title: GeneSifter export of Agilent 4X44K whole mouse genome microarray

status: Public on Oct 31 2008

city: Boston

first: Niels

last: Geijsen

state: MA

address: 185 Cambridge St. CPZN 4-4256

department: Center for Regenerative Medicine

country: USA

institute: Massachusetts General Hospital

organism: Mus musculus

technology: in situ oligonucleotide

description: This Platform was created to accommodate Agilent Whole Mouse Genome Microarray (4x44K) normalized data exported from GeneSifter.

distribution: custom-commercial

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


title: S&S serum biomarker chips, 120 antibodies

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

organism: Homo sapiens

technology: antibody

manufacture_protocol: item 10486077, antibodies dotten onto nitrocellulose coated glass slides


title: INSA Lactococcus lactis IL1403 (S1)

status: Public on Oct 23 2008

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

country: France

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

organism: Lactococcus lactis

technology: spotted DNA/cDNA

description:
aminosilane UltraGAPS slide (Corning)
2.5*7.5 cm
secondary PCR lot1

manufacturer: Eurogentec/Biochips Platform INSA Toulouse France

manufacture_protocol: Manufacture Protocol: Amplicons (PCR) were designed and amplified by Eurogentec. A mean length of 535 bp and final concentrations between 40 and 380 µg/l were obtained. PCR were diluted in DMSO 50 % in 384 wells spot plates and spotted (1 deposits/ spot) in duplicate on aminosilane UltraGAPS slide (Corning) with a Versarray Chipwritter (Biorad) with a 14*12 pattern.


title: Human Promoter Array 1.0R - NCBI build_35

status: Public on Oct 28 2008

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description: For data analysis of the associated Samples, we calculated MAT scores based on the hyridization intensity data of the probes within 500bp windows. The coordinate column in the Platform data table represents the chromosome coordinates for the 500bp window center positions.

first: Shuichi

last: Tsutsumi

manufacture_protocol: Oligonucleotide probes are synthesized in situ complementary to each corresponding sequences. 35 base pair resolution array.


title: University of Texas at Austin Arabidopsis thaliana 29k 70-mer spotted oligoarray

status: Public on Oct 21 2008

city: Bethesda

first: Misook

last: Ha

state: MD

address: NIH

institute: National Heart Lung Blood Institute

organism: Arabidopsis thaliana

technology: spotted oligonucleotide

description: The 70-mer oligo was designed from the 3'end of ATH1.cdna from the ATH1 release 5.0 of the TIGR A. thaliana genome and release 4.0 of the miRNA Registry at the Sanger Institute.

distribution: non-commercial

first: Eun-Deok

last: Kim

first: Z

middle: J

last: Chen

manufacture_protocol: The Arabidopsis thaliana Genome Oligo Set Version 3.0 0 contains 29,110  longmer probes and represents 26,173 protein-coding genes, 28,964 protein-coding gene transcripts, and 87 microRNA genes from A. thaliana. Every 70-mer oligo is spotted once on each slide.


title: SMD Arabidopsis thaliana 12.7K Print_494

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

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_1268

first: Daniel

last: Hogan

address: 279 Campus Dr B439

institute: Stanford University

organism: Saccharomyces cerevisiae


title: Micro-CRIBI Human Oligo Array V_0 (Operon V2.0)

status: Public on Oct 10 2008

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: This set consists of 21,329 70mer oligonucleotides (Operon version 2.0) designed on Human Unigene clusters, mainly in the 3 end terminal region. Each oligonucleotide is spotted by our robotic station Biorobotics Microgrid II, in one replicate on a MICROMAX glass slide SuperChip I (Cat No MPS696) provided by PerkinElmer Life Sciences Inc. The deposition is qualitatively assessed by a scan of the spotted slide at 10 micron resolution, using a GSI Lumonics scanner and a protocol that allows the detection of spotted features through the salts derived from the dried solution in which oligonucleotides are dissolved. Moreover all spotted batch are evaluated for the spot shape and oligo linking onto the slide surface using the vistra green method. Microarray slides that meet the quality standards, are washed as recommended by the supplier and the glass slides are stored, ready for use, in the dark under deep vacuum.

manufacturer: CRIBI University of Padova Microarray facility (http://microcribi.cribi.unipd.it)

first: Stefano

last: Cagnin

first: Beniamina

last: Pacchioni

first: Caterina

last: Millino

first: Barbara

last: Celegato

first: Cristiano

last: De Pitta'

first: Lucia

last: Tombolan

first: Chiara

last: Romualdi

manufacture_protocol:
1.Oligos are arrayed in Genetix 384 Well Microarray Plates (Cat# X7020). Each well contains 600 pmol of 70-mer oligo.
2. Resuspend oligos in 17 µL of Telechem Microspotting solution 1X.
3. Seal plates with Corning seals and after oligos resuspenction print probe with the MicroGrid II Biorobotics spotter.
4. Print is performed with 48 Stealth pins.
5. After printing run plates are stored at -20 C degree.
6. Every 4 months plates are lyophilized and resuspended in adjusted water volume according to the number of spotting runs. This, to maintain the same volume and concentration in all plate well.


title: LSUHSC-S_Shelver_GBS_5K_V1.0

status: Public on Oct 29 2008

city: Shreveport

middle: Wilson

last: Shelver

state: LA

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: LSU Health Sciences Center in Shreveport

organism: Streptococcus agalactiae

middle: W

first: Joshua

middle: D

last: Bryan

manufacture_protocol: The LSUHSC-S_Shelver_GBS_5K_V1.0 was designed according to standard Affymetrix GeneChip protocols.  The array covers the ORFs of Group B Streptococcus (GBS) strain COH1 and 24 PM/MM 25-mer probes were utilized for each ORF.  Probe selection was conducted by Affymetrix.  Each chip contains two copies of each probe.  The chip was manufactured by Nimblegen for Affymetrix via the Affymetrix NimbleExpress program.


title: Print_1270


title: Agilent-012795 C. elegans Oligo Microarray G2518A Option 002 (Probe Name version)

status: Public on Oct 08 2008

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Caenorhabditis elegans

description:
Agilent has made available a new microarray with genome-wide coverage of C. elegans with over 21,000 predicted genes from WormBase, a public C. elegans genome database.

*** 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 GPL2875.

distribution: commercial


title: Chlamydomonas reinhardtii Version_2_plus Microarray

status: Public on Oct 27 2008

city: Bielefeld

first: Anh Vu

last: Nguyen

state: NRW

address: G2-154, CEBITEC, Universitaetsstr. 27

department: Cell and Molecular Biology

country: Germany

institute: Bielefeld University

organism: Chlamydomonas reinhardtii

first: Anh

middle: V

first: Ben

last: Hankamer

first: Jens

last: Ruppprecth

first: Jan

last: Mussgnug

first: Skye

last: Thomas-Hall

first: Olaf

last: Kruse

first: Peer

middle: M

last: Schenk

manufacture_protocol: Reference: "The generation of an oligonucleotide microarray for the analysis of  gene expression in Chlamydomonas reinhardtii" (Eberhard et al. 2006)


title: Print_1271

first: Daniel

last: Hogan


title: Custom Nimblegen aCGH chip targeted to canFam2 segmental duplications.

city: Seattle

first: Thomas

last: Nicholas

state: WA

address: 1705 NE Pacific St. Foege Building

department: Genome Sciences

institute: University of Washington

organism: Canis lupus familiaris

description: Segmental duplications were computationally identified and then were targeted with 368,360 probes.  The remaining available probes were placed in 5kb flanking regions  to the segmental duplications (9,278 probes) and in single copy control regions (8,790 probes).

first: Ze

last: Cheng

first: Mario

last: Ventura

first: Katrina

last: Mealey

first: Evan

middle: E

last: Eichler

last: Akey

manufacture_protocol: Normal Nimblegen parameters were used with relaxed repeat constraints to enable probe placement in segmental duplication regions.


title: Print_627


title: Lactobacillus reuteri F275 44K 60-mer array, Version 1

city: Amsterdam

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

country: Netherlands

institute: Vrije Universiteit Amsterdam

organism: Limosilactobacillus reuteri subsp. reuteri F275

description: This array contains 60-mer probes that are designed for L. reuteri strain F275. The sequence of this organism is present in public databases, Acc. Nr. CP000705 (NC_009513).

first: Filipe

last: Santos

first: Jeroen

last: Hugenholtz


title: Rice Genome Oligo Set V1.0

status: Public on Jan 29 2005

city: Cologne

first: Operon

last: Biotechnologies

institute: Operon Biotechnologies

organism: Oryza sativa

description:
Oryza sativa Genome Oligo Set Version 1.0 was designed by Beijing Genomics Institute (BGI) and contain 60,727 70mer oligos representing both indica and japonica genomes. All oligos were designed from cDNAs, expreseed sequence tag (EST) sequences, predicted genes of BGI rice genome build and other public resources.  Mapping to TIGR rice genome pseudommolecues release 2 is based on the BLAST results, if a oligo has greater than 97% identity to a gene sequence from TIGR pseudomolecules, the oligo represents that gene. If the oligo matches to multiple genes, only one gene ID is randomly chosen. Preference is given to a 100% match.
Keywords = Rice Operon


title: Print_1138


title: Affymetrix GeneChip ParAllele TrueTag 5 K platform

city: Jupiter

first: Mathew

middle: T

last: Pletcher

state: FL

address: 5353 Parkside Dr

institute: Scripps Florida

description: GeneChip® Universal Tag Arrays are available in 3K, 5K, 10k or 25K configurations and contain novel, bioinformatically designed tag sequences that result in minimal potential for cross-hybridization.

manufacture_protocol: see manufacturer's web site


title: Print_626


title: Print_835


title: NCSU_Sulfolobus solfataricus P2_3Karray_version1

city: Raleigh

first: Charlotte

last: Cooper

state: NC

address: 840 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

organism: Saccharolobus solfataricus

first: Sabrina

last: Tachdjian

first: Robert

last: Kelly

manufacture_protocol: A DNA microarray was designed and constructed based on at least 2976 protein-coding sequences in the S. solfataricus genome obtained from the TIGR CMR (http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi). OligoArray 2.1 (Rouillard, 2003) was used to generate one 60-mer (some slightly longer or shorter) oligonucleotide probe sequence for each open reading frame. The probes were synthesized (Integrated DNA Technologies, IA), re-suspended in 50% DMSO, and printed onto Ultragap microarray slides (Corning, NY) using a QArrayMini arrayer (Genetix, UK). Each probe was spotted four times onto each array to fortify statistical analysis.


title: Print_1032


title: Print_1333


title: Agilent-013807 C. familiaris (Dog) Oligo Microarray G2519A option 004

status: Public on Oct 30 2008

last: Agilent Technologies

description:
C. familiaris Oligo Microarray

Arrays of this design have barcodes that begin with 16013807 or 2513807.

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: Exiqon miRCURYTM LNA Array Version 8.1

city: Louisville

first: Amar

last: Singh

state: KY

address: 501 S Preston street

department: Oral Health and Systemic Disease Research Group

institute: University of Louisville

first: Denis

middle: F

last: Kinane

first: Manjunatha

middle: R

last: Benakanakere


title: SMD Arabidopsis thaliana 11.9K Print_376

last: Stanford Microarray Database


title: Agilent-011447 Yeast Oligo Microarray (G4140A) - alternative version

city: RTP

first: Yohan

last: Jin

address: 111 TW Alexander Dr.

institute: NIEHS

description:
This is an alternative version of the official Agilent platform assigned accession number GPL884. The ID column includes the Agilent probe identifiers instead of the Agilent feature IDs.

This oligonucleotide microarray will enable researchers to simultaneously characterize expression of many thousands of yeast genes and identify gene activity during important biological processes, such as yeast growth, adaptation, response to drug candidates and reproduction.


title: Print_1031

first: Daniel

last: Hogan


title: Human_40K_partIII_FCCC_v1.0

city: Philadelphia

first: Julia

last: Santucci-Pereira

state: PA

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. The complete array has 3 sub-arrays- part I, part II and part III.


title: IMB Arabidopsis thaliana 30K operon oligo array

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: The Arabidopsis genome oligo set t(version3.0),comprising  29,110 longmer probes representing26,173 protein-coding genes , 28,964 protein-coding gene transcripts and 87 microRNA genes from Arabidopsis thaliana , 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: PFGRC Aspergillus fumigatus AF293v3

status: Public on Oct 15 2008

city: Bozeman

middle: A.

last: Cramer

state: MT

department: Department of Veterinary Molecular Biology

institute: Montana State University

organism: Aspergillus fumigatus

manufacture_protocol: available from JCVI


title: Ding Lab fruit fly S2 cell small RNAs (454 sequencing)

status: Public on Oct 16 2008

city: Riverside

first: Qingfa

last: Wu

address: 900 University Ave

institute: UC Riverside

organism: Drosophila melanogaster

technology: other

distribution: virtual


title: MSU E. coli 6.1.K Ver. 1.0.2

status: Public on Oct 11 2008

city: East Lansing

first: Thomas

middle: S

last: Whittam

address: 165 Food Safety & Tox

department: Microbiology

institute: Michigan State University

organism: Escherichia coli

manufacture_protocol: 70-mer oligos spotted in duplicate onto Corning UltraGaps slides.


title: Geobacter uraniumreducens Rf4 antisense-detecting array

status: Public on Oct 19 2008

city: Amherst

first: Derek

last: Lovley

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

institute: University of Massachusetts Amherst

organism: Geotalea uraniireducens Rf4

description: each oligonucleotide is synthesized on an array of gold electrodes embedded in a silicon chip.

first: Dawn

last: Holmes

first: Raymond

last: DiDonato

first: Bradley

middle: L

last: Postier

manufacture_protocol: In-situ electrochemically synthesized oligonucleotide array. For reference see: Mauer et al., Electrochemically generated acid and its containment to 100 micron reaction areas for the production of DNA microarrays. PLoS ONE. 2006, Dec 20;1:e34.


title: C. elegans 385K ChIP01

status: Public on Oct 20 2008

city: Chapel Hill

first: Christina

last: Whittle

address: 406 Fordham Hall, CB#3280

department: Biology

institute: University of North Carolina-Chapel Hill

description:
C. elegans whole genome tiling array (3 array set) at 86bp resolution, 385K features per array, 1.15M total features.
Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR,Cerrina F. Maskless fabrication of light-directed oligonuc
leotide microarrays using a digital micromirror array. Nat Biotechnol. 1999 Oct;17(10):974-8. PMID: 10504697

first: Jason

last: Lieb

first: Leo

last: Iniguez


title: Superarray Signal Transduction PathwayFinder PCR Array  APHS-014b

city: Urbana

first: H

middle: Rex

last: Gaskins

state: IL

address: 1207 W Gregory dr

department: Institute for Genomic Biology

institute: University of Illinois

technology: RT-PCR

description: The Human Signal Transduction PathwayFinder™ RT²Profiler™ PCR Array profiles the expression of 84 key genes representative of 18 different signal transduction pathways listed below. Using real-time PCR, you can easily and reliably analyze the expression of a focused panel of genes related to any of the 18 signal transduction pathways that may be involved in your favorite biological response.

first: Matias

last: Attene-Ramos

first: Gerardo

last: Nava

first: Mark

middle: G

last: Muellner

first: Elizabeth

last: Wagner

first: Michael

last: Plewa


title: Micro-CRIBI Mouse Oligo 13.4k Array V_0 (Operon V1.1)

city: Padova

first: Gerolamo

last: Lanfranchi

institute: University of Padova

description: This set consists of 13,440 70mer oligonucleotides (Operon version 1.1) designed on Mouse Unigene clusters, mainly in the 3 end terminal region. Each oligonucleotide is spotted by our robotic station Biorobotics Microgrid II, in one replicate on a MICROMAX glass slide SuperChip I (Cat No MPS696) provided by PerkinElmer Life Sciences Inc. The deposition is qualitatively assessed by a scan of the spotted slide at 10 micron resolution, using a ScanArray LITE (PerkinElmer) scanner and a protocol that allows the detection of spotted features through the salts derived from the dried solution in which oligonucleotides are dissolved. Moreover all spotted batch are evaluated for the spot shape and oligo linking onto the slide surface using the vistra green method. Microarray slides that meet the quality standards, are washed as recommended by the supplier and the glass slides are stored, ready for use, in the dark under deep vacuum.

manufacturer: CRIBI University of Padova microarray facility (http://microcribi.cribi.unipd.it)

first: Stefano

last: Cagnin

first: Beniamina

last: Pacchioni

first: Caterina

last: Millino

first: Barbara

last: Celegato

first: Cristiano

last: De Pitta'

first: Lucia

last: Tombolan

first: Chiara

last: Romualdi

manufacture_protocol:
1.Oligos are arrayed in Genetix 384 Well Microarray Plates (Cat# X7020). Each well contains 600 pmol of 70-mer oligo.
2. Resuspend oligos in 17 µL of Telechem Microspotting solution 1X.
3. Seal plates with Corning seals and after oligos resuspenction print probe with the MicroGrid II Biorobotics spotter.
4. Print is performed with 48 Stealth pins.
5. After printing run plates are stored at -20 C degree.
6. Every 4 months plates are lyophilized and resuspended in adjusted water volume according to the number of spotting runs. This, to permit to maintain the same volume and concentration in all plate well.


title: MPI_IEPE_HomoSapiens_44k_v1.0

status: Public on Oct 17 2008

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

description: Customized oligonucleotide array covering chromosomal region chr14:31170206-41099827 (HG17;NCBI35)

first: Anne

last: Thorwarth

manufacture_protocol: SurePrint Technology


title: Superarray DNA damage signaling APHS-029B

description: The Human DNA Damage Signaling RT² Profiler™ PCR Array profiles the expression of 84 genes involved in DNA damage signaling pathways. The genes featured are those associated with the ATR/ATM signaling network and transcriptional targets of DNA damage response. DNA damage can result in cell cycle arrest, apoptosis, and the stabilization and repair of the cellular genome.


title: ZMOBCombimatrixplatform

first: Stan

last: Martin

address: 1404 Crete Dr.

institute: Science Apps, L3C

organism: Zymomonas mobilis

manufacture_protocol:
A modified semiconductor developed at Combimatrix Inc. utilized integrated circuits which contained arrays of microelectrodes individually addressable using embedded logic circuitry on the chip. When placed in a specially designed flu
idic chamber, the chip digitally directs the molecular assembly of biopolymers in response to a digital command.  Each microelectrode is addressed to selectively generate chemical reagents by means of an electrochemical reaction. These chemical reagents fa
cilitate the in situ synthesis of complex molecules such as DNA oligonucleotides. These molecules are synthesized within a proprietary Porous Reaction Layer (PRL) that coats the chip. Under the direction of a PC the CombiMatrix chip rapidly synthesizes ove
r a thousand different molecules in parallel, each above a distinct electrode.


title: Custom 4x2K miRNA microarray (#4166)

city: Geelong

first: Stephanie

middle: C

last: Bannister

state: Victoria

address: 5 Portarlington Road

department: Livestock Industries

country: Australia

institute: CSIRO

organism:
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: see manufacturer's website


title: PFGRC Porphyromonas gingivalis 70 mer oligo array (condensed version)

status: Public on Oct 09 2008

city: Columbus

first: CHRISTINA

last: IGBOIN

state: OH

address: 305 W 12th Ave

institute: Ohio State University

organism: Porphyromonas gingivalis W83

manufacture_protocol: The Porphyromonas gingivalis microarray was designed to work with Porphyromonas gingivalis strain W83. The full genome array consists of 1907 70-mer oligonucleotides that were designed based on 2083 predicted ORFs from the annotation of strain W83.


title: Agilent-013328 Rat Oligo Microarray (V2) G4130B (Probe Name version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Rattus norvegicus

description:
This microarray contains representative sequences derived from rat RefSeq, high-quality public rat mRNA accessions, homologs to human and mouse RefSeq, EST clusters determined by a leading biopharmaceutical company and the Incyte Zooseq database as well as toxicology markers determined by the National Institute of Environmental Health Sciences (NIEHS) and others. Many of the toxicology markers used in the design of this microarray were released to the public domain for the first time and will be used on this unique microarray product.

*** 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 GPL2882.

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


title: Agilent-020938 S. salar (Salmon) Oligo Microarray (Probe Name version)

organism: Salmo salar

description:
S. salar (Salmon) Oligo Microarray

*** 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 GPL7097.


title: AECOM Nimblegen MM8 gene expression array

city: Bronx

first: Binzhi

last: Qian

state: NY

address: 1300 Morris Park Ave

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

organism: Mus musculus

manufacture_protocol: see http://www.nimblegen.com/index.html


title: Agilent-011842 Magnaporthe grisea Oligo Microarray G4137A (Probe Name version)

organism: Pyricularia grisea

description:
Replaced by 012756, G4137B.  Magnaporthe griesa 1.0.

*** 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 GPL889.


title: Agilent-013324 Arabidopsis 2 Oligo Microarray (V2) G4136B (Probe Name version)

organism: Arabidopsis thaliana

description:
The content on this microarray is derived from the ATH1 v. 3 database of The Institute for Genomic Research (TIGR) and represents 21,500 genes. This microarray will be useful for scientists studying gene activity associated with various plant organ functions, stages of growth, and biotic and abiotic stresses.  Replaces 011839, G4136A

*** 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 GPL2880.


title: Agilent-012756 Magnaporthe Grisea V2 Oligo Microarray G4137B (Probe Name version)

description:
This Magnaporthe grisea 2.0 microarray contains oligos designed after 15,170 predicted Magnaporthe genes and transcripts from the newly annotated data set at the Fungal Genomics Laboratory at North Carolina State University. Included are annotations from the Whitehead Institute at the Massachusetts Institute of Technology. This microarray also contains 6,325 probes designed after ESTs of rice genes.

*** 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 GPL2874.


title: Agilent-012600 Arabidopsis 3 Oligo Microarray G4142A (Probe Name version)

description:
The content on this microarray is derived from the ATH1 v.5 database of The Institute for Genomic Research (TIGR) and from the Arabidopsis MPSS database at the University of Delaware.  Nearly 40,000 features represents 28,500 genes from TIGR and more than 10,000 unannotated transcripts from University of Delaware. This microarray will be useful for scientists studying gene activity associated with various plant organ functions, stages of growth, and biotic and abiotic stresses.

*** 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 GPL2871.


title: Agilent-011871 Human 1B Microarray G4111A (Probe Name version)

organism: Homo sapiens

description:
Consisting of highly-sensitive 60-mer oligonucleotide probes that target human genes present in Incyte LifeSeq Foundation partial sequence database, the Agilent Human 1B Oligo Microarray Kit queries more rare human transcripts where full-length information is not available. The microarray is fully annotated to allow customers to access public or Incyte LifeSeq databases for additional bioinformatics data about the genes.

*** 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 GPL886.


title: Wurdinger/Krichevsky miRNA array IV

city: Charlestown

first: Thomas

last: Wurdinger

state: MA

address: 149 13th Street

institute: MGH

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: An expanded miRNA array was developed as described (Krichevsky et al., 2003) with modified probe design to balance Tm of hybridization to all miRNAs. A total of 407 tri-mer DNA oligonucleotides (anti-sense to microRNAs [Sanger miRBase version 8.0]) were spotted onto GeneScreen Plus (NEN) membranes at a final concentration of 5 µM with a 1536 pin plate replicator (V&P Scientific).


title: DIPROVAL - OPERON Sus scrofa AROS V1.0

city: Reggio Emilia

first: Roberta

last: Davoli

address: Via Fratelli Rosselli 107 -Villa Levi- Coviolo-

department: Dipartimento di Protezione e Valorizzazione Agroalimentare

institute: University of Bologna

organism: Sus scrofa

description: This work was supported by a grant from FIRB of the Ministry of Education, University and Research (MIUR) of Italy –Scientific responsible person: Prof. Vincenzo Russo

manufacturer: MicroCribi - CRIBI Microarray Service - University of Padua, Laboratory: prof. G. Lanfranchi, c/o CRIBI, via Ugo bassi 58/B 35131 PADOVA, tel. 0039-049 8276162, fax 0039-049827 6159, http://microcribi.cribi.unipd.it

first: R

first: S

first: B

first: C

first: G

manufacture_protocol:
The Array-Ready Pig Genome Oligo Set Version 1.0 from Operon Biotechnologies was dissolved in 3XSSC and spotted using a MicroGrid II (BioRobotics) microarrayer onto Micromax SuperChipI glass slides (Perkin Elmer Life Sciences). The oligos were crosslinked (600 mJoules) onto the glass using a Stratalinker UV crosslinker (Stratagene).
Post-spotting treatment: To eliminate salts and materials unlinked the following washes were utilised :
1- 1 % SDS and 3X SSC (1’)by shaking
2- Distilled water (5’) by shaking
3- Boiling distilled water (30”)
Additional information for the oligos is available via the Download Center at Operon Biotechnologies. Present annotation is based on data from OPERON Biotechnologies, Sus scrofa (pig) AROS V1.0, genelist version 1.0.5.


title: EBV regulated microRNAs human 3k array

status: Public on Oct 04 2008

city: New Orleans

first: Erik

middle: K

last: Flemington

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

first: Jennifer

last: Cameron

first: Xiaochuan

last: Zhou

manufacture_protocol:
Array Protocol: LC Mir-Array-Prtl-060518
Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes are made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: Low Density Microvascular Differentiation Array (LD-MDA) version 2.0

city: Zurich

first: Jay

middle: Woo

last: Shin

state: Zurich

address: Wolfgang-Paulistrasse 10; HCI H394

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

description: Microfluidic 384-well TaqMan™  real time RT-PCR platform

manufacture_protocol: Applied Biosystems Primer Assay - gene selection based on LEC vs BEC differential expressions. The 384-well micro-fluidic cards were produced with pre-designed primer pairs and FAM-labeled TaqMan probes for each of the 96 selected genes in duplicate, with two sample reservoirs per card.


title: Low Density Microvascular Differentiation Array (LD-MDA) version 1.0


title: Human 3K BAC/PAC array (Ensembl Ver39)

status: Public on Oct 07 2008

city: London

first: Tomohiko

last: Harada

address: Charterhouse Square

department: Centre for Molecular Oncology

country: United Kingdom

institute: Cancer Research UK

description:
The Platform data table reflects a condensed representation of the array's replicate features.  The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.

All BAC/PAC information has been updated based on Ensembl annotation (Ver49) on 22 Sep 2008. Please refer to GPL7347 for more details.

manufacture_protocol: Spotted BAC/PAC clones arrayed as described in Fiegler H et al. Genes Chromosomes Cancer 36:361-374, 2003


title: Tetrahymena thermophila genome-wide oligonucleotide microarray

status: Public on Oct 01 2008

city: Rochester

first: Martin

last: Gorovsky

address: Hutchison Hall 432

department: Department of Biology

institute: University of Rochester

organism: Tetrahymena thermophila

description:
The complete array includes 384999 60-mer oligonucleotides.
A total of 28,064 T. thermophila sequences from TIGR (http://www.tigr.org/tdb/e2k1/ttg/) including predicted protein-coding genes, non-protein-coding RNA and tRNA genes were used to construct high-density T. thermophila genome-wide oligonucleotide DNA microarrays. For each of the sequences, 13 or 14 unique 60-mer oligonucleotide probes were designed by NimbleGen Systems

Design and gene description files (.ndf, .ngd) appended below as supplementary files.

first: Wei

last: Miao

first: Josephine

last: Bowen


title: UniMelbPea4x2k_ver.1

city: Parkville

first: Chui

last: WONG

address: University of Melbourne

department: Land and Food

institute: University of Melbourne

organism: Lathyrus oleraceus

last: Wong

first: Harald

last: Ottenhof

first: Prem

last: Bhalla

first: Mohan

middle: B

last: Singh

manufacture_protocol: The Combimatrix arrays are semiconductor-based oligonucleotide microarrays and are generated based on CombiMatrix technology (hyperlink) of in situ synthesis as outlined at www.combimatrix.com. The CustomArray™ 4x2k is a microarray that is divided into 4 sectors, each of which can contain up to 2,240 different oligonucleotide probes (spots) and can be hybridized individually with different targets using a provided sectored hybridization cap.


title: BMGC Campylobacter jejuni NCTC 11168 condensed oligo array v.1.0

city: Lethbridge

first: Eduardo

middle: N

last: Taboada

state: Alberta

address: PO Box 640, TWP Rd. 9-1

country: Canada

institute: Public Health Agency of Canada

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

description:
VIDO C. jejuni NCTC 11168 Oligonucleotide Microarray v.1.0.
C. jejuni oligonucleotide microarray from the Campylobacter jejuni Genome Oligo Set Version 1.0 was purchased from Operon Biotechnologies, Inc. (Huntsville, AL35805). This product  contained 1,601 probes 70 bp in length and represented 1,546 open reading frames (ORFs) from C. jejuni subsp. jejuni NCTC 11168 (GenBank sequence AL111168); 51 ORFs from C. jejuni 81-176 virulence plasmid pVir (GenBank sequence AF226280); and four ORFs from C. jejuni plasmid pCJ01 (GenBank sequence AF301164). All 1,601 probes are designed within predicted ORFs by Operon using their proprietary software.  The probes are Tm normalized to 71ºC (±5ºC).  Triplicate spots were included for each ORF on the chip. The microarray slides were produced from this set of oligonucleotides by The Biomedical Genomics Center, University of Minnesota (Minneapolis, MN, USA). Only genes from C. jejuni NCTC11168 (n=1546) were analyzed.

manufacturer: C. jejuni Genome Oligo Set Version 1.0 from Operon Biotechnologies, Inc. (Huntsville, AL35805); Printed at The Biomedical Genomics Center, University of Minnesota (Minneapolis, MN, USA)

first: Sherry

middle: J

last: Hannon

first: Brenda

last: Allan

first: Hugh

last: Townsend

first: Heather

last: Wilson

first: Andrew

last: Potter

first: Cheryl

last: Waldner

first: Lorne

last: Babiuk

first: Margaret

last: Russell

manufacture_protocol:
Array was fabricated at The Biomedical Genomics Center, University of Minnesota (Minneapolis, MN, USA), using modified versions of the DeRisi protocols.
http://www.agac.umn.edu/facilities/microarray/home.html


title: Human 3K BAC/PAC array (Ensembl Ver49)

first: Tomohiko

last: Harada

description:
The Platform data table reflects a condensed representation of the array's replicate features.  The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.

This is exactly the same platform as  Ensembl Ver39 array GPL6181. However, all BAC/PAC information has been updated based on Ensembl annotation (Ver49).


title: INDAC Drosophila melanogaster 15K v5.0

city: Los Angeles

first: Matthew

last: Lebo

state: CA

address: 1040 Child's Way

department: Molecular and Copmutational Biology

institute: University of Southern California

organism: Drosophila melanogaster

first: Laura

last: Sanders

first: Fengzhu

last: Sun

first: Michelle

last: Arbeitman

manufacture_protocol: 15,158 oligonucleotide probes representing all known and predicted open-reading-frames, based on release 4.1 of the Drosophila melanogaster genome were synthesized. The long oligonucleotide sequences were designed by the International Drosophila Array Consortium (INDAC) using a custom implementation of OligoArray2. The oligonucleotides were designed with size ranges between 65-69 nucleotides, a minimal Tm window, bias towards the 3’-ends of transcripts, and minimal sequence similarity to other genes. The oligonucleotide sequences can be downloaded from Flymine


title: 1.5 kb mouse promoter ChIP-chip (MM5, NimbleGen Systems Inc.)

status: Public on Aug 06 2008

city: Turku

first: Lea

last: Sistonen

address: Tykistokatu 6 B

country: Finland

institute: Åbo Akademi University

description:
NimbleGen Design information: Mouse promoter array based on build mm5
Design name: 2005-01-17_MM5_promoter


title: San Francisco State University Petrolisthes_cinctipes_6K_unigene_Array2

city: Tiburon

first: Jonathon

middle: H

last: Stillman

address: 3152 Paradise Drive

department: Romberg Tiburon Center

institute: San Francisco State University

organism: Petrolisthes cinctipes

first: Abderrahmane

last: Tagmount

manufacture_protocol: Spotted PCR products


title: Rosetta/Merck Mouse 430 2.0 RSTA Custom CDF microarray

city: Seattle

first: Amit

middle: V

last: Kulkarni

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description:
Oligonucleotide array on glass.
Contains 60-mer probes (60-mer).
Mouse 430 2.0 RSTA Custom CDF microarray Merck

first: John

last: Castle

manufacture_protocol: This identical to GPL1261 (Affymetrix GeneChip Mouse Genome 430 2.0 Array) but a custom CDF environment was used to extract data. The custom CDF can be found at the link below.


title: Rice Oligonucleotide Array NSF45K-ISU-2

status: Public on Jun 11 2008

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

organism: Oryza sativa

description: This is the 2nd platform for ISU Rice Oligo Array.

manufacture_protocol: The ISU microarray facility printed this platform on UltraGap slides (Corning Life Sciences, Cat. No. 40015) using a PixSys 5500 arrayer (Cartesian Technologies, Irvine, CA). Oligonucleotides were synthesized by Integrated DNA Technologies (Coralville, IA). The platform contains a total of 21,120 spots, though 384 spots were left unfilled. The platform contains two fields named 1 and 2, separately. Field 1 contains 8(meta rows)x4(meta columns)x22(rows)x22(columns) for a total of 15,488 spots. Field 2 contains 4(meta rows)x4(meta columns)x16(rows)x22(columns) for a total of 5,632 spots.


title: Solanum tuberosum 12.3K RLP array Version I

city: Seibersdorf

first: Friederike

last: Trognitz

state: NÖ

address: Seibersdorf

department: Health & Environment

country: Austria

institute: AIT Austrian Institute of Technology GmbH

organism: Solanum tuberosum

first: Jan

last: Rodewald

first: Michael

last: Stierschneider

first: Bodo

manufacture_protocol:
The microarray was based on an enriched, full length cDNA library of S. tuberosum var. Yungay, which had been challenged with Phytophthora infestans complex race for four days. The library was made by VERTIS GmbH (Freising, Germany). The cDNA was inserted to the EcoRI/NotI digestion site using vector pBS IIsk+ and transformed into TransforMax TM Ec100TM-T1 electrocompetent cells. Plasmid DNAs of 3840 clones were obtained by adding a small portion of bacterial culture into TempliPhi DNA Sequencing Template kit (GE Healthcare) according to the manufacturer’s instructions. Inserts were amplified by PCR in 50 µl reactions containing 0.5 µl of a 1:100 dilution of the TempliPhi, 5mM dNTPs (Invitrogen, Oslo, Norway), 2.5 mM MgCl2, 1x BD buffer (Solis Biodyne), 0.5 µM each of primers T7 and T5, and 2 U of Firepol polymerase (Solis Biodyne, Tartu, Estonia). The amplification was done in a GeneAmp PCR System 2700 thermocycler (Applied Biosystems) under the conditions: 95°C for 1 min, 2 min at 50°C and 2 min at 72°C and 30 cycles consisting of 95°C 1min, 56°C 2 min and 72°C for 1 min and a final elongation step at 72°C for 5 min.
In addition to the Yungay cDNA library, another 1173 cDNA clones were ordered from the University of Arizona Genomics Institute corresponding to stress related genes and treated as described above and amplified with the corresponding primers. Furthermore, nine housekeeping genes were included. Gene and primer are listed in the array file (MIAMExpress). They were amplified by using 1 µl of cDNA from S. tuberosum var. Yungay in a mix containing 2.5 mM MgCl2, 0.25 mM dNTPs (Invitrogen, Oslo, Norway), 0.5 µM of each primer, 1x BD buffer (80mM Tris•HCl, 20 mM (NH4)2SO4) (Solis Biodyne, Tartu, Estonia) and 0.2 µl FirePol (Solis Biodyne, Tartu, Estonia) in a PCR reaction of 95°C for 1 min followed by 35 cycles with 95°C 1 min, 55°C 1 min, 72°C 1 min and a final elongation step for 10 min at 72°C.
Twenty µl of all amplicons were lyophilized and then dissolved in 10 µl spotting buffer (3xSSC and 1.5 M betaine). Probes were spotted in duplicate with an Omnigrid 100 (GeneMachines) equipped with 48 TeleChem pins on CAPS II coated slides (Corning) in a 200 µM spot distance and 40% humidity.


title: PICME Sweetpotato 15K Series 1

status: Public on Feb 16 2008

first: Dieter

last: Kopecky

address: Campus Seibersdorf

department: Biogenetics/Natural Resources

institute: Austrian Research Centers GmbH - ARC

organism: Ipomoea batatas

description:
Material generated by Centro Internacional de la Papa - CIP.
This platform represents all slides of the Series 1, i.e. 1_1, 1_2 and 1_3, which are fully identical in their properties except the lot number.
PICME Sweetpotatoe 15K 1_1 uses lot numbers: 19505000B, 18005000B
PICME Sweetpotatoe 15K 1_2 uses lot number: 29205000B
PICME Sweetpotatoe 15K 1_3 uses lot number: 34705000B
Support: Corning GAPS II; Coating: Gamma Amino Propyl Silane
Number of spots: 29.952
Number of pins/blocks: 48
Spottdistance in µm: 170
Recurrances spots/slide: 2
Number of spots vertical: 25
Number of spots horinzontal: 25
Vertical offset of first block in µm: 1200
Horizontal offset of first block in µm: 3150

manufacturer: Austrian Research Centers GmbH - ARC, PICME

first: Silvia

last: Fluch

manufacture_protocol:
Spottingbuffer: 3xSSC+ 1,5MBetain
Spottingplate setting: Biozym 10µl + 20µl
Arrayer Hardware: GeneMachines Omnigrid II
Arrayer Software: OmniGrid Gridder 2.2.13
Humidity: 40%
Dipping time in sec: 1


title: QIMR Haliotis asinina custom 5.5k cDNA array

city: Brisbane

first: Elizabeth

middle: A

last: Williams

state: QLD

address: St Lucia campus

department: School of Integrative Biology

institute: University of Queensland

organism: Haliotis asinina

manufacturer: Radiation Biology Laboratory, Queensland Institute of Medical Research (QIMR)

manufacture_protocol: Microarray chips were created by combining (i) a Haliotis asinina developmental cDNA library (egg to adult) of 4800 clones (Jackson & Degnan 2006), (ii) a H. asinina juvenile mantle tissue cDNA library of 672 clones (Jackson et al. 2006), (iii) several previously characterised abalone genes  (Giusti et al. 2000; O’Brien & Degnan 2000; O’Brien & Degnan 2002; Hinman et al. 2003; Jackson et al. 2005; Degnan et al. 2006; Jackson et al. 2006; Jackson & Degnan 2006; Gunter et al. 2007; Koop et al. 2007), plus (iv) 7 H2O negative controls, 1 PCR product negative control and 3 unique Amphimedon queenslandica (demosponge) clones designed to act as simultaneous positive, negative and orientational controls. Demosponge controls were positioned at positions G8 and H12 on all 60 plates, plus one other well corresponding to plate number (e.g. for Plate 1, A1, Plate 2 A2 etc). This resulted in a microarray chip with a total of 5541 elements spotted onto poly-lysine coated glass slides in duplicate using a GMS 417 Arrayer robot (Genetic Microsystems). Slides were washed post-printing as described in Woods et al. 2004.


title: UMCG_6KBAC_ARRAY

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

institute: Vrije Universiteit Medical Center

description:
Slide E from Scott-Nexterion (germany)
- Epoxysilane coated
- Printing of arrays using Biorobotics Microgrid II printer with 48 nanopins(www.matrixtechcorp.com)
- The arrays consist of 48 subgrids. Each BAC-clone is printed 4 times. Replicate spots are in same/ different subgrids.

first: K

last: Kok

first: P

last: van der Vlies

manufacture_protocol:
High throughput mini-BAC DNA isolation:
Protocol for four 96well plates:
Day1:
1. Add 500µl of LB to each well of a square well block using the multichannel stepper pipet.
2. Inoculate 1µl of the glycerolstock to each well and seal with a Breathseal Sheet
3. Shake at 37°C for 8h with 350rpm
4. Add 1000µl LB to a new 96 well block and inoculate 5µl of the starter culture and seal with a Breathseal Sheet
5. Shake at 37°C for 18h with 350rpm.
Day2:
6. Centrifuge for 7min at 3200 rcf
7. Remove supernatant by inverting the square well blocks above a waste container and remove remaining liquid on a paper towel.
8. Check the presence and absence of bacterial pellets. Use a internal control for a contamination check.
9. Add 30µl GTE, and carefully resuspend the pellet by pipetting 20 times up and down with a multichannel pipette and transfer the liquid into a new non skirted 96 well Microplate.
10. Add 60µl freshly prepared 0,2M NaOH, 1%SDS to each well of plate one.
11. Immediately after finishing one plate, seal it with a Micro-Amp Clear Seal and invert it very, very smoothly for two times.
12. Start to countdown 4min30sec when having inverted the first plate.
13. After 3min and 15sec centrifuge plate1 and 2 in order to spin down the liquid in the centrifuge (2000rpm for one second)
14. After 4min 30 sec start to add 50µl 7,5M Ammoniumacetate to each well of plate one, seal the plate again with a new Micro-Amp Clear Seal and carefully (!) invert the plate immediately after pipetting and put it on ice.
15. Start with the other microplates and repeat from step 11.
16. After finishing the last plate, incubate for 10 minutes on ice. Invert the plates smoothly after 3 minutes of incubating.
17. After 10min centrifuge all plates at 3200 rcf for 30 minutes at room temperature in the Beckmann Allegra centrifuge. Use the stacking tools when placing the microplates in the centrifuge.
18. Place a new 96-wells PCR plate in a rack, mount it on top of the each centrifuged old ones (A1 on A12) and quickly invert it.
19. Centrifuge again for 30min 3200rcf at room temperature.
20. Invert a second time as described at step 19 on a new non skirted 96 well Microplate.
21. Add 70µl isopropanol to each well, seal it with a tape pad and invert it very smoothly for three times.
22. Centrifuge again for 30min at 3200rcf and invert in order to remove supernatant (now the DNA is in the pellet).
23. Add 50µl 70% ethanol and seal it with a Micro-Amp Clear Seal as above
24. Centrifuge at 6000 rcf for 10min at room temperature
25. Invert to remove supernatant, beat several times against a clean tissue in order to completely remove the residual ethanol. Leave the plates inverted on a fresh tissue
26. Add 25µl MilliQ-water to each well, seal with an Adhesive PCR Foil Seal and put them in the refrigerator overnight to solve the DNA.
Day 3
Exonuclease Treatment:
27. Resuspend Exonuclease in 225µl solvent according to the manual of the Large-construct kit.
28. Add to each well 5µl of the following mix: 3µl NEB1, 0,6µl Exonuclease, 0,9µl ATP, 0,15µl RNase and 0,35µl H2O and mix carefully by smoothly pipetting five times up and down.
29. Incubate the plates at 37°C for 4-12h in a PCR machine.
30. Inactivate the exonuclease by heating up the reaction to 75°C for 10min.
Random amplification of BAC-DNA (DOP-PCR)
•Perform for each BAC/PAC-sample three Hot Start PCR reactions according this pipetting schedule:
Mix A 1 reaction:
10x reactionbuffer 3.5 μl
MgCl2 2.0 μl
dNTP's (4x25mM) 0.32 μl
DOP primer (100 pmol/l) 0.8 μl
BAC/PAC-DNA 1 μl
Milli Q water 27,4 μl
----------+
35 μl
Mix B
10x reactionbuffer 0.5 μl
Taq-polymerase 0.5 μl
Milli Q water 4 μl
----------+
5 μl
•Add Mix B to Mix A during the initial denaturation step of the PCR. The PCR is performed in a AB-thermal Cycler 9700 or in a 96wells MJ-Cycler using this program:
94°C 3 min.
94°C 1.5 min.
30°C 2.5 min. 10 cycles
Ramp to 72°C at 0.1 °C per second
72°C 3 min.
94°C 1.0 min.
62°C 1.5 min. 30 cycles
72°C 2.0 min.
72°C 8.0 min.
12°C hold
•Concentrate the PCR-products by precipitation:
-Pool the DOP1, DOP2 and DOP3 products.
-Add 1 μl of Glycogen and mix.
-Add 1 μl of 3M NaAc and 240 l ethanol.
-Spin 30 min. on 6000g in the Beckman Bench top Centrifuge.
-Wash with 100 μl 70% ethanol
-Spin for 10 min. on 6000g.
-Dry the DNA-pellet by spinning the plates upside down on 600rpm for 30s.
-Dissolve the DNA-pellet in 18 μl spotting buffer.
Alternatively it is possible to concentrate the pooled DOP-PCR products by filtrating through a MilliPore Multiscreen PCR filter plate, according to the manual supplied with the kit.
•The amplified BAC/PAC-DNA is now ready for arraying.
Array printing
1. Dissolve oligonucleotide probe or PCR product in the appropriate spotting solution to
obtain the recommended final probe concentration:
DNA Probes Final Spotting Concentration
Oligonucleotides 10 - 20 μM
PCR products 0.1 – 1 mg/ml
2. Transfer an appropriate volume of probes to a microtiter plate.
3. Set up the arrayer according to the manufacturer’s recommendations. If you were
previously using slides that were thicker than 1.0 mm, for optimal spotting you may
need to re-calibrate the distance between the slide surface and the spotting pins.
4. Print the substrates at 40-50% relative humidity at 20 to 25°C.
Dissolve oligonucleotide probe or PCR product in the appropriate spotting solution to
obtain the recommended final probe concentration:
DNA immobilization
1. Incubate printed microarray slides in humidity chamber at room temperature for 30
min (see appendix for details of how to prepare this chamber) to ensure quantitative
immobilization.
2. Proceed to washing.


title: MSU E. coli 6K Ver. 1.0.1

status: Public on Jun 15 2007

city: East Lansing

first: Thomas

last: Whittam

state: MI

address: 165 Food Safety & Tox

department: Microbiology

institute: Michigan State University

organism: Escherichia coli

manufacture_protocol: 70-mer oligos spotted in duplicate onto Corning UltraGaps slides.


title: Rice Oligonucleotide Array NSF45K-ISU-1

manufacture_protocol: The ISU microarray facility printed this platform on UltraGap slides (Corning Life Sciences, Cat. No. 40015) using a PixSys 5500 arrayer (Cartesian Technologies, Irvine, CA). Oligonucleotides were synthesized by Integrated DNA Technologies (Coralville, IA). The platform contains a total of 23,232 spots, though 192 spots were left unfilled. The platform contains two fields named 1 and 2, separately. Field 1 contains 8(meta rows)x4(meta columns)x22(rows)x22(columns) for a total of 15,488 spots. Field 2 contains 4(meta rows)x4(meta columns)x22(rows)x22(columns) for a total of 7,744 spots.


title: Eide Yeast zinc

status: Public on Jul 04 2008

city: Madison

first: CHANG-YI

last: WU

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: UW-Madison

organism: Saccharomyces cerevisiae

manufacturer: The Microarray Core Facility at University of Utah

manufacture_protocol:
1. The PCR amplification products of all the S. cerevisiae open reading frames (ORFs) were purchased from Research Genetics.
2. Each PCR product was reamplified and purified on glass fiber filter plates (Millipore).
3. The reamplified products representing 6000 ORFs (4% not represented) were diluted to 50% Me2SO and spotted in duplicate on 3-aminopropyl-methyldiethoxy silane-coated slides using a Generation III Microarray Spotter (Amersham Biosciences).