title: ENS SGDB Mus musculus NeuroDev v2.2

status: Public on Jun 30 2008

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

country: France

institute: École normale supérieure

organism: Mus musculus

technology: spotted DNA/cDNA

description:
NeuroDev mouse slides were designed using PCR products (produced by the transcriptome platform) that represent around 2000 cDNA by slide linked to the developement of the mouse nervous system. A large part of these clone are a subset of the NIA 15k collection where the clone name have been selected according to their implication in the central nervous system developpement.
Each clone has been spotted in duplicate
PCR products were amplified by the National Sequencing Center.

distribution: non-commercial

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: Applied Biosystems Customized TaqMan Low Density Array (Mouse) _ In vivo T cell gene expression

status: Public on Jun 27 2008

city: Birmingham

first: Karine

last: Serre

state: West Midland

address: Wolfson drive, Edgbaston

department: Infection and Immunity

country: United Kingdom

institute: University of Birmingham

technology: RT-PCR

description:
To probe T cell responses in vivo, naïve OVA-specific transgenic CD4 T (OTII) cells were transferred into normal mice and the chimeras were then immunized with specific forms of OVA driving either a Th1 or a Th2 type of immune responses. This was achieved respectively by following the response in the draining lymph node after immunizing subcutaneously, either with live attenuated Salmonella typhimurium engineered to express an OVA transgene, or alum-precipitated OVA.
Virtual platform listing 384 in vivo T cell polarization-related candidate genes investigated using RT-PCR.

distribution: virtual

first: Elodie

last: Mohr

first: Kai

middle: M

last: Toellner

first: Adam

middle: F

last: Cunningham

first: Samuel

last: Granjeaud

first: Roger

last: Bird

first: Ian

middle: C

last: MacLennan


title: Illumina Arabidopsis thaliana SBS inflorescence (polyA RNA)

status: Public on Jun 10 2008

city: Newark

first: Marcelo

middle: Ariel

last: German

state: DE

address: 15 Innovation Way

country: USA

institute: Delaware Biotechnology Institute

organism: Arabidopsis thaliana

technology: other


title: GIS-Mouse-Solexa-ChIP-seq

status: Public on Jun 12 2008

city: Singapore

first: Chia-Lin

last: Wei

address: 60 Biopolis Street #02-01

department: Genome Technology & Biology

country: Singapore

institute: Genome Institute of Singapore

description: Solexa sequencing


title: Hornfly Haematobia irritans EST array

status: Public on Jun 19 2008

city: Lubbock

first: Scot

last: Dowd

state: TX

address: 4321 Marsha Sharp Fwy

department: MBRI

institute: MBRI

organism: Haematobia irritans

technology: in situ oligonucleotide

description: Hornfly Haematobia irritans EST array

distribution: custom-commercial

middle: E

first: Felix

last: Guerrero

manufacture_protocol: Agilent sureprint technology


title: CampyChip4

status: Public on Jun 11 2008

city: Ottawa

first: John

middle: H

last: Nash

state: Ontario

address: 100 Sussex Drive

department: Institute for Biological Sciences

country: Canada

institute: National Research Council

organism: Campylobacter jejuni

description: Campylobacter jejuni microarray with amplicons corresponding to 1561 genes from strain NCTC 11168 and 238 additional genes from strain RM1221 plus 47 from strain 81-176 as well as selected genes from other strains. All genes are spotted in duplicate and sheared total genomic DNA from strain NCTC 11168 was used as a control.

first: Wendy

middle: A

last: Findlay

first: Brian

last: Agnew

manufacture_protocol: DNA microarrayer (Bio-Rad) equipped with a 48-pin print-heads that uses "quill" pin technology (TeleChem / ArrayIt).


title: Cotton Fiber Oligonucleotide Microarray.V1

first: Thea

last: Wilkins

address: 2500 Broadway,Campus Box 42122

department: Plant and Soil Sciences

institute: Texas Tech University

organism: Gossypium arboreum

technology: spotted oligonucleotide

description: Cotton fiber ESTs were generated from 7-10 dpa fibers from the diploid species, Gossypium arboreum L. cv. AKA8401, at the Cotton Functional Genomic Center (CFGC) at the University of California-Davis (UCD) (cfgc.ucdavis.edu). A Unigene (UG)/Non-redundant (NR) set of 13,947 quality-controlled consensus sequences that define the cotton fiber transcriptome during rapid fiber elongation was assembled by Arpat et al 2004. The UG/NR set was used for designing oligonucleotide probes. A set of 12,227 Oligonucleotides (70-mer) were designed and synthesized by Operon Technologies (Operon, USA). Besides the cotton fiber oligos, the array comprised 71 experimental controls (positives, negatives, internals), transgene and vector controls, six spike-inn controls (Alien Spike mRNA, Stratagene), and blank and buffer controls spotted and replicated ≥ 2. Additional controls included cotton sequences deposited in GenBank, but not found in fiber dbEST.

first: Bulak

last: Arpat

first: Magdy

middle: S

last: Alabady

first: Brad

last: Sickler

manufacture_protocol: Oligonucleotides (oligoNT [70-mers]) were synthesized by Operon Technologies against 12,227 NR fiber ESTs. The cotton fiber microarray platform was fabricated, at CFGC-UCD, by spotting oligo NTs (40 um) in 50% DMSO in duplicates on Corning Ultra GAPS II microarray slides in 23 X 23 subarrays using the Omni Grid arrayer (Genomic Solutions) equipped with 16 (4X4) MicroQuill pins (Majer Precision Engineering).Post-printing processing of slides to chemically cross-link oligomers was performed according to the slide manufacturer’s instructions.


title: TIGR_HUMAN_40k_cDNAarray_1

status: Public on Jun 21 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

organism: Homo sapiens

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 832 spots in a 26 column x 32 row arrangement.

manufacturer: The laboratory of Dr. Norman H Lee at The Institute for Genomic Research

manufacture_protocol: The TIGR_HUMAN_40k_cDNAarray_1 consists of 39,936 elements from the Research Genetics 40K sequence-verified clone human cDNA library. Purified cDNA amplicons were combined with printing buffer to a final buffer concentration of 50% DMSO. The 384-well printing plates were arrayed onto aminosilane glass slides (Corning UltraGAPS) on a custom -built microarray robot from Brooks Automation (Cambridge, MA). Printed arrays were UV cross-linked to ensure binding.


title: VUMC MACF human 19K oligo vSAE4

status: Public on Dec 31 2005

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description:
- oligonucleotide sequences are available via www.ensemble.org after agreeing to Compugen's conditions
- oligonucleotides were mapped by Ensembl to the NCBI35 version of the human genome

first: Paul

last: van den IJssel

first: Bauke

last: Ylstra

manufacture_protocol: The Human Release 1.0 oligonucleotide library, containing 18861 60-mer oligonucleotides representing 17260 unique genes as designed by Compugen (San Jose, CA, USA) was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). The oligonucleotides were dissolved at 10 µM concentration in 150 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink slides (Amersham Biosciences) using a SpotArray Enterprise non-contact microarray printer (Perkin Elmer). After printing slides were processed and blocked prior to use according to the manufacturer’s protocol.


title: Stanford mouse MEEBO oligo arrays, reannotated using MatchMiner

city: Stanford

first: Andrew

last: Gentles

state: CA

address: 1201 Welch Road

institute: Stanford University


title: Nevada Cancer Institute MM8 RefSeq Promoter tiling array 386K

city: Las Vegas

first: Yupo

last: Ma

state: NV

address: 1 Breakthrough Way

institute: Nevada Cancer Institute

description:
Source: UCSC
Build: MM8
Probe Length: 50-75mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
Recommended Storage: Store arrays desiccated at room temperature.

first: Jianchang

last: Yang

first: Li

last: Chai

first: Taylor

last: Fowles

first: Zaida

last: Alipio

first: Dan

last: Xu

first: Louis

last: Fink

first: David

last: Ward

manufacture_protocol: Please see NimbleGen website


title: YZU_E.Coli_152_V1.0

city: yangzhou

first: zhao

last: lixiang

address: 88 Daxue road

department: verterinary school

country: China

institute: Yanzhou university

organism: Escherichia coli

first: Huan

last: Haixia

first: Zhao

last: Lixiang

first: Gao

last: Song

manufacture_protocol:
The confirmed PCR products of those genes were precipitated with isopropanol and redissolved in DNA Spotting Solution (CapitalBio Corp. Beijing, China).  Each gene was printed on amino siland slides in triplicate to facilitate subsequent statistical analysis.  After printing, the slides were baked at 80 °C for 1h and stored dry at room temperature till use.
Prior to hybridyzation, the slides were rehydrated over 65 °C water for 10 seconds, UV cross-linked at 250 mJ/cm2.  The unimmobilized DNAs were washed off with 0.5% SDS for 15 min at 42 °C and SDS were removed by dipping the slides in anhydrous ethanol for 30 seconds.  The slides were spin-dried at 1,000 rpm for 2 min.


title: CNIO-CDC Ratónchip 23K v3

status: Public on Jun 26 2008

city: Madrid

first: Marcos

last: Malumbres

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

description: This chip contains both the NIA15K and the 7.4K clone sets from the National Institute on Aging http://lgsun.grc.nia.nih.gov/cDNA/cDNA.html, plus 800 additional clones specifically associated to cancer, angiogenesis, apoptosis, signal transduction and stress processes obtained either from the Fantom1 collection (RIKEN) or the I.M.A.G.E. Consortium (Research Genetics, Huntsville, AL).

manufacture_protocol: Probes were adquired from the NIA and RICKEN sets of mouse full-lenght cDNAs. Probes were checked by sequencing, aplified by PCR and spotted to the slides


title: DASL Custom Prostate Panel by Probe

status: Public on Jun 23 2008

city: Rochester

first: Robert

middle: B.

last: Jenkins

state: MN

address: 200 First Street SW

department: Laboratory Medicine and Pathology

institute: Mayo Clinic

technology: oligonucleotide beads

description:
Panel contains 526 probe sets (typically three probes/set).  Of these 481 were potentially prostate cancer relevant based upon markers of prostate cancer aggressiveness identified by a Mayo/University of Minnesota Partnership (PMID: 17376245) and previously published studies.
DASL Custom Prostate Panel by Gene may be viewed at GPL5873.
The GPL5831.dap file (linked as a Supplementary file at the foot of the record) is required by BeadStudio for processing Illumina image files.

first: Thomas

last: Kollmeyer

first: Tohru

last: Nakagawa

middle: B


title: UH/MARESH Murine_Operon_V3_V2_Combined_Array

status: Public on Jun 20 2008

city: Honolulu

first: John

last: Maresh

state: HI

address: 651 Ilalo

department: Medicine

institute: University of Hawaii

description: Standard protocol at UT Southwestern

manufacturer: UT Southwestern Medical Center at Dallas MICROARRAY CORE

first: Ria

last: Nag

middle: G

first: Ralph

middle: V

last: Shohet

manufacture_protocol: Standard protocol at UT Southwestern


title: Illumina Fly INDAC 35k Oligo

status: Public on Jun 14 2008

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

organism: Drosophila melanogaster

first: Wim

last: Brugman

manufacture_protocol: The Drosophila INDAC long oligoset (Illumina) containing 15456 oligos of 65-69 bp in length are printed on Amino-Silane Coated Corning UltraGAPS using a GenomicSolutions MicroGrid arrayer. Every oligo is printed from a standard identical concentration.


title: NIH Homo sapiens RAKE

status: Public on Jun 06 2008

city: Bethesda

first: Man Lung

last: Yeung

state: MD

address: 9000 Rockville Pike

institute: NIH

first: Man-Lung

first: Timothy

last: Myers

first: Guojian

last: Jiang

first: Kuan-Teh

last: Jeang

manufacture_protocol:
Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions ( http://www.genomicsolutions.com ) that is fitted with a printhead and 32 SMP3 print tips from Telechem ( http://www.arrayit.com ).
Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl).
The microarrays are printed on Epoxy Slides from Corning (Catalog # 40042) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: OSU-CCC (Ohio State University microRNA microarray v2),

manufacturer: Microarray Shared Resource, Comprehensive Cancer Center, The Ohio State University (OSU-CCC)

manufacture_protocol: Manufacured using GE Healthcare's CodeLink (TM) 3-D Gel Matrix Technology. CodeLink(tm) Activated Slides are designed to covalently immoblize amine-modified DNA for microarrays. The slides are coated with a 3-D surface chemistry comprised of a long-chain, hydrophilic polymer containing amine-reactive groups. This polymer is covalently crosslinked to itself and to the surface of the slide. The crosslinked polymer, combined with end-point attachment, orients the immobilized DNA, and holds it away from the surface of the slide. The 1x printing buffer consists of 50 mM sodium phosphate at pH 8.5. Codelink slides are manufactured by SurModics and were formally sold as 3D-Link(tm) Activated Slides. ¹ Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions that is fitted with a printhead and 16 SMP3 print tips from Telechem. The microRNA microarray probe set is based on 40mer oligonucleotides from Sigma-Genosys. ¹ Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normalized 25 micromolar concentration. The miRNA microarray spot densities are 200 microns (center-to-center). The microarrays are printed on Codelink Activated Slide (PN300011)) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing


title: Daphnia magna cDNA microarray ver. 2

status: Public on Jun 09 2008

city: Boston

first: Helen

last: Poynton

state: MA

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

organism: Daphnia magna

first: Xin

last: Guan

first: Darren

last: Bauer

first: Edward

last: Perkins

first: Chris

last: Vulpe

first: Patricia

last: Holman

manufacture_protocol:
The 5000 randomly selected cDNA clones from the Daphnia Genome Consortium (DGC) library were PCR amplified from the pDNR-LIB vector using the following primers: forward: AGTCGACGGTACCGGACATA and reverse: GCCAAACGAATGGTCTAGAAA.  An additional 2681 cDNAs were constructed at the US Army Engineer Research and Development Center in Vicksburg, MS.  Daphnia magna were exposed to twelve model toxicants for 24 h at the 1/10 LC50 and RNA was isolated using standard protocols for Trizoll (Invitrogen).  Forward and reverse subtracted libraries were created using the PCR-Select cDNA subtractive kit (Clontech).   cDNAs were cloned into the pCR4 vector using the pCR4-TOPO TA cloning Kit from Invitrogen.  PCR products were purified by ethanol precipitation and resuspended in distilled water. cDNA clones were printed onto lysine-coated glass slides (Cheung et al., 1999) by the UCB Nutritional Sciences and Toxicology genomics facility.
Cheung, V. G., Morley, M., Aguilar, F., Massimi, A., Kucherlapati, R. & Childs, G. (1999) Making and reading microarrays. Nat Genet. 21, 15-19.


title: HEEBO Human oligo array

city: Knoxville

first: Seung

middle: Joon

last: Baek

state: TN

address: 2407 River Dr

department: Pathobiology

institute: University of Tennessee

description: Two Color Printed Human Whole Genome Long-Oligo Array

manufacture_protocol: HEEBO long-oligo microarray slides were purchased from Microarray Inc. (Nashville, TN) based on a probe set designed by Illumina (San Diego, http://www.illumina.com) and Stanford University. The HEEBO long-oligo set contains about 39,000 probes for exonic regions and alternative spliced transcripts.


title: MRA-1001 Human miRNA Array versions 7, 9, and 10.1_071219

status: Public on Jun 05 2008

city: Grand Rapids

first: Eric

last: Kort

state: MI

address: 333 Bostwick NE

institute: Van Andel Research Institute

description: NOTE: This platform contains all the probes from three versions of the LC Sciences miRNA arrays: 7, 9 and 10.1_071219.  Naming conventions changed somewhat between platforms, so all variants are listed in this platform.

middle: J

manufacture_protocol: Microarrays designed for genome-wide microRNA expression profiling and built on the flexible and powerful µParaflo® microfluidic on-chip synthesis platform.  The current probe content comes from version 10.1 of the miRBase sequence database which was updated on December 19th, 2007.  (See the 10.1 release summary) (See a comparison to previous versions)


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array [MBNI v10 Entrez Gene ID CDF]

description: This array is identical to GPL570 but the data were analyzed with custom CDF environments created by the MBNI - The version 10 entrez gene ID CDF was used.

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

manufacture_protocol: see the Affymetrix website


title: ULB MEEBO Mouse 39K array version 1

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description:
Probes:
Constitutive Exonic Probes (30,125): that will recognize all known transcripts of a gene.
Alternatively Spliced / Skipped Exonic Probes (4,201): will recognize exons that are present in some, but not all transcripts of a gene.
Non Coding RNA Probes (196): recognizing non-protein coding transcripts (ribosomal RNAs, miRNAs).
BCR / TCR Genic / Regional Probes (372): recognizing transcripts from genes that undergo somatic rearrangement.
Mitochondrial Probes (13): recognizing mouse mitochondrion derived DNA sequences.
Transgenic / Cassette Probes (37): recognizing elements commonly used for transgenic constructs (e.g. GFP, YFP).
Murine Viral Probes (358): recognizing mouse viral pathogen sequences.
Controls:
Negative Controls (317 buffer only and 97): Buffer only and 97 random sequences are positioned throughout the set to assist in determining background.
Positive Controls (1,152): recognizing a small subset of mouse transcripts.
Doped Controls (1,916): recognizing non-mouse sequences that can be spiked into RNA samples.

first: M

last: Fero

manufacture_protocol:
The Mouse Exonic Evidence Based Oligonucleotide (MEEBO) array was developed by a group of researchers from Stanford and UCSF with collaborators from Rockefeller, Basel, and the Stowers Institute. The oligonucleotide set consists of 38,784 70mer probes that were designed using a transcriptome-based annotation of exonic structure for genomic loci.
Tip configuration : 48 tips (4x12)


title: Illumina Arabidopsis thaliana SBS inflorescence (small RNA)

city: Newark

first: Marcelo

last: German

address: 15 Innovation Way

institute: Delaware Biotechnology Institute


title: MIT Caenorhabditis elegans small RNA sequences (Illumina/Solexa)

status: Public on Jun 16 2008

city: San Francisco

first: James

middle: Graham

last: Ruby

address: 1700 4th Street QB3 s404

department: Biochemistry

institute: UCSF

organism: Caenorhabditis elegans


title: Affymetrix GeneChip Pasteurella multocida Array

status: Public on Jun 01 2008

city: Schwabenheim

first: Elena

last: Melnikow

address: Zur Propstei

department: Drug Discovery

country: Germany

institute: Intervet Innovation GmbH

organism: Pasteurella multocida subsp. multocida str. Pm70

description: This GeneChip probe array is a powerful tool for monitoring trascriptional regulation and antimicrobial agent response of P. multocida. The array represents the annotated genome of P. multocida strain PM70 and includes 2,014 protein-coding sequences and a representative of the ribosomal RNA cluster.

first: Hon

last: Tran

first: Volker

last: Spehr

first: Nikolas

last: Gunkel

first: Michael

last: Duszenko

first: Paul

last: Selzer

first: Heinz

last: Ullrich

manufacture_protocol: see manufacturer's web site


title: Print_1223

status: Public on Jun 24 2008

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

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


title: SKI D. melanogaster small RNA sequenced by Solexa

status: Public on Jun 02 2008

city: New York

first: Wei-Jen

last: Chung

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Sloan-Kettering Institute

last: Lai


title: Moniliophthora perniciosa 3.9K glass slides 2

status: Public on Jun 13 2008

city: Campinas

first: Jorge

middle: Maurício Costa

last: Mondego

state: SP

address: Cidade Universitária Zeferino Vaz s/n

department: Genetics and Evolution

country: Brazil

institute: UNICAMP

organism: Moniliophthora perniciosa

description: Glass slides containing whole genome shotgun reads from M. perniciosa. The array has 32 subarrays (8 rows by 4 columns), each subarray consisting of 11 rows by 11 columns.

manufacture_protocol: as described in Laboratorio de Genomica e Expressao protocols


title: dm0603B1

status: Public on Feb 28 2006

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

manufacturer: Jeremy Gollub; CCSR 2255, Stanford, California  94305; 650-736-0075; jgollub@genome.stanford.edu


title: dm0603B2


title: VUMC MACF human 6K BAC v45

status: Public on Dec 19 2005

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

institute: Vrije Universiteit Medical Center

description:
- clones were mapped to the UCSC July 2003 Freeze of the Human Golden Path (NCBI build 34)
- oncobacs were mapped using their overgo-primers and are available via www.ensembl.org

last: van den IJssel

first: Bauke

last: Ylstra

manufacture_protocol: as described in: Carvalho et al (J. Clin. Path.,2004, vol. 57, 644-646). DNA from the 1 Mb resolution Sanger BAC clone set, the OncoBac set, and in house clones of interest, supplemented with clones from the Children’s Hospital Oakland Research Institute (CHORI), amounting to a total of 5284 clones with known chromosomal positions, was isolated according to the CHORI protocol. Amplification of the DNA was done by ligation mediated polymerase chain reaction (PCR) according to Snijders et al. (Nat. Genet.,2001, vol.29, 263-264) and PCR clones were purified using Montage PCR μ96 filter plates (Millipore BV, Amsterdam, the Netherlands). Clones were spotted in triplicate at a concentration of 1 μg/µl, in 150 mM sodium phosphate (pH 8.5), on CodeLink™ slides (Amersham BioSciences, Roosendaal, the Netherlands), using an Omnigrid 100 microarrayer (Genomic Solutions, Ann Arbor, MI, USA) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). After printing slides were processed and blocked prior to use according to the manufacturer’s protocol.


title: KCL_PSD_C.elegans_19,873_v1.1

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

first: Matthew

last: Arno

first: Suresh

last: Swain

middle: R

manufacture_protocol: 19,873 amine modified 70 mer oligonucleotides (Array-Ready Oligo Set™ for the C. elegans genome, version 1.1; Qiagen) representing 20.445 transcripts of the C. elegans genome were spotted on UltraGAPS™ slides using a Genetix QArray 2 microarraying robot.


title: Cunningham Schistosoma mansoni 22K v1.0

status: Public on Jun 10 2008

city: Albuquerque

first: Anthony

last: Aragon

state: NM

address: Castetter Hall Room 214

institute: University of New Mexico

organism: Schistosoma mansoni

manufacture_protocol: Agilent in situ inkjet


title: UCD_Ronald_XOarray_5K_V2.0

city: Davis

first: Malinee

last: Sriariyanun

address: 451 East Health Sciences Drive

department: Plant Pathology

institute: University of California, Davis

organism:
Xanthomonas oryzae pv. oryzae KACC 10331
Xanthomonas oryzae pv. oryzicola BLS256

manufacturer: ArrayCore Microarray Facility at University of California, Davis

first: Young-Su

last: Seo

first: Ki-hong

last: Jung

first: Janice

last: Pfeiff

first: Hui-Hhsien

last: Chou

first: Adam

last: Bogdanove

first: Pamela

last: Ronald

manufacture_protocol:
Oligo Synthesis
Oligos used for spotting were commercially synthesized by IDT (http://www.idtdna.com). As a control, an oligo was designed by Picky to detect hph but not Xo genes. This potential spiking control was included in 2 well positions on each 384-well oligo synthesis plate except last plate with one hph position. Because the positions of this spiking control were randomized across plates, this oligo also serves as check for array printing.
Spotting
All work at ArrayCore is performed in a HEPA-filtered clean room environment to minimize contamination from airborne particles. Oligonucleotides were suspended in 1x Nexterion Spot solution at a final concentration of 20 µM and spotted onto epoxy-coated glass slides (Schott-Nexterion, USA). Oligonucleotides were spotted using a Lucidea Array Spotter (Amersham) in a humidity controlled spotting chamber (70%) at room temperature. Microarrays were deposited using 190 µm column and row pitches, and spot diameters averaged 80 µm under these conditions. After spotting, slides were allowed to sit at 70% humidity overnight at room temperature to maximize oligo binding. Microarrays were allowed to dry at ambient conditions and stored in the dark under Argon at room temperature until use. Slides and spotting plates were tracked using the array spotter’s built in barcode reader and the information was used to generate the gene array layout file of the spotted 5k Xo oligonucleotide microarray.
Amino-blocking Pre-treatment
Prior to hybridization process, oligos-spotted slides were pretreated with blocking step to remove unbound DNA-molecules and buffer substances from the slides by extensive washing to avoid any interference with subsequent hybridization experiments. Spotted slides were incubated in amino blocking solution (5 g succinic anhydride in 315 ml n-methylpyrrolidone, 35 ml 0.2 M sodium borate ph 8.0) at room temperature for 15 mins. Slides were placed in 0.1% SDS solution 20 sec and washed with nanopure water 20 sec 2 timesand then were transferred into the sodium borohydride block solution.
Sodium Borohydride Pre-treatment.
To minimize non-specific autofluorescence from the spotted material , slides were placed into a block solution containing 2x SSC/0.05% SDS/0.25% NaBH4 (Biochemical Technologies, USA) and incubated at 42°C for 20 min. Slides were transferred to 1x SSC for 5 min at room temperature and then sequentially washed with vigorous stirring using fresh 1x SSC (3 × 5 min, room temperature), 0.2x SSC (4 × 2 min, room temperature), and Nanopure water (1 × 2 min, room temperature). Slides were spin-dried (1000 rpm, 10 min) and stored under Argon until use.


title: Agilent- Whole Human Genome Oligo Microarray G4112A condensed

status: Public on Jun 30 2008

city: Woolloongabba

first: Liliana

middle: Beatriz

last: Endo-Munoz

state: Queensland

address: TRI, 37 Kent St

department: Diamantina Institute

country: Australia

institute: University of Queensland

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.
Arrays of this design have barcodes that begin with 16012391 or 2512391.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

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


title: CNIO-CDC RatónBAC 3K

city: Madrid

first: Marcos

last: Malumbres

address: Melchor Fernandez Almagro 3

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

manufacture_protocol:
Spotted BAC probes. This chip contains 3.000 BACs covering the mouse genome every 1 Mb.
BAC probes were checked by sequencing, aplified by PCR and spotted to the slides


title: CSMA [DpnII: Mus musculus] signature list

status: Public on Jun 27 2008

city: Hayward

first: Daixing

last: Zhou

address: 25861 Industrial Blvd

department: Bioinformatics

institute: Solexa

description:
Contains annotation and mapping information for canonical signatures
Unigene Mm.151 and mouse genome sequence (mm7) were used for the annotation


title: SAGE:17:NlaIII:Solanum phureja

last: GEO

organism: Solanum phureja

technology: SAGE NlaIII

description: This is a virtual platform for SAGE libraries generated for Solanum phureja using NlaIII as an anchor enzyme.


title: Homo sapiens microRNA 0.34K version 3

city: New Haven

first: Jun

last: Lu

state: CT

address: 10 Amistad St

department: Yale Stem Cell Center and Department of Genetics

institute: Yale University

description:
Capture oligonucleotides were crosslinked to uniquely-colored Luminex xMap beads, which serve as discriminators of probe identity
This set includes 320 oligonucleotides, designed based on miRBASE v7, as well as 20 control probes.
Many capture oligonucleotides also recognize miRNAs in Mus musculus and Rattus norvegicus

first: Hao

last: Zhang

first: Todd

last: Golub

manufacture_protocol: Luminex xMap beads were coupled with animo-labeled antisense oligonucleotides to microRNAs


title: DASL Custom Prostate Panel by Gene

city: Rochester

first: Robert

last: Jenkins

address: 200 First Street SW

department: Laboratory Medicine and Pathology

institute: Mayo Clinic

description:
Panel contains 526 probe sets (typically three probes/set). Of these 481 were potentially prostate cancer relevant based upon markers of prostate cancer aggressiveness identified by a Mayo/University of Minnesota Partnership (PMID: 17376245) and previously published studies.
DASL Custom Prostate Panel by Probe may be viewed at GPL5831.

first: Thomas

middle: M

last: Kollmeyer

first: Tohru

last: Nakagawa


title: Moniliophthora perniciosa 3.9K glass slides 1

first: Jorge

last: Mondego


title: UCSF_SC_ORF_Uberp10

city: Lexington

first: Gregg

middle: Brooks

last: Whitworth

state: VA

address: 204 West Washington St

department: Biology

institute: Washington and Lee Unversity

organism: Saccharomyces cerevisiae

first: Daniel

last: Coughlin

first: Jeffrey

last: Pleiss

first: David

last: Engelke

manufacture_protocol: Arrays were pin-printed using standard techniques. All protocols are available at http://cat.ucsf.edu/equipment/arrayer/


title: UHNMAC Homo sapiens SS-H19Kv8

city: Sherbrooke

first: Jean-François

last: Beaulieu

state: Québec

address: 3001, 12ème avenue nord

department: Anatomie & biologie cellulaire

institute: Université de Sherbrooke

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

distribution: commercial

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


title: Affymetrix Drosophila Genome Tiling Array 1.0F (Dm35b_MF_v02)

city: Chicago

last: Emerson

state: IL

address: 1101 East 57th Street

institute: University of Chicago

description: Because the original microarray design was unfinished before release 4 of the genome was published, reannotation was undertaken. All 6,553,600 probes were used as queries against the D. melanogaster release 4 Flybase genome with Megablast with a word size of 12. This type of search guarantees successful location of homology maintaining at least 15 (word size + 3) consecutive perfect matches. We kept probes exhibiting the following characteristics: for each probe, both forward and reverse complements are unique on the array; the probe matched the genome perfectly; each probe matched the genome at 100% identity; each probe hit the genome only one time.  We reported the position in the genome that the 13th basepair that the probe maps to, the muller element it maps to, the total number of guanine and cytosine basis in the probe, and the predicted melting temperature of the probe as calculated by the EMBOSS dan program.

manufacture_protocol: See manufacturer's website.


title: VUMC MACF human 5K BAC v22

first: Daoud

last: Sie

department: Pathology

first: Paul

last: van den IJssel

first: Bauke

last: Ylstra

manufacture_protocol: as described in: Carvalho et al (J. Clin. Path.,2004, vol. 57, 644-646). DNA from the 1 Mb resolution Sanger BAC clone set, the OncoBac set, and in house clones of interest, supplemented with clones from the Children’s Hospital Oakland Research Institute (CHORI), amounting to a total of 4678 clones with known chromosomal positions, was isolated according to the CHORI protocol. Amplification of the DNA was done by ligation mediated polymerase chain reaction (PCR) according to Snijders et al. (Nat. Genet.,2001, vol.29, 263-264) and PCR clones were purified using Montage PCR μ96 filter plates (Millipore BV, Amsterdam, the Netherlands). Clones were spotted in triplicate at a concentration of 1 μg/µl, in 150 mM sodium phosphate (pH 8.5), on CodeLink™ slides (Amersham BioSciences, Roosendaal, the Netherlands), using an Omnigrid 100 microarrayer (Genomic Solutions, Ann Arbor, MI, USA) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). After printing slides were processed and blocked prior to use according to the manufacturer’s protocol.


title: dm0603B2

status: Public on Sep 18 2006

city: Salt Lake CIty

first: Mark

last: Metzstein

state: UT

department: Human Genetics

institute: University of Utah


title: NIAID Pfab

status: Public on Feb 10 2005

city: Bethesda

first: Timothy

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

organism: Plasmodium falciparum

description: Printing by NIAID / Microarray Research Facility

manufacturer: NIAID Microarray Research Facility (NIH/NIAID)

manufacture_protocol:
Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions that is fitted with a printhead and 48 SMP3 print tips from Telechem.
Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved at 25um in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) .
The Pfab microarray printing configuration are 4x12, total 6804 oligos are replicated in 48 sub-arrays at 342 spots per sub array wit 18x19 format. Spot densities are 100 Microns, with dot spacing 220 micron (center-to-center).
The microarrays are printed on Epoxy Slides from Corning (Catalog # 40042) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.