Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

Alizadehlab: MeeboChip and HeeboChip Open Source Project

This is an open-source Mouse Exonic Evidence-Based Oligonucleotide Chip (MEEBOChip), and are in the process of building the human counterpart, HEEBOChip. The set of 70mers for MEEBOChip is already available from Illumina, Inc., with synthesis of HEEBOChip 70mers in progress. Both arrays are based on a novel selection of exonic long-oligonucleotides (70-mers) from a genomic annotation of the corresponding complete genome sequences, using a transcriptome-based annotation of exon structure for each genomic locus. Using a combination of existing and custom-tailored tools and datasets (including millions of mRNA and EST sequences), we built and performed a systematic examination of transcript-supported exon structure for each genomic locus at the base-pair level (i.e., exonic evidence). This strategy allowed them to select both constitutive and in many cases alternative exons for nearly every gene in the corresponding genome (e.g., protocadherin locus), allowing an unprecedented exploration of human and mouse biology. Furthermore, they used experimentally derived data to hone the selection of these 70mers, helping maximize their performance under typical fluorescent labeling and hybridization conditions. Specifically, they applied and refined the ArrayOligoSelector algorithm from Joe DeRisis laboratory to select 70mers, considering not only their uniqueness (i.e., hybridization specificity) within the content of the entire genome, but also to overcome the known biases of labeling and hybridization methods (e.g., 3-biased reverse transcription and in vitro transcription reactions).

URL: http://alizadehlab.stanford.edu/

Resource ID: nif-0000-30030     Resource Type: Resource     Version: Latest Version


mouse, exonic, evidence, oligonucleotide, chip, human, array, genomic, annoation, sequence, transcriptome, annotation, dataset, mrna, est, systematic, transcript, exon, locus, biology


MeeboChip and HeeboChip

Funding Information

Stanford University, UCSF, Stowers-Institute, Rockefeller University, Basel University,

Additional Resource Types




Parent Organization

Original Submitter


Version Status


Submitted On

12:00am October 19, 2010

Originated From


Changes from Previous Version

  • Description was changed
  • Funding Information was changed
  • Additional Resource Types was changed

Version 2

Created 2 months ago by Christie Wang

Version 1

Created 5 years ago by Anonymous