Stanford: functional genomics facility
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Mouse Exonic Evidence Based Oligonucleotide (MEEBO) Arrays

The Mouse Exonic Evidence Based Oligonucleotide (MEEBO) array was developed by a group of researchers from Stanford and UCSF with collaborators from Rockefeller, Basel, and the Stowers Institute. The oligonucleotide set consists of 38,784 70mer probes that were designed using a transcriptome-based annotation of exonic structure for genomic loci. An excel worksheet of the oligonucleotide sequences can be downloaded here and the feature set is summarized below.

The MEEBO array contains a collection of oligo probes, largely resultant from constitutively and alternatively spliced exons.

  • Constitutive Exonic Probes (30,125): that will recognize all known transcripts of a gene.
  • Alternatively Spliced / Skipped Exonic Probes (4,201): will recognize exons that are present in some, but not all transcripts of a gene.
  • Non Coding RNA Probes (196): recognizing non-protein coding transcripts (ribosomal RNAs, miRNAs).
  • BCR / TCR Genic / Regional Probes (372): recognizing transcripts from genes that undergo somatic rearrangement.
  • Mitochondrial Probes (13): recognizing mouse mitochondrion derived DNA sequences.
  • Transgenic / Cassette Probes (37): recognizing elements commonly used for transgenic constructs (e.g. GFP, YFP).
  • Murine Viral Probes (358): recognizing mouse viral pathogen sequences.

  • Controls:
  • Negative Controls (317 buffer only and 97): Buffer only and 97 random sequences are positioned throughout the set to assist in determining background.
  • Positive Controls (1,152): recognizing a small subset of mouse transcripts.
  • Doped Controls (1,916): recognizing non-mouse sequences that can be spiked into RNA samples.

  • To facilitate the accurate evaluation of expression results, SFGF has available a suite of exogenous controls for use with our MEEBO arrays. These controls consist of 33 Stanford and XX Commercial premixed controls ready for addition to labeling mixtures. The spike in controls can be ordered below through the SFGF site. We highly recommend the use of these controls when using MEEBO arrays for mRNA expression analysis. Online tools for the interpretation of the results, and error and background modeling, using these mixtures will be available to SFGF users.

    MEEBO MEEBO_Data.txt Order
    Doping Controls Product insert Info.doc Order
    MEEBO Protocols Protocols

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