title: SMD Print_1450 Homo sapiens

status: Public on Mar 26 2010

city: Stanford

first: Andrew

last: Beck

state: CA

address: Stanford

country: USA

institute: Stanford University

organism: Homo sapiens

technology: spotted DNA/cDNA

distribution: non-commercial

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: Chulalongkorn Univ Leptospira interrogans spotted 17K oligo array

status: Public on Mar 31 2010

city: Pathumwan

first: Kanitha

last: Patarakul

state: Bangkok

address: 1873 Rama IV Road

department: Microbiology

country: Thailand

institute: Faculty of Medicine, Chulalongkorn University

organism: Leptospira interrogans

technology: spotted oligonucleotide

manufacturer: The Australian Genomics Research Facility.

manufacture_protocol:
1. Oligos were transferred to 384 well printing plates and resuspended at 250ng/ul in 3xSSC buffer for printing.
2. The prepared oligos were arrayed onto Schott A+ aminosilane glass slides using the ESI Virtek Arraying Robot. DNA was spotted using Point Technology split pins.
3. Slides were baked and UV irradiated at 700MJ to crosslink the DNA.


title: Acropora palmata 2K EST array

status: Public on Mar 25 2010

city: Wilmington

first: Kevin

last: Portune

state: NC

address: 601 S. College Road

institute: University of North Carolina, Wilmington

organism: Acropora palmata

middle: J

first: Christian

middle: R

last: Voolstra

first: Mónica

last: Medina

first: Alina

middle: M

last: Szmant

manufacture_protocol: Microarrays consist of PCR-amplified cDNAs from A. palmata 2,051PCR-amplified cDNAs were spotted in duplicate on poly-lysine-coated slides yielding a microarray with 4,102 total features. cDNAs were chosen from EST libraries described in (Schwarz et al., 2008). To annotate the cDNAs, we performed a BLASTx analysis (E-value cut-off 1e-5) against the GenBank non-redundant DNA and protein database (nr).


title: SMD Print_1322 Homo sapiens


title: TaqMan MicroRNA Assays Human Panel Early Access Kit (Applied Biosystems)

city: Modena

first: Elena

last: Tenedini

state: MO

address: Via Campi, 287

department: Biomedical Sciences

country: Italy

institute: University of Modena and Reggio Emilia

technology: RT-PCR

description: The original platform is composed of two 96-well plates (Plate A and Plate B) whose content is here merged into one single platform. Applied Biosystems Catalog Number: 4365409. Currently no more available for sale.

distribution: virtual


title: Combimatrix Orientia tsutsugamushi customArray 4x2k

city: Seoul

first: Nam-Hyuk

last: Cho

address: 28 Yongon-Dong, Chongno-Gu

department: Microbiology and Immunology

country: South Korea

institute: Seoul National Univ. College of Medicine

organism: Orientia tsutsugamushi

technology: in situ oligonucleotide

description: CustomArray used a specially modified “CMOS” semiconductor to synthesized oligonucleotide probe of a specific sequence of DNA bases in response to a digital command. 27 to 40-mer oligonucleotide probes (1613 probes) were designed for 1472 CDSs of the O. tsutsugamushi genome (GeneBank accession no. AM494475). 1 to 6 probes per CDS were designed and some of the probes were duplicated on the microarray (total 2187 spots on an array). As negative controls, 5 and 15 oligonucleotide probes derived from plant and bacteriophage respectively were spotted on the array at 53 sites per array.

distribution: custom-commercial


title: 25K human oligonucleotide array

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

manufacture_protocol:
The 50 mers 5’amino modified oligonucleotides from the RNG/MRC oligonucleotide collection (see Le Brigand et al, below) (information available at http://www.microarray.fr:8080/merge/index) were diluted to a final concentration of 50 mM in 50% dimethyl sulfoxide (D-8418, Sigma), 100mM potassium phosphate (pH 8.0) and printed onto hydrogel-coated slides (Nexterion H slides, Schott, Jena, Germany) using a microGrid II arrayer (Genomic Solutions, Cambridge, UK).
Le Brigand K, Russel R, Moreillon C, et al. An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. Nucleic Acids Research, 2006 Jul 19; 34(12):e87


title: AB SOLiD System 2.0 (Arabidopsis thaliana)

status: Public on Mar 30 2010

last: GEO

organism: Arabidopsis thaliana

technology: high-throughput sequencing


title: Blue-Chip bovine preimplantion embryo specific cDNA array produced by Sirrard et al. 2005

city: Bonn

first: Dessie

last: Salilew-Wondim

state: NRW

address: Endenicher Allee 15

department: Animal breeding and husbandry group

country: Germany

institute: University of Bonn

organism: Bos taurus

description: Submitter was unable to provide further Platform annotations

manufacture_protocol:
1. Total RNA was extracted from oocyte, blastocyst and somatic tissue using absolutely RNA Microprep Kit
2. Total RNA was then reverse transcribed  and amplified using the BD SMART PCR SYNTHESIS KIT
3. Amplified double stranded cDNA was RsaI digested and purified using the QIAquick PCR Purification Kit
4. Different SSH experiments were then performed for oocytes, blastocyst and somatic tissue
5. Differentially expressed cDNA coming from SSH experiments using oocytes as a tester and blastocyst as a driver, and Blastocyst as a the tester and somatic tissue as a driver were cloned into the pGEM-T Vector systems or into TOPO cloning 5-min PCR Cloning KIt
6. Vectors were then transformed into One Shot MAX efficiency® DH5α-T1R competent cells
7. Transformed bacterial were selected using blue white screening
8. Between 480 and 1152 white colonies per SSH experiment were then picked and resuspended in LB+ampicilin
9. PCR was performed  from bacterial suspension using HotMaster Taq DNA polymerase
10. The PCR product was purified using Unfilter ® 384-well purification plate, speedvac evaporated and resuspended in 3X standard saline citrate
11. cDNA were spotted on GAPS II glas slide using versearray chipwritter proRobot.
12. Slides were then cross-linked with ultravuiolet (UV) rays.


title: [X_tropicalis] Affymetrix Xenopus tropicalis Genome Array

status: Public on Mar 29 2010

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Xenopus tropicalis

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

This array was designed in close collaboration with the Xenopus research community as part of the Affymetrix® GeneChip Consortia Program.

Sequences used in the design of the array were selected from the Xenopus tropicalis UniGene database (Build 30, July 2006), GenBank® mRNAs for Xenopus tropicalis (up to September 12, 2006), and predicted gene sets from both the DOE Joint Genome Institute (Xentr4 transcripts, file creation date August 17, 2005, download date May 25, 2006) and Ensembl (release 40, download date May 2006).

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: USDA-ARS-PSMRU-SalmonellaTEv4

city: Albany

first: Craig

middle: T

last: Parker

address: 800 Buchanan St

department: PSM

institute: USDA ARS

organism: Salmonella enterica

manufacturer: Produce Safety and Microbiology, USDA-ARS, Albany, CA

manufacture_protocol: PCR product microarray of ORF's from S. Typhimurium LT2 and S. Enteritidis PT4. PCR products resuspended to an average concentration of 0.1-0.2 µg µl-1 in 20 µl of 50% dimethyl sulfoxide (DMSO) containing 0.3× Saline-Sodium Citrate (SSC). Spotted on Corning barcoded UltraGAPS slides using a GeneMachine Accent printer with ChipMaker pins.


title: Illumina Genome Analyzer (Glycine max)

organism: Glycine max


title: FGSC-N. crassa-10918-NC_10/04/05 UCB

city: Hanover

first: Chen-Hui

last: Chen

state: NH

address: 702 Remsen

department: Genetics

institute: Dartmouth College

organism: Neurospora crassa

manufacturer: N. Louise Glass's lab in Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.

manufacture_protocol: To construct a gene-specific microarray of N. crassa genome, we designed 70-mer oligonucleotide immobilized probes using ArrayOligoSelector, and the approximately 10,000 open reading frames (ORFs) derived mainly from the N. crassa databases at the Broad Institute and MIPS. ArrayOligoSelector selects a unique segment to identify each ORF considering the predicted sequences of all genes. The program avoids selecting internal self-annealing structures and internal repeat sequences, and preferentially chooses oligonucleotides within a narrow range of GC content, which are biased towards the 3' terminal region of each gene. Oligomers were synthesized (Illumina, San Diego, CA) for all ORFs. Analysis of oligomer placement in predicted genes indicated the desired strong 3' bias. Oligomers were re-suspended in 3x SSC to a final concentration of 20µM, and spotted. Eight 40mM ArrayControl Sense Oligo spots, which were complementary to the eight ArrayControl RNA spikes (Ambion, Austin, TX, USA), were also included.  Amplified DNA may be precipitated in 96-well format with isopropanol, washed with 70% EtOH, and resuspended in a salt spotting solution such as 3X SSC. DNA is commonly spotted on polylysine-coated glass slides or γ-aminopolysilane (GAPS)–coated glass slides (Corning, Corning, NY), using a microarraying robot. GAPS slides are more expensive but have a better shelf life and tend to be less variable in quality than poly-lysine coated slides.  An example of cDNA array can be seen here. 10,918 oligomers are on the chip. 10,526 oligos are based on MIPS or Broad Institute predicted ORFs. 8 oligos are Abmion ArrayControl Sense Oligo Spots (#1781). The remaining 384 oligos (ChIP_Chip) were mainly designed in the intergenic regions. 40uM oligos in 3x SSC were printed onto Corning UltraGAPS slides. Slides are not post-processed. Rehydration is optional. Oligos need to be cross-linked with 600mJ UV. Slides should be stable for a year at room temperature in desiccator.  Slides may display unacceptable levels of green background and the way we know to remove is using the Pronto!™ Background Reduction Kit (Item #40029) from Corning. It is not 100% effective so we recommend prescanning after prehybridization and identifying spots that are 3x standard deviation above background for possible elimination. For fast, easy, successful fist microarrays, we recommend to use Corning/Promega kit: 40076 Pronto Plus Indirect System and RPN5661 Amersham Post-labeling Reactive Dye Pack, which are expensive but always give brilliant results.


title: JCVI PFGRC Streptococcus pneumoniae 15K v8 array designed primarily based on strain MM1 1998

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 3942 oligonucleotides, has 15552 spots distributed in 48 blocks.

manufacture_protocol: 8QSP, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Bacillus cereus ATCC 14579, 3rd design, Agilent 8X15K

city: Wageningen

first: Mara

last: Ceragioli

address: Bomenweg

department: Food Microbiology LAb

country: Netherlands

institute: WUR

organism: Bacillus cereus ATCC 14579

first: Menno

last: van der Voort

first: Roy

last: Moezelaar

first: Tjakko

last: Abee

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


title: Cardiff Caenorhabditis elegans 20K oligo array (Operon oligonucleotide set version 1.1)

status: Public on Mar 23 2010

city: Cardiff

first: Peter

last: Kille

address: Park Place

department: Cardiff School of Biosciences

country: United Kingdom

institute: Cardiff University

organism: Caenorhabditis elegans

description:
Created from Operon C. elegans oligonucleotide set version 1.1.
60-65mer oligonuleotides.

manufacturer: Cardiff School of Bioscience, Cardiff University

manufacture_protocol:
1. The microarrays were printed using Perkin Elmer SpotArray 72 printer (Perkin Elmer, MA, USA).
2. Oligonucleotides  were resuspended in a water/DMSO 50/50 mix to a final concentration of 200 uM and Placed in 384 well plates with appropriate landmarks and oligonucleotides representing the Lucidea ScoreCard (GE Life Sciences).
3. Each array was comprised of (12x4) 48 subarrays, each consisting of (20x22) 440 cDNA spots. In total, each array had 21,120 cDNA spots. This number of spots included the blanks, controls (lucidea scorecard), landmarks and the oligonucleotide reporters.
4. Printing used 48 SMP3 Telechem split pins mounted on a Spotarray 72 (Perkin-Elmer).
5. This printing regime yield spots of approximately 120 µm in diameter. Landmarks were introduced at the left-hand corner of each sub-array (and thus evenly spaced across the whole array) by the introduction of 3 replicates of the Lucida Scorecard (Amersham).
6. Immobilization of the cDNA onto the CMT-GAPSTM coated glass slides was achieved by means of baking and UV crosslinking. The printed slides were initially immobilized by placing them in a UV StratalinkerTM 2400 bench top transilluminator (Stratagene Ltd) for five minutes, in order to initially immobilise the cDNA.
7. The slides were then placed in a lightproof container and baked in an oven at 80oC for 2 hours. The slides were stored in a lightproof desiccator at room temperature, until required.


title: Ovine-Bovine 12K cDNA array

city: St Lucia

first: Sean

last: McWilliam

state: Queensland

address: 306 Carmody Road

department: Agriculture and Food

country: Australia

institute: CSIRO

organism:
Bos taurus
Ovis aries

manufacture_protocol: elements were printed in duplicate onto CMT GAPSII (Corning Inc., Corning, NY, USA) glass slides and Eppendorf (Eppendorf AG, Hamburg, Germany) glass slides using a Virtek Microarrayer with the Stealth 48 pinhead and Micro Spotting Pins (Telechem International Inc., Sunnyvale, CA, USA) at a spacing of 220 µm


title: FSU/NimbleGen Human 2.1M Whole Genome Tiling

status: Public on Mar 24 2010

city: Tallahassee

first: Tyrone

last: Ryba

state: FL

address: 319 Stadium Dr.

department: Biological Science

institute: Florida State University

description: Build: Hg18, NCBI 36

manufacture_protocol: NimbleGen


title: Illumina Genome Analyzer (Oryza rufipogon)

organism: Oryza rufipogon


title: URMITE Rickettsia prowazekii array

city: Marseille

first: LEROY

last: Quentin

address: 27 Boulevard Jean Moulin

institute: URMITE

organism: Rickettsia prowazekii str. Madrid E

description: Oligonucleotide set of 1,411probes representing 545 intergenic regions and 867 ORFs of R.prowazekii madrid E strain.

first: Yassina

last: Bechah

first: Khalid

last: El Karkouri

first: Oleg

last: Mediannikov

first: Quentin

last: Leroy

first: Nicolas

last: Pelletier

first: Chaterine

last: Robert

first: Claudine

last: Medigue

first: Jean-Louis

last: Mege

first: Didier

last: Raoult

manufacture_protocol: Sure Print Technology-In situ synthesis


title: JCVI PFGRC Vibrio parahaemolyticus 21K vt1a array designed primarily based on strain N16961

first: PFGRC

last: JCVI

organism: Vibrio parahaemolyticus

description: This set includes 9232 oligonucleotides, has 21168 spots distributed in 48 blocks.

manufacture_protocol: T1AQVP, with arrayer GENETIX


title: JCVI PFGRC Streptococcus pneumoniae 15K v8 array designed primarily based on strain G54


title: SMD Print_1561 Homo sapiens

first: Andrew

last: Beck

organism: Homo sapiens


title: JCVI PFGRC Streptococcus pneumoniae 15K v8 array designed primarily based on strain TIGR4


title: KSHV tiling microarray AMADID: 017577

city: San Francisco

first: Sanjay

last: Chandriani

address: 513 Parnassus Avenue

institute: UCSF

organism:
Homo sapiens
Human herpesvirus 8 type M

description: Probes based on KSHV (U75698.1) and Homo sapiens for select human transcripts.

manufacture_protocol:
Standard Agilent printing methods.
60-mer tiling oligonucleotides.
Offset = 20nts from both strands of the KSHV genome (U75698.1).
Platform contains both KSHV and human probes, all of which are used in the LOWESS normalization protocol
Platform contains standard Agilent controls probes, including probes that detect spike-in control transcripts.


title: SMD Print_1305 Homo sapiens

city: Stanford

institute: Stanford University


title: RCSI Respiratory Medicine Human TaqMan MicroRNA Arrays v2.0

city: Beaumont

first: Irene

last: Oglesby

address: ERC, beaumont Hospital

department: Medicine

country: Ireland

institute: Royal College of Surgeons in Ireland

manufacture_protocol: The TaqMan® Human MicroRNA Array Set v2.0 is a two card set containing a total of 364 TaqMan® MicroRNA Assays per card. The set enables accurate quantitation of 667 human microRNAs. The content is derived from miRBase v10, and provides close to full coverage of Sanger.


title: Mycobacterium tuberculosis H37Rv proteome microarray

city: Bronx

first: Shajo

last: Kunnath-Velayudhan

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

organism: Mycobacterium tuberculosis H37Rv

technology: spotted peptide or protein

description: This platform is a virtual representation of two .gal versions (see supplementary files).


title: Lactococcus lactis subsp. lactis IL1403 4.2K Eurogentec microarray

status: Public on Mar 22 2010

city: Belfast

first: Guillermo

last: López-Campos

state: Northern Ireland

address: 97 Lisburn road

department: Centre for Experimental Medicine

institute: Queen's University of Belfast

organism: Lactococcus lactis subsp. lactis Il1403

manufacture_protocol: Amplicons were designed using GenomePrimer in combination with UniFrag, amplified by Eurogentec (Belgium), purified using Qiagen 96-wells purifying plates. Amplicons (about 10 microL) diluted 2x with ArrayIT 2x spotting buffer, in Genetix 384 wells spot plates, spotted on aldehyde slides (ArrayIt) with a GenPak spotter at about 55 % humidity. Blocking of reactive aldehyde groups by boric anhydride treatment.


title: Illumina Genome Analyzer (Oryza nivara)

last: GEO

organism: Oryza nivara


title: Illumina Mouse Ref-6 V1

city: Birmingham

first: Molly

middle: Bray

last: Bray

state: AL

address: 720 20th Street S

institute: Univ of Alabama at Birmingham

organism: Mus musculus

technology: oligonucleotide beads

description: Approximately 46,000 RefSeq and EST transcripts are present on the array in the form of oligo-coated (50mer) beads.

manufacture_protocol: See manufacturer web site (www.illumina.com).


title: Taqman Homo sapiens microRNA Low density arrays (TLDA) panel B

status: Public on Mar 20 2010

city: Pittsburgh

first: Monica

last: Panelli

state: PA

address: 5117 Centre Ave

department: Hematology-Oncology

institute: Hillman Cancer Center, University of Pittsburgh

manufacture_protocol: Taqman ® microRNA Low density arrays (TLDA). The ABI Taqman® microRNA Low density arrays (TLDA, Applied Biosystems, Foster City, CA, www.appliedbiosystems.com) were selected as the platform for microRNA melanoma profiling. This platform consists of 2 arrays: TLDA panel A (377 functionally defined microRNAs) and TLDA panel B (289 microRNAs whose function is not yet completely defined) for a total of 666 microRNA assays. Each array/panel includes, among other endogenous controls, the mammalian U6 assay that is repeated four times on each card as a positive control as well as an assay unrelated to mammalian species, ath-miR159a, as negative control


title: Nimblegen-R_aetherivorans_I24-3.5K-v2.0

city: Cambridge

first: Matt

last: Cahill

address: Downing Street

institute: University of Cambridge

organism: Rhodococcus aetherivorans

description: Nimblegen design name 2005-04-27_R_aeth_opt_12plex, design ID 1951.  A total of 3524 genes are represented on the arrays; of these, 41 and 176 are found on the plasmids pRA2 and pRA3, respectively. The number of distinct 24nt probes per gene is variable (1 - 43) with an average of 3. The design includes a variety of control probes.

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


title: SMD Print_1163 Homo sapiens

city: London

first: Simon

last: Waddell

department: Division of Cellular and Molecular Medicine St. George's

institute: University of London Tooting

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


title: JCVI PFGRC Aspergillus fumigatus 22K v3.1 array designed primarily based on strain Af293

status: Public on Mar 19 2010

organism: Aspergillus fumigatus

description: This set includes 9674 oligonucleotides, has 22176 spots distributed in 48 blocks.

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


title: Illumina Genome Analyzer (Gallus gallus)

status: Public on Mar 18 2010

organism: Gallus gallus


title: ARK-Genomics G. gallus 20K v2 (single gene version)

city: Hatfield

first: Zhangrui

last: Cheng

state: Hertfordshire

address: Hawkshead Lane

department: Production and Population Health

institute: Royal Veterinary College

manufacturer: ARK-Genomics, University of  Edinburgh, UK

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


title: University of Cape Town Cowpea 9K drought stress SSH library

city: Pretoria

first: Dave

middle: K

last: Berger

state: Gauteng

address: Room 6-26, Agricultural Sciences Building, University of Pretoria, Lunnon Rd

department: Plant Science, Forestry & Agricultural Biotech. Instit. (FABI)

country: South Africa

institute: University of Pretoria

organism: Vigna unguiculata

manufacturer: ACGT Microarray Facility, University of Pretoria, Pretoria, South Africa (http://www.microarray.up.ac.za )

first: Olivier

last: Nicky

manufacture_protocol:
1. PCR fragments of a cloned cDNA SSH library are arrayed in Genetix X7022 384-well plates.
2. Each well contains a final concentration of 125 ng/µl PCR product in 50% DMSO spotting solution (v/v).
3. Between printing runs the plates are stored at -20°C.
4. Prior to printing the plates are incubated at room temperature for 30 min to aid temperature equilibration.
5. Plates are centrifuged at 2000 x g for 5 minutes prior to printing.
6. Printing is performed on the Molecular Dynamics Generation III spotter.
7. Seals are removed and plates placed in the spotter immediately prior to initiating the printing process to prevent unnecessary evaporation.
8. A relative humidity of 50% is maintained in the spotter cabinet during printing runs.
9. Following completion of the printing run the plates are sealed with a new Abgene adhesive plate seal and stored at -20°C.
10. Each slide is made up of 2144 and 2016 probes from the F and R libraries, respectively, plus 448 probes which are control or blank spots. Each probe is printed twice to make a total of 9216 probes on each array.


title: AGRF Leptospira interrogans spotted oligo array

city: Clayton

first: Miranda

last: Lo

address: Wellington Road

institute: Monash University

organism: Leptospira interrogans

manufacturer: The Australian Genomics Research Facility

manufacture_protocol:
1. Oligos were transferred to 384 well printing plates and resuspended at 250ng/ul in 3xSSC buffer for printing.
2. The prepared oligos were arrayed onto Schott A+ aminosilane glass slides using the ESI Virtek Arraying Robot. DNA was spotted using Point Technology split pins.
3. Slides were baked and UV irradiated at 700MJ to crosslink the DNA.


title: JCVI PFGRC Trypanosoma brucei 19K v4 array designed primarily based on strain TREU927

city: Rockville

institute: J. Craig Venter Institute

organism: Trypanosoma brucei

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

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


title: JCVI PFGRC Salmonella typhimurium 13K v8 array designed primarily based on strain LT2(SGSC1412)

organism: Salmonella enterica subsp. enterica

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

manufacture_protocol: 8QST, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Salmonella typhimurium 13K v8 array designed primarily based on strain 14028


title: JCVI PFGRC Porphyromonas gingivalis 13K v3 array designed primarily based on strain W83

organism: Porphyromonas gingivalis

description: This set includes 1848 oligonucleotides, has 13872 spots distributed in 48 blocks.

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


title: JCVI PFGRC Listeria monocytogenes 21K vt3a array designed primarily based on strain HCC23

organism: Listeria monocytogenes

description: This set includes 6346 oligonucleotides, has 21168 spots distributed in 48 blocks.

manufacture_protocol: T3AQLM, with arrayer GENETIX


title: JCVI PFGRC Listeria monocytogenes 21K vt3a array designed primarily based on strain 4b F2365


title: JCVI PFGRC Salmonella typhimurium 13K v8 array designed primarily based on strain Ty2


title: JCVI PFGRC Escherichia coli 17K v1 array designed primarily based on strain Sakai

organism: Escherichia coli

description: This set includes 7644 oligonucleotides, has 17328 spots distributed in 48 blocks.

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


title: JCVI PFGRC Salmonella typhimurium 13K v8 array designed primarily based on strain CT18


title: JCVI PFGRC Escherichia coli 17K v1 array designed primarily based on strain EDL933


title: JCVI PFGRC Escherichia coli 17K v1 array designed primarily based on strain EC4115


title: JCVI PFGRC Escherichia coli 17K v1 array designed primarily based on strain TW14359


title: JCVI PFGRC Enterococcus faecalis 14K v1 array designed primarily based on strain TX0104

organism: Enterococcus faecalis

description: This set includes 6600 oligonucleotides, has 14688 spots distributed in 48 blocks.

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


title: JCVI PFGRC Enterococcus faecalis 14K v1 array designed primarily based on strain TUSoD_Ef11


title: JCVI PFGRC Campylobacter jejuni 15K v3 array designed primarily based on strain NCTC_11168

organism: Campylobacter jejuni

description: This set includes 6982 oligonucleotides, has 15552 spots distributed in 48 blocks.

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


title: JCVI PFGRC Enterococcus faecalis 14K v1 array designed primarily based on strain HH22


title: JCVI PFGRC Campylobacter jejuni 15K v3 array designed primarily based on strain 81-176


title: JCVI PFGRC Enterococcus faecalis 14K v1 array designed primarily based on strain V583


title: JCVI PFGRC Campylobacter jejuni 15K v3 array designed primarily based on strain RM1221


title: JCVI PFGRC Enterococcus faecalis 14K v1 array designed primarily based on strain TX1322


title: JCVI PFGRC Enterococcus faecalis 14K v1 array designed primarily based on strain ATCC_29200


title: JCVI PFGRC Campylobacter jejuni 15K v3 array designed primarily based on strain 269.97


title: JCVI PFGRC Campylobacter jejuni 15K v3 array designed primarily based on strain CG8421


title: JCVI PFGRC Bacillus anthracis 13K v4 array designed primarily based on strain A2012

organism: Bacillus anthracis

description: This set includes 5821 oligonucleotides, has 13056 spots distributed in 48 blocks.

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


title: Illumina Genome Analyzer (Drosophila mojavensis)

status: Public on Mar 15 2010

organism: Drosophila mojavensis


title: Illumina Genome Analyzer II (Drosophila mojavensis)


title: ACW-universal-95000-v2

status: Public on Mar 16 2010

city: Waedenswil

first: Frederique

last: Pasquer

address: Schloss

department: Plant Protection

country: Switzerland

institute: Agroscope Changins-Waedenswil Research Station ACW

organism: synthetic construct

description: Oligomers contains 2 parts: 13-mer random sequence and 12-mer polyT

first: Cosima

last: Pelludat

first: Brion

last: Duffy

first: Juerg

middle: E

last: Frey

manufacture_protocol:
Roche NimbleGen manufactures custom, high-density DNA arrays based on its proprietary Maskless Array Synthesizer (MAS) technology. The MAS system is a bench top, solid-state, high-density DNA array fabrication instrument comprised of a maskless light projector, a reaction chamber, a personal computer, and a DNA synthesizer. Roche NimbleGen builds its arrays using photo-mediated synthesis chemistry with its MAS system.
At the heart of the system is a Digital Micromirror Device (DMD), similar to Texas Instruments' Digital Light Processor (DLP), employing a solid-state array of miniature aluminum mirrors to pattern 786,000 to 4.2 million individual pixels of light. The DMD creates "virtual masks" that replace the physical chromium masks used in traditional arrays.
These "virtual masks" reflect the desired pattern of UV light with individually addressable aluminum mirrors controlled by the computer. The DMD controls the pattern of UV light projected on the microscope slide in the reaction chamber, which is coupled to the DNA synthesizer. The UV light selectively cleaves a UV-labile protecting group at the precise location where the next nucleotide will be coupled. The patterns are coordinated with the DNA synthesis chemistry in a parallel, combinatorial manner such that 385,000 to 2.1 million unique probe features are synthesized in a single array.


title: Ambion 14K miRChip V1

city: Austin

first: Sachin

last: Sah

state: TX

address: 2150 Woodward St, Suite 100

institute: Asuragen Inc.

organism:
Homo sapiens
Mus musculus
Rattus norvegicus
synthetic construct

manufacture_protocol:
Ambion miRChip V1array, manufactured by Affymetrix, offers the most content, with probes for verified Sanger miRNAs and more than 12,000 predicted miRNAs. Ambion array contains Sanger 9.0 content along with predicted miRNA seqeunces described in papers by: Cummins, Proc Natl Acad Sci USA 103(10):3687-92, 2006); Xie, Nature 434(7031):338-45, 2005); Berezikov, Cell 120(1):21-4, 2005) and Bentwich, Nat Genet. 2005 Jul;37(7):766-70.
The probes are up to 25 mers depending on the mature/putative miRNA length. This array is offered exclusively through Asuragen under the DiscovArray miRNA profiling service. For more information go to http://www.asuragen.com/Services/Solutions/discovarray.aspx


title: miRCURY LNA microRNA Array, v. 9.2 - all organisms

first: Matthew

middle: Jonathan

last: Murray

address: Box 197, Hills Road

department: MRC/Hutchison Research Centre

institute: MRC Cancer Cell Unit

organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

description:
Platform data table annotations represent miRBase 13.0 and unique human microRNAs (miRPlus).
LotNumberRange = 20434-20448

manufacture_protocol: See manufacturers website


title: Affymetrix S. pombe Tiling 1.0FR Array [custom CDF: Sp20b_M_v04]

status: Public on Mar 17 2010

city: Basel

first: Katrina

last: Woolcock

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

organism: Schizosaccharomyces pombe

relation: Alternative to: GPL7715 (Alternative CDF [official])

manufacture_protocol: see the Affymetrix website


title: TMHRI M28 GAS array

city: Warsaw

first: Izabela

last: Sitkiewicz

address: Chełmska 30/34

department: Epidemiology and Clinical Microbiology

country: Poland

institute: National Medicines Institute

organism: Streptococcus pyogenes MGAS6180

first: James

last: Musser

first: Paul

last: Sumby

manufacture_protocol: Standard Affymetrix procedures


title: NimbleGen Clostridium acetobutylicum ATCC 824 4-plex 3.8K expression array

city: Adelphi

first: Christian

last: Sund

address: 2800 Powder Mill Road

institute: US Army Research Laboratory

organism: Clostridium acetobutylicum ATCC 824

description: NimbleGen design name 080303 TI272562 60mer expr X4. Nimblegen catalog number A7307-00-01.  A expression design for 3,847 genes from Clostridium acetobutylicum ATCC 824 and associated plasmid pSOL1 with nine 60-mer probes per gene.  Each probe is replicated 2 times.  The design includes random and other control probes.

middle: D

last: Servinsky

last: Kiel

first: Nicole

middle: F

last: Dupuy

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


title: OSU Streptococcus pyogenes M1 and M18 microarray-SDHHbtail

status: Public on Mar 12 2010

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

organism: Streptococcus pyogenes

description: The oligonucleotides were spotted onto poly-L-lysine microarray slides by a robotic microarrayer (Omni GRAD 100 microarrayer) using 12 pin spotter at the Center of Applied Genomics (CAGE) of the Public Health Research Institute, Newark, NJ. Arrays were distributed in 16 blocks each with 12 columns and 12 rows.

manufacturer: Pancholi Laboratory, OSU, Columbus; Public Health Res Institute-Newark

first: Hong

last: Jin

first: Gregory

last: Boel

manufacture_protocol: Sense strand oligonucleotides with mainly 55-mer, representing the 1,769 open reading frames (ORFs) in the genome of S. pyogenes Type M1, strain SF370 and 175 ORFs (those absent in SF370 strain) of Type M18 (Strain MGAS8232) were designed and produced by Illumina (http://www.illumina.com). They were obtained as 1.35 nmoles quantity at 50 uM concentration in 27 ul of water in shallow well plates.


title: UTHSC/Kotb Streptococcus pyogenes 5.7K

city: Cairo

first: Ramy

middle: Karam

last: Aziz

address: Qasr-El-Einy Street

department: Microbiology and Immunology

country: Egypt

institute: Faculty of Pharmacy, Cairo University

manufacturer: Molecular Resource Center, University of Tenessee Health Sciences Center

manufacture_protocol:
Each array consists of duplicates of 2,328 oligomers (70-mers) that represent all ORFs in M1 GAS, strain SF370 (GenBank accession# NC_002737) in addition to oligomers representing ORFs from prophages in strains MGAS8232 (GenBank accession# NC_003485) and MGAS315 (GenBank accession# NC_004070). The arrays also contained positive and negative controls of streptococcal ribosomal DNA and alien DNA (Stratagene), respectively.
This is a condensed version of the full array.


title: Agilent-015554 RSTA Purple sea urchin 244K v.2.0

status: Public on Mar 13 2010

city: Pacific Grove

first: Melissa

last: Pespeni

state: CA

address: 120 Oceanview Blvd.

department: Biology

institute: Stanford University

organism: Strongylocentrotus purpuratus

manufacture_protocol: in situ oligonucleotide synthesis on glass slide platform; 50bp oligo sequences based on custom designed probes to be centered on all Taq1-alpha restriction cut sites (TCGA) in the purple urchin genome


title: AIST Human EstrArray

status: Public on Mar 11 2010

city: Tokyo

first: zhu

last: yun

address: takanawa 4-21-12

country: Japan

institute: scinet company

organism: Homo sapiens

manufacture_protocol: unknown


title: Agilent-025843 SurePrint G3 Rice CGH Microarray 4x180K (Feature Number version)

status: Public on Mar 10 2010

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Oryza sativa

description:
Rice (O.sativa) CGH 180K Microarray

Arrays of this design have barcodes that begin with 16025843 or 2525843.

Data table annotations based on build IRGSP5:v5:Jun2008.

International Rice Genome Sequencing Project (IRGSP) Build 5:
http://rgp.dna.affrc.go.jp/E/IRGSP/Build5/build5.html

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

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


title: Agilent-025242 SurePrint G3 Bovine CGH Microarray 4x180K (Feature Number version)

organism: Bos taurus

description:
Bovine (bosTau4) CGH Whole Genome Microarray 4x180K

Arrays of this design have barcodes that begin with 16025242 or 2525242.

Data table annotations based on build bosTau4:Btau_4.0:Oct2007.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: University of Heidelberg custom made sulfur 5.4K array

city: Heidelberg

first: Markus

last: Wirtz

address: Im Neuenheimer Feld 360

department: Molecular Biology of Plants

institute: University of Heidelberg

organism: Arabidopsis thaliana

manufacturer: epoxy-coated Nexterion E slides (Peqlab), 50mer Oligonucleotides with aminolinker (Ocimum Biosolutions, Inc.)

manufacture_protocol: 50mer oligonucleotides with an N-terminal amino linker for 920 selected genes were optimized and tested for minimal cross-hybridization with the Smith-Waterman alignment and synthesized by Ocimum Biosolutions. Oligonucleotides were diluted to a concentration of 0.01mM to 1mM in 5xSSC (0.75M sodiumchloride and 0.075M sodium citrate) containing 2.5 M betaine and spotted on epoxy-coated Nexterion E slides (Peqlab) with a MicroGrid robot (Biorobotics) using SMP3 pins (TeleChem International). A microarray contains all probes in four replicates.


title: Agilent-024419 SurePrint G3 Rhesus Macaque CGH Microarray 4x180K (Feature Number version)

organism: Macaca mulatta

description:
SurePrint G3 Rhesus Macaque CGH Microarray 4x180K

Arrays of this design have barcodes that begin with 16024419 or 2524419.

Data table annotations based on build rheMac2:Mmul_051212:Jan2006.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Stanford Caulobacter crescentus 4.1K printing_AB

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

organism: Caulobacter vibrioides

description:
Spotted oligonucleotide array on aldehyde coated glass.
The array contains at least 1 50-mer probe for each ORF in Caulobacter crescentus.

first: Harley

last: McAdams

first: Lucy

last: Shapiro

manufacture_protocol: The microarrays for this study were printed using the GeneMachines Omnigrid Microarrayer with Telechem 16-pin ArrayIt Stealth MicroSpotting Pins. Oligo sequences were chosen to satisfy the following criteria: be a unique sequence in the genome, be located near the 5’ end of the gene, approximately 100 base pairs downstream of the predicted start codon, have similar melting temperatures, and have minimal predicted secondary structure formation. The oligos were modified at the 5’ end with a six-carbon spacer followed by a primary amino group and diluted to 20µM for printing. QMT Aldehyde slides and QMT Spotting Solution I were obtained from Quantifoil.


title: Agilent-024422 SurePrint G3 Chimpanzee CGH Microarray 4x180K (Feature Number version)

organism: Pan troglodytes

description:
SurePrint G3 Chimpanzee CGH Microarray 4x180K

Arrays of this design have barcodes that begin with 16024422 or 2524422.

Data table annotations based on build panTro2:GSCv2.1:Mar2006.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Illumina Genome Analyzer (Danio rerio)

last: GEO

organism: Danio rerio


title: CCG-UNAM Rhizobium etli CFN42 6051 v1.0

city: Cuernavaca

first: Sergio

middle: Manuel

last: Encarnación

state: Morelos

address: Av. Universidad S/N

department: Centro de Ciencias Genomicas

country: Mexico

institute: Universidad Nacional Autonoma de México

organism: Rhizobium etli CFN 42

description: Whole genome expression microarray for Rhizobium etli CFN42, representing the all open reading frames (ORF) of the chromosome and all 6 plasmids (NC_007761, NC007762, NC_007763, NC_007764, NC_004041, NC_007765, NC_007766), included repeat regions, 70mers, Ctrl probes replicated 8 times, negative control probes replicated 16 times.

first: Emmanuel

last: Salazar

first: Javier

last: Díaz-Mejía

first: Gabriel

last: Moreno-Hagelsieb

first: Jaime

last: Mora

manufacture_protocol: The oligonucleotide Rhizobium etli CFN42 70-mers, were designed by using several ad hoc programs written in PERL and other software as follows: A first program read the DNA sequences corresponding to each of the annotated genes of the R. etli CFN42 genome. If the size of the gene permitted it, the program then cut 50 bases from both the 5´ and the 3´ ends. After that, the program scanned, base by base, each possible 70-mer from the sequence, ensuring that there was no single base repeat longer than 7 bp, and a Melting point of 80 ±5 °C (the formula used for calculating TM was: Tm = 81.5 + 16.6 x log[Na+] + 41 x (G + C)/length - 500/length, with Na+ = 0.1 M; length = 70). The resulting candidate oligonucleotides were compared against the complete DNA genome sequence using NCBI’s BLASTALL (blastall –p blastn) with a maximum e-value of 1.0 (-e 1.0), and no masking of low information segments (-F F). The BLAST results were used to ensure that no candidate oligonucleotide would cross-hybridize in the microarray. We used the program PALINDROME from the EMBOSS software suite to find hairpins and filter out any candidate oligonucleotides with potential hairpins longer than 9 bases. Our programs also ensured that no oligonucleotide would have more than 20 bases in common to any other coding sequence. A control was also designed with 4 positive controls and 12 negative controls using the Drosophila melanogaster genome. All oligonucleotides were commercially synthesized without modification by MWG-BIOTECH (Ebersberg, Germany), prepared at 50 uM in Micro Spotting solution (ArrayIt Brand Products) and spotted by duplicate onto SuperAmine coated slides (25 × 75 mm; TeleChem International, INC) using the Virtek Chiprender Professional Arrayer at 20°C and 60% humidity the microarray facility at Instituto de Fisiología Celular, Universidad Nacional Autónoma de México. Finally, the slide was fixed at 80 °C for 4 h.


title: Nimblegen Salmonella enterica 5.0k array v1.0

city: SUMMIT

first: SIYUN

last: WANG

state: IL

address: 6502 S ARCHER ROAD

institute: ILLINOIS INSTITUTE OF TECHNOLOGY

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

description:
NimbleGen design name 2006-08-22_Zhang_60mer, NimbleGen design ID 4587.  Standard expression design for Salmonella typhimurium covering NC_003197, NC_003277, and 500 genes from Salmonella enteritidis. Probes selected for 5027/5027 sequences. Median number of probes/sequence is 19 with an average of 19.00. Each probe will be replicated 4 times on the chip. Probes are randomly distributed over the surface of the array. Unused features have been filled with randomly generated probes of comparable GC content.
native array description file: .ndf
native array description file: .ngd

manufacture_protocol: 385K DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.


title: Bifidobacterium breve 210B array

status: Public on Mar 09 2010

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

institute: University of Verona

organism: Bifidobacterium breve

description:
A total of 2110 probes, representing all the identified ORFs of B. breve 210B genome, of 35-40 bp in length were designed using OligoArray 2.1 software. Oligos were synthesized in 18 replicates on a 2x40k CombiMatrix array (CombiMatrix, Mulkiteo, USA). Replicates were distributed on the chip at random, non-adjacent positions. A set of 29 negative control probes designed on phage and plant sequences were also included on the chip in 60 replicates at randomly distributed positions.
Spots size: 25 microns
Total number of spots: 94928
The Platform data table reflects a condensed representation of the array's replicate features.  The full array layout (gal file) representing all of the individual features is linked as a supplementary file at the foot of this record.

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

first: Francesca

last: Turroni

first: Elena

last: Foroni

first: Mary

last: O’Connell Motherway

last: Bottacini

first: Vanessa

last: Giubellini

first: Aldert

last: Zomer

first: Massimo

last: Delledonne

first: Ziding

last: Zhang

first: Douwe

last: van Sinderen

first: Marco

last: Ventura

manufacture_protocol: Probes are directly synthesized on a 90k Combimatrix array by an in situ oligo synthesis system developed by Combimatrix Corporation (Mukilteo, USA) using the Combimatrix CustomArray synthesizer. Standard synthesis protocol provided by Combimatrix was used.


title: Illumina Genome Analyzer (Nicotiana benthamiana)

status: Public on Mar 05 2010

last: GEO

organism: Nicotiana benthamiana


title: Shanghai Biochip Staph epidermidis 48 oligo array

status: Public on Mar 08 2010

city: Shanghai

first: Tao

last: Zhu

address: 138, Dongan Road

country: China

institute: Fudan university

organism: Staphylococcus epidermidis

manufacture_protocol:
1. 50-mer oligos designed according to the S. epidermidis RP62A genome sequence were synthsized.
2. Poly-L-lysine-coated glass slides of 75 × 25 mm were prepared as described (http://cmgm.stanford.edu/pbrown/MGuide). Slides with aminosilane surface (CMT-GAPS™) were purchased from Corning (Corning, USA). The DNA spotting solution was adjusted to either 45 mM sodium citrate pH 7.0, 450 mM NaCl (3× SSC) or the same composition supplemented with 1.5 M betaine (N,N,N-trimethylglycine; Sigma, Germany).
3. DNA spotting was done with an SDDC-2 DNA Micro-Arrayer from Engineering Services Inc. (Toronto, Canada). A single SMP3 pin (TeleChem International Inc., Sunnyvale, USA) was used to avoid differences between pins. The DNA samples were printed in quadruplicate at a 200 µm centre-to-centre spacing. Slides were left at room temperature overnight and then heat-treated on a metal block at 80°C for 5 s.
4. The DNA was crosslinked to the support by UV irradiation with a total energy of 60 mJ in a Hoefer UV-crosslinker (Amersham Pharmacia Biotech, Freiburg, Germany).
5. For the blocking process, 1 g succinic anhydride (Fluka, Deisendorf, Germany) was freshly dissolved in 200 ml anhydrous 1,2-dichloroethane (DCE; Fluka). To this solution, 2.5 ml of N-methylimidazol (Fluka) was added and immediately poured into the slide chamber. Incubation was for 1 h, placed on an orbital shaker for slight agitation.
6. Subsequently, the slides were briefly washed in 200 ml of fresh DCE and incubated in boiling water for 2 min for DNA denaturation. After a brief rinse in 95% ethanol, they were left to dry at room temperature.


title: UMDNJ Trypanosoma brucei 19K

city: Newark

first: Christopher

last: Utter

state: NJ

address: 225 Warren St.

department: Microbiology and Molecular Genetics

country: USA

institute: University of Medicine and Dentistry of New Jersey-New Jersey Medical School

organism: Trypanosoma brucei

description:
Pathogen Functional Genomics Resource Center
Trypanosoma brucei version 3
70mer oligonucleotide
2x replicate oligo printing

manufacturer: Pathogen Functional Genomic Resources Center

manufacture_protocol: 70mer oligonucleotides are printed in dublicate. Once printed slides are allowed to dry slowly at 65% humidity to insure good spot morphology. Slides are UV cross-linked at 25000uJ (25mJ) and stored in a desiccator until shipped.


title: Boyce/Adler_P. multocida_Combi12K_V1.0_2008

city: St Lucia

first: Jason

last: Steen

address: Carmody Road

department: IMB

institute: University of Queensland

organism: Pasteurella multocida subsp. multocida str. Pm70

middle: A

first: John

last: Boyce

first: Ben

last: Adler

first: Marina

last: Harper

manufacture_protocol:
Probes were designed by Combimatrix as per the published PM70 genome sequence, with 2 probes per ORF >500bp and 1 probe per ORF under 500bp.
Arrays were generated as per the Combimatrix protocols (http://www.combimatrix.com/tech_microarrays.htm)


title: Shanghai Biochip Staph epidermidis 116 cDNA array

manufacture_protocol:
1. Non-homologous DNA fragments of ~500 bp in length were PCR-amplified in 100 µl reactions with the specific primer, purified by an isopropanol precipitation and resuspended in water. The DNA concentration was determined by measuring the fluorescence signal obtained in the presence of the dye Hoechst-33258. Purity of the fragments was checked by agarose gel electrophoresis.
2. Poly-L-lysine-coated glass slides of 75 × 25 mm were prepared as described (http://cmgm.stanford.edu/pbrown/MGuide). Slides with aminosilane surface (CMT-GAPS™) were purchased from Corning (Corning, USA). The DNA spotting solution was adjusted to either 45 mM sodium citrate pH 7.0, 450 mM NaCl (3× SSC) or the same composition supplemented with 1.5 M betaine (N,N,N-trimethylglycine; Sigma, Germany).
3. DNA spotting was done with an SDDC-2 DNA Micro-Arrayer from Engineering Services Inc. (Toronto, Canada). A single SMP3 pin (TeleChem International Inc., Sunnyvale, USA) was used to avoid differences between pins. The DNA samples were printed in quadruplicate at a 200 µm centre-to-centre spacing. Slides were left at room temperature overnight and then heat-treated on a metal block at 80°C for 5 s.
4. The DNA was crosslinked to the support by UV irradiation with a total energy of 60 mJ in a Hoefer UV-crosslinker (Amersham Pharmacia Biotech, Freiburg, Germany).
5. For the blocking process, 1 g succinic anhydride (Fluka, Deisendorf, Germany) was freshly dissolved in 200 ml anhydrous 1,2-dichloroethane (DCE; Fluka). To this solution, 2.5 ml of N-methylimidazol (Fluka) was added and immediately poured into the slide chamber. Incubation was for 1 h, placed on an orbital shaker for slight agitation.
6. Subsequently, the slides were briefly washed in 200 ml of fresh DCE and incubated in boiling water for 2 min for DNA denaturation. After a brief rinse in 95% ethanol, they were left to dry at room temperature.


title: Miltenyi PIQOR (TM) Human Immunology Microarray, antisense

status: Public on Mar 04 2010

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec GmbH

description: The PIQOR (TM) Immunology Microarray is composed of 1070 human-specific cDNAs. These cDNAs include for each array six house-keeping genes as positive controls. In addition, four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer, respectively. All features are spotted in quadruplicate. The Platform data table reflects a condensed representation of the quadruplicate features. This Platform represents two different physical arrays (batch 808 and batch 821) which are identical in terms of spotted cDNA content but differ in the position of some cDNAs.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

manufacture_protocol: Defined 200-400 bp fragments of selected cDNAs were generated by RT-PCR, cloned and sequence-verified. Amplified and purified cDNA inserts were spotted in quadruplicate on PIQOR slides using a proprietary piezoelectric spotter. The PIQOR slides were coated in a 2-step process, generating a surface which covalently binds DNA molecules.


title: Univ of Jyvaskyla Drosophila montana microarray 197

city: Jyvaskyla

first: Maaria

last: Kankare

address: Survontie 9

country: Finland

institute: University of Jyvaskyla

organism: Drosophila montana

description: The primers for the candidate genes of D. montana were designed for one to three unique 200-500 bp regions with Primer3 program (http://www-genome.wi.mit.edu/genome software/other/ primer3.html) or manually, using information on the gene alignments mentioned above. Next, an online program e-Array 5.3 (Agilent) was used to design one to four 60 bp oligonucleotide probes per gene using exon regions. Finally, the probes were synthesized in situ with liquid chemistry and arrayed on an “Agilent 60-mer Multi-Pack Gene Expression Microarray” platform with one-colour system.

first: Tiina

last: Salminen

first: Asta

last: Laiho

first: Laura

last: Vesala

first: Anneli

last: Hoikkala

manufacture_protocol: The species-specific candidate gene microarray constructed for D. montana included 101 genes known to affect circadian clock (25 genes), phototransduction (26 genes), diapause (7 genes) and courtship behaviour (13 genes) as well as responses to cold (2 genes) and heat (28 genes) in D. melanogaster. The genes were selected from the D. melanogaster genome using FlyBase gene ontology searches on biological response (http://flybase.org/). The most conserved regions of the candidate genes were indentified by aligning the exon regions of the D. melanogaster gene to their orthologs in D. virilis with Blat search in UCSC Genome Bioinformatics database (http://genome.ucsc.edu).


title: AQUAFIRST_seabream_18K_Ver1 (condensed)

city: Galway

first: Michael

middle: Taylor

last: Cairns

address: University Road

department: MRI

institute: NUI Galway

organism: Sparus aurata

description: The Platform data table reflects a condensed representation of the array's replicate features.

manufacturer: Richard Reinhardt, MPI Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin-Dahlem, Germany

first: michael

middle: t

last: cairns

first: grace

last: davey

first: josep

last: calduch-giner

first: jaume

last: pérez-sánchez

first: benoit

last: houeix

first: anita

last: talbot

first: richard

last: reinhardt

first: svante

last: winberg

first: per-ove

last: linquist

manufacture_protocol: This array was constructed from a combination of SSH libraries created within AQUAFIRST and libraries within the Marine Genomics project. Two experiments were carried out within AQUAFIRST - one on confinement and one on parasite infection. All AQUAFIRST SSH libraries relate to these experiments. Libraries were made from liver, head kidney, gill and brain for confinment and from head kidney and intestine for pathogen exposure. All clones were sequenced and analysed along with the Marine Genomics clones to select best representation.


title: Solanum tuberosum 12.3K RLP array Version IV

status: Public on Mar 06 2010

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

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: Vanderbilt University/NimbleGen Saccharomyces cerevisiae 11470 Array

city: Nashville

first: Justin

middle: Harrison

last: Layer

state: TN

address: 21st and Garland Avenue, 746 Robinson Research Building

department: Molecular Physiology and Biophysics

institute: Vanderbilt University

organism: Saccharomyces cerevisiae

manufacture_protocol: Nimblegen


title: JCVI PFGRC Campylobacter jejuni 15K v3 array designed primarily based on strain RM1170

city: Rockville

first: PFGRC

last: JCVI

state: MD

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Campylobacter jejuni

description: This set includes 6982 oligonucleotides, has 15552 spots distributed in 48 blocks.

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


title: NIA 15K Mus musculus 15K cDNA array

status: Public on Mar 03 2010

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

organism: Mus musculus

description: The NIA_Mouse_15K_Array platform is composed of cDNAs from the NIA Mouse 15K cDNA clone collection. NIA Mouse 15K is derived from several early embryonic cDNA libraries, including blastocyst, preimplantation, embryonic stem cells, trophoblast stem cells, embryonic germ cells, and others.

manufacture_protocol: spotted cDNA


title: NimbleGen Bos taurus Btau40 WG CGH

city: Beltsville

first: George

last: Liu

address: 10300 Baltimore Ave

institute: United States Department of Agriculture

organism: Bos taurus

first: John

middle: W

last: Keele

manufacture_protocol: Maskless array synthesis was used to construct isothermal arrays. Probes were selected with a median probe spacing of 5.8 kb. Probes were synthesized using an isothermal format (Tm = 76°C) and varied in length from 50 to 75 bp.


title: Illumina Genome Analyzer II (Nicotiana benthamiana)

last: GEO


title: NimbleGen Mouse 2.1 M array 10 of 10

city: Seattle

first: Fan

last: Yang

state: WA

address: 1959 NE pacific street

institute: University of Washington

description:
2007-07-27_MM8_TILE_ChIP_10_HX1
Annotation in this record based on NCBI mouse build 36.

Regions of potential H3K27me3 target genes from mm8, isothermal tiling oligos at 100bp

manufacture_protocol: standard NimbleGen protocol, see manufacturer's web site www.nimblegen.com


title: Illumina Genome Analyzer II (Drosophila melanogaster; synthetic construct)

status: Public on Mar 01 2010

organism:
Drosophila melanogaster
synthetic construct


title: 454 GS FLX (Capsella rubella)

organism: Capsella rubella


title: NimbleGen Cronobacter sakazakii tiling array

city: Nottingham

first: Eva

last: Kucerova

address: Clifton Lane

institute: Nottingham Trent University

organism: Cronobacter sakazakii ATCC BAA-894

first: Fred

last: Long

first: Steffen

last: Porwollik

first: Michael

last: McClelland

first: Stephen

middle: J

last: Forsythe

manufacture_protocol: see Nimblegen site


title: Streptococcus mutans UA159 6k array (condensed)

city: Zurich

first: Danusia

last: Vanoaica

address: Plattenstr. 11

department: Institute for Oral Biology

institute: University of Zurich

organism: Streptococcus mutans UA159

description:
The Platform data table reflects a condensed representation of the array's replicate features.
The uncondensed version of this array is represented in Platform GPL4031.

manufacturer: Helmholtz Centre for Infection Research, Array Facility

manufacture_protocol:
1957 oligonucleotides were deposited onto CodeLink activated slides (Amersham Biosciences) at a concentration of 25 µM in 1.5 x sodium phosphate buffer in a contact-dependent manner using a MicroGrid TAS II spotter (BioRobotics, Freiburg, Germany). All 50-mers were amino-modified at the 5’-end enabling covalent linkage to reactive ester groups provided by the glass surface. Coupling of DNA was ensured by overnight incubation in a saturated sodium chloride chamber and blocking residual reactive groups was done as recommended by the manufacturer (Amersham biosciences). Until they were used, slides were maintained in a desiccated environment. To ensure complete spotting, SYBR-Green staining of three randomly selected microarrays of each printing batch was performed.
The S. mutans UA159 chip consists of 1952 oligonucleotides probing genes specific for ORFs at genomic scale and five Arabidopsis thaliana sequences served as hybridization controls and were used for grid finding. Altogether, three replicates were immobilized per oligonucleotide and array. Two arrays were placed on one slide.


title: 454 GS FLX (Arabidopsis lyrata)

organism: Arabidopsis lyrata


title: UNIFEGM Human 4x44k v1.0

city: Ferrara

first: Matteo

last: Bovolenta

address: 74, Fossato di Mortara

department: Life Sciences and Biotechnology

country: Italy

institute: University of Ferrara

organism: Homo sapiens

manufacture_protocol: 60-mer oligonucleotides spotted with SurePrint technology by Agilent. Probes were designed and identified in the Agilent eArray on-line tool


title: NimbleGen Bos taurus Btau31 WG CGH


title: NIA/NIH Human Focused Immune Array 4600

status: Public on Mar 02 2010

city: Boston

first: Paul

last: McLaren

state: MA

address: 77 Avenue Louis Pasteur, NRB150

department: Medicine

institute: Harvard Medical School

manufacture_protocol: Printed as described in Barrett et al, Restor Neurol Neurosci, 2001;18(2-3):127-35


title: CNRS Paramecium megabase chromosome microarray version 1

city: Gif sur Yvette

first: nicolas

last: Agier

state: Ile de France

address: Avenue de la terrasse

department: transcriptomique

country: France

institute: CNRS

organism: Paramecium tetraurelia

description: GapsII aminosilane coated slides were used

first: Jacek

last: Nowak

first: Marek

last: Juszczuk

first: Robert

last: Gromadka

first: Maria

last: Jerka-Dziadosz

first: Marie-hélène

last: Mucchielli

first: Nicolas

first: Thomas

last: Tang

first: Lawrence

last: Aggerbeck

first: Olivier

last: Arnaiz

first: Jean

last: Cohen

first: Christopher

last: Herbert

first: Hervé

last: Delacroix

first: Linda

last: Sperling

first: Mireille

last: Bétermier

last: Zagulski

manufacture_protocol:
- Array were spotted with the GeneTAC G3 (Genomic solutions)
- cDNA were dried and resuspended in 50% formamide and 1% CHAPs (spotting buffer)
- Each array were qualified after spotting by scan with the axon 4000B
- Each array were designed to contain 3 replicates of each probe


title: Operon_malaria_8K

city: Brummeria

first: John

middle: van Wyk

last: Becker

address: Meiring Naude Road

department: Biosciences

institute: Council for Scientific and industrial Research

organism: Plasmodium falciparum

middle: v

last: Mtwisha

first: Bridget

middle: G

last: Crampton

first: Stoyan

middle: H

last: Stoychev

first: Anna

middle: C

last: van Brummelen

first: Shaun

last: Reeksting

first: Abraham

middle: I

last: Louw

first: Lyn-Marie

last: Birkholtz

first: Dalu

last: Mancama

manufacture_protocol:
Array robot type: robot is a custom design and is not commercially available
Printing Type: Contact printing
Deposition Methodology: ceramic capillary printing pins.
Buffer type: 150mM NaPO4, pH 8.0,
DNA concentration: 40umolar
Substrate type: Schott Epoxide


title: Rosenzweig_E.coli_4290_v1.0

status: Public on Jul 22 2009

city: Missoula

first: Frank

last: Rosenzweig

state: MT

address: 32 Campus Drive, HS 104

department: Division of Biological Sciences

institute: University of Montana

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

description: Corning Gaps II aminosilane coated slides

first: Margie

last: Kinnersley

first: William

middle: E

last: Holben

manufacture_protocol: Microarrays were produced using full-length open reading frame PCR products generated with the Sigma-Genosys ORFmers primer set and reaction conditions and cycling parameters recommended by the manufacturer (Sigma-Genosys, The Woodlands, TX). This set contains primer pairs for all 4290 known and hypothetical ORFs in E. coli K12 MG1655. PCR reactions were repeated and pooled as necessary to obtain at least 3 micrograms of DNA and pooled reactions were ethanol precipitated, resuspended and further purified using a Qiagen MinElute96 UF PCR purification kit. Purified PCR products were run on agarose gels for quantification and to verify PCR product size. Products were standardized to each contain 2 µg, dried, and dissolved in 10 µl 3X SSC for printing. Arrays were printed onto Corning Gaps II aminosilane-coated slides using a 48-pin Stanford-UCSF style arrayer at the Stanford Functional Genomics Facility (Stanford, CA).


title: INRA-BDR Bovine 10k

city: Jouy en Josas

first: Isabelle

last: Hue

address: Domaine de Vilvert

department: PHASE

institute: INRA

description: (22cmx22cm, Amersham Biosciences) - 3x3 pattern - The 10K custom cDNA membrane developed in our laboratory was used for the experiment. Briefly, the array contained 7.800 EST from term placenta (Everts et al., 2005) and we incremented this set by 2.400 new EST from a cDNA library established on young foetuses and early extra-embryonic tissues. This second library (called BE03) was constructed from mRNA isolated from extra-embryonic tissues of bovine embryos from D14 to D24 of gestation and foetuses (D36 and D64). The BE03 library was normalized and subtracted by the 7.8K set using the protocol from Bento Soares. About 10.000 bacterial clones were sequenced. The sequences were repeat-masked using RepeatMasker (05/05/99) and the clustering was performed by CAP3. The CAP3 assembly resulted into 2.400 new EST. In total, 10.214 unique cDNA were spotted onto Nylon N+ membranes (Amersham Biosciences) with a 3x3 pattern (QBot, Proteigene) at the CRB GADIE platform (INRA, Jouy en Josas, France). The “BE03” library is indexed as Lib. 17188 and Lib. 15992 (http://www.ncbi.nlm.nih.gov).

manufacturer: INRA/UMR Biologie du Developpement et Reproduction

first: Severine

last: Degrelle

first: Alvaro

last: Hernandez

first: Robin

last: Everts

first: Cindy

last: Tian

first: Jerry

last: Yang

first: Harris

last: Lewin

first: Jean-Paul

last: Renard

manufacture_protocol: The 10K array contains 7.800 EST from term placenta (Everts et al., 2005), incremented by 2.400 EST from the BE03 cDNA library. The BE03 library was established on extra-embryonic tissues of bovine embryos from D14 to D24 of gestation and fetuses (D36 and D64 and has been indexed in Unigene as Lib. 17188 and Lib.15992. In total, 10.214 unique cDNA were spotted onto Nylon N+ membranes (Amersham Biosciences) with a 3x3 pattern (QBot, Proteigene) at the CRB GADIE platform (INRA, Jouy en Josas, France).


title: Genotypic Designed Agilent Insitu Synthesized Homo sapiens 8x15K array

status: Public on May 30 2009

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

first: Raja

last: Mugasimangalam

first: Rohit

middle: N

last: Shukla

first: Shruti

last: Sinha

first: Madavan

last: Vasudevan

manufacture_protocol: Refer Manufacturer's Protocol


title: UMR BiO3P-INRA Acyrthosiphon pisum 0.4K miRNAs v1

city: Rennes

first: Stephanie

last: Jaubert

address: domaine de la Motte

organism: Acyrthosiphon pisum


title: JCVI PFGRC Vibrio parahaemolyticus 21K v1 array designed primarily based on strain RIMD_2210633

status: Public on Apr 09 2008

first: PFGRC

last: JCVI

organism: Vibrio parahaemolyticus

description: This set includes 9232 oligonucleotides, has 21168 spots distributed in 48 blocks.

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


title: JCVI PFGRC Aspergillus nidulans 25K v2 array designed primarily based on strain FGSC_A4

status: Public on Nov 13 2008

organism: Aspergillus nidulans

description: This set includes 11408 oligonucleotides, has 25392 spots distributed in 48 blocks.

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


title: Vibrio salmonicida 5.5K V1.0.1 AROS

city: Tromsø

first: Erik

last: Hjerde

address: Breivika

department: Department of chemistry

country: Norway

institute: University of Tromsø

organism: Aliivibrio salmonicida

manufacture_protocol:
see manufacturer's web site at www.operon.com
OpArrays are printed on the same side as the barcode (graphic to the right).
70-mer oligos are arrayed in Genetics type G7020 384-well plates. The amount used for printing of each oligo is 300 pmol.


title: CSIR Fungi 20090901 96 v1.0

city: Pretoria

first: Eugenia

last: Barros

state: Gauteng

address: Meiring Naude Rd

department: Building 20

institute: CSIR

organism:
Aspergillus
Aspergillus amstelodami
Aspergillus clavatus
Aspergillus niger
Penicillium
Fusarium
Fusarium oxysporum
Fusarium sporotrichioides
Fusarium acuminatum
Fusarium graminearum
Alternaria alternata
Penicillium expansum
Talaromyces islandicus
Fusarium avenaceum
Aspergillus carbonarius
Fusarium subglutinans
Aspergillus versicolor
Fusarium cerealis
Fusarium equiseti
Penicillium fellutanum
Penicillium corylophilum
Fusarium verticillioides

description: Forty food-borne fungi

manufacturer: CSIR and ACGT Microarray Facility, University of Pretoria, Pretoria, South Africa

manufacture_protocol:
1. Oligonucleotide probes  ranging in size from 16 - 23 bases were transferred to Genetix X7022 384-well plates for arraying.
2. Each well contained a final concentration of 20 µM oligonucleotide probe in 50% DMSO spotting solution (v/v).
3. Between printing runs the plates were stored at -20°C.
4. Prior to printing the plates were incubated at room temperature for 30 min to aid temperature equilibration.
5. Plates were centrifuged at 2000 x g for 5 minutes prior to printing.
6. Printing was performed on the Molecular Dynamics Generation III spotter.
7. Seals were removed and plates placed in the spotter immediately prior to initiating the printing process to prevent unnecessary evaporation.
8. A relative humidity of 50% was maintained in the spotter cabinet during printing runs.
9. Following completion of the printing run the plates were sealed with a new Abgene adhesive plate seal and stored at -20°C.


title: JCVI PFGRC Vibrio parahaemolyticus 21K v1 array designed primarily based on strain AQ3810


title: JCVI PFGRC Listeria monocytogenes 21K v3 array designed primarily based on strain EGD-e

status: Public on Dec 13 2007

organism: Listeria monocytogenes

description: This set includes 6322 oligonucleotides, has 21168 spots distributed in 48 blocks.

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


title: JCVI PFGRC Listeria monocytogenes 21K v3 array designed primarily based on strain 4b H7858


title: Affymetrix GeneChip Mouse Genome 430A array [CDF: mm430mmentrezgcdf]

city: Bar Harbor

first: Gary

last: Churchill

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

organism: Mus musculus

first: Paul

middle: D

last: McDonagh

first: Karl

last: Runge

first: David

last: DeCaprio

first: Ioannis

middle: M

last: Stylianou

first: Sharon

last: Tsaih

first: Bruce

last: Church

first: Iya

last: Khalil

relation: Alternative to: GPL339 (Alternative CDF [official])

manufacture_protocol: This protocol is identical to GPL339 but a custom CDF environment was used to extract data. The CDF can be found at the web link below and as a supplementary file at the foot of the record.


title: JCVI PFGRC Bacillus anthracis 20K v3 array designed primarily based on strain Ames

status: Public on Jun 05 2007

city: Rockville

address: 9704 Medical Center Drive

organism: Bacillus anthracis

description: This set includes 5821 oligonucleotides, has 20160 spots distributed in 48 blocks.

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


title: JCVI PFGRC Trypanosoma cruzi 26K v2 array designed primarily based on strain CL Brener

organism: Trypanosoma cruzi

description: This set includes 11158 oligonucleotides, has 26496 spots distributed in 48 blocks.

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


title: [CAN07a520619F] Candida albicans 11-mer Affymetrix 10K array version1

status: Public on Nov 05 2008

city: Memphis

first: Katherine

middle: S

last: Barker

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

organism: Candida albicans

first: Nico

last: Dunkel

first: Teresa

middle: T

last: Liu

first: Ramin

last: Homayouni

first: Joachim

last: Morschhauser

last: Rogers

manufacture_protocol: We developed a new Affymetrix custom expression array (CAN07, 49-5241 array format with 11 micron features) for C. Albicans.  The nucleotide sequences corresponding to 6,165 open reading frames (ORFs) for C. albicans were downloaded from the Galar Fungail European Consortium (Assembly 6, http://www.pasteur.fr/Galar_Fungail/CandidaDB). We planned to design two separate probe sets for each ORF, each consisting of 11 perfect match and 11 mismatch overlapping 25 bp oligonucleotides, to the 3’ 600 bp region. For ORFs less than 600 bp in length the sequence was divided in two equal segments for subsequent design procedures. For quality control and normalization purposes, we made additional control probesets corresponding to GAPDH (1 probeset), actin (1 probeset) and the 5’ and middle region of Mdr1p (Bmr1p) transcript in addition to the standard Affymetrix controls (BioB, C, D, cre, DAP, PHE, LYS, THR). The probe selection was performed by the Chip Design group at Affymetrix, Inc. using their proprietary algorithm to calculate probe set scores, which includes a probe quality metric, cross-hybridization penalty and gap penalty. The probe sets were then examined for cross-hybridization against all other sequences in the C. albicans genome as well as a number of constitutively expressed genes and rRNA from other common organisms. Consequently, for some target regions we were not able to design high quality probe sets. In the end, the GeneChip contained 10,014 probesets, corresponding to 5,806 unique ORFs. Two probes were represented for 4,208 ORFs, allowing 2 independent measurements of the mRNA level for that particular gene.


title: [CAN04a530004N] Candida albicans affymetrix array

status: Public on Aug 17 2007

first: Kathy

first: Lijing

last: Xu

manufacture_protocol: The nucleotide sequences corresponding to 6165 open reading frames (ORFs) for C. albicans were downloaded from the Galar Fungail European Consortium (Assembly 19, http://www.pasteur.fr/Galar_Fungail/CandidaDB/). Following the Affymetrix Design Guide, we set out to design two separate probe sets for each ORF, each consisting of 13 perfect matches and 13 mismatches overlapping 25 bp oligonucleotides, to the 3’ 600 bp region.  For ORFs less than 600 bp in length the sequence was divided in two equal segments for subsequent design procedures.  For quality control and normalization purposes, we made 2-3 additional probe sets spanning the entire sequence of the C.  albicans 18S rRNA (GenBank Accession M60302), genes encoding GAPDH, actin and Mdr1p (Bmr1p) in addition to the standard Affymetrix controls (BioB, C, D, cre, DAP, PHE, LYS, THR). The probe selection was performed by the Chip Design group at Affymetrix, Inc. using their proprietary algorithm to calculate probe set scores, which includes a probe quality metric, cross-hybridization penalty and gap penalty. The probe sets were then examined for cross-hybridization against all other sequences in the C. albicans genome as well as a number of constitutively expressed genes and rRNA from other common organisms. Consequently, for some target regions we were not able to design high quality probe sets. In the end, the GeneChip contained 10,736 probesets including 9 controls, 6,123 unique ORFs and duplicate probesets for 4,604 ORFs. The duplicate probesets are made to distinct regions of the ORF, thereby allowing 2 independent measurements of the mRNA level for that particular gene. The C. albicans custom Affymetrix NimbleExpress Arrays (CAN04a530004N) were manufactured by NimbleGen Systems per our specification.


title: Mouse custom CGH oligo array 15K (020410)

city: Chiba

first: Takashi

last: Takabatake

state: Chiba

address: Anagawa 4-9-1, Inage-ku

institute: National Institute of Radiological Sciences

manufacture_protocol: see manufacturer's website


title: Tdalmanni Agilent 44K Oligoarray CGH slide

city: College Park

first: Gerald

last: Wilkinson

address: Bldg 144, 4094 Campus Dr

department: Biology

institute: University of Maryland

organism: Teleopsis dalmanni

manufacture_protocol: Custom designed using eArray, chemical synthesis


title: NRC-BRI biofilms 10K v1.0

status: Public on Feb 18 2010

city: Montreal

first: Etienne

last: Yergeau

state: Qc

address: 6100 Royalmount Ave

department: Environmental Microbiology

country: Canada

institute: NRC-BRI

organism: environmental samples

first: John

middle: R

last: Lawrence

first: Charles

last: Greer

manufacture_protocol: Ten microliters of DNA extracted from each of the 33 samples from the Wascana Creek biofilms were pooled together to form one composite DNA sample. This composite sample was fragmented by sonication at a power of 8 W for 5 s and size-selected (400-600bp) on 2% agarose gel. Gel-extracted sonicated DNA was end-repaired using an End-it kit (Epicentre Biotechnologies, Madison, WI) and incubated with Taq DNA polymerase and ATP for 1h at 72°C to create an “A” overhang compatible with UA ligation. End-repaired DNA was then ligated in a pDrive vector (Qiagen, LaJolla, CA) and transformed into XL1-Blue competent cells (Strategene, La Jolla, CA). 9,600 clones were picked by a VersArray colony picker (Bio-Rad, Hercules, CA) at the Concordia University Centre for Structural and Functional Genomics (Montreal, QC, Canada). DNA was extracted from the clones by boiling lysis (5 min at 95°C) and was then amplified by PCR using vector-specific primers and the PCR products were purified using Multi-Screen FB 96 wells purification plates (Millipore, Billerica, MA). Following gel analysis and DNA quantification, 6543 PCR products were classified as “good” (66.2%) and 917 PCR products were classified as “weak” (9.6%). The remaining reactions (2332; 24.3%) showed either no product or multiple bands and were classified as “failed”. All PCR products were then printed in duplicate on amino-silane coated glass slides with a VersArray Chip Writer Pro printer (Bio-Rad).


title: UHN Yeast 6.4kv7

status: Public on Feb 14 2010

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

institute: University of Chile

organism: Saccharomyces cerevisiae

manufacturer: University Health Network Clinical Genomics Center Microarray Centre


title: JCVI PFGRC Vibrio parahaemolyticus 21K v1 array designed primarily based on strain KXV237

first: PFGRC

last: JCVI

institute: J. Craig Venter Institute


title: JCVI PFGRC Listeria monocytogenes 21K v3 array designed primarily based on strain 1/2a F6854


title: [AsprgDTUa520520F] Custom Affymetrix Aspergillus Chip DTU_3Aspergillus_45K_v1.0

status: Public on Feb 10 2008

city: Kgs. Lyngby

first: Mikael

last: Andersen

address: Søltofts plads, bygn 223

department: BioCentrum-DTU

country: Denmark

institute: Technical University of Denmark

organism:
Aspergillus niger
Aspergillus oryzae
Aspergillus nidulans

description: Type: CustomExpress. Feature size: 11-micron. Format: 49-7875

first: Wanwipa

last: Wongsangnak

first: Gianni

last: Panagiotou

first: Irina

last: Borodina

first: Jens

last: Nielsen

manufacture_protocol: Initial probe-design was done using the OligoWiz 2.0 software (Nielsen, 2003, Wernersson, 2005) from CDS sequences of predicted ORFs from the genome sequences of A. nidulans FGSC A4 (Galagan, 2005), A. niger ATCC 1015 (Baker, 2006) and A. oryzae RIB40 (Machida, 2005).  For each gene, a maximum of 11 non-overlapping perfect match probes were calculated using the OligoWiz standard scoring of cross-hybridization, melting temperature, folding, position preference and low complexity. A 3' position preference for the probes was included in the computations. The probes were designed separately for each genome. Pruning of the probe sequences to comply with Affymetrix recommendations was done by removing duplicate probe sequences and shortening probes that were not possible to synthesize in full length. Also included on the chip iss a number of Affymetrix standard controls, custom controls, an A. oryzae EST-collection (courtesy of Novozymes A/S) and probes for ORFs from the S. coelicolor A3(2) (Bentley, 2002) genome.


title: JCVI PFGRC Giardia lamblia 20K v2 array designed primarily based on strain WB_C6

organism: Giardia duodenalis

description: This set includes 7003 oligonucleotides, has 20160 spots distributed in 48 blocks.

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


title: JCVI PFGRC Bacillus anthracis 20K v3 array designed primarily based on strain A2012


title: JCVI PFGRC Streptococcus pneumoniae 15K v8 array designed primarily based on strain R6

status: Public on Mar 26 2010

organism: Streptococcus pneumoniae

description: This set includes 3942 oligonucleotides, has 15552 spots distributed in 48 blocks.

manufacture_protocol: 8QSP, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000