title: JIC Arabidopsis thaliana 130K FCA FPA tiling

status: Public on Dec 31 2009

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

organism: Arabidopsis thaliana

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol: Affymetrix standard protocol


title: UW CombiMatrix Candidatus Accumulibacter phosphatis 12.5K

city: Madison

first: Shaomei

last: He

state: WI

address: 1550 Linden Drive

country: USA

institute: University of Wisconsin-Madison

organism:
uncultured bacterium
Candidatus Accumulibacter phosphatis

manufacture_protocol:
Please see manufacture's descriptions on line at:
http://www.combimatrix.com/tech_microarrays.htm


title: Yeast ncRNA and expression array 45K

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

organism: Saccharomyces cerevisiae

description: Array incorporates the probe set previously developed for analyzing ncRNAs from yeast (PMID 15920104).  Additional probes are included for estimating mRNA expression for ~6000 genes, previously predicted snoRNAs (PMID 17577407) and ncRNAs that were excluded from the original study.

manufacture_protocol: Custom in situ DNA synthesis on glass slides.


title: NimbleGen-Fusarium verticillioides-13K genes-60-mer-v1

city: Peoria

first: Robert

last: Butchko

state: IL

address: 1815 N. University St.

institute: U.S. Dept. of Agriculture

organism: Fusarium verticillioides

description: Array was designed based on a large EST library (Brown et al, Analysis of 87,000 expressed sequence tags reveals alternatively spliced introns in multiple genes of the fumonisin gene cluster, Fungla Genetics and Biology, 42:848-861) and the Fusarium comparative database at the Broad Institute (http://www.broad.mit.edu/annotation/genome/fusarium_verticillioides/MultiHome.html).

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


title: USC/XJZ Human 0.9 K miRNA-940-v1.0

city: Los Angeles

first: Juan

last: Nunez-Iglesias

state: CA

address: 1050 Childs Way, RRI-201

department: Computational Biology

institute: University of Southern California

organism: Homo sapiens

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


title: TIGR NSF rice oligonucleotide microarray A

city: Orono

first: Benildo

middle: G

last: de los Reyes

state: ME

address: 5735 Hitchner Hall

department: School of Biology and Ecology

institute: University of Maine

organism: Oryza sativa

technology: spotted oligonucleotide

description: About 45,000 oligonucleotides corresponding to ORFs encoded by the Nipponbare genome were printed on two separate glass slides (A and B).

distribution: non-commercial

manufacturer: The Institute for Genomic Research (TIGR)

first: Myoung-Ryoul

last: Park

first: Kil-Young

last: Yun

first: Venura

last: Herath

first: Bijayalaxmi

last: Mohanty

first: Song-Joong

manufacture_protocol: Oligonucleotides (~60-mer) corresponding to ORF in the Nipponbare genomic sequence were synthesized and printed on amine coated glass slides by TIGR. Microarray slides were purchased through the NSF rice oligonucleotide microarray project (UC Davis).


title: LC Sciences Human 454 miRHuman_8.2 [condensed version]

city: rome

first: Graziella

last: Curtale

address: viale regina elena 324

country: Italy

institute: "Sapienza" University of Rome

description: This array represents a condensed version of full array which is linked as a supplementary file.


title: Salmonella typhimurium LT2 1.1K

status: Public on Dec 25 2009

city: Fayetteville

first: Arunachalam

last: Muthaiyan

state: AR

address: 2435 N Hatch Ave

department: Food Science

institute: University of Arkansas

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

first: Scot

middle: E

last: Dowd

manufacture_protocol: Using the transcriptome of Salmonella Typhimurium LT2, an oligonucleotide microarray, made up of 43-45 mers, was designed. We choose 1152 genes, that were selected based upon their being associated with virulence or with regulation of virulence genes. Specifications of oligos were based upon various design characteristics such as temperature of melting, 3’ location, specificity, lack of repeat nucleotides, and other consideration as previously described. Oligos were synthesized and normalized in concentration by Integrated DNA Technologies Inc. (Coralville, IA). Oligos were resuspended in Epoxide Slide Spotting Solution and printed onto Epoxide Coated Slides (Corning Inc., Corning, NY) using a GeneMachine’s Omnigrid Accent microarray printer (Genomic Solutions Ann Arbor, MI). Each array also contains duplicate elements for each gene.


title: Arizona_Rice_45K_array

city: Cologne

first: Fernando

last: Andres

address: Carl von Linne 10

department: Plant Developmental Biology

country: Germany

institute: Max Planck Institute for Plant Breeding Research

first: David

middle: W

last: Galbraith

manufacture_protocol: The rice oligonucleotide microarrays are printed on aminosilane-coated “Superamine” slides (Telechem) or “Powermatrix” slides (Full Moon Biosystems), using Telechem Type SMP3 printing pins. Complete protocol description could be found at: http://ag.arizona.edu/microarray/methods.html


title: Bifidobacterium longum NCC2705 Agilent 11K

status: Public on Dec 21 2009

city: Lausanne 26

first: Bernard

last: Berger

address: Vers-Chez-Les-Blanc

department: Nutrition & Health

institute: Nestlé Research Center

organism: Bifidobacterium longum NCC2705

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


title: TIGR NSF rice oligonucleotide microarray B (seedling cold stress)

first: Richard

last: Bruskiewich


title: Custom Aedes aegypti OligoGEArray 500 series

city: Galveston

first: Saravanan

last: Thangamani

state: TX

address: 301 University Blvd

department: Pathology

institute: University of Texas Medical Branch

organism: Aedes aegypti


title: Univ of Montreal Illumina ratRef-12 v1.0 expression beadchip

city: Montréal

first: Luc

last: DesGroseillers

state: Québec

address: 2900 Edouard Montpetit

department: Biochimie

country: Canada

institute: Université de Montréal

organism: Rattus norvegicus

technology: oligonucleotide beads

description: The RatRef-12 Expression BeadChip includes twelve genome-scale, gene expression microarrays built using Illumina’s multi-sample Array of Arrays format. BeadChip content (22,226 probes per array) was selected from theNational Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database.

first: Maher-Laporte

last: Marjolaine

first: DesGroseillers

last: Luc

manufacture_protocol: See manufacturer's web site


title: Yeast 2.7M whole genome tiling array (Sc03b_MR_V04)

first: matteo

last: Pellegrini

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

distribution: commercial

first: Matteo

first: Guillaume

middle: F

last: Chanfreau

first: Tadashi

last: Kawashima

relation: Alternative to: GPL7250 (Alternative CDF [official])

manufacture_protocol: Affymetrxi protocol


title: Affymetrix GeneChip Human Genome U133 Array Set HG-U133A based on a custom CDF (GeneAnnot version 1.4.5)

city: Munich

first: Klaus

middle: H

last: Metzeler

address: Marchioninistr. 15

department: Department of Internal Medicine III

institute: University of Munich

description:
Affymetrix HG-U133A microarrays analysed with custom chip definition files based on the GeneAnnot database.
For further information, see Ferrari F, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli GA, Bicciato S.: Novel definition files for human GeneChips based on GeneAnnot. BMC Bioinformatics. 2007 Nov 15;8(1):446
We used Version 1.4.5 of custom CDF files and R packages based on GeneAnnot version 1.7 and GeneCards version 2.38, available online at http://www.xlab.unimo.it/GA_CDF/

manufacture_protocol: see manufacturer's web site


title: EBT UA Daphnia magna 1.2K version 1

city: Antwerp

first: Tine

last: Vandenbrouck

address: Groenenborgerlaan 171

department: Department of Biology

country: Belgium

institute: University of Antwerp

organism: Daphnia magna

technology: spotted DNA/cDNA

manufacturer: Laboratory for Ecophysiology, Biochemisty and Toxicology, University of Antwerp, Belgium

first: Anneleen

last: Soetaert

first: Nathalie

last: Dom

first: Wim

last: De Coen

manufacture_protocol:
This microarray is composed of 3 cDNA libraries which are the result of 3 SSH procedures. One SSH was performed with adult vs juvenile gene pools, one with ecdyson exposed vs control organisms and one with starved vs well fed organisms (Soetaert et al., 2006; 2007). In general, the differentially expressed genes were ligated in a TA-vector system using the pGEM-T easy vector (Promega, USA). Escherichia coli competent cells (JM109, Promega) were transformed through heat shock. Clones were amplified with vector specific primers (M13 forward and M13 reverse) and purified by an exosap reaction.
In preparation for spotting, cDNA-inserts of the clones were, amplified using adaptor specific primers (nested primers, Clontech), purified by Montage PCR Plate (Millipore, USA) and loaded into 384-well plates (Genetix, UK) in 50% dimethylsulfoxide at ~150 ng/µl. A Qarray Mini Robot (Genetix) with 16-solid pin-head was used to spot each clone in triplicate onto aminosilane coated glass slides (Generoma microarray slides; Asper Biotech, Estonia). In addition, a set of artificial genes control genes (Lucidea Universal Scorecard, Amersham Biosciences, UK) was spotted in 20 replicates spread over each array: 10 calibration controls, 8 ratio controls and 2 negative controls. After rehydration and drying, the slides were fixated by UV-radiation at 300mJ (UV Stratalinker 2400; Stratagene, USA).


title: JCVI PFGRC Campylobacter jejuni 23K array [full array version]

status: Public on Dec 28 2009

city: Ames

first: Yang

last: Wang

state: IA

address: 1113 Vet Med

department: VMPM

institute: Iowa State University

organism: Campylobacter jejuni

manufacturer: Pathogen Functional Genomics Resource Center

first: Jing

last: Han

first: Zhangqi

last: Shen

first: Jianzhong

first: Qijing

last: Zhang


title: TIGR NSF rice oligonucleotide microarray B

first: Benildo

last: de los Reyes

first: Myoung-Ryoul

last: Park

first: Kil-Young

last: Yun

first: Venura

last: Herath

first: Bijayalaxmi

last: Mohanty

first: Song-Joong


title: OGF MWG human 20K print-122

city: Dunedin

first: Aaron

last: Jeffs

address: PO Box 56

country: New Zealand

institute: University of Otago

manufacturer: Otago Genomics Facility, University of Otago, Dunedin, New Zealand

manufacture_protocol:
The oligos on this array are the commercial MWG Biotech human 50-mer 20K set (now owned by Ocimum Biosolutions). Five uL of oligo in 1 x MWG Spotting buffer A (cat no 1190-100100)  was transferred from 96-well source plates to each well of a Whatman polypropylene 384 well V-bottom well printing plate (cat no. 7701_5101). Oligos were printed at a concentration of 35uM.
Oligos were printed onto epoxy coated slides (Schott Nexterion slide E Cat no 1064016) by using an ESI SDDC-2 arrayer with Stealth SMP3 pins (Arraylt). Printing was carried out at room Temperature (18-25C) with humidity maintained at around 55%.
Between print runs, plates were dried at 37C, then stored at 4dC. Before re-use, the appropriate volume of MilliQ water was added to each well, and the dried oligo/buffer was re-dissolved overnight (the intial 5 uL volume was sequentially decreased by 0.25 uL/print to allow for the volume removed by printing). Plates were centrifuged briefly before printing.


title: NUIG_salmon_5K array_V1.0 (condensed array layout)

city: Galway

first: Michael

last: Cairns

address: University Road

department: NCBES

country: Ireland

institute: NUI Galway

organism:
Oncorhynchus mykiss
Salmo salar

description:
Platform data table reflects condensed array layout in which duplicate array features are represented only once.
ONLY CLONES OF INTEREST HAVE BEEN SEQUENCED AND IDENTIFIED
Every sequenced spot has a Genbank Accession Number associated with it.

manufacturer: Liverpool Microarray Facility, School of Biological Sciences, University of Liverpool,Crown St,Liverpool L69 7ZB

middle: T

first: Sophie

last: Hubert

first: Allan

middle: M

last: O'Keeffe

first: Aoife

last: Guiry

first: Samantha

middle: L

last: White

first: Denis

last: Flynn

first: Patrick

last: Forde

first: Olivier

last: LeProvost

first: Margaret

middle: A

last: Hughes

manufacture_protocol: The cDNA microarray contained clones from a number of Suppression Subtractive Hybridisation (SSH) cDNA libraries constructed from different salmon tissues (brain, pituitary, hypothalamus, head kidney, spleen, intestine, gill, testes and ovary) at different developmental stages related to sexual maturation, smoltification and embryo development. Of the 5376 cDNA clones, 4128 were newly generated subtracted cDNA clones and the remaining 1248 clones were other SSH or full-length clones from related salmonid projects. Several candidate genes and controls were also included. At the printing stage DNA sequences were only known for those clones that were used to check library quality/redundancy and for those clones that originated from related salmonid projects. Otherwise clones were only sequenced after microarray analysis had identified a differentially expressed gene. Printed slides consisted of duplicate arrays with sub-arrays in a 4 x 4 format with 336 spots per sub-array.


title: Affymetrix RML Custom Pathogenic chip 7

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

organism: Staphylococcus aureus subsp. aureus USA300

description:
NOTE 1: In general, probesets IDs containing .rc and .m are custom probe-designs covering short regions (intergenic, "non-coding") close to a defined open reading frame.

NOTE 2: GPL8069_probe_tab.txt.gz does not contain sequences

manufacture_protocol: standard Affymetrix protocol


title: University of Freiburg - Prochlorococcus microarray - MD4-9313 (MD4-9313a520062) version GC3.0

city: Freiburg

first: Claudia

last: Steglich

address: Schaenzlestr. 1

department: Biology

institute: University of Freiburg

organism:
Prochlorococcus marinus subsp. pastoris str. CCMP1986
Prochlorococcus marinus str. MIT 9313
Prochlorococcus phage P-SSM4
Tiamatvirus PSSP7

manufacturer: Custom-made high density antisense Affymetrix array

manufacture_protocol: The MD4-9313 array (MD4-9313a520062) is a custom-made high density antisense Affymetrix array. This array detects labeled cDNA that is antisense to the original RNA. It contains probes for the genomes of two cyanobacterial strains, Prochlorococcus MED4 and Prochlorococcus MIT9313. The array contains probe sets to detect all predicted open reading frames with probe pairs approximately every 80 bases. For short open reading frames (ORF), the length of the gap was reduced to ensure a minimum of 11 probe pairs per ORF where possible. Probes were designed for intergenic regions longer than 35 bases and were spaced every ca 45 bases on both strands. For short intergenic regions the gap between probe pairs was reduced to ensure a minimum of 4 probe pairs where possible. For some short sequences, where insufficient high performance probes were designed using this approach, the best probes possible were designed with no regard for their spacing along the genome feature.  Note that the annotation was modified (compared to GPL5471) based on the annotation of Kettler et al. 2007, PLoS Genetics.


title: NUIG_salmon_5K array_V2.0 (full array layout)

description:
Platform data table reflects full array layout in which all duplicate array features are represented.
For funding reasons only those spots identified in subsequent microarray analysis as interesting were sequenced
Every sequenced spot has a Genbank Accession Number associated with it.

relation: Alternative to: GPL8704 (condensed layout)


title: TIGR NSF rice oligonucleotide microarray A (seedling cold stress)

first: Benildo

last: de los Reyes

description: About 45,000 oligonucleotides corresponding to ORFs encoded by the Nipponbare genome were printed on two separate slides (A and B).

first: Myoung-Ryoul

first: Richard

last: Bruskiewich


title: NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 5a

status: Public on Dec 17 2009

city: Nijmegen

first: Gert Jan

last: Veenstra

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

organism: Xenopus tropicalis

description: JGI 4.1 (UCSC xenTro2)

manufacture_protocol: According to manufacturer's protocol (Roche Nimblegen)


title: Bacillus cereus ATCC 14579 - design 3

city: Wageningen

first: Mark

middle: de

last: Been

address: Bomenweg 2

department: Agrotechnology and Food Sciences Group

institute: Wageningen UR

organism: Bacillus cereus ATCC 14579

last: de Been

manufacture_protocol:
Agilent manufacture protocol.
Agilent uses its inkjet technology to print oligos onto glass slides.


title: NimbleGen Xenopus tropicalis Dedicated Promoter v1.0

description: JGI 4.1 (UCSC xenTro2)


title: NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 4

description: JGI 4.1 (UCSC xenTro2)


title: DiSteBa_Homo sapiens_Glioblastoma miRNA 340_v1.0

status: Public on Dec 19 2009

city: Lecce

first: Oscar

middle: Fernando

last: D'Urso

state: Lecce

address: provinciale Monteroni

department: Department of biological science

institute: Salento University

description: The substrates used were Nexterion Slide E epoxy slides.

first: Pietro

middle: I

last: D'urso

first: Pasqualino

last: Ciappetta

manufacture_protocol: Probe set relative to all miRNA were designed by means of ArrayDesigner4. Probes were purchased dry in 384 well plate and resuspended in 3X SSC as spotting buffer. Spotting was performed by means of SpottArray 428 (Perkin Elmer), under humidity range of 50%-60% with optimum setted to 55%. All probes were spotted in duplicate. After printing procedure slides were incubated in a 95% humidity chamber for 30'. After dry to 60° for 20 minutes slides were stored dry and light protected upon usage.


title: NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 3

description: JGI 4.1 (UCSC xenTro2)


title: At35bMR to Arabidopsis Tiling V04-2

status: Public on Dec 30 2009

city: New Haven

first: Hang

last: He

state: CT

address: 165 Prospect St

department: MCDB

institute: Yale University

organism: Arabidopsis thaliana


title: Texas A&M CodeLink Human Whole Genome Array

city: College Station

first: Tarun

last: Bansal

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A & M University


title: SAGE:19:MmeI:Apis mellifera

status: Public on Dec 18 2009

last: GEO

organism: Apis mellifera

technology: other

description: This is a virtual platform for SAGE libraries generated for Apis mellifera using MmeI as an anchor enzyme.

distribution: virtual


title: NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 5b

description: JGI 4.1 (UCSC xenTro2)


title: DKFZ human_naive_T_cells 7_samples v1.0

city: Heidelberg

first: Maximilian

last: Aigner

address: Im Neuenheimer Feld 280

institute: Deutsches Krebsforschungszentrum (DKFZ)

description:
Oligo GEArray 300 Series microarrays can contain up to 276 oligonucleotide spots (including control spots and blanks) which are printed on a 3,8 x 4,8 cm nylon membrane (12 colmns, 23 rows). All oligonucleotide probes are derived from a sequence located at a median distance of approximately 160 nucleotides from the 3’ end of the coding region. Furthermore, gene specificity, sequence complexity, secondary structure, melting temperature and GC content are rigorously evaluated using a SuperArray Bioscience Corporation-proprietary computer algorithm.
The customized Oligo GEArray COH-0005 described in this platform contains 247 different human gene probes, spotted on 253 positions (i.e. some genes are present in replicates) and 23 "non-human" control positions (e.g. sequences derived from E. coli, artificial sequences, or blanks).

manufacture_protocol:
For the Oligo GEArray microarrays the 60-mer oligonucleotide probes are printed on a positively charged, three-dimensional nylon membrane by synQADTM technology (one of the core technologies developed by Genomic Solutions, a Harvard Bioscience company, and marketed under CartesianTM Dispensing Systems). This advanced ink-jet, non-contact dispensing system (10 nL deposition volume only!) is known for its high spotting reproducibility.
The Oligo GEArrays are designed for one-time use only. Each array membrane (containing a unique bar-coded serial number on its reverse side) is packaged, stored and used in its own disposable hybridization tube.


title: NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 2

description: JGI 4.1 (UCSC xenTro2)


title: NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 5c

description: JGI 4.1 (UCSC xenTro2)


title: Pseudomonas fluorescens Pf0-1 chromosome array

city: Tokyo

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

country: Japan

institute: The University of Tokyo

organism: Pseudomonas fluorescens Pf0-1

description: This is an Affymetrix custom-commercial tiling array that covers thePseudomonas fluorescens Pf0-1 chromosome (RefSeq: NC_007492) at 11-bp density. BPMAP files are provided as supplementary files. PFO1b520543F-3-FWD.bpmap represents the forward strand of Pf0-1 chromosome, and PFO1b520543F-3-REV.bpmap represents the reverse strand of Pf0-1 chromosome.

manufacture_protocol: See manufacturer's web site.


title: NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 1

description: JGI 4.1 (UCSC xenTro2)


title: Chicken 44K custom Agilent microarray (2nd version)

first: Huaijun

last: Zhou

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

institute: Texas A&M University

organism: Gallus gallus

first: James

last: Zhu

first: Hsini

last: Chiang

first: Xianyao

last: Li

first: Ying

last: Wang

manufacture_protocol:
Two-Color Microarray-Based Gene Expression Analysis
Protocol
For use with Agilent Gene Expression oligo microarrays
Version 5.0.1
August 2006


title: Streptomyces coelicolor Affymetrix array

status: Public on Dec 14 2009

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

country: United Kingdom

institute: The Genome Analysis Centre

organism: Streptomyces coelicolor A3(2)

manufacture_protocol: Affymetrix genechip arrays were designed by Affymetrix with 13 25bp-oligos targeting each coding sequence. The array contained a total of 226,576 perfect match probes (oligos of length 25bp), including 8205 probe sets targetting coding sequences, 10834 intergenic probe sets (sense and antisense), and 3671 probe sets targetting predicted non-coding RNAs.


title: Applied Biosystems Human TaqMan Low Density Array (TLDA, v1.0)

city: Miami

first: Ricardo

last: Pastori

state: FL

department: Diabetes Research Institute

institute: University of Miami

organism: Homo sapiens

technology: RT-PCR

description: Microfluidic 384-well TaqMan real time RT-PCR platform version 1.0

manufacture_protocol: see manufacturer's website


title: ohlsson_mm6_dedicated

city: Stockholm

first: Rolf

last: Ohlsson

address: Nobels väg 16

department: Microbiology, Tumour and Cell biology

country: Sweden

institute: Karolinska Institute

organism: Mus musculus

description: Customized tiling array was designed based on our genome-wide 4C screening (data not uploaded) for mm6 assembly of mouse genome.


title: ARK-Genomics G. gallus 20K v2 (duplicated spots)

status: Public on Dec 15 2009

first: Haisheng

last: Nie

address: Marijkeweg 40

institute: Wageningen University

manufacturer: ARK-Genomics, Roslin Institute, Roslin, Midlothian, EH25 9PS, United Kingdom

manufacture_protocol: Oligos were resuspended in Corning Pronto Epoxide spotting solution to give a final concentration of 20uM. DNA was printed on Corning Epoxide slides using a Genomic Solutions MicroGrid II arrayer and the MicroSpot 10K pins, according to manufacturer's instructions. All printing was carried out in conditions of constant humidity (52% RH) and temperature (20C) in a room supplied with HEPA filtered air. Prior to printing the pins were cleaned by ultra-sonication in water and if necessary 50mM potassium hydroxide. A test print of all pins was carried out by printing Cy3 streptavidin conjugate dye in printing buffer onto epoxide slides and printing 100 features per pin. When all pins were printing consistent size spots for more than 80 features they were accepted as ready to print. The MicroGrid II was then programmed for the array print run, with a grid layout file prepared to allow duplicate printing atrandom within a patch. At the end of the print run the slides were removed following the program instructions in preparation for post processing. Slides dessicated overnight and then transferred to a humid chamber (45% humidity, 42C) for 8 hours. The slides were then washed in 0.2% SDS (room temperature) for 2 minutes with agitation before being rinsed in three water washes (30seconds, 30 seconds, 1 minute) with agitation. After these steps the slides were then incubated in water at 50C for 20 minutes before spin drying. The slides were then stored in a desiccator in the dark ready for use.


title: Custom Affymetrix Mycoplasma pneumoniae tiling array MPM129b520449F

status: Public on Dec 11 2009

city: Barcelona

first: Marc

last: Güell

address: C/ Dr.Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

organism: Mycoplasmoides pneumoniae M129


title: 85KBGL2V3 ROMA Custom Human Microarray

status: Public on Dec 16 2009

city: Cold Spring Harbor

first: Jude

last: Kendall

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description:
Representational Oligonucleotide Microarray Analysis (ROMA) array.
Genome build: NCBI Build 35, UCSC hg17.

first: Michael

last: Wigler

manufacture_protocol: Photolithography


title: PFGRC_BaumlerLabUCD_Salmonella_Version_4

city: Davis

first: Sebastian

last: Winter

address: One Shields Ave

department: MMI

institute: UC Davis

organism: Salmonella enterica

description:
Number of Grids: 48
Element Type: 70mer Oligonucleotide
Surface Coating: Epoxy
Oligonucleotides Designed: 5462
Replicate Oligo Printings: 5x

The Platform data table is a condensed representation of the array's replicate oligos.
The full array layout file (including oligo sequences) is linked below as a supplementary file. The full layout file was obtained from http://pfgrc.jcvi.org/index.php/microarray/array_description/salmonella_typhimurium/version4.html.

manufacturer: PFGRC / J. Craig Venter Institute (TIGR)

first: Andreas

middle: J

last: Baumler

manufacture_protocol: PFGRC protocol


title: IRCL Human Genome CGH Microarray 44B G4410B (probe version)

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description:
Human Genome CGH Microarray 44B, high-resolution, high performance 60-mer oligonucleotide, allowing genome-wide survey and molecular profiling of DNA copy number changes on a single chip.  It provides comprehensive genome-wide coverage with emphasis on the most commonly studied genomic regions and cancer-related genes.  It consists of ~43,000 60-mer oligonucleotide probes, empirically validated in multiple model systems, spanning coding and noncoding sequences with average spatial resolution of 35kb.  It replaces 44A (G4410A), includes all biological probes from 44A, mapped to the latest NCBI build, 35), plus an additional ~ 2,500 probes to expand coverage in the human genome.  Agilent has taken extra measures to design the microarray that truly represents the coverage and performance needed for this application.  Agilent has developed and optimized assay protocols that enable researchers to use nanogram levels of total genomic DNA without genome complexity reduction.

Arrays of this design have barcodes that begin with 16013282 or 2513282.

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


title: TNO/NimbleGen 60-mer 071112 Bacillus subtilis subsp. subtilis strain 168 4x72K array

city: Zeist

first: Remco

last: Kort

address: Utrechtseweg 48

department: Microbiology

institute: TNO

organism: Bacillus subtilis subsp. subtilis str. 168

description:
NimbleGen design name 071112_Bsub_168_EXP_X4 (each slide contains 4x72,000 probes). A gene expression design for 4,104 genes from B.subtilis subsp. subtilis strain 168 NC_000964 with eight probe pairs (PM/MM) per gene. Each probe is replicated 2 times. The design includes control probes.
Native array description files (ndf, ngd) are linked below as supplementary files.
Multiple different probe sequences per gene.  Probe sequences available in ndf file.

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


title: Gresham Agilent Saccharomyces Cerevisiae isothermal probes Mutation Detection

status: Public on Dec 10 2009

city: New York

first: David

last: Gresham

address: 100 Washington Sq East, 1009 Sliver Center

institute: New York University

organism: Saccharomyces cerevisiae

description: The array was designed using the reference genome of October 2005 obtained from SGD.


title: Oligo GEArray Human DNA Damage Signaling Pathway Microarray

city: Chongqing

first: yi

last: qing

state: Chongqing

address: No.10 Changjiangzhi Rd

department: Daping Hospital and Research Institute of Surgery

country: China

institute: Third Military Medical University

description:
The Oligo GEArray® Human DNA Damage Signaling Pathway Microarray profiles the expression of 113 genes involved in DNA damage signaling pathways. The genes associated with the ATR / ATM signaling network and transcriptional targets of DNA damage response are included on this array. Genes related to cell cycle arrest, apoptosis, and the stabilization and repair of the cellular genome as a result of DNA damage signaling are represented as well. Through a simple side-by-side hybridization experiment you can determine differential gene expression between your samples with this array.Total genomic DNA was spotted on 13 spots for positive control. Nothing was spotted on 2 spot with the aim of negative control. Therefore, a total of 15 spot data were already eliminated from the whole 128 spot data on this array.
HybTube Format.
>>> Functional Gene Grouping <<<
Apoptosis Genes: ABL1, BRCA1, CIDEA, CIDEB, GADD45A, GADD45G, GML, IHPK3, PCBP4, PDCD8, PPP1R15A, RAD21, TP53, TP73.
Cell Cycle Genes:
Cell Cycle Arrest: CHEK1, CHEK2, DDIT3, GADD45A, GML, GTSE1, HUS1, MAP2K6, MAPK12, PCBP4, PPP1R15A, RAD17, RAD9A, SESN1, ZAK.
Cell Cycle Checkpoint: ATR, BRCA1, FANCG, NBS1, RAD1, RBBP8, SMC1L1, TP53.
DNA Repair:
Damaged DNA Binding: ANKRD17, BRCA1, DDB1, DDB2, DMC1, ERCC1, ERCC3, FANCG, FEN1, GTF2H3, MPG, MSH2, MSH3, MSH4, MSH5, MSH6, N4BP2, NBS1, OGG1, PMS2L4, PMS2L9, PNKP, RAD1, RAD18, RAD51, RAD51C, RAD51L1, RAD51L3, REV1L, SEMA4A, XPA, XPC, XRCC1, XRCC2, XRCC3.
Base-excision Repair: APEX1, MBD4, MPG, MUTYH, NTHL1, OGG1, RAD51L3, UNG, UNG2.
Double-strand Break Repair: BRCA2, CIB1, FEN1, G22P1, KUB3, MRE11A, NBS1, PRKDC, RAD21, RAD50, RAD52, XRCC4, XRCC5.
Mismatch Repair: ABL1, ANKRD17, EXO1, MLH1, MLH3, MSH2, MSH3, MSH4, MSH5, MSH6, MUTYH, N4BP2, PMS1, PMS2, PMS2L4, PMS2L9, TP73, TREX1.
Other Genes Involved in DNA Repair: APEX2, ATM, ATRX, BTG2, CCNH, CDK7, CKN1, CRY1, CRY2, ERCC2, ERCC4, ERCC5, GTF2H1, GTF2H2, IGHMBP2, INPPL1, LIG1, LIG3, LIG4, MNAT1, NUDT1, PCNA, RAD23A, RAD23B, RAD54L, RPA1, RPA3, SUMO1, TREX2.


title: 85KBGL2V4 ROMA Custom Human Microarray


title: 454 GS 20 (Drosophila pseudoobscura)

status: Public on Dec 09 2009

last: GEO

organism: Drosophila pseudoobscura

technology: high-throughput sequencing


title: Agilent-021828 Unrestricted Mouse miRNA Microarray (miRNA_105_Dec08)

city: Guangzhou

first: Qin

last: Limei

address: North Third road

institute: SunYatsen University


title: EMBL Mycoplasma pneumoniae Operon Oligonucleotide Array

manufacture_protocol: A custom DNA array has been designed consisting of 688 70mers representing 688 annotated ORFs. The Mycoplasma pneumoniae array consists of oligos (70 bases, amino linker) spotted in the array four times each. The design and synthesis of the 688 oligos (probes) was performed by Operon and the spotting was done in EMBL Genomic Core Facility.


title: KINEXUS KAM-1.1 kinome array

city: Amsterdam

first: Anton

last: Horrevoets

address: van der Boechorststraat 7

department: Molecular Cell Biology

institute: VU University Medical Center

technology: antibody

description: phospho-protein-specific antibody array


title: MWG human 15k oligonucleotide microarray

city: Philadelphia

first: Ilsiya

last: Ibragimova

state: PA

address: 333 Cottman ave, w350

department: ICR

institute: Fox Chase Cancer Center

manufacture_protocol: see manufacturer's web site


title: Plants 4K miRNA LC_MRA-1038_miRNAPlants_11.0 + Bn_PsRNAs

city: Madrid

first: Anja

last: Buhtz

address: Campus de Montegancedo, M40,km38

institute: Centro de Biotecnologia y Genomica de Plantas

organism:
Physcomitrium patens
Pinus taeda
Populus trichocarpa
Arabidopsis thaliana
Brassica napus
Brassica rapa
Brassica oleracea
Glycine max
Medicago truncatula
Oryza sativa
Saccharum officinarum
Sorghum bicolor
Triticum aestivum
Zea mays
Vitis vinifera
Selaginella moellendorffii

description: Plant miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 11.0 and additional custom small RNA sequences from Brassica napus phloem sap (Bn_PsRNAs)

first: Julia

last: Kehr

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


title: Plants 4K miRNA LC_MRA-1038_miRNAPlants_10.0 + Bn_PsRNAs

organism:
Physcomitrium patens
Pinus taeda
Populus trichocarpa
Arabidopsis thaliana
Brassica napus
Glycine max
Medicago truncatula
Oryza sativa
Saccharum officinarum
Sorghum bicolor
Triticum aestivum
Zea mays
Selaginella moellendorffii

description: Plant miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 10.0 and additional custom small RNA sequences from Brassica napus phloem sap (Bn_PsRNAs)


title: SuperArray Mouse Th1-Th2-Th3 PCR Array PCR Array

status: Public on Dec 06 2009

city: Los Angeles

first: Chaim

middle: O

last: Jacob

address: 2011 Zonal Ave

department: Medicine/GI division

institute: University of Southern California

description: The Mouse Th1-Th2-Th3 RT² Profiler™ PCR Array profiles the expression of 84 genes related to the three classes of helper T cells (CD4+ T lymphocytes): Th1, Th2, and Th3. This array includes cytokine genes representative of Th1, Th2 and Th3 cells. The array also contains genes encoding transcriptional factors that regulate the expression of these cytokines as well as other markers of CD4+ T lymphocytes. Genes involved in immune cell activation, in the Th1 and Th2 type immune responses, and genes involved in the antimicrobial humoral response are included on this array as well as other immune response-related genes. Using real-time PCR, you can easily and reliably analyze expression of a focused panel of genes related to helper T cells with this array.

first: Haitao

last: Yang

first: Jacob

last: Chaim

first: Noam

first: William

last: Stohl


title: Huang Lab Human 9K CpG Island Spotted Array

status: Public on Dec 01 2009

city: Columbus

first: Samson

middle: T.

state: OH

address: 420 W. 12th Ave

institute: Ohio State University

manufacturer: Huang Lab using Affymetrix/GMS 417 Arrayer

manufacture_protocol: We used the Affymetrix/GMS 417 microarrayer to dot unpurified PCR products (~0.02 μl per dot 0.1μg/μl) in the presence of 20% DMSO as microdots (150-μm diameter spaced at 300 μm) on poly-L-lysine-coated microscope slides. Spotted DNA was denatured before use.


title: IOLR Lithognathus mormyrus 4608 v2.0

city: Haifa

first: Moshe

last: Tom

department: Marine Biology and Biotechnology

country: Israel

organism: Lithognathus mormyrus

description: Two identical arrays were printed on one 2.5 x 7.5 cm glass (GAPS II slides, Corning) on an area less than 6 x 2 cm. The grid system of each arrray includes 4 x 6 sub-arrays, each containing 9 rows and 15 columns, a total of 1620 unique spots in duplicates, totaling 3240 spots. Not all the spots contained usable DNA.

manufacturer: Moshe Tom's laboratory - Israel Oceanographic and Limnological Research, Haifa, Israel.

first: Yana

last: Yudkovski

first: Meirav

last: Auslander

manufacture_protocol: The protocol for preparation of the array is detailed in: Auslander, M., Yudkovski, Y., Chalifa-Caspi, V., Herut, B., Ophir, R., Reinhardt, R., Neumann, P.M., Tom, M., 2008. Pollution-affected fish hepatic transcriptome and its expression patterns upon exposure to cadmium. Mar. Biotechnol. 10, 250-261. However, the number of printed clones was reduced to 1152, maintaining the original designations of the platform. Two arrays were printed on one slide, each containing duplicates of the printed clones.


title: Gresham Agilent Saccharomyces Cerevisiae 30mer probes Mutation Detection

department: Biology


title: Winzeler Lab Plasmodium tiling array (Pftilingb520509)

city: La Jolla

first: Elizabeth

middle: Ann

last: Winzeler

address: 9500 Gilman Drive 0741

department: Pediatrics

institute: University of California San Diego

organism: Plasmodium falciparum

description: The probe mapping has changed from the original Affymetrix design since the genome assembly has changed. Pftiling_chrprobes_v6.0 contains the probe mapping information relative to the new genome assembly.  Pftiling_probeseqs.txt contains the probe sequence information, and the original .bpmap file from Affymetrix is also provided below.

manufacture_protocol: Whole genome tiling at 2-4 bp spacing, see manufacturer's website.


title: Nimblegen/AECOM Human HG18_HELP array

city: Bronx

first: Reid

last: Thompson

address: 1301 Morris Park Avenue

department: Molecular Genetics

institute: Albert Einstein College of Medicine

description:
Array based on the human genome (hg18), Mar 2006 release.
Custom DNA methylation microarray for the HELP assay, designed to cover 1,135,549 HpaII/MspI fragments of 50-2,000 bp in unique sequence throughout the human genome.

Native NimbleGen files (ndf, ngd, pos) are linked below as supplementary files.

manufacture_protocol: See Roche NimbleGen website ( http://www.nimblegen.com/products/methylation/ ).


title: Cavalieri-Yeast-ORF-7k Array

city: Torino

first: Irene

last: Stefanini

address: via Accademia Albertina

institute: University of Turin

manufacturer: Bauer Laboratory, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA

first: Duccio

last: Cavalieri

first: Keith

last: Morneau

manufacture_protocol: Yeast microarrays were constructed using the amplifying to levels required for preparation of DNA microarrays by PCR (27) a set of clones containing 6218 verified ORFs of the yeast genome obtained from Research Genetics (Huntsville, AL). Some of the longer ORFs were amplified with the GIBCO/BRL Elongase Amplification Kit (Life Technologies, Rockville, MD), using 40 cycles of 1 min at 95 °C denaturation, 1 min at 55 °C annealing, and 10 min at 68 °C elongation. We obtained an amplified product confirmed by agarose gel electrophoresis for 98% of the ORFs. The amplified DNA was precipitated with isopropanol, washed with 70% EtOH, and resuspended in 25 μl Micro Spotting Solution (Telechem, Sunnyvale, CA). The DNA was spotted on CMT-GAPS amino-silane-coated glass slides (Corning), using a microarraying robot with a 16-pin head constructed from a design by Patrick O. Brown (http://cmgm.stanford.edu/pbrown/).


title: Agilent-018586 Bobwhite Quail 15K Microarray

city: Hattiesburg

first: Arun

last: Rawat

state: MS

address: 118 College Drive # 5018

department: Biological Sciences

institute: University of Southern Mississippi

organism: Colinus virginianus


title: UCSF/Sil lab-Histoplasma capsulatum-G217Bprint2

city: San Francisco

first: Anita

last: Sil

address: 513 Parnassus, S-469

department: Microbiology & Immunology

institute: University of California San Francisco

organism: Histoplasma capsulatum

first: Catherine

last: Foo

first: Mark

last: Voorhies

first: Diane

last: Inglis

manufacture_protocol: Spotted using DeRisi arrayer in Center for Advanced Technology, Genentech Hall, Mission Bay.  70-mer oligonucleotides representing each predicted gene are resuspended in 3XSSC and spotted on poly-lysine slides purchased from Erie Scientific.


title: NimbleGen Rat RN4_HELPassay array

organism: Rattus norvegicus

description:
Array based on the rat genome (rn4), Nov 2004 release.
Custom DNA methylation microarray for the HELP assay, designed to cover 38,102 HpaII/MspI fragments of 200-2,000 bp in unique sequence throughout the rat genome.
Native NimbleGen files (ndf, ngd, pos) linked below as supplementary files.

manufacture_protocol: See Roche NimbleGen website


title: Aquilegia formosa x pubescens F2 population oligonucleotide microarray

city: Palmerston North

first: Claudia

last: Voelckel

address: Riddet Road

department: Allan Wilson Centre for Molecular Ecology and Evolution

institute: Massey University

organism: Aquilegia formosa x Aquilegia pubescens

description: NimbleGen design name 2006-05-15_Borevitz, NimbleGen design ID 3448. An isothermal set of oligonucleotide probes (3-35 probes per gene depending on length, Tm 76ºC) were designed for 17,276 Aquilegia genes (The Aquilegia Gene Index, version 2.0, http://compbio.dfci.harvard.edu/cgi-bin/tgi/gimain.pl?gudb=aquilegia) resulting in 352767 probes. A total of 17,246 Aquilegia uni genes were represented by more than three probes and therefore included in expression data analysis (352002 probes).


title: Karenia brevis 11K

city: Charleston

first: Frances

last: Van Dolah

state: SC

address: 219 Fort Johnson Rd

institute: Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research

organism: Karenia brevis

description:
Amadid# 013772
Agilent Design File 013772_D_F_20050913

first: Krisy

middle: B

last: Lidie

first: Jeanine

middle: S

last: Morey

manufacture_protocol: 60-mer oligonucleotide probes were designed from EST contigs derived from Karenia brevis cDNA libraries using Array Designer v 4.0 following Agilent's recommendations for Tm, GC content, and position.  Probes were submitted to Agilent's eArray website for randomization and addition of control probes.  For details on printing see Agilent's website www.agilent.com.


title: 8q24 Nimblegen Homo sapiens 385K custom tiling array

city: Rehovot

first: Gilad

last: Landan

address: PO Box 26

department: Applied Math & Computer Science, Molecular Cell Biology

institute: Weizmann Institute of Science

description:
HG17
Unique array probes were selected to cover all non-repetitive sequence in and around the 8q24 risk loci (chr8:125M–130M) within 5-bps resolution on average.

manufacture_protocol: see manufacturer's web site www.nimblegen.com


title: Angio Chip Microarray

city: Stockholm

first: Liqun

last: He

address: Scheelesvag 2

institute: Karolinska Institute

description: The Angio Chip is a high-density (16K) custom cDNA microarray

first: Elisabet

last: Wallgard

first: Mattias

last: Kalén

first: Mats

last: Hellström

manufacture_protocol: The Angio Chip microarrays were constructed from cDNA libraries from mouse microvascular fragments. It was printed using the MicroGrid II robot (Biorobotics) equipped with MicroSpot 10K pins (Apogent Discoveries) and the software TAS Application Suite (Biorobotics). The microarrays were printed onto CMT GAPS II and UltraGAPS slides (Corning).


title: Gresham Agilent Saccharomyces Cerevisiae 20mer probes Mutation Detection

city: New York

first: David

last: Gresham

address: 100 Washington Sq East, 1009 Sliver Center

institute: New York University


title: Plants 4K miRNA LC_MRA-1038_miRNAPlants_10.1 + Bn_PsRNAs

first: Anja

last: Buhtz

description: Plant miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 10.1 and additional custom small RNA sequences from Brassica napus phloem sap (Bn_PsRNAs)

first: Julia

last: Kehr


title: Oligo GEArray® Mouse Hematopoietic Stem Cells and Hematopoiesis Microarray

status: Public on Jul 23 2009

city: Hackensack

first: Michael

last: Appel

state: NJ

address: 30 Prospect AVE-room 350

department: Oncology Research

institute: Hackensack University Medical Center

description: Hematopoietic stem cells (HSCs) are defined as self-renewing cells with the capacity to differentiate into any of more than eight distinct blood-cell lineages. Hematopoiesis is the development of blood-cell lineages from HSCs through progenitor stem cells. Progenitor stem cells are morphologically indistinguishable from HSCs even while committed to development into specific blood-cell lineages. These progenitor stem cells can be distinguished, however, by lineage-specific molecular markers. The development of HSCs from embryonic stem cells, ex-vivo expansion of HSCs, or hematopoiesis involves specific cytokines, transcription factors, and the Notch and Wnt signaling pathways. This array contains genes encoding lineage-specific markers as well as the cytokines, signaling molecules, and other regulators that are important in stem cell commitment and differentiation. Use this array to study differential expression of genes involved in stem cell development among your experimental samples.

first: Stacey

last: Fanning

middle: Y

first: Stephanie

last: Berger

first: Robert

last: Korngold

first: Thea

last: Friedman

manufacture_protocol:
See manufacturer website
http://www.sabiosciences.com/microarrays.php


title: Albert Einstein College of Medicine RN4_HELP_HD2 array

first: Reid

middle: F

last: Thompson

description:
Array based on the rat genome (rn4), Nov 2004 release.
Custom high-resolution DNA methylation microarray for the HELP assay, designed to cover 917,301 HpaII/MspI fragments of 50-2,000 bp in unique sequence throughout the rat genome.

manufacture_protocol: See Roche NimbleGen website http://www.nimblegen.com/products/methylation/


title: Wuerzburg Neisseria meningitidis 15.4K

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

institute: University of Wuerzburg

organism: Neisseria meningitidis

first: Roland

last: Schwarz

first: Biju

last: Joseph

first: Gabriele

last: Gerlach

first: Kathrin

last: Engelhard

first: Mathias

last: Frosch

first: Christoph

last: Schoen

manufacture_protocol: The oligonucleotides were synthesized by Operon technologies(Germany) and were spotted on Nexterion E epoxy silane coated slides using an OmniGrid scanner after resuspension in the recomended buffers.


title: Biostar Genechip Moniezia expansa 4k microarray

city: Shi Hezi

first: Wenjuan

last: Zhao

state: Xinjiang

address: Wu Yi Road 221#

institute: The Breed & Biotechnology Key Laboratory of Sheep in XinJiang Bingtuan

organism: Moniezia expansa

first: Hui

last: Zhang

first: Xinwen

last: Bo

first: Xinhua

last: Wang

first: Lichao

last: Kang

manufacture_protocol: Biostar Genechip, Shanghai, China. By clustering the 2,642 sequences from the cDNA library, 1,078 unigenes of M.expansa, including full-length and partial cDNAs representing novel or known genes, were obtained for array construction. The negative control spots of non-tapeworm origin in the chip were the rice genes (48 spots). In addition, the array included 9 known genes(54 spots) as positive control genes that were provided by our library and 24 empty spots. Unigenes and all control genes were cloned into plasmid vector.


title: Gresham Agilent Saccharomyces Cerevisiae 25mer probes Mutation Detection

first: David

last: Gresham

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


title: GrapeArray 1.2 developed by the Italian-French Public Consortium for Grapevine Genome Characterization

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

institute: University of Verona

organism: Vitis vinifera

description:
Spots size: 25 microns
Total number of spots: 94928
Number of spots replicates per oligo: 3

manufacturer: University of Verona - Scientific and Technological Department - Plant Functional Genomics Centre

first: Diana

last: Bellin

first: Antoni

last: Chimento

first: Massimo

last: Delledonne

manufacture_protocol: Probes are directly synthesized on a 12k Combimatrix array by an in situ oligo synthesis system developed by Combimatrix Corporation (Mukilteo, USA) using the Combimatrix CustomArray synthesizer. Standard synthesis protocol provided by Combimatrix was used.


title: 454 GS 20 (Drosophila melanogaster)

last: GEO

organism: Drosophila melanogaster


title: EJH Hducreyi Oligo DNA Microarray 1

status: Public on Dec 05 2009

city: Dallas

first: Eric

last: Hansen

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

organism: [Haemophilus] ducreyi 35000HP

first: Maria

last: Labandeira-Rey

manufacture_protocol:
1. Array robot type:  MI's robot is a custom design and is not commercially available
2. Printing Type: Contact printing
3. Deposition Methodology:  MI uses ceramic capillary printing pins.
4. Buffer type: 150mM NaPO4, pH 8.0,
5. DNA concentration: 40umolar
6. Substrate type: Corning UltraGAPS


title: SuperArray Mouse Th-17 pathway PCR Array

city: Los Angeles

first: Chaim

last: Jacob

state: CA

address: 2011 Zonal Ave

institute: University of Southern California

organism: Mus musculus

description: The Mouse Th17 for Autoimmunity & Inflammation RT²Profiler™ PCR Array profiles the expression of 84 genes related to the Th17 Regulatory Network. Th17 is a newly defined subset of CD4(+) T cells that is distinct from the traditional Th1, Th2 and Treg. Th17 is highly proinflammatory and induces severe autoimmunity. This array contains surface molecules, cytokines and receptors, chemokines, matrix metalloproteinases, cell signaling molecules and transcriptional factors. Using real-time PCR, you can easily and reliably analyze expression of a focused panel of genes related to the Th17 regulatory network with this array.

first: Haitao

last: Yang

first: Jacob

last: Chaim

first: Noam

first: William

last: Stohl


title: Bdellovibrio bacteriovorus oligo arrays

city: Nottingham

first: Carey

last: Lambert

state: Notts

address: Queen's Medical Centre

department: Genetics

institute: Nottingham University

organism: Bdellovibrio bacteriovorus HD100

manufacture_protocol: Catalog design for Bdellovibrio bacteriovorus (Taxonomy Id: 264462) covering NC_005363. Probes selected for 3587/3587 sequences. Median number of probes/sequence is 20 with an average of 20. Each probe will be replicated 2 times on the chip. Probes are randomly distributed over the surface of the array. Unused features have been filled with randomly generated probes of comparable GC content.


title: Australian National University Acropora millepora 18k array version 1

status: Public on Dec 07 2009

city: Canberra

first: Lauretta

last: Grasso

state: ACT

address: Biology Place

department: Research School of Biological Sciences

country: Australia

institute: Australian National University

organism: Acropora millepora

manufacturer: Adelaide microarray consortion, University of Adelaide, South Australia

middle: C

first: Andrew

last: Negri

last: Hayward

last: Miller

first: Eldon

middle: E

last: Ball

manufacture_protocol: The amplified cDNAs were spotted onto GAPSII slides using a Biorad Chipwriter Pro (Biorad).  They were then fixed by UV light exposure of 150 mJ followed by baking at 80°C for 3 hours.


title: NimbleGen Polaromonas JS666 385K array v1.0 (condensed)

city: Ithaca

first: James

middle: M

last: Gossett

address: 220 Hollister Hall

department: Civil and Environmental Engineering

institute: Cornell University

organism: Polaromonas sp. JS666

description:
Whole-genome expression arrays were synthesized by NimbleGen Systems, Inc.  Arrays were designed to obtain full coverage of open-reading frames and a 50-bp tiling of the intergenic regions.  A frequency filtering of the intergenic regions was carried out to remove low-complexity regions and repeats.  Long oligos (60-mer) were synthesized on ultra high density, 1-plex arrays containing 385,000 features.  The arrays contained five replicate probes for each of the target sequences. A condensed template is presented below in the Platform data table.
Native NimbleGen files (ndf, ngd) are linked below as supplementary files.

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


title: University of Arizona Vitis buds cDNA array

city: Bet-Dagan

first: Ron

last: Ophir

address: POB 6

department: Fruit Tree Sciences

institute: Agricultire Research Organization

organism:
Vitis vinifera
Vitis riparia

description:
References:

Keilin T, Pang X, Venkateswari J, Halaly T, Crane O, Keren A, Ogrodovitch A, Ophir R, Volpin H, Galbraith D, Or E. Digital expression profiling of a grape-bud EST collection leads to new insight into molecular events during grape-bud dormancy release. Plant Science. 2007 Oct;173(4):446-457.

Mathiason K, He D, Grimplet J, Venkateswari J, Galbraith DW, Or E, Fennell A. Transcript profiling in Vitis riparia during chilling requirement fulfillment reveals coordination of gene expression patterns with optimized bud break. Funct Integr Genomics. 2009 Feb;9(1):81-96. Epub 2008 Jul 17.

manufacturer: Galbraith lab, University of Arizona, Tucson, AZ, USA

first: Etti

last: Or

manufacture_protocol: A total of 7920 cDNA inserts were amplified from the plasmids making up the previously described Vinifera bud EST collection (Keilin et al. 2007). Another 1141 cDNAs were amplified from a Vitis riparia clone collection that was recently described by Mathiason et al. (2008). The PCR products were purified, transferred to 384-well microplates, dried, and resuspended in 3X SSC. A total 9061 PCR products were spotted onto amino-silane-coated slides ("Superamine", Telechem, Sunnyvale, CA). A single array element was printed per clone onto each slide using SMP3 printing pins (Telechem) and a 32-pin head robotic system (‘OmniGrid 100’, GeneMachines, San Carlos, CA) at constant relative humidity (30%). The microarrays contained 9216 spots (including 152 blank spots). Spot diameter was 110 microM, spot spacing was 230 microM and subarray spacing was 460 microM. Slides included 32 grids of 18 columns and 18 rows (rows 17-18 were left empty). The arrays were allowed to air-dry for 10 min and the cDNA spots were immobilized. The quality of the printing process was assessed by hybridization of the first and last array at every print run with Cy3-labeled random 9-mer as described in http://ag.arizona.edu/microarray/Microarraymethod1


title: Yeast Protoarray YA103104 gal file

city: Durham

first: Matthew

last: Foster

state: NC

address: Box 2612 Research Dr.

department: Medicine

institute: Duke University

organism: Saccharomyces cerevisiae

technology: spotted peptide or protein

manufacture_protocol: Yeast GST-tagged ORFs and control proteins printed in duplicate on glass slide. Slides contains 48 blocks.


title: TIFN_Listeria monocytogenes EGD-e_15K_v1.0

status: Public on Nov 25 2009

city: Wageningen

first: Stijn

last: van der Veen

address: Bomenweg 2

department: ATV

institute: Wageningen University

organism: Listeria monocytogenes EGD-e

description: Custom made Listeria monocytogenes EGD-e array

first: Douwe

last: Molenaar

first: Marjon

last: Wells-Bennik

first: Roy

last: Moezelaar

first: Tjakko

last: Abee

first: Willem

last: de Vos


title: Combimatrix microarray of 454 derived grape berry transcripts

first: Alberto

last: Ferrarini

description:
Spots size: 25 microns
Total number of spots: 94928
Number of spots replicates per oligo: 2

first: Diana

last: Bellin

first: Antonio

last: Chimento

first: Massimo

last: Delledonne


title: WiCell HG18 WG CGH 391K v1

status: Public on Nov 14 2008

city: Madison

first: Melodee

last: Patterson

state: WI

address: 510 Charmany Dr Ste 58 & 59

institute: WiCell

organism: Homo sapiens

first: Karen

last: Montgomery

manufacture_protocol: Single array CGH design for whole human genome (hg18; NCBI Build 36). Probes selected from hg18_tiling database using 6000 bp interval and 250 bp window. Isothermal probes with min length of 50 bp and max length of 75 bp and target Tm of 76C. Cycle restricted to 148 synthesis cycles. Interval spacing: 6253 bp (mean); 6270 bp (median). 3553 random probes added. Includes pseudo-autosomal regions from chrX and chrY, though the counts for those regions have been changed to 1 to allow standard analysis.


title: WiCell 2006-07-27 HG18 WG CGH

status: Public on Dec 12 2008


title: Applied Biosystems TaqMan Gene Expression Assays (human)

status: Public on Oct 19 2005

city: Foster City

first: Fangqi

last: Hu

address: 800 Lincoln Center Dr

institute: Life Technologies

description: Pre-designed TaqMan probe and primer sets for quantitative gene expression studies of human genes.

manufacture_protocol: see manufacturer's web site


title: Applied Biosystems TaqMan Gene Expression Assays (mouse)

description: Pre-designed TaqMan probe and primer sets for quantitative gene expression studies of mouse genes.


title: HGS17_min_promoter_set

status: Public on Apr 01 2008

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

description: ChIP-chip promoter microarray based on the HG17 genome build (May 2004) covering approximately 1.5 kb around the transcription start site

first: Ari

last: Melnick

first: John

last: Greally

manufacture_protocol: See Roche NimbleGen website


title: WiCell HG18 WG CGH 385K v2


title: Pseudomonas aeruginosa PAO1 chromosome array

status: Public on Dec 25 2009

city: Tokyo

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

organism: Pseudomonas aeruginosa PAO1

description: This is an Affymetrix custom-commercial tiling array that covers the Pseudomonas aeruginosa PAO1 chromosome (RefSeq: NC_002516) at 11-bp density. BPMAP files are provided as supplementary files. PAO1b520519FF-3.bpmap represents the forward strand of PAO1chromosome, and PAO1b520519FR-3.bpmap represents the reverse strand of PAO1 chromosome.

manufacture_protocol: See manufacturer's web site.