title: University of Minnesota Human miRNA version 2

status: Public on Jul 30 2009

city: Minneapolis

first: Xiaoxiao

last: Zhang

address: 312 Church St. SE

country: USA

institute: University of Minnesota

organism: Homo sapiens

technology: spotted oligonucleotide

distribution: non-commercial

manufacturer: Biomedical Genomics Center Microarray Facility at the University of Minnesota

manufacture_protocol: A miRNA probe set was purchased from Invitrogen, which was designed based on the Sanger miRBase Sequence Database, Release 9.0.  The set contains approximately 1,140 oligonucleotides of 34 to 44 nt long as probes.  They are complementary to C. elegans, Drosophila, zebrafish, mouse, rat, and human miRNAs, and also include a number of internal and negative control probes.  The oligonucleotides were dissolved in 3 x SSC and quadruply printed on Corning® GAPSTM II coated slides  using a BioRobotics Microgrid II spotter


title: Custom Theileria parva oligonucleotide microarray

city: New York

first: Simon

last: Kang'a

state: NY

address: 341 East 25th Street

department: Medical Parasitology

institute: New York University School of Medicine

organism: Theileria parva strain Muguga

manufacturer: Custom made at The Institute for Genomic Research (TIGR), (now J.Craig Venter Institute -JCVI)

first: Vishvanath

last: Nene

first: Bryan

last: Frank

manufacture_protocol: Microarray design and printing was performed by Dr. Simon Kang’a at The Institute for Genomic Research (TIGR), now the J. Craig Venter Institute (JCVI). A total of 4060 unique 70 mer oligonucleotides were designed from an initial 4082 predicted ORF of the Theileria parva (Muguga) genome using the Pick70 program of ArrayOligoSelector software (http://arrayoligosel.sourceforge.net). Oligonucleotide design considerations included uniqueness, avoidance of internal self-annealing structures, narrow annealing temperature (Tm) range over the entire oligonucleotide set, masking of low-complexity regions, balanced base composition (28-30%GC) and proximity to the 3' end. The TIGR genome sequence database containing contigs of the entire T. parva genome was used as the “complete genome source” for screening the 70-mer oligonucleotide sequences for uniqueness using the BLAT feature as implemented in Pick70. The T. parva 70-mer oligonucleotides were also compared by BLAST search against bovine sequences in GenBank and TIGR bovine Gene Index to ensure that they did not cross-hybridize with any bovine host DNA. The 70-mer oligonucleotides were purchased from Illumina (Illumina Inc., San Diego, CA) at a concentration of 50 μM, diluted to 25 μM using an equal volume of Corning Universal Spotting buffer (Corning Inc, Corning, NY) and spotted in quadruplicate onto Corning® UltraGAPS™ aminosilane coated slides (Corning Inc, Corning, NY) using an Intelligent Automation Systems (IAS) arrayer (Cambridge, MA) with a 48-pen print head configuration (12 rows by 4 columns). After printing, the spotted oligonucleotide DNA was cross-linked to the slide surface by UV irradiation at an integrated intensity of 1200 mJ cm-2 using a Stratalink UV Crosslinker (Stratagene, La Jolla, CA). The slides were stored in a desiccator chamber until use.


title: Human-Solexa-ChIP-Seq (NHLBI, NIDDK)

status: Public on Jul 25 2009

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

technology: other

description: Illumina Genome Analyzer

distribution: virtual


title: NHRI Human 46K cDNA array

city: Miaoli County

first: Shu-Chen

last: Liu

address: 35 Keyan Road,Zhunan

country: Taiwan

institute: National Health Research Institutes

technology: spotted DNA/cDNA

manufacture_protocol: The NHRI human cDNA microarray contains 46,657 cDNA clones (IMAGE consortium), representing approximately 26000 unique Unigene clusters. We fabricated cDNA microarrays essentially following protocols  as described by Michael B. Eisen and Patrick O. Brown with minor modification. Briefly, the purified cDNA products were resuspended in spotting solution containing 50% dimethyl sulfoxide. The final concentration of each probe was around 0.2 to 0.5 mg/ml. These probes wererobotically arrayed onto aminosilane-coated UltraGAPS glass microarray slides (Corning) using a home-made robotic microarray spotter. In addition to the human cDNA probes, a series of control DNA probes from the Lucidea Universal ScoreCard (Amersham Bioscience) were also included for quality assessment of the microarray experiment. Totally, there are 49152 probes spotted on a single microarray slides.


title: CombiMatrix_Human_1.6K_miRNA array [condensed version]

status: Public on Jul 31 2009

city: Mukilteo

first: Michael

middle: Joseph

last: Lodes

state: WA

address: 6500 Harbour Heights Pkwy, Suite 303

department: Assay Development

institute: CombiMatrix Corp

technology: in situ oligonucleotide

description:
Arrays for serum miRNA analysis were constructed with 547 human miRNA sequences obtained from the Sanger Database version 10.0 which appeared on 8/2/07.
This array represents a condensed version of full 1.6K array.

distribution: custom-commercial

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: JCVI PFGRC Listeria monocytogenes 17K v4 array designed primarily based on strain HCC23

status: Public on Jul 22 2009

city: Rockville

first: PFGRC

last: JCVI

state: MD

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Listeria monocytogenes

description: This set includes 7704 oligonucleotides, has 17328 spots distributed in 48 blocks.

manufacture_protocol: 4QLM, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: LC Sciences Human miRNA Array

status: Public on Jul 28 2009

city: Debrecen

first: Beata

last: Scholtz

address: Nagyerdei krt 98.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen Medical and Health Science Center

manufacture_protocol: µParaFlo™ microfluidic chip technology


title: Human oligo array from MWG cancerochips_v2009 [condensed array features]

city: Brest

first: Sylvia

last: Quéméner

address: 49 rue Felix le Dantec

country: France

manufacture_protocol: spotted on the Amersham Lucidea spotter. Epoxyslide.


title: JCVI PFGRC Listeria monocytogenes 17K v4 array designed primarily based on strain 4b H7858


title: Solanum tuberosum 12.3K RLP array Version II

status: Public on Jul 24 2009

city: Seibersdorf

first: Friederike

last: Trognitz

state: NÖ

address: Seibersdorf

department: Health & Environment

country: Austria

institute: AIT Austrian Institute of Technology GmbH

organism: Solanum tuberosum

manufacturer: AIT Austrian Research of Technology, Seibersorf, Austria

first: Bodo

first: Jan

last: Rodewald

last: Stierschneider

manufacture_protocol:
The microarray was based on an enriched, full length cDNA library of S. tuberosum var. Yungay, which had been challenged with Phytophthora infestans complex race for four days. The library was made by VERTIS GmbH (Freising, Germany). The cDNA was inserted to the EcoRI/NotI digestion site using vector pBS IIsk+ and transformed into TransforMax TM Ec100TM-T1 electrocompetent cells. Plasmid DNAs of 3840 clones were obtained by adding a small portion of bacterial culture into TempliPhi DNA Sequencing Template kit (GE Healthcare) according to the manufacturer’s instructions. Inserts were amplified by PCR in 50 µl reactions containing 0.5 µl of a 1:100 dilution of the TempliPhi, 5mM dNTPs (Invitrogen, Oslo, Norway), 2.5 mM MgCl2, 1x BD buffer (Solis Biodyne), 0.5 µM each of primers T7 and T5, and 2 U of Firepol polymerase (Solis Biodyne, Tartu, Estonia). The amplification was done in a GeneAmp PCR System 2700 thermocycler (Applied Biosystems) under the conditions: 95°C for 1 min, 2 min at 50°C and 2 min at 72°C and 30 cycles consisting of 95°C 1min, 56°C 2 min and 72°C for 1 min and a final elongation step at 72°C for 5 min.

In addition to the Yungay cDNA library, another 1173 cDNA clones were ordered from the University of Arizona Genomics Institute corresponding to stress related genes and treated as described above and amplified with the corresponding primers. Furthermore, nine housekeeping genes were included. Genes and primers are listed in the array file. They were amplified by using 1 µl of cDNA from S. tuberosum var. Yungay in a mix containing 2.5 mM MgCl2, 0.25 mM dNTPs (Invitrogen, Oslo, Norway), 0.5 µM of each primer, 1x BD buffer (80mM Tris•HCl, 20 mM (NH4)2SO4) (Solis Biodyne, Tartu, Estonia) and 0.2 µl FirePol (Solis Biodyne, Tartu, Estonia) in a PCR reaction of 95°C for 1 min followed by 35 cycles with 95°C 1 min, 55°C 1 min, 72°C 1 min and a final elongation step for 10 min at 72°C.

Twenty µls of all amplicons were lyophilized and then dissolved in 10 µl spotting buffer (3xSSC and 1.5 M betaine). Probes were spotted in duplicate with an Omnigrid 100 (GeneMachines) equipped with 48 TeleChem pins on CAPS II coated slides (Corning) in a 200 µM spot distance and 40% humidity.


title: Campylobacter jejuni 6K whole-ORF array v2.0

city: East Lansing

first: Linda

middle: S.

last: Mansfield

state: MI

address: 181 Food Safety Bldg.

department: Microbiology and Molecular Genetics

institute: Michigan State University

organism: Campylobacter jejuni

description: Array includes ORF coverage from array "Campylobacter jejuni 6.5Kf whole-ORF array v1.0 (GPL7254) plus 46 additional ORFs amplified from strain 11168 using primers designed at Michigan State University.  Also an additional 883 ORFs were amplified from 8 other sequenced C. jejuni strains, primers also manufactured at Michigan State University

manufacturer: Michigan State University Research Technology Support Facility

middle: S

first: Anne

middle: E

last: Plovanich-Jones

first: Julia

middle: A

last: Bell

last: Stanhope

first: Tristan

last: LeFevre

first: Jeff

middle: R

last: Landgraf

manufacture_protocol:
1. First set of Primers were designed at Wayne State University by Jodi R. Parrish, furnished to Michigan State University and are described in “High-Throughput Cloning of Campylobacter jejuni ORFs by in Vivo Recombination in Escherichia coli”, Journal of Proteome Research, Parrish et al., 2004 3(3):582-6.
2. Primers for additional 46 ORFs from C. jejuni 11168 and 883 ORFs from 8 other C. jejuni strains were manufactured at Michigan State University
3. PCR products were amplified from genomic DNA from Campylobacter jejuni 11168 or plasmid DNA obtained from C. jejuni 81-176.  Products were ethanol precipitated, resuspended in 3X SSC, 0.005% SDS print buffer, and run on gels for quality control.
4. 16 pin replicate arrays were printed on Corning UltraGAPS slides using a GenMachines Omnigrid spotting robot and Telechem Chipmaker 3 pins.
5. Each slide contains every spot in duplicate.


title: Salmonid 3600 - Feb 17 2003

status: Public on Feb 11 2004

city: Milwaukee

first: Matthew

middle: Lawrence

last: Rise

state: WI

address: 600 E. Greenfield Ave.

department: Great Lakes WATER Institute

institute: University of Wisconsin - Milwaukee

organism:
Oncorhynchus mykiss
Salmo salar

description:
GRASP ~3600 gene salmonid cDNA microarray
Keywords = Atlantic salmon
Keywords = rainbow trout
Keywords = salmonid

first: Gordon

middle: D

last: Brown

first: Kristian

last: von Schalburg

first: William

last: Davidson

first: Ben

middle: F

last: Koop


title: JCVI PFGRC Listeria monocytogenes 17K v4 array designed primarily based on strain 4b F2365

last: JCVI


title: PC Human Operon 21k v2

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

manufacturer: Microarray Facility - the Prostate Centre at Vancouver General Hospital

manufacture_protocol: This array consists of 21,329 70mer probes representing 21,329 genes ( Operon Version 2.1 of the Human Genome Oligo Set). Oligonucleotides are consolidated into 384-well plates, lyophilized by speed-Vac, and resuspended in 3x SSC to a printing concentration of 30uM. Oligos are printed on aminosilane slides (Erie, Hudson, NH, USA) with a Biorobotics Microgrid II microarray printer (Genomic Solutions). Microspot 10K quill pins (Biorobotics) in a 48-pin tool were used to deposit <0.5 nL per spot onto the slide. The resulting microarrays have a 4 x12 subgrid layout with 392 spots per subgrid, each spot having approximate diameter and pitch of 90 µm and 190µm, respectively. A 280-bp GFP (green fluorescent protein) oligo was printed in subgrid corners to assist in placing on the grid. The slides were crosslinked in a UV Stratalinker 2400 (Stratagene) at 300mJ. Array quality was assessed by visual inspection and hybridization of representative slides from a print run by dye-labelled random 9-mer oligonucleotides. The quality control images were aquired via the ScanArray Express from Perkin Elmer at a 10 micron resolution and quantified with the Imagene 6.0 software suite.


title: Custom Agilent-017087 Human complete chr19 ChIP-on-Chip Microarray 244K

status: Public on Jul 29 2009

city: Montréal

first: François

last: Robert

state: Québec

address: 110, avenue des Pins Ouest

department: Chromatin and Genomic Expression

country: Canada

institute: Institut de recherches cliniques de Montréal (IRCM)

description:
Human complete non-repetitive portions of the chr19, covered with a resolution of ~221bp.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

first: Pierre-Étienne

last: Jacques

first: Sara

last: Hardy

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


title: Prunus persica 5.7K microPEACH1.0

city: Padova

first: Livio

last: Trainotti

address: Via Ugo Bassi 58/B

department: Biology

country: Italy

institute: University of Padova

organism: Prunus persica

description: This set consists of 4,806 70mer oligonucleotides (Operon version 1.0) designed on Prunus persica (peach) Unigene clusters, mainly in the 3 end terminal region. Each oligonucleotide is spotted by our robotic station Biorobotics Microgrid II, in one replicate on a MICROMAX glass slide SuperChip I (Cat No MPS696) provided by PerkinElmer Life Sciences Inc. The deposition is qualitatively assessed by a scan of the spotted slide at 10 micron resolution, using a GSI Lumonics scanner and a protocol that allows the detection of spotted features through the salts derived from the dried solution in which oligonucleotides are dissolved. Moreover all spotted batch are evaluated for the spot shape and oligo linking onto the slide surface using the vistra green method. Microarray slides that meet the quality standards, are washed as recommended by the supplier and the glass slides are stored, ready for use, in the dark under deep vacuum.

manufacturer: Home made MicroCRIBI spotting service, using Operon oligo probes

first: Alice

last: Tadiello

first: Stefano

last: Cagnin

first: Beniamina

last: Pacchioni

first: Caterina

last: Millino

manufacture_protocol:
1.Oligos are arrayed in Genetix 384 Well Microarray Plates (Cat# X7020). Each well contains 600 pmol of 70-mer oligo.
2. Resuspend oligos in 17 µL of Telechem Microspotting solution 1X.
3. Seal plates with Corning seals and after oligos resuspenction print probe with the MicroGrid II Biorobotics spotter.
4. Print is performed with 48 Stealth pins.
5. After printing run plates are stored at -20 C degree.
6. Every 4 months plates are lyophilized and resuspended in adjusted water volume according to the number of spotting runs. This, to maintain the same volume and concentration in all plate well.


title: OSU-CCC MicroRNA Microarray Version 3.0

city: Bethesda

first: Tetsuya

last: Okano

address: 37 Convent Drive, Bldg 37

department: NCI

institute: NIH

organism:
Homo sapiens
Mus musculus

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

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


title: Agilent-019118 Human miRNA Microarray 2.0 G4470B (Probe Name version)

status: Public on Jul 27 2009

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

description:
Agilent Human miRNA Microarray version 2 8x15K (G4470B) annotated against the Sanger miRBASE 12.0 database of miRNAs. The microarray is designed to contain probes specific for each of the human miRNAs in Sanger miRBASE 10.1, as well as probes specific to the human viral miRNAs in this database.

Arrays of this design have barcodes that begin with 16019118 or 2519118.

*** The ID column includes 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 GPL7731.

distribution: commercial


title: Custom Agilent-017092 Human complete chr17 ChIP-on-Chip Microarray 244K

description:
Human complete non-repetitive portions of the chr17, covered with a resolution of ~307bp.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).


title: Compugen Human Oligonucleotide Library 12K

status: Public on Jul 23 2009

city: Nankoku

first: Keisuke

last: Taniuchi

address: Kohasu, Oko

country: Japan

institute: Kochi University Medical School

description: Arrays were custom-printed with a MagnaSpotter robot (BioAutomation Corp.) by a dedicated core facility located at the Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE (by DLK).  They were constructed from a set of sense oligonucleotide (60-mer) probes designed for each human target gene by Compugen Inc., and manufactured by Sigma-Genosys.

manufacture_protocol: Human oligonucleotide probes (60mers) were designed for each target gene (Compugen, manufactured by Sigma-Genosys, Inc). Oligonucleotides (12,135) were resuspended (30µM) in 3X saline sodium citrate (SSC) buffer and spotted onto poly-L-lysine coated slides using a MagnaSpotter robot (BioAutomation) with a 12-pin print head (Telechem) configuration in a humidified, HEPA-filtered hood. After spotting, the DNA was cross-linked to the slides by UV irradiation (350mJ/cm2) with a Stratalinker UV Crosslinker (Stratagene), blocked by succinic anhydride treatment, and rinsed in ethanol. The printed arrays were boxed and stored desiccated at room temperature.


title: Escherichia coli 31K spotted oligonucleotide array

city: Beijing

first: liu

last: hanhua

address: 18 Life Science Parkway

country: China

institute: CBC

organism: Escherichia coli

manufacturer: National Engineering Research Center for Beijing Biochip Technology(CapitalBio corporation), Beijing, China.

manufacture_protocol: The 9, 308 E.coli genome oligo-arrays were constructed by CapitalBio Corp. (Beijing, China) using the 5’-amino-modified 70-mer probe library (Operon, Huntsville, AL). In addition to internal controls, eight intergenic sequences from yeast were used as external controls. All nucleotides were dissolved in DNA Spotting Solution (CapitalBio) at 20 mM and printed on aminosilane-coated glass slides (CapitalBio) using a SmartArrayer-136TM spotter (CapitalBio). After printing, the slides were baked for 1 h at 80°C and stored dry at room temperature until use. Prior to hybridization, the slides were rehydrated over 65°C water for 10 s and UV cross-linked at 250 mJ cm-2 energy. The unimmobilized oligonucleotides were washed off with 0.5% SDS solution for 10 min at 42°C, and SDS was removed by dipping the slides in anhydrous ethanol for 30 s. For hybridization, labeled control and experimental samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed into 80μl hybridization solution (3×SSC, 0.2% SDS, 25% formamide and 5×Denhart’s). Microarrays were hybridized at 42°C overnight and washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C and 0.2% SSC) for 5 min at room temperature.


title: Illumina Human Beta-version microRNA expression BeadChip,

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

technology: oligonucleotide beads

manufacture_protocol: see manufacturer's website


title: Illumina Human-1 Genotyping BeadChip

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

manufacture_protocol: See manufacturer's website


title: National DNA microarray facility of University of Aveiro miRNA chip v1.1

city: Aveiro

first: Patrícia

middle: Matos

last: Pereira

address: Campus Universitário de Santiago

country: Portugal

institute: University of Aveiro

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

first: Patricia

first: Manuel

last: Santos

manufacture_protocol:
miRNA chip v1.1 CONTENTS:
The spotted oligo library was mirVana miRNA probe set V1.0 from Ambion. This library contains 382 42-46mer amine-modified DNA oligonucleotides targeting 281 human, 14 rat and 49 mouse mature miRNA sequences from miRBase Sequence Database version 7.1. In addition, the mirVana miRNA Probe Set includes 33 probes targeting an exclusive set of newly identified human miRNAs, called Ambi-miR™ miRNAs and one positive control and 4 negative controls. The library is provided in 964-well plates in lyophilized form.
The array also included a set of 4 hybridization controls (External Controls) for the detection of RNA spike mixes added to RNA extracts during sample preparation. The control probes were designed so that they had no homology with human, mouse and rat genome and matched in Tm and GC content with mirVana miRNA probe set.
LIQUID HANDLING: The goal was 20 uM oligos in 3XSSC buffer in 384-well plates (Genetix X-6004) ready for robotic spotting.
1. Lyophilized oligos (500 pmol in 96-well plates) were resuspended in 3XSSC to a concentration of 20 uM using a liquid handling station (Sciclone LH 3000, Caliper).
2. After shaking overnight at 4 ºC, at 100 rpm, part of each dissolved oligo was transferred to 384-well plates. The 384-well plate was stored at -80 ºC ready for spotting.
3. The remaining stock in 384-well plates was air dried at room temperature and stored at -80 ºC. When necessary, milliQ water was used to resuspend the oligos accounting for lost volume.
4. The spotting probe set also included 4 External Control (EC) oligos (44mer, lyophilized, provided in separate microfuge tubes). These oligos were resuspended in milliQ water to a concentration of 100 uM. Aliquots for spotting were diluted to a final concentration of 20 uM oligo in 3XSSC. Remaining 100 mM stocks were stored at -20 ºC. Spotting aliquots were air dried at room temperature and stored at -80 ºC, together with the Ambion miRNA probe set.
SPOTTING:
1. The 42-46 mer probes were transfered from the 384-well plates and printed on Nexterion E slides (SCHOTT) with a BioRobotics MicroGrid Compact II spotter (Genomic Solutions) in an environment controlled room. Humidity was 60% ± 2%. Temperature was 21 ºC in the spotter. Quill Pins type MicroSpot2500 (BioRobotics) were used for spotting.
2. For probe fixation, the printed slides were incubated in a humidity chamber at room temperature, overnight.
3. Slides were stored in a desiccator-cabinet (Nalgene, with blue Silica (Sigma)) ready to use (continue with our hybridization protocol).


title: JCVI PFGRC Listeria monocytogenes 17K v4 array designed primarily based on strain 1/2a F6854

first: PFGRC

last: JCVI


title: OSUCCC Human miRNA Expression custom Bioarray

city: Los Angeles

first: Mark

middle: H.

last: Chin

address: 650 Charles E. Young Dr

department: Human Genetics

institute: UCLA

description: Custom array based on Sanger database

manufacturer: Ohio State University Comprehensive Cancer Center


title: Illumina HumanCNV100W v1.0 BeadChip


title: cGRASP Salmonid array, 32K cDNA, version 1, February 2009

city: Nanaimo

first: Shaorong

last: Li

state: British Columbia

address: 3190 Hammond Bay Road

department: Salmon and Freshwater Ecosystems Division

institute: Fisheries and Oceans Canada

description: 32k Salmonid cDNA microarray from cGRASP including features primarily from Atlantic salmon and rainbow trout.

manufacturer: Consortium for Genomic Research on All Salmon Project

manufacture_protocol: Details on the manufacture and testing of the 32k v. 1.0 array may be found on the cGRASP website: http://web.uvic.ca/grasp/


title: JCVI PFGRC Listeria monocytogenes 17K v4 array designed primarily based on strain EGD-e

city: Rockville

address: 9704 Medical Center Drive

institute: J. Craig Venter Institute


title: OciChip Human 40k array

status: Public on Jul 21 2009

city: chennai

first: pavithra

last: shyamsunder

address: iitm

country: India

institute: iit madras

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


title: Illumina HumanCytoSnp-12 Beadchip version 2.0


title: NCI/ATC Mm-MEEBO 30.7k array

city: Frederick

first: Debra

last: Tross

institute: NCI

organism: Mus musculus

description: Derived from GEO Platform GPL4200 03/25/09 - NCI/ATC Mm-MEEBO.

manufacturer: Advanced Technology Center Microarray Facility (NIH/NCI/CCR/ATC)

manufacture_protocol: Microarrays are printed with GeneMachines robotic arrayer from Genomic Solutions (http://www.genomicsolutions.com) that is fitted with a printhead containing 48 SMP2.5 printing pins from Telechem International (http://www.arrayit.com). The mouse long oligonuleotide probe set contains 38,467 optimized 70mers (plus NCI Spotplate #4 controls) obtained from Invitrogen (http://www.invitrogen.com/). The long oligonucleotide probes were purchased in 384-well polypropylene plates (Genetix, 384 microarray) and dissolved print buffer of sodium phosphate (150mM) at ph 8.5 and 4% sodium sulphate at a concentration of 20-30 uM. The microarray spots are printed with 160 micron column x 155 microns row spacing, and one spot is printed per probe per slide. The microarrays were printed on Corning Expoxide slides and post-processed according to the manufacturer's protocol.


title: McGill/Behr lab_M. tuberculosis_10K_v1.0

city: Montreal

first: Pilar

last: Domenech

state: Quebec

address: 1001 Décarie Boulevard

department: IDIGH Program

institute: Research Institute of McGill University Health Centre

organism: Mycobacterium tuberculosis

description:
Contact information for the platform:
Dr. Marcel A. Behr
Division of Infectious Diseases and Medical Microbiology
A5-156, Montreal General Hospital
1650 Cedar Avenue
Montreal, QC  H3G 1A4  Canada

manufacturer: Laboratory of Dr. Marcel Behr  Molecular Epidemiology of Infectious Diseases  Montreal General Hospital Research Institute  McGill University Health Center  Montreal, Quebec, Canada

first: Fiona

last: McIntosh

manufacture_protocol:
1.Oligos are arrayed in Greiner 384-well flat-bottom plates. Each well contains 600 pmol of 70-mer oligo.
2. Resuspend oligos in 3X SSC to 40 uM shake overnight at 4 degrees and rearray 5 µL into 384-well, Genetix polystyrene V-bottom plates (cat# X6004).
3. Seal plates and store at -20 degrees until ready to print.
4. Day of print, thaw plates and centrifuge plates at 2000 rpm for 2 minutes.
5. Remove seals and place plate in the plate cassette.
6. Arrays are spotted using a Virtek robot and the software that runs the system is VersArray ChipWriter Pro 2.1.1
7. Make sure plates rest behind both holding clips in the cassettes. Push plates back into the cassettes as far as they will go, putting them in the proper position for the server arm.
8. After the print run is completed, remove plates, seal and store at -20 degrees.
9. For each subsequent preparation of these plates for a print run, verify if any evaporation has occured.  Add water to the wells if necessary.  The amount of water should be decreased by 0.25 µL per print run, as this is the amount drawn up by the pin capillary during each print.


title: Illumina HumanCytoSnp-12 Beadchip version 1.0


title: University of Gothenburg Rainbow trout 15.5K microarray version 1

status: Public on Jul 19 2009

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

country: Sweden

institute: Chalmers University of Technology

organism: Oncorhynchus mykiss

manufacturer: Department of Neuroscience and Physiology, University of Gothenburg / Febit gmbh, Heidelberg, Germany

manufacture_protocol: Probes were designed according to Gunnarsson et al 2009. Oligonucleotides were then synthesized in situ on one single biochip using the 5’ standard synthesis set for Geniom Instrument (http://www.febit.com/go/en/).


title: Williams lab _Mycobacterium leprae_2.7K oligo array

city: Baton Rouge

first: Diana

middle: L

last: Williams

state: LA

address: Skip Bertman Dr.

department: Laboratory Res Branch

institute: HRSA, BPHC, NHDP

organism: Mycobacterium leprae

manufacture_protocol: Oligos were suspended in 3X SSC and spotted using SMP3 Stealth Spotting Pins from Arrayit. Printing was carried out in a climate-controlled cabinet at 55% humidity and 25°C. Average spot size was approximately 150um and spots were spaced approximately 200um apart. Array contains 1,604 coding genes, 1,116 pseudogenes (2,720 total).


title: DGC r1.0 9k Drosophila custom microarray

status: Public on Jul 18 2009

city: Nantes

first: Mahatsangy

last: Raharijaona

address: Faculte de Medecine - Inserm U915 1 rue gaston Veil

institute: INSERM

organism: Drosophila melanogaster

manufacture_protocol: Gene expression experiment were carried out using home-made nylon microarray provided by the TAGC platform (Marseille-Nice Genopole). They contained 7500 amplification PCR products of unique full length cDNA clones from the Drosophila Gene collection release version 1.0 (Berkeley Drosophila Genome project) and controls. Detailed protocol is available at this URL: http://tagc.univ-mrs.fr/oncogenomics/Nylon_microarrays.php


title: SMD Print_1381 Saccharomyces cerevisiae

status: Public on Jul 15 2009

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

organism: Saccharomyces cerevisiae

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: Whitehead Institute Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F

status: Public on Jul 16 2009

city: Cambridge

first: Shilpa

middle: Manohar

last: Hattangadi

state: MA

address: 9 Cambridge Center

department: Lodish Lab

institute: Whitehead Institute (WIBR)


title: BOMC Bovine 25K v1.0

city: St. Paul

first: John

last: Garbe

state: MN

address: 1988 Fitch Ave

department: Animal Science

institute: University of Minnesota

organism: Bos taurus

manufacturer: Oligos synthesized by Illumina, slides printed by University of Arizona

first: Christine

last: Elsik

first: Scott

last: Fahrenkrug

first: Jerry

last: Taylor

manufacture_protocol: 70-mer oligonucleotides


title: ARK-Genomics G. gallus 20K v3.0

status: Public on Jul 17 2009

city: Roslin

last: Fell

state: Midlothian

address: Roslin Institute

department: Bioinformatics

country: United Kingdom

institute: ARK-Genomics@Roslin Institute

organism: Gallus gallus

description: This is an oligo array containing 20460 elements. Oligos were designed using gene predictions from Ensembl and TIGR, together with full-length cDNAs from the BBSRC UMIST ChickEST database (http://chick.umist.ac.uk/) and chicken bursal EST sequences from Jean-Marie Buerstedde's DT40 database. Sequences from these resources were aligned together and oligos were designed against regions in common to more than one dataset. Oligos were then designed using OligoArray2.0.

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

first: Wilfrid

last: Carre

first: Richard

last: Talbot

first: Andy

last: Law

last: Young

first: Pete

last: Kaiser

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


title: IFR_Salmonella_5.3k_v1.0

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

institute: Institute of Food Research

organism: Salmonella enterica

first: Arthur

last: Thompson

first: Jay

middle: C

last: Hinton

manufacture_protocol: PCR product array of whole ORF's from S. Typhimurium LT2. For description of PCR amplification and printing procedures see Eriksson et al., Molecular Microbiology(2003) 47(1): 103-118.


title: Hebrew University S. pyogenes expression 4Xplex long oligo probe (45-70 mer) array

city: Jerusalem

first: Ilia

last: Belotserkovsky

address: Ein-Kerem Campus

country: Israel

institute: Hebrew University

organism: Streptococcus pyogenes

manufacture_protocol: NimbleGen protocol


title: Ocimum Helicobacter hepaticus Array

status: Public on Jul 14 2009

city: Hannover

last: Josenhans

address: Carl-Neuberg-Strasse 1

department: Institute for Medical Microbiology

country: Germany

institute: Hannover Medical School

organism: Helicobacter hepaticus

manufacture_protocol: see manufacturer's web site


title: Taylor Vibrio 4K

city: Hanover

first: Ronald

middle: K

state: NH

address: N. College Street HB7550

department: Microbiology

country: USA

institute: Dartmouth Medical School

organism: Vibrio cholerae

manufacture_protocol: Oligos were obtained from Illumina. The format is 96-well plates, 50uM 70 and 50-mers. Printing plates were prepared by diluting to 25uM in 100% DMSO. Arrays were printed on Corning Ultra-GAPS slides using a GMS 417 Arrayer. Slides were crosslinked with 600mJ UV.


title: Mus musculus 156K NotSAT tiling array

city: Tokyo

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

institute: Keio University

description: NotSAT array is a tilling array designed for NotI site-related and sense-antisense transcripts (SATs). The fragment value was calculated by corresponding probe values by taking the median probe. Since the normalization was performed after summarizing the fragment value, PLATFORM contains just summarized data. "Raw data file" contains the raw data and the platform table for the raw data.

first: Keiji

last: Hirabayashi

first: Shinya

last: Sato

first: Shintaro

last: Yagi

first: Kunio

last: Shiota

manufacture_protocol: NotSAT array is a tilling array designed for NotI site-related and sense-antisense transcripts (SATs). Each genomic DNA fragments generated by combined HpyCH4IV and TaqI were to be measured by tilling probes covering the region that derives a fragment (corresponding probes). The fragment value was defined as the median value of corresponding probes. Since the normalization was performed after summarizing the fragment value, PLATFORM contains just summarized data. "Raw data file" contains the raw data and the platform table for the raw data.


title: Ambion Human Mouse Rat miRNA microarray (probes_1564V1_Oct05), condensed version

city: Oxford

first: Cecilia

last: Lindgren

address: Roosevelt Drive

institute: Wellcome Trust Centre for Human Genetics, University of Oxford

description: condensed version of Ambion_probes_1564V1_Oct05


title: SMD Print_1380 Saccharomyces cerevisiae

first: Andre

last: Gerber


title: CEA - DSV/IRCM/LEFG : Human 25k oligo v1.0

city: Evry

first: Olivier

last: ALIBERT

address: 2 rue Gaston Crémieux

department: IRCM

institute: CEA

organism: Homo sapiens

first: Maltere

last: Peggy

first: Robert

last: Amelie

first: Tendil

last: Simon

manufacture_protocol: Chip contains 25527 oligonucleotides from human RNG/MRC collection (Le Brigand K et all, An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. Nucleic Acids Res. 2006 Jul 19;34(12)). Oligos printed in phosphate buffer with MicroGridII (BioRobotics).


title: Agilent-012694 Whole Mouse Genome G4122A reannotated using bioconductor package mgug4122a 2.0.1 (Aug/2007)

city: Barcelona

first: Hernando

last: del Portillo

state: Barcelona

address: rosello, 132 (4a)

country: Spain

institute: Barcelona Centre for International Health Research

description:
Designed to truly represent all known genes in the mouse genome and their resulting transcripts, Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts. Content for this microarray was generated from leading public databases, including RefSeq, RIKEN, NIA, Ensembl, RIKEN, UCSC Goldenpath, and Unigene.
Arrays of this design have barcodes that begin with 16012694 or 2512694.
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.
OBS: reannotation of GPL2872 using the bioconductor package mgug4122a 2.0.1 (Aug/2007).

first: Ricardo

middle: Z

last: Vencio

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


title: Print_986

status: Public on Jul 13 2009

city: Kiel

first: Paul-Martin

last: Holterhus

address: Campus Kiel, Schwanenweg 20

department: Pädiatrische Endokrinologie und Diabetologie

institute: Universitätsklinikum Schleswig-Holstein


title: Print_951


title: SMD Print_849

status: Public on Jul 10 2009

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University


title: Print_947


city: Lubbock

first: Scot

last: Dowd

state: TX

address: 4321 Marsha Sharp Fwy

department: MBRI

institute: MBRI

description: sure print 8 x 15K array E coli O157:H7 agilent array full genome based upon EDL933 designed using custom scripts

manufacture_protocol: sure print 8 x 15K array


title: Print_653


title: SMD Print_1354


title: SMD Print_1257


title: SMD Print_1060


title: SMD Print_924


title: SMD Print_989


title: SMD Print_999


title: ROMA 390K Rubble Rep Human Microarray (Design 36)

city: Cold Spring Harbor

first: Nicholas

last: Navin

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description:
Representational Oligonucleotide Microarray Analysis (ROMA) array.

Genome build: NCBI Build 35, UCSC hg17.

Oligonucleotide sequences are available in the supplementary file 'GPL8720_10000036.ndf'.

manufacture_protocol: Photolithography


title: Gang Lab (Agilent)_Z.Officinale/C.Longa_15K array

status: Public on Jul 09 2009

city: Tucson

first: David

last: Gang

state: AZ

address: 1657 E Helen Street

department: Plant Sciences

institute: The University of Arizona

organism:
Zingiber officinale
Curcuma longa

description:
Design Format: 8 X 15K  (each slide has 8 blocks of 15K array)

Number of sequences on each array: 1 (no duplicated spots in each array)

Control Grid: IS-15744-8-V1_8x15K_Gx_EQC_V20060608

first: HyunJo

last: Koo

first: Xiaoqiang

last: Ma

manufacture_protocol:
Application:    Expression
AMADID:    020086
Format:    IS-15744-8-V1
Creation Date:    04/23/2008
Species:    Z.Officinale/C.Longa
Probe#:    15208


title: SMD Print_1126


title: USDA/APHIS/FADDL Pan-viral 15K v4.2

city: Greenport

first: Roger

middle: William

last: Barrette

address: PO Box 848

department: FADDL

institute: USDA-APHIS

organism: Viruses


title: Citrus 22k cDNA microarray v1

city: Valencia

first: Miguel

last: Perez-Amador

state: Valencia

address: Avda. de los Naranjos s/n

institute: Inst. Biologia Molecular y Celular de Plantas (IBMCP-CSIC)

organism: Citrus

manufacturer: Spanish Citrus Funstional Project (http://bioinfo.ibmcp.upv.es/genomics/cfgpDB)

first: MariAngeles

last: Martinez-Godoy

first: MCarmen

last: Marques

first: Julia

last: Santiago

first: Javier

last: Forment

first: Jose

last: Gadea

manufacture_protocol:
cDNA clones being the best representative for each superunigene were selected to be PCR-amplified in a final volume of 100 μL using 4 ng of plasmid template, 400 nM of each primer, and 200 μM dNTPs. The reaction products were analyzed by agarose gels, and purified using the Multiscreen-PCR 96-well Filtration System (Millipore). Only PCR reactions yielding single bands were transferred to printing plates, at a final concentration of 150 ng/μL in PRONTO Universal Spotting Buffer (Corning Life Sciences). PCRs were printed onto UltraGAPS aminosilane Corning slides, using a MicroGrid II arrayer (Genomic Solutions). Printed slides were UV-crosslinked at 150 mJ and store in a desiccator until use. Lucidea Universal ScoreCard (GE Healthcare) spike controls were diluted in 100 ng/μL spotting buffer and printed on the array for quality evaluation. Each calibration and negative controls from the Lucidea kit were spotted several times across the whole area of the array. Every selected clone was spotted once.
Martinez-Godoy MA, Mauri N, Juárez J, Marques MC, Santiago J, Forment J, Gadea J (2008) A genome-wide 20k citrus microarray for gene expression analysis. BMC Genomics 9:318.


title: 85KV4 ROMA Custom Human Microarray (Format 28)

description:
Representational Oligonucleotide Microarray Analysis (ROMA) array.

Genome build: NCBI Build 35, UCSC hg17.

Oligonucleotide sequences are available in the supplementary file 'GPL8581_FORMAT85KBGL2V4.ndf'.

first: Michael

last: Wigler


title: CodeLink™ Rat Whole Genome Bioarray

city: East Lansing

first: Theodora

last: Szasz

state: MI

address: B 445 Life Sciences

department: Pharmacology and Toxicology

institute: Michigan State University

organism: Rattus norvegicus

description:
CodeLink Rat Whole Genome Bioarray is designed to interrogate approximately 34,000 transcripts representing most of the known and predictive genes of the rat genome, as it is described today in the public domain. Each transcript is represented by a 30-mer probe which is designed to conserved exons across the transcripts of targeted genes. The probe sequences, representing well annotated, full length and partial rat gene sequences, were designed based on sequences selected from the NCBI UniGene build #129, RefSeq database (April 1, 2004 release) and dbEST database (March 20, 2004 release).
This platform submission has a different layout compared to the manufacturer original GPL2896. IDs in the first column are associated with the unique GE probe names sorted alphabetically in the PROBE_NAME column. Positive controls, negative controls and CodeLink unique sequences have a blank GB_ACC entry.

manufacture_protocol: See the manufacturer's website


title: Campylobacter jejuni 2K whole-ORF array v1.2

status: Public on Jul 08 2009

first: Linda

middle: S.

last: Mansfield

address: 181 Food Safety Bldg.

department: Microbiology and Molecular Genetics

organism: Campylobacter jejuni

description: Array includes ORF coverage from array "Campylobacter jejuni 6.5K whole-ORF array v1.0" (GPL7254) plus an additional 46 ORFs amplified from strain 11168 using primers designed at Michigan State University.

middle: S

first: Anne

last: Plovanich-Jones

first: Jodi

last: Parrish

first: Russell

last: Finley

first: Dave

last: Wilson

first: Tom

last: Whittam

last: Dewitt

last: Bell

first: Jeff

last: Landgraf

first: Jenna

last: Gettings

first: Jessica

last: St. Charles

first: John

middle: P

last: Jerome

manufacture_protocol:
1.) Primers were designed at Wayne State University by Jodi R. Parrish, furnished to Michigan State University, and are described in “High-Throughput Cloning of Campylobacter jejuni ORFs by in Vivo Recombination in Escherichia coli”, Journal of Proteome Research, Parrish et al., 2004 3(3):582-6.  Additional primers were designed at Michigan State University to amplify 46 additional ORFs or putative ORFs from strain 11168.
2.) PCR products were amplified from genomic DNA from Campylobacter jejuni 11168 or plasmid DNA obtained from C. jejuni 81-176. Products were ethanol precipitated, resuspended in 3X SSC, 0.005% SDS print buffer, and run on gels for quality control.
3.) 16 pin replicate arrays were printed on Corning UltraGAPS slides using a GenMachines Omnigrid spotting robot and Telechem Chipmaker 3 pins.
4.) Each slide contains every spot once.


title: JCVI PFGRC Salmonella typhimurium 13K v6 array designed primarily based on strain 14028

city: Rockville

first: PFGRC

last: JCVI

state: MD

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Salmonella enterica subsp. enterica serovar Typhimurium

description: This set includes 5936 oligonucleotides, has 13872 spots distributed in 48 blocks.

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


title: JCVI PFGRC Salmonella typhimurium 13K v6 array designed primarily based on strain CT18


title: JCVI PFGRC Staphylococcus aureus 22K v7 array designed primarily based on strain Mu50

organism: Staphylococcus aureus

description: This set includes 4510 oligonucleotides, has 22176 spots distributed in 48 blocks.

manufacture_protocol: 7QSA, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Staphylococcus aureus 22K v7 array designed primarily based on strain MSSA476


title: altMouseA_exon-exon_junction_array

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

organism: Mus musculus

manufacture_protocol: Affymetrix Standard Protocol


title: sciTracer Staphylococcus aureus 2005

city: Muenster

first: Jochen

last: Seggewiss

address: Roentgenstr. 21

department: Integrated Functional Genomics

institute: University of Muenster

manufacture_protocol: Can be obtained from the supplier. These microarrays arrays are cDNA arrays.


title: JCVI PFGRC Trypanosoma brucei 19K v3 array designed primarily based on strain TREU927, full array version

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

organism: Trypanosoma brucei

description: This set includes 8375 oligonucleotides, has 19200 spots distributed in 48 blocks.

manufacture_protocol: 3QTB, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Moss Human 15k rRNA v1.0

status: Public on Jul 11 2009

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

institute: EPFL

description:
Agilent-017983
60-mer probes were designed to tile Human rDNA (GenBank accession U13369) on both strands using ArrayOligoSelector (Wardle et al., 2006). A total of 1,146 different non-overlapping probes (573 for each DNA strand) were designed to cover the 43 kb of human rDNA.

manufacture_protocol: See manufacturer's web site.


title: JCVI PFGRC Staphylococcus aureus 22K v7 array designed primarily based on strain N315


title: JCVI PFGRC Salmonella typhimurium 13K v6 array designed primarily based on strain Ty2


title: JCVI PFGRC Salmonella typhimurium 13K v6 array designed primarily based on strain LT2 (SGSC1412)


title: CSU TBVTRM Mycobacterium tuberculosis 4.2K DNA Microarray

city: San Antonio

first: Deepak

last: Kaushal

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

organism: Mycobacterium tuberculosis

manufacturer: Colorado State University TB Vaccine Testing and Research Materials Contract

first: Noton

last: Dutta

first: Smriti

last: Mehra


title: Human oligo array from MWG cancerochips_v2009

city: Nantes

first: Raluca

last: TEUSAN

address: 1, rue gaston veil

institute: INSERM U915

first: Catherine

last: Chevalier

first: Isabelle

last: Guisle

manufacture_protocol: spotted on the  Amersham Lucidea spotter. Epoxyslide.


title: NSF Rice Oligonucleotide Array 45K One Chip Version

status: Public on Jul 01 2009

city: Ames

first: Hui-Hsien

last: Chou

state: IA

address: 503 Science II

department: Genetics, Development and Cell Biology

institute: Iowa State University

organism: Oryza sativa

description: GenePix Array List rice_45k.v4.feb1706.gal provided

manufacture_protocol: Visit http://www.ricearray.org


title: JCVI PFGRC Staphylococcus aureus 22K v7 array designed primarily based on strain MW2


title: JCVI PFGRC Staphylococcus aureus 22K v7 array designed primarily based on strain COL


title: Beijing Institute of Microbiology and Epidemiology Vibrio parahaemolyticus 4.7K

status: Public on Jul 07 2009

city: Beijing

first: Ruifu

last: Yang

address: No.20, DOngdajie, Fengtai

organism: Vibrio parahaemolyticus

manufacture_protocol:
Based on the whole-genome sequences of Vibrio parahaemolyticus strain RIMD2210633, a total number of 4770 annotated open reading frames (ORFs) were selected after the exclusion of ORFs encoding IS protein, integrase, and transposase (The word “gene” will be used in the following part of this paper in reference to the ORF). Those highly homologous to each other at nucleotide level were also excluded. Gene specific primer pairs (16bp to 18bp in length) were designed to amplify nearly the full length of each gene. All primers were synthesized by Illumina Co. (San Diego, CA, U. S. A).
300µl of PCR product was obtained for each gene. PCR amplifications were performed in 96-well plates by using a DNA thermocycler (Biometra UNOII). 100 µl of PCR reaction mixture, containing 50 mM KCl, 10 mM Tris-HCl (pH8.0), 2.5 mM MgCl2, 0.001% gelatin, 0.1% BSA, 150 µM of each dATP, dCTP, dGTP and dTTP, 0.6 µM of each primer, 5 units of Taq DNA polymerase (MBI Fermentas), and 20 ng of template DNA, was predenatured at 95°C for 5 min. Then 30 cycles of 94°C for 1 min, 60°C for 1 min 30 sec and 72°C for 2 min were performed with a final extension at 72°C for 10 min. Each PCR product was verified by agarose gel electrophoresis and was scored as successful if a single band of the expected mobility was detected. DNA smear, multiple bands, or single band of unexpected size were characterized as unsuccessful reactions. Primer pairs from unsuccessful PCR reactions were re-amplified with altered annealing temperatures to get the desired single band of products. A few primers had to be redesigned to ensure successful amplification. In the end, 4669 genes were amplified successfully.
PCR products were purified by using 96-well Multiscreen PCR plates (Millipore) following the user manual’s instruction. The purified DNAs were air dried at 65°C, and were resuspended in 30 µl of 50% DMSO solution. 10 µl of the purified PCR product was transferred into Genetix 7020 384-well Polystyrene Plates for microarray printing. Each of the PCR products was spotted in duplicate on CSS-1000 silylated glass slides (CEL) by using a SpotArray72 Microarray Printing System (Perkin Elmer Life Sciences) with 32 Telechem SMP3 Stealth Pins (4×8 Layout). Genomic DNA of strain S072（its genomic content is almost identical to that of pandemic O3:K6 strain RIMD2210633）, salmon sperm DNA and 50% DMSO solution were included in the microarray design as internal control elements. The spotted slides were stored in dry environment at room temperature for at least 12 hr, and then were crosslinked twice by using a UV Stratalinker (Hoefer) each at a total energy of 60 microjoules. The spotted CSS-1000 silylated slides need not any blocking procedure, such as the blocking of unreacted aldehyde groups and the prehybridization. The microarray slide to be hybridized was simply washed in water for 2 min to remove the unbounded DNA and then was blown to dry with hot air.


title: JCVI PFGRC Staphylococcus aureus 22K v7 array designed primarily based on strain MRSA252


title: CDRI Mycobacterium tuberculosis H37Rv Whole Genome Microarray 4.1k

city: Lucknow

first: Ranjana

last: Srivatsava

address: Chattar Manzil Palace

institute: Central Drug Research Institute

organism: Mycobacterium tuberculosis H37Rv

description:
Genotypic Designed M.tuberculosis H37Rv Whole Genome Microarray 4.1k
M.tuberculosis H37RV microarray was custom designed using multiple 60mer oligonucleotides covering all known transcripts of M.tuberculosis H37Rv genome. Array was designed at Genotypic Technology using Agilent Technologies e-Array platform. All 60mer oligo sequences were designed based on the H37Rv sequences available from Sanger, Tuberculist and NCBI databases. Probe validation was done using the following criteria: The 60mer oligonucleotide has to be specific for the H37Rv genome only (Sequence Identity shall be 100% identical only to H37Rv), Average Tm would meet the recommended DNA hybridization standards.  39986 unique probes were designed for 4080 genes at an average of 9 probes per gene. Carefully selected 60mer probes were printed insitu using Agilent’s Inkjet technology.
The Platform data table reflects a condensed representation of the array's replicate features.  The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.

last: Srivastava

first: Brahm

first: Amita

last: Yadav

first: Ravi

last: Gupta

manufacture_protocol: Refer to manufacturer website http://www.opengenomics.com


title: Rice NimbleGen 390K tiling array (2006-11-14_ggb_rap1_3tile_101706)

city: Yong in

first: Nam-gun

last: Kim

address: Myongi Univ.

country: South Korea

institute: GGBIO

description: Rice genome build information requested but not provided.

first: Yeon-Ki

manufacture_protocol: The profiling was conducted with the Rice 3'Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon and with shifting 10 bp so 10 probes cover 150 bp in the 3' region of the gene. Genes from chloroplast (123) and mitochondria (74) and selection markers such as gfp, gus, hyg, bar, and kan are included. In total, 270,000 probes were designed with the average size of probe is 60-nt long to have its Tm value 75 to 85 ¡ÆC. The microarray was manufctured at NimbleGen inc (http://www.nimblegen.com/). Random GC probes (38,000) to monitor the hybridization efficiency and four corner fiducial controls (225) were included to assist with overlaying the grid on the image.


title: NimbleGen Streptomyces avermitilis 4.7K

status: Public on Jul 02 2009

city: Shanghai

first: Lei

last: Chen

address: 300 Fenglin Road

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

organism: Streptomyces avermitilis

description:
NimbleChip Expression Oligonucleotide Customer Microarrays (Roche NimbleGen, USA) designed for S. avermitilis were employed. For each gene, 10 different oligonucleotides were designed and every oligonucleotide was repeated 5 times on each slide. Each slide contains 385,000 60mer oligonucleotides. The array containing a total of 7645 ORFs of S. avermitilis was manufactured as described before (Nuwaysir et al., 2002)
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: Lc Sciences Human 470 miRHuman 9.0

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

institute: Consiglio Nazionale delle Ricerche (CNR)

manufacture_protocol: see manufacturer's website


title: Spodoptera frugiperda 7k (v1-inra)

status: Public on Jun 24 2009

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

organism: Spodoptera frugiperda

first: Frederique

last: Hilliou

manufacture_protocol: spotted microarray


title: Spodoptera frugiperda 7k (v3-toulouse)


title: Rosetta/Merck Mouse 44k 1.0 microarray (with 2D spot locations)

city: Albuquerque

first: Matthew

middle: Luke

last: Fero

state: NM

address: 1201 Camino de Salud

department: Internal Medicine

institute: University of New Mexico

description: Oligonucleotide array on glass. Contains 60-mer probes (60-mer).

first: Peter

last: Linsley

first: Bruce

middle: E

last: Clurman

first: Daniel

middle: A

last: Kuppers

first: Aimee

last: Jackson

first: Harry

last: Hwang

manufacture_protocol: Prodcuced by Agilent, Inc. for Rosetta Inpharmatics / Merck Pharmaceuticals.  Identical to GEO platform GPL3677 with the addition of 2D feature location information.


title: FilgenArray miRNA Homo sapiens V11

status: Public on Jun 20 2009

city: Nagoya

first: Manabu

last: Harada

state: aichi

address: 15-1 Nakanoshima, Ohdaka-cho, Midori-ku

department: Biosciences

institute: Filgen,Inc.

manufacture_protocol: CustomArray™ uses a specially modified “CMOS” semiconductor to direct the molecular assembly of a specific sequence of DNA bases in response to a digital command. Each feature on the array (a microelectrode) is digitally addressed to selectively generate acid, by means of an electrochemical reaction which, in-turn, controls the detritylation reaction during phosphoramidite synthesis. A software program is used to control the microelectrodes, and thus, the detritylation pattern applied on the chip during synthesis.


title: Hofmann A. burtoni 16K brain_pinky_array_print4

status: Public on Jan 25 2008

city: Portland

first: Suzy

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

organism: Haplochromis burtoni

description:
synonym: Astatotilapia burtoni
the array consists of 48 blocks (4#12) of 400 spots each (20X20)
the physical array contains an adition set of yeast control features that are not included in the GEO platform
NO EMPTY FEATURES NOR UNRELIABLE SPOTS (BAD PCR PRODUCT) ARE INCLUDED IN THIS PLATFORM

first: Hans

last: Hofmann

first: Walter

last: Salzburger

manufacture_protocol: This array is built primarily from two Cichlid cDNA libraries. Library 1: Brain2000 was made in the lab of Russ Fernald using brains from all sexes, stages, and phenotypes. Library 2: Pinky2003 was made by Walter Salzburger using mixed tissues including gonads, liver, skin, muschle from all stages. this library was normalized Both libraries represent Astatotilapia burtoni 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 candidate genes cloned in the Hofmann and Fernald labs as well as yeast control genes and a few other positive and negative controls


title: mirVANA miRNA Bioarray V9.2

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description:
Manufactured using GE Healthcare’s CodeLink (TM) 3-D Gel Matrix Technology
Surface type: non-adsorptive
Attachment: covalent
The mirVana miRNA Bioarrays are an Ambion product that is manufactured by GE Healthcare and incorporates the CodeLink™ 3-D Gel Matrix slide surface. This aqueous environment elevates the probes away from the surface of the slide, allowing for maximum interaction between the probes and targets.

manufacture_protocol:
CodeLink(tm) Activated Slides are designed to covalently immobilize amine-modified DNA for microarrays. They are easy to use and are compatible with most available arraying and scanning instruments. CodeLink Activated Slides are coated with a novel 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.
Technical specifications:
Slide dimensions: 25 × 75 × 1 mm
1× Printing buffer: 50 mM sodium phosphate at pH 8.5
Codelink slides are manufacured by SurModics and were formally sold as 3D-Link(tm) Activated Slides.


title: SBC Rat cDNA Microarray ver2.0

status: Public on Mar 01 2006

first: Huasheng

last: Xiao

address: No.151,Libing Rd.,Zhangjiang Hi-Tech Park,Pudong

department: Department of Genechip

institute: Shanghai Biochip Co., Ltd.

first: Jiajing

last: Zhou

first: Zhidong

last: Zhu

first: Junsong

last: Han

first: Yucheng

first: Qi

last: Wang

manufacture_protocol: The cDNA fragments of selected genes were amplified by PCR and the final concentration is ranged from 200 ng/µl to 250 ng/µl. The cDNA fragments were spotted on poly-lysine coated slides by using OmniGrid 100 spotter and cross linked in 400 mJ UV. Keep temperature(room temperature: around 20℃) and the humidity(50%-55%).


title: mirVANA miRNA Bioarray V2

status: Public on Apr 20 2007


title: Murine Operon V4 Array

status: Public on Mar 28 2009

city: Honolulu

first: John

last: Maresh

state: HI

address: 651 Ilalo

department: Medicine

institute: University of Hawaii

description: 36K array with Operon V4 murine set of oligonucleotides

first: April

last: Darrow

middle: G

first: Ralph

middle: V

last: Shohet

manufacture_protocol: Pin spotted onto glass slide


title: IFR_Salmonella_7.3k_v1.0

status: Public on Aug 30 2007

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

institute: Institute of Food Research

organism: Salmonella enterica

first: Arthur

last: Thompson

first: Jay

last: Hinton

manufacture_protocol:
PCR product microarray of ORF's from S. Typhimurium LT2, S. Typhimurium SL1344, S. Typhimurium DT104, S. Enteritidis PT4, and S. Gallinarum 287/91. For the description of PCR amplification and printing procedures see:
Clements et al., (2002) PNAS 99(13): 8784-8789;
Nagy et al., (2006) Infect. Immun. 74(10):5914-5925


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array [CDF: Hs133P_Hs_REFSEQ_8]

status: Public on Jul 15 2009

city: Cincinnati

first: Nancy

last: Ratner

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

organism: Homo sapiens

description: This is identical to GPL570 but a custom CDF environment was used to extract data. The custom CDF (Hs133P_Hs_REFSEQ_8) was described by Dai et al., NAR 2005 33(20), PMID: 16284200. The cdf can be found at the link below.

manufacture_protocol: see manufacturer's web site