title: D. pseudoobscura Male Head 454 2007

status: Public on Feb 14 2008

city: Chicago

first: Chung-I

last: Wu

state: IL

address: 1101 57th East

department: Ecology and Evoluation

country: USA

institute: University of Chicago

organism: Drosophila pseudoobscura

technology: other

distribution: virtual

manufacture_protocol: see www.454.com


title: AGENAE_TroutGeneric2_9216

status: Public on Apr 22 2006

city: Jouy-en-Josas

first: Sylvain

last: Marthey

address: Domaine de Vilvert Bat 320

department: Animal Genetics

country: France

institute: INRA

organism: Oncorhynchus mykiss

technology: spotted DNA/cDNA

description: spotted DNA/cDNA

distribution: non-commercial

manufacture_protocol: as described in Institute Labs manual


title: Mouse Small RNA 42K array

status: Public on Feb 22 2008

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

country: Canada

institute: Best Institute

organism: Mus musculus

technology: in situ oligonucleotide

description: small RNA array

distribution: custom-commercial

first: Edyta

last: Marcon

first: Gordon

last: Chua

first: Tim

last: Hughes

first: Peter

last: Moens

manufacture_protocol: see manufacturer's website


title: Identification of protein variations in closely related Salmonella serovars

status: Public on Feb 27 2008

city: London

first: Vesela

last: Encheva

state: Greater London

address: 61 Colindale Avenue

department: Centre for Infections

country: United Kingdom

institute: Health Protection Agency

organism: Salmonella enterica

technology: MS

description: Examination of protein expression patterns of closely related Salmonella serovars using 2D GE and MS/MS


title: XC3 (TCR beta-based oligonucleotide microarray)

status: Public on Feb 13 2008

city: Memphis

first: Deanna

middle: Cole

last: Naeve

state: TN

address: 332 N. Lauderdale

institute: St. Jude Children's Research Hospital

organism: Homo sapiens

technology: spotted oligonucleotide

description:
The Platform data table reflects a condensed representation of the multiply-printed oligos.
The full array layout (GPL4259_complete_layout.txt) is linked as a supplementary file at the foot of this record.

manufacturer: St. Jude Children's Research Hospital, Functional Genomics lab

first: Xiaohua

last: Chen

first: Gregory

middle: A

last: Hale

first: Geoffrey

last: Neale

first: James

last: Knowles

first: Raymond

last: Barfield

first: Yong-Dong

last: Wang

first: Deepak

last: Kaushal

middle: C

first: Clayton

middle: W

first: Rupert

last: Handgretinger

manufacture_protocol: The array contains 27 TCR Vbeta probes and 13 Jbeta probes. The oligonucleotides are 50-62-mer sequences for Vbeta genes and 38-56-mer for Jbeta genes designed according to published sequences by using Vector NTI 9.0.0 software. The similarity of the probes was analyzed with Vector NTI 9.0.0 software. Oligonucleotides were synthesized by using phosphoramidite chemistry and were purified by using a cartridge system (Applied Biosystems, Foster City CA) in the Hartwell Center for Bioinformatics and Biotechnology Macromolecular synthesis lab at St Jude Children’s Research Hospital. Oligonucleotides were resuspended in 3xSSC to a concentration of 40µM and printed on poly-L-lysine-coated 1x3-inch glass slides by using an Omnigrid microarray printer (Genomic Solutions, Ann Arbor MI) with 16 CMP4 pins (Telechem, Sunnyvale CA) in the Functional Genomics lab of Hartwell Center. Each oligonucleotide was printed 48 times with 12 consecutive spots in each of 4 different semi-random areas across the array. After printing, slides were rehydrated, snap-dried and cross-linked by using a Stratalinker (Stratagene, La Jolla CA) and blocked with succinic anhydride.


title: Chicken 44K custom Agilent microarray

status: Public on Feb 29 2008

city: College Station

first: Huaijun

last: Zhou

state: TX

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

organism: Gallus gallus

last: Zhu

first: Hsini

last: Chiang

first: Xianyao

last: Li

first: Ying

manufacture_protocol:
Analysis
Protocol
For use with Agilent Gene Expression oligo microarrays
Version 5.0.1
August 2006
See list of components or package insert for storage conditions


title: MSU_Rose_Env_Vir_v3

status: Public on Feb 28 2008

city: East Lansing

first: Mark

last: Wong

state: MI

address: 3 Natural Resources

department: Crops and Soil Sciences

organism: Viruses

first: Jean-Marie

last: Rouillard

first: Erdogan

last: Gulari

first: Joan

middle: B

last: Rose

manufacture_protocol:
Oligonucleotide probes are synthesized in-situ using conventional DMT-protected phosphoramidite chemistry. A photogenerated acid (PGA) is used instead of the conventional acid DMT deprotection step. In photogenerated acid deprotection, deprotection is initiated by directing light at selected three-dimensional chambers in microfluidic chips. Upon activation, acid forms in seconds, removing DMT group.
An incoming phosphoramidite nucleoside monomer is then coupled to the growing oligomer chain. The synthesis cycle is repeated for each additional monomer until an array of thousands of oligonucleotides is formed.


title: SIPPE Brassica napus 8.1K cDNA Microarray (v1.0)

status: Public on Feb 26 2008

city: Shanghai

first: Hong-Wei

last: Xue

state: Shanghai

address: 300 Fenglin Road

department: molecular genetics

country: China

institute: Institute of Plant Physiology & Ecology

organism: Brassica napus

description: The genechip is a glass-based cDNA chip. The chip has 8192 spots, including 8095 Brassica Napus genes, 81 blanks and 16 negative controls. The chip is divided into 32 sub-matrix. There is 16*16 spots in every sub-matrix. The distance between two spots is 0.281 millimeter.

manufacturer: United Gene Scientific Tech.(Group) Co., Ltd.

first: Guo-Zhang

last: Wu

first: Ya

last: Niu

first: Rui

last: Ye

first: Wen-Hui

last: Lin

first: Qiu-Ming

last: Shi

first: Xiao-Dong

last: Xu

first: Rao

first: Yu-Guang

last: Du

manufacture_protocol:
1、Amplify the insertions (in pBSF vector) by PCR using T3 and T7 primers;
2、Check the quality of the PCR products through electrophoresis;
3、Purify the products using isopropyl alcohol;
4、Dissolve the PCR products(in 96-well plates) in spotting buffer;
5、Transfer the products into 384-well plates;
6、Spotting the genechip using OmniGrid Arraying System with MicroQuill 2000 Pins;
7、Hydrate the chip for 30 min in Arraying System, dry the chip for 2 hour at room temperature;
8、Block the chip for 15 min with blocking buffer, wash it with water, dry it at room temperature.


title: SHFE2

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

manufacturer: Stanford Functional Genomics Facility,  Stanford School of Medicine

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


title: Keratinocyte Lab Mouse 112

status: Public on Feb 20 2008

city: Cambridge

first: Josema

last: Torres-Ibanez

address: Tennis Court Road

institute: Wellcome Trust Centre for Stem Cell Research

last: Torres

first: Fiona

middle: M

last: Watt

manufacture_protocol: A small scale cDNA microarray was carried out using NF-κB target gene array kit (Panomics, Inc., Redwood City, CA). A long sense-strand oligonucleotide for each of the 107 mouse genes that have been previously shown to be regulated by NFkB signaling pathway was spotted in duplicate on the nitrocellulose membrane. Biotinylated DNA was spotted along the right and bottom sides of the array membrane as control of the array. The arrays were performed according to the manufacturer’s instructions. Briefly, 20 micrograms of Total RNA extracted from ES cells grown in the presence or absence of Leukemia Inhibitory Factor were used to prepare biotin-labeled cDNA probes through incorporation of biotin-dUTP into cDNA via reverse transcription reactions. Each biotin-labeled cDNA probe was hybridized to an array membrane at 42°C overnight in a hybridization incubator. The membrane was washed after hybridization and subject to incubations with blocking buffer and subsequent streptavidin-conjugated horseradish peroxidase (HRP). The detection was carried out through chemiluminescence reactions and 10 seconds exposures to Kodak BioMax XAR films (Sigma, Dorset, UK).  The dots of the array were quantified through densitometric analysis using ImageJ (Rasband, W.S., ImageJ, U. S. National Institutes of Health, Bethesda,Maryland, USA, http://rsb.info.nih.gov/ij). The 2 spots intensities acquired for each gene were averaged to obtain the VALUE. Empty spots were used as background values. Ratio (minus:plus LIF) was used to determine the effect of ES cell differentiation on the gene regulation.


title: Agilent Mouse 11k Sense-Antisense Transcript Microarray

city: Tsuruoka City

first: Yuki

last: Okada

address: Nipponkoku 403-1, Daihouji

department: Institute for Advanced Biosciences

country: Japan

institute: Keio University

description: Mouse natural sense-antisense transcripts

first: Chiaki

last: Tashiro

first: Koji

last: Numata

first: Kazufumi

last: Watanabe

first: Hajime

last: Nakaoka

first: Naoyuki

last: Yamamoto

first: Kazue

last: Okubo

first: Rieko

last: Ikeda

first: Rintaro

last: Saito

first: Akio

last: Kanai

first: Kuniya

last: Abe

first: Masaru

last: Tomita

first: Hidenori

last: Kiyosawa

manufacture_protocol: See manufacturer's web site


title: ProtoArray Human Protein Microarray v3.0

first: Li

last: Li

address: 300 pastuer dr.,

department: Pediatric

technology: spotted peptide or protein

first: Persis

last: Wadia

first: Rong

last: Chen

first: Neeraja

last: Kambham

first: Maarten

last: Naesens

first: Tara

last: Skgdel

first: David

last: Miklos

first: Minnie

last: Sarwal

first: Atul

last: Butte

manufacture_protocol:
The ProtoArray® Human Protein Microarray is a high-density protein microarray containing thousands of purified human proteins for protein interaction screening. Each human open reading frame (ORF) is expressed as an N-terminal GST fusion protein using a baculovirus expression system, purified from insect cells, and printed in duplicate on a nitrocellulose-coated glass slide. The human proteins spotted on the microarray are expressed in insect cells using an optimized process to maximize the production of soluble recombinant proteins
in a high-throughput format (Schweitzer et al., 2003). Proteins are expressed at high levels in insect cells which are similar to mammalian cells with respect to protein folding and post-translational modifications such as phosphorylation and glycosylation (Bouvier et al., 1998; Hollister et al., 2002; Predki, 2003) in contrast to proteins expressed in E. coli. This allows protein interaction detection at a functional level.
http://www.invitrogen.com/protoarray


title: Rat Oligo array V3.0.5 27648 spots

city: Stockholm

first: Roxana

last: Merino

address: L8:01 karolisnka Hospital

country: Sweden

institute: Karolinska Institute

organism: Rattus norvegicus

description: Spotted 27K oligonucleotide microarrays. 70 mer gene specific oligonucleotide probes from Operon Rattus Norvegicus AROSv3.0.5

first: Carolina

middle: E

last: Gustavsson

last: Merino-Martinez


title: SHFA

first: Jonathan

last: Pollack


title: SHFS


title: IntegratedGenomics_Ecoli_14K_v12-1

status: Public on Feb 19 2008

city: Los Angeles

first: Jason

last: Ernst

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

organism: Escherichia coli

manufacture_protocol: As described in (Tong et al. 2004, Biochemical and Biophysical Research Communications, 322: 347-354): "unique cDNA fragments corresponding to each predicted ORF of E. coli MG1655 were produced by PCR amplification from genomic DNA. To ensure that each primer pair would amplify the most unique 200–350 base pair region within each ORF, the PCR amplification product sequences were compared with all others in the genome by BLAST analysis. Sequences producing the minimum E values, relative to all other ORFs in E. coli, were selected. Of the 4485 E. coli ORFs listed in the ERGO database [Integrated Genomic, Chicago, IL], unique primers were found for 4442 ORFs (sequences available upon request). Most of the remaining ORFs represent genes that are shorter than 240 bp. Thus, each predicted ORF of E. coli MG1655 was represented by a fragment predicted to minimally cross-hybridize with other E. coli MG1655 sequences. These fragments varied in length from 200 to 350 bp, with a median length of ~300 bp. After two rounds of PCR amplification the final products were purified on 384-well format ArrayIt PCR purification Kits (TeleChem International). PCR products were resuspended in 15 μl spotting buffer (3× SSC (1× SSC is 0.15 M NaCl plus 0.015 M sodium citrate), 1.5 M betaine) and printed in triplicate onto amino-alkylsilane coated slides (Sigma) with an OmniGrid arrayer (Gene Machines) equipped with Telechem SMP3 split pins. The DNA was cross-linked to the slides with UV light and baked in a vacuum oven at 60 °C for at least two hours. Residual salt and unbound DNA were removed by rinsing the slides with 0.5% sodium dodecyl sulfate and water. The slides were stored desiccated at room temperature until use." Note that this array design is the same as IntegratedGenomics_Ecoli_14K_v1-12 except for a reordering of the location of the probes.


title: Mouse tRNA 42k array

first: Tomas

last: Babak

description: tRNA array

first: Dan

last: Coughlin

first: C

last: Nihranz

first: Timothy

last: Hughes

first: DR

last: Engleke

manufacture_protocol: in situ - custom design


title: University of Washington Human original custom 2-plex 166K array, version 1

status: Public on Feb 17 2008

city: Seattle

first: Heather

last: Mefford

state: WA

address: 1705 NE Pacific St

department: Genome Sciences

institute: University of Washington

manufacture_protocol: per Nimblegen protocol


title: Compugen mouse 22K array (Adelaide)

city: Melbourne

first: Yi Mo

last: Deng

state: Victoria

address: Royal parade

department: Medicine

country: Australia

institute: University of Melbourne

manufacturer: Microarray Facilicty, University of Adelaide, Australia

first: Yi-Mo

manufacture_protocol: CompuGen Mouse OligoLibrary V2.0 comprising 21,991 65-mers representing 21,587 unique genes. Additional locally made control plate spotted. Spots printed onto Corning CMT-GAPS slides using a 4x16 pinhead robot. Each print head printed an array of 480 spots arranges as a 24 rows by 20 columns (23040 features per array). See the Adelaide Microarray Facility website for printing details.


title: INSA Lactococcus lactis IL1403 (lot de PCR n°1)

status: Public on Feb 23 2008

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

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

organism: Lactococcus lactis

description:
nylon membranes positively charged
8*12 cm

manufacturer: Eurogentec/Biochips Platform INSA Toulouse France

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 (4 deposits/ spot) in duplicate on positively charged nylon membranes (Roche) with a Biogrid spotter (Biorobotics) with a 4*4 pattern.


title: Emory_University Mouse-6 Expression BeadChip 47K

city: Atlanta

first: Colleen

middle: D

last: McCabe

state: GA

address: 615 Michael St

institute: Emory University

technology: oligonucleotide beads

description: The Sentrix Mouse-6 BeadChip can be used to study expression of over 47,000 mouse transcripts based on MEEBO, RefSeq and RIKEN FANTOM2 content. researchers can generate whole-genome expression profiles for 6 samples in parallel on a single BeadChip. Each array is composed of 3 micron features with average feature redundancy of 30-fold . All features are QCed by a sequential hybridization process called array decoding. The probes are fully screened all-full-length 50-mers and the assay requires 50-100ng of total RNA input.


title: IntegratedGenomics_Ecoli_14K_v1-12

manufacture_protocol: As described in (Tong et al. 2004, Biochemical and Biophysical Research Communications, 322: 347-354): "unique cDNA fragments corresponding to each predicted ORF of E. coli MG1655 were produced by PCR amplification from genomic DNA. To ensure that each primer pair would amplify the most unique 200–350 base pair region within each ORF, the PCR amplification product sequences were compared with all others in the genome by BLAST analysis. Sequences producing the minimum E values, relative to all other ORFs in E. coli, were selected. Of the 4485 E. coli ORFs listed in the ERGO database [Integrated Genomic, Chicago, IL], unique primers were found for 4442 ORFs (sequences available upon request). Most of the remaining ORFs represent genes that are shorter than 240 bp. Thus, each predicted ORF of E. coli MG1655 was represented by a fragment predicted to minimally cross-hybridize with other E. coli MG1655 sequences. These fragments varied in length from 200 to 350 bp, with a median length of ~300 bp. After two rounds of PCR amplification the final products were purified on 384-well format ArrayIt PCR purification Kits (TeleChem International). PCR products were resuspended in 15 μl spotting buffer (3× SSC (1× SSC is 0.15 M NaCl plus 0.015 M sodium citrate), 1.5 M betaine) and printed in triplicate onto amino-alkylsilane coated slides (Sigma) with an OmniGrid arrayer (Gene Machines) equipped with Telechem SMP3 split pins. The DNA was cross-linked to the slides with UV light and baked in a vacuum oven at 60 °C for at least two hours. Residual salt and unbound DNA were removed by rinsing the slides with 0.5% sodium dodecyl sulfate and water. The slides were stored desiccated at room temperature until use." Note that this array design is the same as IntegratedGenomics_Ecoli_14K_v12-1 except for a reordering of the location of the probes.


title: University of Washington Human custom 2-plex 166K array for 15q13 region, A1 version 1


title: Agilent Human 11k Sense-Antisense Transcript Microarray

first: Yuki

last: Okada

first: Chiaki

last: Tashiro

first: Koji

last: Numata

first: Kazufumi

last: Watanabe

first: Hajime

last: Nakaoka

first: Naoyuki

last: Yamamoto

first: Kazue

last: Okubo

first: Rieko

last: Ikeda

first: Rintaro

last: Saito

first: Akio

last: Kanai

first: Kuniya

last: Abe

first: Masaru

last: Tomita

first: Hidenori

last: Kiyosawa


title: D. simulans Male Head 454 2007

city: Chicago

first: Chung-I

last: Wu

address: 1101 57th East

organism: Drosophila simulans

manufacture_protocol: see www.454.com


title: University of Washington Human custom 2-plex 166K array for 15q13 region, A2 subarray version 1

first: Heather

last: Mefford


title: IAH Salmonella typhimurium whole genome 10K cDNA array version 1

status: Public on Feb 12 2008

city: Roslin

first: Michael

middle: Bryan

last: Watson

state: Midlothian, EH25 9PS

address: Roslin Biocentre

department: ARK-Genomics

institute: The Roslin Institute

organism: Salmonella enterica subsp. enterica serovar Typhimurium

first: Paul

last: Barrow

first: Philippa

last: Adams

manufacture_protocol:
Oligos were synthesised commercially and spotted to Epoxy-coated glass slides using a Microgrid II robot (Biorobotics) using previously published protocol [1]
1. Burton, J.E., et al., Development of a multi-pathogen oligonucleotide microarray for detection of Bacillus anthracis. Mol Cell Probes, 2005. 19(5): p. 349-57.


title: MSU/JMT Exiguobacterium sibiricum 70mer array v. 1.0

status: Public on Feb 11 2008

first: Debora

middle: Frigi

last: Rodrigues

address: 540 Plant and Soil Science Bldg.

department: Microbiology and Molecular Genetics

institute: Michigan State University

organism: Exiguobacterium artemiae 255-15

manufacturer: oligonucleotides were commercially synthesized without modification by MWG Biotech Inc. (High Point, NC), Dr. Zhou from University of Oklahoma spotted the oligos into arrays

manufacture_protocol: The design criteria of the 70 mer probes were as follows: (i) 85% sequence similarity, 18-base stretch, and -35 kcal/mol free energy for gene-specific probes; and (ii) 96% sequence similarity, 55-base stretch, and -90 kcal/mol free energy for group-specific probes. Based on those criteria, 2931 CDS had gene-specific probes; 25 CDS were covered by six group-specific probes; no qualified probes were selected for 22 CDS. In addition, 10 human and 10 Arabidopsis probes were designed as controls. All designed oligonucleotides were commercially synthesized without modification by MWG Biotech Inc. (High Point, NC). The concentration of oligonucleotides was adjusted to 100 pmol µl-1. Oligonucleotide probes prepared in 50% DMSO (Sigma Chemical Co., MO) were spotted onto UltraGAPS glass slides (Corning Life Science, NY) using a Microgrid II robotic arrayer (Genomic Solutions Inc., MI). Each oligonucleotide probe had two spots on a single slide.  Additionally, six different concentrations (5~300 ng µl-1) of genomic DNA were also spotted (four duplicates on a single slide) as positive controls. After printing, the oligonucleotide probes were fixed onto the slide by UV cross-linking at 600 mJ of energy (Corning Life Science, NY). The oligo design information provided in the supplementary file.


title: D. melanogaster Male Head 454 2007

institute: University of Chicago

organism: Drosophila melanogaster


title: Eurogentec Candida albicans 6k microarray (condensed)

city: Jena

first: Bernhard

last: Hube

address: Beutenbergstr. 11a

country: Germany

institute: Hans Knoell Institute

organism: Candida albicans

description:
C. albicans is an opportunistic yeast that causes severe infections in immunocompromised individuals. Infections can be localized, such as vaginal infections and oral infections, which cause a considerable degree of discomfort. In some patient groups, whose defense system is severely compromised (premature infants, leukemics, burnt persons, and Aids patients), the yeast can turn into a deadly pathogen causing systemic infections up to 50 % of the patients infected die as a result. Although fluconazole has been an effective drug for a number of years, resistance is increasing. Alternatives such as amphotericin B have serious drawbacks, including such side effects as nephrotoxicity and severe discomfort. Few new antifungals are on the horizon, and more knowledge about the mechanism of pathogenicity of fungi as well as about their general biology is crucial if new drug targets are to be identified.
MicroArray content (the physical array contains ~13k data features):
* 98 % of C. albicans genes were spotted twice in a single glass slide
* Tags (GFP, TAP, GST)
* Marker genes Kan, Leu2, LacZ
* Luciferase gene to spike mRNA samples
* Negative controls (intergenic regions)
* Cross hybridization S. cerevisiae genes having 70 %, 50 % and 30 % sequence identity with S. pombe genes cDNA quality controls
* Dynamic range controls
* Spatial hybridization controls

The GPL6453 data table is a condensed representation of the physical microarray (~13k features).

manufacture_protocol:
The C. albicans MicroArray has been developed in collaboration with the European Galar Fungail Consortium (www.pasteur.fr/recherche/unites/Galar_Fungail/).
The Stanford Genome Technology Center generated the nucleotide sequence data for C. albicans with fundings from the NIDCR, NIH and the Burroughs Wellcome Fund. Information about coding sequences and proteins were obtained from the CandidaDB database: www.pasteur.fr/recherche/unites/Galar_Fungail/CandidaDB/, which has been developed by the Galar Fungail European Consortium.
Specific primers were designed to amplify all 6039 putative ORFs. The primers were selected carefully to amplify only a specific region of each ORF.
Universal sequences of 15 bases were incorporated on the 5' of each specific forward and reverse primer.
The two-step PCR method has been employed to generate 5' amino-modified PCR for covalent attachment to the aldehyde-coated support. All the amplicons have an average length of 300 bp and they were controlled systematically by electrophoresis on 2 % agarose gels. Two independent probes per gene were selected to represent 34 genes. The MicroArray covers nearly 98 % of the annotated C. albicans genes and includes twelve mitochondrial genes, five intergenic regions, five S. cerevisiae genes and five genes for hybridization quality control, human glycerol-3-phosphate dehydrogenase and actin gene. We include in the MicroArray probes to evaluate the dynamic range of signal intensities, reverse transcription efficiency and spatial hybridization.
The C. albicans MicroArrays are manufactured by printing PCR amplicons suspended in optimized spotting buffer for high coupling efficiency of DNA to the most consistent aldehyde coated glass slides. This spotting chemistry provides us the highest hybridization intensities, which is a consequence of a better binding of the probe to the slides and their accessibility to the cDNA targets. We use ChipWriter™ Pro (Virtek) which is a high precision dispensing robot to spot the PCR products onto aldehyde glass slides. The robot is designed to collect 100 nl of DNA solution and to deposit 0.6 nl per spot. For C. albicans MicroArray, we use simultaneously 32 pins to place the spots in area of 3.6 x 1.8 cm. In order to generate high quality spots, the printing procedure is performed under a tight controlled humidity and temperature environment. This allows having the complete control on the spot morphology, the spot diameter and uniformity. This configuration of the robot generates 32 blocks, each containing 20 x 20 dots with 200 microns spacing center to center with a spot diameter of 100 microns.


title: Custom Tiling array of 920 regions (HG18)

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

first: William

middle: L

first: Raga

last: Krishnakumar

first: Matthew

middle: J

last: Gamble

manufacture_protocol: see NimbleGen website


title: Genotypic/UHN Human ss-H19K7 cDNA Array

status: Public on Feb 09 2008

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

distribution: commercial

manufacturer: Microarray Center - University Health Network (UHN) - The Toronto Medical Discovery Tower - 101 College Street - Rm 9-301 - Toronto, Ontario - M5G 1L7 - Canada

manufacture_protocol:
Human ss-H19K8, Arrayer used - SDD26, Slide type - Corning ultraGAP
Microarrays are printed on UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol and are ready-to-use. Most of the quantification packages available for microarray analysis require certain parameters in order to provide grids to mark off spots. Below are the required specifications for all our arrays. Specifications of array layouts are defined based on the slide barcode located on the bottom of the scanned image.
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. Negative control features include Arabidopsis, blank, and 3XSSC buffer.


title: NimbleGen custom murine genomic tiling array

city: Urbana

first: jun

last: cai

address: Springfield Ave, DCL

institute: UIUC

description: annotations based on mm5 genome build

first: Huck

middle: H

last: Ng

manufacture_protocol:
1.Contain probes interrogating 402 genes and 4 gene clusters at a 100bp tiling interval.
2.Sequences derived from 20 miRNA genes; 7 imprinted loci; 7 germ cell marker genes; 1 oocyte gene; 155 genes expressed in ES cells; 129 genes expressed in differentiated cells.
3.The single array contains more than 360,000 50mer probes selected from 57 megabases of murine sequence and we surveyed 50 kb surrounding each gene.


title: University Health Network Microarray Centre 19k human cDNA microarray

status: Public on Feb 10 2008

city: Toronto

first: Susan

last: Done

address: 610 University Ave

institute: Ontario Cancer Institute

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


title: High-throughput pyrosequencing of small RNAs in Arabidopsis thaliana

status: Public on Feb 25 2008

city: Norwich

first: Frank

last: Schwach

address: University of East Anglia

department: School of Computing Sciences

institute: University of East Anglia

organism: Arabidopsis thaliana

description: The dataset contains Arabidopsis thaliana endogenous small RNA sequences in the range 16 to 31 nucleotides. High-throughput sequencing was carried out at 454 Life Sciences. Please see www.454.com for details of the technology. Total RNA was extracted from mixed-stage flower buds grown under 16h light.

first: Rebecca

last: Mosher

first: David

last: Studholme

last: Baulcombe

manufacture_protocol: see manufacturer website www.454.com


title: SHGC

city: Stanford

first: Lucinda

last: Thompson

address: Fairchild Bldg., D035, 299 Campus Dr

department: Microbiology and Immunology, School of Medicine

institute: Stanford University

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


title: SHFT


title: RTSF Lactobacillus reuteri 2.3K v1.0

status: Public on Feb 05 2008

city: East Lansing

first: Robert

last: Britton

address: 6144 BPS Building  Michigan State University

organism: Limosilactobacillus reuteri

manufacturer: Michigan State University Research Technology Support Facility

first: Jeff

last: Landgraf

manufacture_protocol:
Oligos arrayed in low volume Greiner 384 well plates in 3X SSC at a final concentration of 30uM.
Arrays printed using a GeneMachines Omnigrid 100 robot with TeleChem Chipmaker 3 pins.
Printing conditions: room temperature, 60% humidity.
Oligo plates sealed with Erie Scientific Titer-Tops, placed in a zip-loc bag and stored frozen at -20C.


title: Genotypic/UHN Human ss-H10K8 cDNA Array

manufacture_protocol:
Human ss-H10K8, Arrayer used - SDD26, Slide type - Corning ultraGAP
Microarrays are printed on UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol and are ready-to-use. Most of the quantification packages available for microarray analysis require certain parameters in order to provide grids to mark off spots. Below are the required specifications for all our arrays. Specifications of array layouts are defined based on the slide barcode located on the bottom of the scanned image.
This set includes 10752 cDNA clones from the IMAGE consortium, single spotted array containing 10,752 characterized and unknown human ESTs. The clone set has been sequence-verified at the Microarray Centre and the sequences can be downloaded for validation. Negative control features include Arabidopsis, blank, and 3XSSC buffer.


title: P. gingivalis W83 microarray glass slides (version 2)

status: Public on Feb 01 2008

city: Gainesville

first: Paulo

state: FL

address: 1600 Archer Rd

department: Oral Biology

institute: University of Florida

organism: Porphyromonas gingivalis

manufacturer: J. Craig Venter Institute (TIGR - www.tigr.org)

manufacture_protocol: The microarrays consisted of 1,907 70-mer oligonucleotides representing 1,990 open reading frames. The full 70-mer complement is printed four times on the surface of each microarray slide. Additional details regarding the arrays are available at http://pfgrc.tigr.org/slide_html/array_descriptions/P_gingivalis_2.shtml.


title: Dehalococcoides ethenogenes strain 195 1.6K

city: Dübendorf

middle: R

last: Johnson

address: Uberlandstrasse 133

department: Environmental Microbiology

country: Switzerland

institute: Eawag

organism: Dehalococcoides mccartyi 195

first: Eoin

last: Brodie

first: Alan

last: Hubbard

first: Gary

last: Andersen

first: Stephen

last: Zinder

first: Lisa

last: Alvarez-Cohen

manufacture_protocol:
Prokaryotic midi format (format 100)
Affymetrix control probe-sets: 45
Dehalococcoides ethenogenes specific probe-sets: 1560


title: SHGE

status: Public on Nov 14 2007

city: Basel

first: Martin

last: Buess

state: CH

address: Petersgraben 4

department: Medizinische Onkologie

institute: University Hospital Basel


title: Osaka University E. coli O157 Sakai Oligo Array 5.5K ver2

city: Suita

first: Toru

last: Tobe

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine

institute: Osaka University

manufacturer: Molecular Gene Technics, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.

manufacture_protocol: Oligonucleotide probes were prepared for all the protein-coding genes on the O157 Sakai genome (5,447 genes in total).  Principles for the probe design were 60-mer in length and one probe per gene/CDS.  For each gene, we designed 60-mer probe except one 44 or 45-mer probes for 7 genes.  In total, 5447 probes were synthesized (Sigma-Aldrich Japan, Tokyo, Japan), and each probe was spotted onto poly-L-Lysine coated glass slides (SD10011; Matsunami Glass Ind., Osaka, Japan) using SPBIO (Hitachi Software Engineering, Tokyo, Japan).


title: SHFU


title: SHEX

status: Public on Oct 20 2007

city: Kiel

first: Paul-Martin

last: Holterhus

address: Campus Kiel, Schwanenweg 20

department: Pädiatrische Endokrinologie und Diabetologie

institute: Universitätsklinikum Schleswig-Holstein


title: UCD_Ronald_XOarray_5K_V1.0

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: Microarray Core Facility. University of California, Davis

first: Young-Su

last: Seo

first: Li

last: Wang

first: Jirapa

last: Phetsom

first: Ki-Hong

last: Jung

first: Michael

last: Shultz

first: H

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 to undergo to sodium borohydride pre-treatment.
Sodium Borohydride Pre-treatment.
To minimize non-specific autofluorescence from the spotted material (Raghavachari et al. 2003), 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: SHGF

organism: Homo sapiens


title: UHN cDNA microarray

status: Public on Jan 23 2008

first: Susan

last: Done

manufacture_protocol: see manufacturer's website


title: WashU Operon Array-Ready Yeast Oligo set (Yeast_V1.1.2)

city: Claremont

first: Laura

middle: L. Mays

last: Hoopes

address: 175 6th Street

department: Biology

institute: Pomona College

organism: Saccharomyces cerevisiae

description:
epoxy
full platform linked as supplementary file

first: Gloria

last: Yiu

first: Alejandra

last: McCord

first: Alison

last: Wise

first: Rishi

last: Jindal

first: Jennifer

last: Hardee

first: Allen

last: Kuo

first: Michelle

middle: Y

last: Shimogawa

first: Laty

last: Cahoon

last: Wu

first: John

last: Kloke

first: Johanna

last: Hardin

manufacture_protocol: Operon Array-Ready Yeast Oligo set was printed on epoxy slides according to the yeast gal file for 2005-6 on the GCAT website at: http://www.bio.davidson.edu/projects/GCAT/GCATprotocols.html#yeast


title: NCSU/FBG_Poplar_miRNA_v1.0

status: Public on Dec 31 2007

city: Raleigh

first: Ying-Hsuan

last: Sun

state: NC

address: 2500 Partners II, 840 Main Campus Drive

department: Forestry and Environmental Resources

institute: North Carolina State University

organism: Populus trichocarpa

first: Shanfa

last: Lu

first: Vincent

last: Chiang

manufacture_protocol: This is custom designed poplar miRNA microarray platform. Probes were designed based on the miRNA genes.


title: SHEL

status: Public on Oct 03 2007

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology


title: SHGI

first: Paul-Martin

last: Holterhus


title: Clostridium difficile 630/QCD32g58 array

city: Ithaca

first: Tavan

last: Janvilisri

state: NY

address: Veterinary Research Tower, College of Veterinary Medicine, Cornell University

institute: Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University

organism: Clostridioides difficile

description: The genome sequences of C. difficile 630 and QCD-32g58 were used as a source of the genes used in this study. The final arrays consisted of 13,824 spots corresponding to 4227 coding sequences present in both or either strains, with many genes represented by multiple spots. Genes that lacked unique regions were excluded (126 genes from the strain 630 and 34 genes from the strain QCD-32g58).

first: Yung-Fu

last: Chang

first: Joy

last: Scaria

manufacture_protocol: Oligonucleotides of 55 to 70 bp with a matched melting temperature of ~60 C were designed to be specific for each gene. The probes (70 mer) were synthesized (Operon) and suspended in 50% dimethyl sulfoxide and spotted as triplicates onto Corning UltraGAPS slides using a custom-built microarrayer and Telechem 946 pins at the Cornell University Microarray Core Facility (www.bigredspots.cornell.edu). Autoblank (buffer without oligos) was used as a negative control. The slides were processed according to the slide manufacturer’s instructions, using hydration and UV irradiation, and stored in a dark, dust-free environment.


title: SHFM2


title: SHEZ

status: Public on Aug 27 2007

city: San Francisco

first: Xin

last: Chen

institute: UCSF


title: Homo sapiens 0.9 K allele specific expression 1

status: Public on Jan 05 2008

city: Baltimore

first: Aik Choon

last: Tan

state: MD

address: 1650 Orleans Street, RM 1M86

department: The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins

institute: Johns Hopkins University

manufacture_protocol: See Supplementary file


title: SHEW


title: SHEU

status: Public on Aug 17 2007

city: Stockholm

first: Annika

last: Saaf

department: Department of Molecular Medicine & Surgery

institute: Karolinska Institute, Karolinska University Hospital, Solna


title: Agilent-016808 Custom Human 244K CGH Microarray

status: Public on Dec 23 2007

city: Santa Clara

first: Nick

last: Sampas

address: 5301 Stevens Creek Blvd

department: Life Science and Nanotechnology Department

institute: Agilent Technologies

description:
Agilent Custom Human 244K CGH Microarray consisting of 60-mer oligonucleotides mapped to UCSC hg17 human genome (NCBI build 35).
Reference: Bovee et al. Nature Genetics, 2007
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 FeatureNum column represents the Agilent Feature Extraction feature number.

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


title: GeneChip ENCODE01 1.0 Array - NCBI build 36

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The 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.

The supplementary files (linked below) also report the 500bp window start and end positions (and also sequence of 500bp unit region for used for analysis).

first: Kerstin

middle: S

last: Wendt

first: Keisuke

last: Yoshida

first: Takehiko

last: Itoh

first: Masashige

last: Bando

first: Birgit

last: Koch

first: Erika

last: Schirghuber

first: Hiroyuki

last: Aburatani

first: Jan-Michael

last: Peters

manufacture_protocol: Oligonucleotide probes are synthesized in situ complementary to each corresponding sequences. 22 base pair resolution array.


title: SHDP

status: Public on Aug 13 2007

city: Oslo

first: Therese

last: Sorlie

address: Montebello

department: Genetics

country: Norway

institute: The Norwegian Radium Hospital


title: SHFC


title: Atlantic halibut 40K Array

city: Halifax

first: Jason

last: Williams

state: Nova Scotia

address: 1411 Oxford Street

department: Institute for Marine Biosciences

institute: National Research Council

organism: Hippoglossus hippoglossus

first: Susan

last: Douglas

first: Michael

last: Reith

first: Miroslava

last: Cuperlovic-Culf

first: Adrian

last: Culf

manufacture_protocol:
Oligonucleotide DNA probes were designed from approximately 13000 available Atlantic halibut ESTs.  The majority of the ESTs were derived by sequencing from the 5’ end of clones from 13 different normalized libraries from eight different tissues and five different developmental stages (Douglas et al., 2007). All EST data have been deposited in GenBank (accession numbers EB029285-EB041700 & EB080851-EB080975), and preliminary annotations are available on the Pleurogene website (www.pleurogene.ca).  Additional unique ESTs from other research groups that were present in GenBank were also used.  Oligonucleotide probes wFere designed using ArrayDesigner software (Premierbiosoft, Palo Alto, CA, USA). Probe sequences were selected to have minimal secondary structure, a GC ratio between 40-60%, a melt temperature of 75 ± 5oC and to be 45-55-mer in length. Uniqueness of the selected probes was ensured by BLAST comparison against all of the ESTs and the zebrafish genome.
Halibut DNA probes were synthesized at the Atlantic Microarray Facility (Moncton, NB, Canada) by the phosphoramidite method at a 40 nmole scale on a Gene Machines PolyPlex 2 oligonucleotide synthesizer (Genomic Soutions, Ann Arbor, MI, USA). Isolated DNA was analyzed by ESIElectrospray ionisation-Mass Spectrometry using an Agilent VL1100MSD mass spectrometer (Agilent Technologies, Inc., Mississauga, ON, Canada). DNA of low quality was re-synthesized. In addition to the halibut probes, 1344 control spots containing buffer only, and 92 control spots containing an oligonucleotide specific to the chlorophyll synthetase G4 from Arabidopsis thaliana (GenBank Acc. U19382) were included.   Solutions (20 M) in sodium phosphate Schott-Nexterion Spot buffer (Schott, Jena, Germany) were prepared in 384-well plates (Genetix X7020)
and spotted in quadruplicate on epoxide microarray slides (Schott) to give 39936-feature microarrays. An OmniGrid 100 microarrayer (Genomic Solutions) equipped with SMT-S50 silicon print pins (Parallel Synthesis Technology, Santa Clara, CA, USA) was used.
Spotted microarrays were analyzed by SpotQC (IDT Inc., Coralville, IA, USA) for any defects in spotting that may have occurred. Microarrays were stored at room temperature in vacuum-sealed microarray pouches (Corning Inc., Corning, NY, USA).


title: SHDM


title: SHCU

first: Annika

last: Saaf


title: SHED

status: Public on Jun 28 2007

city: Paris

first: Karine

last: Clement

address: place du parvis Notre-Dame

department: Service de Medecine et Nutrition

institute: Hotel-Dieu


title: University of Pennsylvania/Nathanson Lab_HomoSapiens_4575 unique BACS_FGA042003

status: Public on Apr 21 2007

city: Philadelphia

first: Carmen

middle: Elisa

last: Oquendo

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

description: ULTRA GAPS (Gama Amino Propyl Silane)

manufacturer: Weber Laboratory/School of Medicine/University of Pennsylvania

manufacture_protocol:
This BAC array platform consisted of 4575 unique BACs spotted in-house on CorningCMT Ultra-Gap slides (Corning, USA) using two replicates printed on each slide. Details of array construction are described elsewhere (Greshock et al., 2004)
Greshock J, Naylor TL, Margolin A, Diskin S, Cleaver SH, Futreal PA, deJong PJ, Zhao S, Liebman M, Weber BL. 2004. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 14(1):179-87.


title: SHEY


title: SHDX


title: NGEL miRMAX microRNA Oligo Microarray

status: Public on May 11 2007

city: Bryan

first: Rajesh

last: Miranda

state: TX

address: MREB, 8447 Riverside Parkway

department: Neuroscience

institute: Texas A&M HSC

organism:
Caenorhabditis elegans
Drosophila melanogaster
Homo sapiens
Mus musculus
Rattus norvegicus

description: Oligos designed by IDT

first: Ron

last: Hart

first: Jessica

last: Bowers

first: Loyal

last: Goff

first: Yang

last: Maocheng

first: Getts

last: Robert

first: Padgett

last: Richard

manufacture_protocol: contact NGEL


title: SHDS2

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


title: SHEF

status: Public on Mar 07 2007

first: Xin

last: Chen


title: Operon Human 21k Oligo Arrays

status: Public on Aug 15 2007

city: San Antonio

first: Xinyu

last: Wang

address: 3400 Rawley E. Chambers Ave., Bldg. 3611

institute: US Army Institute of Surgical Research

description: Spotted long oligonucleotide array using the Operon Human Genome Oligo Set Version 2.0

first: Phillip

last: Bowman

first: James

last: Bynum

manufacture_protocol: The Human Array Ready Oligo Set Version 2 contains arrayable 70mers representing 21,329 well-characterized human genes from the UniGene Database. This database is located at the National Center for Biotechnology Information (see www.ncbi.nlm.nih.gov/UniGene/). All 70mer oligonucleotides in the Human Genome Oligo Set Version 2 were designed after the representative sequences in the UniGene Database, Build Hs 147.The 70mers have also been Tm normalized to 78°C (±5 C). The Tm normalization allows for a more stringent hybridization at higher temperatures. When a 70-mer could not be designed within the specified Tm range, a shorter or longer length oligo was substituted to maintain the stringent Tm conditions. There are also 12 positive controls and 12 negative controls provided in 16 replicates.


title: Affymetrix S. cerevisiae tiling 1.0R (Sc03b_MR_v03.bpmap)

status: Public on Oct 16 2006

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

description:
Strain S288C
Design based on October 2003 cerevisiae genome

manufacture_protocol: Affymetrix


title: Eurogentec Candida albicans 13k microarray

status: Public on Jan 31 2007

city: Jena

first: Bernhard

last: Hube

address: Beutenbergstr. 11a

institute: Hans Knoell Institute

relation: Alternative to: GPL6453 (Condensed layout)

manufacture_protocol:
Construction of C. albicans MicroArray
The C. albicans MicroArray has been developed in collaboration with the European Galar Fungail Consortium (www.pasteur.fr/recherche/unites/Galar_Fungail/). The Stanford Genome Technology Center generated the nucleotide sequence data for C. albicans with fundings from the NIDCR, NIH and the Burroughs Wellcome Fund. Information about coding sequences and proteins were obtained from the CandidaDB database: www.pasteur.fr/recherche/unites/Galar_Fungail/CandidaDB/, which has been developed by the Galar Fungail European Consortium. Specific primers were designed to amplify all 6039 putative ORFs. The primers were selected carefully to amplify only a specific region of each ORF. Universal sequences of 15 bases were incorporated on the 5' of each specific forward and reverse primer. The two-step PCR method has been employed to generate 5' amino-modified PCR for covalent attachment to the aldehyde-coated support. All the amplicons have an average length of 300 bp and they were controlled systematically by electrophoresis on 2 % agarose gels. Two independent probes per gene were selected to represent 34 genes. The MicroArray covers nearly 98 % of the annotated C. albicans genes and includes twelve mitochondrial genes, five intergenic regions, five S. cerevisiae genes and five genes for hybridization quality control, human glycerol-3-phosphate dehydrogenase and actin gene. We include in the MicroArray probes to evaluate the dynamic range of signal intensities, reverse transcription efficiency and spatial hybridization.
Spotting design
C. albicans MicroArrays are manufactured by printing PCR amplicons suspended in optimized spotting buffer for high coupling efficiency of DNA to the most consistent aldehyde coated glass slides. This spotting chemistry provides us the highest hybridization intensities, which is a consequence of a better binding of the probe to the slides and their accessibility to the cDNA targets. We use ChipWriter™ Pro (Virtek) which is a high precision dispensing robot to spot the PCR products onto aldehyde glass slides. The robot is designed to collect 100 nl of DNA solution and to deposit 0.6 nl per spot. For C. albicans MicroArray, we use simultaneously 32 pins to place the spots in area of 3.6 x 1.8 cm. In order to generate high quality spots, the printing procedure is performed under a tight controlled humidity and temperature environment. This allows having the complete control on the spot morphology, the spot diameter and uniformity. This configuration of the robot generates 32 blocks, each containing 20 x 20 dots with 200 microns spacing center to center with a spot diameter of 100 microns.
MicroArray content
98 % of C. albicans genes were spotted twice in a single glass slide.
Tags (GFP, TAP, GST)
Marker genes Kan, Leu2, LacZ
Luciferase gene to spike mRNA samples
Negative controls (intergenic regions)
Cross hybridization S. cerevisiae genes having 70 %, 50 % and 30 % sequence identity with S. pombe genes
cDNA quality controls
Dynamic range controls
Spatial hybridization controls
Quality control
The C. albicans MicroArrays are certified to generate a high quality data.
All printed slides are previously selected for coating uniformity and low intrinsic background.
The MicroArrays are visually inspected for spotting quality (doughnuts), uniformity, integrity and for perfect alignment of spots and grids.
From each batch of printed MicroArray, three are randomly chosen for further quality control. We use the Terminal Transferase reaction to assess the amount of DNA covalently attached to the slides. Finally, we perform a real hybridization using labeled cDNA obtained from heat-choc cultured cells.


title: SHDQ

first: Therese

last: Sorlie


title: Agilent-014699 Mouse Genome CGH Microarray 105A (G4416A)

status: Public on Aug 15 2006

city: Palo Alto

last: Agilent Technologies

state: CA

organism: Mus musculus

description:
This kit provides two arrays per slide, each containing over 98,000 60-mer oligonucleotide probes. These probes, specifically optimized for copy-number measurement, span coding and non-coding genomic sequences with median spacing of 15.7 kb and 36.8 kb respectively. This microarray is designed for use with Agilent’s optimized assay protocols, enabling researchers to use nanogram levels of total genomic DNA without complexity reduction.

Arrays of this design have barcodes that begin with 16014699 or 2514699.

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: SHEA

last: Clement


title: Rice small RNA MPSS signatures

status: Public on May 26 2006

city: Davis

first: Blake

middle: C.

last: Meyers

address: 451 Health Sciences Dr.

department: UC Davis Genome Center

institute: University of California - Davis

organism: Oryza sativa

technology: MPSS

description:
small RNA MPSS signatures represent the 5' end of endogenous small RNA (e.g. miRNA and siRNA that average 21-24 nt). These molecules are typically associated with gene silencing, not mRNA expression.
All MPSS was performed essentially as described by Brenner et al. (Nat Biotechnol. 2000 18:630).
The specific modifications to the method for the MPSS sequencing of small RNAs are described in the paper Lu et al. (Science 2005, 309:1567).

middle: C


title: y10

status: Public on May 23 2006

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)


title: Agilent-014698 Human Genome CGH Microarray 105A (G4412A)

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

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

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column 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: University of Pennsylvania/Nathanson Lab_HomoSapiens_4798 unique BACS_FGA72904

status: Public on Apr 20 2007

last: Oquendo

description: ULTRA GAPS (Gama Amino Propyl Silane)

manufacture_protocol:
This BAC array platform consisted of 4798 unique BACs spotted in-house on CorningCMT Ultra-Gap slides (Corning, USA) using two replicates printed on each slide. Details of array construction are described elsewhere (Greshock et al., 2004)
Greshock J, Naylor TL, Margolin A, Diskin S, Cleaver SH, Futreal PA, deJong PJ, Zhao S, Liebman M, Weber BL. 2004. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 14(1):179-87.


title: University of Pennsylvania/Nathanson Lab_HomoSapiens_5217 unique BACS_FGA061005

description: Ultra GAPS (Gama Amino Propyl Silane)

manufacturer: Nathanson Laboratory/School of Medicine/University of Pennsylvania

manufacture_protocol:
This BAC array platform consisted of 5217unique BACs spotted in-house on CorningCMT Ultra-Gap slides (Corning, USA) using two replicates printed on each slide. Details of array construction are described elsewhere (Greshock et al., 2004)
Greshock J, Naylor TL, Margolin A, Diskin S, Cleaver SH, Futreal PA, deJong PJ, Zhao S, Liebman M, Weber BL. 2004. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 14(1):179-87.


title: AY7

status: Public on Jan 04 2006


title: ORF_intergenic_M

status: Public on Dec 30 2005


title: SHFE

status: Public on Aug 25 2006

first: Howard

last: Chang

address: CCSR 2142

department: Dermatology

institute: Stanford University


title: AY5

status: Public on Dec 21 2005


title: yB5

status: Public on Dec 15 2005


title: SHGS

status: Public on Apr 07 2007

city: South San Francisco

first: Adam

last: Adler

address: 1 DNA Way

institute: Genentech


title: YYN4

status: Public on Dec 03 2005


title: SHFC2

status: Public on Nov 01 2005

first: Hongjuan

last: Zhao

department: Urology, Edwards Building R116


title: Eurogentec S. pombe ORF array (B190D)

status: Public on Mar 19 2007

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

institute: Karolinska Inst

organism: Schizosaccharomyces pombe

first: K

first: T

last: Wright

first: D

last: Talibi

first: S

middle: A

last: Haas

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


title: SHDU


title: Agilent-014584 Human Genome 244K CGH Microarray (Alpha Test)

status: Public on Nov 09 2006

description:
Alpha test array -- final design is Agilent-014693, P/N G4411B.

Arrays of this design have barcodes that begin with 16014584 or 2514584.

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: SHDJ


title: SHFE3


title: SHES

status: Public on Oct 05 2006

first: Julie

middle: B.

last: Sneddon

address: Beckman Center, Room 400

department: Stanford Biochemistry

institute: Stanford


title: SHFM


title: SHFQ


title: SHFJ


title: y21-22

status: Public on Oct 15 2005


title: ORF_intergenic_B

status: Public on Sep 24 2005


title: SHDS


title: Agilent-013903 Human Proximal Promoter ChIP-on-Chip Set, Microarray 2 of 2 G4481A

status: Public on Aug 14 2006

description:
The Human Proximal Promoter ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to promoter regions spanning    -0.8KB upstream to +0.2KB downstream of the transcriptional start sites. The two slide set provides coverage for ~17,000 of the best defined human transcripts.

Arrays of this design have barcodes that begin with 16013903 or 2513903.

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: YB1

status: Public on Sep 10 2005


title: Human 32k tiling BAC array

status: Public on Sep 16 2005

city: Nijmegen

first: Joris

middle: Andre

last: Veltman

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: This set includes 32462 BAC clones, amplified by DOP-PCR, selected by fingerprint mapping to cover the entire human genome in a tiling fashion.

first: Eric

middle: F

last: Schoenmakers

first: Erik

last: Huys

first: Martin

last: Elferink

first: Walter

last: van der Vliet

first: Lisenka

middle: E

last: Vissers

first: Irene

middle: M

last: Janssen

first: Simon

last: van Reijmersdal

first: Leisink

last: Martijn

first: Rolph

last: Pfundt

first: Ad

last: Geurts van Kessel

manufacture_protocol: as described in MFN manual


title: YYM2

status: Public on Jul 23 2005

last: Stanford Microarray Database


title: SHCD

status: Public on May 08 2006

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A


title: Agilent-013902 Human Proximal Promoter ChIP-on-Chip Set, Microarray 1 of 2 G4481A

last: Agilent Technologies

institute: Agilent Technologies

description:
The Human Proximal Promoter ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to promoter regions spanning    -0.8KB upstream to +0.2KB downstream of the transcriptional start sites. The two slide set provides coverage for ~17,000 of the best defined human transcripts.

Arrays of this design have barcodes that begin with 16013902 or 2513902.

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: y19_&_y20

status: Public on Jul 22 2005


title: Operon Human V3.0.2 printed oligonucleotide array

status: Public on Mar 01 2007

city: Durham

first: Holly

middle: Kloos

last: Dressman

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University Medical Center

manufacturer: Duke Microarray Facility (manufactured printing of arrays)


title: y11 b


title: Spectral Genomics 2600

status: Public on May 04 2006

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

institute: Queensland Facility for Advanced Bioinformatics

description: The 2600 Human BAC Array contains 2,632 nonoverlapping BAC clones from the RPCI BAC library. Approximately 60 picogram of each BAC is spotted in duplicate. The BACs span the genome at approximately 1 Mb intervals. Genomic loci of all the BACs have been verified by Spectral Genomics by doing end sequencing from both ends, FISH verifying by at least a third party and by using the latest genomic build available. Spots are 250 microns across. Center to center spacing of spots is 300 microns. BAC arrays have been pre-treated and are ready for direct hybridization.


title: YYN2


title: RAKEv2

status: Public on Apr 25 2006

first: Don

last: Baldwin

address: 277 John Morgan, 3620 Hamilton Walk

department: Pathology and Lab Medicine

organism:
Arabidopsis thaliana
Homo sapiens
Mus musculus
Rattus norvegicus

description: Printed glass slide microarray for RNA-primed Array-based Klenow Enzyme assay for detection of microRNAs

manufacture_protocol: contact printing on CodeLink glass slides


title: y12 -

status: Public on Jul 21 2005


title: y6k_6400 b


title: SHT


title: AY4

status: Public on Dec 21 2005


title: SCA-A

status: Public on Jul 16 2005


title: SAGE:10:NlaIII:Gallus gallus

status: Public on Nov 30 2004

last: GEO

organism: Gallus gallus

technology: SAGE NlaIII

description:
This is a virtual platform for SAGE libraries generated for Gallus gallus using NlaIII as an anchor enzyme.
Platform_anchor: NlaIII


title: SHFB

status: Public on Nov 01 2005

first: Hongjuan

last: Zhao


status: Public on Apr 21 2005

city: Aarhus N

first: Karen

last: Koed

address: Brendstrupgaardsvej

department: Dept. of Clinical Biochemistry

country: Denmark

institute: Aarhus University Hospital, Skejby Sygehus

description: The Affymetrix GeneChip Mapping 10K Early Access Array enables genotyping of greater than 10,000 Single Nucleotide Polymorphism (SNP) loci on a single array. The SNPs on the array were chosen from The SNP Consortium (TSC) database. Technical information can be found at the Affymetrix website: http://www.affymetrix.com/support/technical/byprodukt.affx?product=10k Basically, the early access array has the same features as the GeneChip® Human Mapping 10K Array, but as it was an early version a few of the probes have been removed later due to poor performance.


title: SHER


title: SAGE:10:NlaIII:Meleagris gallopavo

status: Public on Mar 19 2003

organism: Meleagris gallopavo


title: SAGE:10:NlaIII:Sus scrofa

status: Public on Jun 01 2004

organism: Sus scrofa

description:
This is a virtual platform for SAGE libraries generated for Sus scrofa using NlaIII as an anchor enzyme.
Platform_anchor: NlaIII


title: SAGE:10:NlaIII:Medicago truncatula

status: Public on May 29 2002

organism: Medicago truncatula


title: SAGE:10:NlaIII:Arabidopsis thaliana

status: Public on Dec 04 2001

organism: Arabidopsis thaliana


title: SHEO


title: SHEB


title: y25

status: Public on Oct 15 2005


title: y24n

status: Public on Sep 24 2005


title: y7_1C

status: Public on Aug 24 2005


title: YYN3

status: Public on Jul 23 2005


title: y13 -


title: yB14n


title: yB7


title: yB8


title: yB4


title: SAGE:17:NlaIII:Gallus gallus

status: Public on Oct 04 2004

description:
This is a virtual platform for longSAGE 17 libraries generated for Gallus gallus using NlaIII as an anchor enzyme.
Platform_anchor: NlaIII


title: Human 6k Chip

status: Public on Mar 15 2005

city: Bethesda

first: Alan Lap-Yin

last: Pang

address: 49 Convent Drive, Room 2C08, MSC 4429

department: NICHD/LCG/SDG

institute: National Institutes of Health

description: Human 6000 cDNA Clones

first: Ekwere

middle: T

last: Ifon

first: Alan

middle: L

first: Warren

last: Johnson

first: Kathleen

last: Cashman

first: Sharon

last: Zimmerman

first: Sumitra

last: Muralidhar

first: Wai-Yee

last: Chan

first: John

last: Casey

first: Leonard

middle: J

last: Rosenthal


title: SAGE:17:NlaIII:Oryza sativa (japonica cultivar-group)

status: Public on Dec 08 2003

organism: Oryza sativa Japonica Group

description:
This is a virtual platform for SAGE libraries generated for Oryza sativa (japonica cultivar-group) using NlaIII as an anchor enzyme.
Platform_anchor: NlaIII


title: SAGE:10:NlaIII:Pinus taeda

status: Public on Aug 08 2003

organism: Pinus taeda


title: Florida

status: Public on Sep 10 2005

last: Stanford Microarray Database


title: University of Washington Human Itsara PWS 388K custom design array, version 1

status: Public on Feb 17 2008

city: Seattle

first: Heather

last: Mefford

state: WA

address: 1705 NE Pacific St

department: Genome Sciences

institute: University of Washington

organism: Homo sapiens

description: Ultra high-density coverage of Prader-Willi region on chr15

manufacture_protocol: manufactured per NimbleGen protocol. The design utilized b35 coordinates, with 385,000 spaced over 15258127bp, corresponding to a final probe density of 1 oligo per 39 bp.