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一种用于酿酒酵母的全基因组微阵列探针的新颖设计，可最大限度地减少交叉杂交。

A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization.

作者信息

Talla Emmanuel, Tekaia Fredj, Brino Laurent, Dujon Bernard

机构信息

Institut Pasteur, Unité de Génétique Moléculaire des Levures (URA 2171 CNRS, UFR 927 Université PM Curie), 25 rue du Docteur Roux, F-75724 Paris cedex 15, France.

出版信息

BMC Genomics. 2003 Sep 22;4(1):38. doi: 10.1186/1471-2164-4-38.

DOI:10.1186/1471-2164-4-38
PMID:14499002
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC239980/
Abstract

BACKGROUND

Numerous DNA microarray hybridization experiments have been performed in yeast over the last years using either synthetic oligonucleotides or PCR-amplified coding sequences as probes. The design and quality of the microarray probes are of critical importance for hybridization experiments as well as subsequent analysis of the data.

RESULTS

We present here a novel design of Saccharomyces cerevisiae microarrays based on a refined annotation of the genome and with the aim of reducing cross-hybridization between related sequences. An effort was made to design probes of similar lengths, preferably located in the 3'-end of reading frames. The sequence of each gene was compared against the entire yeast genome and optimal sub-segments giving no predicted cross-hybridization were selected. A total of 5660 novel probes (more than 97% of the yeast genes) were designed. For the remaining 143 genes, cross-hybridization was unavoidable. Using a set of 18 deletant strains, we have experimentally validated our cross-hybridization procedure. Sensitivity, reproducibility and dynamic range of these new microarrays have been measured. Based on this experience, we have written a novel program to design long oligonucleotides for microarray hybridizations of complete genome sequences.

CONCLUSIONS

A validated procedure to predict cross-hybridization in microarray probe design was defined in this work. Subsequently, a novel Saccharomyces cerevisiae microarray (which minimizes cross-hybridization) was designed and constructed. Arrays are available at Eurogentec S. A. Finally, we propose a novel design program, OliD, which allows automatic oligonucleotide design for microarrays. The OliD program is available from authors.

摘要

背景

在过去几年中，已在酵母中进行了大量DNA微阵列杂交实验，使用合成寡核苷酸或PCR扩增的编码序列作为探针。微阵列探针的设计和质量对于杂交实验以及后续的数据分析至关重要。

结果

我们在此展示了一种基于基因组精细注释的新型酿酒酵母微阵列设计，目的是减少相关序列之间的交叉杂交。努力设计长度相似的探针，最好位于阅读框的3'端。将每个基因的序列与整个酵母基因组进行比较，并选择没有预测交叉杂交的最佳子片段。总共设计了5660个新型探针（超过97%的酵母基因）。对于其余143个基因，交叉杂交不可避免。使用一组18个缺失菌株，我们通过实验验证了我们的交叉杂交程序。测量了这些新微阵列的灵敏度、重现性和动态范围。基于此经验，我们编写了一个新程序来设计用于完整基因组序列微阵列杂交的长寡核苷酸。

结论

这项工作定义了一种在微阵列探针设计中预测交叉杂交的有效程序。随后，设计并构建了一种新型酿酒酵母微阵列（将交叉杂交降至最低）。阵列可从Eurogentec S. A.获得。最后，我们提出了一个新的设计程序OliD，它允许自动设计用于微阵列的寡核苷酸。OliD程序可从作者处获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fb78/239980/78037fcb6f58/1471-2164-4-38-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fb78/239980/e4b827a9b82d/1471-2164-4-38-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fb78/239980/30e207535c03/1471-2164-4-38-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fb78/239980/14c0d76a1f02/1471-2164-4-38-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fb78/239980/3ce4fe747c30/1471-2164-4-38-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fb78/239980/62912731b117/1471-2164-4-38-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fb78/239980/78037fcb6f58/1471-2164-4-38-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fb78/239980/e4b827a9b82d/1471-2164-4-38-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fb78/239980/30e207535c03/1471-2164-4-38-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fb78/239980/14c0d76a1f02/1471-2164-4-38-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fb78/239980/3ce4fe747c30/1471-2164-4-38-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fb78/239980/62912731b117/1471-2164-4-38-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fb78/239980/78037fcb6f58/1471-2164-4-38-6.jpg

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