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Human Exonic Evidence Based Oligonucleotide (HEEBO) Arrays
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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.
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| Probes:
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.
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| 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
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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.
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