案概述 Affymetrix公司作为全球销量第一的基因芯片厂家，以其完备的芯片设计，稳定可靠的分析结果和强大的生物信息学分析能力，帮助研究人员在最短的时间内获得大量可靠的结果，为后续研究提供重要的线索和帮助。Affymetrix公司目前已经在纳斯达克上市，在基因芯片领域中成为行业标准。 Affymetrix公司的巨大优势在于为客户提供“完整的基因芯片解决方案”，即提供全套的基因芯片相关产品。 包括：1. 性能优异、种类齐全的各类研究应用系列芯片产品；2. Affymetrix基因芯片相关试剂和试剂盒；3. 基因芯片杂交、洗涤、扫描检测仪器系统及相关分析软件工具；4. 基因芯片相关技术手册及使用指南等。 独特的原位光刻技术；独特的PM-MM探针设计；严密的质控步骤；种类齐全，应用广泛的基因芯片；强大的配套分析软件，强大的网上注释及分析工具；还有发表的研究论文和项目合作及技术培训，想要了解Affymetrix芯片最具特色的技术特点，详细资料请点击进入.Affymetrix生物芯片解决方案概述部分文章及链接（点击文章标题可以浏览全文）胚胎及成体干细胞表达谱分析 SCIENCE VOL302 2003Comment on Stemness: Transcriptional Profiling of Embryonic and Adult Stem Cells and A Stem Cell Molecular Signature (I)AbstractRamalho-Santos et al. (1) and Ivanova et al. (2), comparing the same three stem cells embryonic stem cells (ESCs); neural stem cells (NSCs), referred to as neural progenitor/stem cells (NPCs) in the present study; and hematopoietic stem cells (HSCs)with their differentiated counterparts, each identified a list of commonly expressed stemness genes, proposed to be important for conferring the functional characteristics of stem cells. The ability to capture expression profiles of cells using microarrays offers the possibility of defining a stem cell by its constellation of active genes. An intriguing question, however, is whether the functional commonalities (self-renewal and pluripotency) (3) among stem cells can be defined at the genetic level. Do all stem cells express a similar set of stemness genes necessary for their unique properties, or do different stem cells express different sets of genes that confer stemness?拟南芥基因组插入突变表达谱分析 SCIENCE VOL301 2003Genome-Wide Insertional Mutagenesis of Arabidopsis thalianaAbstractOver 225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space. The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 of the 29,454 predicted Arabidopsis genes. Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels. Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.寡核苷酸微阵列技术对结肠腺瘤、腺癌的基因表达谱分析 CancerResearch 61(7), 3124-30, 2001Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arraysAbstractUsing an oligonucleotide array containing sequences complementary to 3200 full-length human cDNAs and 3400 expressed sequence tags (GeneChip, Affymetrix), mRNA expression patterns were probed in 18 colon adenocarcinomas and 4 adenomas. Paired normal tissue was available and analyzed for each of the tumors. Relatively few changes in transcript expression are associated with colon cancer. Nineteen transcripts (0.48% of those detected) had at least 410.5-fold higher mRNA expression in carcinoma compared with paired normal samples, whereas 47 transcripts (1.3% of those detected) had at least 438-fold or lower expression in the tumor tissue compared with the normal samples. Some of these differences were confirmed by reverse transcription-PCR. Many of these transcripts were already known to be abnormally expressed in neoplastic tissue in general, or colon cancer in particular, and several of these differences were also observed in premalignant adenoma samples. A two-way hierarchical clustering algorithm successfully distinguished adenoma from adenocarcinoma and normal tissue, generating a phylogenetic tree that appropriately represented the clinical relationship between the three tissue types included in the analysis. This supports the concept that genome-wide expression profiling may permit a molecular classification of solid tumors.利用DNA微阵列监测药物代谢及毒理相关基因的表达 Physiological Genomics 5(4), 161-70, 2001Monitoring expression of genes involved in drug metabolism and toxicology using DNA microarrays.AbstractOligonucleotide DNA microarrays were investigated for utility in measuring global expression profiles of drug metabolism genes. This study was performed to investigate the feasibility of using microarray technology to minimize the long, expensive process of testing drug candidates for safety in animals. In an evaluation of hybridization specificity, microarray technology from Affymetrix distinguished genes up to a threshold of 90% DNA identity. Oligonucleotides representing human cytochrome P-450 gene CYP3A5 showed heterologous hybridization to CYP3A4 and CYP3A7 RNAs. These genes could be clearly distinguished by selecting a subset of oligonucleotides that hybridized selectively to CYP3A5. Further validation of the technology was performed by measuring gene expression profiles in livers of rats treated with vehicle, 3-methylcholanthrene (3MC), phenobarbital, dexamethasone, or clofibrate and by confirming data for six genes using quantitative RT-PCR. Responses of drug metabolism genes, including CYPs, epoxide hydrolases (EHs), UDP-glucuronosyl transferases (UGTs), glutathione sulfotransferases (GSTs), sulfotransferases (STs), drug transporter genes, and peroxisomal genes, to these well-studied compounds agreed well with, and extended, published observations. Additional gene regulatory responses were noted that characterize metabolic effects or stress responses to these compounds. Thus microarray technology can provide a facile overview of gene expression responses relevant to drug metabolism and toxicology.表达图谱分析揭示不同细胞遗传学背景下的急性粒细胞白血病的生物学本质的区别 11241129 PNAS January 30, 2001 vol. 98 no. 3Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogeneticsAbstractAcute myeloid leukemia (AML) is a heterogeneous group of diseases. Normal cytogenetics (CN) constitutes the single largest group, while trisomy 8 (+8) as a sole abnormality is the most frequent trisomy. How trisomy contributes to tumorigenesis is unknown. We used oligonucleotide-based DNA microarrays to study global gene expression in AML+8 patients with +8 as the sole chromosomal abnormality and AML-CN patients. CD34+ cells purified from normal bone marrow (BM) were also analyzed as a representative heterogeneous population of stem and progenitor cells. Expression patterns of AML patients were clearly distinct from those of CD34+ cells of normal individuals. We show that AML+8 blasts overexpress genes on chromosome 8, estimated at 32% on average, suggesting gene-dosage effects underlying AML+8. Systematic analysis by cellular function indicated up-regulation of genes involved in cell adhesion in both groups of AML compared with CD34+ blasts from normal individuals. Perhaps most interestingly, apoptosis-regulating genes were significantly down-regulated in AML+8 compared with AML-CN. We conclude that the clinical and cytogenetic heterogeneity of AML is due to fundamental biological differences.利用SNP微阵列进行小细胞肺癌的杂合性的丢失（LOH）分析 Nature Biotechnology 18(9), 1001-5, 2000Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arraysAbstractHuman cancers arise by a combination of discrete mutations and chromosomal alterations. Loss of heterozygosity (LOH) of chromosomal regions bearing mutated tumor suppressor genes is a key event in the evolution of epithelial and mesenchymal tumors. Global patterns of LOH can be understood through allelotyping of tumors with polymorphic genetic markers. Simple sequence length polymorphisms (SSLPs, or microsatellites) are reliable genetic markers for studying LOH, but only a modest number of SSLPs are used in LOH studies because the genotyping procedure is rather tedious. Here, we report the use of a highly parallel approach to genotype large numbers of single-nucleotide polymorphisms (SNPs) for LOH, in which samples are genotyped for nearly 1,500 loci by performing 24 polymerase chain reactions (PCR), pooling the resulting amplification products and hybridizing the mixture to a high-density oligonucleotide array. We characterize the results of LOH analyses on human small-cell lung cancer (SCLC) and control DNA samples by hybridization. We show that the patterns of LOH are consistent with those obtained by analysis with both SSLPs and comparative genomic hybridization (CGH), whereas amplifications rarely are detected by the SNP array. The results validate the use of SNP array hybridization for tumor studies.小肠内寄主与微生物之间共生关系的分子水平分析 Science 291(5505), 881-4, 2001Molecular analysis of commensal host-microbial relationships in the intestineAbstractHuman beings contain complex societies of indigenous microbes, yet little is known about how resident bacteria shape our physiology. We colonized germ-free mice with Bacteroides thetaiotaomicron, a prominent component of the normal mouse and human intestinal microflora. Global intestinal transcriptional responses to colonization were observed with DNA microarrays, and the cellular origins of selected responses were established by laser-capture microdissection. The results reveal that this commensal bacterium modulates expression of genes involved in several important intestinal functions, including nutrient absorption, mucosal barrier fortification, xenobiotic metabolism, angiogenesis, and postnatal intestinal maturation. These findings provide perspectives about the essential nature of the interactions between resident microorganisms and their hosts.生物时钟对拟南芥信号传导途径中相关基因的表达调控 Science 290(5499), 2110-3, 2000Orchestrated transcription of key pathways in Arabidopsis by the circadian clockAbstractLike most organisms, plants have endogenous biological clocks that coordinate internal events with the external environment. We used high-density oligonucleotide microarrays to examine gene expression in Arabidopsis and found that 6% of the more than 8000 genes on the array exhibited circadian changes in steady-state messenger RNA levels. Clusters of circadian-regulated genes were found in pathways involved in plant responses to light and other key metabolic pathways. Computational analysis of cycling genes allowed the identification of a highly conserved promoter motif that we found to be required for circadian control of gene expression. Our study presents a comprehensive view of the temporal compartmentalization of physiological pathways by the circadian clock in a eukaryote.利用寡核苷酸芯片在果蝇全基因组分析免疫应答 PNAS 98(26), 15119-24, 2001A genome-wide analysis of immune responses in DrosophilaAbstractOligonucleotide DNA microarrays were used for a genome-wide analysis of immune-challenged Drosophila infected with Gram-positive or Gram-negative bacteria, or with fungi. Aside from the expression of an established set of immune defense genes, a significant number of previously unseen immune-induced genes were found. Genes of particular interest include corin- and Stubble-like genes, both of which have a type II transmembrane domain; easter- and snake-like genes, which may fulfil the roles of easter and snake in the Toll pathway; and a masquerade-like gene, potentially involved in enzyme regulation. The microarray data has also helped to greatly reduce the number of target genes in large gene groups, such as the proteases, helping to direct the choices for future mutant studies. Many of the up-regulated genes fit into the current conceptual framework of host defense, whereas others, including the substantial number of genes with unknown functions, offer new avenues for research.在酿酒酵母全基因组筛选与紫外辐射敏感相关的基因 Proceedings of the National Academy of Sciences of the United States of America 98(22), 12608-13, 2001A genome-wide screen in Saccharomyces cerevisiae for genes affecting UV radiation sensitivityAbstractThe recent completion of the deletion of essentially all of the ORFs in yeast is an important new resource for identifying the phenotypes of unknown genes. Each ORF is replaced with a cassette containing unique tag sequences that allow rapid parallel analysis of strains in a pool by using hybridization to a high-density oligonucleotide array. We examined the utility of this system to identify genes conferring resistance to UV irradiation by using a pool of 4,627 individual homozygous deletion strains (representing deletions of all nonessential genes). We identified most of the nonessential genes previously shown to be involved in nucleotide excision repair, in cell cycle checkpoints, in homologous recombination, and in postreplication repair after UV damage. We also identified and individually confirmed, by replacing the genes, three new genes, to our knowledge not previously reported to confer UV sensitivity when deleted. Two of these newly identified genes have human orthologs associated with cancer, demonstrating the potential of this system to uncover human genes affecting sensitivity to DNA-damaging agents and genes potentially involved in cancer formation.老龄化与小鼠下丘脑皮层表达谱研究 PNAS | February 13, 2001 | vol. 98 | no. 4 | 1930-1934The effects of aging on gene expression in the hypothalamus and cortex of miceAbstractA better understanding of the molecular effects of aging in the brain may help to reveal important aspects of organismal aging, as well as processes that lead to age-related brain dysfunction. In this study, we have examined differences in gene expression in the hypothalamus and cortex of young and aged mice by using high-density oligonucleotide arrays. A number of key genes involved in neuronal structure and signaling are differentially expressed in both the aged hypothalamus and cortex, including synaptotagmin I, cAMP-dependent protein kinase C , apolipoprotein E, protein phosphatase 2A, and prostaglandin D. Misregulation of these proteins may contribute to age-related memory deficits and neurodegenerative diseases. In addition, many proteases that play essential roles in regulating neuropeptide metabolism, amyloid precursor protein processing, and neuronal apoptosis are up-regulated in the aged brain and likely contribute significantly to brain aging. Finally, a subset of these genes whose expression is affected by aging are oppositely affected by exposure of mice to an enriched environment, suggesting that these genes may play important roles in learning and memory.Affymetrix 芯片在自体免疫屏蔽研究中的应用 Science, Vol. 298, Issue 5597, 1395-1401, November 15, 2002Projection of an Immunological Self Shadow Within the Thymus by the Aire ProteinAbstractHumans expressing a defective form of the transcription factor AIRE (autoimmune regulator) develop multiorgan autoimmune disease. We used aire- deficient mice to test the hypothesis that this transcription factor regulates autoimmunity by promoting the ectopic expression of peripheral tissue- restricted antigens in medullary epithelial cells of the thymus. This hypothesis proved correct. The mutant animals exhibited a defined profile of autoimmune diseases that depended on the absence of aire in stromal cells of the thymus. Aire-deficient thymic medullary epithelial cells showed a specific reduction in ectopic transcription of genes encoding peripheral antigens. These findings highlight the importance of thymically imposed central tolerance in controlling autoimmunity.人类白血病细胞体内药物刺激后基因表达谱差异特异性 Nat Genet. 2003 May;34(1):85-90.Treatment-specific changes in gene expression discriminate in vivo drug response in human leukemia cells.AbstractTo elucidate the genomics of cellular responses to cancer treatment, we analyzed the expression of over 9,600 human genes in acute lymphoblastic leukemia cells before and after in vivo treatment with methotrexate and mercaptopurine given alone or in combination. Based on changes in gene expression, we identified 124 genes that accurately discriminated among the four treatments. Discriminating genes included those involved in apoptosis, mismatch repair, cell cycle control and stress response. Only 14% of genes that changed when these medications were given as single