Stacking the deck: double-tiled DNA microarrays

Microarrays—high-throughput platforms for analyzing the gene expression and features of total genomic DNA, among other applications—are gaining in popularity as researchers discover ever more uses for their unbiased and broad feature sets. At present, microarray analyses are limited by the number of individual features that can be placed on each array. Here we describe a double-tiling method that significantly increases the number of sequences present on an array, and we show that successful transcriptional profiling is possible and straightforward with such arrays. With this method, we and others can save money and precious samples by using fewer arrays to cover a region, or can carry out investigations at significantly higher resolution without incurring prohibitive costs or increasing the amount of sample required for the experiment.

[1]  R. Stoughton,et al.  Experimental annotation of the human genome using microarray technology , 2001, Nature.

[2]  G. Helt,et al.  Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution , 2005, Science.

[3]  Gordon K Smyth,et al.  Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2004, Statistical applications in genetics and molecular biology.

[4]  Mark Gerstein,et al.  An efficient pseudomedian filter for tiling microrrays , 2007, BMC Bioinformatics.

[5]  S Rozen,et al.  Primer3 on the WWW for general users and for biologist programmers. , 2000, Methods in molecular biology.

[6]  Lisa Z. Scheifele,et al.  Transposon insertion site profiling chip (TIP-chip) , 2006, Proceedings of the National Academy of Sciences.

[7]  T. A. Brown,et al.  A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. , 1990, Nucleic acids research.

[8]  J. Ecker,et al.  Applications of DNA tiling arrays for whole-genome analysis. , 2005, Genomics.

[9]  Thomas E. Royce,et al.  Global Identification of Human Transcribed Sequences with Genome Tiling Arrays , 2004, Science.

[10]  Mark Gerstein,et al.  Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery , 2005, Chromosome Research.

[11]  John Quackenbush,et al.  Multiple-laboratory comparison of microarray platforms , 2005, Nature Methods.

[12]  P. Brown,et al.  Yeast microarrays for genome wide parallel genetic and gene expression analysis. , 1997, Proceedings of the National Academy of Sciences of the United States of America.