title: Compugen mouse 22K array (UQ)

status: Public on Feb 27 2008

city: Melbourne

first: Yi Mo

last: Deng

state: Victoria

address: Royal parade

institute: University of Melbourne

manufacturer: SRC Microarray Facility, University of Queensland, Australia

first: Yi-Mo

manufacture_protocol:
POLY-LYSINE SLIDE PREPARATION:
This protocol follows the Stanford protocol (Pat Brown Lab at Stanford), except for the exception of glass source and then number of slides processed (max is 20 Vs 60 due to slide racks we use and spinning restrictions). We have tried a variety of glass types and found Menzel& Glaser suprefrost plus to be a great substrate.
Background problems: We have made an awful lot of crap batches of poly-lysine slides. Common causes of bad batches include using dirty glassware or forceps, using cheap ethanol, using slide racks not dedicated to this process and having talc run off wet gloves during the rinsing steps and onto the slides.
Plunging: One of the major factors in getting a uniform coating on slides is the thoroughness of the slide agitation when moved between different solutions. It is essential that slides be plunged in and out to ensure no gradient of mixed solution is left between the slides. We have found that "jiggling" the slides in the rack ensures an even coating, even to the edge of the slide that is resting in the rack. Getting the knack of this can be tricky. Excessive jiggling leads to all the slides coming out of the rack..
Reagents Qty
Slides  2 pkts Menzel & Glasser Superfrost PlusTM microscope slides.
MilliQ H2O  760mL
NaOH  190 g
95% Ethanol  1140 mL
Poly-L-lysine  70 mL Sigma #P 8920
PBS  70 mL
Equipment
Oven (45oC)  1
Slide rack  4 Kartel polypropylene slide rack with handle (holds 20 slides). We Shorten the handles down to approximately 5cm long so that the rack can be directly spun in a bench top centrifuge with microtitre plate buckets.
2L Beakers  4 2L beakers should dedicated to slide preparation.
Slide storage box  1 (holds 100 slides).
Stirring bar  2
Stirring unit  2
Stirring bar cover  2 Home made arch that goes over the stirring bar to allow mixing. while washing and coating slides.
Flat nose Forceps  1 Used for loading slides into racks.
Large forceps  2 Used for handling slide racks
2L measuring cylinders  2 Polypropylene.
POLY-LYSINE SLIDE PREPARATION:
Place 80 slides into 4 slide racks using forceps.
Prepare cleaning solution as follows: Dissolve 190 g NaOH in 760 mL H2O. Add 1140 mL of analytical grade ethanol. Place a stirring bar in the bottom of the beaker and mix until completely dissolved. CAUTION, THIS SOLUTION IS EXTREMELY CAUSTIC.
Place a "stand" over the stirring bar. We use a polypropylene lid of a p200 micropipette tip box with the ends cut off as an arch over the stirring bar.
Submerge slides in their racks 2-3 times to ensure even wetting. Jiggle in the rack just enough to have the slides momentarily lose contact with the rack. Stack on top of the arch and stir as quickly as possible for 2 hr.
Fill 2L beakers with ddH20. Handle the slide racks with clean forceps and quickly transfer one rack at a time to 1.8L of ddH2O. Rinse vigorously by plunging racks up and down. Plunging should once again jiggle the slides so they lose contact with the sides of the rack.
Repeat rinses 5X with fresh ddH2O each time. It is critical to remove all traces of NaOH-ethanol. Once slides are clean, they should be exposed to air as little as possible. Dust particles will interfere with coating and printing.
Prepare Poly-lysine solution as follows: 200 mL poly-L-lysine + 200 mL tissue culture PBS in 1600 mL water. Use plastic graduated cylinder and beaker.
Transfer slides to circulating poly-lysine solution. Jiggle 5 times, and shake for 1 hr.
Transfer rack to fresh chambers filled with ddH2O. Plunge up and down 5X to rinse.
Centrifuge slides on micro-titer plate carriers (place paper towels below rack to absorb liquid) for 5 min. @ 500 rpm. Transfer slide racks to plastic slide chambers with covers.
Dry slide racks in 450C vacuum oven for 10 min. (Vacuum is optional).
Store slides in closed slide box (without rubber or cork mat in the bottom).
ELEMENT PREPARATION:
Elements are normally prepared from plasmid DNA or cleared bacterial lysates. The percentage of PCR failure for both methods is typically 5-7%. Plasmid DNA templates were also for sequencing of elements for QC purposes.
Cleared bacterial lysates: from Biotechniques, 29(3), Sept 2000,548-562
Selected clones are inoculated into a 96 well, U bottom plate containing 100 µl of LB/10% glycerol/Ampicillin (50µg/ml) using a biomek 2000 HDRT or 5µl of liquid culture. The plate is sealed and incubated o/n at 37ºC.
5µl of culture suspension are transferred into a 96 well U-bottom plate containing 95µl of MilliQ water and heated to 95oC for 10 minutes in a laboratory oven to lyse the cells and release the plasmid clones. Caution: some ploy carbonate plates warp at this temperature.
Precipitate cellular debris by centrifugation at 1500´g for 5 minutes
Take 5µl of lysate as template for PCR. Store the remainder frozen. Re-spin before further use.
Plasmid preparation:
This protocol is a modified version of the Beckman plasmid preparation procedure for the Biomek 200 but we use multi-channel pipettes instead. Protocol yields small amounts of DNA for a mini prep but the DNA is good enough to be sequenced if coming from the IMAGE bug strain.
Aliquot Inoculate 1.1ml of LB broth + ampicillin 50µg/ml into 2.2ml deep 96 well plates ABgene. Square well, round bottom plates are best as they are easier to remove supernatant from. Cover plate with sealable lid and shake at 250rpm (minimum) overnight at 37oC.
Spin down bacterial pellet by spinning plate at 3K for 15min 4oC. Tip off supernatant and pat dry on towel. Resuspend bacterial pellet in 100µl of Buffer P1 (10mM Tris pH8.0, 1mM ETDA pH 8.0, 100µg/ml RNAse A and RNAse T1. Leave for 5' at RT.
Add 100 µl of Buffer P2 (0.2%SDS, 0.2M NaOH) Leave on ice for 5min
Add 100µl of 3M Na Acetate pH 4.8 and leave at -20oC for 30min.
Spin plate at max speed for 60min, 4oC and transfer 125µl to a new 96 well plate. Add 125µl of iso-propanol and precipitate at -20oC for at least one hour. Precipitate plasmid DNAs by spinning the plate at 3000g for 60min at 4oC. Tip out supernatant. Wash with 500µl of 70% Ethanol. Spin 3100rpm for 10min at 4oC.
Leave plate to dry on bench Resuspend in 50 µl of TE and run 5µl on a gel to check the prep. Dilute 10µl down to 10ng/µl for generating PCR products.
PCR AMPLIFICATION:
PCRs are set up as follows:
Reagent Per Rxn Per 4x 96 Rxns
--------------------------------------------------------------------------------

10x PCR Buffer 10µl 4.8µl
25mM MgCl2 7µl 4.0µl
100mM NH2-M13F* 0.3µl 140µl
100mM NH2-M13R* 0.3µl 140µl
5U/µl Taq (AB biotech) 0.8µl 320µl
H20 to  48ml
*The primers have a 5' NH2 modified. The primer sequences are:
M13 FWD: 5' GTT TTC CCA GTC ACG ACG TTG 3'
M13 REV: 5' TGA GCG GAT AAC AAT TTC ACA CAG 3'
The bulk mix is then aliquoted into 96 well plates (thermofast, AB biotech). These are skirtless poly-propylene plates. While they don't fit into the arrayer, the have wells deep enough to allow product precipitation and are cheap. Template (5µl) is then added to each reaction. These DNAs had been previously diluted down to approximately 10ng/µl in water.
Reactions are carried out in a MJ research tetrad PCR machine under the following conditions: (Temperature of block is calculated, plate option is selected, volume of reaction selected is 100µl in the program setup).
1 x  94oC for 3min
35 x  48oC for 20sec
72oC for 3min
94oC for 40sec
5µl of the PCR reaction is run out on a 96 lane gel (AB biotech) to determine success of the PCR. PCRs are scored for presence of a product, number of bands and intensity.
PRODUCT PURIFICATION:
Isopropanol precipitation:
Immediately after running out products, add 10µl of 3M Na Acetate (pH5.2) and 100µl iso-propanol. Reseal the plate and precipitate at -20oC overnight. Element is recovered by spinning at 4,100 rpm is approximately 3,100g for 60min at 4oC. Plates are turned over on absorbent towel and gently tapped dry. Pellets are often just visible. Sigma make a rotor that will spin plates at 5,100rpm (approx 4000g) which would be preferable for precipitating these elements.
Pellets can be washed in 70% ethanol but we have found you can often leave this step out with out obvious problems.
Leave to air dry for 60min to overnight. Plates are sealed in a storage box and left at -20oC until you are ready to array.
Prior to arraying, resuspend pellets with the addition of 30µl of H2O and orbital shaking for 60min. Aliquot 10µl material into array working plate. Dry down and resuspend
Millipore purification derived from Biotechniques, 29(3), Sept 2000,548-562
Transfer PCR product (50ml) to the Millipore filter plate.
Place the filter plate on a vacuum manifold filtration system (Qiagen, Cat # 19504 or Millipore Cat. No # MAVM0960R) and filter at a pressure of 15in (380 mm) Hg for 10 minutes or until the plate is dry.
Add 30ml of MilliQ water to each well and filter at 15mm (380 mm) Hg for 5-10 minutes or until the plate is dry.
Repeat step 3.
Remove plate from the manifold filtration system. Add 60ml of MilliQ water to each well and place on a shaker. Shake vigorously for 10 minutes to resuspend the DNA.
Transfer the purified product to a new 96 well plate.
Plates containing the purified PCR products are then stored at 4oC for future arraying.
POST-ARRAY FIXATION:
Once again, this protocol was adapted from the Brown web site.
I have taken their protocol and removed the following steps: We have omitted snap drying of the slides. We have omitted post array rehydration.
Succinic anhydride 6g Aldrich #23,969-0
1-Methyl-2-pyrrolidinone 325mL Aldrich #32,863-4
Sodium borate (1M, pH 8) 15mL <= Use boric acid and adjust pH with NaOH
ddH2O ~1 L
2L beaker 1
95% ethanol 350mL Use high grade ethanol
Mark boundaries of array on back of slide using diamond scriber. Array will become invisible after post-processing.
UV crosslink DNA to glass with Stratalinker set for 65 mJ. (Set display to "650", which is 650 x 100 mJ.)
Prepare BLOCKING SOLUTION: Have 3 x 350 ml glass chambers and a large round glass beaker with dH2O ready in the microwave. At this time, prepare the 15ml sodium borate in a 50 mL conical tube.
Dissolve 6g succinic anhydride in approx. 325-350 mL 1-methyl-2-pyrrolidinone. Rapid addition of reagent is crucial. Immediately after the last flake of the succinic anhydride dissolves, add the 15 mL sodium borate.
Immediately after sodium borate solution mixes in, pour solution into empty slide chamber. Plunge slide rack rapidly and evenly in solution. Vigorously shake up and down for a few seconds, making sure slides never leave solution.
Mix on orbital shaker 20 min (50rpm). Meanwhile, heat water 1L of H2O in a microwave (4min max power).
Gently plunge slide rack in 95oC water (just stopped boiling) for 2 min.
Plunge slide rack 5X in ice cold (taken out of the -200C freezer) 95% ethanol.
Centrifuge slides and rack for 2 min. @ 500 rpm at room temperature. Use gloves and forceps when loading to avoid contact with oil and talc.
Store in slide box. Slides are normally used the following day. Some people recommend leaving at least one week to mature.


title: NHGRI_HumanKnownGene24k_cDNA chips 2003

status: Public on Mar 11 2008

city: Bethesda

first: Bin

last: Yan

state: MD

address: 10 Center Dr. Bldg 10, Rm 5D55

department: NIDCD

country: USA

institute: National Institute of Health

organism: Homo sapiens

technology: spotted DNA/cDNA

description: This is a 24k cDNA microarray spotted on glass prepared from PCR amplification of clones from the IMAGE Consortium cDNA library. The chips contain a total of 23220 spots, which includes known genes (12270), ESTs, hypothetical genes and control spots.

distribution: non-commercial

manufacturer: National Human Genome Research Institute Microarray core, National Institute of Health, Bethesda, Maryland

manufacture_protocol: detailed on the web site http://research.nhgri.nih.gov/microarray/main.html, and have also been published in Current Protocols in Human Genetics.


title: MEEBO Mus musculus 39k spotted oligo array (MOE series)

status: Public on Feb 22 2008

city: Honolulu

first: rich

last: allsopp

state: HI

address: 651 Ilalo St

department: anatomy & reprod biol

institute: university of hawaii

organism: Mus musculus

technology: spotted oligonucleotide

distribution: custom-commercial

first: Richard

last: Allsopp

manufacture_protocol: THe MEEBO (Mouse Exonic Evidence Based Oligonucleotide) olionucleotide library is composed of 38784 unique 70mer probes that was developed using a transcriptome-based annotation for exonic structure of murine genomic loci.  Hence this oligo probe set largely corresponds to constitutive (30,125) and alternatively spliced (4,201) exons. The particular batch of MEEBO arrays used for this platform are the MOE series.


title: Human 17K cDNA-GeneTrack

status: Public on Feb 01 2008

city: Seoul

first: DONG HYUK

last: KI

address: sinchon-dong 134

country: South Korea

institute: NBRC

first: Chiwang

last: Yoon

manufacture_protocol:
1.  cDNAs are amplified in Sorenson 96 well PCR plate (cat#21970) with 50 ul reaction volume and purified PCR products using Sephadex G-50 Fine (Amersham Biosciences, cat#17-0573-02).
2. Transfer purified PCR products to Nunc 96 well V-bottom plates (cat#442587) and allow plates to dry through passive water evaporation in a protective environment (e.g., chemical hood).
3. Resuspend cDNAs in 50% DMSO to 100-500 ng/ul (total volume 12 ul) and Seal plates with Corning seals
4. Incubated plates at 60oC for 30 minutes to aid resuspension of cDNA and rearray 10 ul into 384-well, Genetix polystyrene V-bottom plates (cat# X6004). This can be done the night before a print run is started.
5. Seal plates with Corning seals.
6. Centrifuge plates at 2000 rpm for 3 minutes.
7. Remove seals and cover with plate lids. Place in appropriate location of plate cassette. This should be done with first plates just before print run is started to minimize evaporation time before printing. For second and third cassettes, wait until 30 minutes before next cassette is needed to begin centrifugation.
8. Make sure plates rest behind both holding clips in the cassettes. Push plates back into the cassettes as far as they will go, putting them in the proper position for the server arm.
9. After the print run is completed, back plates to 4oC refrigerater.


title: Phalanx Mouse OneArray

status: Public on May 14 2008

city: Hsinchu Science Park

first: Phalanx

middle: Biotech

last: Group Inc.

state: Hsinchu

address: 6 Technology Road 5, 6th Floor

department: Bioinformatics

country: Taiwan

institute: Phalanx Biotech

description:
Phalanx Biotech Group's Mouse OneArray contains 31,082 features, 29,922 detection probes and 1880 control probes, spotted onto class slides using a proprietary non-contact printing method. Detection probes are annotated against the human genome and grouped into the following categories:

Group 1 - gene specific: exon
Group 2 - intron hit
Group 3 - intergenic
Group 4 - multi-gene hits
Group 5 - no hit to genome
Group 6 - >200 hits to genome

distribution: commercial

manufacture_protocol: See http://www.phalanxbiotech.com/ for updated protocols


title: Sidney Kimmel Cancer Center Human Promotor 19K Array, v13, set-A

status: Public on Feb 05 2008

city: San Diego

first: Yipeng

last: Wang

state: CA

institute: Vaccine Research Institute of San Diego

manufacturer: Sidney Kimmel Cancer Center Genomics Core

first: Fred

last: Long

first: Shilpi

last: Arora

first: Saynur

last: Vardar-Sengul

first: Dan

last: Mercola

first: Michael

last: McClelland

manufacture_protocol: Human promoter sequences (1000bp upstream and 500bp downstream from transcription initiation site) were utilized for fabrication of the arrays.  Approximately 5000 sequences were retrieved batch-wise from GoldenPath. Primers for amplification of these sequences were generated batchwise using Primer 3 (Rozen and Skaletsky 2000) designed to generate an average amplicon of 1200 nts. An additional ~ 13,000 sequences were prepared using the primer set developed by the Whitehead Institute Center for Microarray Technology (http://www.wi.mit.edu/CMT/Downloads.html) designed to generate and average amplicon of ~840 nts. The promoter sequences were amplified purified and spotted onto UltraGAPS coated slides (Corning Incorporated, Corning, NY) in the presence of 50% DMSO. The products of all amplification were visualized by agarose gel electrophoresis. Over 70% of all amplifications yielded single products of the expected size.  Failed amplifications were recorded and ignored in the subsequent robot-assisted selection for spotting using Biomek FX (Beckman Coulter, Inc). Promoter arrays were printed on two slides, set A and set B. Each array contains triplicate of 6400 spots. In total, promoter microarray contains 12186 promoter sequences (including 192 oligos), 544 non-promoter controls, 32 salmonella controls, 32 Cy Dye controls and 6 blank spots. Many of the promoters on the array are from genes of particular relevance to cancer and the array includes promoters from most of the genes that are known to be regulated by methylation in cancer. Human promoter array have been used for high-throughput DNA methylation assay and ChIP-on Chip analysis (Hayakawa, Mittal et al. 2004; Wang, Hayakawa et al. 2005).


title: Sidney Kimmel Cancer Center Human Promotor 19K Array, v13, set-B


title: Center for Functional Analysis of Human Genome Human 21K

status: Public on Mar 26 2008

city: Daejon

first: Seon-Young

last: Kim

address: 52 Eoeun-dong, Yuseong-gu

department: Genome Research Center

institute: Korea Research Institute of Bioscience and Biotechnology

manufacture_protocol: cDNA microarrays were fabricated in our core facility using a robotic arrayer (PixSYS 5500, Cartesian; Ann Arbor, MI). The 21K microarray contains 21,168 genes from KUGI unigene library. All the clones were verified by sequencing in our facility. The cDNA inserts were amplified by PCR, and after purification, spotted onto silylated glass slides (CSS-100; Telechem, Sunnyvale, CA). Each microarray slide contained control genes to normalize the effect of different fluorescent dyes.


title: Agilent-013275 Mouse Promoter ChIP-on-Chip Set 44k, Microarray 1 of 2

status: Public on Jan 27 2008

city: Los Angeles

first: Yin

last: Shen

address: 695 Charles E. Young Dr.

institute: UCLA

technology: in situ oligonucleotide

description:
Mouse Promoter ChIP-on-Chip Set 44K 1 of 2
Arrays of this design have barcodes that begin with 25132751.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

first: Shaun

middle: D

last: Fouse

first: Guoping

last: Fan

manufacture_protocol: see manufacturer's web site at http:/www.agilent.com/


title: CCDTM Hs_CCDTM36k - version 1

status: Public on Jul 24 2008

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

manufacturer: NIH Clinical Center, Dept. of Transfusion Medicine, Immunogenetics Section (NIH/CC/DTM)

manufacture_protocol: Microarrays are printed with GeneMachines robotic arrayer from Genomic Solutions (http://www.genomicsolutions.com) that is fitted with a printhead containing 48 SMP3 printing pins from Telechem International (http://www.arrayit.com). The human oligo probe set is purchased from Operon Human Genome Array-Ready Oligo Set[tm] (AROS) Version 4.0 which contains 35,035 oligonucleotide probes, representing approximately 25,100 unique genes and 39,600 transcripts excluding control oligos. The human version 4.0 is constructed based on the Ensembl human database build (NCBI-35c), with a full coverage on NCBI human Refseq dataset (04/04/2005). In addition, it integrates a significant portion of unique full-length cDNA clone sequences from H-Invitational Database (release 1.8). The microarray spot densities are 157.5 microns (center-to-center), and one spot is printed per probe per slide. The microarrays are printed on Epoxy coated slide (ThermoFisher) and post processed according to manufacture instruction.


title: Agilent-013276 Mouse Promoter ChIP-on-Chip Set 44k, Microarray 2 of 2

description:
Mouse Promoter ChIP-on-Chip Set 44K 2 of 2
Arrays of this design have barcodes that begin with 20050525.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Rosetta/Merck Rat 25k v1.0 microarray

status: Public on Jan 22 2008

city: Seattle

first: Amit

middle: V

last: Kulkarni

state: WA

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

organism: Rattus norvegicus

description:
Oligonucleotide array on glass.
Contains 60-mer probes (60-mer).

first: John

last: Castle

manufacture_protocol: see manufacturer's website


title: Illumina HumanCNV370-Duov1 DNA Analysis BeadChip (HumanCNV370v1)

status: Public on Jun 23 2008

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

technology: oligonucleotide beads

description: contains the standard SNP content featured on our HumanHap300-Duo Genotyping BeadChip, with an additional 52,167 markers designed to specifically target nearly 14,000 copy number variant (CNV) regions of the genome, for a total of over 370,000 markers

manufacture_protocol: See manufacturer's website


title: Bovine oviduct and endometrium (BOE) cDNA array version 1

status: Public on Dec 31 2007

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

organism: Bos taurus

manufacturer: Laboratory for Functional Genome Analysis (LAFUGA) - Genomics Unit, Gene Center of the LMU Munich, Munich, Germany

manufacture_protocol: Fifteen microliters of PCR reactions of amplified cDNA clones were transferred to 384 well microtiter plates (AbGene, Epsom, Surrey, UK) containing 15 µl of 2 x spotting buffer (40 mmol/l Tris-HCl pH 8, 2 M NaCl, 2 mmol/l EDTA, and bromphenol blue). PCR products were spotted onto amphoterous nylon membranes (Nytran plus, Schleicher & Schuell, Dassel, Germany) within an area of 2 x 5 cm. For spotting an Omnigrid Accent microarrayer (GeneMachines, San Carlos, CA) was used with solid pins (0.015 inches in diameter, SSP015; Telechem International; Sunnyvale, CA). Spotting was performed 6 times for each PCR product on the same position for sufficient and equal application. Twenty-eight arrays were produced simultaneously. The spotted DNA was denatured with 0.5 N NaOH for 20 min at room temperature. DNA was immobilized by baking for 30 min at 80 °C and UV crosslinking (120 mJ/cm2).


title: Agilent-015092 Whole Human Genome Microarray 4x44K

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: Content sourced from the UCSC hg17 human genome (NCBI build 35, May 2004)

manufacture_protocol: see manufacturer's web site (www.agilent.com)


title: Geschwind Ren 6k promoter array-2

first: Daniel

middle: H

last: Geschwind

address: 695 Charles E Young Drive

department: Neurology

first: Elizabeth

last: Spiteri

first: Genevieve

last: Konopka

first: Giovanni

last: Coppola

first: Jamee

last: Bomar

last: Oldham

first: Bing

last: Ren

manufacture_protocol: PCR products from promoter regions


title: Filgen Array Mouse 32K Version 3.0

status: Public on Dec 05 2007

city: Nagoya

first: Manabu

last: Harada

state: aichi

address: 15-1 Nakanoshima, Ohdaka-cho, Midori-ku

department: Biosciences

country: Japan

institute: Filgen,Inc.

manufacture_protocol: Array-Ready Oligo Set for Mouse Genome Version 3.0 from Operon Biotechnologies, Inc. was spotted using a GeneMachines OmniGrid Arrayer . The microarrays printed on Corning Ultra-GAPS slides (Item #40018) coated with amino-silane and post-processed according to the manufacturer's protocol.


title: Stanford Human cDNA SHEW

status: Public on Nov 16 2007

city: Boston

first: Bao Jian

state: MA

address: MEEI, 243 Charles Street

department: Ophthalmology

institute: Harvard Medical School

manufacture_protocol:
Preparation of Slides to be used to make microarrays.
Last updated: October 6, 1999
Materials
Qty
Order info
Notes
Glass microscope slides
60
Gold Seal #3010
Slide rack
2
Shandon Lipshaw #121 (800-245-6212)
Each rack holds 30 slides
Slide chamber
6
Shandon Lipshaw #121
Each chamber holds 350 mL
ddH2O
~5 L
NaOH
70 g
95% Ethanol
420 mL
Poly-L-lysine
70 mL
Sigma #P 8920
Tissue culture PBS
70 mL
Vacuum oven (45C)
Slide box (plastic only)
1
VWR #48443-806
1. Place slides in slide racks. Place racks in chambers.
2. Prepare CLEANING SOLUTION:
a. Dissolve 70 g NaOH in 280 mL ddH2O.
b. Add 420 mL 95% ethanol. Total volume is 700 mL (= 2 X 350 mL); stir until completely mixed.
c. If solution remains cloudy, add ddH2O until clear.
3. Pour solution into chambers with slides; cover chambers with glass lids. Mix on orbital shaker for 2 hr. Once slides are clean, they should be exposed to air as little as possible. Dust particles will interfere with coating and printing.
4. Quickly transfer racks to fresh chambers filled with ddH2O. Rinse vigorously by plunging racks up and down. Repeat rinses 4X with fresh ddH2O each time. It is critical to remove all traces of NaOH-ethanol.
5. Prepare POLYLYSINE SOLUTION:
a. 70 mL poly-L-lysine + 70 mL tissue culture PBS in 560 mL water.
b. Use plastic graduated cylinder and beaker.
6. Transfer slides to polylysine solution and shake 15 min. - 1 hr.
7. Transfer rack to fresh chambers filled with ddH2O. Plunge up and down 5X to rinse.
8. Centrifuge slides on microtiter plate carriers (place paper towels below rack to absorb liquid) for 5 min. @ 500 rpm. Transfer slide racks to empty chambers with covers for transport to vacuum oven.
9. Dry slide racks in 45C vacuum oven for 10 min. (Vacuum is optional.)
10. Store slides in closed slide box (plastic only, without rubber mat bottom)
11. BEFORE PRINTING ARRAYS:
a. Check that polylysine coating is not opaque.


title: Duke Operon Mouse v4.0

status: Public on Dec 04 2007

city: Durham

first: Mary

middle: Elizabeth

last: Jones

state: NC

address: Jones Bldg, Research Dr.

department: Immunology

institute: Duke University

manufacturer: Oligo print set from Operon, Array printing done by Duke University Microarray Facility

manufacture_protocol: Operon oligos in the whole genome print set are synthesized to 70 base pairs.  Arrays were printed using an Omnigrid 300 arrayer by Genomic Solutions.


title: FHCRC Human Prostate PEDB cDNA Array v2

status: Public on Oct 25 2007

first: Denise

last: Mauldin

address: 1100 Fairview Ave N D4-100

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

first: Peter

middle: S

last: Nelson

middle: E

last: Abbott

first: Ruth

last: Dumpit

manufacture_protocol: As cited.


title: PIQOR Custom Ischemia

status: Public on Dec 01 2007

city: Cologne

first: Bernhard

last: Gerstmayer

address: Stockheimer Weg 1

country: Germany

institute: Miltenyi Biotec GmbH

description: The PIQOR Custom Ischemia Microarray comprises 737 immune related rat and mouse specific cDNAs. These cDNAs include 5 house-keeping genes as positive controls. In addition 4 E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. 2 negative controls are given by spotted herring sperm DNA and buffer. Spotting in quadruplicate results in 2948 spots exclusive of the spots for the negative controls and the E. coli positive controls.

first: B.

first: K.

last: Hofmann

first: A.

last: Bosio

manufacture_protocol: Defined 200-400 bp fragments of selected cDNAs were generated by RT-PCR, cloned and sequence-verified. Amplified and purified cDNA inserts were spotted in quadruplicate on PIQOR slides using a proprietary piezoelectric spotter. The PIQOR slides were coated in a 2 step process generating a surface which covalently binds DNA molecules.


title: NIA 15K BHAM

status: Public on Nov 06 2007

city: Birmingham

first: Hong

last: Lin

address: Vincent Drive

department: Anatomy

country: United Kingdom

institute: Institute of Biomedical

manufacturer: The NIA 15K mouse cDNA library was purchased through the UK Medical Research Council and printed onto glass slides by the Genomics and Proteomics Laboratory, U.Birmingham (www.genomics.bham.ac.uk)

first: Vibhor

last: Gupta

first: Matthew

last: VerMilyea

first: Francesco

last: Falciani

first: Jeannie

middle: T

last: Lee

first: Laura

middle: P

last: O’Neill

first: Bryan

middle: M

last: Turner

manufacture_protocol: The slides were printed in duplicate using an Advalytix Automated Hybrydization Station.


title: Gladstone Core Operon Mouse V 2.0 spotted array

status: Public on Oct 04 2007

city: Novato

first: Eric

last: Verdin

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

first: Christopher

last: Barker

first: Yangxia

last: Hao

manufacture_protocol: The Mouse version 2.0 oligonucleotide set from Operon was spotted on polylysine-coated glass arrays


title: Arizona Gallus gallus 20.7K Oligo Array v1.0

status: Public on Oct 26 2007

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

organism: Gallus gallus

manufacturer: Genomics Research Laboratory, Steele Children's Research Center, University of Arizona

first: Nares

last: Trakooljul

first: Jay

last: Konieczka

first: Adam

last: Hoying

first: Parker

middle: B

last: Antin

first: Tom

last: Porter

middle: A

manufacture_protocol:
1. Oligo Design.
The chicken oligos were designed by Carre et al. (2007) using gene predictions from Ensembl, TIGR, full-length cDNAs from the BBSRC UMIST ChickEST database, and chicken bursal EST sequences from Jean-Marie Buerstedde's DT40 database. Sequences from these resources were aligned and 70mer oligos designed against regions common to more than one aligned sequence. Oligos were then designed using OligoArray2.0.
2. Oligo Array Manufacturer.
The chicken oligo set [Gallus gallus (chicken) Roslin/ARK CoRe Array V1.0] was manufactured by Operon Technologies, Inc.. The chicken oligo set (Catalog # 851102) contains 20,460 long oligo probes (300 pmol) arrayed in 54 384-well plates. Four wells in each of the 54 384-well plates contained the Operon Production Tracking Oligo opHsV04NC000001, which is a randomly-generated oligo sequence with a length of 30 bases.
3. Printing.
This 20.7K chicken oligo array contains 20,676 features that include 20,460 70mer oligos and 216 control spots of the Operon Production Tracking Oligo opHsV04NC000001. The oligos (300pmol) were dissolved in 8 microliters of 50% DMSO for printing. The chicken oligo array was printed on Corning® UltraGAPSTM aminosilane coated slides (Cat # 40018) using a Virtek ChipWriter Pro (Model # HCO1-M) robot fitted with 48 TeleChem (SMP2.5) pins. The slides were printed in a HEPA-filtered positive-pressure chamber maintained at 24 degrees C and 48% relative humidity (RH)(± 2 %RH). The printed slides were dried overnight at room temperature (22-25 degrees C with 20-40 %RH). The slides were then stored in a chemical (Drierite) desiccator at room temperature until use.


title: UH/MARESH_mus_musculus_32K_V3

status: Public on Sep 20 2007

city: Honolulu

first: John

last: Maresh

address: 651 Ilalo

department: Medicine

institute: University of Hawaii

description: V3 array, murine 32K, UTSouthwestern Microarray Core

middle: G

first: Ralph

last: Shohet

manufacture_protocol: Unknown


title: Operon Human V3.0.2 printed oligonucleotide array

status: Public on Aug 25 2007

middle: R.

last: Cullen

address: CARL Bldg 427, Research Drive

institute: Duke University Medical Center

manufacturer: Duke Microarray Facility (manufactured printing of arrays)

first: Holly

middle: K

last: Dressman


title: MRC MGU Harwell NIA 15K Spotted cDNA Microarray

status: Public on Oct 24 2007

city: Cambridge

first: Akhilesh

middle: Basi

last: Reddy

address: Hills Road

department: Institute of Metabolic Science

institute: University of Cambridge

manufacturer: MRC Mammalian Genetics Unit, Harwell, UK


title: UCSF 7Hs version 2 human long oligo array

status: Public on Oct 08 2007

city: San Francisco

first: Donna

last: Albertson

department: Comprihensive Cancer Center

institute: University of California San Francisco

description: Spotted long oligonucleotide array produced using Operon Human Genome Oligo Set Version 2 probes. This set includes 21329 oligonucleotides (mostly 69-mers) designed based upon representative sequences in build 147 of the human UniGene database. 12 negative control oligos are also included on these arrays.

manufacture_protocol: Please Contact UCSF Shared Microarray Facility


title: 3D-Gene Human Immunity & Metabolic Symdrome 9k

status: Public on Aug 11 2007

city: Kamakura

first: Satoko

last: Takizawa

state: Kanagawa

address: 6-10-1 Tebiro

department: New Frontiers Research Laboratories

institute: TORAY Industries, Inc.

description: Ultra-sensitive DNA chip for human gene expression analysis, specially in the studies of immunology and the metabolic syndrome.

manufacture_protocol: See manufacurer's web site


title: DKFZ/Operon Human 11K Oligo Set v2.1

status: Public on Jul 29 2007

city: Heidelberg

first: Hendrik

last: Reuter

department: Moleculare Genetics B060

institute: DKFZ

description:
Spotted long oligonucleotide array produced using the Operon Human Genome Oligo Set Version 2.1 (21,329 70mer oligonucleotides, based on build #147 of the Human UniGene database).
Keywords = spotted
Keywords = human
Keywords = long oligonucleotide
Keywords = oligo
Keywords = 70mer
Keywords = Operon
Spotted long oligonucleotide array produced using the Operon Human Genome Oligo Set Version 2.1 (21,329 70mer oligonucleotides, based on build #147 of the Human UniGene database).
Keywords = spotted
Keywords = human
Keywords = long oligonucleotide
Keywords = oligo
Keywords = 70mer
Keywords = Operon

manufacturer: Division Molecular Genetics, DKFZ Heidelber, Germany

first: Meinhard

last: Hahn

first: Peter

last: Lichter

manufacture_protocol: 70mer oligonucleotides were diluted at 40 µM in FBNC buffer (G. Wrobel et al., Nucleic Acids Res 31 e67, 2003) and spotted as array duplicates using epoxy-silane coated glass slides (Schott Nexterion) and stainless steel split pins (SMP3, Telechem) at 20°C and 40% rH. Slides were dried (60' @ 60°C) and DNA was UV-crosslinked with 240 mJ/cm2 @ 254 nm. Slides were stored, sealed airtight and dry, at 4°C.


title: Mm_FCRF_UniGEM2

status: Public on Sep 01 2007

city: Bethesda

first: Jeffrey

last: Green

address: Rm 4054, 37 Convent Drive

institute: NCI

description: The mouse cDNA probe set is based on 9984 PCR products from Incyte's mouse UniGEM 2.0 library (http://www.incyte.com).

first: Kristin

last: Deeb

first: Aleksandra

last: Michalowska

first: Cheol-yong

last: Yoon

first: Scott

last: Krummey

first: Mark

middle: J

last: Hoenerhoff

first: Claudine

last: Kavanaugh

first: Ming-chung

last: Li

first: Francesco

last: Demayo

first: Ilona

last: Linnoila

first: Chu-xia

last: Deng

first: Eva

last: Lee

first: Daniel

last: Medina

first: Joanna

last: Shih

first: Jeffery

manufacture_protocol: Printing by the NCI-Frederick/LMT Microarray Research Facility with BioRobotics TAS II robotic arrayer from Genomic Solutions (http://www.genomicsolutions.com) on Fisher Premium microscope slides coated with poly-L-lysine and post-processed according to the procedures on the NCI website http://nciarray.nci.nih.gov/. http://nciarray.nci.nih.gov/reference/NCIReference.shtml


title: Nimblegen_yeast_expression_24mer

city: Yokosuka

first: Fumiyoshi

last: Abe

address: 2-15 Natsushima-cho

department: Extremobiosphre Research Center

institute: Japan Agency for Marine-Earth Science and Technology

organism: Saccharomyces cerevisiae

manufacture_protocol: High-density microarrays based on Maskless Array Synthesizer (MAS) technology. At the heart of the MAS technology is the Digital Micromirror Device (DMD), an array of 786,000 tiny aluminum mirrors, arranged on a computer chip, where each mirror is individually addressable. Using these tiny aluminum mirrors to shine light in specific patterns, coupled with the photo deposition chemistry, produces arrays of oligonucleotide probes.


title: LA Biomed_candida albicans_6266_1.0

status: Public on Jul 18 2007

city: Torrance

first: Hyunsook

last: Park

address: 1124 W carson st

department: Infectious Diseases

institute: Los Angeles Biomedical Research Institute at Harbor-UCLA medical center

organism: Candida albicans

last: Filler

first: Haoping

last: Liu

first: Norma

last: Solis

manufacture_protocol:
www.operon.com
www.amersham.com


title: UNAM HUMAN 10K v1.0

city: Rio de Janeiro

first: Ulisses

middle: Gazos

last: Lopes

state: Rio de Janeiro

address: Cidade Universitaria- CCS

department: Molecular and Structural Biology

country: Brazil

institute: Federal University of Rio de Janeiro

manufacturer: Unidad de Microarreglos de DNA - UNAM - Mexico

first: Jorge

last: Ramirez

first: Alessandra

last: Saliba

manufacture_protocol: 50 mer oligos purchased from MWG, collection A. 10000 oligos. Number of applications 2, total number of applications 20000, array area 18X36 mm, distance between applications 185uM. Bio-Rad Versarray chipwriter hardware


title: CNIO Human Oncochip 2.0

status: Public on Jul 25 2007

city: Madrid

first: Barbara

last: Angulo

address: Melchor Fernandez Almagro, 3

department: Molecular Pathology Program

country: Spain

institute: Spanish National Cancer Centre

description: CNIO Human Oncochip 2.0 is a cDNA microarray which consists of 27648 features, with 11768 cDNA clones representing over 9300 genes. This microarray is specially designed to study the genes involved in cancer, it includes: 1) genes with known molecular function and involved in cell processes related to cancer like cell cycle control, apoptosis, angiongenesis, cell adhesion, etc.; 2) tissue specific genes; 3) housekeeping genes as positive controls and non human genes as negative controls. Since the microarray spotter is equipped with 48 capillary pins, the spots are arrayed over the entire length of the slide in 48 subarrays, arranged in 4 meta-columns and 12 meta-rows. Each subarrays consists 24 columns x 24 rows.

manufacturer: Genomic Unit, Biotechnology Program, Spanish National Cancer Research Centre

manufacture_protocol:
1.- Individual I.M.A.G.E. Consortium [LLNL] clones were grown in 96-well plates at 37°C for 6 hours.
2.- The bacterial cultures were used for PCR amplification.
3.- PCR products were purified by ultrafiltration, verified by agarose gel electrophoresis and quantified by gel image densitometry.
4.- Probe concentrations were adjusted in 50% DMSO at about 100-150 ng/ul.
5.- Probes were printed onto Gamma Amino Silane Coated glass slides (CMT-GAPS Corning) using the spotter Multigrid II (BioRobotics).
6.- After printing, the slides were baked for 4 hours at 80ºC and stored desiccated in the dark, under vacuum and at room temperature.


title: NMC Homo sapiens 21K Hs-OperonV2

status: Public on Sep 30 2007

city: Oslo

first: Nur

last: Duale

address: Lovisenbergg. 8, P.O.Box 4404 Nydalen,

department: Division of Climate and Environment Health

country: Norway

institute: Norwegian Institute of Public Health

description:
•Printing plates: 384 well low profile plates from Genetix (Cat# X60004)
•Spotting conditions: 20–22°C and at 45–55% RH.
•Slide post-processing: Slides are stored in a desicator cabinet to dry for 24-48 hours after spotting, and UV-crosslinked at 800 mJ/cm2
(active side up) using a UV-Stratalinker 2400 from Stratagene Inc. The arrays are stored in Corning slide boxes before use.

manufacturer: Norwegian Microarray Consortium (Radiumhospital, Oslo, Norway)

first: Gunnar

last: Brunborg

manufacture_protocol:
Array Production Details:
•Spotting Instrumentation: MicroGrid II arrayer (model# 600),
MicroSpot pin tool (Cat# BR001482),
MicroSpot 10 K Split pins (Cat# BR001489),
BioRobotics (see the description for the MicroGrid arrayer at the Genomic Solutions website)
•Slide substrates: CMT UltraGAPS slides (25x75 mm) , Aminosilane coating (Corning Cat# 40016)
•Oligonucleotide consentration: 40 μM (600 pmol oligonucleotide dissolved in 15 μL 50% DMSO)
•Spotting buffer: 50% Dimethyl Sulphoxide (DMSO), (Sigma Cat# D-8418)


title: Operon Human V2; print layout 2

status: Public on Jul 03 2007

city: Boston

first: Geoffrey

last: Cooper

address: 5 Cummington St

department: Biology

institute: Boston University

description: Custom spotted oligonucleotide print of Operon's Human Array-Ready Oligo Set Version 2, layout 2.

first: John

middle: W

last: Tullai

first: Michael

last: Schaffer

first: Steven

last: Mullenbrock

first: Gabriel

middle: D

last: Sholder

first: Simon

last: Kasif

manufacture_protocol: Microarrays were fabricated by resuspending 21,329 70-mer oligonucleotides from OperonÕs Human Genome Array-Ready Oligo Set Version 2.0 in 3X SSC to a final 30 micromolar concentration, and spotted onto amino-silane coated GAPS II slides (Corning) with an OmniGrid Accent microarrayer (GeneMachines).  After drying, the slides were post-processed according to the oligonucleotide manufacturerÕs protocol.  Briefly, to promote spot uniformity, the microarrays were rehydrated with nuclease-free water and snap-dried on a 100 degree C hot plate.  The slides were UV crosslinked with 65 mJ of energy and shaken for 20 min in a blocking solution of 1-methyl-2-pyrrolidinone, 171 mM succinic anhydride, and 43 mM sodium borate.  Finally, the slides were washed successively in water and 95% ethanol, then centrifuged at 800 rpm for 5 min to dry.


title: ConPath Chip 4600

status: Public on Jul 06 2007

city: Yokohama

last: DNA Chip Research Inc.

institute: DNA Chip Research Inc.

description: ConPath Chip 4600

manufacture_protocol: see manufacturer's web site


title: UHNMAC Homo sapiens 19K Hu19Kv8

status: Public on Jul 31 2007

city: Toronto

first: Mark

last: Cameron

state: Ontario

address: 3-913 TMDT, MaRS Centre, 101 College St.

country: Canada

institute: UHN

description: This set includes 19200 cDNA clones from the IMAGE consortium, single spotted array containing 19,008 characterized and unknown human ESTs. The clone set has been sequence-verified at the Microarray Centre and the sequences can be downloaded for validation.

first: Jim

last: Woodget

first: Neil

last: Winegarden

first: Patrick

last: Yau

first: Bryan

last: McNeil

first: Eric

last: Ho

manufacture_protocol: as described on the UHN Microarray Centre website (www.microarrays.ca)


title: NIAID_Mouse_16475_Mmbe-62-02

status: Public on Jul 11 2007

first: Stephen

middle: John

last: Davies

address: 4301 Jones Bridge Road

department: Microbiology and Immunology

institute: USUHS

first: Erika

last: Lamb

last: Pesce

first: Emily

last: Crow

first: Sean

last: Maynard

first: Thomas

last: Wynn

first: Brian

middle: C

last: Schaefer

manufacture_protocol:
Oligonucleotides manufactured to following specifications:
Length: 70 bases
Modification: 5'-C6 amino modifier
Oligo synthesis efficiency: < 99%
Reduced propensity to form secondary structure
Minimized cross-hybridization potential to non-target mouse or human genes
Consistent theoretical melting temperature with all other oligonucleotides
Bias to the 3' end of the gene for enhanced cDNA labeling
Targeted sequence region of high sequence fidelity and accuracy
Positive and negative controls provided
Oligonucleotides are purified for enriched full-length product and desalted.


title: Sentrix Human-6 v2 Expression BeadChip

status: Public on Nov 13 2007

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

manufacture_protocol: Enables genome-wide expression analysis of multiple samples in parallel on a single microarray. Researchers can profile more than 48,000 transcript probes per sample.


title: Illumina mouse-6 v1.0 expression beadchip

status: Public on Dec 13 2007

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

description:
The Mouse-6 BeadChip can be used to study expression of over 47,000 mouse transcripts based on MEEBO, RefSeq and RIKEN FANTOM2 content. researchers can generate whole-genome expression profiles for 6 samples in parallel on a single BeadChip.

Please use the GEO Data Submission Report Plug-in v1.0 for Gene Expression which may be downloaded from https://icom.illumina.com/icom/software.ilmn?id=234 to format the normalized and raw data.  These should be submitted as part of a GEOarchive.  Instructions for assembling a GEOarchive may be found at http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html

relation:
Alternative to: GPL6283
Alternative to: GPL6333
Alternative to: GPL5798

manufacture_protocol: see manufacturer's website


title: Illumina humanRef-8 v1.0 expression beadchip

description:
The HumanRef-8 Expression BeadChip contains eight arrays of > 24,000 probes derived from the RefSeq database.

Please use the GEO Data Submission Report Plug-in v1.0 for Gene Expression which may be downloaded from https://icom.illumina.com/icom/software.ilmn?id=234 to format the normalized and raw data.  These should be submitted as part of a GEOarchive.  Instructions for assembling a GEOarchive may be found at http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html


title: Operon Human V2; print layout 1

first: Geoffrey

last: Cooper

description: Custom spotted oligonucleotide print of Operon's Human Array-Ready Oligo Set Version 2, layout 1.

first: John

last: Tullai

first: Michael

middle: E

last: Schaffer

last: Mullenbrock

last: Sholder

last: Kasif


title: NHGRI Homo sapiens 29k cDNA Agilent

status: Public on Jul 01 2007

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

first: Paul

middle: S

last: Meltzer

manufacture_protocol: Agilent


title: 3D-Gene Human Oligo chip 25k

first: Satoko

last: Takizawa

description: Ultra-sensitive DNA chip for human genome wide gene expression analysis

manufacture_protocol: See manufacurer's site


title: YN Human 36K (sets1-8)

status: Public on Jun 01 2007

city: Tokyo

first: Hidewaki

last: Nakaagwa

state: Tokyo

address: 4-6-1 Shirokanedai, Minato-ku,

department: Institute of Medical Science

institute: The University of Tokyo

description: Human genome-wide cDNA microarray with 36,864 elements spotted (sets1-8)

manufacturer: Laboratoryof Molecular Medicine, Instutute of Medical Science, the University of Tokyo

first: Yusuke

last: Nakamura

first: Toyomasa

last: Katagiri

last: Nakagawa

manufacture_protocol: 36,864 transcripts including ESTs were chosen as target cDNAs, and their sequences were retrieved from the UniGene database (National Center for Biotechnology Information; build# 131). A mixture of pooled mRNA from the liver, spleen, thyroid, placenta, skeletal muscle, small intestine, brain, heart, fetal lung, fetal liver, fetal kidney, and fetal brain (Clontech) were used for target cDNA preparation. Each RNA was reverse transcribed using oligo(dT) primer and Superscript II reverse transcriptase (Invitrogen). We amplified cDNA segments of 200-1100-bp long without repetitive or polyadenylated sequences by PCR using the specific primer sets to each gene or EST. The 36,864 PCR products were purified and spotted in duplicate on type 7 or Alice glass slides (Amersham Pharmacia Biotech) using a Microarray Spotter Generation III (Amersham) or Lucidea Microarray Spotter (Amersham), separated on eight or four slides. Each slide contained 52 housekeeping genes, to normalize the signal intensities of the different fluorescent dyes. Spotted DNAs were cross-linked with slides by SPECTRO LINKER (SPECTRONIC Corp.).


title: SMCmou8400A Mus musculus 8k cDNA array

status: Public on Jun 09 2007

city: Beaverton

first: Valerie

last: Matagne

state: OR

address: 505 nw 185th Ave

department: Neuroscience

institute: OHSU

description: Array format is 16 grids, with four rows (metarows) and four columns (metacolumns) of grids.  Grids are 23 x 23.  Each array was printed twice per slide.  The array contains replicates of the Stratagene SpotReport 10 cDNA validation system.  These are Arabidopsis thaliana genes that have no known homology to mammalian genes.  The labels for these in the genelist are A.thaliana_Cab, A.thaliana_RCA, A.thaliana_rbcL, A.thaliana_LTP4, A.thaliana_LTP6, A.thaliana_XCP2, A.thaliana_RCP1, A.thaliana_NAC1, A.thaliana_TIM, and A.thaliana_PRKase.  Included in the SpotReport material is also human_beta_actin.  Genes not identified in the primarily library listing are noted as NoGeneID.  Locations printed with only buffer are listed as LeftBlank.

manufacturer: Oregon Health and Science University Spotted Microarray Core

first: Robert

middle: P

last: Searles

first: Julie

last: Patch

first: Aaron

last: Kabb

first: David

last: Lee

manufacture_protocol:
1.  PCR products were derived from the first 88 plates of the NIA 15k Mouse cDNA clone set.  The reference for the library is:  Tanaka TS, et al. (2000). Genome-wide expression profiling of mid-gestation placenta and embryo using a 15000 mouse developmental cDNA microarray. Proc. Natl. Acad. Sci. USA, 97: 9127-9132.
2.  cDNAs were amplified by PCR using DynaZyme Ext polymerase (MJResearch) using 0.5 units of enzyme per reaction.  Amplification protocol was 94 C for 45 sec, 55 C for 45 sec, and 72 C for 2 min 30 sec for 32 cycles.  Amplifications were performed in an MJResearch PTC-225 Thermal Cycler fitted with four 96-well heads.
3.  PCR products were separated from unincorporated nucleotides using Millipore Multiscreen PCR filter plates and recovered from the filter in 100 ul of water.  2 microliter aliquots were removed and run on 0.8% agarose gels for quality control. Purified PCR products were reduced from 98 microliters to dryness in a LabConCo CentriVap concentrator.  Dried DNA was resuspended in 30 microliters of 50% DMSO and stored frozen at -20C.
4.  Three microliters of each PCR product were transferred to Whatman 384-well microtiter plates for printing.  Printing plates were used up to 7 times.  Plates were stored at -20 C between print runs.  Prior to each print run, thawed plates were spun at 3000 rpm in a Sorvall RT7plus tabletop centrifuge for 10 minutes.
5.  Arrays were printed on Corning UltraGAPS slides using a Cartesian PixSys 5500XL array printer with a Pegasus plate handler attachment.  The plate handler chamber was maintained at 70% relative humidity; the print chamber was maintained at 50% relative humidity.  Printing was done with 16 Telechem CMP-2 array printing pins.  Printing used twenty-two 384-well microtiter plates and took approximately 24 hours.  Printed arrays were baked at 80 C for 3.5 hours in a baking oven.  Arrays were stored in the dark in a sealed desiccator until use.  Prior to use, arrays were blocked for 1 hour at 55 C in 5X SSC, 1.0% SDS, and 2.0% BSA.


title: Operon Homo sapiens 21K (Hs Operon Vw)

status: Public on Apr 19 2007

first: Yuanyuan

last: Xiao

address: 185 Berry Street, Lobby4, Suite 5700

department: Epidemiology and Biostatistics

institute: UCSF

manufacturer: Printed by UCSF Functional Genomics Core Facility

manufacture_protocol: Long oligonucleotides were designed and synthesized by Operon Biotechnologies (Operon Biotechnologies, Huntsville, AL). The Human Genome Oligo Set Version 2 includes 21,329 oligonucleotides, mostly 69-mers that were based upon UniGene build 147. Oligonucleotides were dissolved in 3XSSC at a concentration of 40um in preparation for spotting on aminosilane-coated slides (Schott Nexterion, Elmsford, NY). A custom-built microarrayer equipped with Majer Precision MicroQuill 2000 pins was used to print each batch of 255 slides. A detailed description of the microarrayer (MGuide) is available at the Brown lab's website (Stanford Univeristy). After printing, the slides were stored at room temperature in desiccators.


title: UVicHelbing XenRanaMAGEX 434 ver1

status: Public on May 10 2007

city: Victoria

first: Caren

last: Helbing

state: British Columbia

address: PO Box 3055 Stn CSC

department: Biochemistry and Microbiology

institute: University of Victoria

organism:
Xenopus laevis
Aquarana catesbeiana

first: D

last: Crump

first: K

last: Werry

first: N

last: Veldhoen

first: G

last: van Aggelen

first: C

manufacture_protocol:
The protocol for designing the array is described in detail in Crump, D, Werry, K, Veldhoen, N, van Aggelen, G, and Helbing, CC (2002) Environmental Health Perspectives 110: 1199-1205.
Preparation of RNA. Total RNA was obtained from preserved tadpole tissue using TRIzol reagent as described by the manufacturer (Invitrogen Canada Inc., Burlington, Ontario, Canada). We subsequently resuspended isolated RNA in RNase-free water and stored it at –70°C. Poly(A)+ RNA was isolated from total RNA using the Oligotex mRNA isolation mini kit (Qiagen Inc., Mississauga, Ontario, Canada). Array target sequence selection and primer design. The frog MAGEX (multispecies analysis of gene expression) cDNA array was designed using Xenopus and Rana complete cDNA information obtained from GenBank (GenBank 2001). The abundance of Xenopus cDNA sequences compared to Rana sequences on the array reflects their relative abundance in GenBank. The cDNA sequences chosen encode structurally and functionally important products involved in regulation of amphibian development (embryogenesis and metamorphosis) as well as basal cell metabolism (ViagenX Biotech, Inc. 2002). We selected X. laevis ribosomal L8 (GenBank accession no. U00920) cDNA for normalization, as its mRNA transcript levels remain relatively constant between different developmental stages (Shi and Liang 1994). We included 420 cDNA sequences on the array, of which 390 are X. laevis and 30 are R. catesbeiana in origin. All primers were designed with Primer Premier V4.1 software (Premier Biosoft International, Palo Alto, CA, USA) and synthesized by AlphaDNA (Montreal, Québec, Canada). Primers of 18 to 20 base pairs with an optimal annealing temperature between 50° and 55°C were designed to amplify sequences of between 450 and 550 base pairs within each target cDNA. Primer pairs were combined and diluted to a final concentration of 10 μM. Total cDNA preparation. We prepared individual cDNA target sequences which form the basis of the array clone bank from total RNA isolated from untreated Xenopus tadpoles (NF stages 47 and 58; Nieuwkoop and Faber 1956) and oocyte tissues and Rana tadpoles (stage XV; Taylor and Kollros 1946) using TRIzol reagent as described by the manufacturer (Invitrogen). Total RNA was annealed with 500 ng random hexamer oligonucleotide (Amersham Biosciences, Baie d’Urfe, Québec, Canada) and cDNA was generated using Superscript II RNase H-reverse transcriptase as described by the manufacturer (Invitrogen). The 20-μL reaction was incubated at 42°C for 2 hr and diluted 20-fold before DNA amplification. Amplification, cloning, and verification of target cDNAs. Each 50-μl DNA amplification reaction contained polymerase chain reaction buffer (20 mM Tris-HCl, pH 8.4, 50 mM KCl, 1.5 mM MgCl2), 200 μmol dNTP, 20 pmol of each gene specific primer, 1 μL of a 20-fold dilution of X. laevis or R. catesbeiana total cDNA, and 2.5 U Taq DNA polymerase (Invitrogen). Amplification was carried out in a DNA Thermal Cycler 480 (Perkin-Elmer, Wellesley, MA, USA). The thermocycle program included a denaturation step at 94°C (7 min); 45 cycles of 94°C (1 min), 52°C (1 min), and 72°C (1 min); and a final elongation step at 72°C (7 min). Amplified DNA products were separated on a 1.5% agarose gel and visualized by ethidium bromide staining on a ChemiImager 4000 (Alpha Innotech Corp., San Leandro, CA, USA). We excised DNA bands within the correct size range (450–550 base pairs) from the gel and extracted them by freeze-thaw centrifugation (Smith 1980). We confirmed purified samples by electrophoresis on a 1.5% agarose gel. Polymerase chain reaction products were cloned into pCR II-TOPO vector using the TOPO TA Cloning Kit (Invitrogen). We purified plasmid DNA using the QIAprep Spin Miniprep Kit (Qiagen) and confirmed the presence of insert sequence by restriction analysis using EcoRI (Amersham Biosciences). Cloned cDNA was sequenced and compared by BLAST to sequences available in GenBank. Clones that matched the correct target sequence were included in the plasmid clone bank. Preparation of cDNA fragments for spotting on the array. We prepared specific cDNA fragments for the frog MAGEX cDNA array using the plasmid clone bank. Individual amplification reactions were assembled in 96- well amplification plates (VWR International, Mississauga, Ontario, Canada). Each 100-μl reaction was similar to that described above, except that the target DNA comprised 1 ng of each plasmid clone, and 1 U AmpliTaq polymerase (Applied Biosystems, Foster City, CA, USA) was used. Amplification was carried out in an MJ Research Gradient Cycler PTC-255 (MJ Research, San Francisco, CA, USA). The thermocycle program included a denaturation step at 95°C (2 min); 35 cycles of 95°C (30 sec), 52°C (30 sec), and 72°C (1 min); and a final elongation step at 72°C (10 min). We separated amplified DNA products by electrophoresis on a 1.5% agarose gel and purified them using the QIAquick PCR purification kit and the Qiagen Biorobot 3000. Purified cDNA fragments were resuspended in 3SSC (20SSC contains 3 M NaCl, 0.3 M Na citrate, pH 7.0) to a final concentration of 0.5 μg/μL. The prepared cDNA was then loaded into 384-well plates (VWR International), and 90 nL/spot was spotted in duplicate on Biodyne B positively charged nylon membranes (PALL Gelman Laboratory, Ann Arbor, MI, USA) using the Biorobotics Total Array System (Biorobotics Ltd., Woburn, MA, USA). The spotted membranes were UV-crosslinked and stored at –20°C.


title: AGRF Drosophila melanogaster 16K oligonucleotide microarray

status: Public on Mar 21 2007

city: Parkville

first: Lee

last: Willoughby

state: Victoria

address: 30 Flemington Road

department: Genetics

country: Australia

institute: University of Melbourne

organism: Drosophila melanogaster

description: This spotted oligonucleotide microarray is composed of over 14000 transcript specific features as well as a number of controls, including non-Drosophila targets, spotting buffer and empty wells.  The oligonucleotides were designed by the International Drosophila Array Consortium (INDAC: details at www.INDAC.net).

first: Philip

last: Batterham

manufacture_protocol: Oligonucleotide features were designed by the International Drosophila Array Consortium (INDAC: www.INDAC.net).  The oligonucleotides were synthesised by Illumina  (www.illumina.com).  The microarrays were printed on Corning GAPS II slides (Corning), using a Virtek SDDC2 microarrayer (Virtek Vision International Inc.), by the Australian Genome Research Facility (www.AGRF.org.au).


title: Buck Institute_Homo sapiens_25K_verC

status: Public on May 23 2007

city: Hamilton

first: Adeel

last: Safdar

state: ON

address: 1200 Main Street West

department: Kinesiology

institute: McMaster University

manufacture_protocol: Print plate cDNA was amplified with a standard PCR protocol. cDNA samples were purified and verified with a gel. Purification and gel used robotics (Tecan and Quadra) to process 384-well plates. After purification, cDNA samples were dried down in a speed vacuum and resuspended in a 3XSSC+1.5M Betaine print buffer. Using a Gene Machines Omni grid printer and Telchem Stealth print pins, samples were arrayed in a 32 block, print format on MGM epoy slides.


title: Chinnaiyan Lab Human 34K cDNA microarray-Jan2006

status: Public on Mar 02 2007

city: Navi Mumbai

first: Chandan

last: Kumar

state: Maharashtra

address: Kharghar Node

department: ACTREC

country: India

institute: Tata Memorial Center

manufacturer: Arul Chinnaiyan Lab, Department of Pathology, University of Michigan, Ann Arbor, MI, USA

manufacture_protocol: PCR amplified and purified cDNA inserts from ResGen clones printed on poly-L-lysine coated slids using quill-type pins.


title: FilgenArray Human35k

status: Public on Apr 20 2007

city: Nagoya

first: Manabu

last: Harada

address: 15-1 Nakanoshima, Ohdaka-cho, Midori-ku

department: Biosciences

institute: Filgen,Inc.

manufacture_protocol: Array-Ready Oligo Set for Human Genome Version 3.0 from Operon Biotechnologies, Inc. was spotted using a GeneMachines OmniGrid Arrayer . The microarrays printed on Corning Ultra-GAPS slides (Item #40018) coated with amino-silane and post-processed according to the manufacturer's protocol.


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array [MBNI v6 Entrez Gene ID CDF]

status: Public on Jun 12 2007

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: This array is identical to GPL570 but the data were analyzed with custom CDF environments created by the MBNI - The version 6 entrez gene ID CDF was used.

relation: Alternative to: GPL570 (Alternative CDF [official])

manufacture_protocol: see the Affymetrix website


title: GMRCL Human 7K

status: Public on May 29 2007

city: Teipei

first: Yun-Shien

address: No.199, Tunghwa Rd.,

institute: Chang Gung Memorial Hospital

description: UltraGAPS Coated slides (Corning).

manufacturer: Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital;

first: Tzu-Hao

last: Wang

manufacture_protocol: cDNA microarrays were spotted using PCR products obtained with the Incyte Genomics. Spotters: Qarray Genetix, with split pins (ArrayIt Brand Products, ChipMaker CMP4). Double stranded DNA in Microarray Spotting Solution (Genetix, GSS-50) were binding to the UltraGAPS Coated slides (Corning), by UV-mediated crosslinking.


title: ACTREC Homo sapiens 23K

status: Public on Mar 07 2007

manufacturer: A Private Commercial Organization (Name withheld)

manufacture_protocol: Spotted microarrays printed on UltraGAPS™ slides (Corning Inc.) using Genomics Solutions' Omnigrid Microarrayer


title: Conway Institute Candida parapsilosis 3851 v1.0

status: Public on Mar 01 2007

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

organism: Candida parapsilosis

manufacturer: University College Dublin, Conway Institute

first: Tristan

last: Rossignol

first: Mary

last: Logue

manufacture_protocol:
Oligonucleotides were designed from the genome sequence survey of C. parapsilosis CLIB214 (Logue, M. E., S. Wong, K. H. Wolfe, and G. Butler. 2005. A genome sequence survey shows that the pathogenic yeast Candida parapsilosis has a defective MTLa1 allele at Its Mating Type Locus. Eukaryot Cell 4:1009-1017).
Oligonucleotides were synthesized by Operon Biotechnologies and resuspended in printing buffer from Genetix at a final concentration of 50 µM.  In total, 3851 oligonucleotides representing 3849 putative genes and the 2 positive controls were printed in duplicate on UltraGAPS coated slides (Corning) using a Q-array robot (Genetix) controlled with Qsoft software (Genetix). The general design is 2 subarrays of 16 blocks each, with all oligonucleotides spotted in duplicate, one copy per block. The slides were air dried for 2 days and DNA was cross-linked to the slide by UV at 6200 mJ cm-2 in an UV-linker (Stratagene). The slides were pre-soaked in a solution consisting of 75 % PBS, 25 % ethanol and 0.5% sodium borohydride (Alfa Aesar) for 4 h at 42ºC to remove potential spot autofluorescence. The slides were subsequently washed 3 times in water, 1 time in isopropanol, dried, and stored.


title: UCSF Gladstone Genomics Core Mus Musculus 16k Oligo array (2005)

status: Public on Apr 03 2007

city: San Francisco

first: Sergio

last: Baranzini

state: CA

address: 513 Parnassus Ave

department: Neurology

institute: University of California San Francisco

description: This set includes 16496 oligonucleotides, mostly 60- to 70-mers

manufacture_protocol: Please Contact UCSF Gladstone Genomics Core


title: Aviva-6khu-promoter

status: Public on May 01 2007

city: Chicago

first: Jindan

last: Yu

state: IL

address: 303 E. Superior St.

department: Medicine - Hem/Onc

institute: Northwestern University

description: This 6144-element (8 blocks, 12 rows, 64 columns) array contain spotted DNAs of promoter regions (800-1000 bp on average) typically from 650bp upstream to 250bp downstream of transcription start sites.

first: Arul

middle: M

last: Chinnaiyan


title: NIA Mouse 22.4K cDNA array_Hepatotoxicity

status: Public on Feb 27 2007

city: Lucknow

first: Sanjeev

last: Noel

state: Uttar Pradesh

address: M G Marg

department: Toxicology

institute: Central Drug Research Institute

first: Srikanta

last: Rath

manufacture_protocol: The clone sets from NIA were PCR amplified and purified before spotting on CMT-GAP II slides (Corning). Post Printing Quality Control tests include a real hybridization using commercially available mouse RNA, vector probe labeling and terminal transferase tailing method to assess spot morphology, background quality and intensity of signal. More information is available on http://www.microarrays.ca


title: SBTM Microarray Laboratory Operon Mouse v4.0

status: Public on Feb 23 2007

city: Temple

first: Vincent

last: VanBuren

state: TX

address: 702 SW HK Dodgen Loop

department: Systems Biology and Translational Medicine

institute: Texas A&M Health Science Center

manufacturer: The SBTM Microarray Laboratory, Systems Biology, 702 SW HK Dodgen Loop, Temple, TX 76504

first: Robert

last: Jamroz

first: Reza

last: Forough

manufacture_protocol: The Array-Ready Mus musculus Genome Oligo Set Version 4.0 from Operon Biotechnologies, Inc. was spotted using a GeneMachines OmniGrid Arrayer (Arrayer manual/spotting protocol available at the Genomic Solutions website; complete genelists, annotations, and datasheets for oligos available at the Operon Biotechnologies website). Array descriptions may be found at the SBTM Microarray Laboratory website.


title: NIA Mouse 15K cDNA array_Hepatotoxicity

manufacture_protocol:
The mouse 15k bacterial clone sets from NIA were PCR amplified and purified before spotting on CMT-GAP II slides (Corning). Post Printing Quality Control tests include a real hybridization using commercially available mouse RNA, vector probe labeling and terminal transferase tailing method to assess spot morphology, background quality and intensity of signal. More information is available on http://www.microarrays.ca
Duplicate adjacent spots on the array.


title: VIB Crohn 7k version 2

status: Public on May 03 2007

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
The arrray design contains 15,552 features printed in a layout of 12 meta rows and 4 meta columns, consisting out of 18 rows and 18 columns per block.  The array measures the expression of 6,779 features, spotted in duplicate.  Meta column 1 is a replicated in meta column 2 and meta column 3 is replicated in meta column 4.  The Lucidea Universal ScoreCard controls (Amersham Biosciences Buckinghamshire, UK) are added, making a total of 384 controls, also spotted in duplicate (i.e., 768 control spots).  A set of 1,226 spots remained empty.
The Platform data table reflects a condensed representation of the array. The complete array layout file representing the duplicate-spotted features is linked as a supplementary file.

first: Debby

last: Laukens

first: Pieter

last: Rottiers

first: Paul

last: Van Hummelen

manufacture_protocol:
Equipment:
1. Generation III microarray spotter (Amersham Biosciences, Buckinghamshire, UK).
2. 384 microtiter plates (Amersham Biosciences, Buckinghamshire, UK).
3. UV-crosslinker (Biolink, BLX-254, Vilber Lourmat, France).
4. Type VII silane coated slides (cat#: RPK0174, Amersham BioSciences, Buckinghamshire, UK).
Spotting:
1. Dissolve cDNA array elements in 50% DMSO at concentrations ranging between 100-200ng/µl and array in 20 384 microtiter plates.
2. Set spotter: normal mode, 69% humidity, 65% inside humidity, spot diameter: 224, spot buffer: 30, and pen deflection:0.508mm.
3. Make sure room temperature is between 20-24 degrees Celsius.
4. Place microtiter plates in the plate hotel with A1 in upper right corner.
5. Place 75 slides on the slide-deck and perform 2 manual pin-washes.
6. After spotting, let slides dry at 55% humidity for 3 hours and cross-link at 50 mjoules.
7. Block slides in %SSPE for 30 minutes at room temperature rinse in water and dry in centrifuge.
8. Slides can be stored for at least 6 months in a dry-cabinet.


title: Custom cDNA array from NIA mouse clone set

status: Public on Mar 08 2007

city: Bethesda

first: TIN-LAP

last: LEE

state: MD

address: 2C08 Building 49

department: NICHD

country: USA

institute: National Institutes of Health

description: Custom cDNA array based on NIA mouse 15k clone set.

manufacturer: Department of Pathology, Loyola University Medical Center, Maywood, IL 60153, USA

first: Wai-Yee

last: Chan

first: Tin-Lap

last: Lee

first: Michael

last: Leung

first: Yan

last: Su

first: Owen

last: Rennert

manufacture_protocol: The arrays was fabricated from NIA mouse 15k cDNA clone set by standard 96-well plate protocol and printed onto glass slide surface (20x60mm) by ink-jet mechanism.


title: MLRG/DrosoIndac Drosophila melanogaster 15K

status: Public on Apr 24 2007

city: Montpellier

first: Laurent

last: Journot

address: 141 rue de la Cardonille

country: France

institute: MGX - Montpellier GenomiX

description: The Drosophila melanogaster INDAC Oligo-chip contain 14,444 70mer probes representing 13,900 genes and 19,239 transcripts (see the International Drosophila Array Consortium website for details), All probes are designed from gene transcript sequences from the Flybase release 4.2 database (see the Flybase website for details). The library also included sets of positive and negative controls that were used for quality control purposes. Arrays were printed using the Amersham Biosciences Lucidea Array spotter on aminosilane-coated mirror glass slides (Exprexions™ slideGenExprex).

manufacturer: Montpellier Génopole Microarray core facility

first: Dany

last: Severac

first: Cindy

last: Aknin

first: Christelle

last: Dantec

manufacture_protocol: The Drosophilia Indac oligo set were spotted using the Amersham Biosciences Lucidea Array spotter on aminosilane-coated mirror glass slides (7 Star, Amersham Biosciences). Negative and positive control oligo were also printed into 24 different sectors of each slide. After printing, the slides were stored at room temperature in a dessicator.


title: SBTM Microarray Laboratory Operon Human v2.1

first: Vincent

last: VanBuren

manufacture_protocol: The Array-Ready Homo sapiens Genome Oligo Set Version 2.1 from Operon Biotechnologies, Inc. was spotted using a GeneMachines OmniGrid Arrayer (Arrayer manual/spotting protocol available at the Genomic Solutions website; complete genelists, annotations, and datasheets for oligos available at the Operon Biotechnologies website). Array descriptions may be found at the SBTM Microarray Laboratory website.


title: ViagenX MAGEX 401 ver1

first: Caren

last: Helbing

first: D

last: Crump

first: K

last: Werry

first: N

last: Veldhoen

first: G

last: van Aggelen

first: C

manufacture_protocol:
The protocol for designing the array is described in detail in Crump, D, Werry, K, Veldhoen, N, van Aggelen, G, and Helbing, CC (2002) Environmental Health Perspectives 110: 1199-1205.
Preparation of RNA. Total RNA was obtained from preserved tadpole tissue using TRIzol reagent as described by the manufacturer (Invitrogen Canada Inc., Burlington, Ontario, Canada). We subsequently resuspended isolated RNA in RNase-free water and stored it at –70°C. Poly(A)+ RNA was isolated from total RNA using the Oligotex mRNA isolation mini kit (Qiagen Inc., Mississauga, Ontario, Canada). Array target sequence selection and primer design. The frog MAGEX (multispecies analysis of gene expression) cDNA array was designed using Xenopus and Rana complete cDNA information obtained from GenBank (GenBank 2001). The abundance of Xenopus cDNA sequences compared to Rana sequences on the array reflects their relative abundance in GenBank. The cDNA sequences chosen encode structurally and functionally important products involved in regulation of amphibian development (embryogenesis and metamorphosis) as well as basal cell metabolism (ViagenX Biotech, Inc. 2002). We selected X. laevis ribosomal L8 (GenBank accession no. U00920) cDNA for normalization, as its mRNA transcript levels remain relatively constant between different developmental stages (Shi and Liang 1994). We included 420 cDNA sequences on the array, of which 390 are X. laevis and 30 are R. catesbeiana in origin. All primers were designed with Primer Premier V4.1 software (Premier Biosoft International, Palo Alto, CA, USA) and synthesized by AlphaDNA (Montreal, Québec, Canada). Primers of 18 to 20 base pairs with an optimal annealing temperature between 50° and 55°C were designed to amplify sequences of between 450 and 550 base pairs within each target cDNA. Primer pairs were combined and diluted to a final concentration of 10 μM. Total cDNA preparation. We prepared individual cDNA target sequences which form the basis of the array clone bank from total RNA isolated from untreated Xenopus tadpoles (NF stages 47 and 58; Nieuwkoop and Faber 1956) and oocyte tissues and Rana tadpoles (stage XV; Taylor and Kollros 1946) using TRIzol reagent as described by the manufacturer (Invitrogen). Total RNA was annealed with 500 ng random hexamer oligonucleotide (Amersham Biosciences, Baie d’Urfe, Québec, Canada) and cDNA was generated using Superscript II RNase H-reverse transcriptase as described by the manufacturer (Invitrogen). The 20-μL reaction was incubated at 42°C for 2 hr and diluted 20-fold before DNA amplification. Amplification, cloning, and verification of target cDNAs. Each 50-μl DNA amplification reaction contained polymerase chain reaction buffer (20 mM Tris-HCl, pH 8.4, 50 mM KCl, 1.5 mM MgCl2), 200 μmol dNTP, 20 pmol of each gene specific primer, 1 μL of a 20-fold dilution of X. laevis or R. catesbeiana total cDNA, and 2.5 U Taq DNA polymerase (Invitrogen). Amplification was carried out in a DNA Thermal Cycler 480 (Perkin-Elmer, Wellesley, MA, USA). The thermocycle program included a denaturation step at 94°C (7 min); 45 cycles of 94°C (1 min), 52°C (1 min), and 72°C (1 min); and a final elongation step at 72°C (7 min). Amplified DNA products were separated on a 1.5% agarose gel and visualized by ethidium bromide staining on a ChemiImager 4000 (Alpha Innotech Corp., San Leandro, CA, USA). We excised DNA bands within the correct size range (450–550 base pairs) from the gel and extracted them by freeze-thaw centrifugation (Smith 1980). We confirmed purified samples by electrophoresis on a 1.5% agarose gel. Polymerase chain reaction products were cloned into pCR II-TOPO vector using the TOPO TA Cloning Kit (Invitrogen). We purified plasmid DNA using the QIAprep Spin Miniprep Kit (Qiagen) and confirmed the presence of insert sequence by restriction analysis using EcoRI (Amersham Biosciences). Cloned cDNA was sequenced and compared by BLAST to sequences available in GenBank. Clones that matched the correct target sequence were included in the plasmid clone bank. Preparation of cDNA fragments for spotting on the array. We prepared specific cDNA fragments for the frog MAGEX cDNA array using the plasmid clone bank. Individual amplification reactions were assembled in 96- well amplification plates (VWR International, Mississauga, Ontario, Canada). Each 100-μl reaction was similar to that described above, except that the target DNA comprised 1 ng of each plasmid clone, and 1 U AmpliTaq polymerase (Applied Biosystems, Foster City, CA, USA) was used. Amplification was carried out in an MJ Research Gradient Cycler PTC-255 (MJ Research, San Francisco, CA, USA). The thermocycle program included a denaturation step at 95°C (2 min); 35 cycles of 95°C (30 sec), 52°C (30 sec), and 72°C (1 min); and a final elongation step at 72°C (10 min). We separated amplified DNA products by electrophoresis on a 1.5% agarose gel and purified them using the QIAquick PCR purification kit and the Qiagen Biorobot 3000. Purified cDNA fragments were resuspended in 3SSC (20SSC contains 3 M NaCl, 0.3 M Na citrate, pH 7.0) to a final concentration of 0.5 μg/μL. The prepared cDNA was then loaded into 384-well plates (VWR International), and 90 nL/spot was spotted in duplicate on Biodyne B positively charged nylon membranes (PALL Gelman Laboratory, Ann Arbor, MI, USA) using the Biorobotics Total Array System (Biorobotics Ltd., Woburn, MA, USA). The spotted membranes were UV-crosslinked and stored at –20°C.


title: SPOC1_MMCC

status: Public on Feb 06 2007

city: Irvine

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

organism: Salmonella enterica

first: Steffen

last: Porwollik

first: Carlos

last: Santiviago

first: Xiao-Qin

last: Xia

manufacture_protocol: Custom made Salmonella oligo array


title: RNG-MRC Mus musculus 25k STRASBOURG

status: Public on Feb 02 2007

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

last: Le Brigand

first: Pascal

last: Barbry

first: Bernard

last: Jost

first: Philippe

last: Kastner

manufacture_protocol: Spotted microarray


title: CNIO Homo sapiens Oncochip 2 (27.648)

status: Public on Feb 09 2007

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

institute: Genomics Consulting

manufacturer: Spanish National Cancer Centre (CNIO Genomics Unit)

first: Gema

last: Moreno-Bueno

manufacture_protocol:
[spotted] cDNA microarrays
The CNIO Oncochip contains about 11,500 cDNA clones representing 9,300 genes (UniGene clusters) plus several hundred not included in UniGene


title: SRC Mouse Compugen Printed Long Oligonucleotide 22K run 118

status: Public on Feb 01 2007

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

institute: Institute for Molecular Bioscience, Uni of Qld

manufacture_protocol: Please see the SRC microarray facility website


title: FHCRC Human Prostate PEDB cDNA Array v9

city: Seattle

first: Denise

last: Mauldin

state: WA

address: 1100 Fairview Ave N D4-100

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: FHCRC Human Prostate PEDB cDNA Array v9

first: Peter

last: Nelson

first: Ilsa

last: Coleman

first: Ruthy

last: Dumpit

last: Abbott

manufacture_protocol: DNA spotted onto polylysine-coated glass microscope slides


title: FHCRC Human Prostate PEDB cDNA Array v8

description: FHCRC Human Prostate PEDB cDNA Array v8


title: FHCRC Human Prostate PEDB cDNA Array v5

description: Version 5 of the Prostate Expression Database Array.


title: MRC Homo sapiens 6K Hs030602

status: Public on Jan 26 2007

city: Leicester

first: Jerry

last: Styles

state: Leicestershire

address: Robert Kilpatrick Building, Univ. Leicester

department: Cancer Studies and Molecular Medicine

institute: University of Leicester

first: Ayman

last: Ewies

first: Farook

last: Al-Azzawi

first: Mona

last: El-Shafie

first: Jin

last: Li

first: Adrian

last: Stanley

first: Bryan

last: Williams

first: John

last: Thompson

first: Ian

middle: N

last: White

manufacture_protocol:
5680 EST clones were obtained from Research Genetics (Human known gene set). The actual clones were obtained from the IMAGE collections held at the MRC Human Genome Mapping Project. These clones were sequence verified prior to arraying. All of the plasmid inserts were amplified by use of a universal primer set and a standard PCR mix (ABGene) employed. The products were all electrophoresed on an agarose gel and the gel images stored for future reference.
All PCR products that failed an initial amplification or produced multiple bands were re-amplified using plasmid specific primers. The size of the insert sequence was determined from the agarose gel by comparison with ladder using MultiAnalyst software (BioRad). After PCR the reaction products were precipitated and prepared for array using the methods described by Eisen and DeRisi (DeRisi et al., 1997; Eisen et al., 1999).
Arrays were printed on poly-L-lysine coated slides and UV crosslinked and blocked prior to use (DeRisi et al., 1997; Eisen et al., 1999). The arrays were printedusing an arrayer built essentially according to the Stanford designs and can be seen at the MRC toxicology website. The centre to centre distance of the features was 210 um and each feature was 90-100 um in diameter


title: SRC Mouse Compugen Printed Long Oligonucleotide 22K set Run 30

status: Public on Jan 24 2007


title: RNG-MRC_HU2k_v4

status: Public on Jan 06 2007

first: Kevin

last: Lebrigand

last: Le Brigand

first: Pascal

last: Barbry

first: Bernard

last: Mari


title: FHCRC Human Prostate PEDB cDNA Array v6

last: Mauldin

description: FHCRC Human Prostate PEDB cDNA Array v5

last: Nelson


title: FHCRC Human Prostate PEDB cDNA Array v7

description: FHCRC Human Prostate PEDB cDNA Array v7

last: Coleman

last: Dumpit


title: FHCRC Human Prostate PEDB cDNA Array v10

last: Abbott


title: Agilent Human 1 cDNA with custom annotation and filtering

status: Public on Jan 15 2007

city: Brussels

first: Vincent

last: Detours

address: 808 Route de Lennik

department: School of Medicine

institute: Free University of Brussels

description: 12430 unique human clones.

first: Laurent

last: Delys

manufacture_protocol:
For manufacturing see Agilent Human 1 cDNA plateform (GEO accession GPL875).

Feature were re-annotated from munufaturer-supplied GenBank IDs using R/Bioconductor AnnBuilder package 1.4.4, Locuslink as available on 10/31/2003 and Unigene #163.

All control and "Fiducial" spots were filtered out. Expression were averaged over duplicated GenBank accessions.


title: NimbleGen_1500b_Promoter_Array

status: Public on Jan 25 2007

city: Columbus

first: Victor

middle: X

last: Jin

state: OH

address: 333 West 10th Ave

department: Biomedical Informatics

institute: OSU Medical Center

first: Henny

last: O'Geen

first: Sushma

last: Iyengar

first: Roland

last: Green

first: Peggy

last: Farnham

manufacture_protocol:
CHIP_Protocol decribes the process for immunoprecipitation and amplification by WGA (Sigma) of samples derived from cultured eukarotic cells.
Hybridization_Protocol describes the process for hybridization of samples prepared by chromatin immunoprecipitation and amplified by WGA on NimbleGen DNA microarrays.
Scan_Protocol describes the process of scanning NimbleGen two-color arrays with Axon GenePix 4000B Scanner and associated software.


title: Rosetta/Merck Mouse 25k v1.9 microarray

status: Public on Dec 26 2006

city: Rahway

first: Olivia

last: Fong

state: NJ

department: Molecular Profiling

institute: Merck & Co.

description:
Oligonucleotide array on glass.
Contains 60-mer probes (60-mer).

manufacturer: Rosetta Inpharmatics / Merck Pharmaceuticals

first: Amit

last: Kulkarni

last: Castle

manufacture_protocol: see manufacturer's web site


title: Bando (Agilent Whole Human Genome Oligo Microarray)

status: Public on Nov 28 2006

city: Tokushima

first: Bando

last: Mika

address: 3-18-15 Kuramoto

institute: University of Tokushima

description:
This is a custom representation of Agilent's Whole Human Genome Oligo Microarray.

This platform is formatted specifically for this users normalized data and should not be referenced by other users.

manufacture_protocol: see manufacturer's web site at http://www.agilent.com/


title: UHNMAC Human 19K v7

status: Public on Jan 09 2007

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description: This set includes 19200 cDNA clones from the IMAGE consortium, single spotted array containing 19,008 characterized and unknown human ESTs. The clone set has been sequence-verified at the Microarray Centre and the sequences can be downloaded for validation."

first: Jim

last: Woodget

first: Neil

last: Winegarden

first: Patrick

last: Yau

last: McNeil

first: Eric

last: Ho

manufacture_protocol: as described on the UHN Microarray Centre website (www.microarrays.ca)


title: Qiagen Human V3 35K Oligo array (HV3)

status: Public on Dec 02 2006

city: bethesda

first: abdel

last: elkahloun

address: 50 south dr

institute: nih

first: Abdel

middle: G

last: Elkahloun

manufacture_protocol: please see the NHGRI Microarray Core Facility website


title: NCI/Staudt mouse 12K v1

status: Public on Nov 24 2006

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

first: Art

last: Shaffer

manufacture_protocol: See reference Alizadeh et al. The lymphochip: a specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes. Cold Spring Harb Symp Quant Biol. 64, 71-8 (1999).


title: NimbleGen/UW-Madison_Drosophila_whole_genome_v1

status: Public on Nov 23 2006

city: Clemson

first: Brad

last: Hersh

state: SC

address: 132 Long Hall

department: Biological Sciences

institute: Clemson University

manufacture_protocol:
Manufacturing protocol described in the following publication:
Nuwaysir et al. 2002. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12:1749-55.
24nt oligonucleotide probes


title: C. elegans 22k 60 mer array

city: Haren(GN)

first: Yang

last: Li

address: Kerklaan 30

institute: Groningen Bioinformatics Center

organism: Caenorhabditis elegans

manufacture_protocol: as described in Genome Sequencing Center's protocols and workflow


title: Illumina Human 49K Oligo array (HEEBO-7 set)

manufacture_protocol: Please see the NHGRI Microarray Core Facility website.


title: SRC Mouse Compugen Printed Long Oligonucleotide 22K set Run 54

status: Public on Nov 09 2006

first: Darrin

last: Taylor

manufacture_protocol: Please see the SRC microarray facility website http://microarray.imb.uq.edu.au/


title: NimbleGen/UW-Madison Drosophila wing validation array


title: Van Andel Institute Mouse 15K cDNA Array - rel4

status: Public on Oct 28 2006

city: Las Vegas

first: Sheri

last: Holmen

state: NV

address: 10441 W. Twain Ave.

department: Drug Development

institute: Nevada Cancer Institute

manufacture_protocol: see the The Molecular Diagnostics Laboratory at the Van Andel Institute web site


title: Human 22K long oligo array

status: Public on Nov 08 2006

city: Beijing

first: yu

last: jian

state: Beijing

address: Qinghuayuan

department: Medical Systems Biology Research Center

country: China

institute: Tsinghua University

description: This set includes 22k oligonucleotides, mostly 70-mers, designed based upon representative sequences in the human UniGene database.

first: Yu

last: Jian

first: Zhang

last: Liang

manufacture_protocol: The 22 K oligonucleotide microarrays were constructed in CapitalBio Corp. (Beijing, China) using the Human Genome Oligo Set Version 2.1 (Operon, Huntsville, AL), which consist of 21,329 5'-amino-modified 70-mer probes. In addition to internal controls provided by the Oligo Set vendor, eight intergenic sequences from the yeast used as external controls were synthesized. All nucleotides were dissolved in DNA Spotting Solution (CapitalBio Corp.) at 20 M and printed on amino silaned glass slide using a SmartArrayTM microarrayer (CapitalBio Corp.). After printing, the slides were baked for 1 h at 80oC and stored dry at room temperature untill use. Prior to hybridization, the slides were rehydrated over 65oC water for 10 seconds and UV cross-linked at 250 mJ/cm2 energy. The unimmobilized oligonucleotides were washed off with 0.5% SDS for 10 min at 42oC and SDS was removed by dipping the slides in anhydrous ethanol for 30 seconds. The slides were spin-dried at 1000 rpm for 1 min. An aliquot of 5 µg total RNA was used to produce fluorescent dye-labeled cDNA with Eberwine’s linear RNA amplification method and subsequent enzymatic reaction according to a previous published protocol (Guo et al., 2005). The labeled DNA was purified with PCR Clean-up NucleoSpin kits (Macherey-Nagel), resuspended in Elution buffer, and quantified by UV spectrophotometry. Labeled control and test samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed into 80 µL hybridization solution (3×SSC, 0.2% SDS, 25% formamide and 5×Denhart’s). DNA in hybridization solution was denatured at 95oC for 3 min prior loading on a microarray. Hybridization was performed under LifterSlipTM (Erie Company), which allows for even dispersal of hybridization solutions between the microarray and coverslip. The hybridization chamber was placed on a 3D-Tilting Agitator (CapitalBio Corp.) to facilitate the microfluidic circulation under the coverslip. The array was hybridized at 42oC overnight and washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42℃ for 5 min, and 0.2% SSC for 5 min at room temperature). After hybridization, microarrays were scanned with a confocal LuxScanTM scanner (CapitalBio Corp.), and the data of obtained images were extracted with SpotData Software (CapitalBio Corp.). The raw data was normalized using a space and intensity-dependant LOWESS program (Yang et al., 2002). The data from faint spots was removed, in which the intensity was lower than the average intensity plus 2 standard deviations of the negative controls on the array. For each test and control sample, two hybridizations were performed by using a dye-swap strategy.


title: 5808-v4-1q

status: Public on Oct 27 2006

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

institute: Institute of Cancer Research

description: cDNA 5808 version 4 with 1q clones

manufacturer: Cell Transformation Team, Section of Molecular Carcinogenesis, Institute of Cancer Research

manufacture_protocol: as described in Institute Labs manual


title: MPIIB custom human (AMADID 011412)

city: Berlin

first: Marc

last: Jacobsen

address: Chariteplatz 1

department: Immunology

institute: Max-Planck-Institute for Infection Biology

first: Hans-Joachim

last: Mollenkopf

first: Stefan

middle: H

last: Kaufmann

manufacture_protocol: 'sure print' in situ


title: NIMH Mus musculus 35.9K Mm-NIMH36Kb

status: Public on Sep 21 2006

city: Bethesda

first: Babru

middle: Bahan

last: Samal

address: 9000 Rockville Pike

department: SMN

institute: NIMH/NIH

first: Charlie

last: Xiang

manufacture_protocol: Mouse cDNA microarray with 36,250 elements were printed on poly-L-lysine-coated glass slides using an OmniGrid arrayer (GeneMachines, San Carlow, CA). The methods used to make the cDNA microarrays, including slide coating with poly-L-lysine, array fabrication, and post-processing, can be found on the website the Brown lab at Stanford University and the National Human Genome Research Institute (NHGRI). The cDNA clones were obtained from Bento Soares (University of Iowa, Iowa City, IA) and are part of the BMAP (Brain Molecular Anatomy Project) set.


title: NIMH Mus musculus 36.3K Mm-NIMH36Kb


title: ORF_intergenic_K

status: Public on Aug 22 2006

city: Chapel Hill

first: Jason

last: Lieb

state: NC

address: 203 Fordham Hall

department: Biology

institute: University of North Carolina at Chapel Hill

manufacture_protocol:
Tip Configuration: Standard 32-tip
Columns per Sector: 24


title: FHCRC Fly 7K v2.0

status: Public on Sep 09 2006

first: Ryan

last: Basom

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

manufacture_protocol: The Fly 7K microarray is comprised of PCR amplified clones from the following sources:  1) 5929 clones from the DGCr1 (BDGP), 2) 192 randomly selected clones from the CK and LD libraries (Research Genetics), and 3) 138 clones from the Northwest Flychip Consortium.  Clones from the CK and LD libraries, as well as from the Northwest Flychip Consortium, are represented on the array in duplicate.  Additionally, a combination of 8 positive and negative controls are represented on the array in quadruplicate.  Individual PCR products were verified as unique via gel electrophoresis, purified, and mechanically spotted onto glass microscope slides using an OmniGrid high-precision robotic gridder (GeneMachines, San Carlo, CA).


title: CapitalBio Operon Human MAQC (BIO and BIO1, two- and one-color)

status: Public on Sep 08 2006

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

institute: Fudan University

description:
The human genome-wide long oligonucleotide microarray was constructed inhouse at CapitalBio Corporation. Briefly, 5′-amino-modified 70-mer probes representing 21,329 H. sapiens genes from the Human Genome Oligo Set Version 2.1 (Operon/Qiagen), and internal and external controls, were printed on amino silaned glass slides using a SmartArray microarrayer (CapitalBio Corp.). Fluorescent-labeled DNA (Cy3 and Cy5-dCTP) was produced through Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described in detail (Guo, Y. et al. J. Virol. 79, 14392-14403, 2005). Briefly, double-stranded cDNA containing T7 RNA polymerase promoter sequence was synthesized with 5 µg of total RNA using Reverse Transcription System, RNase H, DNA polymerase I and T4 DNA polymerase, according to the manufacturer’s recommended protocol (Promega). The resulting labeled DNA (labeled control and test samples) was quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed into 80-µl hybridization solution (3× SSC, 0.2% SDS, 25% formamide and 5× Denhart’s). Individually labeled cRNAs were not pooled before hybridization.
Hybridization on a microarray (see hybridization configurations above) was performed under LifterSlip (Erie Company). The hybridization chamber was laid on a three-phase Tiling Agitator (CapitalBio Corp.) to facilitate the microfluidic circulation under the coverslip. The microarray was hybridized at 42°C overnight and washed with two consecutive washing solutions (0.2% SDS, 2× SSC at 42°C for 5 min, and 0.2% SSC for 5 min at 22 °C) before scanning with a confocal LuxScan scanner (CapitalBio Corp.). For two-color microarrays, the scanning setting for the Cy3 and Cy5 channels was manually balanced by visual inspection of the external control spots. The data from the obtained images were extracted with SpotData software (CapitalBio Corp.).

manufacture_protocol: CapitalBio Corporation


title: NIA Mouse 44K Microarray v2.2 (Whole Genome 60-mer Oligo)

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: The Agilent's Mouse Development Oligo Microarray 44K is formatted on a 1x3 inch (25mm x 75mm) glass slide.  Each 44,290-feature microarray contains 41,999 (60-mer) probes representing all empirical and predicted mouse genes and transcripts from the NIA Mouse Gene Index.  The sequence and associated annotation information is based on the NIA Mouse Gene Index 4.0 http://lgsun.grc.nia.nih.gov/geneindex4, which combines genome assembly sequences from public databases (RefSeq, Ensembl, Riken), and the NIA collection of public EST libraries derived from stem cells and early stage of mouse embryos, along with human-curated genetic databases to form structure models of over 40,000 genetic loci4.  Furthermore, a set of synthetic spike-in control probes are included to control variations in target labeling and hybridization, and to provide more quantitative information on transcripts5.

manufacture_protocol: As descripted by Agilent manuals under Platform_web_link


title: UAF Arctic Ground Squirrel Illumina BeadArray 1A

status: Public on Aug 03 2006

city: Fairbanks

first: Jun

last: Yan

state: AK

address: 311 Irving Building

department: Institute of Arctic Biology

institute: University of Alaska Fairbanks

organism:
Urocitellus parryii
Ictidomys tridecemlineatus
Callospermophilus lateralis

description: This array (1A) contains the first 707 genes designed from the mixed sequences of three close-related ground squirrel species: golden-mantled ground squirrel; thirteen-lined ground squirrel; arctic ground squirrel. Two 50bps probes were designed for each gene.

first: Franziska

last: Kohl

first: Brian

last: Barnes

first: Thomas

last: Marr


title: FHCRC Mouse Prostate MPEDB cDNA Array v1

status: Public on Aug 01 2006

city: Seattle

first: Denise

last: Mauldin

address: 1100 Fairview Ave N D4-100

department: Human Biology

first: Peter

last: Nelson

first: Colin

last: Pritchard

last: Abbott

first: Ruth

last: Dumpit

manufacture_protocol: As cited