第十一讲tilingarrayandexonarray.pptVIP

Tiling array and exon array Tiling芯片 全基因组测序的完成，使新的全基因组实验手段成为可能 Tiling Arrays提供了一个解读基因组序列的方法（a physical readout of a genome） Tiling指贴，盖，搭的意思，Tiling芯片指叠瓦式阵列芯片，也指嵌合芯片，是非常适合全基因组分析的针对所有转录本的DNA微阵列 密集的探针数才能保证对整个基因组全转录本的扫描，保证一个都不会少 genome tiling探针来源 Oligos：synthesized directly on the slides or prepared in solution and then deposited PCR products tiling typically of ~1-kb in length PCR产物用于tiling的缺点 芯片上的双链形态对杂交的影响 难以规模化，制备 ~1-kb PCR 产物的tiling芯片仅以chromosome 22 (roughly 1% of the human genome)为例就需要 20 000 次PCR反应。 A PCR tiling of the entire human genome would require approximately two million PCR reactions at the same resolution。不仅PCR反应量大，而且相应的生物信息学处理要求也很大。 分辨率低 GeneChip Tiling Arrays feature 25-mer oligonucleotides for optimal hybridization specificity High-resolution arrays for the most accurate detection used to build annotations, particularly in genomic regions previously thought to be “genome deserts.” 一般采用等长移位法，按照靶序列从头到尾选取一定长度（16－25nt－36nt）的互补核苷酸序列形成一组探针组合，其中相邻探针序列相差一个或多个碱基，覆盖的碱基数目是恒定的。 Tiling Array Design Tiling Array Design Probes：non-repetitive（Repetitive elements were removed by RepeatMasker），throughout coding and non-coding sequences， Tiling arrays labeled with “R” are complementary to the reverse (-) strand of a genome and F arrays are complementary to the forward (+) direction. Promoter tiling array Whole-Genome Tiling Array Sets Results oligonucleotide microarrays representing 1.5 Gb of nonrepetitive genomic DNA from each strand of the human genome A total of 51,874,388 36-nucleotide (nt) probes, positioned every 46 nt on average, were selected to interrogate sense and antisense strands of the genome and synthesized at a feature density of about 390,000 probes per array 发现了上千条新的转录区，验证了全基因组水平经序列预测得到的基因转录产物的表达。 得到比以前更为详尽的关于基因表达的注释（extensive and diverse） 很多新的转录产物与在小鼠中已经充分研究的蛋白序列上保守，证明这些新发现的转录产物中的绝大部分都是功能性的转录产物。 很多保守的转录序列都位于已知基因的远端，而且相当一部分的蛋白编码产物在300个氨基酸以上。 Chromatin Immunoprecipitation multiple regulation pathways interacting, regulatory networks. Chromatin im