title: Human Cancer Chip v4.0 1.2k

status: Public on Mar 11 2011

city: Athens

first: George

middle: I

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

institute: National and Kapodistrian University of Athens

description: The microarray slide has the dimensions of a regular microscopy slide. Its grid/sub-grid structure is in the uploaded raw data file.

manufacture_protocol: Takara's microarrays contain denatured double stranded cDNAs arrayed on glass slides. Spot size of the present platform is 150um with space between spots 300um. The grid structure of this platform is 2 x 2 (2 meta-rows x 2 meta-columns). Each subgrid has a structure of 16x18 (16 rows x 18 columns). It has 886 unique genes. Glass slides contain silica-bearing amino residues which facilitate electrostatic coupling attachment of DNA fragments. Finally, chips are printed with a 12-pin robotic head.


title: Genotypic Technology designed "Custom Agilent Mus Musculus 8x15k GE Microarray (AMADID-016270) "

status: Public on Feb 27 2011

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

organism: Mus musculus

technology: in situ oligonucleotide

distribution: commercial

first: Raja

middle: C

last: Mugasimangalam


title: KTH Hum 34k Oligo Microarray

status: Public on Feb 10 2011

city: Uppsala

first: Katarina

last: Edfeldt

address: Akademiska Sjukhuset

department: Surgical Sciences

country: Sweden

institute: Uppsala University

organism: Homo sapiens

technology: spotted oligonucleotide

distribution: custom-commercial

manufacturer: KTH Microarray Center http://www.biotech.kth.se/molbio/microarray/

manufacture_protocol:
Version 3.0 of the Human Genome Oligo Set contains 34,580 70mer probes representing 24,650 genes and 37,123 gene transcripts. The design is fully based on the Ensambl (http://www.ensambl.org/) Human 13,31 Database and Human Genome Sequencing Project and directly deals with alternative splicing variants using common , partial common, or individual transcript oligos. The oligo set comes with complete annotation including Gene Ontology (GO), oligo chromosome coordinates, comparative genome analysis, and other functional annotation (InterPro, Online Mendelian Inheritance in Man [OMIM] disease, and protein family) For probe design state-of-the-art methodology was used and proprietary software. An amino linker is attached to the 5`end of each oligo. http://www.operon.com/arrays/oligosets_human.php
The 34,580 70mer probes were dissolved in 30% DMSO to a concentration of 18 µM. The microarrays were printed with a QArray2 (Genetix) instrument with 48 K2805 pins (Genetix) on Ultra GAPS slides (Corning). The 34,580 longmer probes were spotted in a 28x28 pattern within each block and with a feature center-to-center distance of 155 µm. The quality of the spotted slides was assessed by staining with Syto61 (Molecular Probes) and with hybridization with random nonamers. The slides were UV cross-linked at 150 mJ/cm2.


title: IntelliGene II Human CHIP 1

technology: spotted DNA/cDNA

manufacture_protocol: Takara's microarrays contain denatured double stranded cDNAs arrayed on glass slides. Spot size of the present platform is 200um with space between spots 355um. The grid structure of this platform is 12 x 1 (12 meta-rows x 1 meta-columns). Each subgrid has a structure of 8x50 (8 rows x 50 columns). It has 3893 genes from which 3864 are unique. Glass slides contain silica-bearing amino residues which facilitate electrostatic coupling attachment of DNA fragments. Finally, chips are printed with a 12-pin robotic head.


title: Homo sapiens 8.5k CpG island array

status: Public on Feb 07 2011

city: Leiden

first: Eddy

last: van Roon

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: LUMC

distribution: non-commercial

first: Judith

middle: M

last: Boer

first: Hans

last: Morreau

manufacture_protocol: This platform is an LGTC spotted microarray and is based on the CpG island clone library developed by Tim Huang and Pearlly Yann (GPL9542). All clones were amplified using vector-specific primers and subsequently spotted at the LGTC (detailed information available upon request).


title: Agilent-024724  Genotypic Technology Pvt. Ltd designed Custom Rattus Norvegicus 8x15k (Probe Name version)

status: Public on Feb 19 2011

organism: Rattus norvegicus

first: Rohit

middle: N

last: Shukla

first: Shruthi

last: Sinha


title: ASB Mouse 8K v1.0

status: Public on Feb 01 2011

city: wuhan

first: haifang

last: qiu

address: lion street 1

country: China

institute: Huazhong Agricultural University

description: mouse promoter array, M8K (Aviva Systems Biology, San Diego, CA), containing 8000 40-mer oligonucleotide probes targeting gene promoters

manufacture_protocol: see manufacturer website - AVIVA Systems Biology


title: CodeLink Human Whole Genome Bioarray

status: Public on Jan 20 2011

city: Kansas City

first: Douglas

last: Bittel

state: MO

address: 2401 Gillham Rd

department: Genetics research

country: USA

institute: Childrens Mercy Hospital


title: CCDTM Hs_CCDTM36k - version 1 (derived from GPL7088)

status: Public on Jan 24 2011

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-016322] Agilent Yeast 8X15K conversion (Probe Name version)

status: Public on Jan 18 2011

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

organism: Saccharomyces cerevisiae

description:
Yeast 8X15K conversion
Agilent-016322

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


title: Illumina HumanHT-12 WG-DASL V4.0 expression beadchip

status: Public on Jul 18 2011

city: San Diego

last: Illumina Inc.

state: CA

address: 9885 Towne Centre Drive

institute: Illumina Inc.

technology: oligonucleotide beads

manufacture_protocol: see manufacturer's website


title: SMD Print_1149 Mus musculus

status: Public on Jan 16 2011

city: Stanford

first: Michael

last: Longaker

address: 257 Campus Drive

department: Department of Surgery

institute: Stanford University

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine

manufacture_protocol: Material is transferred from microtiter plate wells to the slide surface by an automated print head


title: [hGlue2_0_v1] Glue Grant Human Transcriptome Array version 2.0 (GG-H) [transcript-level]

status: Public on Jan 27 2011

city: Palo Alto

first: Weihong

last: Xu

address: 855 California Ave

department: Department of Biochemistry

institute: Stanford Genome Technology Center

description: Inflammation and the Host Response to Injury Program

first: Wenzhong

last: Xiao

first: Ronald

last: Davis

last: Tompkins

manufacture_protocol: See Manufacturers website


title: Custom Whole Genome Mouse 8x60k designed by Genotypic Technology Pvt. Ltd.  (Agilent-026986)

status: Public on Apr 09 2011

last: technology

last: Mugasimangalam

manufacture_protocol: Agilent Technologies


title: Konyang-homo sapiens-Macarrray4.5k-v1.0

status: Public on Jan 10 2011

city: Seu-gu

first: Jaeku

last: Kang

state: Daejeon

address: 685, Gasuwon-dong

department: Department of Pharmacology

country: South Korea

institute: College of Medicine, Konyang University


title: Homo sapiens 22K Oligo micrarray V2.0 (Capitalbio)

status: Public on Jan 15 2011

city: Beijing

first: Hongyan

last: Guo

address: Chengfu

department: School of Medcine

institute: Tsinghua University

manufacture_protocol: As described in CapitalBio Corporation Manual


title: Agilent-019644 Human Genome CGH Microarray 105A (G4425A), version 1

status: Public on Dec 31 2010

city: Spokane

first: Blake

middle: C.

last: Ballif

address: 2820 North Astor Street

department: Research & Development

institute: Signature Genomic Laboratories

description: Platform annotations based on UCSC hg18 (NCBI Build 36, March 2006).

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


title: Agilent-015223 Rat Genome CGH Microarray 244A

city: Shanghai

first: Zhi-Qiang

last: Ye

address: No. 320 of Yueyang Road

institute: Shanghai Institutes for Biological Sciences

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


title: UHN Human 19K cDNA microarray

city: Toronto

first: Susan

last: Done

state: ON

address: 200 Elizabeth Street, 11E444

country: Canada

institute: University Health Network

manufacturer: University Health Network Microarray Centre, Toronto, Canada (www.microarrays.ca)

manufacture_protocol: See manufacturer's website for manufacture protocol


title: NHGRI Human 30k cDNA array

status: Public on Mar 31 2011

city: Bethesda

first: Phillip

middle: A

last: Dennis

state: MD

address: 37 Convent Dr.

department: MOB, CCR

institute: NCI

manufacture_protocol: The cDNA microarrays contained over 28,798 cDNA clones representing over 23,600 unique UniGene clusters. These cDNA clones were obtained from the sequence-verified IMAGE clone selection from Research Genetics (Invitrogen Corporation, Inc). After PCR amplification and purification, the cDNA inserts were resuspended in 3x SSC solution and spotted on poly-lysine-coated slides. The slides were then blocked by regular succinic Anhydre solution, denatured in boiling water and dried by centrifugation. The gene names are listed according to UniGene build 141 (www.ncbi.nlm.nih.gov/UniGene).


title: Affymetrix OncoScan™ FFPE Express

status: Public on Mar 29 2011

city: Santa Clara

first: Bioinformatics

last: Services

address: 3420 Central Expressway

institute: Affymetrix, Inc.

description:
A platform that offers high-quality copy number, genotype, and somatic mutation data with whole-genome coverage and high resolution in cancer genes for FFPE samples. This array should be used together with the MIP (Molecular Inversion Probes) technology.

Annotations correspond to NCBI build 36.

manufacture_protocol: See manufacturer's web site.


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf]

status: Public on May 18 2011

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

manufacture_protocol: See manufacturer's web site


title: Agilent Eichler Human CNP 180K v3.0

first: Catarina

middle: D

last: Campbell

address: 3720 15th Avenue NE

institute: Univerisity of Washington

description:
Custom microarray for assaying copy number polymorphisms (CNPs).
Platform annotations based on human genome UCSC hg18.


title: Agilent-017479 Nelson Whole Mouse Genome Microarray 4x44K

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center


title: Agilent-027242 Genotypic Technology Pvt. Ltd. designed human gene expression microarray (Probe Name version)

status: Public on Dec 21 2010

city: Bangalore

first: Genotypic

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

first: Raja

first: Rohit

last: Shukla

first: Shruthi

last: Sinha


title: NCAUR/USDA-ARS Yeast 70-mer oligo array

city: Peoria

first: Z Lewis

last: Liu

state: IL

address: 1815 N University

institute: USDA-ARS

manufacture_protocol:
1. 70-mer universal RNA controls were synthesized with AminoC6 modification at the 5' end
2. Oligos are stored in Greiner 384-well flat-bottom plates. Each well contains 600 pmol of 70-mer oligo.
3. Oligos stored at -80℃
4. Allow oligos to thaw at room temperature
5. Shake plate for 1 min
6. Centrifuge plates at 2500 rpm for 1 min
7. Remove seals and cover with plate lids
8. Load the plates in a proper order onto a plate tower
9. Array design with replicated genome in separated blocks
10.Microarray spotting with a humidifier to keep constnet moisture in the chamber
11. Array platform is properly leveled and examined for each direction
12. Printing pins washed with sonication to avoid smaple contamination carry over


title: Agilent Eichler Human CNP 180K v2.1


title: FCCU_Human_Agilent_44k

status: Public on Dec 02 2010

city: Cambridge

first: Nicholas

middle: B

last: Shannon

address: Robinson Way

department: Oncology

country: United Kingdom

institute: Cambridge Research Institute

manufacture_protocol: For information contact Agilent


title: CapitalBio 36K Mouse Genome Array

status: Public on Nov 30 2010

first: Weibin

last: Jiang

address: 518,Ziyue ARd

institute: Shanghai Institute of Veterinary Research, Chinese Academy of Agricultural Sciences

manufacture_protocol: as described in CapitalBio Corporation Manual


title: Agilent-015066 Xenopus Gene Expression Microarray (Probe Name version)

status: Public on Dec 01 2010

last: Agilent Technologies

institute: Agilent Technologies

organism: Xenopus laevis

description:
Xenopus laevis (Frog) Oligo Microarray by Agilent Technologies

Arrays of this design have barcodes that begin with 16015066 or 2515066.

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 Probe Name.


title: [CG_AGPa520460F] Affymetrix Adenoma Biomarker 46K Gene Chip v1.0

status: Public on Nov 13 2010

city: North Ryde

first: Iain

last: Beeston

state: NSW

address: 11 Julius Avenue

country: Australia

institute: Clinical Genomics

manufacture_protocol: custom Express design. See manufacturer's website


title: Illumina Human Sentrix-8, ChipID 4403827059

status: Public on Nov 11 2010

city: Heidelberg

first: Ulrike

middle: Mareike

last: Litzenburger

state: Baden-Württemnberg

address: INF 280

department: neuroimmuology

country: Germany

institute: DKFZ


title: Rocky Mountain Regional Center of Excellence Mouse 38K V4.0

status: Public on Nov 01 2010

city: Fort Collins

first: Luke

last: Kingry

state: CO

address: 2025 IDRC at Foothills Campus Delivery

institute: Colorado State University

description: Array contains 250 negative control spots  spaced randomly throughout the array.  100 housekeeping genes printed in triplicate randomly throughout the array for positive controls and normalization

manufacture_protocol: Oligo  Arrays were spotted using a BioRad Chipwriter Pro Software and printer in a 4 by 12 grid array on poly amine coated slides.  Arrays were printed in humidity controlled cabinet (55% humidity) at room temperature using 48 ArrayIt Smp3 pins.


title: Agilent-017278 whole human genome (hg17) custom 4×44k array

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH


title: UB Mus musculus 22K v1

city: Barcelona

first: Felix

last: Junyent

address: Avda/Diagonal

country: Spain

institute: Universitat de Barcelona

manufacture_protocol:
Printing of arrays:
A mus musculus 22 thousand 63-mer oligo library from SigmaGenosys sets was resuspended to 50 mM in the Micro Spotting solution (Arraylt Brand Products). SuperAmine-coated slides 25 x 75 mm (TeleChem International, Inc.) were printed in duplicate, and fixed at 80ºC for 4 fours. For pre-hybridization, the slides were re-hydrated with water vapor at 60ºC and fixed two cycles of UV light (1,200J). After boiling for 2 min at 92ºC, the slides were washed with 95% ethanol for 1 min and prehybridized in 5 x SCC, 0.1% SDS, and 1% BSA for 1 h at 42ºC. The slides were the washed and dried for further hybridization.
Probe Preparation and Hybridization to Arrays:
For cDNA synthesis, 10 g of total RNA was used as the template, incorporating dUTP-Cy3 or dUTP-Cy5 with the CyScribe First-Strand cDNA labeling kit (Amersham). Incorporation of the fluorophore was analysed by evaluating the absorbance at 555 nm for Cy3 and 655 nm for Cy5. Equal quantities of labeled cDNA were hybridized for 14 hours at 42ºC to the 22 thousand oligo mice arrays in UniHyb hybridization solution (TeleChem Interbational, Inc).
Data Acquisition and Analysis of Array Images:
The acquisition and quantification of the array images were performed in a ScanArray 4000 using the accompanying software (Packard BioChips). All images were captured at a 50% scan rate using 65% PMT gain, 70 to 75% lase power, and 10 m resolution. For each spot, the Cy3 and Cy5 mean density value and the Cy3 and Cy5 mean background value were calculated with ArrayPro Analyzer software (Media Cibernetics). In all cases, the fluorescence signal was between seven to ten times more intense than the background signal, and the background was evaluated just beside the labeled spot.
Data analysis:
Microarray data analysis was performed with the GenArise software, developed by the Computing Unit at the Cellular Physiology Institute of the UNAM. GenArise carries out a number of transformations: background correction, lowest normalization, intensity filter, replicate analysis, and selection of differentially expressed genes. The goal of GenArise is to identify good evidence that the genes are differentially expressed, and it has been successfully used in recent studies. The software identifies differentially expressed genes by calculating an intensity-dependent z-score. It uses a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and it defines a z-score that measures the number of standard deviations a data point is from the mean: zi = (Ri - mean(R)) / sd(R)
Where zii is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. Applying these criteria, the elements with a z-score > 2 standard deviations are genes likely to be differentially expressed.


title: WHOI Zebrafish 44k v1.0 custom-commercial Chemical Defensome

status: Public on Oct 21 2010

city: Woods Hole

first: Jared

last: Goldstone

state: MA

address: Redfield 3-52 MS#32

department: Biology

institute: Woods Hole Oceanographic Institution

organism: Danio rerio


title: Agilent-016299 Nelson Whole Mouse Genome Microarray 4x44K (Feature Number version)

status: Public on Oct 18 2010

city: Seattle


title: JLUGiMM-rattus norvegicus-35k-v1.0

status: Public on Oct 20 2010

city: Giessen

first: Andreas Christian

last: Geisler

address: Frankfurter Str. 107

department: Med. Mikrobiologie

institute: Justus Liebig Universität Giessen

manufacture_protocol: see GE Healthcare


title: St. George's Hospital, Clostridium difficile 7.5K array [condensed version]

status: Public on Oct 09 2010

city: Boston

first: Abraham

middle: L

last: Sonenshein

address: 136 Harrison Avenue

department: Molecular Biology & Microbiology

institute: Tufts University

organism: Clostridioides difficile 630

description: ArrayExpress (accession number A-BUGS-20)

manufacturer: Bacterial Microarray Group, St. George's Hospital, London, UK (http://bugs.sgul.ac.uk/A-BUGS-20)


title: VUMC Agilent-019445 ch16_199k_plus44k

status: Public on Sep 10 2010

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

institute: Vrije Universiteit Medical Center


title: Exiqon Drosophila miRNA arrays

status: Public on Oct 29 2010

city: Philadelphia

first: Bonini

last: Nancy

state: PA

address: 415 S University Ave

institute: University of Pennsylvania

organism: Drosophila melanogaster

description: miRBase=Release 8.1

manufacture_protocol: See manufacturers website


title: CapitalBio 32K Mouse Genome Array

status: Public on Sep 28 2010

city: Urumqi

first: guo

middle: dong

last: lv

state: Xinjiang

address: liyushan

department: clinical cases reserch center

institute: Xinjiang medical hospital


title: CapitalBio 36K Mouse Genome Array


title: Agilent-24598 Genotypic-designed C. albicans and C. dubliniensis Cross Species CGH Microarray 4x180k

status: Public on Sep 24 2010

first: Genotypic

last: technology

organism:
Candida albicans
Candida dubliniensis

first: Mugasimangalam

last: Raja

first: Shukla

last: Rohit

first: Sinha

last: Shruthi

manufacture_protocol: Refer to www.opengenomics.com


title: MouseRef-8 v2.0 Expression BeadChip

city: Los Angeles

first: ren

last: liu

address: 1441 Eastlake Avenue

institute: University of Southern California

description: entered as a custom platform since official Illumina IDs could not be supplied

manufacture_protocol: see manufacturer's website


title: Illumina MouseRef8 Ver1.1

status: Public on Aug 31 2010

city: Hobart

first: Minghui Jessica

last: Chen

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

institute: Menzies Research Institute

manufacture_protocol: See manufacturer's website


title: F-IVI_Human_44k_v1

status: Public on Aug 15 2010

city: Valencia

first: Jose

middle: Antonio

last: Martinez-Conejero

address: C/ Guadassuar 1, bajo

institute: iGenomix

first: Irene

last: Cervello

first: Claudia

last: Gil-Sanchis

first: Aymara

last: Mas

first: Francisco

last: Delgado-Rosas

first: Amparo

last: Galán

first: Alicia

last: Martínez-Romero

first: Sebastian

last: Martinez

first: Ismael

last: Navarro

first: Jaime

last: Ferro

last: Horcajadas

middle: J

last: Esteban

middle: E

last: O'Connor

first: Antonio

last: Pellicer

first: Carlos

last: Simón

manufacture_protocol: See manufacturer instructions


title: Operon Array-Ready Oligo Set Mouse Whole 34K version 4.0.1 array

status: Public on Jul 24 2010

city: Seoul

first: Tae Hoon

last: Kim

state: Socho-gu

address: 505 Bonpo-dong

department: Pathology

institute: Medical College of the Catholic University

manufacture_protocol: Please see linked supplementary file.


title: Agilent Mouse 60K Genotypic Designed Array

status: Public on Jul 21 2010

city: Bangalore

first: madavan

last: vasudevan

address: Kasturi Nagar

institute: Theomics International Private Limited

first: Raja

last: Mugasimangalam

first: Rohit

last: Shukla

first: Shruti

last: Sinha

manufacture_protocol: Please refer to www.chem.agilent.com


title: Agilent-019921 Sheep Gene Expression Microarray (Probe Name version)

status: Public on Dec 20 2010

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Ovis aries

description: *** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL10427.


title: Agilent-021531 Whole Human Genome Oligo Microarray 4x44K (Feature Number version)

status: Public on Jul 01 2010

description:
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.

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


title: KIST custom metabolite Agilent 4x44 K array

first: Sailendra

middle: Nath

last: Sarma

address: P.O. Box 131, Cheongryang

institute: Korea Institute of Science and Technology

manufacturer: BioMicro Systems, Inc. 1290 West 2320 South, Suite D Salt Lake City UT 84119

first: Youn-Jung

first: Jae-Chun

manufacture_protocol:
Materials
MAUI Mixer A4 Hybridization Chambers (Cat No. 02-A008-25)
A4/LC Hinged Clamp Assembly (Cat No. 02-A004-00)
SL/A4/LC Assembly/Disassembly Jig (Cat No. 02-033-03)
Gasket Brayer (Cat No. 02-054-00)
MAUI Humid Cover (Cat No. 02-D0031-00)
M-100 Microman® Pipette (Cat No. 01-014-00)
CP-100 Pipette Tips (Cat No. 01-015-00)
Port Plugs (Cat No. 03-D0002-00)
Port Plug Insertion Tool (Cat No. 04-D0005-00)
Cotton Swabs
1.5 ml Eppendorf® Tubes
Hybridization Buffer (see recipe below)
250 μl Pipette Conditioning Solution (see recipe below- used only to eliminate air from the pipette tip prior to filling the
hybridization chamber and not for the actual hybridization)
Additional BioMicro Systems Instructions & Procedures
Replacing Bay Clamp Assemblies on MAUI Hybridization Systems (CDP-02)
MAUI Humid Cover for the MAUI Hybridization System (CDP-12)
MAUI Mixer Sealing Using Port Plugs (CDP-13)
MAUI Mixer-Slide Assembly Procedure (see MAUI Hybridization System User’s Guide) (CDP-14)
MAUI Mixer Filling and Sealing Procedure (see MAUI Hybridization System User’s Guide) (CDP-14)
Modifications to Agilent Two-Color Microarray-Based Gene Expression Analysis --
Quick Amp Labeling and Hybridization Protocol
Below is a list of key adaptations made to the Agilent gene expression array labeling (Quick Amp Labeling) and
hybridization protocol when using the MAUI Hybridization System and 4x44k CGH arrays.
Table 1: Protocol Differences
Agilent SureHyb® System MAUI Hybridization System
Labeled Target(s) - Dry using a SpeedVac®
Final Sample Volume
4 x 44K array 110 μl 25 μl
Hybridization Mixture No formamide Add formamide for a final
concentration of 16%
Hybridization Temperature 65ºC 55ºC
Hybridization Time
4 x 44K array 17 hours 17 hours
Total RNA labeling should be performed according to Agilent Quick Amp Labeling protocol. For the microarray
hybridization process, following removal of the unincorporated dyes it is necessary to reduce the volume of the labeled
target in order to load it into the ultra-low volume MAUI Mixers. The following modifications have been made to the
protocol of Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling, version 5.7, March
2008):
MAUI® Mixer A4 on Agilent® 4 x 44K Gene Expression Arrays
Following the purification of the labeled and amplified RNA (step 9, page 24).
1. Combine the appropriate purified Cy5 and Cy3 labeled RNA samples.
2. Dry combined samples using an appropriate speed vacuum under low heat and protect samples from light during the
process (e.g. using aluminum foil). This may take 20 minutes or longer depending on the degree of vacuum, the
sample volume and total number of samples being prepared.
3. Prepare the hybridization mixture according to the following recipe at room temperature.
Note: Make the appropriate volume of hybridization mixture based on the number of samples prepared.
Table 2: Hybridization Mixture Recipe
Component Volume
Nuclease-Free Water 80.6 μl
Agilent 10X GE Blocking Agent 25 μl
25x Fragmentation Buffer 4.4 μl
Final Hybridization Mixture Volume 110 μl
4. Add 11 μl of the above hybridization mixture to each dried sample in a 1.5 ml Eppendorf Tube. Completely
resuspend the labeled sample(s) by gently pipetting the hybridization mixture up and down several times (avoid
causing bubbles). Briefly spin.
5. Incubate the samples at 60ºC for exactly 30 minutes to fragment RNA.
6. Add 4 ul of high-quality de-ionized formamide and 10 μl of 2x GE Hybridization Buffer to each sample to stop the
fragmentation reaction and make a final total volume of 25 μl for each array. Mix well but gently by pipetting. To
avoid introducing bubbles, do not vortex. Please note that the final concentration of formamide is 16% and the final
concentration of Agilent 2x GE hybridization buffer in the final hybridization mixture is 0.8x (not 1x), which is
optimized specifically for the MAUI Hybridization system.
Final Volume = Chamber Volume + (5 to 10 μl).
Note: The chamber volumes may vary slightly from lot to lot of MAUI Mixers. The actual chamber volume for each MAUI
Mixer is indicated on the MAUI Mixer packaging.
7. Spin tubes (highest speed for 1 minute) to collect the buffer at the bottom of the tubes and load samples as soon as
possible.
Protocol
Prior to using Agilent microarrays with the MAUI Hybridization System you will need to replace the standard bay clamp
assemblies with A4/LC bay clamp assemblies (see Bay Clamp Replacement Instructions CDP-02).
1. Set the MAUI Hybridization System temperature to 55ºC.
2. Prepare 250 μl of Pipette Conditioning Solution in a 1.5 ml Eppendorf tube and warm to 55ºC. The purpose of this
solution is to eliminate air from the pipette tip prior to aspirating the hybridization mixture for injection into the MAUI
Mixer hybridization chamber.
Table 3: Pipette Conditioning Solution Recipe
Component Volume
Nuclease-Free Water 80.6 μl
Agilent 10X Blocking Agent 25 μl
25x Fragmentation Buffer 4.4 ul
Agilent 2x GE Hybridization Buffer 100 μl
High Quality De-Ionized Formamide 40 μl
Final Pipette Solution Volume 250 μl
- 3 -
CDP-20-REVA DEC 2008
3. Place the solution at 55ºC a few minutes before use.
4. Open a single MAUI Mixer A4. Attach the mixer to the Agilent microarray slide using an SL/A4/LC
Assembly/Disassembly jig, as described in the MAUI Hybridization System User’s Guide. Make sure the “active
array side” of the slide faces up and the barcode end slides into the jig first.
Note: Completely bray all portions of the adhesive gasket. The adhesive gasket will appear clear (not cloudy) when sealed
correctly. Do not use excessive pressure when braying directly over the microarray surface, as this may result in damage to
the array.
BioMicro Systems highly recommends that you practice assembling and loading MAUI Mixers with used Agilent microarrays
and Pipette Solution containing 1% Bromophenol Blue.
5. Fill a single chamber of the MAUI Mixer A4.
a. Set the M-100 Microman Pipette to 3μl more than the chamber volume indicated on the MAUI Mixer
package label.
b. Use a new CP-100 pipette tip and slowly pipette the pipette conditioning solution (step 2) up and down until
all air bubbles are removed from the tip.
c. With the pipette plunger depressed, transfer the pipette tip into the tube containing the hybridization
solution.
d. Slowly aspirate hybridization solution (being careful not to introduce bubbles into the tip).
e. Insert the pipette tip into the fill port of the desired chamber. Be sure to hold the pipette tip as vertically as
possible.
MAUI Mixer A4
f. With a continuous motion, slowly inject the hybridization solution into the chamber. After filling, DO NOT
wipe hybridization solution from fill and vent ports.
6. Seal the chamber using port plugs (see Port Plug Instructions).
a. Hold the star shaped port plug carrier to the side of the MAUI Mixer (not over it) with the raised marks on
the handle facing up.
b. Center a port plug over the fill port. You should be able to feel the end of the plug insert into the port.
c. Vertically center the port plug insertion tool over the aligned port plug. Using the tool, lightly (~ 2-4 lbs. of
pressure) push the port plug into the fill port. Tilt the tool slightly toward the carrier (away from the center of
the MAUI Mixer) and gently pull the carrier away from the tool. The edge of the port plug tool will cut/snap
the port plug off of the carrier.
d. Move the port plug tool back to a vertical position and push with just enough force to fully insert plug. Avoid
using excessive force, which may disrupt the gasket seal.
e. Slowly release the pressure on the port plug insertion tool to prevent air from being pulled into the vent port.
f. Seal the vent port in the same manner (always seal fill port first and then the vent port).
g. Use a cotton swab to blot excess buffer from around the sealed port plugs until the cotton swab appears
dry.
- 4 - CDP-20-REVA DEC 2008
h. Press lightly on the center


title: MEEBO Mouse 38,976-element spotted oligo microarray, 070321 printing

status: Public on Aug 04 2010

city: Storrs

first: Mark

middle: Gerald

last: Carter

state: CT

address: 1392 Storrs Road

department: Center for Regenerative Biology

institute: University of Connecticut

manufacturer: W.M. Keck Center, University of Illinois Urbana-Champaign

manufacture_protocol: MEEBO microarrays were printed on Corning UltraGAPS slides using an OmniGrid 100 microarray printer (Genomic  Solutions) with Arrayit SMP2.5 capillary print pins. Oligos were prepared in 384 well plates at a final concentration of 20 uM in 150 mM Sodium Phosphate print buffer. Slides were fogged and cross-linked in a Stratalinker at 6,000 μJoules/cm2.


title: [Agilent-021439] University of Chicago-Dual Species (Homo sapiens and Mus musculus) 87K array

status: Public on Jul 22 2010

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

organism:
Homo sapiens
Mus musculus

manufacture_protocol: Agilent 4x44K array protocol


title: BWH Human Release 3.0 oligonucleotides

status: Public on Jun 22 2010

first: Zhijian

last: Gao

address: Longwood 221

institute: BWH, Harvard Medical School

description: The Human Release 3.0 oligonucleotide library containing 60-mer oligonucleotides representing 44,000 probe sets, was used for this microarray analysis.

manufacture_protocol: The oligonucleotides were dissolved at 10 mM concentration in 50 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink slides, using an OmniGrid 100 microarrayer (Genomic Solutions, Ann Arbor, MI) at the Advanced Technology Center (Rockville, MD)


title: Agilent 4x44k Horse Gene Expression microarrays (AMADID 021322)

status: Public on Jun 30 2010

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: Equus caballus

manufacturer: Agilent Technologies Inc., Santa Clara, USA

manufacture_protocol: see Agilents homepage for SurePrint technology


title: University Hospital Regensburg Human promoter 243K array

status: Public on Jun 06 2010

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

description: Custom designed oligonucleotide array comprising roughly 17.000 annotated promoter regions (-4000 - +1000 around transcription start sites). In addition, four selected loci are tiled over a large genomic interval, including CHIT1/CHI3L1 (170 kb), CCL13 (140 kb), SPI1 (60 kb), and TLR4 (75 kb).


title: Genotypic designed Agilent in situ synthesised Mus musculus & Staphylococcus aureus gene expression profiling microarray

status: Public on Aug 10 2010

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

organism:
Staphylococcus aureus
Mus musculus

middle: C


title: Custom Agilent/Univ Antwerp Human Cell 15K

status: Public on Jun 01 2010

city: Antwerp

first: Caroline

last: Vanparys

address: Groenenborgerlaan 171

country: Belgium

institute: University of Antwerp

description: Combination of in-house custom MCF-7, H295R and C3a arrays.

manufacture_protocol: In situ printing of 60-mer oligonucleotides.


title: KCL-Danio_rerio-16K-pronto-v1.0

status: Public on May 20 2010

city: Cardiff

first: Peter

last: Kille

address: Park Place

department: Cardiff School of Biosciences

institute: Cardiff University

manufacturer: King’s College London Genomics Centre, UK.

manufacture_protocol:
Oligonucleotides include 16,399 designed and synthesised by Compugen and Sigma Genesys as a Zebrafish OligoLibrary ready set, which represent 15,806 LEADS™ clusters plus 171 controls (http://www.labonweb.com/chips/libraries.html). In addition, 331 customised oligonucleotides and 23 controls from Amersham Lucidea Universal ScorecardTM were added to the array set.
All oligonucleotides were resuspended to a concentration of 25uM in Pronto buffer (Corning).
The Zebrafish oligonucleotides arrays were spotted on UltraGAPS™ coated slides (Corning Life Sciences, Promega), using 48 SMP3 Telechem split pins mounted  Qarray2 robot (Genetix Ltd) .
Printing conditions include: Humidity range - 40 – 50 %, temperature range = 20 – 25 ºC, Inking time: 3 sec, Inking depth: about 1mm below the solution surface, Printing depth: adjust to high enough to make all pins just touch, Stamping time (dwell time): 50msec, Maximum number of prints per inking: up to 400 without losing intensity but avoid re-inking, Spot diameter = 100 microns, Spot spacing = 215 microns, five blots are performed prior to printing, pins are washed using 3x5sec water wash and 2x5sec ethanol wash between sample printing.
Immobilization of the cDNA onto the Ultra-GAPS coated glass slides was achieved by means of baking and UV crosslinking. The printed slides were initially immobilized by placing them in a UV StratalinkerTM 2400 bench top transilluminator (Stratagene Ltd)
The slides were then placed in a lightproof container and baked in an oven at 80oC for 2 hours. The slides were then stored in a lightproof desiccator at room temperature, until required.


title: Affymetrix GeneChip Mouse Genome 430 2.0 Array [CDF: Mm_ENTREZG_11]

status: Public on May 26 2010

city: Zeist

first: Marijana

last: Radonjic

address: Utrechtseweg 48

institute: TNO

description: For annotation of probes and summarization of signals from probes representing one gene, the MNBI custom CDF annotation file was used (EntrezGene, version 11.0.2, mouse4302mmentrezg.db_11.0.2.zip, at http://nugo-r.bioinformatics.nl/Packages_Prior_to_R2.10.html)

relation: Alternative to: GPL1261 (Alternative CDF [official])

manufacture_protocol: This array is identical to GPL1261 but a custom, remapped CDF environment is used to extract data. The EntrezGene, version 11 custom CDF is linked below as a supplementary file.


title: UHN Human H1.7k3_SDDC2_v2

status: Public on Mar 31 2010

city: Toronto

first: Christine

last: Ichim

address: 2075 Bayview Avenue

department: Molecular and Cell Biology

institute: Sunnybrook Research Institute

description: Double-spotted array containing 1,718 well-characterised human ESTs.

manufacturer: University Health Network (UHN) Microarray Facility

manufacture_protocol: UHN microarrays are printed on UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol. For detailed information see http://www.microarrays.ca/


title: MGX_Human_35K_AROSV4.0.2

status: Public on Jun 17 2010

city: Montpellier

first: Laurent

last: Journot

address: 141 rue de la Cardonille

country: France

institute: MGX - Montpellier GenomiX

description: Coating : epoxysylane

manufacture_protocol: Operon protocol. Microarray Inc.


title: Zebrafish 23K oligo_COMP-GIS_v4

status: Public on Jun 29 2010

city: Singapore

first: zhengyuan

last: wang

address: 14 Science Drive 4

department: Biological Sciences

country: Singapore

institute: National University of Singapore

manufacture_protocol: See GISMADB homepage


title: MRC Toxicology Unit, Mus musculus, oligo MEEBO microarrays

city: Leicester

first: Amy

last: Pointon

address: Lancaster Road

department: Systems Toxicology Group

institute: MRC Toxicology Unit

manufacturer: MRC Toxicology Unit, Systems Toxicology Group

manufacture_protocol:
1.Oligos are in 101 384 well plates (MEEBO set) (Cat OL -10-122).  Each well contains 200 pmol of 70-mer oligo.  Print split over 2 slides – A and B.
2. Resuspend oligos in 20ul printing buffer to 10uM.  Printing buffer is 1.5M betaine, 3xSSC.
3. Seal plates with adhesive PCR film from Applied Biosystems (cat. AB-0558).
4. Shake plates on a multi plate shaker for about 15 minutes This resuspends the dried down oligo in the printing buffer.
5. Centrifuge plates at 3000rpm for 5 minutes.
6. Remove seal immediately prior to use. Place one plate at a time in appropriate location of plate holder on arrayer.  Screw to keep in position.  Attach 32 pin head to standford design arrayer and start print run.  After all 384 samples have been printed software will request next plate be placed in position.  Remove previous plate, reseal and replace with next plate.


title: Duke Human Operon 36k v4.0 spotted microarray

status: Public on May 19 2010

city: Manassas

first: Margaret

middle: Claire

last: Emblom-Callahan

address: 10900 University Blvd.

department: Molecular and Microbiology

institute: George Mason University

manufacture_protocol: Human Operon 4.0 spotted microarray prepared by the Duke Institute for Genome Sciences and Policy.


title: NIAS Agilent Bovine 11K Oligo Microarray v1

status: Public on Mar 27 2010

city: Tsukuba City

first: Koichi

last: Ushizawa

state: Ibaraki

address: Ikenodai 2

department: Animal Science Department

country: Japan

institute: National Institute of Agrobiological Sciences

organism: Bos taurus

first: Toru

last: Takahashi

first: Misa

last: Hosoe

first: Kanako

last: Kaneyama

first: Keiichiro

last: Kizaki

first: Kazuyoshi

last: Hashizume

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


title: UHN Microarray Centre Human 8.1K CpG island microarray

status: Public on Apr 27 2010

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

institute: The George Washington University School of Medicine and Health Sciences

manufacturer: UHN Microarray Centre, University of Toronto, Canada

manufacture_protocol: Our microarrays are printed on UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol. Single-spotted array containing 8,109 CpG-island clones consolidated from the UHN's HCGI12K set and an independent 8.5K set obtained from Tim Huang at the Ohio State University (Columbus, OH).* This library and array was described in Heisler L, et. al., CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. NAR (2005) 33:2952-2961.


title: Nanjing University 22K Human Genome Array

status: Public on May 06 2010

city: Nanjing

first: Yu

last: Tang

state: Jiangsu Province

address: 321 Zhongshan Road

department: Department of Rheumatology and  Immunology

institute: The Affiliated Drum Tower Hospital of Nanjing University Medical School

manufacture_protocol:
1.The labeled DNA was puriﬁed with a PCR PuriﬁcationKit (Qiagen), resuspended in Elution buffer and quantiﬁed.
2. Labeled samples were quantitatively adjusted based on the efﬁciency of Cy-dye incorporation and mixed into 80μl hybridization solution (3×SSC, 0.2%SDS, 25%formamide, and 5×Denhart’s).
3. DNA in hybridization solution was denatured at 95℃ for 3 min prior loading on a microarray.
4. The array was hybridized at 42℃ overnight
5. The array was washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42℃for 5min, and 0.2% SSC for 5 min at room temperature)


title: Affymetrix Human Genome U133 Plus 2.0 Array [CDF from AffyProbeMiner]

status: Public on Apr 17 2010

city: Namur

first: conny

last: mathay

address: 61, rue de Bruxelles

institute: FUNDP

description: This identical to GPL570 but a custom cdf environmnet was used to extract data. The cdf can be found at the link below.

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

manufacture_protocol: see the Affymetrix website


title: Illumina MouseWG-6 v2.0 expression beadchip (gene version 2)

status: Public on Nov 02 2010

city: Indianapolis

first: Randall

middle: J.

last: Roper

state: IN

address: 723 W. Michigan Street., SL306

department: Biology

institute: Indiana University-Purdue University Indianapolis

description:
The MouseWG-6 v2.0 Expression BeadChip offer the most up-to-date content for whole-genome expression profiling in the mouse. Featuring content derived from the National Center for Biotechnology Information Reference Sequence (NCBI RefSeq) database (Build 36, Release 22).

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

manufacture_protocol: see manufacturer's website


title: Affymetrix GeneChip Human Genome 133 Plus 2.0 Array [CDF: Brainarray Version 11, hgu133plus2hsentrezg]

status: Public on May 01 2010

city: leiden

first: joyce

middle: AM

last: emons

institute: lumc

description: This identical to GPL570 but a custom cdf environmnet was used to extract data. The cdf can be found at the link below. We used the entrez version 11 for HGU-133_plus2.

first: Joyce

last: Emons

first: Carsten

last: Sticht

manufacture_protocol: see manufacturer's web site


title: Human CpG Island Microarray 244K (Agilent-014791) with extended custom annotation

first: Michael

last: Rehli

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


title: Capitalbio 22K Human oligo array version 1.0

status: Public on Apr 02 2010

city: Beijing

first: Jianqing

last: Zhao

address: 18 Life Science Parkway

institute: Capitalbio. Crop

manufacture_protocol: as described in Capitalbio Human 22K oligo array Manual


title: HGU-MRC-Bickmore Mouse Hoxb/d 22K tiling v1.0

status: Public on Mar 04 2010

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

description: Tiling path array of oligos on HoxB and HoxD clusters :1 oligo / 250 bp in the core region containing the Hox genes,1 oligo / 500 bp in the flanking regions,1 oligo / 50kb outside flanking regions.These tiling oligos are designed alternatively on each strand. The position number (NCBI built m35) in the files is the 5’ base for the forward oligos and the 3’ for the reverse oligos (so one given oligo and the corresponding reverse oligo have the same position number). Other regions on the array are:Oct4  exons, promoter, flanking regions with low resolution,Sox2 exons, promoter, flanking regions with low resolution, Nanog  exons, promoter. Control genes for array are; Ncl : exons, promoter, flanking regions with low resolution, RPL19  exons, Rrm2 exons, HPRT exons, promoter, c-myc, exons and other regions contains MAR and CTCF binding sites, Hbb-b1 exons and regulatory elements, Cdkn1a exons, promoter and regulatory elements, Oprk1 exons and regulatory elements and  Mouse major and minor satellite DNA. Mismatch control oligos are the same as the oligos in exons but containing 1, 3, 5,7 ,10 mismatches. (NB : the Ncl mismatch oligos have been designed on the wrong strand). Other control probes are NM_000015.1 and Drosophila sequences.

manufacturer: University of Liverpool Microarray Facility

first: Clémence

last: Kress

first: Nick

last: Gilbert

first: Wendy

middle: A

last: Bickmore

manufacture_protocol: Amine-modified oligos were spotted at 20uM in 1 x Nexterion Spot buffer containing 0.005% triton X100 onto Codelink activated slides


title: CapitalBio Human 22k oligonucleotide microarray

status: Public on Mar 05 2010

city: Guangzhou

first: Li

middle: Xu

last: Yan

state: Guangdong

address: 651# Dong Feng Road East

department: Department of Pathology

institute: Sun Yat-Sen University Cancer Center

manufacture_protocol: As described in National Engineering Research Center for Beijing Biochip Technology(CapitalBio Corporation) manual


title: Operon Homo sapiens 34K (updated)

status: Public on Feb 24 2010

city: Seoul

first: Sailendra

last: Sarma

address: P.O. Box 131, Cheongryang

institute: Korea Institute of Science and Technology

middle: N

first: Youn-Jung

last: Kim

first: Jae-Chun

last: Ryu

manufacture_protocol:
Manufacture protocol Date 2/7/2007 OpArraysTM Protocol
www.operon.com Page 1
Operon Homo sapiens 31K
Operon Biotechnologies GmbH, BioCampus Cologne, Nattermannallee 1, 50829 Cologne, Germany
When conducting your experiment, remove only the OpArrays slides you plan to use immediately and immediately return the remaining OpArrays to the pouch, leaving the desiccant pack in place. For added protection, OpArrays slides may be kept in their storage pouch in a desiccator.
OpArrays Storage
OpArrays microarrays are printed on epoxide slides, pre-processed and supplied ready-to-use.
° The microarray slides should be stored in their original container at room temperature in dry conditions (preferably desiccated) and protected from light.
° The slide box containing OpArrays is shipped in a re-sealable storage pouch containing desiccant which is ideal for continued storage.
° Both the storage pouches and slide storage boxes are manufactured from materials that minimize out-gassing and effectively block exposure to foreign contaminants that can elevate background levels in your experiments.
° When properly stored, OpArrays slides will remain hybridization competent for 4 months or more.
Array Position on OpArrays Slides
OpArrays slides are printed on the same side as the barcode (graphic to the right). The array area is 18mm wide, 54mm long, and is located 8mm from the top of the slide (barcode at bottom). The size and location are compatible with standard 22mm x 60mm cover slips and other equipment for handling microarrays printed on this substrate size. A list of previously tested equipment can be found in Appendix A.
Technical Note: To reduce possible sources of experimental variation, which may effect experimental results, Operon strongly advises OpArrays users to gather completed OpArrays experimental data by scanning the OpArrays as soon as practical once the experiment is completed. Please schedule your experiments appropriately. Degradation of fluorescent dyes is reported post-hybridization; these effects are attributed to a variety of sources. There are several reports regarding reduction of Cy5 signal intensity relative to Cy3 due to the concentration of atmospheric ozone above 5 ppb in the atmosphere. The major consideration in preventing this effect seems to be in the transition from a wet to dry array surface. This protocol is designed to minimize these effects.
Date 2/7/2007 OpArraysTM Protocol
www.operon.com Page 2


title: Agilent RISET 2.0 8x15K 60mer oligonucleotide microarray

status: Public on May 25 2010

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

manufacture_protocol: see www.agilent.com


title: cGRASP 32K (Salmonid) cDNA - Release Date 02/08

city: Québec

first: Christopher

last: Sauvage

state: QC

address: 1030 Avenue de la médecine - Pavillon Marchand

institute: University Laval

organism: Salmo salar

description:
Described in A salmonid EST genomic study: genes, duplications, phylogeny and microarrays. Koop et al., BMC Genomics 2008 Nov 17;9:545
Annotation file, see: http://web.uvic.ca/grasp/microarray/32KArrayData_IE007/32KcDNA_data.html


title: Biological Research Center Agilent human 14k custom platform

status: Public on Feb 23 2010

city: Szeged

first: Agnes

last: Zvara

address: Temesvari krt 62

country: Hungary

institute: Biological Research Center

first: Laszlo

middle: G

last: Puskas

first: Liliana

middle: Z

last: Feher

first: Csaba

last: Vizler

first: Ferhan

last: Ayaydin

first: Erzsebet

last: Raso

first: Eszter

last: Molnar

first: Istvan

last: Magyary

first: Ivan

last: Kanizsai

first: Gabriella

last: Fabian

first: Klaudia

last: Farkas

first: Peter

last: Hegyi

first: Ferenc

last: Baska

first: Bela

last: Ozsvari

first: Klara

last: Kitajka

manufacture_protocol: Agilent protocol


title: Agilent-016162 PEDB Whole Human Genome Microarray 4x44K

status: Public on Feb 17 2010

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center


title: Homo sapiens 3K Immunoarray2 HTLV-1 JH

status: Public on Feb 14 2010

city: Montreal

first: Eduardo

last: Hernandez

state: Quebec

address: 3755 Cote-Sainte-Catherine Road

department: Molecular Oncology Group

institute: Lady Davis Institute for Medical Research (JGH)

last: Wilkinson

manufacture_protocol: As posted in the website www.microarray.ca for to color hybridizations


title: Affymetrix GeneChip Human Genome HG-U133 Plus 2 Array [CDF: Brainarray Version 11, HGU133Plus2_Hs_ENTREZG]

status: Public on Jan 31 2010

city: Mannheim

first: Tobias

last: Czymai

state: Baden-Württemberg

address: Theodor-Kutzer-Ufer 1-3

department: Dermatology

institute: University Medical Center Mannheim, University of Heidelberg

description:
This is identical to GPL570 but a custom CDF environment was used to extract data [Brainarray Version 11, HGU133Plus2_Hs_ENTREZG].
CDF is linked below as a supplementary file.


title: Agilent_UNIFEGM Human 8x15k array v1.0

status: Public on Jan 28 2010

city: Ferrara

first: Matteo

last: Bovolenta

address: 74, Fossato di Mortara

department: Life Sciences and Biotechnology

country: Italy

institute: University of Ferrara

description:
CGH-v4_95_Feb07
genome version: hg18,NCBI36,Mar2006

manufacture_protocol: 60-mer oligonucleotides printed with SurePrint technology by Agilent. Probes were both designed and identified in the Agilent eArray on-line tool


title: SMD Print_1015 Homo sapiens

city: Amsterdam

first: Lisa

last: van Baarsen

address: Meibergdreef 9

department: Div. of Clinical Immunology and Rheumatology

country: Netherlands

institute: EULAR & FOCIS Center of Excellence

manufacture_protocol: Material is transferred from microtiter plate wells to the slide surface by an automated print head


title: Agilent SurePrint G3 CGH array (4X180K) CCA_VUMC design AMADID#022522

status: Public on Jun 17 2010

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

description:
170k BaBo UMCG plus Cancer Census.
Arrays of this design have barcodes that begin with 16022522 or 2522522.

first: B

last: Ylstra

last: Eijk


title: Illumina mouseRef-8 v1.0a expression beadchip

status: Public on Jan 26 2010

first: Lynn

middle: M

last: Amon

address: 1100 Fairview, M1-C108

department: Division of Public Health Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

description: The Mouse-8 BeadChip can be used to study expression of over 24,000 mouse transcripts based on MEEBO, RefSeq and RIKEN FANTOM2 content. researchers can generate whole-genome expression profiles for 8 samples in parallel on a single BeadChip.


title: 32K_Mouse_Genome_Array_gene list

status: Public on Jan 27 2010

first: Bin

last: Wan

address: 18 shuangqing road, Haidian District

country: China

institute: Research centre for eco-environmental sciences, CAS

manufacture_protocol: The microarray was purchased from CapitalBio Inc. This 32K Mouse Genome Array consists of 32256 70mer oligo DNA that were purchased (Operon, Huntsville, AL) and printed on a 75×25 mm silanized glass slides using a SmartArrayTM microarrayer (CapitalBio). A detailed description and list of genes can be found on the CapitalBio website (CapitalBio Corp., Beijing, China).


title: Duke Taeniopygia guttata 45K

status: Public on Jan 16 2010

city: Durham

first: Osceola

last: Whitney

state: NC

address: Research Drive, Bryan Research Building, Room 401E

department: Neurobiology

institute: Duke University Medical Center

organism: Taeniopygia guttata

first: Andreas

last: Pfenning

first: Jason

last: Howard

first: Erich

last: Jarvis

manufacture_protocol: Using Agilent eArray 5.4, a web-based application, we designed custom microarrays. The microarrays are manufactured using a proprietary non-contact industrial inkjet printing process, in which oligo monomers are deposited uniformly onto specially-prepared glass slides. This in situ synthesis process prints 60-mer length oligonucleotide probes, base-by-base, from digital sequence files. The precise inkjet process enables the delivery of extremely small, accurate volumes (picoliters) of the chemicals to be spotted. Standard phosphoramidite chemistry used in the reactions allows for very high coupling efficiencies to be maintained at each step in the synthesis of the oligonucleotide. Agilent’s real time quality control inspection system verifies chemical deposition at each step in the process to minimize or eliminate feature drop-out and premature truncation of the oligonucleotide probe.


title: Agilent-015580 Mouse 44K ChIP-on-Chip Set, 1 of 2

status: Public on Dec 09 2009

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

manufacture_protocol: see the manufacturer's website


title: 36K Mouse Genome Array

status: Public on Jan 01 2010

first: changyan

last: li

address: 27 Taiping Road

institute: Beijing Institute of Radiation Medicine

manufacture_protocol: as described in CapitalBio Corporation Manual


title: Agilent-015580 Mouse 44K ChIP-on-Chip Set, 2 of 2


title: CCDTM Homo sapiens 17.5k version 2.1

status: Public on Dec 05 2009

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

description: Derived from GPL5959 07/01/09 - CCDTM Hs_CCDTM17.5k version 2

manufacture_protocol: Microarrays are printed with GeneMachines robotic arrayer from Genomic Solutions (http://www.genomicsolutions.com) that is fitted with a printhead containing 32 SMP2.5 printing pins from Telechem International (http://www.arrayit.com). The human cDNA probe set is based on RG_HsKG_031901 8k clone set and 9k clones from the RG_Hs_seq_ver_070700 40k clone set from Research Genetics (http://clones.invitrogen.com). The set includes 12,072 uniquely named genes, 875 duplicates of named genes and all remainder consisted of expression sequence tags (about 4053 EST). In addition, 194 selected cDNA clones from Stratgene and 218 custom designed 60mer oligo representing transcripts with immunological function were added to the probe set. The cDNA probes were amplified by PCR and distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in 3XSSC print buffer at a concentration of 50-100 ug/ml. The microarray spot densities are 280 microns (center-to-center), and one spot is printed per probe per slide. The microarrays are printed on Fisher Premium microscope slides (cat# 12-544-1) coated with poly-L-lysine and post-processed according to the procedures on the NCI website http://madb.nci.nih.gov/.


title: OciChip Zebrafish 14K

status: Public on Dec 25 2009

city: San Marcos

first: Dana

last: Garcia

address: 601 University Drive

institute: Texas State University-San Marcos

first: Katherine

middle: E

last: Saul

first: Joseph

middle: R

last: Koke

manufacture_protocol: contains 50-mer probes representing 8,839 genes in 14,067 spots


title: IRCL Human Genome CGH Microarray 4x44K (G4426B) (probe version)

status: Public on Dec 16 2009

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description:
Transfer of the Human Genome CGH Microarray 44B to the 4x44K format
Arrays of this design have barcodes that begin with 16014950 or 2514950.


title: Saccharomyces cerevisiae_GE06388_UCM

status: Public on Dec 01 2009

city: Barcelona

first: Benjamin

last: Pina

address: Jordi Girona, 18

institute: IDAEA-CSIC

description:
Budding yeast. 70-mer oligonucleotides.
YeastGenomeUG6388_2.gal

manufacturer: Genomics Unit. Scientific Park of Madrid (Spain).

manufacture_protocol: 6,388 oligonucletides (70 mer) in duplicate, representing 6,388 ORFs from Saccharomyces cerevisiae (Yeast Genome Oligo Set, OPERON, Cologne, Germany). Printed on aminosylane-treated slides (Corning, 25x75 mm), and covalently linked with UV light and heat. 48 blocks, 18 columns, 16 Rows.


title: Saccharomyces cerevisiae_GE06388_UCM_4x4

description:
Budding yeast. 70-mer oligonucleotides.
YeastGenomeUG6388 (4x4)(2).gal


title: TwinChip Rat 5K array

status: Public on Dec 02 2009

city: Gangneung

first: Dojun

last: Yoon

state: Gangwon

address: 522 Naegokdong

department: Biochemistry, Medical College

country: South Korea

institute: Kwandong University

manufacture_protocol: see manufacturer's web site


title: CASPUR Aristaeus 95K version 1.0

status: Public on Nov 30 2009

city: Viterbo

first: Alessio

last: Valentini

address: via San Camillo de Lellis

department: IBAF

institute: University of Tuscia

description: High-density (90k) in situ synthesized microarray for Ovis aries, designed by means of a pipeline of software instruments that, starting from unannotated redundant EST sequences deposited at NCBI, selects oligonucleotides suitable for in situ generation on chip. The chip carries 21,743 non-redundant Ovis aries features in quadruplicate, 73.4% of which are fully annotated and correspond to 10,190 genes, thus representing a good coverage of the sheep genome.

first: Giovanni

last: Chillemi

first: Lorraine

last: Pariset

first: Susana

last: Bueno

first: Gianluca

last: Prosperini

first: Silvia

last: Bongiorni

first: Giordano

last: Mancini

manufacture_protocol: CustomArray uses a specially modified “CMOS” semiconductor to direct the molecular assembly of a specific sequence of DNA bases in response to a digital command. Each feature on the array (a microelectrode) is digitally addressed to selectively generate acid, by means of an electrochemical reaction which, in-turn, controls the detritylation reaction during phosphoramidite synthesis. A software program is used to control the microelectrodes, and thus, the detritylation pattern applied on the chip during synthesis.


title: Affymetrix Human Genome U133A Array [CDF: XLab gahgu133a_1.5.0]

status: Public on Dec 03 2009

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

description: NCBI36/hg18 assembly

relation: Alternative to: GPL96 (Alternative CDF [official])

manufacture_protocol: See GPL96 platform for the complete description of HG-U133A manufacture protocol


title: Lovett/WUSTL 0.7k TFarray v3

city: Saint Louis

first: Kara

last: Powder

state: MO

address: 4566 Scott Ave

department: Genetics

institute: Washington University in St Louis

organism:
Gallus gallus
Homo sapiens
Mus musculus

description: The majority of probes interrogate transcription factors and are designed to coding regions.

last: Lovett

first: David

last: Alvarado

manufacture_protocol: Microarrays were printed on a GMS 417 Arrayer (Affymetrix, Santa Clara, CA) within the Washington University Division of Human Genetics.


title: Agilent-015435 Copy_of_Mouse Promoter ChIP-on-Chip Set 244K Microarray 1 of 2

status: Public on Nov 17 2009

city: Boston

first: Frederic

middle: Emile

last: Bienvenu

state: MA

address: 1 Jimmy Fund Way

department: Cancer Biology

institute: Dana-Farber Cancer Institute

organism: Mus musculus

description:
Mouse Promoter ChIP-on-Chip Set 244K, Microarray 1 of 2

Arrays of this design have barcodes that begin with 16015435 or 2515435.

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.

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


title: Agilent-019597 custom fathead minnow 60mer (8x15k)

status: Public on Jul 30 2010

city: Vicksburg

first: Kurt

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

organism: Pimephales promelas


title: SMD Print_982  Mus musculus

status: Public on Feb 17 2010

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)


title: NCI_human_7657_001

city: Lübeck

first: Jens

middle: K

last: Habermann

address: Ratzeburger Allee 160

department: Department of Surgery

institute: University Clinic Schleswig-Holstein (UKSH), Campus Lübeck

organism: Homo sapiens

description: Arrays were used from one print batch and composed of 9,128 cDNAs denatured and immobilized on a poly-L-lysine-coated glass surface.  The gene annotation file (GAL file) used (Hs-UniGEM2-v2px-32Bx18Cx18R.gal) can be found at the facilities website http://nciarray.nci.nih.gov.

manufacture_protocol: Based on Incyte Human UniGem


title: Agilent-015436 Copy_of_Mouse Promoter ChIP-on-Chip Set 244K Microarray 2 of 2

description:
Mouse Promoter ChIP-on-Chip Set 244K, Microarray 2 of 2

Arrays of this design have barcodes that begin with 16015436 or 2515436.

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: Operon Homo Sapien V4 36K

city: Lyon

first: Frantz

last: Bouhallier

address: 29 rue Soeur Bouvier

institute: INSERM U418


title: Human ten thousand 50-mer oligo library from MWGBiotech Oligo sets (http:/www.mwgbiotech.com)

status: Public on Nov 13 2009

city: Mexico City

first: Carmen

last: Sánchez-Torres

department: Molecular Biomedicine

country: Mexico

institute: CINVESTAV-IPN

manufacturer: DNA Microarray unit of Cellular Physiology Institute, UNAM, Mexico

manufacture_protocol:
1. Oligo sets (http:/www.mwgbiotech.com) were resuspended to 50µM in Micro Spotting solution (ArrayIt Brand Products.).
2. SuperAmine coated slides 25x75 mm (TeleChem International INC) were printed in duplicate, and fixed at 80 ºC for 4 hours.
3. For pre-hybridization, slides were re-hydrated with water vapor at 60 ºC, and fixed with two cycles of UV light (1200J). After boiling for two minutes at 92 ºC, slides were washed with 95% ethanol for one minute and prehybridzed in 5X SSC, 0.1% SDS and 1% BSA for one hour at 42 ºC. The slides were washed and dried for further hybridization


title: [mjay] Custom Affymetrix Mouse Exon Junction Array

status: Public on Nov 04 2009

city: Cleveland

first: Donny

middle: D

last: Licatalosi

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve University

manufacture_protocol: see manufacturer's website


title: Human 9K CGI Array

status: Public on Jan 22 2010

city: Beijing

first: Kunlin

last: Zhang

address: DaTun Road A4

institute: Chinese Academy of Sciences

manufacture_protocol: Clone:pGEM-5Zf(-)/Primers:5'-CGG CCG CCT GCA GGT CGA CCT TAA- 3';5'-AAC GCG TTG GGA GCT CTC CCT TAA- 3';oligo synthesize/strandedness:Methylation tolerant E.coli strain XLI-BLUE MRF'/Length:760 bp(Average insert size);Arrayer Harderware:Aminosilane Coated Glass Slides/Software:Arrays were scanned with a confocal LuxScanTM scanner (CapitalBio Corp.), and obtained images were analyzed with LuxScan3.0 TM software (CapitalBio Corp);Spotting protocol:The PCR products were precipitated with ethanol and re-dissolved in EasyArrayTM Spotting Solution (CapitalBio Corp.), then printed in triplicate on Aminosilane Coated Glass Slides using a SmartArrayTM microarrayer (All from CapitalBio Corp.).


title: Eurogentec S. pombe IGR + ORF array (A290G and K060F)

status: Public on Nov 03 2009

city: Gothenburg

first: Claes

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

organism: Schizosaccharomyces pombe

description: 22176 IGRs and ORFs were spotted in duplicate on a glass slide

first: Paulina

last: Wanrooij

first: Olga

last: Khorosjutina

first: Karl

last: Ekwall

first: Julian

last: Walfridsson

manufacture_protocol:
Primary PCR: The PCR reactions are performed using tagged genome specific primers in the presence of genomic DNA (provided by your laboratory). We normally achieve a success rate of 93 % of PCR reactions. For the failed PCR reactions we perform three different protocols of PCR conditions, which include different MgCl2 concentrations and different Taq polymerase. We should normally get an additional 2 % working and reach a success rate of 95 % in total. We check 5 % of the total oligos by Mass Spectrometry and will re-synthesize maximum 2 % of the oligos based on a newly designed primer. We will perform the PCR reactions with the new designed oligonucleotides with the standard PCR protocol. Following this process we reach usually 97 % success rate.
Secondary PCR: amplifications will be performed using a single pair of primers annealing to tag sequences introduced on primary PCR primers. These PCR amplifications will also be controlled by agarose gel electrophoresis and repeated if required reaching a minimum of 95 % success rate. The final PCR products will contain an amino group at their 5' end to promote the attachment of the predicted gene coding DNA strand to the treated glass slides.


title: Kanazawa University/Hitachisoft AceGene Mouse Oligo Chip 30k 1 Chip Version

status: Public on Nov 11 2009

city: Kanazawa

first: Hiroshi

last: Ootsuji

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Disease Control and Homeostasis

institute: Kanazawa University Graduate School of Medical Science


title: University of North Carolina School of Medicine Whole Human Genome Oligo Microarray G4112A (Probe Name version)

status: Public on Oct 30 2009

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

description: This condensed platform contains 8 ids (A_23_P377735, A_23_P330490, A_23_P398545, A_23_P359596, A_23_P422222, A_23_P313394, A_23_P355433, A_23_P323814, A_23_P356088, A_23_P337837) that are absent from GPL6848.


title: SMD H. sapiens 40K IMAGE cDNA array

status: Public on Nov 01 2009

city: Palo Alto

first: Kunju

middle: J

last: Sridhar

address: 3801 Miranda Ave, bldg 100, Rm E4-230

department: Hematology

institute: Stanford University

manufacture_protocol: Material is transferred from microtiter plate wells to the slide surface by an automated print head


title: MusV29K

city: Marseille

first: Isabelle

last: Lesur Kupin

address: 163 av. de Luminy - case 928

department: Bioinformatics

institute: INSERM U928

first: Catherine

last: Nguyen

manufacture_protocol:
The microarrays MUSV29K contain 7771 sequences. The following cDNA libraries were used: the NIA Mouse 15K cDNA clone set, 2NbMT (thymus), NbMLN (lymph node), and 3NbMS (spleen). Detailed descriptions of these cDNA libraries are available at the UniGene database website (2NbMT: Lib.544, 3NbMS: Lib. 553, NbMLN: Lib.567, NIA 15K: Lib. 8622). All of the libraries were cloned into pT3T7D-Pac vector, exept for the NIA 15K Mouse cDNA clone set, which was cloned into pSPORT1 vector. The NIA 15K Mouse cDNA clone set is a rearrayed and resequenced set of 15 000 bacterial clones derived from 11 embryo cDNA libraries. 2NbMT, NbMLN and 3NbMS are sequenced I.M.A.G.E libraries. These libraries contain 84127 clones. We used the Microarrays Quality Control tool to select clones matching a single region on the mouse genome and for which at least one 3' EST and one 5'EST have been identified. We selected 7771 bacterial clones matching 6622 mouse genes. 73% (4833) of the genes are represented by a single cDNA clone and about 27% (1789) of the genes included in this gene set are represented by two or more different cDNA clones, providing internal controls to assess the reproducibility of gene expression measurements. We also added 8 positive controls (poly-A LBP2S and Cot1, a mix of DNA fragments containing repeated sequences) and 2205 negative controls (empty spots and CG03, an Arabidopsis thaliana cDNA sequence). In summary, the MUSV29K mouse microarray we designed contains 9984 spots, identifying 6622 mouse genes.
PCR amplifications were performed in 96-well microliters plates using the following primers: 5'-CCAGTCACGACGTTGTAAAACGAC-3' and 5'-GTGTGGAATTGTGAGCGGATAACAA-3'. The reactions were performed as described in Diehl et al. by transferring few Escherichia coli from a growth culture with a plastic 96pins replicator (Proteigene, #X5055) to 100µl of PCR mix pH8,5 containing 1,5mM MgCl2, 1M Bétaine, 375µM dATP, dTTP, dGTP, dCTP, and 5U of GoTaq DNA polymerase (Promega, #M3171). The plates were incubated for 6 min at 94°C, before 38 cycles of 94°C for 30s, 65°C for 45s and 72°C for 3min30s, followed by a final elongation phase at 72°C for 10 min. Amplification products were not quantitated, but their quality was systematically checked on 1% agarose gels. 11,03% of the bacterial clones were estimated to be nonamplified and 4,38% showed multiple bands after PCR amplification. Unpurified PCR products were then transfered to 384-well microplates using the TECAN Genesis workstation 150, before being evaporated, taken up to 30µl of distilled water, and spotted onto nylon membranes (Hybond-N+; Amersham Bioscience). This step was conducted using a MicroGrid-II arrayer (Apogent Discoveries) equipped with a 64-pin biorobotics printhead. Microarrays were hybridized with  ƔdATP 33P-labelled probe, whose oligonucleotide sequence is common to all spotted PCR product (LBP2S 5'-TCACACAGGAAACAGCTATGAC-3'). It showed uniform signal intensities across individual membranes.


title: NimbleGen Mouse 60-mer Expression Array 42.5K

status: Public on Nov 02 2009

city: Tallahassee

first: Ichiro

last: Hiratani

state: FL

address: 319 Stadium Dr

department: Biological Science

institute: Florida State University

description:
Build: MM8, NCBI 36
native array description file: 2006-08-03_MM8_60mer_expr.ndf
native array description file: 2006-08-03_MM8_60mer_expr.ngd

manufacture_protocol: NimbleGen


title: SMD Print_1128 Mus musculus

status: Public on Oct 18 2009

first: Alexander

last: Red Eagle

address: 3230 CCSR

institute: Alexander Red Eagle


title: Rosetta/Merck Mouse 23.6K 3.0 A1 microarray

status: Public on Dec 08 2009

city: Seattle

first: Amit

middle: V

last: Kulkarni

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description: Contains 60-mer probes (60-mer).

first: John

last: Castle

manufacture_protocol: Oligonucleotide array on glass.


title: UCSD Fly 4.7K v1.0

status: Public on Oct 15 2009

city: St Louis

first: Paul

last: Shaw

address: 660 S Euclid

department: Anatomy

institute: Washington University School of Medicine

manufacturer: University of California, San Diego Biogem Biomedical Microarray Facility

manufacture_protocol:
1. Specific DNA primers were used to amplify ecdysone-regulated control genes by polymerase chain reaction (PCR).
2. Vector-specific primers were used for 5853 cDNA EST clones.  More than 30,000 cDNA EST clones were selected for low levels of redundancy by the bioinformatics group at the Berkeley Drosophila Genome Project (BDGP) to obtain this set of 5853.
3. This set was arrayed into 96-well plates by Research Genetics. These clones were obtained from embryonic (LD), female germ line (GM), or head (HL) cDNA libraries provided by the Berkeley/Howard Hughes Medical Institute Drosophila EST Project.
4. Forward and reverse vector-specific primers were made for either the pBS vector (ESTf, GAACAGCTATGACCATGATTACGCC; ESTr, CGGCCAGTGAATTGTAATACGACTC) or the pOT2 vector (OTf, AATGCAGGTTAACCTGGCTTATCG; OTr, AACGCGGCTACAATTAATACATAACC).
5. All PCR primers were picked with Primer3 software developed at the Whitehead Institute and are available at www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi.
6. PCR reactions were done in 96-well plates with reaction volumes of 100 µl per well under the following conditions: 0.2 µg each of forward and reverse primers, 2 mM MgCl2, 10 µl of 10× PCR buffer, 0.25 mM each dNTP, 1.5 U of Taq DNA polymerase, and 0.025 U of Pfu DNA polymerase, for 35 cycles at 94°C for 30 s, at 65°C for 30 s, and at 72°C for 5 min.
7. Several microliters of bacterial liquid culture containing the cDNA EST clone were transferred from a master plate to each well in the PCR reaction plate by means of a 96-pin transfer device.
8.  All PCR reactions were analyzed by agarose gel electrophoresis.
9. The following categories of amplified product were obtained: no product, 731; light single band, 604; double band, 221; double band with one much fainter than the other, 412; streak, 5; other anomaly, 19; and single intense band, 3861.
10. These PCR products were then mechanically spotted on glass microscope slides.


title: SMD Saccharomyces cerevisiae 7k Print_781

status: Public on Sep 23 2009

first: Barbara

last: Dunn

organism: Saccharomyces cerevisiae


title: SMD Saccharomyces cerevisiae 8.6k Print_778


title: Hs-OperonV2-vB1.1

status: Public on Oct 02 2009

city: Houston

first: Samuel

last: Mok

address: 1515 Holcombe Blvd

institute: University of Texas M.D. Anderson Cancer Center

manufacturer: NCI, Advanced Technology Center (Rockville Maryland).

manufacture_protocol: 1. The Human Release 1.0 oligonucleotide library, containing 60mer oligonucleotides representing 22,000 unique genes were obtained from Sigma-Genosys (Sigma, St. Louis, MI).


title: Affymetrix Human Genome U133B Array [CDF: XLab gahgu133b_1.5.0]

status: Public on Dec 03 2009

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

institute: University of Rostock

description: NCBI36/hg18 assembly

relation: Alternative to: GPL97 (Alternative CDF [official])

manufacture_protocol: See GPL97 platform for the complete description of HG-U133B manufacture protocol


title: SMD Saccharomyces cerevisiae 8.4k Print_55


title: SMD Saccharomyces cerevisiae 13.8K Print_1204


title: Print_1320

status: Public on Oct 13 2009

city: Manchester

first: Kimberly

last: Mace

address: Michael Smith Building, Oxford Road

department: Division of Cell Matrix Biology & Regenerative Medicine

country: United Kingdom

institute: University of Manchester


title: SRI Human 27K version 2 slide 1

status: Public on Aug 27 2009

city: Toronto

first: Azza

last: Al-Mahrouki

address: 2075 Bayview Avenue

department: Radiation Oncology & Imaging Research

country: Canada

institute: Radiation Oncology, Sunnybrook Health Sciences Centre

manufacturer: SRI Genomics Core Facility, Sunnybrook Health Science Centre.

manufacture_protocol: Using epoxy coated slides under 50% humidity and Perkin Elmer SpotArray 72 in 4 x 12 pin configuration and 18 x 17 spot configuration of each subarray.


title: Print_1223

status: Public on Sep 18 2009

city: Paris

first: Karine

last: Clement

address: place du parvis Notre-Dame

department: Service de Medecine et Nutrition

institute: Hotel-Dieu


title: MouseWG-6 V2

status: Public on Aug 31 2009

city: Seoul

first: YoungJi

address: 28 Yongon-dong Chongno-gu

institute: Seoul National University Biomedical Informatics

manufacturer: Illumina Inc. San Diego, California, USA


title: Print_1201

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine


title: University of Goettingen, Custom Agilent Rat Immuno Microarray 8x15K G2509F (Feature Number Version)

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

organism: Rattus norvegicus

description: Designed to represent all known genes from immunological processes in the rat genome and their resulting transcripts. Content for this microarray was generated from leading public databases.

first: Peter

last: Novota

first: Reiner

last: Hitt

first: Lennart

last: Opitz

first: Ralf

last: Dressel


title: Duke Operon Rat 27k V3.0 printed oligonucleotide array

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Operon Rat genome arrays printed in 3XSSC buffer onto Corning CGAP slides using OmniGrid300 arrayer by Institute for Genome Sciences and Policy of Duke University Medical Center

manufacturer: Duke Microarray Facility (manufactured printing of arrays)


title: Illumina Sentrix 6 Mouse V1.1 BeadChip

status: Public on Aug 26 2009

city: Townsville

first: Catherine

last: Rush

state: Queensland

address: Douglas Campus

department: Medicine

country: Australia

institute: James Cook University


title: University of Southern California/Agilent Mouse Genome CGH Microarray 244A

status: Public on Aug 14 2009

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California


title: Agendia_DiscoverPrint_v2

status: Public on Aug 17 2009

city: Amsterdam

last: Roepman

address: Science Park 406

institute: Agendia

manufacture_protocol: Microarrays were prepared by Agilent technologies using their Agilent SurePrint Technology. Breifly, 60-mer oligonucleotides are synthesized base-by-base in repetitive print layers on a solid glass substrate, using standard phosphoramidite chemistry.


title: Ajou University Mus musculus Array 24K

status: Public on Aug 09 2009

city: Suwon

first: Sangdun

last: Choi

address: Woncheon-dong, Yeongtong-gu

department: Department of Molecular Science and Technology

institute: Ajou University


title: 36K_mouse_genome_array V4.0

status: Public on Jul 08 2009

city: Beijing

first: Bin

last: Wan

address: 18 shuangqing road, Haidian District

institute: Research centre for eco-environmental sciences, CAS

manufacture_protocol: Genome Array consisting of 35852 70mer oligo DNA representing 25,000 genes and 38,000 gene transcripts that were purchased (Operon, Huntsville, AL) and printed on a 75×25 mm silanized glass slides using a SmartArrayTM microarrayer (CapitalBio). A detailed description and list of genes can be found on the CapitalBio website (www.capitalbio.com).


title: PF - Agilent-014850 Whole Human Genome Microarray 4x44K

status: Public on Oct 16 2009

city: Toulouse

first: Stéphane

last: VISPE

address: 3 Rue des Satellites

institute: Laboratoires Pierre Fabre

description:
This multi-pack (4X44K) formatted microarray represents a compiled view of the human genome as it is understood today. The sequence information used to design this product was derived from a broad survey of well known sources such as RefSeq, Goldenpath, Ensembl, Unigene and others. The resulting view of the human genome covers 41K unique genes and transcripts which have been verified and optimized by alignment to the human genome assembly and by Agilent's Empirical Validation process.
Arrays of this design have barcodes that begin with 16014850 or 2514850.
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.


title: Adelaide Micoarray Facility Compugen Oligolibrary Mouse 22K V4.0

status: Public on Jun 15 2009

city: Brisbane

first: Ashley

last: Connolly

address: St Lucia

institute: University of Queensland

description: 4x16 print groups, 24 rows x 20 columns per print tip group. The platform contains a single copy of the Compugen mouse oligonucleotide library V2.0 (IDs start with CGEN), plus an inhouse produced control plate (IDs start with AMC). This spotting layout is version 4 and is similar to version 1 and version 3 but with a different array list.

manufacturer: Adelaide Microarray Facility IMVS Adelaide Australia

first: Mark

last: Vanderhoek

first: Christopher

last: Wilkinson

manufacture_protocol: Compugen mouse oligonucleotide library V2.0 comprising 21,991 65-mers representing 21,857 unique genes. Additional locally made controls spotted. Oligos printed onto Corning CMT-Gaps slides using a 4x16 pinhead robot. Each pinhead printed an array of 480 features arranged in 24 rows x 20 columns (23040 features per array). See www.microarray.adelaide.edu.au for further details).


title: Rosetta/Merck Human P4 Array1

status: Public on Jun 09 2009

city: Seattle

first: Amit

last: Kulkarni

address: 401 Terry Ave N

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description:
Oligonucleotide array on glass.
Contains full length probes

first: John

last: Castle

manufacture_protocol: see Merck's web site


title: Agilent-014698 Human Genome CGH Microarray 105A (G4412A) [Probe Name version]

status: Public on Aug 21 2009

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
This kit provides two arrays per slide, each containing over 99,000 60-mer oligonucleotide probes. These probes, specifically optimized for copy-number measurement, span coding and non-coding genomic sequences with median spacing of 18.9 kb and 50.6 kb respectively. This microarray is designed for use with Agilent’s optimized assay protocols, enabling researchers to use nanogram levels of total genomic DNA without complexity reduction.

Arrays of this design have barcodes that begin with 16014698 or 2514698.

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 includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL4093.

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


title: Eurogentec AG S. pombe Microarray Platform

status: Public on Sep 12 2009

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

institute: Karolinska Inst

first: A

middle: P

last: Wright

first: D

last: Talibi

first: S

last: Hass


title: LBEG Dmel/UChile

status: Public on Jul 01 2009

city: Santiago

first: Alejandro

last: Zúñiga

address: Macul 5540

country: Chile

institute: INTA - Universidad de Chile

manufacturer: Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile

manufacture_protocol: Clones were picked from -80°C stocks and grown overnight in 96 well plates in 200 µl LB plus 50 µg/mL of ampicillin. PCR amplification of bacterial cultures and quality verification of the products were performed as described in González-Agüero et al (2008). PicoGreen ds-DNA Quantitation Kit (Molecular Probes) was used according to manufacturer instructions to quantify and standardize PCR products concentration. Twenty µl of the PCR products were arrayed in 96-well plates and mixed with an equal volume of 50% dimethyl sulfoxide. PCR products (70 ng) were spotted in duplicate on 8 x 12 cm Nylon membranes (GeneScreen Plus, Biorad) using an 8 pins print-head (Arraylt model SSP015) and the arraying robot Versarray Chip Writer Compact (BioRad). The membranes were treated as described in González-Agüero et al. (2008). In addition to the library clones, the following controls were spotted onto membranes: (1) a fragment of the vector pBluescript II obtained by amplification with the T7 and SP6 universal primers; (2) several spots of DMSO 50%; (3) PCR amplified fragment of genes serendipity α, twist, tinman, fog and snail as positive controls, and (4) actin, tubulin, and RP49 as housekeeping, and (5) four dilutions of a PCR amplified fragment from a B. subtilis dap cDNA (ATCC; number 87486), which hybridizes to an in vitro synthesized poly(A)-RNA that was added to the embryo RNA samples (dilution 1/200) prior to the labelling process and used as spike mRNA (Kane et al., 2000).


title: [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array - custom CDF (tinesath1cdf)

status: Public on Jun 02 2009

city: Gent

first: Nathalie

last: Gonzalez

address: Technologiepark 927

department: Plant System Biology

country: Belgium

institute: VIB

organism: Arabidopsis thaliana

description: see manufacturer's web site/ data processing:an alternative CDF ("tinesath1cdf") was used, where each probe is assigned uniquely to one transcript and is excluded if it aligns to a different transcript with 24 or more perfect matches (Casneuf et al. 2007)

relation: Alternative to: GPL198 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: Stanford_MMArray_mouse_43k

status: Public on May 27 2009

city: San Antonio

first: stephen

middle: e

last: harris

address: 7703 Floyd Curl Drive

department: Periodontics

institute: U. of Texas Health Sci Center at San Antonio

manufacturer: Stanford Functional Genomics Facility, Stanford, CA


title: Experimental Therapeutics Centre Human Ref-8 version 2

status: Public on Sep 01 2009

city: Singapore

first: Meng Ling

last: Choong

address: 31 Biopolis Way, #03-01 Nanos

department: Drug Discovery

country: Singapore

institute: Experimental Therapeutics Centre

description:
Alternative platform created for Experimental Therapeutics Centre Assay Development Group.
Equivalent official platform: GPL6104


title: USDA 9.6K avian intestinal intraepithelial lymphocyte cDNA microarray (AVIELA) version 1

city: Beltsville

first: Hyun

last: Lillehoj

state: MD

address: USDA-ARS, Bldg. 1040, BARC-East

department: Animal Research Service

institute: US Department of Agriculture

organism: Gallus gallus

manufacturer: Lab of Dr. Hyun Lillehoj, Animal Parasitic Diseases Laboratory, ARS, US Department of Agriculture (USDA)

manufacture_protocol: The microarray was constructed from 9,668 EST clones selected from an intestinal IEL cDNA library. PCR products of the ESTs were dried and resuspended in 3X SSC, 0.01% SDS, followed by spotting in duplicate  onto MicroMax glass slides (Perkin Elmer, Boston, MA) using an OmniGrid Accent spotter (GeneMachines, San Carlos, CA).  The elements were organized into duplicated 24 subarrays, each as a 21 x 21 spot grid.  The PCR products were fixed by UV cross-linking, followed by assessment of spotting quality by staining with SYBR-Green II according to the manufacturer's protocol (Invitrogen, Carlsbad, CA).  Greater than 90% of the spots possessed an average diameter of 150-200 µm.


title: Aviva Systems Biology Human H20K ChIP-DSL

first: Yongfeng

last: Shang

address: 38 Xue Yuan Road

department: Biochemistry and Molecular Biology

institute: Peking University

manufacture_protocol: as described in Aviva Systems Biology Manual. Microarray chips containing 20,000 human promoters.


title: Saccharomyces cerevisiae 9.2K Print_1137

status: Public on May 12 2009

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

manufacture_protocol: Material is transferred from microtiter plate wells to the slide surface by an automated print head


title: Hsbb-20

status: Public on May 14 2009

city: Bethesda

first: Sasisekhar

last: Bennuru

address: 10 Center Dr, Bldg 10, Rm 11N208

department: LPD

institute: NIH/NIAID

description: The custom microarrays are manufactured by the Microarray Research Facility of the National Institute of Allergy and Infectious Diseases (NIH/NIAID). Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions (http://www.genomicsolutions.com ) that is fitted with a printhead and 48 SMP3 print tips from Telechem (http://www.arrayit.com ). The human microarray (Hsbb) probe set is based on 70mer oligonucleotides from Qiagen's Human Genome Oligo Set V2.0 ( http://oligos.qiagen.com/arrays/omad.php ). A comprehensive gene list is also available at http://madb.niaid.nih.gov/

first: Thomas

middle: B

last: Nutman

manufacture_protocol: Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved to a normalized 25 micromolar concentration in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl). The Hsbb microarray spot densities are 190 microns (center-to-center). The microarrays are printed on MWG Epoxy Slides (MWG Biotech Inc., # 1150-000000) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: SMD Print_668 Mus musculus

status: Public on May 13 2009

city: Richmond

first: Paul

last: Fawcett

state: VA

address: 1101 E. Marshall St.

institute: Virginia Commonwealth University


title: Rosetta/Merck Mouse 25k_v3

status: Public on May 30 2009

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

institute: Best Institute

first: Hunter

last: Fraser

first: Eric

last: Schadt

manufacture_protocol: Inkjet in situ synthesis


title: Affymetrix GeneChip Human HJAY Array 17K

status: Public on May 05 2009

city: Iowa City

first: Yi

last: Xing

state: IA

address: 3294 CBRB, 285 Newton Rd

department: Internal Medicine, Biomedical Engineering

institute: University of Iowa

manufacture_protocol: See manufacturers website


title: Duke Mouse 36K oligonucleotide array Operon V4.0

status: Public on Aug 12 2009

city: Prairie View

first: Dumitru

last: Iacobas

address: Ann Preston St

institute: Prairie View A&M University

description: Operon Mouse genome arrays printed in 3XSSC buffer onto Corning CGAP slides using OmniGrid300 arrayer by Institute for Genome Sciences and Policy  of Duke University Medical Center


title: Gallus gallus 55k 080317_Chicken_galGal3_expr

status: Public on May 01 2009

city: Beijing

first: Yeshi

last: Yin

address: NO.1 West Beichen Road, Chaoyang District

institute: Institute of Microbiology

description: The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.


title: Duke Mouse 30k Oligonucleotide Array Operon V3.0.1

status: Public on Aug 07 2009

description:
Operon Mouse genome arrays printed in 3XSSC buffer onto Corning CGAP slides using OmniGrid300 arrayer by Institute for Genome Sciences and Policy of Duke University Medical Center.
Spotted sequences in GPL4783.
Reannotated on 27/07/09 through http://smd.stanford.edu/cgi-bin/source/sourceBatchSearch

middle: A


title: State Key Lab_Human_13K_cDNA array

status: Public on Aug 01 2009

city: Bristol

first: Hai

last: Fang

address: Woodland Road

department: Department of Computer Science

institute: University of Bristol

manufacturer: State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology

manufacture_protocol: Microarrays with 12,630 cDNA clones representing 10,647 genes were fabricated in-house using a Generation III spotter (Amersham Biosciences). The cDNA clones were sequence verified and enriched with genes expressed in hematopoietic cells (Mao et al. 1998; Zhang et al. 2000). Among these cDNA clones include commercial clones from Invitrogen. The Scorecard plate including positive control, negative control, dynamic range control, ratio control and housekeeping genes were spotted on each slide. Microarray slides were obtained from Fullmoon BioSystems (Sunnyvale, CA, USA). The clones were spotted in a final concentration of 200-400 fmol/µl in spotting buffer (50% DMSO) using 12 microspot pins to reach a complexity of 12,630 spots per slide. After spotting, the slides were UV cross-linked (400 mJoules) and stored at room temperature.


title: FHCRC Human Oligo Array v3.2

status: Public on Apr 01 2009

first: Robert

last: Strauss

state: WA

address: 1705 NE Pacific st.

institute: University of Washington

manufacturer: Fred Hutchinson Cancer Research Center, Genomics Resource

first: Pavel

last: Sova

first: David

last: Pritchard

first: Ying

last: Liu

last: Lieber

manufacture_protocol: Human Oligonucleotide 22K microarray ("Human Oligo 22K array") manufactured by the Genomics Resource of the Fred Hutchinson Cancer Research Center (FHCRC). The array was manufactured using version 3.2 of the Operon Human Genome Oligo Set which contains 21,329 70mer probes representing 21,329 genes. A majority of the probes (21,322) were designed from the UniGene Database Build Hs147 (February 2002) and the Human Reference Sequence (RefSeq) Database with the exception of 7 probes designed from the UniGene Database Build Hs 152.