title: CapitalBio 29K Rat Genome Version 3.0.5 Array

status: Public on Nov 30 2010

city: Shanghai

first: Weibin

last: Jiang

address: 518,Ziyue ARd

country: China

institute: Shanghai Institute of Veterinary Research, Chinese Academy of Agricultural Sciences

organism: Rattus norvegicus

technology: spotted oligonucleotide

distribution: custom-commercial

manufacture_protocol: as described in CapitalBio Corporation Manual


title: Illumina HiSeq 2000 (Locusta migratoria manilensis)

status: Public on Nov 24 2010

last: GEO

country: USA

organism: Locusta migratoria manilensis

technology: high-throughput sequencing

distribution: virtual


title: University of Cape Town Arabidopsis thaliana 7200 cDNA array

status: Public on Nov 22 2010

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: Arabidopsis thaliana

technology: spotted DNA/cDNA

distribution: non-commercial

manufacturer: University of Cape Town, Microarray facility, South Africa

first: Katherine

middle: J

last: Denby

first: Sally

last: Walford

manufacture_protocol:
1. Mendel Biotechnology L35 collection of Arabidopsis ecotype Col-0 cDNA library were amplified using vector specific primers (5'CGCTCTAGAGGATCCAAGCTTACGT-3' and 5'ACCGGTCCGGAATTCCCGGGTCGAC-3')
2. PCR fragments were purified using Multiscreen PCR purification plates
3. Purified PCR fragments were arrayed in Genetix X7022 384-well plates.
4. Each well contained a final concentration of 125 ng/µl PCR product in 50% DMSO spotting solution (v/v).
5. Between printing runs the plates were stored at -20°C.
6. Prior to printing the plates were incubated at room temperature for 30 min to aid temperature equilibration.
7. Plates were centrifuged at 2000 x g for 5 minutes prior to printing.
8. Printing was performed on the Molecular Dynamics Generation III spotter.
9. Seals were removed and plates placed in the spotter immediately prior to initiating the printing process to prevent unnecessary evaporation.
10. A relative humidity of 50% was maintained in the spotter cabinet during printing runs.
11. Following completion of the printing run the plates were sealed with a new Abgene adhesive plate seal and stored at -20°C.


title: TNO/NimbleGen 60-mer 080328 L. monocytogenes 4bF2365 4x72K array

status: Public on Nov 26 2010

city: Zeist

first: Remco

last: Kort

address: Utrechtseweg 48

department: Microbiology

country: Netherlands

institute: TNO

organism: Listeria monocytogenes serotype 4b str. F2365

technology: in situ oligonucleotide

description:
NimbleGen design name 080328 L monocytogenes 4bF2365 expr X4 (each slide contains 4x72,000 probes). An expression design for 2,821 genes from L.monocytogenes NC_002973 with twelve probe pairs (PM/MM) per gene. Each probe is replicated 2 times. The design includes control probes.
Native array description files (ndf, ngd) 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: TNO/NimbleGen 60-mer TI224308 Bacillus subtilis subsp. subtilis strain 168 array

status: Public on Nov 28 2010

organism: Bacillus subtilis subsp. subtilis str. 168

description: NimbleGen design name TI224308_60mer_expr. An expression design for 4,104 genes from B.subtilis subsp. subtilis strain 168 NC_000964 with eight probe pairs (PM/MM) per gene. Each probe is replicated 2 times. The design includes control probes.


title: SAGE:15:NlaIII:Lentinula edodes

status: Public on Nov 18 2010

organism: Lentinula edodes

technology: SAGE NlaIII

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


title: NimbleGen T. reesei 2.1M HD2 arrayCGH

city: VTT, Espoo

first: Marika

last: Vitikainen

address: Tietotie 2

country: Finland

institute: VTT Technical Research Centre

organism: Trichoderma reesei

description: Build: Trichoderma reesei v2.0 (http://genome.jgi-psf.org/Trire2/Trire2.home.html)

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


title: Exiqon miRCURY array

city: Verona

first: Mirco

last: Galiè

address: via Le Grazie, 8

department: Neuroscience, Biomedicine and Movement Sciences

country: Italy

institute: University of Verona

organism: Mus musculus

description: LNA-based microRNA profiling

manufacture_protocol: Exiqon (Vedbaek, Denmark)


title: Madhani lab S. pombe 43K euchromatin tiling array

city: San Francisco

first: Hiten

last: Madhani

state: CA

department: Biochemistry and Biophysics

institute: University of California, San Francisco

organism: Schizosaccharomyces pombe

description: Coordinates of oligos are based on sequence downloaded prior to April 2009

manufacture_protocol: Oligonucleotides were synthesized and applied using inkjet technology developed by Agilent


title: Agilent-023287 Salm_enterica_14028_tiling_array

status: Public on Nov 20 2010

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

organism: Salmonella enterica subsp. enterica serovar Typhimurium

description:
A tiling array for Salmonella enterica serovar Typhimurium 14028. Arrays of this design have barcodes that begin with 16023287 or 2523287.
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.

first: Marcus

last: Jones

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


title: E.coli_12k_Combimatrix

city: Ljubljana

first: Spela

last: Baebler

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

organism: Escherichia coli

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


title: Human Inflammatory Response and Autoimmunity PCR Array

city: North Chicago

first: Kenneth

last: Beaman

state: IL

address: 3333 Green Bay Rd

department: Microbiology and Immunology

institute: Rosalind Franklin University of Medicine and Science

organism: Homo sapiens

technology: RT-PCR


title: Human 21K

status: Public on Nov 27 2010

city: Chieti

first: Rosa

last: Mancinelli

state: Chieti

address: via Dei Vestini 29

department: Dept. Basic and Applied Medical Sciences

institute: University "G. d'Annunzio" Chieti-Pescara, Chieti

description: Operon oligos, oligo sequence not available

manufacture_protocol: Details of the design of the slide and sequence selection can be found at the manufacturer’s website (http://microcribi.cribi.unipd.it/e-index.htm)


title: Madhani lab S. pombe 41K heterochromatin tiling array


title: DTU Agilent Pseudomonas putida KT2440 15K

city: Kgs Lyngby

first: Gamze

last: Gulez

address: Miljoevej 113

department: Environmental Engineering

country: Denmark

institute: Technical University of Denmark

organism: Pseudomonas putida KT2440

first: Arnaud

last: Dechesne

first: Chris

last: Workman

first: Barth

middle: F

last: Smets

manufacture_protocol: array (8x15) is spotted using Agilent 60-mer SurePrint technology,  with 2 to 4 spot replicates for each probe (http://www.genomics.agilent.com/GenericB.aspx?PageType=Custom&SubPageType=Custom&PageID=2011)


title: Superarray Bioscience Corporation - custom array COM-0088

manufacture_protocol: Superarray Bioscience Corporation


title: Lactobacillus johnsonii NCC533 Agilent 11K

city: Lausanne 26

first: Bernard

address: Vers-Chez-Les-Blanc

department: Nutrition & Health

country: Switzerland

institute: Nestlé Research Center

organism: Lactobacillus johnsonii


title: Habitat specific dsrAB targeted functional gene microarray

city: Vienna

first: Doris

last: Steger

state: Vienna

address: Althanstrasse 14

department: Department of Microbial Ecology

country: Austria

institute: University of Vienna

organism: uncultured sulfate-reducing bacterium

first: Manuel

last: Hofer

first: Alexander

last: Loy

manufacture_protocol: Probes targeting dsrA or dsrB were designed using the probe tools of the ARB software package and a dsrAB ARB database containing approximately 500 sequences (>1500 nucleotides) from pure cultures and environmental studies. Based on a distance matrix tree of all previously published dsrAB clone sequences retrieved from Schlöppnerbrunnen I+II system, 146 probes with an average length of 30 bases were designed targeting different clone groups from the study site. Thermodynamic properties of the probes were calculated using the two-state hybridization server of DINAMelt (default settings: linear DNA, 37°C, 1 M Na+, 0 M Mg2+, 0.1 mM strand concentration). Probes lengths were adjusted to obtain similar theoretical free energy (deltaG) values. Final probes had a length of 27 to 34 nucleotides with an average deltaG of -41.0 ± 0.7 kcal/mol. The in silico specificity and number of weighted mismatches to non-target dsrAB sequences of each probe were determined using probeCheck. Oligonucleotides for microarray spotting were synthesized by Microsynth (Balgach, Switzerland). The 5’-end of each oligonucleotide probe carried a T-spacer consisting of 30 dTTP molecules and the 5’-terminal dTTP was aminated to allow covalent coupling of the oligonucleotides to aldehyde group-coated VSS-25 glass slides. Each probe was adjusted to a concentration of 50 pmol/µl in 50% dimethyl sulfoxide and printed on the slide by using a BioRobotics MicroGrid spotter (Genomics Solutions, Ann Arbor, MI, USA) under constant temperature (20°C) and humidity (min. 50%) conditions. Each microarray contained three and six replicate spots of each dsrA/dsrB-targeted probe and control probe, respectively. Freshly spotted DNA microarrays were incubated overnight at room temperature in a humid chamber. Slides were further treated with sodium borohydride as described previously.


title: "Dehalococcoides ethenogenes" strain 195 with Methanogens and Fosmids, Base Composition Method

city: Ithaca

first: Cresten

last: Mansfeldt

state: NY

address: 220 Hollister Hall

institute: Cornell University

organism: Dehalococcoides mccartyi 195

description: "Dehalococcoides ethenogenes" strain 195 with additional community members and luciferase. Arrays of this design have barcodes that begin with 16021465 or 2521465. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent. 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.

first: Ruth

middle: E

last: Richardson

first: Annette

last: Rowe

first: Laura

last: Hug

first: Gretchen

last: Heavner


title: QIMR/Agilent-023536 Schistosoma japonicum 44k array_New 2009 Sj

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

organism: Schistosoma japonicum

description:
Arrays of this design have barcodes that begin with 16023536 or 2523536.
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.

first: Donald

last: McManus


title: Aquafirst_Trout

city: Galway

first: Michael

middle: Taylor

last: Cairns

address: University Road

department: MRI

country: Ireland

institute: NUI Galway

organism: Oncorhynchus mykiss

first: P

last: Prunet

first: S

last: Winberg

first: C

last: Secombes

first: M

middle: T

middle: C

last: Johnson

last: Linquist

first: T

last: Wang

first: B

last: Houeix

first: A

last: Talbot

first: G

last: Le borgne

last: Mmativet

manufacture_protocol: Oligos were designed and manufactured by Eurogentec, printed on E Nexterion slides from Schott


title: Agilent-017166 Brevibacterium aurantiacum ATCC9174 Array

status: Public on Nov 25 2010

city: Thiverval-Grignon

first: Marie-Pierre

last: FORQUIN

address: Aveniue de la Bretigniere

department: MICA

country: France

institute: INRA

organism: Brevibacterium aurantiacum

manufacture_protocol: see Agilent website


title: Affymetrix human microbiota probiotic transcriptional platform

city: Ann Arbor

first: Eric

middle: Charles

last: Martens

state: MI

address: 1150 West Medical Center Drive

department: Dept. of Microbiology and Immunology

institute: University of Michigan Medical School

organism:
Bacteroides thetaiotaomicron
Streptococcus thermophilus
Lacticaseibacillus casei
Lactobacillus delbrueckii
Bifidobacterium animalis
Agathobacter rectalis
Bifidobacterium longum

description:
probiota520522F
Affymetrix high-density 25-basepair oligonucleotide array.

Multiple human gut bacteria and/or food supplements.

first: Justin

last: Sonnenburg

first: Erica

first: Jeffrey

last: Gordon

manufacture_protocol: See manufacturer's website.


title: Agilent-027313 Yersinia pestis CO92 tiling array [YP_tiling_244k]

status: Public on Nov 23 2010

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Yersinia pestis CO92

description: Yersinia pestis tiling array. Arrays of this design have barcodes that begin with 16027313 or 2527313.. 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: Maize oligo array version 1.4 slide set (slides A and B)

city: St. Louis

first: Nicole

middle: Christina

last: Riddle

state: MO

address: 1 Brookings Dr.; CB1137

department: Biology

institute: Washington University

organism: Zea mays

manufacturer: Maize Oligonucleotide Project, University of Arizona; www.maizearray.org

manufacture_protocol:
REHYDRATION AND PRINTING OF THE OLIGONUCLEOTIDE MICROARRAYS Add 15 uL of 3XSSC to each well of the 300 pM oligonucleotide set to make a 20 μM oligonucleotide solution. Transfer onto an orbital shaker for 1 h at RT at 100 rpm. The oligonucleotides are now ready for printing. The Arabidopsis oligonucleotide microarrays are printed on aminosilane-coated “Superamine” slides (Telechem) or “Powermatrix” slides (Full Moon Biosystems), using Telechem Type SMP3 printing pins. Printing conditions: Single array element printed per oligonucleotide, 48 pins in the print head, 31% relative humidity, redipping after every 50 slides. The print head Z- velocity is set to a maximum of 10 mm/sec. Bake slides for 2h at 80oC. Store dry and in darkness at RT.
IMMOBILIZATION OF THE OLIGONUCLEOTIDE ARRAY ELEMENTS Rehydrate the microarray slide over 50oC water for 10 seconds; snap-dry on a 65oC heating block for 10 seconds. Repeat this step 4 times. Crosslink the oligonucleotides to the slide surface by exposing the DNA-side of the microarray to UV irradiation (65mJ). Wash the slides in 1% SDS dissolved in sterile ddH2O for 5 min at RT. Rinse the slides by plunging slide into sterile ddH2O. Rinse in 100% ETOH for 30 seconds to 5 min, with gentle shaking. Spin dry the slides in a slide centrifuge for 3 min. Store the slides in a light-proof box under cool dry conditions.


title: RIPCM H. Pylori 3.2K 1576 v1.0

city: Moscow

first: Kuvat

last: Momynaliev

address: Malaya Pirogovskaya 1A

country: Russia

institute: Research Institute for Phys-Chim Medicine

organism: Helicobacter pylori 26695

manufacture_protocol: Primers set for PCR were purchased from Eurogentec. 3242 primers were designed and synthesized to amplify the complete ORFs in the H. pylori genome of strain 26695. The primers were designed to amplify each ORF beginning at the start codon and ending at the stop codon. The PCR reactions were performed using 96-well plates in a 100 mkl reaction volume in an MJ Research (Cambridge, MA) PTC-225 DNA Engine Tetrad thermal cycler under the following conditions: 94°C 5 min, followed by 30 rounds of 30 seconds at 94°C, 30 seconds at 500C, and 4 min at 72°C, followed by one round of 10 min at 72°C. To control the yield and the specificity of the amplified ORFs, all PCR reactions were analyzed by electrophoresis on a 1% agarose gel. The 1576 PCR products that were successfully obtained (97%) were spotted robotically (Qpix, Genetix, England) in duplicate onto positively charged nylon membrane (Amersham) of 12X8 cm. After spotting, the nucleic acid samples were alkali denatured and fixed by baking the membrane at 80°C for 60 min.


title: PMCC Human 10.5K

city: Melbourne

first: Holger

last: Schlueter

state: Victoria

address: Locked Bag 1

department: Research

institute: Peter Mac Callum cancer Centre

manufacture_protocol:
PRINTING: Arrays were printed on Telechem Superamine slides. The DNA concentration we print at is 200ng/ul. DNA concentrations in every well always differ. In the past have worked out the concentrations of random wells and assumed 8ug/100ul. PCR product is dried down and resuspended in 40ul to give 200ng/ul. One 384 well plate is made up of four 96 well plates.
Cleaned up PCR product - 6ul is transferred to a 384 well plate, dried down then resuspended in 6ul of filtered 150mM NaPhosphate buffer pH 8 in a fridge overnight, ready for printing. After this, plates are resuspended in filtered Milli Q water. Plates are spun down in the centrifuge at a speed of 2800 rcf for 5 mins before resuspending in the fridge overnight, then placed on the shaker for 10 minutes then spun down again before printing. PCR foil seals were used to cover the 384 well plates during resuspension. After printing the arrays were dried down and covered with clear seal and stored in the -20C freezer. Pins take up ~0.25ul each time, so after a plate is printed, if dried down the plate was resuspended at 0.25ul less for the next print run.Scorecard aliqouts were resuspended in 5ul.
PHOSPHATE BUFFER: For pH8: 95ml 0.5M Na (2) HPO (4) 5ml 0.5M NaH (2) PO (4). Water used for the array and for washing the pins is distilled water bought from Coles. Human 10.5K array. 4 x 6 = 24 pins = 16 pick ups per 384 well plate. Consists of 27 plates + scorecard = 28 plates


title: mTOR Signaling Phospho Specific Antibody Microarray

city: louisville

first: huizhi

last: wang

state: kY

address: 501 S.Preston St. Room 211B

department: PEDH

institute: University of Louisville

technology: antibody

description: PI3K/mTOR specific Phospho-antibody array

manufacture_protocol:
see manufacturer's website
http://www.fullmoonbiosystems.com/protocols/AntibodyArrayUserGuide.pdf


title: NimbleGen Homo sapiens HG18 60mer expr (385k)

status: Public on Nov 17 2010

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description: NimbleGen design HG18 60mer expr (DESIGN_ID: 4542). Expression design for human (hg18; NCBI Build 36). 8 60mer probes per gene. 47633 exemplar genes representing a total of 63780 transcripts/variants.

distribution: commercial

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


title: TaqMan Array miRNA Card-A

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description: format: 384-well plate

manufacture_protocol: See manufacturer's website (http://www.appliedbiosystems.com/).


title: Candida albicans ENS oligo array version 1.0

city: New Delhi

first: Rajendra

last: Prasad

state: Delhi

address: New Mehrauli Road

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

organism: Candida albicans

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 Corning buffer to 20 uM and rearray 10 µL into 384-well, Genetix polystyrene V-bottom plates (cat# X6004).
3. Shake plates near maximum rotational speed on flat-bed shaker for 1 minute.
4. Centrifuge plates at 2000 rpm for 3 minutes.
5. Print oligonucleotides in duplicate on corning ultragaps II slides, using a Biorobotics spotting device and 16 pins.
6. Fix DNA on slides using UV treatment (1200 mJ default set up in a stratalinker device)


title: 454 GS FLX (unidentified)

status: Public on Nov 15 2010

last: GEO

organism: unidentified


title: NCHU Tsaiya duck magnum triplicate array (condensed version)

status: Public on Nov 16 2010

city: Taichung

first: Mu-Chiou

address: 250 Kuo-Kuang Rd

country: Taiwan

institute: National Chung-Hsing University

organism: Anas platyrhynchos

description:
Tsaiya duck (Anas platyrhynchos)
Sex: female
Tissue type: magnum
Spotted cDNA array
The Platform data table reflects a condensed representation of the array's triplicate features.  The full array layout representing all of the individual features is linked below as a supplementary file.

ONLY CLONES OF INTEREST HAVE BEEN SEQUENCED AND IDENTIFIED.

manufacturer: National Chung-Hsing University, 250 Kuo Kuang Rd., Taichung 402, Taiwan

manufacture_protocol: Printing was performed under the conditions of 60% relative humidity and 300-μm dot space. The 2912 amplicons were printed onto GAPS II coated glass slides (Corning Life Sciences) using an OmniGrid AccentTM microarrayer (GeneMachine); each amplicon was spotted in triplicate, resulting in 8736 spots on each slide.


title: Illumina Genome Analyzer II (Methanobrevibacter smithii)

organism: Methanobrevibacter smithii


title: Silkworm 23K oligo array version 2.0

city: Chongqing

first: Ling

last: Gan

address: 160#Xue Yuan Road,RongchangCounty

department: 1The Department of Veterinary Medicine

institute: Southwest University

organism: Bombyx mori

manufacture_protocol: The 23 K oligonucleotide microarrays were constructed in CapitalBio Corp. (Beijing, China), which consist of 23,134 5'-amino-modified 70-mer probes. In addition to internal controls, eight intergenic sequences from the yeast used as external controls were synthesized. The oligonucleotide probes were printed on amino silaned glass slides using a SmartArray microarrayer (CapitalBio Corp.). An aliquot of 5 µg total RNA was used to produce fluorescent dye-labeled cDNA with Eberwine’s linear RNA amplification method and subsequent enzymatic reaction according to a previous published protocol (Guo et al., 2005). The labeled DNA was purified with PCR Clean-up NucleoSpin kits (Macherey-Nagel), resuspended in Elution buffer, and quantified by UV spectrophotometry. Labeled control and test samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed into 80 µL hybridization solution (3×SSC, 0.2% SDS, 25% formamide and 5×Denhart’s). DNA in hybridization solution was denatured at 95oC for 3 min prior loading on a microarray. Hybridization was performed under LifterSlipTM (Erie Company), which allows for even dispersal of hybridization solutions between the microarray and coverslip. The hybridization chamber was placed on a 3D-Tilting Agitator (CapitalBio Corp.) to facilitate the microfluidic circulation under the coverslip. The array was hybridized at 42oC overnight and washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42℃ for 5 min, and 0.2% SSC for 5 min at room temperature). After hybridization, microarrays were scanned with a confocal LuxScanTM scanner (CapitalBio Corp.), and the data of obtained images were extracted with SpotData Software (CapitalBio Corp.). The raw data was normalized using a space and intensity-dependant LOWESS program (Yang et al., 2002).


title: Array-Ready Operon Mouse Genome Oligo Set v3.0

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

organism: Mus musculus

manufacture_protocol: see the Microarray Consortium of Norwegian University of Science and Technology website


title: Illumina Genome Analyzer II (Methanobrevibacter smithii ATCC 35061)

organism: Methanobrevibacter smithii ATCC 35061


title: University of Michigan E_coli_CFT073 5.4K array

first: Harry

last: Mobley

address: 5641 Medical Sciences II  1150 W. Medical Center Dr.

institute: University of Michigan

organism: Escherichia coli CFT073

description: NimbleGen design name 2006-07-27_TI199310_60mer.


title: Listeria monocytogenes 12K whole genome array

city: Würzburg

first: Frederike

last: Fritsch

address: Am Hubland

country: Germany

institute: Uni Würzburg

organism: Listeria monocytogenes

description:
ARRAY PRINTING
1. Dissolve oligonucleotide probe or PCR product in the appropriate spotting solution to obtain the
recommended final probe concentration:
DNA Probes Final Spotting Concentration
Oligonucleotides 10 - 20 micromolar
PCR products 0.1 – 1 mg/ml
2. Transfer an appropriate volume of probes to a microtiter plate.
3. Set up the arrayer according to the manufacturer’s recommendations. If you were previously
using slides that were thicker than 1.0 mm, for optimal spotting you may need to re-calibrate
the distance between the slide surface and the spotting pins.
4. Print the substrates at 40-50% relative humidity at 20 to 25°C.
DNA IMMOBILIZATION
1. Incubate printed microarray slides in humidity chamber at room temperature for 30 min (see
appendix for details of how to prepare this chamber) to ensure quantitative immobilization.
2. Proceed to washing
HANDLING OF PRINTED ARRAYS
The volume of washing solution should be at least 250 ml per 5 slides. Make sure that slides
do not dry out between washing steps, or between the washing and blocking step.
WASHING
1. Wash slides to remove unbound probe molecules and buffer substances to avoid
interference with subsequent hybridization experiments.
a. Rinse 1 x 5 min in 0.1% Triton X-100 at room temperature.
b. Rinse 2 x 2 min in 1 mM HCl solution at room temperature.
c. Rinse 1 x 10 min in 100 mM KCl solution at room temperature.
d. <optional> Denaturation step for arrays spotted with PCR-probes: 1 x 3 min in
boiling diH2O.
e. Rinse 1 x 1 min in diH2O at room temperature.
2. Proceed to Blocking immediately.
BLOCKING
1. Block the slides with Nexterion® Blocking Solution or alternatively with 50 mM
ethanolamine, 0.1% SDS (add freshly before use) in 0.1 M Tris, pH 9.0 as follows:
a. Incubate slides 1 x 15 min in 1x Nexterion® Blocking Solution at 50°C. The
volume of blocking solution should be at least 100 ml for 5 slides.
b. Rinse 1 x 1 min in diH2O at room temperature.
• Dry the Nexterion® Slide E in an oil-free air or nitrogen stream or by centrifugation
(200 x g for 5 min) to avoid any water stains on the slide surface.
• Proceed to hybridization.
HYBRIDIZATION
1. Re-suspend the dried, labeled target to be applied to the array in Nexterion® Hyb. In
case the target is already dissolved in a different buffer or in water, the sample can
also be diluted in Nexterion Hyb to get at least 90% (v/v) buffer in the final
hybridization solution.
2. Denature the suspended target by heating at 95°C for 3 min in a heat block, perform
a quick spin in a microcentrifuge, then pipette the appropriate volume onto the array
surface of a blocked slide under the coverslip or inside a hybridization station.
POST-HYBRIDIZATION WASHING
1. Place the array into a slide rack and immerse in a dish containing 2x SSC and 0.2%
SDS. Wash in the above solution 1 x 10 min at room temperature.
2. Wash 1 x 10 min in 2x SSC.
3. Wash 1 x 10 min in 0.2x SSC at room temperature.
4. Dry the array in an oil free air or nitrogen stream or by centrifugation (200 x g for 5
min) to avoid water stains on the slide surface.
5. Protect the array from light, dust and abrasion of the array surface, until ready for
scanning. Ensure that the laser and filter set of the scanner is compatible with the
fluorescent labeling of the probe molecules.

manufacturer: Institute for Hygiene and Microbiology, University of Wuerzburg

manufacture_protocol: oligonucleotides purchased from Operon Biotechnologies, Inc.


title: SMD Print_1448 hox

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism: Homo sapiens

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: SMD Print_1447 how


title: Baseman Mycoplasma genitalium oligo array

city: San Antonio

first: Wenbo

last: Zhang

state: TX

address: 7703 Floyd Curl Drive

department: Microbiology and Immunology

institute: The University of Texas Health Science Center at San Antonio

organism: Mycoplasmoides genitalium

description: This array includes spotted 70-mer oligonucleotides, designed to represent 484 open reading frame in the annotated M. genitalium genome.

first: Joel

middle: B

last: Baseman

manufacture_protocol: Standard company protocol


title: 454 GS (Saccharomyces cerevisiae)

status: Public on Nov 03 2010

organism: Saccharomyces cerevisiae


title: Streptomyces clavuligerus 7.4K Whole Genome MicroArray Release I

status: Public on Nov 10 2010

city: Delft

first: Wilbert

last: Heijne

address: A.Fleminglaan 1

institute: DSM Biotechnology Center

organism: Streptomyces clavuligerus

manufacture_protocol: see manufacturer's website


title: SMD Print_1437 hov


title: NimbleGen Bos taurus Whole-genome CGH 385k Array (Btau_4.0 version)

status: Public on Nov 09 2010

city: Bologna

first: Pier Luigi

last: Martelli

address: via Irnerio 42

institute: University of Bologna

organism: Bos taurus

description:
A cattle genome array for cross species experiment (Goat, Sheep).

Custom tiling arrays designed on the bovine (Bos taurus) genome, Btau_4.0 version, including a fraction of BTA13 of the University of Maryland (UMD) Bos taurus v. 2.0 assembly (ftp://ftp.cbcb.umd.edu/pub/data/Bos_taurus/Bos_taurus_UMD_2.0/). Arrays contained ~385,000 probes on a single slide to provide an evenly distributed coverage with an average interval of ~6 kb for the Btau_4.0 genome. The BTA13 of the UMD v. 2.0 assembly was included from nucleotide position 48 M bp to nucleotide position 78 M bp (4,673 oligonucleotides and average spacing of ~6 kb). This chromosome region was analysed as internal control because it contains the ASIP gene, not assembled in the BTA13 of the Btau_4.0 version.

first: Luca

last: Fontanesi

first: Pier

middle: L

first: Francesca

last: Beretti

first: Valentina

last: Riggio

first: Stefania

last: Dall'Olio

first: Michela

last: Colombo

first: Rita

last: Casadio

first: Vincenzo

last: Russo

first: Baldassarre

last: Portolano

manufacture_protocol:
See manufacturer's website at http://www.nimblegen.com/.
Probes were designed on the Btau_4.0 version of the Bos taurus genome and on the UMD version 2.0 for part of chromosome 13.
NimbleGen manufactures high-density DNA microarrays using its proprietary Maskless Array Synthesizer (MAS) technology. At the heart of the system is a Digital Micromirror Device (DMD) that uses a solid-state array of miniature aluminum mirrors to create “virtual masks” that replace the physical chromium masks used in traditional arrays. The DMD directs a pattern of UV light projected onto a microscope slide, which when coupled with UV-mediated DNA synthesis in a parallel, combinatorial manner, can generate up to 2.1 million unique probes on a single microarray.


title: SMD Print_1372 hor


title: Penaeus monodon 5K UniShrimp chip

status: Public on Nov 04 2010

city: Pathumthani

first: nitsara

last: karoonuthaisiri

state: Pathumthani

address: Paholyothin

department: Central

country: Thailand

institute: BIOTEC

organism: Penaeus monodon

manufacture_protocol: Array Design:    Amplification  Approximately 5000 sequences will be amplified either from plasmids of EST clones or from the first strand cDNA template.  For amplification from EST clones, PCR reactions were optimized considering the following parameters: (1) amounts of template, (2) types of Taq DNA polymerase, (3) units of Taq DNA polymerase, and (4) MgCl2 concentrations.   In all experiments, the reactions were performed using purified plasmids as templates in a 96-well format PCR plate (Axygen) with final concentrations of the following components: 0.3 mM dNTPs, 1X buffer, 0.4 M each primer (LM13F: CAC GAC GTT GTA AAA CGA CGG CCA G and LM13R: CAT GGT CAT AGC TGT TTC CTG T, BioBasic).  Amplification was carried out for 35 cycles at the following settings: 940C for 30 sec, 600C for 30 sec, 720C for 3 min.    For amplification from first strand cDNA, PCR reactions were optimized considering the following parameters: (1) amounts of template, (2) MgCl2 concentrations, (3) units of Taq DNA polymerase, and (4) reaction volumes.   In all experiments, the reactions were performed using cDNA as templates in a 96-well format PCR plate (Axygen) with final concentrations of the following components: 0.4 mM dNTPs, 1X buffer, 0.6 uM each gene-specific primer (designed as described below; IDT, Singapore). Amplification was carried out for 38 cycles at the following settings: 940C for 30 sec, 570C for 60 sec, 720C for 3 min.  The resulting amplicons were electrophoretically analyzed on 1.5% agarose gel prepared in 0.5X TBE buffer.  Purification  The PCR products were purified using Multiscreen PCR 96 well purification plate (Millipore, #MSNU03050). Briefly, PCR products were thoroughly loaded to the purification plate and placed under a vacuum manifold.  The bound DNA on the plate will be washed with sterile water once in vacuo until completely dried.  To collect the purified products, sterile water was added to the Millipore plate and let stand for 5-10 min before resuspended into a polysterene V-shape 96-well plate (Corning, CoStar # 3897)   Microarray fabrication    Fifteen plates of 384-well print plates were used as source plates for microarray fabrication. Source plates were resuspended in 7 uL of 3xSSC buffer (Invitrogen, cat no.15557-044) and incubated at 4C overnight before printing. The cDNA microarrays were fabricated using Nanoprint LM210 microarray spotter (ArrayIt, USA) fitted with a 24-pin head on GAPS II amino-silane coated slides (CORNING, cat no.40005). A 11,136 spots/array pattern was designed by 24 X 20 spots per block, containing a total of 24 arrays. Each amplicon was spotted in replicate. The printed slides were UV-crosslinked at 200 mJ of energy (GS Gene Linker UV chamber, BIO-RAD) and stored at room temperature in a dry incubator.


title: Princeton Biocomplexity Project, BC010 array, Salt marsh fertilization experiment

status: Public on Nov 13 2010

city: Boston

first: Jennifer

last: Bowen

state: MA

address: 100 Morrissey Blvd

department: Biology Department

country: USA

institute: University of Massachusetts Boston

organism: uncultured bacterium

manufacture_protocol: 70-mer oligonucleotides, spotted using DiRisi type arrayer


title: NimbleGen GDR Malus domestica EST UnigeneV4 array

status: Public on Nov 05 2010

city: Wenatchee

first: Yanmin

last: Zhu

state: WA

address: 1104 N. Western Ave

institute: USDA ARS

organism: Malus domestica

description:
NimbleGen design name: 080501_GDR_Malus_EST-V4_EXP
NimbleGen design ID: 7552


title: UCSF/Kornberg-Drosophila Incyte array - 14151 features

city: San Francisco

first: Brian

last: Biehs

state: CA

address: 505 Parnassus Ave

institute: UCSF

organism: Drosophila melanogaster

manufacture_protocol: 14,151 specific primer pairs (Incyte Genomics) were used for PCR amplification of 100-600 bp long fragments of annotated open reading frames. Reactions were arrayed into 384-well plates and printed on poly-L-lysine-coated glass slides using a linear servo arrayer and ArrayMaker version 2 control software. Slides were then processed as described at http://www.microarrays.org/protocols.html.


title: ARK-Genomics bovine 25k array v1

status: Public on Nov 06 2010

city: Roslin

first: Michael

middle: Bryan

last: Watson

state: Midlothian, EH25 9PS

address: Roslin Biocentre

department: ARK-Genomics

country: United Kingdom

institute: The Roslin Institute

first: R

last: Talbot

manufacture_protocol: cDNAs 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: Illumina Genome Analyzer (Carthamus tinctorius)

last: GEO

organism: Carthamus tinctorius


title: NimbleGen Caenorhabditis elegans Gene expression 4x72K Array

status: Public on Nov 08 2010

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Caenorhabditis elegans

description:
Design Name: CE WS160 60mer expr X4
Format: 4x72K
Source: Wormbase
Build: 160
Probe Length: 60mer
Genes: 23,336
Probes/ Target: 3
Replicates: 1

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


title: Candida albicans 27.6K genome array

city: Shanghai

first: Feng

last: Yang

address: Guohe Road

country: China

institute: Second Military Medical University

organism: Candida albicans

manufacture_protocol: as described in CapitalBio Corporation Manual


title: custom Agilent 4x44K rabbit microarray

city: Chicago

first: Pan

last: Du

state: IL

address: 676 N ST Clair St, 1200#

institute: Northwestern University

organism: Oryctolagus cuniculus

description:
Agilent has developed a transcriptome-wide rabbit, Oryctolagus cuniculus, microarray to enable scientists to study gene expression profiling at the global level and enhance the understanding of biology and gene functions.
Customized probes were designed for this array by a Univ. of Florida group and are not publically available.


title: UCSC-Cryptococcus neoformans H99 gene expression microarray

city: Roma

first: ada

last: florio

state: Roma

address: Largo A. Gemelli 8

department: Microbiology

institute: Catholic University of Sacred Heart

organism: Cryptococcus neoformans H99

first: Ada

middle: R

last: Florio

first: Selene

last: Ferrari

first: Elena

last: De Carolis

first: Giovanni

last: Fadda

first: Maurizio

last: Sanguinetti

first: Dominique

last: Sanglard

first: Brunella

last: Posteraro

manufacture_protocol: C. neoformans H99 microarrays were designed following the Agilent eArray Design guidelines by first creating two separate sets of 60-base nucleotide probes for each of the 6,967 open reading frame (ORF) sequences as downloaded from the Broad Institute website (http://www.broadinstitute.org/annotation/genome/cryptococcus_neoformans/MultiHome.html). The probe selection was performed using the GE Probe Design Tool; probes were filtered following their base composition and distribution, cross-hybridization potential, and melting temperature to yield final duplicate probes representing 6,823 ORFs to cover 97.9% of the whole C. neoformans H99 genome. C. neoformans custom arrays were manufactured in the 8 x 15k format by Agilent Technologies (Santa Clara, Calif.). For quality control and normalization purposes, 157 probes were selected randomly and spotted 10 times throughout each array. Standard controls (Agilent Technologies) were also included.


title: CapitalBio miRNA microarray V4.0

status: Public on Nov 02 2010

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: See the manufacturer's website.


title: Rainbow trout 8k

city: Moscow

first: Tim

last: Cavileer

state: ID

address: BioSci LSS 252

department: Biological Sciences

institute: Tim Cavileer

organism: Oncorhynchus mykiss

description: 49 - NimbleExpress sense design

manufacture_protocol: maskless photolithographic process. http://twistedoctopus.com/affymetrix/mini_site/nimbleexpress.asp


title: NimbleGen-Homo_sapiens-2.1M-hg18

status: Public on Nov 01 2010

city: Seattle

first: Vitalina

last: Komashko

address: 1100 Fairview Ave N

institute: Sage Bionetworks

description:
design ID: 5173
design description: 0701_HG18_TILE_27
native array description file:  0701_HG18_TILE_09_HX1.ndf
native array description file: 0701_HG18_TILE_09_HX1.pos

manufacture_protocol: HD2 array level design for human tiling set (hg18; NCBI Build 36). Probes selected from hg18_tiling probe database using interval of 75 bp and window size of 25 bp, allowing up to 5 close matches in the genome.


title: Illumina Genome Analyzer (Apis mellifera)

organism: Apis mellifera


title: Viro4AG-15k

first: Charles

last: Chiu

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

organism: Viruses

description: This platform includes ~15,000 oligonucleotides derived from ~1,200 viral species.  The sequences of the 70mer microarray probes on this platform are identical to the Viro4 probes as previously reported

first: E

last: Chen

first: J

last: DeRisi

first: C

middle: Y


title: Agilent Kluyveromyces latic 15K Array

first: Lauren

middle: N

last: Booth

address: 600 16th Street, N374

department: Micobiology and Immunology

organism: Kluyveromyces lactis

first: Brian

last: Tuch

first: Alexander

middle: D

last: Johnson

manufacture_protocol: see the Agilent website


title: BAMC-DCI GAS 12K ver1.0 [condensed version]

first: Jeffrey

last: Livezey

address: 3400 Rawley E Chambers Ave

department: Clinical Investigation

institute: Brooke Army Medical Center

organism:
Streptococcus pyogenes M1 GAS
Streptococcus pyogenes SSI-1
Streptococcus pyogenes MGAS315
Streptococcus pyogenes MGAS5005
Streptococcus pyogenes MGAS6180
Streptococcus pyogenes MGAS9429
Streptococcus pyogenes MGAS2096
Streptococcus pyogenes MGAS10750

description: The full array layout file provided as a supplementary file.

manufacture_protocol: Probe sets were 30-40mers in length, sense strand and were selected using a Combimatrix probe selection algorithm taking into account gene (>90% BLAST score) and serotype specificity, Tm, hairpins and GC content. Arrays were constructed using the CustomArray Synthesizer at Combimatrix. 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. Seventy factory built in negative controls and 327 quality control probes are also included in the microarray.


title: Bacillus cereus Bc14579 - 3rd design (11K array)

city: Wageningen

first: Clint

last: van Melis

address: Bomenweg 2

department: Agro- & Food Science Group

country: Netherlands

institute: Wageningen University and Research centre

organism: Bacillus cereus ATCC 14579

first: Masja

last: Nierop Groot

first: Marcel

last: Tempelaars

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: NIAID Ssca -- Strongyloides stercoralis 4K - mAdb version

status: Public on Oct 27 2010

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

organism: Strongyloides stercoralis

description:
Oligonucleotide probes were designed to hybridize 3,572 contigs generated by the Strongyloides sequencing project. Microarrays were manufactured by Agilent SurePrint(TM) to produce spotted glass slide arrays. The spot density was 22K spots per array. Of the 6 oligos designed per target, 1 was designed using the Array Designer program from Premier Biosoft, 2 were designed using using E-Array (Agilent) using "base composition" method) (replicated twice), 2 were designed using E-array "best Tm" method, the last one was a 40-mer designed using Array Designer. Probes were selected to avoid cross-hybridization to other sequences in the target (contig) dataset.
Agilent designID: 015083

first: Kathleen

last: Meyer

first: Esther

last: Asaki

first: John

middle: I

last: Powell

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


title: Ocichip Human 40 K Set (chip A)

city: Delhi

first: Vibha

last: Tandon

address: University of Delhi

department: Department of Chemistry

institute: University of Delhi

organism: Homo sapiens

manufacture_protocol: Human 40 K A Ocichip consisting of 20160 spots and Human 40 K B Consisting of 19968 spots were printed on Corning® epoxy coated glass slides using Omnigrid (Gene Machines). Chip has been printed using 4x12 SMP4 pins on 75.5x 25.5x1.3mm microarray glass slides. The origin offset values were 0 for X direction and 0 for Y direction. The dot to dot distance is 220 um; distance between subarrays is 150um and no of dots per array is 20x21=420. Oligos were printed using spotting buffer A from Ocimum Biosolution at 50% humidity and temperature at 22°C. The time taken by the robotic gridder to print Human 40 K A and B slides altogether was 50 hrs. Each probe was checked for its performance by standard QC process followed at Ocimum Biosolutions. Printed slides were stored in a light-tight box in a bench-top dessicator, with desiccant and were kept at 4°C until they were used for hybridization.


title: 44K multiplex chip, Agilent (Tailor-made microarray, condensed version)

status: Public on May 15 2010

city: Straubing

first: Jochen

last: Schmid

address: Schulgasse 16

department: Chair of Chemistry of Biogenic Resources

institute: Technische Universität München

organism: Agroathelia rolfsii

description:
Tailor-made microarray (44K multiplex chip, Agilent) was designed by imaGenes (Berlin, Germany) using an in-house developed method for empirical selection of best performing probes for each gene (Pre Selection Strategy). Briefly, up to ten probes were designed for each of the 454 unigenes (60 bp long oligomers). The 244K Agilent test array was hybridized with pooled Cy3-labeled cRNAs gained form EPSmax13 and EPSmin17 cultures and (in average) two of the best performing oligos were selected for each unigene.

Full physical array layout file linked as a supplementary file, GPL10247_44K_Design.txt.
The oligonucleotide sequences can be found in the GPL10247_44K_Design.txt.gz file.


title: Ocichip Human 40 K Set (chip B)


title: [DM_5chip_4] Affymetrix GeneChip Drosophila Tiling 7BP Array 4

status: Public on Dec 11 2008

city: Woodbury

first: Chris

last: Zaleski

state: NY

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Labs

description:
*** Note: Before submitting Affymetrix hybridization Sample data based on the Drosophila Tiling 7BP Array, please contact us at geo@ncbi.nlm.nih.gov for additional instructions.

Based on BDGP genome release 5

25-mer oligonucleotide probes interrogate the entire genome with an average 7-base-pair spacing

"1lq format" files submitted in lieu of platform data table.
1lq Format information:
ftp://ftp1.nci.nih.gov/pub/CGAP/transcriptome/sci_21_22_paper/format_1lq.html

manufacture_protocol: see manufacturer's web site


title: [DM_5chip_3] Affymetrix GeneChip Drosophila Tiling 7BP Array 3


title: [DM_5chip_5] Affymetrix GeneChip Drosophila Tiling 7BP Array 5


title: [DM_5chip_2] Affymetrix GeneChip Drosophila Tiling 7BP Array 2


title: [DM_5chip_1] Affymetrix GeneChip Drosophila Tiling 7BP Array 1


title: Agilent-011592 Custom Agilent Ciona intestinalis 22K Array

status: Public on Jun 20 2007

city: Sapporo

first: Sorin

middle: Vasile

last: Sabau

address: 5-1-1-1 Minamisawa, Minamiku

country: Japan

institute: Tokai University

organism: Ciona intestinalis

first: Nori

last: Satoh

manufacture_protocol: The microarray was manufactured by Agilent Technologies. The details can be found in their web site http://www.chem.agilent.com/Scripts/PCol.asp?lPage=494


title: hoptag07A

status: Public on Oct 24 2008

city: Baltimore

first: Daniel

last: Yuan

address: 733 N. Broadway, Suite 351

department: Molecular Biology and Genetics

institute: Johns Hopkins Univ School of Medicine

organism: Saccharomyces cerevisiae

description:
Comprehensive array of the sequence TAGs ("barcodes") designed for incorporation into the Yeast Knockout strain collection. Updated from GEO accession GPL1444 to include the YKOv2 strains, five-fold replicate features for most sequences, and 3x more negative controls. Also includes selected TAGs from TAG resequencing projects.
Two Platform supplementary files are included for data analysis.

middle: S

first: Jef

last: Boeke

manufacture_protocol: Proprietary "Maskless Array Synthesizer" based on a "Digital Micromirror Device" for light-controlled in-situ oligonucleotide synthesis. See http://www.nimblegen.com/technology/manufacture.html


title: [Tgondiia520372] Affymetrix Toxoplasma gondii Custom GeneChip (CDF: ToxoDB version 5)

status: Public on Feb 02 2010

city: Philadelphia

first: David

last: Roos

state: PA

address: 304B Carolyn Lynch Laboratories

department: Department of Biology

institute: University of Pennsylvania

organism: Toxoplasma gondii

description: Affymetrix custom CDF [Tgondiia520372]

relation: Alternative to: GPL7186 (Alternative CDF)

manufacture_protocol: see manufacturer's website


title: Illumina Genome Analyzer II (Bos taurus)

last: GEO

organism: Bos taurus