MEEBOChip & HEEBOChip:
Information Page

Welcome. In collaboration with researchers at Stanford, UCSF, Stowers-Institute, Rockefeller, and Basel University, we designed and built 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 (see below for more details).

To see sample MEEBO hybridizations from various laboratories, click here for a hybridization at Stanford by Kate Rubins, click here for a hybridization at UCSF by Caroline Mrejen, click here for a hybridization by Emily Buck of Anita Sil's laboratory at UCSF, or feel free to contribute your own.

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 us 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, we used experimentally derived data to hone the selection of these 70mers, helping maximize their performance under typical fluorescent labeling and hybridization conditions. Specifically, we applied and refined the ArrayOligoSelector algorithm from Joe DeRisi’s 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).

Finally, we have integrated an unprecedented set of control features -- corresponding to both endogenous mouse/human transcripts as well as a diverse array of over 200 spiked doping control RNAs -- within both microarrays. These features allow users of these arrays to examine in detail the performance of any given hybridization, including assessment of sensitivity, specificity, dynamic range, normalization, linearity, and to explore various biases.

For infomation about MEEBOChip, please see:

• a description of the MEEBO content (PDF)
• MEEBO oligo naming conventions
• MEEBO printing instructions
• an updated version (051705) of these the MEEBO Oligo annotations (TXT)

For more information on MEEBOChip, you can also see the Illumina site, where you can find the data-sheet (PDF) and the original oligo-annotation file (XLS), or the UCSF Mouse Microarray Consortium, or the UCSF Functional Genomics Core Laboratories.

For more information about HEEBOChip, please see:

• the HEEBO oligos as a track on the hg16/July 2003 genome browser
• a description of the HEEBO content, naming conventions, statistics for each oligo category as well as oligo annotations with gene names (updated 051805) as a ZIP compressed Excel file (6.5 MB).

There are currently more than 100 publications that have used MEEBOChips and/or HEEBOChips. You may find them here.

If you have purchased a MEEBO/HEEBO set and have not been receiving e-mail updates regarding contents, controls, etc., please e-mail me and I will add to the mailing list (no spam).

Ash Alizadeh, Max Diehn, Chris Seidel, Brown Lab, and SFGF

Last updated Wednesday, Dec. 17, 2014 6:00 PM