Preamble
Due to the complexity of genes in most metazoan species, creating ALEXA designs can be a time consuming and
computationally intense exercise. For species such as human the design process requires the creation of a
very large number of probes to profile all exons, introns, exon-junctions and exon-boundaries. Testing
the specificity and thermodynamic properties of such a large number of sequences can be a challenge for
centres that do not have convenient access to substantial computational resources (a 'Beowulf' style cluster
for example). For this reason and others it may be desirable to simply download a completed design for the
species of interest. To date we have generated such designs for ten EnsEMBL genomes. Some summary statistics
and links to related materials are provided for each of these below. Each of these designs was created
using the same parameters as those used in our validation experiments in which arrays were manufactured for
our designs using the NimbleGen platform and hybridized with their
50-mer hybridization protocol (originally designed for CGH arrays). Alternate array manufacturers are listed below.
Download
The designs described can be downloaded from our FTP server.
See the Platform section for instructions on how to import these designs and create your own array
design submission file.
Requests
If you are interested in a design not represented below (alternate species or design parameters) and you do not have
access to the bioinformatic or computational resources neccessary to use the ALEXA platform, please
Contact Us.
Design Synthesis
The designs described below are not specific to any particular array manufacturer. Once you have finalized
your design, the actual microarrays can be printed or synthesized on numerous platforms. We used NimbleGen
because they allow variable probe lengths and a density of 385,000 features on a single array. Other
possibilities include Affymetrix, Agilent,
IDT,
Illumina, Operon,
SuperArray,
The Scripps Research Institute, etc.
Designs
ALEXA_ce_45_170b (C. elegans)
Species: Caenorhabditis elegans Common name: Worm (nematode) Source EnsEMBL Database: caenorhabditis_elegans_core_45_170b
Gene count: 21,249 Known exon skipping events: 2,472 Probe count (unfiltered): 6,063,626
Detailed information
ALEXA_cf_42_2 (DOG)
Species: Canis familiaris Common name: Dog Source EnsEMBL Database: canis_familiaris_core_42_2
Gene count: 22,874 Known exon skipping events: 6,595 Probe count (unfiltered): 8,340,667
Detailed information
ALEXA_dm_42_43 (FLY)
Species: Drosophila melanogaster Common name: Fruit Fly Source EnsEMBL Database: drosophila_melanogaster_core_42_43
Gene count: 14,701 Known exon skipping events: 4,476 Probe count (unfiltered): 5,615,401
Detailed information
ALEXA_dr_42_6c (ZEBRAFISH)
Species: Danio rerio Common name: Zebrafish Source EnsEMBL Database: danio_rerio_core_42_6c
Gene count: 28,508 Known exon skipping events: 13,927 Probe count (unfiltered): 8,116,906
Detailed information
ALEXA_gg_42_2 (CHICKEN)
Species: Gallus gallus Common name: Chicken Source EnsEMBL Database: gallus_gallus_core_42_2
Gene count: 17,358 Known exon skipping events: 3,715 Probe count (unfiltered): 10,077,586
Detailed information
ALEXA_hs_35_35h (HUMAN - NCBI Build 35)
NOTE: This design was used for Validation experiments
Species: Homo sapiens Common name: Human Source EnsEMBL Database: homo_sapiens_core_35_35h
Gene count: 34,270 Known exon skipping events: 12,602 Probe count (unfiltered): 11,270,011
Detailed information
ALEXA_hs_41_36c (HUMAN - NCBI Build 36)
Species: Homo sapiens Common name: Human Source EnsEMBL Database: homo_sapiens_core_41_36c
Gene count: 31,185 Known exon skipping events: 26,317 Probe count (unfiltered): 15,621,632
Detailed information
ALEXA_mm_41_36b (MOUSE)
Species: Mus musculus Common name: House Mouse Source EnsEMBL Database: mus_musculus_core_41_36b
Gene count: 27,964 Known exon skipping events: 7,652 Probe count (unfiltered): 13,995,763
Detailed information
ALEXA_pt_41_21 (CHIMP)
Species: Pan troglodytes Common name: Chimpanzee Source EnsEMBL Database: pan_troglodytes_core_41_21
Gene count: 25,510 Known exon skipping events: 16,682 Probe count (unfiltered): 13,431,332
Detailed information
ALEXA_rn_43_34m (RAT)
Species: Rattus norvegicus Common name: Norway Rat Source EnsEMBL Database: rattus_norvegicus_core_43_34m
Gene count: 27,249 Known exon skipping events: 15,497 Probe count (unfiltered): 11,939,250
Detailed information
ALEXA_sc_41_1d (YEAST)
Species: Saccharomyces cerevisiae Common name: Baker's Yeast Source EnsEMBL Database: saccharomyces_cerevisiae_core_41_1d
Gene count: 7,096 Known exon skipping events: 0 Probe count (unfiltered): 1,527,330
Detailed information
Acknowledgements
The images depicted for each species above were taken from the corresponding EnsEMBL build.
For more details on the input EnsEMBL build used to generate each design follow the 'Source EnsEMBL Database' link
for the species of interest or visit the EnsEMBL home page and find the appropriate species and version
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