Harvard-Lipper Center for Computational Genetics

Oligonucleotide Sequences for Human and Mouse RNA Assays

We have designed a potentially shareable set of oligonucleotides for use in a variety of microarray and/or PCR measures of DNA and/or RNA. This consists of a simple list of one 70-mer per "gene" (i.e. dominant RNA.) Subsequent separate pages will have two or more oligos per RNA (often more than one RNA per gene.)

We expect to maintain this as an archival list with version-tracking and connections to NCBI resources for each RNA. The longer lists will contain the shorter list as a subset as much as possible.

We chose "unique" 70-mers on the assumption that smaller overlapping unique oligomers could be chosen from these as needed and still be referenced to a "standard" region. Seventy bases is also the maximum length seen for human oligos in various commercially available comprehensive oligo sets.

The criteria we use are listed below

Specificity

Uniqueness: evaluated by BLAST alignment (bit score < 50)

Sensitivity:

Uniformity: Tm between 72.5 and 83.5 (same range used by Operon)

Sequence Complexity: compressibility score below 35 (described in documentation)

Secondary Structure: Gibbs energy of secondary structure formation (using RNAfold – described in documentation)

open source code and data sets description of criteria, methods, and the algorithm

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We thank the following for their support of this work. These oligonucleotides are under consideration for distribution on microarrays as part of our resource center.
DOE Genome Projects  
NHLBI - Program for Genomic Applications :
   and
Dana Farber / Harvard Cancer Center,