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Affymetrix
Equipment and Software Tools
The Genomics Core Facility
processes GeneChips using the Affymetrix Hybridization Oven, GeneChip
Fluidics Station 400, and the GeneArray Scanner. The fluidics station
and scanner are computer controlled through Microarray Suite version
5.0 software. Microarray Suite v5.0 along with Affymetrix MicroDB
and Data Mining Tool v3.0 allow for flexible data management, data
filtering, expression result sorting, replicate analysis, clustering
and matrix analyses.
The Process
for Doing a GeneChip Experiment
1. Contact
the Genomics Core Facility and set up a consultation to discuss the
aims of your experiment. We accept fully prepared cRNA samples or
biotinylated cRNA requiring fragmentation for overnight hybridization,
washing and staining on fluidics station, and chip scanning on confocal
laser scanner. Procedures for RNA isolation and cRNA target preparation
will be discussed during your consultation and can be found here on
the 'protocols' page .
2. Researchers will be contacted when their chips are ordered and
arrive, and a date for chip processing will be scheduled.
3. The day before samples are scheduled to be processed, researchers
should submit their prepared cRNA and an
Affymetrix Sample Submission form.
4. Researchers will be contacted by e-mail by the core facility to
arrange an appointment for the review and return of data.
Fee
structure for Affymetrix GeneChip experiments
GeneChip
processing
We accept fully prepared
cRNA samples for overnight hybridization, washing and staining on
fluidics station, and chip scanning on confocal laser scanner.
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| UAB |
non-UAB academic |
non-UAB/non-academic |
| $75/chip |
$150/chip |
$225/chip |
Per chip price applies
to expression chips and test arrays alike.
We also accept biotinylated
cRNA samples requiring fragmentation and hybridization cocktail preparation
for a fee of $15/cRNA sample in addition to the chip processing fee
listed above.
Data
Extraction and Management
Initial extraction of absolute
results, comparison of experimental vs. control samples using Microarray
Suite, simple data filtration, comparison of multiple experimental
vs. control samples using MicroDB and Data Mining Tool. All data files
are provided in .txt format on CD ready for import into other analysis
programs.
| UAB |
non-UAB academic |
non-UAB/non-academic |
| $70/hr |
$70/hr |
$70/hr |
GeneChip
Prices
Gene Expression Chips
The price of Affymetrix GeneChips vary according to species and type.
Test 3 Array
It is recommended that each labeled cRNA target be hybridized to a
Test 3 array to evaluate the quality of the target cRNA prior to hybridizing
the genomic array.
Chip prices listed reflect academic and volume discounts. Non-UAB/non-academic
users are not eligible for these discounts and will be billed list
price for chips.
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| Species |
Array |
Description |
Price |
| Human |
U133
set (1A + 1B) |
Set
covers ~33,000 well substantiated Human genes, derived from UniGeneBuild
133, April 2001 |
$800/set |
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U133
A |
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$400/chip |
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U133
B |
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$400/chip |
| Mouse |
430
set (1A + 1B) |
Set
covers ~34,000 well substantiated Mouse genes, derived from UniGeneBuild
107, June 2002 |
$800/set |
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430A |
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$400/chip |
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430B |
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$400/chip |
| Rat |
230
set (1A + 1B) |
Set
covers >28,000 well substantiated Rat genes, derived from UniGeneBuild
99, June 2002 |
$800/set |
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230A |
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$400/chip |
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230B |
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$400/chip |
| All |
Test
3 |
For
cRNA Evaluation |
$100/chip |
| Drosophila |
Genome |
Covers
>13,500 transcripts |
$300/chip |
| Arabidopsis |
ATH1
Genome |
Covers
>24,000 genes |
$300/chip |
| Yeast |
Genome
S98 |
~6400
well recognized ORFs (SGD, Dec 1998) |
$300/chip |
| E.Coli |
Antisense
Genome |
>4200
ORFs + 1350 intergenic regions |
$300/chip |
| C.
elegans |
Genome |
>22,500
transcripts |
$300/chip |
| P.
aeruginosa |
Genome |
>5500
ORFs from strain PAO1, 100 intergenic regions, 117 genes from
strains other than PAO1 |
$300/chip |
Previously listed
arrays (Human U95 series, Mouse U74v2 series, Rat U34 series, Rat
Toxicology, Rat Neurobiology) may still be available from Affymetrix.
Check the Affymetrix website for availability.
* For a more detailed description of each GeneChip, please refer to
the products section of the Affymetrix website, http://www.affymetrix.com
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Protocols:
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