title: Agilent Homo sapiens 21.6K custom array

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

country: Japan

institute: Aichi Cancer Center

manufacture_protocol: see manufacturer's website


title: Agilent custom 105K array (Agilent-019507)

status: Public on Jul 18 2009

city: Newcastle Upon Tyne

first: Vikki

last: Rand

state: Tyne and Wear

address: Paul O'Gorman Building, Newcastle University

department: Northern Institute for Cancer Research

country: United Kingdom

institute: Newcastle University

organism: Homo sapiens

technology: spotted oligonucleotide

description: as per GPL4093 with additional oligonucleotides spanning pseudoautosomal region 1 on Xp/Yp

distribution: custom-commercial

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


title: LUH Human Genome CGH Microarray 244A

status: Public on Apr 01 2009

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

technology: in situ oligonucleotide

description: This microarray is Agilent’s premium product for human DNA copy-number profiling. Over 236,000 60-mer oligonucleotide probes, specifically optimized for copy-number measurement, span coding and non-coding genomic sequences with median spacing of 7.4 kb and 16.5 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.


title: NIBI mouse oligo-DNA 10K microarray

status: Public on Jun 30 2009

city: Ibaraki

first: Naoki

last: Osada

state: Osaka

address: 7-6-8 Saito-Asagi

department: Division of Biomedical Research Resources

institute: National Institute of Biomedical Innovation

organism: Mus musculus

distribution: non-commercial

first: Yosuke

last: Kameoka

manufacture_protocol: The microarrays were printed on Corning Ultra-GAPS slides coated with amino-silane and post-processed according to the manufacturer's protocol.


title: SweGene Homo Sapiens-35.327 12.6k oligo array

status: Public on Jun 05 2009

city: Las Palmas de Gran Canaria

first: Luis

last: Henriquez

state: Las Palmas

address: C/ Dr. Pasteur s/n

country: Spain

institute: University of Las Palmas de Gran Canaria

manufacturer: SweGene DNA Microarray resource center (Lund University, Sweden)

manufacture_protocol: Homo Sapiens-35.327 human 70-mer oligonucleotides were spoted on glass slides (Corning). Probes set obtained are from Origen


title: Agilent-012700 Human Genome CGH Microarray 44A G4410A_beta (Feature Number version)

status: Public on Mar 27 2009

city: Helsinki

first: Henrik

last: Edgren

address: Tukholmankatu 8

country: Finland

institute: Institute for Molecular Medicine, University of Helsinki

description:
Represents a beta-/trial version of Agilent-012750 Human Genome CGH Microarray 44A G4410A (GEO accession number GPL2873).

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: NimbleGen Human Promoter Array 1.0

status: Public on Mar 17 2009

city: San Diego

first: Yipeng

last: Wang

state: CA

country: USA

institute: Vaccine Research Institute of San Diego

first: Fred

last: Long

first: Michael

last: McClelland


title: Affymetrix GeneChip Human HJAY Array r1

status: Public on Jul 01 2009

city: Santa Clara

first: Jason

middle: Wray

last: Hubbard

address: 3380 Central Expressway

institute: Affymetrix Inc

manufacture_protocol: See manufacturers website


title: WU Mouse_Illumina_46k_v6-1.1

status: Public on Mar 08 2009

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

technology: oligonucleotide beads

description: Same as platform GPL6105.

manufacture_protocol: See manufacturer's website.


title: Wistar microarray facility custom human array Ha05+Ha06

status: Public on Feb 28 2009

city: West Point

last: Nebozhyn

state: PA

address: Mail Stop WP53B-120, 770 Sumneytown Pike, Building 53, P.O. Box 4

department: GpGx/Computational System biology

institute: Merck, Inc

technology: spotted DNA/cDNA

manufacturer: Genomics Facility, the Wistar institute, Philadelphia, PA

manufacture_protocol: In house protocol


title: Duke Operon Human Oligo Arrays 35K version 3.0

status: Public on Mar 04 2009

city: Durham

first: Pedro

last: Gonzalez

state: NC

address: Erwin Road Box 3802

department: Ophthalmology

institute: Duke University

manufacturer: Duke Microarray Facility (manufactured printing of arrays)

first: Coralia

middle: C

last: Luna

first: Guorong

last: Li

first: Paloma

middle: B

last: Liton

first: David

middle: L

last: Epstein


title: Illumina Mouse-8 Expression BeadChip

status: Public on Apr 04 2009

city: Daejon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine


title: HudsonAlpha Illumina Homo sapiens Methyl-seq

status: Public on Mar 09 2009

city: Stanford

first: Rami

last: Rauch

address: 300 Pasteaur Dr

institute: Stanford U

technology: other

description: 1G Genome Analyzer sequencing machine

distribution: virtual


title: PGA Mouse v1.1

status: Public on Mar 16 2009

city: Cambridge

last: Sawada

state: MA

address: 65 Landsdowne Street

institute: Brigham and Women's Hospital

manufacturer: Massachusetts General Hospital Microarray Core

manufacture_protocol: The microarray was a glass-based array containing PGA Mouse v1.1 probe set (19,549 70-mer oligonucleotides), which provides complete coverage of the 2002. Mouse genome, built off the GenPept database. The information on the probe set including the gene ID and oligo sequences can be found at: https://dnacore.mgh.harvard.edu/microarray/files/anno_dist-MGH_Mm_11_total.txt


title: Aguiar Human 41K miRNA CGH

city: Boston

first: Cheng

address: 44 Binney St

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

manufacture_protocol: The miRTile platform was designed using the eArray interface  (Agilent Technologies). In brief, the genomic coordinates from 474 miRNA genes  (miRBase release V9.0, October 2006) were extracted and used to search for all  oligonucleotide probes available in the Agilent catalogue located within a ~ 35kb area  surrounding each precursor miRNA sequence. Probes were available to cover all but 3  miRNA loci (miR511-1, miR-511-2 and miR-550-2) included in the miRBase release  V9.0. Thus, our platform effectively tiled the loci for 471 miRNAs. In addition, probes  mapping to the entire genomic locus of 17 mRNA genes that are known to play a role in  microRNA biogenesis were also identified and included in this platform (Supplementary  Table 2 of the paper). These high density tilling arrays were printed in the 4 X 44K slide format  including 41631 oligoprobes (~55bp long, 44-59bp) with a total genomic coverage of  11.6 Mb encompassing 309 unique chromosomal regions Backbone probes between  microRNA gene loci were included in the array at approximately 1 Mb intervals.


title: Print_470

status: Public on Feb 26 2009

city: Hanover

last: Whitfield

state: NH

address: 7400 Remsen

department: Genetics

institute: Dartmouth Medical School

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: OPERON_AROSV1.1.2_Candida_albicans_array

status: Public on Feb 21 2009

first: Robert

middle: J

last: Bastidas

address: 322 CARL, Research Drive Box 3546

department: Molecular Genetics and Microbiology

organism: Candida albicans

manufacture_protocol: Proprietary


title: Print_457


title: Su Lab Mouse 23K cDNA microarray

status: Public on Feb 09 2009

city: Bethesda

first: Tomoshige

last: Kino

address: 10 Center Drive MSC 1109

department: Program in Reproductive and Adult Endocrinology

institute: National Institute of Child Health & Human Development

description: This array includes the NIA mouse 15K and 7.4K cDNA clones as well as 0.2K controls

first: Yan

middle: A

last: Su

first: Jun

last: Wu

manufacture_protocol:
1. cDNA clones of the mouse 23K genes are amplified by PCR using published methods (Su YA and Trent JM, in Methods in Molecular Medicine, B. J. Nickoloff, Ed. [The Human Press Inc., Totowa, NJ, 2001], pp. 15-29.)
2. The PCR-amplified DNA fragments are arrayed in 96-well V-bottom plates (Matrix Cat#4914). Each well contains approximately 0.2 micrograms cDNA in 10 microlitters 3 X SSC
3. Dry the DNA-containing solution via evaporation at room temperature in stainless drawers within a class 10,000 clean room the day before printing.
4. Two hours before printing, add 10 µL of ultrapure water to each well.
5. Seal plates with Corning seals.
6. Incubate at room temperature for at least two hours to aid resuspension of DNA.
7. Shake plates near maximum rotational speed on flat-bed shaker for 1 minute.
8. Spin plates at 2000 rpm (Sorvall Super T21) at room temperature for 5 minutes.
9. Remove seals and cover with plate lids. Place plates in the Server Arm cassettes of GeneMachine OmniGrid 100 at 70% humidity.
10. Make sure plates rest behind both holding clips in the cassettes. Push plates back into the cassettes as far as they will go, putting them in the proper position for the server arm.
11. After the print run is completed, allow plates to dry through passive evaporation in a protected environment (same as the step 3 above)
12. For each subsequent preparation of these plates for a print run, the amount of ultrapure water added should be decreased by 0.25 µL per print run, as this is the amount drawn up by the pin capillary during each print cycle.


title: CDMC_Drosophila_Oligo

status: Public on Apr 03 2009

city: Johnson City

first: Lev

last: Yampolsky

state: TN

address: ETSU

department: Biological Sciences

institute: East Tennessee State University

organism: Drosophila melanogaster

description:
The CDMC_Drosophila_Oligo14k1 and The CDMC_Drosophila_Oligo14k2 platforms are oligonucleotide-based glass microarrays. Transcript-specific probes were designed by the International Drosophila Array Consortium (INDAC, www.indac.net) based on release 4.1 of the D. melanogaster genome and synthesized by Illumina (www.Illumina.com). This array is produced by the Canadian Drosophila Microarray Centre located at the University of Toronto. It is available for distribution to academic labs.
condensed version of GPL3603

manufacture_protocol: The CDMC_Drosophila_Oligo14kv1 and Oligo14kv2 arrays are printed on CMT-UltraGAPS slides (Corning Inc, Acton, MA) with an aminosilane coating using a SpotArray 72 microarrayer (Perkin Elmer, Boston, MA). There are 32448 spots on each array in a 12 row by 4 column arrangement of blocks (sub-grids). Each block contains 672 spots arrayed in a 26 row by 26 column grid. Spots designated as 'EMPTY' contain only NaPO4 spotting buffer for the 14kv1 arrays or 3x SSC for the 14kv2 arrays and occupy positions 23 through 26 of the 26th row. The blocks are spaced at 4500 micron intervals and the spot-to-spot distance is 166 microns. The nominal spot diameter is 125 microns. Further information including information regarding printing conditions and post-print treatments can be found at http://www.flyarrays.com/index.php?option=com_content&task=view&id=15&Itemid=38


title: Illumina HumanWG6_V2 chip

status: Public on Mar 03 2009

city: Philadelphia

first: Gao

last: Zhang

address: 3601 SPRUCE ST

department: Molecular and Cellular Oncogenesis Program

institute: Wistar Institute

description: This platform lets you assay more than 46,000 transcripts and profile six samples simultaneously on a single HumanWG-6 BeadChip.

first: Zhang

last: Gao


title: KRIBB_Human_14K

status: Public on Feb 13 2009

city: Daejeon

first: Kyung-Suk

last: Suh

first: Je-Geun

last: Lee

first: Sun-Hoo

last: Park

first: Chul-Ju

last: Han

first: Sang-Bum

first: Sook-Hyang

last: Jeong

first: Young-Il

last: Yeom

first: Chang-Min

first: Su-Jin

last: Cho

first: Ja-June

last: Jang

first: Dong-Wook

last: Choi

first: Kee-Ho

manufacture_protocol: Microarray chips contain ~13,000 cDNA clones originated from 14 libraries of cancer cell lines, 1 of carcinoma, and 5 of nontumor tissues. The PCR products were spotted on glass slides using an Array Spotter Generation III. The detailed information about clones and manufacture protocols can be found at website of Korean Unigene Information (http://kugi.kribb.re.kr).


title: LU/IBL_D.rerio_44k_015747

status: Public on Jan 29 2009

city: Neuherberg

first: Katharine

last: Webb

address: Ingolstaedterlandstr. 1

department: Institute for developmental genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

organism: Danio rerio

description: The micro-array slides were custom designed by Agilent Technologies. The slides contain in total 43.371 probes of a 60 oligonucleotide length. Of these probes a total of 21.496 probes were identical to the probes present on the Agilent probe set that is commercially available under catalog number 013223_D.  Most of the additional probes were designed using the eArray software from Agilent Technologies (https://earray.chem.agilent.com/earray/).  Settings used were based on the following settings: base composition methodology, best probe methodology and design with 3’ bias. The Agilent D.rerio transcriptome was used as a reference database. A small number of probes were manually designed based on knowledge of particular polymorphisms for genes encoding protein families such as 14-3-3 proteins, chitinase-like proteins and Toll-like receptors  in order to obtain gene-specific probes.

first: Annemarie

last: Meijer

first: Herman

middle: P

last: Spaink

manufacture_protocol: the arrays were produced according to manufacturer's protocol, check website: http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/default.aspx


title: SMD human Print_950

status: Public on Jan 21 2009

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine


title: Agilent Mouse Promoter ChIP-on-Chip Set 244K Combined Arrays (Slide 1 & 2) mm7 build

status: Public on Jan 27 2009

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

department: Biological Chemistry

institute: UCLA

first: Rupa

last: Sridharan

first: Jason

last: Tchieu

first: Mike

last: Mason

first: Qing

last: Zhou

first: Steve

last: Horvath

relation:
Alternative to: GPL4128
Alternative to: GPL4129

manufacture_protocol: Agilent Mouse Promoter Arrays 2x244K (Slide 1 and 2).  Data from both arrays were combined.


title: Agilent Mouse Promoter ChIP-on-Chip Set 244K Combined Arrays (Slide 1 & 2) mm8 build

manufacture_protocol: Agilent manufacturing protocol


title: SMD Human Print_886


title: Lovett/WUSTL_TFarray_v4

status: Public on Feb 06 2009

city: Saint Louis

first: Kara

last: Powder

state: MO

address: 4566 Scott Ave

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.

first: Michael

last: Lovett

first: David

last: Alvarado

middle: E

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


title: Agilent-016047 Walbot Zea mays 4x44K array

status: Public on Mar 01 2009

first: John

middle: F

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

organism: Zea mays

description: designed by Walbot Lab (same probes as 1x44)

manufacture_protocol: 43K 60-mer oligo probes were designed from the TIGR maize contigs and synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry on glass slides.


title: SMD Human Print_731


title: SMD Human Print_673


title: SMD Human Print_654


title: SMD Human Print_633


title: Fusion gene microarray, human, 69k, v.1.0.

status: Public on Jan 19 2009

city: Oslo

first: Gard

middle: Olav

last: Thomassen

address: Radiumhospitalet, Rikshospitalet HF

department: Institute for Cancer Research

country: Norway

institute: Rikshospitalet

manufacture_protocol: In-house made oligo design script, see original publication.


title: SMD mouse Print_1273

status: Public on Jan 15 2009


title: Saccharomyces cerevisiae 10.9K Print_1137

status: Public on Jan 14 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

organism: Saccharomyces cerevisiae

description: Nexterion epoxy slides

manufacturer: Center for Integrative Genomics, University of Lausanne, Switzerland


title: Custom Human Agilent Array 11k, Chromosome 6, Expression

status: Public on Dec 31 2008

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

distribution: commercial

first: Marco

last: Henneke

first: Lennart

last: Opitz

first: Jutta

last: Gaertner

manufacture_protocol: see manufacturer's web site


title: LU/IBL_D.rerio_44k_015747

status: Public on Mar 02 2009

city: Leiden

first: Anna

middle: Magdalena

last: Zakrzewska

address: Wassenaarseweg 64

department: IBL

country: Netherlands

institute: University of Leiden

first: Annemarie

last: Meijer

first: Herman

last: Spaink


title: SMD Mus musculus 38.8K Print_1376 Run:mof

status: Public on Jan 09 2009

last: Stanford Microarray Database


title: INSERM-Agilent-014850 Whole Human Genome Microarray 4x44K (G4112F)

status: Public on Dec 22 2008

city: Paris

middle: M

last: Mutch

address: Centre de Recherche des Cordeliers (CRC), 15 rue de l'école de médecine

department: Nutrition and Metabolism

country: France

institute: INSERM UMRS U872 (Eq 7) Nutriomique

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.

Alternative version of GPL4133

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


title: KTH Human 30k v1.0

status: Public on Dec 11 2008

city: Stockholm

first: Johan

last: Lindberg

address: Roslagstullsbacken 21, Floor 3

institute: Royal Institute of Technology

manufacturer: Royal Institute of Technology, Stockholm, Sweden

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. For the probe design we use state-of-the-art methodology 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: Agilent-scanner-UNC-custom-4X44K-without-Virus [Probe Name version]

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

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

manufacture_protocol: agilent printing protocol


title: Hs-OperonV2-vB2.2

status: Public on Dec 03 2008

city: Durham

first: Chaitanya

middle: R

last: Acharya

address: 203 Research Drive,Medical Sciences Research Building, Suite 433

department: Dept. of Surgery

institute: Duke University

manufacture_protocol: The human long oligonuleotide probe set obtained from Operon (http://www.operon.com/ ).


title: Illumina HumanRef-6 v2.0 expression beadchip

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

first: Rod

last: Bremner

first: Mohamed

last: Abou El Hassan

manufacture_protocol: see manufacturer's website


title: Ramaciotti Centre for Gene Function Analysis MWG Saccharomyces cerevisiae 7K array v3

status: Public on Dec 23 2008

city: Randwick

first: Anthony

middle: G.

last: Beckhouse

state: NSW

address: High St

department: BABS

country: Australia

middle: G

first: Victoria

last: Gauci

last: Lyons

first: Vincent

last: Higgins

manufacture_protocol:
Single stranded (sense) 40mer oligonucleotides were obtained from MWG, diluted and spotted onto glass Schott Nexterion Slide A+ with amino-link coating using a 24 pin ESI scanner. A total of 13824 features were spotted onto 120 slides within a run where 24 subarrays were added (6x4) with each containing 24 vertical by 24 horizontal features. Features are 100 microns in diameter and attached via an amino-epoxide bond with a separation size of 180 microns.
This is a condensed version of 14K array. The full array layout linked as a supplementary file.


title: Print_730

status: Public on Dec 17 2008

first: Annika

last: Saaf

department: Department of Molecular Medicine & Surgery

institute: Karolinska Institute, Karolinska University Hospital, Solna

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


title: Operon human v3 ~35K 70-mer two-color oligonucleotide microarrays.

city: Groningen

first: Rudolf

middle: Stephan Nicolaas

last: Fehrmann

state: Groningen

department: Gynecologic Oncology

institute: University Medical Center Groningen

manufacturer: The Netherlands Cancer Institute, Central Microarray Facility

manufacture_protocol: Operon v3.0 oligo arrays from the central microarray facility (CMF) at the Netherlands Cancer Institute (NKI) were used for hybridization. A complete list of genes and controls present on the slides is available on the CMF web site (http://microarrays.nki.nl/download/geneid.html). The 70-mer oligo’s, dissolved in a 3x SSC solution, were printed on UltraGaps slides (Corning, Cat# 40018) with a BioRobotics MicroGrid II (Genomic Solutions) print robot. The oligo’s were cross linked to the slide’s amino silane surface by treating the slide with 600 millijoule of UV irradiation (Stratagene, Cat# Stratalinker 2400). Slides were subsequently backed for 3 hours at 80°C.


title: Agilent Human Promoter ChIP-on-Chip Set 244K, combined Microarray (slides 1 and 2) HG17 build

status: Public on Feb 09 2009

first: Wei

last: Xie

address: 611 Young Dr. East, Boyer Hall Rm 332, UCLA

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


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

status: Public on Nov 29 2008

first: Holly

middle: Kloos

last: Dressman

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University Medical Center

description: We print the Operon Mouse genome arrays in 3XSSC buffer onto Corning CGAP slides using OmniGrid300 arrayer


title: Fusion gene microarray, human, 69k, v.1.0. (long version)

first: Gard

last: Thomassen


title: Takara Bio Inc. Human 16K cDNA array set (Array A)

status: Public on Dec 01 2008

city: Nishinomiya

first: Yoshie

last: Yoshikawa

state: Hyogo

address: 1-1 Mukogawa-cho

department: Genetics

institute: Hyogo College of Medicine

first: Takashi

last: Okado

manufacture_protocol:
1. About 300 bp of cDNA are amplified for each gene, purified, and resuspended to 0.1 ug/ul dH2O. The 5'-end of primer used with amplification is labeled with amino residue.
2. Add equal volume of the spotting buffer to the cDNA solution.
3. Spot to TaKaRa-Hubble Slide Glass.
4. After the print run is completed, process the fixation protocol of the glass.


title: Hitachisoft Hypergene Yeast Chip Ver. 2.0

status: Public on Nov 26 2008

city: Osaka

first: Thai

middle: Nho

last: Dinh

address: 2-1 Yamadaoka, Suita

department: Biotechnology

institute: Osaka University


title: Takara Bio Inc. Human 16K cDNA array set (array B)


title: UH/MARESH Mus musculus 32K

status: Public on Nov 15 2008

city: Honolulu

first: John

last: Maresh

state: HI

address: 651 Ilalo

department: Medicine

institute: University of Hawaii

description: The Operon V3 and V2  murine set

manufacturer: UT Southwestern Medical Center at Dallas MICROARRAY CORE

first: Ralph

middle: V

last: Shohet

first: Matthew

last: Reed

last: Campen

manufacture_protocol: Standard protocol at UT Southwestern.


title: Human_40K_partII_FCCC_v1.0

status: Public on Oct 30 2008

city: Philadelphia

first: Julia

last: Santucci-Pereira

address: 333 Cottman Ave, P2051

institute: Fox Chase Cancer Center

manufacturer: Microarray Facility at Fox Chase Cancer Center, Philadelphia, PA

manufacture_protocol: Mirror glass slides used for robotically spotting 40000 cDNAs representing 28000 distinct human transcripts, 10000 identified by expressed sequence tags, and 2000 controls and blank spots.


title: Human_40K_partI_FCCC_v1.0

manufacture_protocol: Mirror glass slides used for robotically spotting 40000 cDNAs representing 28000 distinct human transcripts, 10000 identified by expressed sequence tags, and 2000 controls and blank spots. The complete array has 3 sub-arrays- part I, part II and part III.


title: Inserm Homo sapiens 1.1K myoARRAY

status: Public on Oct 22 2008

city: Rouen Cedex

first: Olivier

last: Boyer

address: 22 Bd Gambetta

department: Faculty of Medicine and Pharmacy

institute: INSERM

first: Maud

last: Vaillant-Maho

first: Laurent

last: Drouot

manufacture_protocol: Specialized macroarray of genes differentially expressed in various myopathies including inflammatory myopathies (506 non-redundant genes) and genes with known or suspected roles in immunological processes (265 non-redundant genes). Also contains 201 various control probes.


title: Human oligo array from Ocimum (20k)

status: Public on Nov 25 2008

city: Nantes

first: Raluca

last: TEUSAN

address: 1, rue gaston veil

institute: INSERM U915

manufacturer: Plateforme Transcriptome - OUEST Genopole (Nantes)

first: Catherine

last: Chevalier

first: Isabelle

last: Guisle

manufacture_protocol: spotted on the  Amersham Lucidea spotter. Epoxyslide.


title: SMD Mus musculus 38.8K Print_1429

city: South San Francisco

first: Adam

middle: S

last: Adler

address: 1 DNA Way

institute: Genentech


title: SMD Homo sapiens 41.5K Print_1225


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

last: Dressman

description: We print the Operon Human genome arrays in 3XSSC buffer onto Corning CGAP slides using OmniGrid300 arrayer


title: IMB Mus musculus 32K operon oligo array

status: Public on Oct 21 2008

city: Taipei

first: Shu-Yun

last: Tung

state: Taiwan

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description: Mouse array-ready oligo nucleotide set(version3.0),comprising  31,769 longmer probes representing 24,878 genes and 32,829 gene transcripts , were obtained from Operon Inc (http://www.operon.com).

manufacturer: Microarray Core Facility of the Institute of Molecular Biology, Academia Sinica, TW

manufacture_protocol: Probes were dissolved in 50mM sodium phosphate buffer(pH8.0) at a concentration of 40uM. The microarrays were printed on active codelink slide(GE) using ommniGrid 100 arrayer(genomic solution) equipped with CMP# 3 pin(Telechem) and post-processed according to codelink’s protocols


title: INSERM-Agilent-012391 Whole Human Genome Oligo Microarray G4112A

first: David

last: Mutch

description:
This single 44K 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.

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.

Alternative version of GPL1708


title: Operon Rat V3.0 printed oligonucleotide array

status: Public on Oct 11 2008

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

organism: Rattus norvegicus

first: Holly

middle: K


title: UH/ShohetWalton Mouse 31.8k oligo array_v3

status: Public on Oct 15 2008

first: Chad

middle: Brian

last: Walton

address: 651 Ilalo Street, JABSOM BSB 222-18

department: Center for Cardiovascular Research

description: Standard protocol at UT Southwestern

middle: B

first: Raffi

last: Bekeredjian

first: Fred

last: Kruse

first: Joel

middle: T

last: Outten

last: Sutcliffe

first: Robert

middle: D

last: Gerard

first: Richard

last: Bruick

manufacture_protocol: Standard protocol at UT Southwestern


title: NuGO array (mouse) NuGO_Mm1a520177 [CDF: Mm_ENTREZG_10]

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description:
CDF file was created by Microarray Lab at the Molecular and Behavioral Neuroscience Institute at the University of Michigan.
Oligonucleotide probes on GeneChips were reorganized based on the latest genome and transcriptome information. In this particular case the Entrez Gene database (build: Sept 11, 2006) was used as source.
For the CDF file based on Entrez Gene:
A probe must hit only one genomic location;
Probes that can be mapped to the same target sequence in the correct direction are grouped together in the same probe set;
Each probe set must contain at least three oligonucleotide probes and probes in a set are ordered according to their location in the corresponding exon.
For detailed description please see the paper and website.

relation: Alternative to: GPL7440 (Alternative CDF [official])

manufacture_protocol: This array is identical to GPL7440 but a custom, remapped CDF environment is used to extract data. This is version 10 of the remapped CDF. The CDF for various platforms can be found at the link below.


title: Agilent-012799 Mouse Developmental Microarray 44K G2519A Option 002 (Probe Name version)

status: Public on Oct 08 2008

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
The Mouse Development Oligo Microarray 44K array represents the first commercial whole mouse genome microarray based on the NIA (National Institute on Aging) Mouse Gene Index, which is optimized for stem cell and developmental research.

*** 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 GPL2876.

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


title: SCCPRR_Mouse_19549_v1.1

status: Public on Oct 01 2008

city: Santa Monica

first: Adrian

last: Anghel

address: 2825 Santa Monica Blvd. Suite 200

institute: University of California, Los Angeles (UCLA)

manufacturer: SCCPRR Gene Array Facility, University of Washington, Seattle, WA

first: Christina

middle: A

last: Jamieson

first: Justin

last: Young

middle: E

last: Ghods

first: Kabirullah

last: Lutfy

first: Yanjun

last: Liu

first: Theodore

last: Friedman

manufacture_protocol: This array was made using the PGA mouse 70mer oligo library generated at Massachusetts General Hospital. The 19,556 oligos were designed using the OligoPicker software generated at the facility and available for free download at http://pga.mgh.harvard.edu/oligopicker/. Oligos were selected using a stringent set of filters to ensure specific representation of all protein-coding sequences in the NCBI GenPept database. The program designs the oligos to have a Tm within a set 10°C range, to ensure hybridization under similar conditions. Also, OligoPicker avoids sequences that are likely to cross-hybridize with other genes or to self-anneal (form primer dimers). The sequence specificity of each oligo is tested with a global BLAST score and all oligos with a BLAST score above a threshold are discarded. Additional information about the library, including sequences of oligos, is available on the MGH website: https://dnacore.mgh.harvard.edu/microarray/index.shtml.


title: UTHSCSA Agilent Whole Human Genome Microarray 4x44K

status: Public on Oct 07 2008

city: San Antonio

first: Luiz

last: Penalva

address: 8403 Floyd Curl Drive

department: GCCRI

institute: UTHSCSA

description:
Microarray Specifications:
Slide Format: 4x44K
Microarrays/Slide: 4
Features/Microarray: 45,015
#Biological Features: 43,376
#Unique Probes: 41,000
Replicates of Biological Probes: 264 x 10
#Positive Controls: 1,468
Replicate #E1A Probes: 10 x 32
#Negative Controls: 153

first: Jennifer

last: Rebeles

first: Suzanne

last: Burns

first: Tarea

last: Burton

first: Raquel

last: Abreu


title: Univ of Liverpool Agilent Mouse TIR QTL regions 56K CGH Array

status: Public on Nov 08 2008

city: Manchester

first: Catriona

last: Rennie

address: Oxford Rd

department: Faculty of Life Sciences

institute: The University of Manchester

description:
Probes on the array were from NCBI mouse build version 34. The probes cover 3 regions (which are known trypanosoniasis infection response QTLs):
Chr1 from 94999974 to 124998700
Chr5 from 75000128 to 88999877
Chr17 from 29000114 to 33999682
For the chromosome 1 region there are 40k probes, the chosen region for probe design was from 95Mb to 125Mb.
For the chromosome 5 region there are 40k probes, the chosen region for probe design was from 75Mb to 89Mb.
For the chromosome 17 region there are 17k probes, the chosen region for probe design was from 29Mb to 34Mb


title: IMB yeast 7K operon oligo array

status: Public on Sep 16 2008

first: Jun-Yi

last: Leu

address: 128 Academia Road, Section 2, Nankang

department: Insititute of Molecular Biolody

first: S

middle: Y

last: Tung

manufacture_protocol: Arrays were printed by standard protocols on CodeLink Activated slides ( GE Healthcare) using a Gene Machine(San Carlos, CA) OmniGrid 100 Instrument.


title: Human 1A Microarray G4110A/G4110B

status: Public on Sep 15 2008

city: Phoenix

first: Yoga

last: Balagurunathan

state: AZ

address: 445 N. Fifth street

institute: TGEN

description: The data table represents common probes extracted from Human 1A Microarray G4110A and Human 1A Microarray G4110B (v1 & v2).


title: VMSR Human 30k oligonucleotide microarray

status: Public on Sep 05 2008

city: Atlanta

first: Arianne

last: Theiss

state: GA

address: 615 Michael St

institute: Emory University

middle: L

first: Matam

last: Vijay-Kumar

first: Tracy

last: Obertone

first: Jason

middle: M

last: Hansen

first: Dean

middle: P

last: Jones

first: Andrew

last: Gewirtz

first: Didier

last: Merlin

first: Shanthi

last: Sitaraman

manufacture_protocol: Microarrays containing all oligonucleotides from the Compugen Human Release 2.0 OligoLibrary were resuspended in 150mMol phosphate buffer and arrayed by Microarrays Incorporated on amine-coated glass slides from Genexprex, crosslinked using 80mjoules of ultraviolet energy (Stratagene Stratalinker, LaJolla, CA), baked for two hours at 70C, and stored until use.


title: Mouse NCI/ATC Mm-CGEN2.0 22k oligo array

status: Public on Aug 31 2008

city: Yokohama

first: Reiko

last: Kurotani

state: Kanagawa

institute: Yokohama City University School of Medicine

manufacturer: Advanced Technology Center Microarray Facility (NIH/NCI/CCR/ATC)

first: Shioko

last: Kimura

manufacture_protocol: see manufacturer's web site (http://arraytracker.nci.nih.gov/)


title: Print_1186

status: Public on Sep 08 2008

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

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: Print_1182


title: PRHU06-S1-0002 (PC Human Operon v3 36K)

status: Public on Aug 28 2008

city: Vancouver

first: Shawn

last: Anderson

address: The Prostate Centre at Vancouver General Hospital, 2660 Oak Street

department: Urological Sciences

country: Canada

institute: University of British Columbia

manufacturer: Microarray Facility - the Prostate Centre at Vancouver General Hospital

first: Jamie

last: Rosner

first: Robert

middle: H

last: Bell

manufacture_protocol: This array consists of 34,580 longmer probes representing 24,650 genes and 37,123 gene transcripts ( Version 3.0 of the Human Genome Oligo Set). Oligonucleotides are consolidated into 384-well plates, lyophilized by speed-Vac, and resuspended in 3x SSC to a printing concentration of 30uM. Oligos are printed on aminosilane slides (Erie, Hudson, NH, USA) with a Biorobotics Microgrid II microarray printer (Genomic Solutions). Microspot 10K quill pins (Biorobotics) in a 48-pin tool were used to deposit <0.5 nL per spot onto the slide. The resulting microarrays have a 4 x12 subgrid layout with 392 spots per subgrid, each spot having approximate diameter and pitch of 90 µm and 190µm, respectively. A 280-bp GFP (green fluorescent protein) oligo was printed in subgrid corners to assist in placing on the grid. The slides were crosslinked in a UV Stratalinker 2400 (Stratagene) at 300mJ. Array quality was assessed by visual inspection and hybridization of representative slides from a print run by dye-labelled random 9-mer oligonucleotides. The quality control images were aquired via the ScanArray Express from Perkin Elmer at a 10 micron resolution and quantified with the Imagene 6.0 software suite.


title: SNU/Agilent Whole Mouse Genome Array (GenePix version)

status: Public on Sep 11 2008

city: Seoul

first: Seong

last: Je kyung

institute: Seoul National University

description: This platform design was submitted specifically for the (GenePix) data being provided and may not be suitable for other data being submitted by the general Agilent community.


title: Sentrix Mouse-6 Expression BeadChip (3)

status: Public on Jul 30 2008

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

manufacture_protocol: see manufacturer's website


title: Swine Protein-Annotated Oligonucleotide Microarray

status: Public on Nov 04 2008

city: East Lansing

first: Catherine

middle: W.

last: Ernst

state: MI

address: 3330 Anthony Hall

department: Animal Science

institute: Michigan State University

organism: Sus scrofa

manufacturer: Illumina (Oligo synthesis); University of Arizona (Array printing)

manufacture_protocol:
Printing protocols available at:
http://ag.arizona.edu/microarray/protocol1A.doc
Information on oligonucleotide design available at:
http://www.pigoligoarray.org/


title: SMD Mus musculus 42K Print_942

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)


title: Sentrix MouseRef-8 Expression BeadChip

status: Public on Aug 22 2008

description: The Sentrix MouseRef-8 BeadChip can be used to study expression of approximately 24,000 well-annotated transcripts from the NCBI RefSeq database. Researchers can generate whole-genome expression profiles for 8 samples in parallel on a single BeadChip. The array is composed of 3 micron features with average feature redundancy of 30-fold. All features are quality controlled by sequential hybridizations process called array decoding. Probes are fully screened, full-length 50-mers. Assay requires 50-100ng of total RNA input.


title: Agilent Mouse 4X44K plus 2500 MEEBO

status: Public on Aug 17 2008

city: San Francisco

first: Andrea

middle: J

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

description:
This array contains the following:
1. The entire Agilent whole genome mouse 4x44K probe set  (design# 014868)
2. 2500 MEEBO sequences that were not represented in the Agilent set (randomly selected from a larger group of ~3000)
3. MEEBO probes for tectonic, kif2a, OFD1. The Agilent probe set also contained sequences for these genes.
4. All transgene probes from the MEEBO set
5 Probes designed from the full length sequences for tectonic 2 and 3 ( these were not represented on the MEEBO or Agilent arrays). There are 2 probes for tectonic 3 (splice variants).
Additional probes are replaced the “empty” slots on the original Agilent mouse whole genome chip.

first: Weihong

last: Xu

manufacture_protocol: Agilent’s non-contact industrial inkjet printing process uniformly deposits oligo monomers onto specially-prepared glass slides. Both the catalog and custom microarrays are manufactured using Agilent’s non-contact in situ synthesis process of printing 60-mer length oligonucleotide probes, base-by-base, from digital sequence files. This is achieved with an inkjet process which delivers 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 full-length oligonucleotide. Precise quantities are reproducibly deposited “on the fly.” This engineering feat is achieved without stopping to make contact with the slide surface and without introducing surface-contact feature anomalies, resulting in consistent spot uniformity and traceability.


title: SMD Homo sapiens 37.6K Print_843

status: Public on Oct 21 2008


title: DKFZ Division of Molecular Genome Analysis Human Operon 4.0 oligo Array 35k

status: Public on Sep 17 2008

city: Heidelberg

first: Alberto

last: Calabro

address: INF 580

institute: DKFZ

first: Ruprecht

last: Kuner

first: Tim

last: Beissbarth

first: Holger

last: Sultmann

first: Annemarie

last: Poustka

manufacture_protocol: The microarrays contains 35,035 oligonucleotide probes, representing approximately 25,100 unique genes and 39,600 transcripts excluding control oligos spotted on epoxysilane glass slides (Quantifoil, Jena, Germany) using the VersArray ChipWriter Pro System (Biorad, Munich, Germany) and SMP3 pins (Telechem, Sunnyvale, CA, USA). Spotting was performed in the division of Molecular Genome Analysis with a spacing of 28x29 Spots in 4x12 Subarrays (top-down to left-right). After spotting, microarrays were rehydrated, and the DNA was denatured with boiling water prior to washing with 0.2% SDS, water, ethanol, and isopropanol. The arrays were dried with air pressure.


title: Agilent Human oligo 22k A

status: Public on Jul 29 2008

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

institute: university Paris Sud11

description: array 22k spotted on 1 glass slide.

first: Christophe

last: Desterke

manufacture_protocol:
Oligo Microarray Agilent 60 mers spotted.
Commercial spotting


title: Duke University Murine Operon v.3.0 spotted Array

status: Public on Aug 08 2008

city: Cincinnati

first: Gary

last: Shull

state: OH

address: 231 Albert Sabin Way ML0524

institute: University of Cincinnati

manufacture_protocol: The Operon mouse oligonucleotide library,version 3.0, comprised of 70-mer oligonucleotides representing 24,878 unique mouse genes, was printed on poly-L-lysine-coated glass slides. The library also included sets of positive and negative controls that were used for quality control purposes. Oligonucleotides were spotted using a GeneMachines Omnigrid arrayer by the Duke University Microarray facility. Details can be found at http://mgm.duke.edu/genome/dna_micro/core/spotted.htm.


title: MWG Rat 10K oligo array

status: Public on Jul 23 2008

city: Little Rock

first: Radhakrishnan

last: Nagarajan

state: AR

address: 4301 W Markham, Slot 781, Room: 3234

department: Department of Biostatistics

institute: University of Arkansas for Medical Sciences

first: Esther

last: Dupont-Versteegden


title: Print_850

status: Public on Jul 01 2008

first: Li-Fen

last: Lee

address: 299, Campus Dr.

department: Microbiology and Immunology

institute: Stanford University


title: Illumina Sentrix mouse-6.v1 bead array

status: Public on Jul 16 2008

first: anton

middle: j

last: horrevoets


title: Operon Homo sapiens 34K

first: Sailendra

middle: Nath

last: Sarma

address: P.O. Box 131, Cheongryang

institute: Korea Institute of Science and Technology

manufacturer: Operon Biotechnologies GmbH, BioCampus Cologne, Nattermannallee 1, 50829 Cologne, Germany

middle: N

first: Youn-Jung

last: Kim

first: Jae-Chun

last: Ryu

manufacture_protocol:
Date 2/7/2007 OpArraysTM Protocol
www.operon.com Page 1
OpArraysTM Protocol
___________________________________________________________
When planning or preparing for an experiment, please read through this protocol completely before
proceeding. 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
Target Preparation for OpArrays
___________________________________________________________
Isolation of Total RNA
Total RNA can be isolated employing commonly described procedures (such as Sambrook et al.,
2000). However, depending on the organism and tissue type, the method of choice may require
different modifications. Operon recommends selecting a procedure that is best suited for the tissue
type that you are working with. If you are having problems isolating suitable RNA samples, you
may wish to refer to the collection of RNA isolation methods described by Farrell (2005).
Total RNA Cleanup
After isolating total RNA using the method of your choice, a subsequent RNA purification helps to
remove most of the inhibitory contaminants; such as organic (phenol),and cytosolic
(polysaccharide, polyphenols). Operon recommends using Qiagen’s RNeasy MinElute kit to purify
total RNA samples. This method works consistently well for RNA samples isolated from a wide
range of tissue types such as brain, kidney, liver, testis, and ovary from human, mouse and rat,
Arabidopsis seedlings, roots, leaves, flower, Maize leaves, roots, and endosperm, rice leaves and
roots, and the leaves of Medicago truncatula and Vitis vinifera (grape). Additional details
concerning the capacity of the columns and other technical details can be found in the Qiagen
RNeasy Mini Handbook.
Materials
° RNeasy MinElute Column (Qiagen Cat# 74204)
° Agilent RNA 6000 Nano LabChip Kit
° Refrigerated microcentrifuge
° RNAase-free microfuge tubes and tips
° 100% Ethanol
° DEPC-treated H2O
° 80% Ethanol (prepared with DEPC treated water)
Method
Note: Buffer RPE is supplied with the RNeasy MinElute kit as a concentrate. Ensure that ethanol was
added prior to use.
1. Preheat 50 μL RNAase-free DEPC-treated H2O to 55°C.
2. Adjust sample (10 μg total RNA) to a volume of 100 μL with RNAase-free water.
3. Add 350 μL RLT buffer and mix thoroughly by pipetting.
4. Add 250 μL 100% ethanol to the sample, and mix thoroughly by pipetting.
5. Prepare the RNeasy MinElute spin column for use by placing it in a 2 mL collection tube.
6. Add the sample to the RNeasy MinElute and spin column. Close the tube gently.
7. Centrifuge for 1 minute at 10,000xg.
8. Discard the liquid from the 2 mL collection tube.
9. Pipette 500 μL RPE buffer to the RNeasy MinElute spin column. Close the tube gently.
10. Centrifuge for 1 minute at 10,000xg.
11. Discard the liquid from the 2 mL collection tube.
12. Add 500 μL 80% ethanol to the RNeasy MinElute spin column. Close the tube gently.
13. Centrifuge for 1 minute at 10,000xg.
14. Discard the liquid from the 2 mL collection tube.
15. Close the RNeasy MinElute spin column.
16. Centrifuge the spin column at 10,000xg for 3-5 minutes.
17. Discard the 2 mL collection tube.
18. Transfer the RNeasy MinElute spin column to a new 2 mL or 1.5 mL RNAase-free
microfuge tube.
Date 2/7/2007 OpArraysTM Protocol
www.operon.com Page 3
19. Pipette 40 μL DEPC-treated H2O (pre-heated to 55°C in step 1) directly onto the center of
the membrane. Close the tube gently.
20. Incubate at room temperature (RT) for 2 minutes.
21. Centrifuge for 1 minute at maximum speed to elute.
22. Immediately place the RNA solution on ice after elution.
Note: Since RNA samples are labile it is important to keep RNA solutions on ice after elution.
23. Measure the RNA amount using a NanoDrop.
24. Analyze the total RNA quality of your sample using a Bioanalyzer or Experion follow the
manufacturer’s directions to operate the instrument.
Total RNA Analysis using the Bioanalyzer or Experion
Only samples that have a large percentage of intact RNA will produce a uniform amplification.
Degraded samples will produce unpredictable RNA amplification which may cause variation in
subsequent microarray hybridization experiments. Therefore, we insist that you check the RNA
quality before proceeding to the next step. Operon recommends the use of the Bioanalyzer (Agilent
Technologies) or Experion (BioRad) to verify the quality of the total RNA sample. Typically, these
instruments require very small quantity of RNA for the analysis (100-150 ng/sample).
Figure 1. Electropherogram of total RNA from Arabidopsis leaf tissue was analyzed using the
Bioanalyzer. (CP = Chloroplast RNA)
Figure 2. Gel-like image file output from the Bioanalyzer. Sample 12 is the unpurified total RNA,
and samples 1-11 are the cleaned-up RNA samples from Arabidopsis leaf tissues.
Date 2/7/2007 OpArraysTM Protocol
www.operon.com Page 4
aRNA Amplification
___________________________________________________________
An Overview
A typical microarray experiment requires 30-50 μg total RNA that is equal to ~1 μg polyA+ RNA.
This large amount of total RNA requirement makes RNA amplification techniques essential for
experiments involving limited amounts of starting material. Most RNA amplification techniques are
based on Eberwine methods (van Gelder et al., 1990), employing double-stranded cDNA synthesis
using oligo dT primers incorporating one of the T3 or T7 viral promoters, followed by in vitro
transcription (IVT) as a means to linearly increase the concentration of messenger RNA. The
optimized Eberwine method is capable of amplifying mRNA up to ~103 fold for one round of
amplification, and up to ~105 fold for two rounds of amplification (Wang et al., 2000; Baugh et al.,
2001). Employing two rounds of RNA amplification, one can successfully perform a microarray
experiment using as lit-dye modified UTP during
the process of in vitro transcription, or (2) indirect labeling, by incorporating aminoallyl modified
UTPs during in vitro transcription, followed by mono reactive Cy-dye coupling. The OpArrays
protocol takes advantage of the second approach. Aminoallyl UTP (aaUTP) does not contain a bulky
side chain modification, which allows ~100% replacement of the UTP with aaUTP during RNA
synthesis. Operon recommends using a 1:1 ratio of UTP:aaUTP.
61. Prepare the IVT Reaction Master Mix by adding the reagents in the following order:
Single Reaction
Amount Ingredient
2 μL aaUTP Solution (50 mM)
12 μL ATP, CTP, GTP Mix (25 mM)
2 μL UTP Solution (50 mM)
4 μL T7 10X Reaction Buffer
4 μL T7 Enzyme Mix
Note: When processing more than one sample include ~5% overage to cover pipetting error.
62. Add 24 μL IVT Reaction mix to 16 μL double-stranded cDNA sample.
63. Mix the reaction mix by pipetting up and down several times.
64. Centrifuge at 3,000xg for 30 seconds.
Date 2/7/2007 OpArraysTM Protocol
www.operon.com Page 8
65. Incubate the tube for 4-14 hours at 37°C in a PCR machine with lid temperature set at
40°C.
66. After incubation, stop the reaction by adding 60 μL DEPC-treated H2O to each sample,
bringing the final volume to 100 μL.
67. Mix thoroughly by gentle vortexing.
68. Proceed to aRNA Purification or store the reaction tubes at -80°C.
aRNA Purification
Materials
° Aminoallyl Message Amp II kit (Ambion Cat# 1753)
° RNAase-free tips, tubes
° Refrigerated Microfuge centrifuge
° 100% EtOH
° DEPC-treated H2O
Method
Become familiar with the steps before proceeding and have all reagents ready to use. This
procedure will remove all the unincorporated nucleotides from the aRNA.
69. Add 350 μL aRNA Binding Buffer to each aRNA sample, mix by pipetting up and down
three times.
70. Add 250 μL ACS grade 100% ethanol to each aRNA sample.
71. Mix by pipetting the mixture up and down three times.
72. Quickly transfer the sample onto the center of the filter in the aRNA spin column.
73. Centrifuge at 10,000xg, for at least 1 minute or until the liquid has passed through the
filter.
74. Discard the liquid from the collection tube.
75. Replace the aRNA filter cartridge back into the aRNA collection tube.
76. Apply 650 μL Wash Buffer to each aRNA filter cartridge.
77. Centrifuge at 10,000xg, for at least 1 minute or until the liquid has passed through the
filter.
78. Discard the liquid from the collection tube.
79. Centrifuge the aRNA filter cartridge for an additional 3 minutes to remove trace amounts
of Wash Buffer.
80. Transfer filter cartridge(s) to a fresh aRNA collection tube.
81. Add 100 μL DEPC-treated H2O to 55°C to the center of the filter.
82. Incubate at room temperature for 2 minutes.
83. After incubation, centrifuge at 10,000xg, for at least 1.5 minutes or until the liquid has
passed through the filter.
84. Discard the aRNA filter.
85. Place your aRNA sample tube(s) (~100 μL volume) on ice.
Date 2/7/2007 OpArraysTM Protocol
www.operon.com Page 9
Quantitation
Determine the concentration of aRNA using either the NanoDrop or a conventional
spectrophotometer. In general, you can expect a yield of ~40-60 μg amplified aa-aRNA from 1 μg
total RNA as starting material, and 80-120 μg of aa-aRNA from 2 μg of total RNA as starting
material. If the amplification is significantly less, it is likely that either inhibitory contaminants
present in the total RNA sample or there may have been partial degradation of the starting RNA
sample or traces of washing buffer (ethanol) in the cDNA from step 60.
Sample Preparation
86. Prepare an aliquot for Bioanalyzer (5 μL of aRNA 150-200 ng/μL concentration).
87. Aliquot 4 μg aRNA in 1.5 mL microfuge tube (if aRNA is limited, as little as 1 μg should be
enough).
88. Completely dry the sample using a Speedvac centrifuge set at 45°C or lower.
89. Store the remaining aRNAs samples at -80°C for further use.
aRNA Analysis using the Bioanalyzer
Follow the procedure recommended by the manufacturer for analysis of the RNA samples. In
general, 1 μL of RNA sample (100-200 ng/μL) is sufficient for analysis using a Nano chip.
Figure 3. Typical results of aRNA Analysis using the Bioanalyzer.
Date 2/7/2007 OpArraysTM Protocol
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Coupling of AA-aRNA to the Cy Dye Ester
___________________________________________________________
Materials
° Cy3 Monoreactive dye (Amersham Pharmacia; Cat# PA23001)
° Cy5 Monoreactive dye (Amersham Pharmacia; Cat# PA25001)
° DMSO (Sigma; Cat# D8418)
° Hydroxylamine (Sigma Cat# 159417)
° 0.2 M Sodium Carbonate Buffer
Note: Typically, the Sodium Bicarbonate Buffer is supplied with the Aminoallyl Message Amp II kit (Ambion
Cat# 1753). If the buffer is not provided with the kit follow the procedure described below to make RNAasefree
0.2 M Sodium Bicarbonate buffer.
Preparation of 0.2 M Sodium Carbonate Buffer: pH 9.0.
° Solution I: Dissolve 0.84g NaHCO3 in 50 mL DEPC H2O in a disposable sterile Falcon tube.
° Solution II: Dissolve 1.05g Na2CO3, in 50 mL DEPC H2O in a disposable sterile Falcon tube.
° Mix 45 mL of Solution I and 2.75 of mL Solution II in a disposable sterile Falcon tube.
° Check the pH by aliquoting 5 mL into a new 15 mL Falcon tube, if needed adjust the pH by
adding appropriate amount of Sol-I or Sol-II. Never check the pH directly in the stock
solution as that is a common source of RNAase contamination.
° Aliquot 0.2 mL into RNAase-free tubes, store at -20°C. Discard the tube after use or 24
hours, whichever comes first.
Preparation of Cy3 and Cy5 Monoreactive Dye
These dyes are supplied in 5 aliquots; the content of each tube is sufficient for at least 4-5 labeling
reactions.
Preparation of Cy-dyes Prior to Reaction
° Dissolve the entire contents of a single tube in 27 μL DMSO by flicking the tube several
times.
° Leave at RT for at least 30 minutes protected from light.
° Centrifuge at 1,000xg for 30 seconds to collect the dye at the bottom of the tube. The dye
is now ready for use, but can be stored at -20°C for up to one month. Protect the dye from
light by wrapping with aluminum foil.
Method
90. Dissolve the dried aRNA sample in 5 μL 0.2 M NaHCO3 buffer (make sure the aRNA
completely dissolved in to the solution by pipetting the buffer along the sides of the tube).
91. Incubate the tube at RT for at least 20 minutes.
92. Add 5 μL Cy3 or Cy5 (in DMSO) to each aRNA sample.
93. Mix thoroughly by flicking the tube several times.
94. Centrifuge the tube at 1,000xg for 30 seconds.
95. Cover each tube with aluminum foil or otherwise protect the samples from light exposure.
96. Incubate the aRNA dye mixture at RT for 2 hours.
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Post Dye-Coupling aRNA Purification
___________________________________________________________
Materials
RNeasy MinElute column (Qiagen Cat# 74204)
° RNAase-free tips and tubes
° Refrigerated centrifuge
° Hydroxylamine (Sigma Cat# 159417)
Preparation of 4 M Hydroxylamine:
° Dissolve 2.7g of Hydroxylamine Hydrochloride salt in 7 mL DEPC treated water.
° Bring the solution to 10 mL total volume.
° Aliquot the 4 M hydroxylamine solution into 100 μL aliquots in RNAase-free microfuge tubes.
° Store excess tubes at -20°C.
Quenching Reaction
This optional step involves quenching any unreacted Cy-dye by adding an excess of primary
amines.
97. Add 4.5 μL 4 M hydroxylamine into the dye coupling reaction.
98. Mix well.
99. Incubate for 15 minutes in the dark at RT.
Removal of Unincorporated Dye
___________________________________________________________
Note: The Qiagen RNeasy MinElute column is used for this purpose. Become familiar with the steps before
proceeding and have all reagents ready-to-use. RPE buffer is supplied as a concentrate; ensure that ethanol is
added before use. Work through this procedure to remove all the unincorporated dye.
100. Adjust sample volume to 100 μL with DEPC-treated H2O.
101. Add 350 μL of RLT (kit) buffer.
102. Mix thoroughly.
103. Add 250 μL 100% ethanol to the sample.
104. Mix thoroughly by pipetting.
105. Apply the sample to an RNeasy MinElute Spin Column in a 2 mL collection tube.
106. Close the tube gently.
107. Centrifuge at 10,000xg, for at least 1 minute or until the liquid has passed through the
filter.
108. Discard the liquid from the collection tube.
109. Pipette 500 μL RPE buffer onto the spin column.
110. Close the tube gently.
111. Centrifuge at 10,000xg, for at least 1 minute or until the liquid has passed through the
filter.
112. Discard the liquid from the collection tube.
113. Add 500 μL of 80% ethanol to the RNeasy MinElute Spin Column.
114. Close the tube gently.
115. Centrifuge at 10,000xg, for at least 1 minute or until the liquid has passed through the
filter.
116. Discard the liquid from the collection tube.
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117. Centrifuge at 10,000xg, for at least 1 minute or until the liquid has passed through the
filter.
118. Transfer the spin column to a new microfuge tube.
119. Apply 20 μL warm DEPC water (55°C) to the center of the spin column.
120. Close the tube gently.
121. Incubate at RT for 2 minutes.
122. Centrifuge at 12,000xg for 1 minute.
123. Repeat the elution with an additional 20 μL of warm DEPC water (55°C).
Measure the amount of dye incorporated into aRNA using a NanoDrop or conventional
spectrophotometer.
Estimation of Dye Incorporation
___________________________________________________________
Overview
The Beer-Lambert equation is used to correlate the calculated absorbance with concentration:
A = E * b * c where A is the absorbance represented in absorbance units, E is the wavelengthdependent
molar absorption coefficient (or extinction coefficient) with units of liter/mol-cm, b is
the path length in cm, and c is the analyte concentration in moles/liter or molarity (M).
Dye Incorporation
Use the table below to estimate the amount of dye incorporation. The NanoDrop instrument
contains built-in software (the Microarray Concentration module) that uses the general form of the
Beer-Lambert equation to automatically calculate the fluorescent dye concentrations.
Table of Extinction Coefficients for Typical Dyes Used in Microarray Experiments
Dye Type Extinction Coefficient (liter/mol-cm) Measurement Wavelength (nm)
Cy3 150000 550
Cy5 250000 650
Alexa Fluor 488 71000 495
Alexa Fluor 546 104000 556
Alexa Fluor 555 150000 555
Alexa Fluor 594 73000 590
Alexa Fluor 647 239000 650
Alexa Fluor 660 132000 663
Cy3.5 150000 581
Cy5.5 250000 675
Date 2/7/2007 OpArraysTM Protocol
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Figure 4. Estimation of Cy3 and Cy5 incorporation into aRNA targets using the NanoDrop
spectrophotometer.
Note: If NanoDrop is not available, a spectrophotometer may be used to measure dye incorporation.
Incorporation for Cy5 is measured as its absorption at 650 nm, and incorporation of Cy3 at 550 nm. To
calculate the amount of dye incorporated in your sample please see the "Incorporation Calculator" the Pangloss website.
Microarray Hybridization
___________________________________________________________
Materials
° OpArrays Hybridization Buffer kit (OPHYB-1)
° Microscope slide staining dish (Ted Pella Cat# 21078-1) or mBox (Erie scientific, Cat# BXIM-
20ERIE)
° Microscope slide holders (Ted Pella Cat# 21078)
° 10 mL disposable pipette
° Sterile measuring cylinder
° Extra-deep Hybridization Cassette (Telechem International Cat# AHCXD)
° LifterSlip™ (Erie Scientific Company Cat# 24X601-2-4733)
° 50 mL Falcon tubes
° Incubator set to 42°C (Boekel Shake N Bake Hybridization Oven)
° Sterile diH2O
OpArrays slides are always printed on the same side as the barcode on the slide. The array area is
18mm wide, 54mm long, and is located 9mm from the top of the slide (barcode at bottom).
OpArrays slides are supplied in a pre-processed, ready-to-use format.
Date 2/7/2007 OpArraysTM Protocol
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Pre-Hybridization
If you have a centrifuge equipped with a microplate centrifugation, use mBox (Erie scientific, Cat#
BX-IM-20ERIE) or Microscope slide holder to dry the slides, this will speed up the process and
produce less variation between the slides.
Note: Do not allow the slides to dry during the pre-hybridization and washing procedure.
Caution note: mBox may require more buffer than described in the procedure.
124. Pre-warm an appropriate volume of OpArrays Pre-Hyb Solution to 42°C by placing the
pre-hyb buffer in a 42°C incubator for 30 minutes.
125. Using a large enough volume of buffer to ensure that all slides are completely covered,
incubate slides in OpArrays Pre-Hyb Solution for 60 minutes at 42°C.
126. During the pre-hybridization step, prepare Wash Solution 1 by diluting OpArrays Wash B
1:40 with diH2O. Prepare 50 mL per slide (i.e. 1.25 mL OpArrays Wash B, add diH2O to
50 mL).
127. Wash slides for 5 minutes in Wash Solution 1 at 20-25°C.
128. Immediately transfer the slides to a container with sterile DH2O, and rinse for 30 seconds.
Repeat this step for at least two times.
129. Dry the slides using a nitrogen or oil free air jet or dry by centrifugation at 200xg for 5
minutes using a microplate rotor. If microplate rotor is not available use 50 mL Falcon
tubes for drying.
130. Preparation of 50 mL Falcon tube for slide drying.
a. Pack bottom of 50 mL plastic disposable centrifuge tube with Kimwipes.
b. Using forceps, carefully place slide into tube with label at the bottom.
c. Spin the slides at 200xg for 5 minutes, if any liquid remains on the slide, repeat for
an additional 5 minutes.
Hybridization
Note: Excessive amount of labeled target causes precipitation of Cy3, leading to very high background on the
microarray. Therefore we recommend using a maximum of 0.8 pmol Cy5-labeled target/ μL of hybridization
solution and 0.8 pmol of Cy3-abeled target/ μL hybridization solution.
131. Mix 2.5 μL of Cy5-labeled targets (40 pmol), 2.5 μL of Cy3-labeled targets (40 pmol) and
45 μL of OpArrays Hyb Buffer.
Note: The OpArrays Hyb Buffer can be diluted to a maximum of 90% [v/v] therefore if necessary,
concentrate the labeled targets using a speedvac. Store the tubes in ice until the next step.
132. Rinse the Hybridization Cassette with sterile diH2O and dry thoroughly.
133. Make sure the flexible rubber gasket is seated evenly in gasket channel.
134. Add 15 μL sterile diH2O to the lower groove inside the cassette chamber.
135. Insert the OpArrays slide into the cassette chamber, DNA side up (barcode side up).
136. Place the LifterSlip over the microarray slide.
137. Make sure the white stripe of the LifterSlip is at the lower side and properly positioned on
the slide surface.
138. Denature labeled target solution from Line 131 by incubating in the tube at 65oC for 5
minutes.
139. Apply the labeled target solution directly onto the slides or place on ice immediately.
140. Apply the denatured target solution slowly to one end of the LifterSlip and let it disperse
across the OpArrays surface.
141. Quickly place the clear plastic cassette lid on top of the cassette chamber.
142. Apply downward pressure and manually tighten (clockwise) the four sealing screws.
143. Check all four screws again to confirm a tight seal.
144. Place the cassette into a hybridization oven set at 42°C.
145. Hybridize for 14-16 hours.
Date 2/7/2007 OpArraysTM Protocol
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Post-Hybridization Washing
Note: Do not allow the slides to dry during the hybridization and washing procedure. Wash Solutions 2, 3,
and 4 should be prepared in advance. Use at least 50 mL solution per slide.
146. Prepare all post-hybridization washing solutions:
Wash Solution 2:
° 50 mL OpArrays Wash A
° 25 mL OpArrays Wash B
° Bring Wash Solution 2 final volume to 500 mL with sterile diH2O
Wash Solution 3:
° 50 mL OpArrays Wash A
° Bring Wash Solution 3 final volume to 500 mL with sterile diH2O
Wash Solution 4:
° 5 mL OpArrays Wash A
° Bring Wash Solution 4 final volume to 500 mL with sterile diH2O
147. Pre-warm the Wash Solution 2 to 42°C.
148. After hybridization, remove cassette from the hyb oven and manually loosen the four
sealing screws (counterclockwise) to remove the lid.
149. Place the hybridized OpArrays slides into a slide rack removing them from the cassette
chamber using forceps.
150. Place the slide tray containing the OpArrays slide into a dish with Wash Solution 2 at 42°C
for 10 minutes.
151. Transfer the slide tray into a dish with Wash Solution 3.
152. Incubate at 20-25°C (RT) for 10 minutes.
153. Transfer the slide tray into a dish with Wash Solution 4.
154. Incubate at RT for 5 minutes.
155. Transfer the slide tray into another dish with fresh Wash Solution 4.
156. Incubate at RT for 5 minutes.
157. Dry the slides by either using an oil-free nitrogen (or air) jet or by centrifugation (200xg
for 5 minutes).
158. Protect the array from light, dust, and abrasion of the array surface. Scan as soon as
practical.
Note: There are several reports regarding reduction of Cy5 signal due to the atmospheric ozone above 5 ppb.
The Ozone induced Cy5 degradation is prudent particularly in the summer months. We advise taking
appropriate preventive measures such as increasing the Nitrogen in the microarray lab, or setting up
appropriate AIR filtration system to eliminate the Ozone. As a general practice we also recommend completing
the scanning as soon as the washing process is completed.
Date 2/7/2007 OpArraysTM Protocol
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Scanning of the Microarray Slides
___________________________________________________________
Please follow all manufacturer recommendations for Microarray scanner operation and
maintenance.
° Turn on the scanner at least 20 minutes before the scanning to warm up the scanner.
° Place the slide into the slide cartridge and close the scanner.
° If the slides are hybridized with two color targets, select Cy5 channel (650 nm) and Cy3
channel (532 nm), otherwise select appropriate wavelength.
° If the option is available, select the preview scan, and scan entire slide.
° Examine the image and if the option is available check the histogram.
° Adjust the laser power or PMT settings to obtain ration of 1 between these two channels.
If the microarrays hybridized with targets with single color make sure to follow a single
setting or similar setting to obtain a consistent result.
° After adjusting the setting to get a ratio of 1 between the Cy5 and Cy3 channel, perform
high resolution scanning (usually 10 microns).
° Save a multicolor TIFF image, otherwise save single channel TIFF images.
Feature Extraction
Feature extraction is one of the most critical steps in any microarray experiment. In this step you
will convert the optical image to numerical values for comparing the results among samples and for
drawing conclusions from your experiment. To facilitate feature extraction with any of the
commercially or publicly-available microarray analysis software, Operon provides files in the
standard *.gal configuration. Other configurations may be available through the Operon website
or upon request.
Operon Contact Information
North America
Global Headquarters
Europe
Japan
Customer Service: 800-688-2248
Technical Support: 800-688-2248
Fax: (251) 252-7794
Email: oligo-us@operon.com
Customer Service: 00 800-67 673377
Toll Free: +49-221-17090270
Fax: +49-221-17090170
Email: oligo-eu@operon.com
Customer Service: +03-5914-1200
Technical Support: +03-5914-3750
Fax: +03-5914-3751
Email: oligo-jp@operon.com
Mailing Address
Operon Biotechnologies, Inc.
2211 Seminole Drive
Huntsville, AL 35805
USA
Mailing Address
Operon Biotechnologies GmbH
BioCampus Cologne
Nattermannalle 1
50829 Cologne
Germany
Mailing Address
Operon Biotechnologies K.K.
1-29-10 Maenocho, Itabashiku
Tokyo 174-0063
Japan
Date 2/7/2007 OpArraysTM Protocol
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References
___________________________________________________________
Biochem Biophys Res Commun. 300: 915-920.
Aoyagi K, Tstsuta T, Nishigaki M, Akimoto S, Tanabe C, Omoto Y, Hayashi S, Sakamoto H,
Sakamoto M, Yoshida T, Terada M, and Sasaki H (2003). A faithful method for PCR-mediated
global mRNA amplification and its integration into microarray analysis on laser-captured cells.
Nucleic Acids Res. 29:No5,E29.
Baugh LR, Hill AA, Brown EL, Hunter CP (2001). Quantitative analysis of mRNA amplification by in
vitro transcription. Nucleic Acids Res. 29: No5, E29.
Farrell R (2005). RNA Methodologies: A Laboratory Guide for Isolation and Characterization, 3rd
ed. (Elsevier Academic Press, 2005).
Neurochem Res. 10:981-992.
Ginsberg SD and Che S (2002). RNA amplification in brain tissues.
Nat Biotechnol. 20:940-943.
Iscove NN, Barbara M, Gu M, Gibson M, Modi C, and Winegarden N (2002). Representation is
faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA.
J Mol Diagn. 5:9-14.
Luzzi V, Mahadevappa M, Raja R, Warrington JA and Watson MA (2003). Accurate and reproducible
gene expression profiles from laser capture microdissection, transcript amplification, and high
density oligonucleotide microarray analysis.
Sambrook J, Fritsch EF and Maniatis T (2000). Molecular Cloning: A Laboratory Manual, 2nd. ed.
Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
J Biochem Biophys Methods. 55:53-66.
Seth D, Gorrell MD, McGuinness PH, Leo MA, Lieber CS, McCaughan GW, and Haber PS (2003).
SMART amplification maintains representation of relative gene expression: quantitative validation
by real time PCR and application to studies of alcoholic liver disease in primates.
Proc Natl Acad Sci USA 87: 1663-1667.
Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH (1990). Amplified
RNA synthesized from limited quantities of heterogeneous cDNA.
Nat. Biotechnol. 18:457-459.
Wang E, Miller LD, Ohnamacht GA, Liu ET, and Marincola FM (2000). High-fidelity mRNA
amplification for gene profiling. Nat. Biotechnol. 18:457-459.
Biotechniques 34:386-388.
Xiang CC, Chen M, Kozhich OA, Phan QN, Inman JM, Chen Y, and Brownstein MJ (2003). Probe
generation directly from small numbers of cells for DNA microarray studies.
Date 2/7/2007 OpArraysTM Protocol
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Appendix A
___________________________________________________________
There are many models of scanners, hybridization stations, and analysis software which are
compatible with Operon OpArrays products. The items listed below have been specifically reviewed,
however, additional equipment if configured to accept a standard microarray slide will likely be
compatible with OpArrays. Please contact Operon Technical Support with any specific questions
regarding the OpArrays protocol. See contact information on page 16.
Specifically-Tested Equipment
Compatible Microarray Scanners
° Axon 4000B
° Axon 4100A
° Axon 4200AL
° Agilent DNA Microarray Scanner
° PerkinElmer Scanarray GX
° PerkinElmer Scanarray HT
° PerkinElmer ProScann
° PerkinElmer Scanarray Express
° Telechem International Spotlight-2
° Alpha Innotech NovaRay
° Genomic Solutions UC4 Scanner
° GE Healthcare ArrayWoRx Scanner
° Tecan Microarray Scanner
° Genetix aQuire scanner
° Innopsis Microarray Scanner
Microarray scanners NOT compatible with OpArrays Slides
° Affymetrix Scanner
° Illumina Bead array Scanner
° ABI 1700 Chemiluminescent Microarray Analyzer
Compatible Automated Hybridization Stations
° MAUI Hyb Station
° ArrayBooster™
° GeneMachines HybStation
° GeneTAC Hybridization Station
° CapitalBio Biomixer
° a-Hyb™ Hybridization Station
° Tecan HS400 Hyb-station
Compatible Manual Hybridization Chambers/Cassettes
° Glass array Hybridization Cassette; Ambion
° International Hybridization Chambers; Telechem


title: UHN Microarray Centre - Single Spot Human 19K4 (or 19K6, 19K7, 19K8 etc.)

status: Public on Sep 30 2008

city: Toronto

first: Irene

last: Andrulis

state: ON

address: 600 University Avenue

department: Research

institute: Mount Sinai Hospital

manufacturer: University Health Network (UHN) Microarray Centre, Ontario Cancer Institute (OCI), Toronto, Canada. The cDNA microarray can be purchased at UHN Microarray Centre. The web link: http://www.microarrays.ca.

manufacture_protocol: All current human clones are from Image Consortium. EST clones are PCR amplified and printed on UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol and are ready-to-use.  Each array contains 19008 characterized and unknown human ESTs.  The clone set has been sequence-verified at the Microarray Centre and the sequences can be downloaded for validation  (http://www.microarrays.ca/products/glists.html).


title: Print_1149


title: Agilent-019118 Human miRNA Microarray 2.0 G4470B (Feature Number version)

status: Public on Dec 03 2008

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Agilent Human miRNA Microarray version 2 8x15K (G4470B) annotated against the Sanger miRBASE 12.0 database of miRNAs. The microarray is designed to contain probes specific for each of the human miRNAs in Sanger miRBASE 10.1, as well as probes specific to the human viral miRNAs in this database.

Arrays of this design have barcodes that begin with 16019118 or 2519118.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL8936

relation:
Alternative to: GPL8227
Alternative to: GPL8936
Alternative to: GPL15006
Alternative to: GPL16541


title: SWEGENE Rat 70mer oligonucleotide array version 1.0

status: Public on Oct 01 2008

city: Skövde

first: Sandra

last: Karlsson

address: Högskolevägen 1

department: School of Life Sciences

institute: University of Skövde

manufacturer: Swegene DNA Microarray Resource Center, Lund, Sweden

manufacture_protocol: Arrays were produced by the Swegene DNA micro array resource center at Lund University.


title: UHN Human 19K cDNA Array SS-H19Kv8 with Unigene Human Build 211

status: Public on Jul 10 2008

first: Dong-Yu

last: Wang

address: 610 University Ave

institute: UHN-PMH-OCI

description: This set includes 19,200 spots containing 18,981 cDNA clones from the IMAGE consortium and printed on UltraGAPS™ slides. The Single spotted array contains 18,827 characterized and unknown human ESTs. The clone set has been sequence-verified at the Microarray Centre and the sequences can be downloaded for validation.

manufacturer: University Health Network Microarray Center, Toronto, Ontario

manufacture_protocol: As described on the UHN Microarray Centre website


title: Print_1128

manufacturer: Stanford Functional Genomics Facility,  Stanford School of Medicine


title: ENS SGDB Mus musculus NIA 15k

status: Public on Jun 30 2008

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

institute: École normale supérieure

description:
This cDNA clone set was prepared by researchers at the National Institute on Aging. The clone set has been distributed widely and is currently in use by a number of other microarray programmes.
The set has the following characteristics:
~ 15,000 'unique' cDNA clones were rearrayed from 52,374 ESTs from pre- and periimplantation embryos, E12.5 female gonad/mesonephros, and newborn ovary.
Up to 50% are derived from novel genes.
~ 1.5 kb average insert size.
Clones were sequenced from 5' and 3' termini to obtain longer reads and verify sequence. Sequence information is available from their web site (NIA/NIH Mouse Genomics Home Page).
PCR products were amplified by the National Sequencing Center.

manufacturer: ENS Biology Department Transcriptome Platform

first: Stephane

last: Le Crom

first: Piotr

last: Topilko

first: Veronique

last: Tanty

first: Corinne

last: Blugeon

manufacture_protocol:
Slide spotted using a MicroGrid II (Genomic Solution)
Spotting conditions: Temperature of 20¡C more or less 5¡C. Hygroscopy of 50% more or less 5%.
Before each spotting:
1.	Printing tips (Geneworx 10k) are tested on glass slides.
2.	The spotting robot is put in operation and water tanks filled with distilled water.
3.	Corning glass slides are deposited on plates.
4.	The spotting program specific for each slide bacth is launched.


title: Nimblegen MM8 Mouse Promoter Array

status: Public on Jun 28 2008

city: Boston

first: Will

last: Renthal

state: MA

address: 60 Fenwood Rd.

institute: Brigham and Women's Hospital

manufacture_protocol: See www.nimblegen.com.


title: Duke University Operon Mouse 32K V3.0.1 printed oligonucleotide array [Mus musculus]

status: Public on Jun 03 2008

city: Durham

first: Alisa

last: Ray

state: NC

address: DUMC Box 3209

department: Neurobiology

institute: Duke University

manufacture_protocol:
Duke Microarray Facility
http://microarray.genome.duke.edu/services/copy_of_print_req/


title: MWG Biotech mouse 30K array

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

manufacture_protocol: Standard MWG commercial protocol


title: Operon Mouse V3.0 printed oligonucleotide array

status: Public on May 26 2008

first: Neelanjan

last: Mukherjee

address: 101 Science Drive

department: Institute for Genome Sciences & Policy

manufacturer: Duke Microarray Facility (manufactured printing of arrays)

manufacture_protocol: see the Duke IGSP Microarray Facility website


title: MDC Illumina MEEBO 38K

status: Public on Jun 19 2008

city: Loma Linda

first: Robert

last: Chadwick

department: Molecular Genetics Division

institute: Musculoskeletal Disease Center

description: Corning UltraGAPS (Gamma Amino Propyl Silane)

first: Kristen

last: Govoni

first: Jon

last: Wergedal

first: Apurva

middle: K

last: Srivastava

first: Subburraman

last: Mohan

manufacture_protocol: Spotted in 25% DMSO using a Genetix Q-Array 2 robotic spotter.  The MEEBO set comprises 38,467 oligo probes (70mers).  Each probe was spotted once using silicon 50 micron split pins (Parallel Synthesis, Inc.)


title: Mouse custom CGH oligo array 244K (chr18, 018812)

status: Public on May 02 2008

city: Chiba

first: Takashi

last: Takabatake

state: Chiba

address: Anagawa 4-9-1, Inage-ku

institute: National Institute of Radiological Sciences

first: Hiroshi

last: Ishihara

first: Yasushi

last: Ohmachi

first: Izumi

last: Tanaka

first: Masako

last: Nakamura

first: Katsuyoshi

last: Fujikawa

first: Tokuhisa

last: Hirouchi

first: Shizuko

last: Kakinuma

first: Yoshiya

last: Shimada

first: Yoichi

last: Oghiso

first: Kimio

manufacture_protocol: As descripted by Agilent manuals under Platform_web_link


title: UMGC-IRCNA 9k B

status: Public on May 07 2008

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

institute: ICO (Integrated Center of Oncology Nantes)

first: Stéphane

last: Minvielle

first: Florence

last: Magrangeas

first: Pascal

last: Jézéquel

manufacture_protocol:
One channel DNA microarrays were constructed from EST cDNA clones (based on Homo sapiens).
End-sequence-verified I.M.A.G.E. clones were purchased from RZPD German Resource Center for Genome Research (Berlin, Germany) or provided by the Human Genome Mapping Project Resource Centre (Hinxton, UK) and sequenced by MilleGen (Labege France).
The cDNA clones were amplified in 96-well microtiter plates with universal primers.
PCR products were spotted onto nylon using a robot-based high-speed contact spotting facility which ensures high precision positioning and constant droplet volumes of cDNA samples to provide an reproducible spot morphology and DNA content over the whole array.
The process is performed under dust free, temperature-and humidity controlled conditions.
The spotted cDNA is covalently bound by U.V. rays to the nylon surface.
The feasibility, reproducibility and sensitivity of spotting procedures onto nylon membrane currently used in our laboratory to produce cDNA arrays have been previously described (Nguyen et al., Genomics. 1995;29:207-216; Bernard et al., Nucleic Acids Res. 1996;24:1435-1442; Bertucci et al. Hum Mol Genet. 1999;8:1715-1722; Magrangeas F et al. Blood. 2003;101:4998-5006.).


title: Agilent_human_1A_22k

status: Public on May 01 2008

city: Denver

first: Ivana

middle: V

last: Yang

state: CO

address: 1400 Jackson Street

department: Medicine

institute: National Jewish Health

manufacture_protocol: In situ synthesized 60-mer oligos


title: Mouse custom CGH oligo array 244K (015151)

manufacture_protocol: see manufacturer's website


title: VMSR Compugen Human Oligo P6G5

status: Public on Apr 29 2008

city: Nashville

first: Braden

last: Boone

state: TN

address: 465 21st Ave South

department: Vanderbilt Microarray Shared Resource

institute: Vanderbilt University

manufacture_protocol: Microarrays containing all oligonucleotides from the Compugen Human Release 2.0 OligoLibrary were resuspended in 150mMol phosphate buffer and arrayed according to the manufacturers recommendations.  Microarrays were produced by Microarrays Incorporated (www.microarrays.com) utilizing custom, high precision robotics and amine-coated glass slides from Genexprex.  The microarrays were then crosslinked using  80mjoules of ultraviolet energy (Stratagene Stratalinker, LaJolla, CA).  Following crosslinking, the arrays were baked for two hours at 70C in a standard oven and stored under low humidity conditions until use.


title: CapitalBio Human 22k oligonucleotide microarray

city: Beijing

first: bo

last: kong

address: 167 Beilishi Road

country: China

institute: Cardiovascular Institute and Fuwai Hospital,CAMS&PUMC

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


title: Illumina mouse-6 v1.1 expression beadchips

status: Public on May 21 2008

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH


title: Print_1185

status: Public on Apr 09 2008

city: Stanford

first: David

last: Wong

address: 269 Campus Drive

institute: Stanford University

description: SHGE

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: Print_1225

description: SHGS


title: Duke University Human Operon v.3.0 spotted Array

status: Public on Mar 21 2008

first: Vasantha

last: Rao

address: 2351 Erwin Rd

department: Ophthalmology

institute: Duke University Medical Center

manufacturer: Institute for Genome Science Policy, Duke University

first: Min

last: Zhang

first: Rupalatha

last: Maddala

first: Vasanth

manufacture_protocol: The Operon Human oligonucleotide library,version 3.0, comprised of 70-mer oligonucleotides representing 35,324 unique human genes, was printed on poly-L-lysine-coated glass slides. The library also included sets of positive and negative controls that were used for quality control purposes. Oligonucleotides were spotted using a GeneMachines Omnigrid arrayer by the Duke University Microarray facility. Details can be found at http://mgm.duke.edu/genome/dna_micro/core/spotted.htm.


title: TIGR_RAT_27k_cDNAarray_1

status: Public on Mar 04 2008

city: Washington, DC

first: Norman

last: Lee

state: DC

address: 2300  I Street, N.W.

department: Pharmacology & Physiology

institute: The George Washington University Medical Center

description: The arrays are printed on the barcoded side of the slide with approximate distance from the top, left side and right side of 3 mm. The array consists of 48 grids with each grid representing 576 spots in a 24 x 24 arrangement.

first: Bina

last: Joe

first: Bryan

middle: C

last: Frank

manufacture_protocol:
TIGR Department of Mammalian Genomics protocol.
The TIGR RAT 27k cDNAarray consists of 26,501 probe elements representing 20,465 unique genes.
Purified cDNA amplicons were combined with the printing buffer to a final  buffer percentage of 50% DMSO. The printing plates were arrayed onto aminosilane glass slides on a custom-built microarray robot from Brooks Automation (Cambridge, MA). Printed arrays were UV cross-linked to ensure binding.


title: Print_1214

description: SHGH


title: NIH NIAMS gene array facility human cDNA array 8K

status: Public on Mar 11 2008

city: rockville

first: Mike

last: havert

address: 1401 Rockville Pike

institute: CBER/FDA

first: Christian

last: Jacobson

first: Santosh

last: Nanda

last: Havert

manufacture_protocol: CDNA clones purchased from commercial supplier, spotted and immobilized on glass slides


title: NCI Qiagen Homo sapiens 36K v3 cgh expression

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

first: Rosemary

last: Balleine

first: Lucy

middle: R

last: Webster

first: Elizabeth

last: Salisbury

first: Robert

last: Walker

first: Karen

last: Byth

first: Christine

last: Clarke

first: Paul

middle: S

last: Meltzer

manufacture_protocol: Human qiagen/operon version 3 longmer (~70-mer) spotted onto glass