Stanford: functional genomics facility
Email FAQ Register


Human Exonic Evidence Based Oligonucleotide (HEEBO) Arrays

The Human Exonic Evidence Based Oligonucleotide (HEEBO) array was developed by a group of researchers from Stanford University with collaborators from UCSF, Rockefeller, Basel, and the Stowers Institute. The oligonucleotide set consists of 44,544 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.
Also you can use the HEEBO oligos as a track on the hg16/July 2003 to compare Heebo to Illumina
or compare with Operon and Agilent. From the genome browser you can also open up tracks for the Affymetrix U133 Human Genome Array as well as the Affymetrix Human Exon 1.0 ST array.
  • Constitutive Exonic Probes (30,718): that will recognize all known transcripts of a gene.
  • Alternatively Spliced / Skipped Exonic Probes (8,441): will recognize exons that are present in some, but not all transcripts of a gene.
  • Non Coding RNA Probes (196): recogning non-protein coding transcripts (ribosomal RNAs, miRNAs).
  • BCR / TCR Genic / Regional Probes (372): recognizing transcripts from genes that undergo somatic rearrangement.
  • Other Probes (843): recognizing human mitochondrion derived DNA sequences.

  • Controls:
    A total of 4,189 controls are included in the set, including
  • Negative Controls (398 and 194 buffer only): Buffer only and 410 random sequences are positioned throughout the set to assist in determining background.
  • Positive Controls (864): recognizing a small subset of human transcripts.
  • Doped Controls (1,384): recognizing non-human 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 HEEBO arrays. These controls consist of 33 Stanford and 18 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 HEEBO 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.

    HEEBO HEEBO_Human_Set_v1.00.xls Order
    Doping Controls Product Insert Info.doc Order
    HEEBO Protocols Protocols
    HEEBO oligos as a track on the hg16/July 2003 UCSC genome browser

    about home contact
    © 2008 Copyright The Board of Trustees of Leland Stanford Junior University
    All Rights Reserved