affymetrix基因芯片产品培训课件.pptVIP

Affymetrix基因芯片产品 Up to ~7,000,000 features / chip 5-11µm RNA target Thousands of copies of a specific oligonucleotide probe in each feature Raw data image with 1-6.9 million different complementary probes Oligonucleotide probe 1.28 cm Hybridized probe cell 5” 5” 芯片产品分类 表达谱芯片-mRNA 3’IVT WT MicroRNA芯片 lncRNA芯片 SNP/CNV芯片 甲基化转录因子芯片 表达谱芯片 3’IVT Human U133 Plus 2.0 Mouse U430 2.0 Rat U230 2.0 PrimeViewAlmac Xcel WT Human/Rat/Mouse Gene1.0 ST Human/Rat/Mouse Exon1.0 ST HTA2.0 表达谱芯片探针设计 表达谱芯片实验步骤 样本RNA抽提质检 cDNA合成及片段化 生物素标记 芯片杂交-洗脱-扫描 芯片数据标准化 Gene系列芯片 Transcript coverage of the array Human Gene 1.0 ST Array Human Gene 2.0 ST Array Total RefSeq transcripts covered 36,079 40,716 NM ? RefSeq coding transcript, well-established annotation 32,020 30,654 NR ? RefSeq non-coding transcript, well established annotation 2,967 5,638 XM ? RefSeq coding transcript, provisional annotation 579 996 XR ? RefSeq non- coding transcript, provisional annotation 513 3,428 lincRNA transcripts 466 11,086 RefSeq (Entrez) gene count 21,014 24,838 EXON系列芯片 Design Statistics Summary Probe Sets 1.4 million Exon Clusters 1 million Supported by Putative Full-Length mRNA 289,961 probe sets Supported by Ensembl Transcripts 306,583 probe sets Supported by EST 665,175 probe sets Supported by Mouse or Rat mRNA 220,262 probe sets Supported by Gene Prediction 883,105 probe sets Probe Selection Region Along the entire length of the transcripts Probes/Probe Selection Region 4 Background Subtraction Strategy Median intensity of up to 1,000 background probes with the same GC content Total Features Per Array 5,500,000 Interrogated Strand Sense² HTA2 Array content Protein coding content Non-protein coding content Genes (transcript clusters) 44,699 22,829 Transcripts 245,349 40,914 Exons 560,472 109,930 Exon clusters 296,058 82,444 Splice junctions (probe sets) 339,146 0 表达谱芯片应用 U133——经典，相对旧，无价格优势，不做推荐 Gene系列——基本，仅满足一般表达量检测需求 Exon系列——全面，精确表达量检测 HTA2——最佳，最全最精确表达量 EG1.0——最佳，唯一能够获得转录本表达量 MicroRNA芯片 MicroRNA 4.0 m