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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)

C elegans image for alternative expression microarray design 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)

Dog image for alternative expression microarray design 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)

Fly image for alternative expression microarray design 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)

Zebrafish image for alternative expression microarray design 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)

Chicken image for alternative expression microarray design 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)

Human image for alternative expression microarray design 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)

Human image for alternative expression microarray design 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)

Mouse image for alternative expression microarray design 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)

Chimp image for alternative expression microarray design 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)

Rat image for alternative expression microarray design 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)

Yeast image for alternative expression microarray design 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
Button link to main ALEXA home page Button link to ALEXA-Arrays home page Button link to ALEXA-Seq home page Button link to acknowledgements of funding and other support for Malachi Griffith and Marco Marra Button link to contact information for Malachi Griffith and Marco Marra