title: University of Amsterdam Bacillus subtilis 168 9.2K Array Version 2

status: Public on Jan 07 2008

city: Leiden

first: Anna

middle: Magdalena

last: Zakrzewska

address: Wassenaarseweg 64

department: IBL

country: Netherlands

institute: University of Leiden

organism: Bacillus subtilis

technology: spotted oligonucleotide

description: This is a condensed platform of the full 9.2K array. The full layout is linked as a supplementary file.

distribution: non-commercial

manufacturer: Microarray department (MAD) Amsterdam, www.microarray.nl

first: Alex

last: Ter Beek

first: Bart

middle: J

last: Keijser

first: Andre

last: Boorsma

first: Rick

last: Orij

first: Gertien

last: Smits

first: Stanley

last: Brul

manufacture_protocol: The B. subtilis oligonucleotide libraries (Cat # BACLIB384) were obtained from Sigma-Compugen Incorporated. Technical support was supplied by LabOnWeb company. The libraries represent in total 4128 oligos, which represent 4106 B subtilus genes, 10 controls from E.coli and the Brome mosaic virus and 12 random oligos LEADS™ clusters plus 231 controls. The oligonucelotide library was printed with a Lucidea Spotter (Amersham Pharmacia Biosciences, Piscataway, NJ, USA) on commercial UltraGAPS slides (amino-silane-coated slides, Corning 40017) and processed according to the manufacturer’s instructions.


title: klingenkhh_BAC_32K_Full

status: Public on Jan 24 2008

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

organism: Homo sapiens

technology: spotted DNA/cDNA

description: The 32k BAC Re-Array set Ver. 1.0 (32,433 BAC clones) was obtained from the BACPAC Resource Center at Children's Hospital Oakland Research Institute, Oakland (CA, US). The average resolution of the whole genome tiling clone set is 46kb. Clones were mapped to human genome build 17 (UCSC Human Genome Browser)

manufacture_protocol: Arrays were produced using amplified genomic DNA from BAC clones. Amplification was performed using degenerate oligonucleotide primed PCR and products were purified by size-exclusion filtration and verified by agarose gel electrophoresis. After purification, products were dried down, recovered in 50% DMSO to a concentration of 500-1000ng/µl, and printed on amino-silane-coated glass slides (UltraGAPS from Corning) using a MicroGrid2 robot (BioRobotics) equipped with MicroSpot2500 pins (BioRobotics).


title: PDP Mouse 11k BMAP

status: Public on Jan 25 2008

city: Winnipeg

first: stephanie

last: booth

address: 1015 Arlington St

country: Canada

institute: PHAC

organism: Mus musculus

first: Stephanie

middle: A

last: Booth

manufacture_protocol: Libraries and clones derived from brain regions of adult mouse (strain C57BL/6) were obtained from Research Genetics. The 11 136 clones represent expressed sequence tags (ESTs) from some 5471 unique known genes and 5665 as-yet-uncharacterized mRNAs and form part of a library that was created as part of the Brain Molecular Anatomy Project (BMAP). Each insert from this BMAP 3' EST library was amplified by PCR. cDNA was purified by using Millipore multiwell purification plates and lyophilized PCR products were resuspended in 1x Micro-spotting Solution Plus (TeleChem) at a concentration of 0·25–0·75 µg µl–1. DNA was spotted onto CMT–GAPS-coated glass slides (Corning) by using Stealth micro-spotting pins (TeleChem)


title: Ecoli_pangenome_CBSDTU_v1

status: Public on Jan 21 2008

city: Kgs. Lyngby

first: Hanni

last: Willenbrock

address: Kemikalievej, bygning 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: DTU

organism: Escherichia coli

technology: in situ oligonucleotide

distribution: custom-commercial

first: Peter

middle: F

last: Hallin

manufacture_protocol: NimbleGen in situ synthesis


title: Print_633

status: Public on Jan 20 2008

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

country: USA

institute: Stanford University

description: SHCK

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: UCSF/Haqqlab_Human_36574_GEMINAL_v1.0

status: Public on Jan 30 2008

city: San Francisco

first: Scot

middle: M

last: Federman

address: 499 Illinois St

department: Biochemistry

institute: UCSF

manufacture_protocol:
See the following reference for details:
Fox, M.S., Ares, V.X., Turek, P.J., Haqq, C. and Pera, R.A.R. (2003) Feasibility of global gene expression analysis in testicular biopsies from infertile men. Mol. Reprod. Dev., 66, 403 – 421.


title: Singapore Grouper Iridovirus 0.5K genomic DNA microarray

status: Public on Jan 28 2008

city: Guangzhou

first: yong

last: teng

address: 135 West Xingang Road

country: China

institute: Sun yet-san university

organism: Iridovirus

manufacturer: National Engineering Research Center for Beijing Biochip Technology, 18 Life Science Parkway, Changping District, Beijing 102206, People’s Republic of China.

manufacture_protocol: A SGIV cDNA microarray was constructed following a PCR product-based microarray method. In brief, an in-house high-throughput computer algorithm based on Linux operating system and Phython programming language was employed to design PCR primers for 162 open reading frames (ORFs) of SGIV genome. The fundamental rules of our computer algorithm include that all the primers should have a close annealing temperature with PCR products length about 150-1100 bp and amplicons should have a minimum sequence similarity. The PCR amplifications were performed in 100 µl reaction volume and PCR successes were confirmed by agarose gel electrophoresis. The confirmed PCR products were precipitated with isopropanol and redissolved in 50% dimethyl sulphoxide (DMSO). Two house-keeping genes: Piscine 18S ribosomal RNA (18S rRNA) gene and ß-actin gene from host cells were also amplified to act as positive controls. PCR products (in 50% DMSO, 20 µM) were spotted with SmartArrayTM microarrayer (CapitalBio Corp., Beijing, China). Each gene was printed on amino silaned slides in triplicate to facilitate subsequent statistical analysis. After printing, the slides were baked at 80°C for 1h and stored dry at room temperature till use. Prior to hybridization, the slides were rehydrated over 65°C water for 10 sec. UV cross-linked at 250 mJ/cm2. The unimmobilized DNAs were washed off with 0.5% SDS for 15 min at 42°C and SDS were removed by dipping the slides in anhydrous ethanol for 30 sec. The slides were spin-dried at 1,000 rpm for 2 min.


title: Univerisity of Wisconsin Gene Expression Center_Escherichia coli_4.2K_Eco15

status: Public on Jan 22 2008

city: Northampton

first: Christine

middle: Ann

last: White-Ziegler

state: MA

address: Clark Science Center

department: Biological Sciences

institute: Smith College

first: Amy

last: Malhowski

first: Sarah

middle: D

last: Young

manufacture_protocol: Microarray consists of full-length PCR products from all 4,290 annotated open reading frames (ORFs) in E. coli mg1655 (1).  PCR products are printed in replicate on standard, 1” X 3”, poly-l-lysine coated glass microscope slides.  Greater than 95% have been shown to migrate as a single band, of the predicted molecular weight, as determined by gel electrophoresis and ethidium bromide staining.  Also printed on each microarray are >200 control spots consisting of: fragmented E. coli genomic DNA, non-specific salmon sperm DNA, 3X SSC, and >25 different yeast ORF PCR products (see master table). These microarrays are printed using a 16-pin configuration, resulting in a pattern of 32 sub-arrays each having geometry of 17 rows by 18 columns with spot diameter averaging 100 microns. To aid in locating the array, the top and bottom array boundaries are etched on the back of the microscope slide.  A unique serial number is also etched on the array side at the bottom of the slide (see diagram in master table). The integrity and quality of each set of microarrays have been verified by hybridization with fluorescent-labeled cDNA and genomic DNA.


title: hop

status: Public on Jan 27 2008

first: David

last: Wong

address: 269 Campus Drive


title: SHFF Human 41K cDNA Array

status: Public on Jan 23 2008

city: Hannover

first: Doris

last: Steinemann

state: Niedersachsen

department: Cell and Molecular Pathology, Theoretische Institute II

country: Germany

institute: Medical School Hannover


title: Stintzi Lab Campylobacter jejuni 1.9k array, version 4.0

city: Ottawa

first: Alain

last: Stintzi

state: Ontario

address: 451 Smyth road

department: Biochemistry, Microbiology and Immunology

institute: University of Ottawa

organism: Campylobacter jejuni

description: Campy version 4.0; spotted PCR products.

manufacture_protocol: A set of 3,308 oligonucleotides were designed with Primer 3 (code available at http://www.genomewi.mit.edu/genome_software/other/primer3.htm) to amplify, via PCR, an internal fragment from each of the 1,654 predicted open reading frames (ORFs) identified in the annotated genomic sequence of C. jejuni NCTC 11168. Genomic DNA (20 ng) was used as a template in the first round of PCR amplifications with standard methods in a 96-well plate format. The PCR products were analyzed by agarose gel electrophoresis. Successful PCR products were reamplified to reduce the amount of residual genomic DNA carried over from the first PCR. PCRs without product or with incorrectly sized products were performed again by modifying the reaction conditions or by designing new primers.   DNA fragments were obtained for approximately 98% of the ORFs. PCR products were purified with the Millipore PCR96 cleanup kit and quantified with the PicoGreen double-stranded DNA quantitation reagent from Molecular Probes. They were diluted in a 50% dimethyl sulfoxide solution at a concentration of 75 ng/µl and rearrayed into a 384-well format. They were then printed on aminosilane-coated glass microscope slides (CMT GAPS-II; Corning Inc., Corning, N.Y.) with an arrayer robot (Molecular Dynamic). Finally, the DNA fragments were immobilized onto the slides by baking at 80°C for 4 h.


title: ISQ Chip Folsomia candida Collembola VU version 1.0

status: Public on Jan 19 2008

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

institute: Sanquin

organism: Folsomia candida

description: 2*11K format. In total 5,131 different experimental probes representing 5,112 EST contigs are in duplicate on the microarray.

manufacture_protocol: 60-mer oligo probes were designed from Collembase EST contigs, using OligoArray v2.0 and synthesized in situ by an ink-jet printing (Agilent) method on glass slides.


title: Chr. Hansen A/S_Streptococcus thermophilus_2304_v1.0

status: Public on Jan 18 2008

city: Cadorago

first: Martin

middle: Bastian

last: Pedersen

state: CO

address: Via Manzoni 29

department: R&D

country: Italy

institute: Sacco Srl

organism: Streptococcus thermophilus

description: Full array layout file (ie, gal file) linked below as a Supplementary file.

first: Ondrej

last: Valina

middle: B

manufacture_protocol: DNA oligos were purchased from Bioneer Corporation at 50nmol synthesis scale with BioRP purification and in lyophilized state (Daedeok-gu, Daejeon, South Korea). Oligos were dissolved at 10uM in 50% DMSO and printed in 4 replicates on UltraGAPS slides (Corning B.V., Schiphol-Rijk, The Netherlands) using a Genpak ARRAY 21 arrayer (Genetix Ltd., Hampshire, United Kingdom) with 16 SMP3 pins, (TeleChem International Inc., Sunnyvale, CA) giving a spot diameter of 100-120mm. Washing was performed between each print cycle for 20s in water followed by 20s in 70% ethanol. The relative humidity was kept at 48 ± 5% by placing a water bath at the appropriate temperature below the air inlet of the arrayer. The oligos were cross-linked to the surface using a Stratalinker 1800 UV Crosslinker set at 70mJ/cm2 (Stratagene). Printed arrays were stored in aluminium pouches with five arrays each and silica gel to remove humidity.


title: Sunflower organ-specific medium-scale cDNA array

status: Public on Jan 29 2008

city: Castelar

first: Paula

last: Fernandez

state: Buenos Aires

address: N. Repetto y Los Reseros S/N

country: Argentina

institute: INTA Castelar

organism: Helianthus annuus

first: Julio

last: Di Rienzo

first: Horacio

middle: E

last: Hopp

first: Norma

last: Paniego

first: Ruth

last: Heinz

manufacture_protocol: Five ul from each purified PCR cDNA products (317 in total) were transferred into 384 well plate containing 5 ul of DMSO 100%,spotted onto coated glass-slides in the working solution plates and  printed onto UltraGap Slides (Corning) using a Versarray chipwriter (Bio-Rad) with Stealth Micro Spotting quill pins (Telechem). Humidity was set at 45%, and temperature was 22-25°C. Pins were loaded in the working plate during 0.5 sec. Distance between spots was 400 um, Dwell time for printing was 0.05 sec. Four replicas from each cDNA were spotted per slide. Pins were loaded in the working plate and before printing the slides, a blotting slide was printed 5 times in order to discard the excess of cDNA on the pins. After printing on slides, and before loading a new cDNA, pins were washed with 3 cycles of 5 sec. wash with water, followed by 1 sec vacuum and a final 10 sec vacuum time . After printing was completed, cDNA were UV crosslinked to the slides on a CL-1000 UV crosslinker (UVP). Printed slides were stored in a dissecator.


title: Lactobacillus johnsonii NC533 microarray project

status: Public on Jan 17 2008

city: Lausanne

first: Emmanuel

last: Denou

state: vaud

address: vers chez les blancs

department: Nutrition & Health

country: Switzerland

institute: Nestlé Research Center

organism: Lactobacillus johnsonii NCC 533

manufacturer: Eurogentec - parc industriel d'Ivoz-Ramet 21 - 4400 - Ivoz-Ramet - Belgium

manufacture_protocol:
Primer synthesis of 1876 pairs of primers in 96 well Multiplex format
Each Forward primer carries a Tag sequenceand a total number of 9 different tags have been designed for covering all Forward primers. All reverse primers contains a unique tag
Following a 96 well plate map, a specific arrangement of these 9 tags provides a way to eliminate one major source of DNA contamination during the secondary amplification by locating one tagged PCR product away from the adjacent one that will be amplified with identical tags. Basically, tags 1 to 9 are arranged in a row starting from position A1 to A9, and this is repeated in the next positions and second lane of the plate, i.e. well plates B1 and B2 will contain primers tagged with 4 and 5, respectively
Primary PCR amplification: The reverse primers were mixed with the corresponding Forward primers and diluted each to 5 mM final concentration to prepare a 10-fold concentrated solution of specific primers
A master mix is prepared with EuroTAQ incubation buffer, EuroTAQ thermostable polymerase (EGT), 0.2 mM each dNTPs (EGT), 1.8 mM MgCL2, LA-1 genomic DNA (5 ng), and dispensed by 90 µl to the 96 well PCR plates.
PCR amplification were performed in Applied Biosystem thermocycler GeneAmp PCR system 9700 with 1 min at 94°C for initial denaturation followed by 30 cycles (94°C, 1 min; 50°C, 30 sec; 72°C, 1 min), and finally a final step at 72°C for 5 min.
An aliquot of each PCR mix (5 µl) was resuspended in EthBr loading buffer and analyzed by agarose gel electrophoresis (1% in TAE buffer).
The size of amplicons were determined with the help of  the molecular weight DNA ladder Smart Ladder (EGT).
Secondary PCR amplification : The unique Reverse Tag primer was mixed with the corresponding Forward primers 1 to 9 in order to prepare a template 96 well plate that was used for transferring the tag primer couples at the good locations in all 96 well PCR plates (10 µl, 5 mM final concentration)
We obtained 98.6% of the aminated secondary PCR products, which covers 1876 ORFs
PCR purification was performed by using the Millipore Multiscreen 96 well Filter Plates.
Based on differential binding of DNA molecules on silica matrix, this system is adapted for centrifugation with a throughput of 17 plate per centrifuge.
A binding buffer (Guanidine-HCl7 M; MES 200 mM pH = 5.6) is first added to the PCR plates.
Following up and down pipetting, the samples are transferred to the purification plate for binding onto the glass fibers during centrifugation.
One step centrifugation washing is done with Ethanol 80 %. Amplicons are recovered in H20 buffered at pH 8 (120 µl).
Water have been removed by evaporation and DNA samples were resuspended to a final volume of 30 µl 3x SSC printing buffer (average concentration 100-200 ng/µl).
An aliquot of each first lane (A1 to A12 well) from 96 well plates (1 µl) was resuspended in EthBr loading buffer and analysed by agarose gel electrophoresis (1% in TAE buffer).
For arraying the aminated PCR products, the samples were transferred from 96 well plates to V-bottom 384 well plates (Genetix #7020).
Additional controls (printing buffer, C1, C2, C3 and luciferase cDNA from Renilla) were added in the last 384 well plate in order to place these controls in each subgrid of the array (16 subgrids in total).
We used the Virtek ChipWriterPro, equipped with 16 SMP3 quill pins (Array It, Telechem) for arraying the library in close duplicates with 200 µm dot spacing onto CMT-GAPS II Corning glass slides.
Each subgrid contains 16 columns and 16 rows.
In order to provide an area for normalising the laser intensities for working at an optimal dynamic range and the scans for normalisation on intensities recovered from spike control RNA (LuxA control RNA available at Promega), we added an extra lane located outside of the main array frame that contains serial two-fold dilutions of sonicated LA-1 genomic DNA, Luciferase cDNA and CAT cDNA.
Following printing, the slides were dried overnight at room temperature in the gridder chamber and processed according to the Anhydride succinic acid protocol recommended by Corning.
Printed microarray slides were incubated in MilliQ water for 2 min at 95°C for DNA denaturation.
For checking the quantity and quality of DNA spotted onto the glass slides, we performed a Cy5-dCTP Terminal Transferase labelling (Roche) of bound DNA molecules onto the ready-to-use LA-1 microarray glass slides (one slide per 40 slides-batch).
For this purpose, we directly added to the printed glass slide area, 20 µl of dCTP labelling reactional mix according to the manufacturer’s recommendations.
A coverslip was applied onto the array and the glass slide was incubated for 15 min at 37°C.
The glass slide was then washed 5 min in 0.2x SSC, 0.1% SDS and 5 min in 0.2x SSC and finally spin-dried.
Microarray glass slides were scanned with Genepix 4000 scanner (Axon instruments, Inc.) and arrays analysed with Genepix 4.0 software.


title: JCVI PFGRC Streptococcus pneumoniae 17K v5 array designed primarily based on strain R6

city: Rockville

first: PFGRC

last: JCVI

state: MD

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Streptococcus pneumoniae

description: This set includes 3314 oligonucleotides, has 17280 spots distributed in 96 blocks.

manufacture_protocol: 6QSP, with arrayer GENETIX, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 7383017, pen id 10181, pen cycles -1, operator bj, humidity control On, humidity set point65


title: Deinococcus radiodurans 6K cDNA microarray (NC_001263, NC_001264, NC_000958, NC_000959)

status: Public on Jan 31 2008

city: Hangzhou

first: Yuejin

last: Hua

state: Zhejiang

address: 268 KaiXuan Road

department: Institute of Nuclear-Agricultural Sciences

institute: Zhejiang University

organism: Deinococcus radiodurans

manufacturer: The Bioinformatics and Molecular Regulation Laboratory, Zhejiang University

first: Songnian

last: Hu

first: Huan

last: Chen

manufacture_protocol: The predicted ORFs of Deinococcus radiodurans (NC_001263, NC_001264, NC_000958, NC_000959) are PCR amplified. The PCR amplicons are deposited onto poly-L-lysine slide in duplicate. There are 48 blocks on the array. In each block, there are 12 columns and 12 rows. See detailed description on manufacture protocol in "Transcriptional profile in response to ionizing radiation at low dose in Deinococcus radiodurans" (Progress In Natural Science. Vol 17 No.5: 529-536).


title: Mus musculus MEEBO 38.5K oligo array

status: Public on Jan 16 2008

city: Mississauga

first: Ashley

last: Monks

address: 3359 Mississauga Road

department: Dept. of Psychology

institute: University of Toronto

description: Full genome M. musculus array containing all oligonucleotides from the MEEBO mouse genome set (http://mmc.ucsf.edu/Meebo.html), representing 25,000 genes.

first: Kaiguo

last: Mo

first: Pengcheng

last: Rao

first: Tim

last: Westwood

first: Douglas

manufacture_protocol: Microarrays were produced by Microarrays Inc. (www.microarrays.com) using high precision robotics and amine-coated glass slides from Genexprex.


title: Homo sapiens oncogene oligo 2.3k array

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

description: Epoxy-silane coating.

first: Derek

last: Zieker

first: Bettina

last: Knapp

manufacture_protocol: 65mer Oligos were designed by Sigma Aldrich. Oligos were spotted using a Affymetrix 417 spotter.


title: Maize oligonucleotide array 46K version

city: Tucson, AZ

first: Jack

last: Gardiner

state: AZ

address: 303 Forbes Building, University of Arizona

institute: Maize Oligonucleotide Array Project

organism: Zea mays

description: Spotted 70-mer oligo array on glass. The maize array set 46K version contains ~46,000 unique probes from maize

manufacture_protocol:
REHYDRATION AND PRINTING OF THE OLIGONUCLEOTIDE MICROARRAYS
1.Add 15 uL of 3XSSC to each well of the 300 pM oligonucleotide set to make a 20 μM oligonucleotide solution.
2.Transfer onto an orbital shaker for 1 h at RT at 100 rpm. The oligonucleotides are now ready for printing.
3.The maize oligonucleotide microarrays are printed on aminosilane-coated “Superamine” slides (Telechem) using Telechem Type 946 SMP2.0 printing pins.
4.Printing conditions:
Single array element printed per oligonucleotide, 48 pins in the print head, 31% relative humidity, redipping after every 50 slides. The print head Z- velocity is set to a maximum of 10 mm/sec.
5.Bake slides for 2h at 80oC. Store dry and in darkness at RT.
The microarrays are sent out to recipient scientists at this point. Prior to hybridization, these next steps should be followed:
IMMOBILIZATION OF THE OLIGONUCLEOTIDE ARRAY ELEMENTS
1.Rehydrate the microarray slide over 50oC water for 5-10 seconds; snap-dry on a 65oC heating block for 5 seconds. Repeat this step 4-6 times, examining the slides under a dissection microscope (or using red reflectance imaging) to verify complete re-hydration of all the spots. If re-hydration is not complete, repeat the process several more times.
2.Crosslink the oligonucleotides to the slide surface by exposing the DNA-side of the microarray to UV irradiation. We employ a Stratalinker set at an energy level of 180 mJ.
3.Wash the slides in 1% SDS dissolved in sterile ddH2O for 5 min at RT.
4.Rinse the slides by plunging 10 times into sterile ddH2O.
5.Rinse in 100% ETOH for 30 seconds to 5 min, with gentle shaking.
6.Spin dry the slides in a centrifuge at 1000 rpm for 2 min.
7.Store the slides in a light-proof box under cool dry conditions.


title: SuperArray Oligo GEArray® Mouse Extracellular Matrix and Adhesion Molecules Microarray OMM-013

status: Public on Jan 12 2008

city: Frederick

first: SuperArray

last: Bioscience Corporation

address: Suite 101, 7320 Executive Way

institute: Technical Support

description: The Oligo GEArray® Mouse Extracellular Matrix (ECM) and Adhesion Molecules Microarray profiles the expression of 113 genes key to the functions of cell adhesion. This array contains extracellular matrix proteins including basement membrane constituents, collagens, and genes playing a role in ECM structure. Proteases involved in degradation of the ECM are included as well as their inhibitors. This array also represents molecules important to cell adhesion including molecules involved in cell-cell and cell-matrix adhesion, transmembrane molecules, and others. Through a simple side-by-side hybridization experiment you can determine differential gene expression between your samples.

distribution: commercial

manufacture_protocol: see manufacturer's website


title: CIW-8_09-02a

status: Public on Jan 10 2008

city: Taipei

first: Laurent

last: Zimmerli

address: Roosevelt road

country: Taiwan

institute: National Taiwan University

organism: Arabidopsis thaliana


title: Lactobacillus plantarum WCFS1_LpGn 3K DNA array

status: Public on Jan 15 2008

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

institute: Vrije Universiteit Amsterdam

organism: Lactiplantibacillus plantarum WCFS1

description: Lactobacillus plantarum LpGn

manufacturer: Department of Molecular Genetics, university of Groningen, the Netherlands

first: Marc

last: Stevens

first: Michiel

last: Kleerebezem

first: Anne

last: De Jong

first: Oscar

last: Kuipers

manufacture_protocol: See Van Hijum et al, 2005, PMID: 15907200 and Hendriksen et al, 2006, PMID: 17085554


title: University of Texas UTHSC-H Candida albicans 6K v1.0

status: Public on Jan 09 2008

city: University

first: Ameeta

last: Agarwal

state: MS

address: NCNPR, Room 2049

department: National Center for Natural Products Research

institute: University of Mississippi

organism: Candida albicans

middle: K

first: Tao

last: Xu

first: Melissa

middle: R

last: Jacob

first: Qin

last: Feng

first: Michael

middle: C

last: Lorenz

first: Larry

last: Walker

first: Alice

last: Clark

manufacture_protocol: The C. albicans Genome Oligo Set consisting of 70mer probes representing 6266 C. albicans genes was obtained from Qiagen (Valencia, CA), and printed on glass slides by Microarrays, Inc (Nashville, TN).


title: Stintzi Lab Campylobacter jejuni 1.9k array, version 3.0

status: Public on Jan 21 2008

first: Alain

last: Stintzi

description: Campy version 3.0; spotted PCR products.


title: Print_1126

status: Public on Jan 20 2008

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

institute: Stanford University

description: SHFV

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


title: Print_951

description: SHEK


title: Wakimoto Drosophila melanogaster heterochromatin tiling

city: Seattle

first: Barbara

last: Wakimoto

state: WA

address: University of Washington, Box 351800

department: Biology

institute: University of Washington

organism: Drosophila melanogaster

first: Jiro

last: Yasuhara

middle: T

manufacture_protocol: see the Nimblegen website for details


title: Arizona Microarray Qiagen-Operon Arabidopsis Genome Set 31K Version 3.0

status: Public on Jan 25 2008

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

manufacturer: University of Arizona, Department of Plant Sciences

manufacture_protocol:
- add 15 μL of 3XSSC to each well of the 300 pM oligonucleotide set (Qiagen-Operon Arabidopsis Genome Array Ready Oligo Set Version 3.0) to make a 20 μM oligonucleotide solution
- transfer onto an orbital shaker for 1 h at RT at 100 rpm. The oligonucleotides are now ready for printing.
- Arabidopsis oligonucleotide microarrays are printed on aminosilane-coated “Superamine” slides (Telechem)
- Printing conditions:
Single array element printed per oligonucleotide, 48 pins in the print head, 31% relative humidity, redipping after every 50 slides.  The print head Z- velocity is set to a maximum of 10 mm/sec.
- Bake slides for 2h at 80oC. Store dry and in darkness at RT.


title: Agilent-015686 Custom Human 244K CGH Microarray

status: Public on Jan 24 2008

city: Santa Clara

first: Peter

last: Tsang

address: 5301 Stevens Creek Blvd.

department: Agilent Labs

institute: Agilent Technologies

description:
Agilent Custom Human 244K CGH Microarray consisting of 60-mer oligonucleotides
Publication: Perry et al. Nature Genetics, 2007
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The FeatureNum column represents the Agilent Feature Extraction feature number.

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


title: klingenkhh_BAC_3.7k_condensed_array

city: Lund

first: Karolin

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

institute: Lund University

manufacture_protocol: The array contains 3700 probes spotted in triplicate on glass slides. The BAC set is distributed by the Welcome Trust Sanger Institute (Hinxton, UK), and comprises of 1 mb spaced probes, a set of subtelomeric sequences for each chromosome arm, and a few hundred probes selected for their involvement in oncogenesis. Reference: Knijnenburg J, Szuhai K, et.al. Am J Med Genet A. 2005 Jan 1;132(1):36-40. Insights from genomic microarrays into structural chromosome rearrangements.


title: SHDK

department: Pathology


title: Print_1161

description: SHFN


title: OSU subolesin dsRNA injected SSH library

city: Stillwater

first: Patricia

last: Ayoubi

state: OK

address: 246 NRC

department: Biochemistry and Molecular Biology

institute: Oklahoma State University

organism: Ixodes scapularis

manufacture_protocol: Total RNA was isolated from pooled guts and salivary glands of I. scapularis female ticks injected with subolesin dsRNA or injection buffer at 9 dpi (8 days of feeding) using TriReagent (Sigma) according to manufacturer’s instructions. SSH was performed at Evrogen JCS (Moscow, Russia) as described previously (Naranjo et al., 2006; de la Fuente et al., 2007b). Tester and driver RNAs were subtracted in both directions to construct two SSH libraries enriched for differentially expressed cDNAs in subolesin dsRNA-injected (reverse-subtracted) and saline-injected (forward-subtracted) ticks.  Tick cDNA fragments (384 from each of the reverse and forward subtracted SSH libraries) were amplified by PCR using pAL-16 vector-specific primers, purified (MultiScreen PCR plates, Millipore, Billerica, MA, USA). Eight pools of 12 clones each from an unsubtracted I. scapularis cDNA library (de la Fuente et al., 2005a) and subolesin cDNA were also arrayed and used to validate normalization.   The PCR products were purified using Millipore Multi-screen plates and resuspended in 3x SSC to a concentration of about 500ng/ul.  Each probe was then arrayed in quadruplicate onto gamma amino propyl silane coated GAPS II slides (Corning, Lowell, MA, USA).at room temperature and 50% relative humidity using a GeneMachines Omnigrid 100 (Genomic Solutions; Ann Arbor, MI) robot fitted with 4x2 TeleChem SMP4 pins. Printed slides were baked at 80°C for 2 hours.  Slides with immobilized probes were then stored in slide holders and placed in a desiccator at room temperature until use.


title: Agilent-015685 Custom Human 244K CGH Microarray

organism: Homo sapiens

description:
Agilent Custom Human 244K CGH Microarray consisting of 60-mer oligonucleotides
publication: Perry et al. Nature Genetics, 2007
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The FeatureNum column represents the Agilent Feature Extraction feature number.


title: Print_771

description: SHDI


title: SHEN


title: Yale University MCDB Rice japonica NimbleGen 390K Oligo Array version1

status: Public on Jan 04 2008

city: New Haven

first: Hang

last: He

state: CT

address: 165 Prospect St

department: MCDB

institute: Yale University

organism: Oryza sativa

first: Xueyong

last: Li

first: Xiangfeng

last: Wang

first: Kun

first: Yeqin

last: Ma

first: Ning

last: Su

first: Viktor

last: Stolc

first: Waraporn

last: Tongprasit

first: Weiwei

last: Jin

first: Jiming

last: Jiang

first: Songgang

first: XingWang

last: Deng

manufacture_protocol:
1. Oligo length: 36
2. Minimum oligonucleotide Tm: 80
3. Maximum oligonucleotide Tm: 95
4. Temperature to use during secondary structure prediction (an oligo will be rejected if it can fold into a stable secondary structure at this temperature): 65
5. Threshold to report putative cross-hybridizations (all targets hybridizing with a given oligo with a Tm exceeding this threshold are reported): 70
6. Minimum oligonucleotide GC content: 40
7. Maximum oligonucleotide GC content: 73 for gene models; 77 for TARs
8. Minimum distance between the 5' end of two adjacent oligos: 1


title: Print_1257

first: Jonathan

last: Pollack

state: CA

description: SHGU


title: SNU_Breast_CGH_v1.0

city: Seoul

first: Wonshik

last: Han

address: 28 Yongon-dong, Chongno-gu

department: Dept. of Surgery

country: South Korea

institute: Seoul National University College of Medicine

manufacture_protocol:
Construction of BAC library
The array used in this study consists of 4,045 human Bacterial Artificial Chromosomes (BACs), which were spaced approximately 1 Mb on average across the entire genome (MacArrayTM Karyo4000 from Macrogen, Inc., Seoul, Korea). BAC clones were selected from the proprietary BAC library of Macrogen, Inc. Briefly, the pECBAC1 vector was digested with HindIII and size-selected HindIII-digested pooled male DNAs were used to generate a BAC library. These vectors were then transformed into and grown in the Escherichia coli DH10B strain.
Construction of BAC-mediated array CGH microarray
All clones were two-end sequenced using an ABI PRISM 3700 DNA Analyzer (Applied Biosystems, Foster City, CA, USA), and their sequences were blasted and mapped according to their positions described in the University of California, Santa Cruz (UCSC) human genome database (http://www.genome.ucsc.edu). Confirmation of locus specificity of the chosen clones was performed by removing multiple loci-binding clones by individual examination under standard fluorescence in situ hybridization (FISH) as described previously. These clones were prepared by the conventional alkaline lysis method to obtain BAC DNA. The DNA was sonicated to generate ~3-kb fragments before mixing with 50% DMSO spotting buffer. The arrays were manufactured by an OmniGrid arrayer (GeneMachine, San Carlos, CA, USA) using a 24-pin format. Each BAC clone was represented on an array as triplicate spots and each array was pre-scanned using a GenePix 4200A scanner (Axon Instruments Inc., Foster City, CA, USA) for proper spot morphology.


title: JCVI PFGRC Streptococcus pneumoniae 17K v5 array designed primarily based on strain TIGR4

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

institute: J. Craig Venter Institute


title: Human tiling 1.0F array, chip 7 of 14

status: Public on Jan 01 2008

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

manufacture_protocol: See manufacturer's web site


title: JCVI PFGRC Streptococcus pneumoniae 17K v6 array designed primarily based on strain G54

city: Rockville

manufacture_protocol: 6QSP, with arrayer GENETIX, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 7383017, pen id 10181, pen cycles -1, operator bj, humidity control On, humidity set point65


title: Human tiling 1.0F array, chip 4 of 14


title: Human tiling 1.0F array, chip 5 of 14


title: Human tiling 1.0F array, chip 2 of 14


title: Human tiling 1.0F array, chip 1 of 14


title: Human tiling 1.0F array, chip 14 of 14


title: NimbleGen Mouse 385k custom array [deLaat_4C_2005_11A]

city: Rotterdam

first: Wouter

last: de Laat

address: Dr. Molewaterplein 50

department: Cell Biology

institute: Erasmus MC

organism: Mus musculus

first: Robert-Jan

last: Palstra

manufacture_protocol: Details on the manufacture protocol can be found on http://www.nimblegen.com/technology/index.html


title: Nimblegen Macaque Whole genome CGH 385K array

city: Boston

first: Arthur

middle: S

last: Lee

state: MA

address: 221 Longwood Ave.

institute: Harvard Medical School

organism: Macaca mulatta

manufacture_protocol: Whole genome CGH design for Macaca mulatta (rhesus monkey; rheMac2). Probes were selected from rheMac2_tiling database using an interval spacing of 5950 bp and a window size of 500 bp. 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: 6455 bp (mean); 6476 bp (median). Added 4306 random probes.


title: Mitoligo

status: Public on Jan 13 2008

city: Angers

first: Matthieu

last: Arvier

address: 4 rue larrey

department: UMR 694

country: France

institute: INSERM

organism:
Homo sapiens
Rattus norvegicus

first: Jean-François

last: Dumas

first: Yves

last: Malthièry

first: Gilles

last: Simard

first: Patrick

last: Ritz

first: Catherine

last: Chevallier

first: Jean

last: Leger


title: Human tiling 1.0F array, chip 12 of 14


title: Human tiling 1.0F array, chip 10 of 14


title: Ecole Normale Superieure/Lopez_Phaeodactylum tricornutum_7K_v1.0

city: La Jolla

first: Andrew

last: Allen

address: 11149, North Torrey Pines Road, Suite 220

department: Deptartment of Environmental Genomics

organism: Phaeodactylum tricornutum

first: Pascal

last: Lopez

first: Chris

middle: P

last: Bowler

first: Julie

last: LaRoche

manufacture_protocol: Oligo array, spotted at Ecole Normale Superieure


title: DKFZ/Operon Human Oligo Set v4.0

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
Spotted long oligonucleotide array produced using the Operon Human Genome Oligo Set Version 4.0.
Keywords = human
Keywords = long oligonucleotide
Keywords = oligo
Keywords = 70mer
Keywords = Operon

first: Kolja

last: Freier

first: Karl

last: Knoepfle

first: Christa

last: Flechtenmacher

first: Susanne

last: Pungs

first: Christof

last: Hofele

first: Meinhard

last: Hahn

first: Stefan

last: Joos

first: Peter

last: Lichter

manufacture_protocol: 70mer oligonucleotides were diluted at 40 µM in FBNC buffer (G. Wrobel et al., Nucleic Acids Res 31 e67, 2003) and spotted as array duplicates using epoxy-silane coated glass slides (Schott Nexterion) and stainless steel split pins (SMP3, Telechem) at 20°C and 40% rH. Slides were dried (60' @ 60°C) and DNA was UV-crosslinked with 240 mJ/cm2 @ 254 nm. Slides were stored, sealed airtight and dry, at 4°C.


title: LC Sciences Human 4k microRNA array

city: New Orleans

first: Erik

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

institute: Tulane Health Sciences Center

description: MicroRNA array platform for EBV LMP1 regulated microRNA Analysis

first: Xiaochuan

last: Zhou

first: Jennifer

last: Cameron

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


title: CodeLink UniSet Mouse I Bioarray

first: David

last: Sullivan

address: 20 Staniford Street

institute: Schepens Eye Research Institute

description:
CodeLink UniSet Mouse I Bioarray contains single-stranded oligonucleotide probes derived from a large majority of publicly available, well-annotated mRNA sequences found in the Mouse UniGene set of unique clusters. Each bioarray contains probes for an independent assay of all 10,000 genes in the set.

This is a user-specific platform not meant to be shared by others.


title: Pyrococcus Horikoshii OT3_proteomics study

city: Cambridge

first: Yasunobu

last: Murata

address: 77 Massachusetts Ave, MIT 46-4151

institute: MIT

organism: Pyrococcus horikoshii OT3

technology: MS

description: The list of genes encoded in Pyrococcus Horikoshii OT3 genome, based on the Refseq annotation.

distribution: virtual

first: Hideki

last: Matsuzaki

first: Chizu

last: Kuroishi

first: Masashi

last: Miyano

first: Koji

last: Takio

first: Hisaaki

last: Taniguchi


title: LGTC_Mouse_SigmaCompugen_Mu22K_Rosetta

city: Leiden

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

institute: Leiden University Medical Center

manufacture_protocol: Spotting of 20 uM oligonucleotide solutions in 50% DMSO on poly-L-coated glass slides


title: 32K Cotton cDNA array

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

institute: College of life sciences, Peking University

organism: Gossypium hirsutum

manufacturer: CapitalBio Corporation, National Engineering Research Center for Beijing Biochip Technology, 18 Life Science Parkway, Beijing 102206, China

manufacture_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine's linear RNA amplification method and subsequent enzymatic reaction. In detail, double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 10 ¦Ìg total RNA using the cDNA synthesis system according to the manufacturer's protocol (TaKaRa). A T7-oligo(dT) primer (5'-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTTTTTTTTTTTTTTTTT-3') was used instead of the poly-T primer provided in the kit. After completion of double-stranded cDNA synthesis, cDNA products were purified using a PCR purification kit (Qiagen) and eluted with 60 ¦ÌL elution buffer. One-half of the eluted double-stranded cDNA products were vacuum evaporated to 8 ¦ÌL and subjected to 20-¦ÌL in vitro transcription reactions at 37¡ãC for 3 h using the T7 RiboMAX Express large scale RNA production system (Promega). The amplified RNA was purified using the RNeasy mini kit (Qiagen). Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 2 ¦Ìg amplified RNA was mixed with 2 ¦Ìg random hexamers, denatured at 70¡ãC for 5 min, and cooled on ice. Then, 4 ¦ÌL of first-strand buffer, 2 ¦ÌL of 0.1 M DTT, 1 ¦ÌL 10 mM dNTP, and 1.5 ¦ÌL SuperScript II (Invitrogen) were added. The mixtures were incubated at 25¡ãC for 10 min, then at 42¡ãC for 60 min. The cDNA products were purified using a PCR purification kit (Qiagen) and vacuum evaporated to 10 ¦ÌL. The cDNA was mixed with 2 ¦Ìg random nanomer, heated to 95¡ãC for 3 min, and snap cooled on ice. Then, 10 ¦ÌL buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (Amersham Pharmacia Biotech) were added to final concentrations of 120 ¦ÌM dATP, 120 ¦ÌM dGTP, 120 ¦ÌM dTTP, 60 ¦ÌM dCTP, and 40 ¦ÌM Cy-dye. Klenow enzyme (1 ¦ÌL; TaKaRa) was then added, and the reaction was performed at 37¡ãC for 60 min. Labeled cDNA was purified with a PCR purification kit (Qiagen) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed with 30 ¦ÌL hybridization solution (50% formamide, 1x hybridization buffer; Amersham Biosciences). DNA in hybridization solution was denatured at 95¡ãC for 3 min prior to loading onto a microarray. Arrays were hybridized at 42¡ãC overnight and washed with two consecutive solutions (0.2% SDS, 2x SSC at 42¡ãC for 5 min, and 0.2x SSC for 5 min) at room temperature.


title: SAGE:10:NlaIII:Rhipicephalus microplus

status: Public on Jan 08 2008

last: GEO

organism: Rhipicephalus microplus

technology: SAGE NlaIII

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


title: Homo sapiens 1.2 K allele specific expression 2

status: Public on Jan 05 2008

city: Baltimore

first: Aik Choon

last: Tan

address: 1650 Orleans Street, RM 1M86

department: The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins

institute: Johns Hopkins University

technology: oligonucleotide beads

manufacture_protocol: See Supplementary file


title: Human 70-mer oligonucleotide microarray

city: Jinan

first: Xiao-Lin

last: Zhang

state: Shandong Province

address: West Wen Hua Road 107

department: Department of Hematology

institute: Qilu Hospital, Shandong University

first: Xiao

middle: L

first: Jun

last: Peng

first: Zhi

last: Sun

first: Ming

last: Hou

manufacture_protocol: A human genome 70-mer oligonucleotide microarray was obtained from CapitalBio Corporation (Beijing, China) Briefly, a human genome oligonucleotide set (version 2.0) consisting of 5’ amino acid-modified 70-mer probes and representing 21,329 well-characterized Homo sapiens genes was purchased from Operon. Then Oligonucleotides were dissolved in EasyArrayTM spotting solution (CapitalBio Corp) , and printed on PolymerSlide, in which the surface is covered by a thin layer of aldehyde group modified three-dimensional polymer chain (CapitalBio Corp.).


title: Thalassiosira pseudonana NimbleGen 36mer-oligo gene-specific array

city: Seattle

first: E.

middle: Virginia

last: Armbrust

address: Ben Hall IRB, 616 NE Northlake Pl, Room 306

department: Oceanography

institute: University of Washington

organism: Thalassiosira pseudonana CCMP1335

description: Only probes matching Thalassiosira pseudonana genome version 3 are listed.  Any probes matching more than 4 duplicate positions in Thalassiosira pseudonana genome version 3 are not represented here.

manufacturer: University Wisconsin, Madison; Biotechnology Center

first: Matthew

last: Rodesch

last: Robison

first: Sandra

last: Splinter BonDurant

first: Kathryn

last: Richmond

first: Manoj

last: Samanta

manufacture_protocol:
1.  Gene-specific array design:  A gene-specific array was designed with 176,320 36-mer genomic probes that were selected from the preliminary set of 15,906 transcribed units (TUs) based on the tiling arrays, existing EST data and the version 2 JGI models. The design included up to 68 probes from each gene or transcribed regions. Each array also included ca. 500 random duplicated probes for normalization and noise estimation purposes. The location of the probes on each array was randomized in order to eliminate any positional bias in the synthesis and hybridization.
2. Synthesis: Six complete sets (in quadruplicate for each growth condition (biological replicates)) of the gene-specific microarrays were synthesized for hybridization with labeled cDNA from the control, low silicon, nitrogen, iron, temperature and alkaline pH. Microarrays were fabricated using a modified Maskless Array Synthesizer (MAS) as described previously (Sing-Gasson et al. 1999, Nuwaysir et al. 2002) on SuperClean (ArrayIT) glass substrates functionalized with N-(3-Triethoxysylylpropyl)-4-hydroxy-butryamide (Gelest Inc). Delivery of standard DNA synthesis reagents (Proligo) and NPPOC phosphoramidite (Nimblegen) was performed via an Expedite DNA synthesizer.
3. Array Processing: After synthesis, microarrays were deprotected by immersion in EDA/EtOH (1:1 vol) for two hours at room temperature.  Arrays were then washed in water, dried with argon, and stored desiccated prior to hybridization.  Hybridization was performed with 10ug of fragmented cRNA in 300ul in the presence of 100mM MES, 1M Na, 20mM EDTA and 0.01% tween20 for 17 hours at 45C.  After hybridization, arrays were washed with a non stringent wash buffer (NSWB) (6X SSPE and 0.01% Tween 20) followed by incubation with a stringent wash buffer (100mM MES, 0.1M Na+, 0.01% Tween 20) for 30 minutes at 45C.  Arrays were stained with streptavidin-cy3 (Amersham) for 25 minutes at room temperature, washed with NSWB, rinsed with Final Wash Buffer (Nimblegen) and dried under argon. Arrays were scanned using an Arrayworx scanner (Applied Precision).  Array feature intensity was extracted from images using in-house software.


title: Chaetoceros neogracile 1.8 Kb cDNA microarray platform

status: Public on Dec 13 2007

city: seoul

first: Gyeongseo

last: Jung

address: 17 haengdang-dong, seongdong-gu

institute: Hanyang university

organism: Chaetoceros neogracilis

first: EonSeon

last: Jin

manufacture_protocol: We constructed the cDNA microarrays from the Chaetoceros neogracile cDNA library (Jung et al., 2007). 2500 selected expressed sequence tags (ESTs) from each clone, including housekeeping genes like ribosomal binding proteins, were amplified by PCR using M13 primers and recovered by a MultiScreen PCR Filter Plate (Millipore, Billerica, MA, USA). Each cDNA chip was designed with 1774 successfully amplified PCR products from the cDNA library. Additionally, several control clones from the Saccharomyces cerevisiae intergeneic sequences were included. Microarrays were produced using a fully automated system by robotic operation at Digital Genomics (Seoul, South Korea). The cDNA PCR products were spotted onto amine-coated GAPSII slides (Corning Inc., Corning, NY, USA) using MG II (Biorobotics Inc., Woburn, MA, USA) with a 240 um pitch between spots as a twin format. There were 22 x 22 spots per block, and the spot diameter was 100~140 um. To evaluate fabrication, a cDNA microarray was stained with Syto61 (Molecular Probes, Eugene, OR, USA).


title: UAB 32K v1

status: Public on Nov 09 2007

city: Birmingham

first: Jan

last: Dumanski

state: AL

address: 720 20th Street South

department: Department of Genetics

institute: University of Alabama

manufacturer: Howell and Elizabeth Heflin Center for Human Genetics, University of Alabama at Birmingham (UAB)

first: Carl

last: Bruder

first: Arek

last: Piotrowski

manufacture_protocol: The 32,450 BAC clones were amplified using three independent DOP PCR amplifications, followed by pooling of the DOP PCR products and re-amplification using a universal amino-modified primer. The amino-PCR-products were then purified using Millipore filter plates, eluted with printing buffer. Quality control agarose gel electrophoresis was performed for all clones after the universal amino PCR, and the gel images were stored in an image database. All DNA transfers were performed using a Hydra 96 channel micro-dispenser (Matrix Technologies, Hudson, NH) and a Biomek FX robot (Beckman-Coulter, Fullerton, CA). The aminogroup attached at the 5’ end of the universal primer, allows for covalent attachment of DNA fragments to the CodeLink HD slide surface (GE Healthcare, Piscataway, NJ). We used the spotting solution recommended for these slides (GE Healthcare). Printing of the clones was carried out using a high throughput printing robot (http://www.heflingenetics.uab.edu/CORE/array_printing.shtml). The center-to-center distance between the spots was 160 micrometers using a hexagonal printing pattern.


title: Yale University MCDB Rice japonica NimbleGen 390K Oligo Array for H3K4Me2 and H3K4Me3 version1

city: New Haven

first: Hang

last: He

address: 165 Prospect St

institute: Yale University

first: Xuyong

last: Li

first: Xiangfeng

last: Wang

first: Kun

first: Yeqin

last: Ma

first: Ning

last: Su

first: Viktor

last: Stolc

first: Waraporn

last: Tongprasit

first: Weiwei

first: Jiming

last: Jiang

first: Songgang

first: XingWang

last: Deng


title: BIARC Portunus pelagicus 5000

status: Public on Jan 03 2008

city: Maroochydore DC

first: Anna

middle: Viktoria

last: Kuballa

state: Queensland

address: University of the Sunshine Coast

department: Faculty of Science, Health and Education

country: Australia

institute: University of the Sunshine Coast

organism: Portunus pelagicus

middle: V

first: Timothy

last: Holton

first: Abigail

last: Elizur

manufacture_protocol: cDNA clones, generated using the SMART cDNA library construction kit (Clonetech, Mountain View, CA, USA), were amplified using kit supplied primers and spotted (split pin spotter) onto glass, aminosilane slides.  The slides were baked and UV cross linked to bind the DNA.


title: Black tiger shrimp subtractive hybridization cDNA array

city: Charleston

first: Enrique

last: de la Vega

state: SC

address: 331 Fort Johnson Road

department: Biochemistry

institute: Medical University of South Carolina

organism: Penaeus monodon

manufacturer: Australian Institute of Marine Science / University of Queensland

first: Michael

last: Hall

first: Kate

middle: J

last: Wilson

first: Antonio

last: Reverter

first: Rick

middle: G

last: Woods

first: Bernard

last: Degnan

manufacture_protocol:
Construction of cDNA libraries
Suppression subtractive hybridization (SSH) (Diatchenko et al. 1996), was used to generate cDNA libraries enriched for genes that are regulated under different types of environmental stress exposure. Double stranded cDNA was prepared from 2 µg poly A RNA extracted from shrimp haemocytes (pool of three shrimp), digested with Rsa I, and tester and driver cDNAS generated for treatments and controls using the PCR-Select cDNA Subtraction Kit (Clontech) according to the manufacturer’s instructions. The PCR-amplified cDNA fragments generated by SSH were then ligated into the plasmid pGEM-T Easy (Promega) and used to transform High Efficiency JM109 competent cells (Promega) according to the manufacturer’s instructions. Six different SSH cDNA libraries were constructed enriching for both up and down regulated genes during osmotic, hypoxic and hyperthermic environmental stress exposure. A total of 1248 random recombinant colonies were hand-picked, cored and further amplified in 96 well plates with LB ampicillin.
A full-length enriched cDNA haemocyte library in λ TriplEx2 was also constructed from haemocytes of a single hyperthermic stressed shrimp using the SMART cDNA library construction kit (Clontech) following manufacturer’s instructions for long distance PCR. The cDNA ligated into λ TriplEx2 arms was packaged using the Gigapack III Gold ® packaging system (Stratagene) and the phage used to infect E. coli, strain XL1-blue cells. A total of 2688 random recombinant plaques were cored and the phage eluted in SM buffer.
PCR amplification and construction of cDNA microarray
The insert from each of the 3936 cDNA fragments from the SSH libraries and the non-subtracted haemocyte library was PCR-amplified using either pTriplEX2 sequencing forward and reverse primers (Clontech) for clones from the pTriplEx2 cDNA library or SSH nested primers 1 and 2R (Clontech) for clones from the SSH libraries. PCR products were assessed by agarose gel electrophoresis (Holloway et al. 2003), isopropanol precipitated, washed with 70% ethanol and resuspended in 60 μl of 4X SSC, 0.1% sarkosyl.  The 4032 DNA elements composed of PCR products from the different cDNA libraries and a series of controls were spotted in duplicate onto polylysine-coated glass slides using a GMS 417 Arrayer robot (Genetic Microsystems). Post-processing of the slides was accomplished as previously described (Woods et al. 2004 Development 131(12): 2921-2933.).


title: Saccharopolyspora erythraea 7K (Saccaroa520128F)

status: Public on Jan 02 2008

city: Segrate - Milan

first: Giorgio

last: Corti

address: via Fratelli Cervi 93

department: Institute of Biomedical Technologies

institute: National Research Council

organism: Saccharopolyspora erythraea

description:
the chip is contains: total probes = 218544; Affymetrix control probes = 1422; Saccharopolyspora specific probes = 217122
the probes are organized into: total probesets 7060; Affymetrix control probesets: 45; Saccharopolyspora specific probesets: 7015

manufacture_protocol: in situ oligonucleotide synthesis


title: Human tiling 1.0F array, chip 9 of 14

city: Yokohama

first: Takahiro

last: Suzuki

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN

manufacture_protocol: See manufacturer's web site


title: MWG_Zebrafish_14K

city: Taipei

first: Ming Yi

last: Chou

state: Taiwan

address: 128 Sec. 2 Acdemia Rd.

department: Cellular and Organismic Biology

institute: Acdemia Sinica

organism: Danio rerio

first: MY

first: ST

last: Liu

first: FC

last: Ting

first: BK

last: Liao

manufacture_protocol:
Zebrafish 14K array comprising 14067 zebrafish genes is an important tool for general biomedical research. Oligonucleotides were calculated using 1800 zebrafish gene sequences from the NCBI and a database of 12768 putative open reading frames (ORF). The ORFs were established in-house using NCBI zebrafish EST sequence information.
The commercial zebrafish 14K oligonucleotides set (MWG
Biotech AG, Ebersbach, Germany) were obtained and were printed on UltraGAPS Coated slide (Corning, New York, NY ) with use of the OmniGrid 100 microarrayer (Genomic Solutions, Ann Arbor, MI) according to the manufacture’s instructions. The 14,067 oligonucleotides represent 9666 genes (7009 singlet genes and 2657 redundant genes), and the redundancy of this chip is 31 %. The detailed description of the oligonucleotides information can be obtained on the Ocimun Biosolution website (http://www.ocimumbio.com/web/default.asp).


title: AppChip1 (NRC-IBS Actinobacillus pleuropneumoniae L20)

status: Public on Apr 13 2006

city: Ottawa

first: John

middle: H

last: Nash

state: Ontario

address: 100 Sussex Drive

department: Institute for Biological Sciences

organism: Actinobacillus pleuropneumoniae

description: PCR primers were designed for 2025 ORFs from a draft genomic sequence of Actinobacillus pleuropneumoniae L20 which comprised 2091 ORFs on 66 contigs. For AppChip1, all genes are spotted in duplicate on the microarray and sheared total genomic DNA from A. pleuropneumoniae L20 and porcine DNA were spotted in the top row of each subarray as controls.

first: Wendy

middle: A

last: Findlay

first: Brian

last: Agnew

first: Simon

last: Foote

manufacture_protocol: Primers were synthesized at the Biotechnology Research Institute (BRI-NRC) in Montreal. ORF-specific amplicons were produced from 30 ng of genomic DNA template by standard PCR amplification methods. Amplicon quality was evaluated by agarose gel electrophoresis. Amplicons were purified, lyophilized, and sent to BRI-NRC for printing onto microarray slides.


title: E. coli array print #4

status: Public on Sep 14 2005

city: Los Angeles

first: Katy

last: Kao

address: 420 Westwood Plaza/5805 Boelter Hall

department: Chemical Engineering

institute: University of California, Los Angeles

organism: Escherichia coli

manufacture_protocol: primer set purchased from Sigma Genosys


title: Human tiling 1.0F array, chip 8 of 14

organism: Homo sapiens


title: Human tiling 1.0F array, chip 6 of 14


title: E. coli array print #1


title: Human tiling 1.0F array, chip 3 of 14


title: Human tiling 1.0F array, chip 13 of 14


title: Hofmann-cichlid-brain-array

status: Public on Feb 05 2004

city: Austin

first: Hans

middle: A.

last: Hofmann

state: TX

address: 1 University Station - C0930

department: Section of Integrative Biology

institute: Universit of Texas at Austin

organism: Haplochromis burtoni

description:
This array is built from a Cichlid cDNA library first made in the lab of Russ Fernald.  mRNA from brains of all ages and stages of the species Astatotilapia burtoni was used.  colony picking, PCR amplification, and array printing have been done at Harvard's Bauer Center for Genomics Research in the lab of Hans Hofmann.  the array also includes yeast control genes and a few other positive and negative controls
Keywords = cichlid
Keywords = brain

first: Susan

last: Renn

first: Nadia

last: Aubin-Horth


title: Human tiling 1.0F array, chip 11 of 14

department: Center for Integrative Medical Sciences


title: DSO/GIS lab Full_Burkholderia_pseudomallei_Genome v2

city: Singapore

first: Sim

middle: Siew

last: Hoon

address: 27 Medical Drive

department: MCB

country: Singapore

institute: DSO National Laboratories

organism: Burkholderia pseudomallei K96243

description:
spotted DNA
This set includes 8836 PCR probes (30 mers) designed in-house using Primer 3

first: Patrick

last: Tan

manufacture_protocol: as described in DSO/GIS Labs manual


title: Surrey S. coelicolor Microarray for DNA/DNA analysis of S. rimosus

status: Public on Jan 11 2008

first: Ralph

last: Kirby

address: Li-Nong Road

institute: National Yang-Ming University

organism: Streptomyces coelicolor

manufacture_protocol: see the Surrey web site below


title: Eurogentec Bacillus subtilis microarray

city: Vancouver

first: Heather

last: Maughan

state: BC

address: Life Sciences Centre

department: Zoology

institute: University of British Columbia

organism: Bacillus subtilis

manufacture_protocol:
Product description

The B. subtilis genome contains 4096 putative open reading frames (ORFs). 8192 primers were designed and synthesized to amplify 4096 ORFs in the B. subtilis genome. The primers were designed to amplify each ORF beginning at the start codon and ending at the stop codon. Each primer contains 15-base non-variable sequence at the 5’-end followed by 18 to 22 bases of ORF-specific sequence. A high fidelity PCR system was used to obtain PCR products. The PCR reactions were performed in two rounds using 96-well plates in a 100 ml reaction volume. The first round of PCR reaction (primary PCR) was done using 10 ng of DNA genomic as template and the specific part of the oligo. The second round of PCR reactions (secondary PCR) was performed in the presence of 5 ul of 40-fold diluted primary PCR products and the C12-NH2 modified universal primers. The entire primary and the secondary PCR reactions were controlled on standard gel electrophoresis for yield and for the expected size. Using these two-step methods we have successfully amplified up to 96 % of 4096 B. subtilis ORFs. The 5’-aminated PCR products were purified using Millipore 96-well purification kit, concentrated to 200 to 500 ng per microliter and then covalently immobilization onto aldehyde coated glass slide through a well-known Schiff base reaction.

Spotting design

B. subtilis MicroArrays are manufactured by printing PCR amplicons suspended in optimized spotting buffer for high coupling efficiency of DNA to the most consistent aldehyde coated glass slides. This spotting chemistry provides us the highest hybridization intensities, which is a consequence of a better binding of the probe to the slides and their accessibility to the cDNA targets. We use ChipWriter™ Pro (Virtek) which is a high precision dispensing robot to spot the PCR products onto aldehyde glass slides. The robot is designed to collect 100 nl of DNA solution and to deposit 0.6 nl per spot. For B. subtilis MicroArray, we use simultaneously 16 pins to place the spots in area of 1.8 x 1.8 cm. In order to generate high quality spots, the printing procedure is performed under a tight controlled humidity and temperature environment. This allows having the complete control on the spot morphology, the spot diameter and uniformity. This configuration of the robot generates 16 blocks, each containing 22 x 24 dots with 180 microns spacing center to center with a spot diameter of 100 microns.


title: JCVI PFGRC Streptococcus pneumoniae 21K v6 array designed primarily based on strain R6

city: Rockville

first: PFGRC

last: JCVI

state: MD

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Streptococcus pneumoniae

description: This set includes 3367 oligonucleotides, has 21168 spots distributed in 48 blocks.

manufacture_protocol: 6QSP, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: STv7bIII_MMCC

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

organism: Salmonella enterica

first: Steffen

last: Porwollik

first: Monica

last: Ponder

first: Pui

last: Cheng

first: Carlos

last: Santiviago

manufacture_protocol: custom made Salmonella PCR product array


title: JCVI PFGRC Streptococcus pneumoniae 21K v6 array designed primarily based on strain TIGR4


title: IFR OGT Salmonella SL1344 22k v1.0

status: Public on Sep 10 2007

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

country: United Kingdom

institute: Institute of Food Research

organism: Salmonella enterica subsp. enterica serovar Typhimurium

first: Marcus

last: Harrison

first: Jay

last: Hinton

manufacture_protocol: The microarrays were designed and produced by Oxford Gene Technology (Kidlington, UK). They consist of 21,939 60-mer oligonucleotides tiled throughout the S. Typhimurium SL1344 NCTC13347 genome and 636 control oligonucleotides. The S. Typhimurium SL1344 sequences were obtained from the Sanger Institute (Hinxton, UK) website (http://www.sanger.ac.uk/Projects/Salmonella/).


title: GUTHRIE_YEAST_SPLICINGARRAY_v20060215a

status: Public on Aug 21 2007

city: Lexington

first: Gregg

middle: Brooks

last: Whitworth

state: VA

address: 204 West Washington St

department: Biology

institute: Washington and Lee Unversity

organism: Saccharomyces cerevisiae

manufacturer: Guthrie Lab, University of California, San Francisco

first: Jeffrey

last: Pleiss

middle: B

first: Megan

last: Bergkessel

first: Christine

last: Guthrie

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


title: University of Pennsylvania/Nathanson Lab_HomoSapiens_5215 unique BACS_FGA011806

status: Public on Apr 20 2007

city: Philadelphia

first: Carmen

middle: Elisa

last: Oquendo

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

description: ULTRA GAPS (Gama Amino Propyl Silane)

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

manufacture_protocol:
This BAC array platform consisted of 5215 unique BACs spotted in-house on CorningCMT Ultra-Gap slides (Corning, USA) using two replicates printed on each slide.  Details of array construction are described elsewhere (Greshock et al., 2004)
Greshock J, Naylor TL, Margolin A, Diskin S, Cleaver SH, Futreal PA, deJong PJ, Zhao S, Liebman M, Weber BL. 2004. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 14(1):179-87.


title: Pinus taeda cDNA (Mårten Lind)

status: Public on Aug 24 2007

city: Raleigh

first: Chris

last: Smith

state: NC

address: 840 Main Campus Dr

department: Bioinformatics Research Center

institute: NCSU

organism: Pinus taeda

description: The microarray contains ESTs selected from 6 Xylem libraries: 1. NXCI - ESTs from juvenile compression wood of Pinus taeda (loblolly pine) 2. NXLV - ESTs from transitional/mature late wood of Pinus taeda (loblolly pine) 3. NXNV - ESTs from mature normal wood of Pinus taeda (loblolly pine) 4. NXPV - ESTs from transitional planings wood of Pinus taeda (loblolly pine) 5. NXRV - ESTs from root wood of Pinus taeda (loblolly pine) 6. NXSI - ESTs from juvenile side wood of Pinus taeda (loblolly pine) , a Pollen Cone library, and a Shoot tip library.

first: Mårten

last: Lind

first: Aleksandra

last: Adomas

first: Guosheng

last: Li

first: Debbie

last: Craig

first: Gunnilla

last: Swedjemark

first: Åke

last: Olson

first: Len

last: van Zyl

first: Bo

last: Karlsson

first: Roger

last: Finlay

first: Ron

last: Sederoff

first: Jan

last: Stenlid

first: Frederick

middle: O

last: Asiegbu

manufacture_protocol: DNA from 1965 ESTs was printed in two replications onto amino-silane coated CMT-GAPS slides (Corning Inc; Corning, NY, USA) using a Lucidea Array Spotter (Amersham Biosciences, USA). After printing, the DNA was cross linked using 250 mJ of UV-C radiation. The slides were subsequently baked at 75ºC for 2 hrs.


title: CBS - 7 genomes E. coli microarray

status: Public on Aug 29 2006

city: Kgs. Lyngby

first: Hanni

last: Willenbrock

address: Kemikalievej, bygning 208

department: Center for Biological Sequence Analysis

institute: DTU

description:
Microarray design covers 7 E. coli strains:
O157:H7 EDL933, O157:H7 RIMD0509952, K-12 MG1655, K-12 W3110, CFT073, O42 and E2348/69

first: Anne

last: Petersen

first: David

middle: W

last: Ussery

manufacture_protocol: NimbleExpress


title: JCVI PFGRC Mycobacterium smegmatis 30K v2 array designed primarily based on strain MC2

status: Public on Sep 09 2006

first: PFGRC

last: JCVI

organism: Mycolicibacterium smegmatis

description: This set includes 6635 oligonucleotides, has 30000 spots distributed in 48 blocks.

manufacture_protocol: 2QMS, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: E. coli array print #3

first: Katy

last: Kao


title: E. coli array print #2


title: JCVI PFGRC Streptococcus pneumoniae 21K v6 array designed primarily based on strain G54


title: URGV Arabidopsis thaliana 25K CATMA_v2.3

status: Public on Jan 25 2008

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

institute: INRA

organism: Arabidopsis thaliana

description: Corning Ultra-GAPS (TM) slides are spotted with 64 pins (8x8) therefore the spotted area is divided into 3 metablocks, each containning 64 blocks of 144 spots (12x12)

first: Jean-Pierre

last: Renou

first: Ludivine

last: Taconnat

first: Vincent

last: Thareau

first: Pierre

last: Hilson

first: Olivier

last: Voinnet

manufacture_protocol:
A.thaliana genes were predicted with Eugene software (Foissac S. et al., Nucleic Acids Res., 2003) and gene-specific sequence tags were automatically designed (Thareau et al. Bioinformatics, 2003 Nov 22). Two rounds of PCR were performed and PCR products were finally purified and dissolved in 50% DMSO in TE at concentrations ranging between 50-200ng/ul and re-arrayed in 1536 microtiter plates. The pins are washed in 0.1% SDS at 50 °C then three times in bi-distilled water. Spotter settings are 45-55% humidity, and a pitch = 180 um. The room temperature is set between 19 and 21 degrees Celsius and below 40 % humidity. The microtiter plates are placed in the biobank. The four trays are cleaned and 100-120 slides placed on them (30 slides per tray). The spotting lasts 25 hours. The slides are stored in the dark in a dry-cabinet for 3 days and UV-cross-linked at 300 mJ. After crosslinking, the slides are stored in the dark in a dry-cabinet.
- 24576 Gene Specific Tags (GST)
- 48 Non Protein Coding (NPC)
- 1207 micro-RNA precursors