title: SAGE:17:NlaIII:Aureococcus anophagefferens

status: Public on Apr 21 2010

last: GEO

country: USA

organism: Aureococcus anophagefferens

technology: SAGE NlaIII

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

distribution: virtual


title: SAGE:17:NlaIII:Aedes aegypti

status: Public on Apr 27 2010

organism: Aedes aegypti

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


title: Affymetrix RML Custom Pathogenic chip 6

status: Public on Apr 19 2010

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

organism: Salmonella enterica subsp. enterica serovar Typhimurium

technology: in situ oligonucleotide

description: custom pathogenic Affymetrix chip 6 manufactured for RML (RMLchip6a520533F)

distribution: non-commercial

manufacture_protocol: standard Affymetrix protocol


title: OSU-CCC MicroRNA Microarray Version 2.0 (Homo sapiens only)

status: Public on Apr 16 2010

city: Columbus

first: Pei-Yin

last: Hsu

state: OH

address: BRT836, 460W 12th Ave

institute: OSU

organism: Homo sapiens

technology: spotted oligonucleotide

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

manufacture_protocol: Manufacured using GE Healthcare's CodeLink (TM) 3-D Gel Matrix Technology. CodeLink(tm) Activated Slides are designed to covalently immoblize amine-modified DNA for microarrays. The slides are coated with a 3-D surface chemistry comprised of a long-chain, hydrophilic polymer containing amine-reactive groups. This polymer is covalently crosslinked to itself and to the surface of the slide. The crosslinked polymer, combined with end-point attachment, orients the immobilized DNA, and holds it away from the surface of the slide. The 1x printing buffer consists of 50 mM sodium phosphate at pH 8.5. Codelink slides are manufactured by SurModics and were formally sold as 3D-Link(tm) Activated Slides. Â¹ Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions that is fitted with a printhead and 16 SMP3 print tips from Telechem. The microRNA microarray probe set is based on 40mer oligonucleotides from Sigma-Genosys. Â¹ Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normalized 25 micromolar concentration. The miRNA microarray spot densities are 200 microns (center-to-center). The microarrays are printed on Codelink Activated Slide (PN300011)) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: ORNL DesulfovibrioG20 3.8k Array

status: Public on Apr 25 2010

city: Raleigh

first: Stan

last: Martin

state: NC

address: 1404 Crete Dr.

institute: Science Apps, L3C

organism: Oleidesulfovibrio alaskensis G20

technology: spotted DNA/cDNA

description: Desulfovibrio G20

manufacture_protocol: ORNL internal protocol.  The probes were designed and the arrays printed at ORNL.


title: Agilent Custom Human 244K CGH Array

city: Santa Clara

first: Nick

last: Sampas

state: CA

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 hg18 human genome (NCBI build 36).

Novel Sequence Array for Kidd et al 2010 AMADID 21331

distribution: custom-commercial

first: Jeffrey

middle: M

last: Kidd

first: Francesca

last: Antonacci

first: Tina

last: Graves

first: Robert

last: Fulton

first: Hillary

middle: S

last: Hayden

first: Can

last: Alkan

first: Maika

last: Malig

first: Mario

last: Ventura

first: Giuliana

last: Giannuzzi

first: Joelle

last: Kallicki

first: Paige

last: Anderson

first: Anya

last: Tsalenko

last: Yamada

first: Peter

last: Tsang

first: Rajinder

last: Kaul

first: Richard

middle: K

last: Wilson

first: Laurakay

last: Bruhn

first: Evan

middle: E

last: Eichler

manufacture_protocol: in situ synthesized oligonucleotide array


title: The Human Apoptosis RT² Profiler™ PCR Array (PAHS-012)

status: Public on Apr 24 2010

city: Jefferson

first: Rohan

last: Kulkarni

state: AR

address: 3900 NCTR Road

department: Div. of Genetic and Reproductive Toxicology

institute: National Center for Toxicological Research

technology: RT-PCR


title: Homo sapiens 0.66K AndroChip-2

status: Public on Apr 15 2010

city: Rome

first: Daniela

last: Minella

state: Italy

address: Via Montpellier 1

department: Dept. of Biopathology

country: Italy

institute: Tor Vergata University

manufacture_protocol: The oligonucleotide set (50 mer, Ocimum Biosolutions, Indianapolis, USA) was mechanically “spotted” in triplicate onto UltraGAPS glass slides (Corning, Schiphol-rijk, The Netherlands) using TheRoboArrayerTM (Microgrid Compact Plus, BioRobotics). Printed slides were dried overnight and cross-linked with UV light at 600 mJ using a Strata-linker 2400 (Stratagene, Glenville, VA) and stored in a desiccator at room temperature. See also the related website http://www.geneticaumana.net/ricerca_news_scheda.php?id=53


title: NimbleGen Agrsci Bovine 6.3M v1, Design 2

status: Public on Apr 22 2010

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

organism: Bos taurus

description:
High density, custom Nimblegen HD2 CGH tiling arrays were planned in 3 designs. Each design covers a specific set of chromosomes with 2.1M probes, which yields 420 bp of average probe spacing (301 bp median probe spacing).
Design_ID: 8026
Design_name: 080804_Btau4_design2_CGH_03
Description: HX1 CGH for Bos taurus release 4.0, chr 1,4,6,7,9,13,15,20,22,26,27,M; selection at i300w50.
Annotation in this array is based on the bovine genome assembly, version 4.0 (Btau_4.0).
Probe sequences are available in the 'PROBE_SEQUENCE' column of the 'GPL9220_080804_Btau4_design2_CGH_HX1.ndf' supplementary file.

manufacture_protocol: See manufacturer's web site (www.nimblegen.com).


title: miRXplore TM Microarray (848)

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

country: Germany

institute: Miltenyi Biotec GmbH

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: The miRXplore TM Microarray is composed of 5288 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 1977 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 1977 miRNA sequences covered sequence verified miRNAs of the species human (743) mouse (588) and rat (428) as well as viral miRNAs (151) and further mammalian species (76) as deposited in the miRBase sequence database version 10.1. The 97 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (43 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 36 positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 13 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences. Microarrays were manufactured by Miltenyi Biotec. Briefly, 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides in quadruplicates using a customized piezoelectric spotter.

distribution: commercial

manufacturer: Miltenyi Biotec GmbH, Bergisch Gladbach, Germany

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

manufacture_protocol: 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted four times on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides using a customized piezoelectric spotter.


title: NimbleGen-Streptococcus agalactiae-X4 expression design

status: Public on Apr 29 2010

city: Seattle

first: Lakshmi

last: Rajagopal

state: WA

address: 1900 9th Ave

department: Pediatric Infectious Disease

institute: Seattle Children's Hospital Research Institute

organism: Streptococcus agalactiae A909

description: 071112 Sagal A909 EXP X4, 1978 genes, 18 probes/target, 4 X 72000 probes, 2 replicates, NC_007432

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


title: UMR745 INSERM Human NF1 8x15K v1.0

city: Paris

first: Eric

last: Pasmant

address: Faculté de Pharmacie de Paris, 4 avenue de l’Observatoire

country: France

institute: Paris Descartes University

description: Probes were selected either from catalog probes of Agilent’s 44K commercial array CGH or from Agilent’s eArray library (Agilent Technology,Inc. Santa Clara, CA).

manufacture_protocol: Agilent manual (Protocol v5.0, June 2007, Agilent technologies)


title: NimbleGen Agrsci Bovine 6.3M v1, Design 3

description:
High density, custom Nimblegen HD2 CGH tiling arrays were planned in 3 designs. Each design covers a specific set of chromosomes with 2.1M probes, which yields 420 bp of average probe spacing (301 bp median probe spacing).
Design_ID: 8029
Design_name: 080804_Btau4_design3_CGH_03
Description: HX1 CGH for Bos taurus release 4.0, chr 2,3,5,10,11,14,16,17,23,24,25; selection at i300w50.
Annotation in this array is based on the bovine genome assembly, version 4.0 (Btau_4.0).
Probe sequences are available in the 'PROBE_SEQUENCE' column of the 'GPL9221_080804_Btau4_design3_CGH_HX1.ndf' supplementary file.


title: LC_MRA-1001_miRHuman_11.0_080411 (miRNA ID version)

status: Public on Apr 26 2010

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

description: Human miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 9.2

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: TaqMan® Array Human MicroRNA Panel v1.0

city: Rotterdam

first: Su Ming

last: Sun

address: Dr. Molewaterplein 50

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center


title: Pangenomic Ostreococcus microarray (8K)

status: Public on Apr 20 2010

city: Rennes

first: annabelle

last: monnier

address: 2 avenue du Professeur Léon Bernard

institute: UMR 6061 Génétique et Développement

organism: Ostreococcus tauri

manufacturer: Transcriptomic platform (Rennes - France)

manufacture_protocol:
1. 8096 gene-specific oligonucleotides (50-mers) were designed and synthesized by Eurogentec.
2. Oligonucleotides were resuspended at a 30 microM concentration in Nexterion Spot Solution 2X (Schott Nexterion).
3. Oligonucleotides were spotted in triplicate on Nexterion Slides E (Schott) using a Biorobotics MicroGrid II spotter (Genomic Solutions).  24k feature array comprises technical triplicates.
4. Positives (Cy3 labelled oligonucleotides) and negatives (spotting buffer) controls were added
5. Quality of spotting was checked by slide scanning using an Agilent G2565BA Microarray scanner (Agilent Technologies).


title: [mpiUstilagoa] MPI UstilagoA

status: Public on Apr 25 2006

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

organism: Mycosarcoma maydis

description:
Whole genome Affymetrix array, based on a map based assembly supplied by BayerCropScience.
Information available at http://mips.gsf.de/genre/proj/ustilago/

first: Mario

last: Scherer

first: Regine

last: Kahmann

manufacture_protocol: Affymetrix protocol, 33 match/mismatch probe pairs for 800 bp 3´region of each gene.


title: miRCURY LNA microRNA Array, v.11.0 - hsa, mmu & rno [probe-level]

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

manufacture_protocol: see manufacturer's website


title: NimbleGen-Staphylococcus aureus-X4 expression design

organism: Staphylococcus aureus subsp. aureus COL

description:
catalog design 081003_Saur_COL_exp_X4 + pseudogene SACOL1232; 9 probes per target, 3 copies of probes on array,genome accession NC_002951, NC_006629
native array description file:  090327_Saur_COL_SACOL1232_expr.ndf
native array description file:  090327_Saur_COL_SACOL1232_expr.ngd


title: Marine microbial communities 0.26 K

city: Tucson

first: Virginia

middle: Isabel

last: Rich

state: AZ

address: 1041 E. Lowell St.

institute: University of Arizona

organism:
uncultured crenarchaeote 4B7
Prochlorococcus marinus subsp. pastoris str. CCMP1986
uncultured marine alpha proteobacterium
uncultured marine gamma proteobacterium EBAC31A08
uncultured marine group II euryarchaeote 37F11
uncultured Pseudomonadota bacterium
uncultured crenarchaeote 74A4
uncultured marine bacterium 440
uncultured marine bacterium 577
uncultured marine bacterium 583
uncultured gamma proteobacterium eBACHOT4E07
uncultured marine bacterium EB0_41B09
uncultured proteobacterium 60D04
uncultured proteobacterium 65D09
uncultured marine group II euryarchaeote EF100_57A08
uncultured marine bacterium EB000_55B11

description: update to platform GPL6012. DeLongLab_GenomeProxyArray_v2.0_268targets. Note supplementary platform for full array design and sequences of probes.

manufacturer: DeLong Lab, Massachusetts Institute of Technology

manufacture_protocol: Glass slides with poly-lysine coating. The expanded genome proxy array was designed as in (Rich et al., 2008). Briefly, each genotype was targeted using suites of ~20 70-mer oligonucleotide probes designed using the program ArrayOligoSelector (Zhu et al., 2003). Probes had approximately the same %GC (40%) and were distributed across the target genome or genome fragment, with no more than one probe per gene and avoiding 16S and 23S rRNA genes. The probes were selected solely based on theoretical thermodynamic properties and GC content; that is, probe selection did not focus on specific genes or regions, but simply produced the “optimal” probes for each genome proxy based on the probes’ predicted hybridization properties. The array included positive and negative control probes designed using the same method, to Halobacterium salinarum NRC-1 and a random genome sequence, respectively.    The expanded array had a broader scope than the prototype of Rich et al., 2008 (268 target genotypes, as opposed to the prototype’s 14) and included a co-spot oligo for spot alignment and gridding purposes (using the “alien” oligo sequence of (Urisman et al., 2005). The targets were selected from fully-sequenced marine microbial genomes, publicly-available marine-derived BAC and fosmid clone sequences, and fully-sequenced clones from the lab’s Monterey Bay and Hawaii environmental BAC- and fosmid-based genomic libraries. Targeted genotypes are detailed in Table S1, summarized in Table S2, and presented in a schematic phylogenetic overview in Fig. 1. Previously-unpublished sequences used for array design were submitted to Genbank under accession numbers GU474833-GU474949.    Oligonucleotides were synthesized (Illumina, San Diego, CA), suspended in 3X SSC to a concentration of 40 pmol ml-1, and spotted on homemade poly-L-lysine-coated glass slides using a QArray 2 microarraying robot (Genetix, Hampshire, UK). Six replicates of each probe were spotted.


title: NimbleGen Agrsci Bovine 6.3M v1, Design 1

description:
High density, custom Nimblegen HD2 CGH tiling arrays were planned in 3 designs. Each design covers a specific set of chromosomes with 2.1M probes, which yields 420 bp of average probe spacing (301 bp median probe spacing).
Design_ID: 8023
Design_name: 080804_Btau4_design1_CGH_03
Description: HX1 CGH for Bos taurus release 4.0, chr 8,12,18,19,21,28,29,U,X; chrU is all chrUn scaffolds concatenated with 10-base run of N's as separator; selection at i200w50.
Annotation in this array is based on the bovine genome assembly, version 4.0 (Btau_4.0).
Probe sequences are available in the 'PROBE_SEQUENCE' column of the 'GPL9219_080804_Btau4_design1_CGH_HX1.ndf' supplementary file.


title: Affymetrix Mouse Genome UG 430 2.0 Array [CDF: Mouse4302_Mm_UG_v11.cdf]

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

institute: University Heidelberg

organism: Mus musculus

description: Custom CDF (Brainarray v11); UniGene

relation: Alternative to: GPL1261 (Alternative CDF[official])

manufacture_protocol: see manufacturer's web site


title: SR ferret 44K v2.0

city: Birmingham

first: Carl

last: Bruder

state: AL

address: 2000 9th Ave South

department: Viral Biochemistry

institute: Southern Research Institute

organism: Mustela putorius furo

manufacture_protocol: Agilent e-array, default settings (60 mers)


title: ARIM-GX

city: yokohama

first: kenjiro

last: ikuta

state: kanagawa

address: 10-1, Daikoku-cho, Tsurumi-ku

country: Japan

institute: MITSUBISHI RAYON CO.,LTD

description: Oligo nucleotide probes were covalently attached to hydrophilic gel which bond to inner wall of plastic hollow fiber.

first: Tatsunobu

last: Fukushima

manufacture_protocol:
The oligonucleotide probes were designed by 200 of innate immune related genes and to be the same annealing temperature throughout a microarray. Probes were also designed within 1 kb from 3’-end of each genes.
To manufacture the DNA microarray of 200 genes, we used the Genopal(TM) (Mitsubishi Rayon) system as described below. Bundled plastic hollow fibers, in which oligonucleotide capture probes were chemically bonded to hydrophilic gel were embedded in resin, then polymerize and sliced it into thin chips.


title: Adelaide Microarray Facility CompuGen Human 19K Oligo Array

status: Public on Apr 17 2010

city: Adelaide

first: Benjamin

last: Lewis

state: South Australia

address: Frome Road

department: Sansom Institute

country: Australia

institute: University of South Australia

first: Tamara

middle: A

last: Crittenden

first: Peter

middle: L

last: Wigley

first: Allan

last: Evans

first: Ross

last: McKinnon

manufacture_protocol: See microarray.adelaide.edu.au for printing details


title: 3D-Gene Human miRNA Oligo chip v12-1.00

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

manufacture_protocol: See manufacturer's web site


title: miRXplore TM Microarray (857)

status: Public on Apr 23 2010

first: Silvia

last: Rueberg

description: The miRXplore TM Microarray is composed of 5668 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 2027 miRNA sequences and 95 controls with all probes spotted in quadruplicates. The 2027 miRNA sequences covered sequence verified miRNAs of the species human (754) mouse (597) and rat (451) as well as viral miRNAs (150) and further mammalian species (75) as deposited in the miRBase sequence database version 10.1. The 95 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (4 sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (1 sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (43 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 36 positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 11 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences. Microarrays were manufactured by Miltenyi Biotec. Briefly, 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides in quadruplicates using a customized piezoelectric spotter.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio


title: Capitalbio mammal microRNA V3.0

city: Beijing

first: Jianqing

last: Zhao

address: 18 Life Science Parkway

country: China

institute: Capitalbio. Crop

manufacture_protocol: as described in Capitalbio mammal microRNA V3.0 oligo array Manual


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array [CDF: Hs133P_Hs_ENTREZG.cdf]

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

institute: Erasmus MC

first: Lonneke

last: Gravendeel

first: Mathilde

middle: C

last: Kouwenhoven

first: Olivier

last: Gevaert

first: Johan

middle: J

last: de Rooi

first: Andrew

middle: P

last: Stubbs

first: Elza

last: Duijm

first: Anneleen

last: Daemen

first: Fonnet

last: Bleeker

first: Linda

middle: B

last: Bralten

first: Nanne

last: Kloosterhof

first: Bart

last: de Moor

last: van der Spek

last: Kros

last: Sillevis Smitt

first: Martin

last: van den Bent

manufacture_protocol: The platform used is the HU133 plus 2.0 array from Affymetrix and is manufactured as such. 17,527 genes were extracted from the array using updated array annotation (Dai et al., 2005) based on reorganizing probes to gene specific probe sets, excluding inaccurate or wrongly annotated probes.


title: Illumina Genome Analyzer (Homo sapiens; Mus musculus)

status: Public on Apr 14 2010

last: GEO

organism:
Homo sapiens
Mus musculus

technology: high-throughput sequencing


title: SMD Print_1566 Homo sapiens

city: Stanford

first: Rajnish

last: Gupta

address: CCSR Room 2155

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: ASU Brucella melitensis 13K oligo array v1.0

city: College Station

first: Jenni

last: Weeks

address: 4467 TAMU

institute: Texas A&M University

organism: Brucella melitensis

manufacturer: Western Regional Center of Excellence (WRCE) Pathogen Expression Core (Arizona State University)

first: Stephen

last: Johnston

first: Mitchell

last: McGee

first: Rhonda

last: Friedberg

first: Jonathan

last: Lawson

manufacture_protocol: A set of unique 70-base oligonucleotides representing 3,227 ORFs of B. melitensis strain 16M and unique/divergent genes from B. abortus and B. suis were designed at the Pathogen Expression Core and purchased from Sigma-Genosys (The Woodland, TX). Oligonucleotides were suspended in 3X SSC (Ambion) at the final concentration of 40 uM before robotic arraying in triplicate onto ultraGAPS coated glass slides (Corning) using a Spotarray 72 microarray printer (Perkin Elmer, Downer’s Grove, ILL). Printed slides were steamed and UV cross-linked and stored in a desiccator until use.


title: Agilent-026657 Whole Rat Genome Microarray 4x44K v2 (Feature Number version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Rattus norvegicus

description:
Rat Design content refresh 44k

Arrays of this design have barcodes that begin with 16026657 or 2526657.

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

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

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


title: Nimblegen human 60-mer gene expression array, design version 2003_10_27

city: Richland

first: Katrina

last: Waters

address: 902 Battelle Blvd; MSIN J4-18

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

manufacture_protocol: Whole human genome expression array, design version 2003_10_27, using GenBank annotation from 06/14/2003


title: R & D Human Cytokine Array

city: Central

first: R A P

last: Perera

address: 34, Hospital road

department: Faculty of Dentistry

country: Hong Kong

institute: The University of Hong kong

technology: spotted peptide or protein

manufacture_protocol: Proteome Profiler 96 Microplate-based Antibody Arrays consist of a 96-well microplate pre-spotted with multiple capture antibodies in each well. Experimental samples are added and target proteins present in the samples bind to the immobilized antibodies. All wells also contain Reference Spots, which provide a strong positive signal to allow easy visualization of well location. A cocktail of biotinylated detection antibodies and Streptavidin-HRP or an HRP-conjugated pan anti-phospho-tyrosine antibody is subsequently used to detect the bound proteins. Chemiluminescent substrate reagents produce a signal that is proportional to the amount of analyte bound. A compatible digital imaging system capable of chemiluminescent detection is used to determine the intensity of light emitted from individual spots.


title: [HsAirwaya520108F] Custom Affymetrix HsAirway array

city: Iowa City

first: Bartley

middle: Joseph

last: Brown

state: IA

institute: The University of Iowa

manufacture_protocol: See manufacturer's website


title: Illumina Genome Analyzer (Cymbidium ringspot virus; Nicotiana benthamiana)

status: Public on Apr 11 2010

organism:
Nicotiana benthamiana
Cymbidium ringspot virus


title: Illumina Genome Analyzer (Neurospora crassa)

status: Public on Apr 12 2010

organism: Neurospora crassa


title: AB SOLiD System 3.0 (Candida albicans)

organism: Candida albicans


title: Agilent/CCFFT Escherichia coli K12 MG1655 8x15k v1.0

city: Tallinn

first: Ranno

last: Nahku

address: Akadeemia tee 15b

country: Estonia

institute: TFTAK

organism: Escherichia coli str. K-12 substr. MG1655

description:
Steps/settings in Earray (http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/gp50660.aspx):
a. Design Wizards - Create a Microarray Design from Target Transcripts
b. Selected Method - Tm matching methodology
c. Selected Parameters:
Probe Length - 60bp
Probes per Target - 3
Probe Orientation - Sense
Design Options - Best Distribution Methodology
NO - "Design with 3' Bias" and "Allow Probes to be Trimmed"
Preferred Probe Tm - 85C
Target File Details - Upload Gene Sequence File
Note: "e.coli.nuc" file was downloaded from the KEGG ftp site (ftp://ftp.genome.jp/pub/kegg/genes/organisms/eco/ )
Transcriptome Details - Use Target File as Transcriptome
d. 8x15K platform was used


title: Agilent Xenopus laevis 22k AMADID-013665

city: Bethesda

first: Biswajit

last: Das

state: MD

address: 18 Library Drive, Building 18T, Room 106

department: Laboratory of Gene Regulation and Development

institute: National Institutes of Health/National Institute of Child Health and Human Development

organism: Xenopus laevis

description: This in situ synthesized 60-mer oligonucleotide contains 21495 spots and is designed from NCBI Unigene database (build 63/64) for Xenopus laevis. It is designed using Agilent e-Array.

first: Agilent

last: Technologies

manufacture_protocol: Please see manufacturer's web site


title: SuperArray GEArray Q Series Mouse Neurotrophin and Receptors Microarray [cat# OMM-031]

city: Frederick

first: SuperArray

last: Bioscience Corporation

address: Suite 101, 7320 Executive Way

institute: Technical Support


title: Agilent yeast array

status: Public on Apr 09 2010

first: Gavin

last: Sherlock

address: 300 Pasteur Drive

department: Genetics

organism: Saccharomyces cerevisiae

manufacture_protocol: Agilent


title: Human Platelet Gene Arrays 0.5 K

city: Stony Brook

first: Wadie

last: Bahou

state: NY

institute: Stony Brook University

organism: Homo sapiens

manufacturer: microarrays custom manufactured at Stony Brook University, Center for Biotechnology Applied Bioscience Lab and Microarray Facility

manufacture_protocol: 432 platelet-expressed, 43 leukocyte-expressed gene probes, and series of positive and negative spike controls, including housing genes and arabidopsis probes; synthetic 70mer oligonucleotides spotted onto coated glass slides (Corning UltraGAPS) using GenPak 21 microarraying system


title: SMD Print_857 Homo sapiens

first: Ash

last: Alizadeh

address: 269 Campus Drive, CCSR 1145c

department: Medicine, Divisions of Hematology and of Oncology

institute: Stanford University School of Medicine


title: UHN Homo sapiens 19.2K cDNA array

city: Pune

first: Ashwin

last: Kelkar

state: Maharashtra

address: Ganeshkhind

department: Department of Zoology

country: India

institute: University of Pune

first: Deepti

last: Deobagkar

manufacture_protocol:
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 the arrays. Specifications of array layouts are defined based on the slide barcode located on the bottom of the scanned image.


title: Illumina Genome Analyzer II (Equus caballus)

status: Public on Apr 08 2010

last: GEO

organism: Equus caballus


title: Ectocarpus siliculosus tiling array ChIP2

status: Public on Apr 07 2010

city: Los Altos

first: Manoj

last: Samanta

address: 2240 Homestead Court #309

institute: Systemix Institute

organism: Ectocarpus siliculosus

description:
50-mer probes tiling the entire Ectocarpus siliculosus genome
Control probes were placed on all arrays for monitoring hybridization quality and data normalization.

manufacture_protocol: Synthesized on glass-based slides using a maskless array synthesizer (Nimblegen technology).


title: SAGE:16:DpnII:Schizophyllum commune

organism: Schizophyllum commune

technology: other

description: This is a virtual platform for SAGE libraries generated for Schizophyllum commune using DpnII as an anchor enzyme.


title: Ectocarpus siliculosus tiling array ChIP1


title: FUNDP/URBM_Brucella.melitensis.16M_v.1.0

city: Namur

first: Jean-Jacques

last: Letesson

address: rue de Bruxelles, 61

department: URBM

country: Belgium

institute: University of Namur

organism: Brucella melitensis bv. 1 str. 16M

description: The design (.ndf) file and description (.ngd) file are available as Supplementary files (at the foot of this record).

first: Sophie

last: Uzureau

first: Julien

last: Lemaire

first: Anthoula

last: Gaigneaux

first: Xavier

last: De Bolle

manufacture_protocol: Microarray design and experimentation were made by NimbleGen Systems, INC from catalogue design for B. melitensis 16M chromosomes I (NC_003317) and II (NC_003318) with 20 probes per gene (10 perfect matches and 10 mismatches).  Each probe (24 mer) was replicated three times on chip (design includes random GC probes). Triplicate samples of each strain were mixed and one chip was made per strain.


title: NIAID Cgda -- Candida glabrata 6K - mAdb version

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

organism: Nakaseomyces glabratus CBS 138

description: The array probes were designed against all NCBI RefSeq mRNA sequences available for Candida glabrata CBS138 as of September 2008. Length 60-base DNA sequences were selected using the e-Array software (Agilent Technologies) specifying one “best probe” per transcript and “3-prime bias”. Custom microarrays with 5,125 unique probes (one for each target transcript), replicated to eight spot features per probe, were manufactured by Agilent in the 4x44K format.


title: NHGRI Human_Mouse_Rat miRNA microarray (condensed version)

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

institute: The George Washington University School of Medicine and Health Sciences

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description:
Organisms represented on array: Human, Rat, Mouse, and others
The Platform data table reflects a condensed representation of the array's replicate features.

manufacturer: The Microarray CORE Facility of the National Human Genome Research Institute (NHGRI, NIH, Bethesda, MD)

manufacture_protocol: We used the same custom-printed miRNA array that was previously used by our collaborators, Zhou et al (Neuropsychopharmacology (2009) 34:1395-1405) which included human, mouse, and rat miRNA on the mirVana miRNA Probe Set 1564V2.  The entire probe set was printed by the National Human Genome Research Institute (NIH, Bethesda, MD) microarray CORE facility for the convenience of multiple users, who also requested the inclusion of additional ncRNA (aside from miRNA).


title: GE Healthcare CodeLink Human Whole Genome Bioarray (GB_ACC version)

status: Public on Apr 10 2010

city: Pittsburgh

first: Latha

last: Satish

state: PA

address: 320 E North Avenue

department: Center for Genomic Sciences

institute: Allegheny-Singer Research Institute

manufacture_protocol: see manufacturer's website


title: Ocimum Biosolutions E.coli K12 V2 OciChip

city: Hyderabad

first: Ocimum

last: Biosolutions

email: govind.a@ocimumbio.com, sandhya.p@ocimumbio.com, hazira.b@ocimumbio.com, anwaruddin.m@ocimumbio.com

state: Andhra Pradesh

address: Banjara Hills Road No., 1 VI Floor Reliance Classic

department: Bioinformatics

institute: Ocimum Biosolutions

organism: Escherichia coli K-12

first: Govind

last: Roa

first: Sandhya

last: Kiran

first: Hazira

last: Begum

manufacture_protocol: E.coli K12 V2 Ocichip consists of 4608 spots printed on Corning® epoxy coated glass slides using Omnigrid (Gene Machines). Chip has been printed using 4x4 SMP4 pins on 75.5x 25.5x1.3 mm microarray glass slides with a spot area of 18x18 cm. The origin offset values were 0 for X direction and 10000 for Y direction. The dot to dot distance is 260 mm; distance between subarrays is 150 mm and no of dots per array is 16x18=288. Oligos were printed using spotting buffer A from Ocimum Biosolution at 50% humidity and temperature at 22°C. The time taken by the robotic gridder to print was 16 hrs. Each probe was checked for its performance by standard QC process followed at Ocimum Biosolutions. Printed slides were stored in a light-tight box in a bench-top dessicator, with desiccant and were kept at 4°C until they were used for hybridization.


title: Ruhr-Universität Bochum/NimbleGen A_tumefaciens_C58_4x72K array

city: Bochum

first: sonja

last: klüsener

address: Universitätsstrasse 150

institute: Ruhr-Universität Bochum

organism: Agrobacterium fabrum str. C58

description: NimbleGen design name 080630_A_tumefaciens_C58_expr; NimbleGen design ID 7811; The 4-plex NimbleGen Gene Expression Array for A. tumefaciens represents 5344 genes and is based on NCBI reference sequences NC_003062, NC_003063, NC_003064 and NC_003065. Each gene is represented by 6 probes (45mer-60mer oligonucleotides), each in two copies on different locations on the array.

manufacture_protocol: See manufacturer's website at http://www.nimblegen.com/.


title: Rhodobacter capsulatus Affymetrix GeneChip RCAP_ex1a520469F

city: St. John's

first: Ryan

last: Mercer

state: Newfoundland

address: 232 Elizabeth Avenue

department: Biology

country: Canada

institute: Memorial University

organism: Rhodobacter capsulatus

manufacture_protocol: Contructed using Affymetrix protocols for Rhodobacter capsulatus chromosome and plasmid. Contains oligonucleotide probes for 3635 ORF and 1452 intergenic regions greater 90 bp.


title: Ectocarpus siliculosus tiling array ChIP8

status: Public on Apr 06 2010

state: CA


title: Agilent-015279 Mouse CpG Island ChIP-on-Chip Microarray 2x105K  (Probe Name version)

last: Agilent Technologies

institute: Agilent Technologies

organism: Mus musculus

description:
Mouse CpG Island ChIP-on-Chip Microarray 2x105K
Enriched content sourced from UCSC mm8, NCBI build 36 (February 2006)
16,030 CpG islands
97,652 probes in or within 95bp of CpG Islands
2 x 105K slide format printed using Agilent's 60-mer SurePrint technology

*** The ID column represents the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL7099.


title: Ectocarpus siliculosus tiling array ChIP7


title: Ectocarpus siliculosus tiling array ChIP5


title: Ectocarpus siliculosus tiling array ChIP4


title: Ectocarpus siliculosus tiling array ChIP6


title: Ectocarpus siliculosus tiling array ChIP3


title: DNA Chip Research AceGene Human Oligo Chip 31K

status: Public on Apr 05 2010

city: Yahata-nishi, kitakyushu

first: Junichi

last: Sakabe

state: Fukuoka

address: 1-1 Iseiga-oka

department: Graduate School of Medicine

institute: University of Occupational and Environmental Health

manufacture_protocol: see manufacturer's web site at http://hitachisoft.jp/dnasis/acegene/


title: JIVAN Homo sapiens 38.4K array for Glioblastoma Splicing

status: Public on Apr 02 2010

city: San Antonio

first: Jonathan

middle: Adam

last: Gelfond

address: Mail Code 7933, 7703 Floyd Curl

department: Epidemiology & Biostatistics

institute: UT Health Science Ctr San Antonio

description: Custom designed Agilent Array for alternative splicing in cancer.

first: Luiz

middle: O

last: Penalva

manufacture_protocol: Per manufacturer protocol


title: Illumina Genome Analyzer (Populus trichocarpa)

last: GEO

organism: Populus trichocarpa


title: NimbleGen_Ppu_pSL1_5.3k array v1.0

status: Public on Apr 01 2010

city: Tsukuba

first: yong

last: wang

state: Ibaraki

address: 3-1-3 Kannondai

department: Environmental Biofunction Division

institute: National Institute for Agro-Environmental Sciences

organism: Pseudomonas putida KT2440

description:
NimbleGen design name 2007-08-09_GFC234_Pput_60mer_expr, NimbleGen design ID 6223. Sample species Pseudomonas putida KT2440.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files 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: CBM_UCE_Mouse_12K_v2.0

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

institute: CBM

manufacture_protocol: CombiMatrix uses a bench-top synthesizer (produced in-house) and proprietary electrochemical synthesis approaches (U.S. patents and foreign equivalents) that employ standard phosphoramidite chemistries. CombiMatrix commercial 12K semiconductor CustomArray® microarray has 12,544 features (electrodes or spots) and is manufactured by ST Microelectronics. There are 13 silver pads on the chip that provide connections between a controller instrument and each electrode on the array. Each electrode is an independent transducer that can convert an electrical signal to a chemical reaction and, likewise, convert a chemical reaction on its surface into an electrical signal. Using a serial bus (SPI), all 12,544 electrodes can be addressed individually in less than one second. For oligonucleotide array synthesis, the semiconductor chip is coated with a porous layer and a single phosphoramidite (thymidine) is added. An electrical current sent to an individual electrode decreases th e proximal pH, which deprotects the thymidine and makes it react with a subsequent phosphoramidite that is introduced into the reaction chamber. The synthesis of different DNA probes at individual electrodes is possible by repeating this process through approximately 100 cycles an array of 35-40mers. Probes as large as 100mers can be synthesized, but best results are obtained with 35-40mers.


title: Human 40K A OciChip array

city: NOTTINGHAM

first: SHAILENDA

last: SINGH

address: QUEEN'S MEDICAL CENTRE, DERBY ROAD

department: DIVISION OF THERAPEUTICS AND MOLECULAR MEDICINE

country: United Kingdom

institute: UNIVERSITY OF NOTTINGHAM

manufacture_protocol: see manufacturer's website (http://www.ocimumbio.com/web/arrays/download.asp)


title: Exiqon Homo sapiens 0.56K miRNA array [208000v8]

status: Public on Apr 03 2010

city: Chongqing

first: jingyi

last: li

address: Gao Tan Yan

department: institute of immunology

institute: the third millitary medical university

manufacture_protocol: Exiqon’s microRNA arrays feature Tm-normalized LNA™-enhanced capture probes, designed for excellent specificity and sensitivity even for AT-rich microRNAs.


title: UWBMC Armigeres subalbatus 18K v1.0

city: Madison

first: Bruce

middle: M

last: Christensen

state: WI

address: 1656 Linden Drive

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

organism: Armigeres subalbatus

manufacturer: University of Wisconsin Gene Expression Center

manufacture_protocol:
Six cDNA libraries from adult female mosquitoes were used to generate 8,020 Expressed Sequence Tag (EST) clusters (Mayhew et al. 2007) from which 60-mer oligonucleotides were synthesized that represent 6,143 unique EST clusters.  Oligos were designed using OligoArray v 2.1, and these 6,143 oligonucleotides were used to construct our Armigeres microarray.  Ar. subalbatus microarray slides (Corning Ultragaps) were printed using a Genomic Solutions GeneMachines Omnigrid arrayer and SMP3 pins from TeleChem International (23˚C and 50% humidity) following established printing protocols.  Sixty-mer oligonucleotides were re-suspended at 40 μM in Pronto spotting buffer (Promega, Madison, WI).  Each microarray (19,200 total tool spots) was printed using 16 pins, resulting in 48 subgrids (20 x 20 at 0.215 mm pitch).  Features were printed in triplicate across the slide.

Cytochrome C oxidase was printed at all four corners of each of the 48 subgrids and served as a positive control.  Negative controls on the array included blanks (spotting buffer with no oligo) and two mouse oligos, Mus 1 and Mus 2.  Blanks were interspersed within all subgrids, and Mus 1 and 2 were printed in triplicate like all other features.  A scanning control, Mus 3, was added because of its ability to be mixed with both Cy3 and Cy5 reactions, resulting in a 1:1 ratio on the array.  Mus 3 RNA (2.5 ng) was added as a spike during cDNA synthesis.  Forty-eight spots appeared as empty, i.e. a spot touched down on the slide but visited an empty well for its source visit.  These allow for new features to be added to the array without changing the general design.  Overall, the array had 6,143 unique features printed in triplicate (= 18,429 spots, including Mus 1 and 2), 192 positive control spots, 48 Mus 3 spots printed once per subgrid, and 495 blank spots.


title: AB SOLiD System 2.0 (Mus musculus)


title: Danio rerio dedicated 15k array

city: Amsterdam

first: Mark

middle: de

last: Jong

address: Kruislaan 318

institute: University of Amsterdam

organism: Danio rerio

first: M

last: de Jong

first: H

last: Rauwerda

first: O

last: Bruning

first: J

last: Verkooijen

last: Spaink

last: Breit

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


title: JCVI PFGRC Salmonella typhimurium version 5

status: Public on Jan 08 2010

city: Fayetteville

first: Jeong Nam

last: Kim

state: AR

address: 1260 W Maple St. POSC L-115

department: Cell and Molecular Biology

institute: University of Arkansas

organism: Salmonella enterica subsp. enterica serovar Typhimurium

description:
Number of Grids: 48
Element Type: 70mer Oligonucleotide
Oligonucleotides Designed: 5462
Replicate Oligo Printings: 4x
Salmonella typhimurium/typhi version 5

manufacture_protocol: Contact PFGRC Bioinformatics group (http://pfgrc.jcvi.org/)


title: UNIBI-Ps6kOLI1-Pisum sativum-16k-Microarray

city: Villeneuve d'Ascq

first: Lucau

last: Anca

address: Cité Scientifique SN2/302

department: Stress Abiotiques et Différenciation des Végétaux Cultivés

institute: UMR  USTL / INRA 1281

organism: Lathyrus oleraceus

description:
Each microarray contains 5.376 triplicate spots (total number of spots: 16.128) in 48 grids of 19 rows and 18 columns; all triplicates are spotted in the same grid. The 48 grids were arrayed in a 4x12 pattern of 4 metacolumns and 12 metarows. In each grid, 6 positions are not arrayed leading to 288 positions that do not contain spots across the arrays.
The spots contain 5276 different 70mer oligonucleotides.
A total of 42 empty wells containing no 70mers but only spotting buffer are distributed across the Ps6kOLI1 arrays in 3 duplicates giving a total of 126 background controls designated EMPTYWELLS.

manufacturer: Institute of Genome Research (IfG), Center of Biotechnology (CeBiTec), Bielefeld University, Germany

first: Toitot

last: Clarisse

manufacture_protocol:
Ps6kOLI1 oligonucleotide microarray represent 5.220 EST-clusters derived from 11930 Pisum sativum ESTs. These were donated by Hans Weber and Ruslana Radchuk (IPK Gatersleben; 8412 ESTs from cotyledons and seed coats), Aymeric Duclert (INRA Evry and Génoplante; 2816 ESTs from stipules, epicotyls, leaves, stems and seeds) and Julie Hofer (JIC Norwich; 702 ESTs from lateral and apical shoot tips before and during flowering). Automatic blast comparisons against GenBank "nr", the TIGR M. truncatula and Glycine max Gene Indices as well as the directionally cloned JIC and IPK collections were used to establish the orientation of the EST clusters obtained and all clusters were subsequently converted to "sense"
orientation. In case of 300 clusters with ambiguous directionality due to (1) lack of polyA tails or (2) lack of significant homologies, both "sense" and "antisense" orientations were selected.
Including a collection of 26 marker genes for P. sativum seed, stem and flower development (supplied by J. Hofer, JIC Norwich; C. Rameau, INRA Versailles and R. Radchuk, IPK Gatersleben) a total of 4946 non-redundant EST clusters are represented on the arrays.
All oligonucleotides were spotted in 3 replicates. Oligonucleotides serving as controls were spotted in more replicates in some cases.
Control oligos detecting different transgenes (bar, nptII, gusA, gfp, luc, hph)
• PSGAPDH-5-100/-C-100/-3-100 oligonucleotides covering the 5', the central and the 3' region of the GAPDH gene that can serve as controls for the processivity of labeling
• PSGAPDH-C-100 to C-74 oligonucleotides that can serve as controls to assess crosshybridization.
• NCPS01- NCPS06 oligonucleotides serve as alien controls to detect unspecific hybridization.
• Alien1- Alien10 oligonucleotides serve as alien controls to detect unspecific hybridization
• PCPS01 – PCPS26 oligonucleotides serve as positive controls representing expressed genes
• EMPTYWELLS only containing spotting buffer. These can be used to adjust the flagging for lowintensity ("empty") spots that give signals very close to background
More information : www.cebitec.uni-bielefeld.de/legume/microarrays/microarrays.html


title: PFGRC Trypanosoma cruzi Oligonucleotide Array v1

status: Public on Aug 01 2009

city: Athens

first: Todd

last: Minning

state: GA

address: Rm 310 Coverdell

department: CTEGD

institute: University of Georgia

organism: Trypanosoma cruzi

manufacturer: PFGRC - Pathogen Functional Genomics Resource Center

manufacture_protocol: sense strand


title: Applied Biosystems TaqMan Gene Expression Assays (rat)

status: Public on Oct 19 2005

city: Foster City

first: Fangqi

last: Hu

address: 800 Lincoln Center Dr

institute: Life Technologies

organism: Rattus norvegicus

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

manufacture_protocol: see manufacturer's web site


title: Agilent/WalbotLab Zea mays + Ustilago maydis (dual organism) 4x44K array

city: Stanford

first: John

middle: F

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

organism:
Zea mays
Mycosarcoma maydis

description: designed by Walbot Lab

manufacture_protocol: 36K maize and 6800 Ustilago maydis 60-mer oligo probes were designed from known cDNAs and synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry on glass slides.


title: Mouse OpArray OPMMV4

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

manufacture_protocol: See manufacturer website


title: Washington University School of Medicine Microarray Core Brugia malayi microarray V.2

city: Bonn

first: Uta

last: Strübing

address: Sigmund-Freud-Str. 25

department: Institute for Medical Microbiology, Immunology and Parasitology

institute: University Hospital Bonn

organism:
Brugia malayi
Onchocerca volvulus
Wuchereria bancrofti
Wolbachia endosymbiont strain TRS of Brugia malayi

manufacture_protocol:
The Brugia malayi Version 2 (V.2) array contains 18,153 oligonucleotides, 878 based on Wuchereria bancrofti ESTs, 1,016 based on Onchocerca volvulus gene indices, 804 from the Wolbachia complete genome, and the remaining 15,455 based on B. malayi ESTs, TIGR gene indices, TIGR gene models, and L3 ESTs.

Oligonucleotide selection:
We patterned our oligo selection algorithm after PICK70 (J. DeRisi, personal communication). The algorithm utilizes two input files in oligo selection: the first is a fasta format file of all genes to be used for oligo selection and the second is a fasta format file of the entire genome sequence. For the input gene sequences, we bias selection of oligos to the 3?-most 1000 bases of sequence (for genes greater than 1000 bp in length) by pre-masking all sequences upstream of this cutoff. The initial portion of the oligo selection routine is designed to mask out any repetitive sequence elements or any highly similar portions (e.g. to other genes) of the input gene sequences. This masking is accomplished by BLAST comparison of genes to genome, using a stringent cut-off to mask out any sequence with 70% or greater similarity to any other sequence in the genome that extends over 66% of the desired oligo length. Once the input gene sequences are masked, they are subjected to the oligo selection algorithm. Here, the algorithm examines each sequence one at a time, starting from base number one and looking at the first contiguous 65 bases (or whatever the input desired oligo length is) with respect to the following parameters, in order:
1.Ensures that all of the bases being considered are either A, C, G or T (e.g. no N?s or masked bases are contained in the putative oligo sequence). If all bases do not conform, the algorithm shifts to base two of the sequence and reiterates the check.
2.If all bases conform, examines the input bases for whether they collectively fall in the desired G/C range of the oligo. If not, the sequence is rejected and the algorithm shifts to base two of the input sequence and reiterates step one, etc.
3.If all bases and the G/C range conform, the algorithm examines the input bases for whether they collectively fall in the desired Tm range of the oligo. If not, the sequence is rejected and the algorithm shifts to base two of the input sequence and reiterates step one. The Tm calculation currently used is nearest-neighbor calculation.
For the next series of checks, the algorithm assigns ?scores? for the input oligo, rather than outright rejection of non-conforming sequence. The score assigned indicates the relative deviation of the oligo from the desired parameter, where a score of zero means that the oligo conforms to the parameter.
4.If the bases conform to the Tm range desired, then the algorithm examines the oligo for percentage of G/C content across the oligo, using a sliding window. If any window has a G/C content that deviates from the average G/C content of all windows by more than a specified amount (the default is 10% of the overall oligo Tm) the oligo score is incrementally increased. This ensures uniformity of G/C content across the oligo.
5.Once the sequence G/C uniformity is scored, the algorithm examines the oligo for homopolymers greater in length than the cut-off length set by the user (we typically stipulate that the same base cannot occur more than 4 times in a row or the oligo score is increased from zero). The number of homopolymer runs in the oligo greater than the cut-off length and the total number of bases encompassed by these runs is also determined and stored.
6.Once the homopolymer content is assessed, the algorithm calculates secondary structure potential. This is done using a fasta comparison of the sequence to itself. The optimal score of the fasta alignment is used here as the score reported for the oligo. An optimal fasta score of zero indicates no potential for self-annealing. The optimal score increases as more regions of potential self-alignment are found. Our examination of many such alignments indicates that oligos with a reverse fasta score lower than 100 lack significant secondary structure.
7.If the algorithm passes through all these checks with the oligo starting at base one of the input sequence, it writes that oligo and its scores to a temporary database and starts over with the next input oligo (bases 2-66 in this example). The algorithm reiterates over the entire input gene and then passes to the next gene.
8.In some stretches of input sequence, multiple oligos will result that differ by only one base in succession, but all conform to the desired oligo parameters. In these cases, the algorithm selects the best scoring sequence for all parameters and selects it as the best oligo sequence representing a particular region.
9.In some input genes, the algorithm may not find any oligos within the desired Tm range. In these cases, the algorithm will lengthen or shorten the oligo length according to the length range input, and re-iterate at each length to determine whether the desired Tm range can be met. If not, the algorithm selects the best oligo that falls outside the range, with the corresponding Tm appearing in the final output file.
10.The final output of the algorithm is a text document containing the optimal oligo for each gene examined, including the oligo names (gene name plus oligo start position as an extension) and sequences, followed by the output of all parameter scores for that sequence
For genes that do not result in an oligo selection, we manually examine the input sequences and then relax certain algorithmic parameters in order to select an oligo (typically we relax the constraint on similarity in the initial masking step, up to 80% identity). In some instances, no oligo that uniquely represents a gene can be found since no sufficient length of the gene sequence is left unmasked due to gene family similarities at the nucleotide level.
Oligos were synthesized from the consensus sequence of selected clusters (n=3569) by standard methods by Illumina (San Diego, CA). The oligonucleotides (50nM in 3x SSC with 0.75M betaine) were printed in duplicate on MWG Epoxy slides (MWG Biotech Inc, High point, NC) by a locally constructed linear servo arrayer.


title: CERI_Medaka-array 4x44K ver.1.0

first: Katsuyuki

last: Kadota

address: Tokodai 5-13-11

department: Research

institute: Japan Pulp and Paper Research Institute, Inc.

organism: Oryzias latipes

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


title: NIAID Mmeb -- Mouse 44k - mAdb version

status: Public on Oct 15 2009

city: Bethesda

first: Timothy

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description: NIAID Mmeb 44k (37.5k reporters) derived from Operon Mouse V4 oligo set. Length 60 bp probe sequences were generated by extracting base 10 through base 69 from the original 70 bp Operon probe. Agilent design number is 017138. For direct access, please contact tmyers@nih.gov.


title: ChickenOligo 20.6K 70-mer microarray v2

status: Public on Feb 26 2009

city: Jouy-en-Josas

first: Sylvain

last: Marthey

address: Domaine de Vilvert Bat 320

department: Animal Genetics

institute: INRA

organism: Gallus gallus

description:
Roslin/ARK Cooperative Research Chicken Array set.
The oligo set (20,673) were designed by ArK using ENSEMBL genes transcripts, the BBSRC fully sequenced set and the DT40 full length sequencing set.
This oligo set was synthesized by Operon (2007).

first: Diane

last: Esquerré

first: Céline

last: Ducroix-Crepy

first: Jerome

last: Lecardonnel

manufacture_protocol:
Resuspending
1-1. Oligos from 20K set are arrayed by Operon in 384-well V-bottom plates (Genetix). Each well contains 1 nmol of oligo.
1-2. Resuspend oligos in water (20µM) on Staccato RapidPlate (Caliper).
1-3. Incubate at room temperature during a night shaking plates to aid resuspension of DNA.
1-4. Deep freeze and defrost centrifuging plates at 1000 rpm for 16 minutes then 2000 rpm for 3 minutes.
1-5. Take 5 µl of oligos solution and put it in new polypropylene v-bottom plates (cat# X7022, Genetix)
1-6. Add 5 µL of 1X Pronto! Universal Spotting Solution (Corning) to each well and mix.
Spotting
2-1. Centrifuge plates at 2000 rpm for 3 minutes.
2-2. Oligos are ready for spotting.
2-3. Spotting on glass slides (Corning, Ultragaps), with 48 Microspotting pins Stealth 3 on Chipwriter (Virtek), with control of humidity (45-50%).
2-4. Fixation of the oligos slides with UV (600 mJoules).
2-5. Storage the slides in a vacuum.
2-6. After the print run is completed, cover oligos plates with seals and deepfreeze them at -20°C in a protected environment.


title: Illumina Genome Analyzer II (Rattus norvegicus)

last: GEO


title: Mussel MytArray 1.1

status: Public on Mar 31 2010

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

organism: Mytilus galloprovincialis

manufacturer: C.R.I.B.I.-Biotechnology Centre and Dept. Biology (University of Padova)

first: Cristiano

last: De Pittà

first: Beniamina

last: Pacchioni

first: Caterina

last: Millino

first: Barbara

last: Celegato

first: Stefano

last: Cagnin

first: Paola

last: Venier

first: Alberto

last: Pallavicini

first: Francesco

last: Marsano

first: Laura

last: Varotto

manufacture_protocol: MytArray 1.1 is a cDNA platform, that consists of 1,712 different clones obtained from systematic sequencing of multiple Mytilus galloprovincialis tissues cDNA library and 46 unrelated controls (ESTs from Coffea and bacterial species) printed in duplicate and twice per slide. This library was produced using a strategy that allows the selection of a short 3’-end region of mRNAs and the tagging of each transcript with an unique probe. Moreover, since the 3’-end non coding region is the least conserved part of the genes, a microarray constructed in this way greatly reduces the cross hybridization of different mRNAs derived from genes with high homology in the coding region to the same probe. The strategy was also designed to obtain 3’-tags with very uniform size (400-800 bp). This feature ensures that all the cDNA clones of the collection can be PCR-amplified and spotted with comparable efficiency and that production of microarrays with uniform hybridization characteristics be obtained.


title: [TTHB8401a520105F] Riken Thermus thermophilus HB8 4K mRNA custom array, library Rev.2

status: Public on Sep 18 2009

city: Hyogo

first: Yoshihiro

last: Agari

address: 1-1-1, Kouto, Sayo

department: RIKEN SPring-8 Center

institute: RIKEN Harima Institute

organism: Thermus thermophilus HB8

first: Akeo

last: Shinkai

first: Seiki

last: Kuramitsu

manufacture_protocol: Affymetrix custom array standard protocol. Please see http://www.affymetrix.com for more information.