title: Illumina Genome Analyzer (Epinephelus tauvina)

status: Public on Jan 27 2011

last: GEO

country: USA

organism: Epinephelus tauvina

technology: high-throughput sequencing

distribution: virtual


title: UHN Mouse 22.4k mouse cDNA array

status: Public on Jan 21 2011

city: Pune

first: Sanjay

last: Mukherjee

state: Maharashtra

address: Ganeshkhind

department: Department of Zoology

country: India

institute: University of Pune

organism: Mus musculus

technology: spotted DNA/cDNA

distribution: non-commercial

manufacturer: University Health Network, Canada Microarray Centre


title: 454 GS (Cicer arietinum)

status: Public on Jan 31 2011

organism: Cicer arietinum


title: 021301-MLU Fusarium graminearum 8x15K v1.0

status: Public on Jan 26 2011

city: Halle/Saale

first: Rayko

last: Becher

address: Betty-Heimann-Str. 3

department: Department of Phytopathology and Plant Protection

country: Germany

institute: Martin-Luther-University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences

organism: Fusarium graminearum

technology: in situ oligonucleotide

description: The microarray was designed in collaboration with an Agilent-certified service provider (imaGenes, Berlin, Germany) that applied an in-house developed approach for selection of the best performing probes for each gene (http://www.imagenes-bio.de/services/microarray/pss/mechanism). Using the  F. g. genome annotation v3.0 annotation (FG3), for each gene model, several 60mer oligonucleotides were selected by the software eArray (https://earray.chem.agilent.com/earray/) and were then filtered by proprietary software (imaGenes). In addition to the 13,332 genes of the F. g. genome annotation v3.0, available cDNA sequences of the TRI (= trichothecene biosynthesis) gene cluster from nivalenol (NIV) producing strains of F. graminearum were chosen for oligonucleotide selection.  Several suitable oligonucleotides per gene were assembled on a pre-selection array (2x105K format) and hybridized against Cy3-labeled genomic DNA and cRNA (from a pooled RNA sample),  respectively. Based on the RNA hybridization results, for each gene the relative ratio of probes was determined that yielded significant signal intensities. In case that this ratio was 60% higher than the background, a gene was considered expressed. For these genes, final oligonucleotide selection relied on the results from RNA hybridization, whereas for genes considered non-expressed hybridization results from genomic DNA were used. The final 15K array design comprises 15,744 features (15,208 F. g. - specific oligos + 536 internal controls). 11,476 genes and 10 TRI cluster ESTs were represented by one oligonucleotide, 1,854 genes and 7 TRI cluster ESTs two probes were chosen.

distribution: custom-commercial

first: Stefan

middle: G

last: Wirsel

manufacture_protocol: The microarray is manufactured by Agilent using its proprietary SurePrint inkjet technogy that synthesizes 60mer oligonucleotides onto specially-prepared glass slides. For detailed information see manufacturer's web site http://www.agilent.com/.


title: 454 GS FLX Titanium (Equus caballus)

organism: Equus caballus


title: Illumina Genome Analyzer II (Nostoc sp. PCC 7120)

status: Public on Jan 24 2011

organism: Nostoc sp. PCC 7120 = FACHB-418


title: Agilent-023310 ISB Sulfolobus 244K 60mer tiling array

status: Public on Jun 26 2011

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

organism: Saccharolobus solfataricus P2

description:
Whole genome tiling array for Sulfolobus solfataricus P2
Agilent designID: 023310

first: Sung-Ho

first: J

middle: C

last: Bare

first: David

middle: J

last: Reiss

first: Nitin

middle: S

last: Baliga

manufacture_protocol: 60-mer probes were tiled every 25 nt. Plus extras, random control probes, and replicate probes. See manufacturer's web site at http://www.agilent.com/


title: Illumina Genome Analyzer (Schistosoma japonicum)

status: Public on Jan 25 2011

organism: Schistosoma japonicum


title: UNIS_S COELICOLOR_SCo3_8149 (unique gene version)

status: Public on Jan 28 2011

city: Norwich

first: Govind

last: Chandra

state: Norfolk

address: Norwich Research Park

department: Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

organism: Streptomyces coelicolor

technology: spotted oligonucleotide

description: Derived from GPL5136 by excluding all the control probes and taking only one of duplicate spots for each probe.

manufacturer: University of Surrey http://www2.surrey.ac.uk/fhms/microarrays/

manufacture_protocol:
1. Arrays are printed in 12X4 blocks using a Genetix QArray2 high-throughput spotting robot with tungsten split pins at room temperature, 45% Humidity and a spotting buffer containg 150mM PO4/0.005% SDS/Tween20.
2. After printing, the arrays stay on the platform in the printing chamber overnight (printing starts in early afternoon).
3. Next day the oligo arrays are cross linked at 600 mJ/cm2.


title: Illumina Genome Analyzer II (Trypanosoma cruzi)

status: Public on Jan 20 2011

organism: Trypanosoma cruzi


title: Exonhit Apoptosis SpliceArray

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

organism: Homo sapiens

distribution: commercial

manufacturer: designed by Exonhit (manufactured by Agilent)

manufacture_protocol: see designer's (http://www.exonhit.com) and manufacturer's (http://www.chem.agilent.com) web sites


title: MAS bovine BlueChip v3

city: Charlestown

first: Petr

last: Vodicka

state: Massachusetts

address: 114 16th Street

department: Department of Neurology

institute: Massachusetts General Hospital

organism: Bos taurus

manufacturer: Centre de Recherche en Biologie de la Reproduction, Département des Sciences Animales, Université Laval, Sainte-Foy, Québec, Canada G1K 7P4

manufacture_protocol: The custom bovine developmental cDNA microarray (v3) used in this study contains 2,441 ESTs derived from different subtracted libraries.Clones coming from those libraries were used for the preparation of the cDNA microarray slides (Vallée et al. Reproduction, 2009, 138,95-105). The PCR products of  selected clones were purified using Unifilter 384-well purification plates (Whatman, Clifton, NJ) according to the manufacturer's instructions.  Purified PCR products were speedvac-evaporated, resuspended in a mixture of equal parts H2O/DMSO, and spotted on ultra-GAPS glass slides (Corning, Corning, NY) using a VersArray Chip WriterPro robot (Bio-Rad). Each clone is spotted three times on the array, for a total of 9408 spots. Additionally, control spots were added to the cDNA array for hybridization quality control. SpotReport Alien cDNA Array Validation System (Stratagene, La Jolla, CA) was printed as negative controls and a cDNA fragment of the Green Fluorescent Protein (GFP) was used as an exogenous positive control.


title: Illumina Genome Analyzer II (Globobulimina pseudospinescens)

status: Public on Jan 18 2011

organism: Globobulimina pseudospinescens


title: IMP Genomics Mouse (Composite)

city: Vienna

first: Daniel

last: Schramek

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

description: Composite of three arrays (46MM, 47MM, 51MM). Design files included as supplementary data linked to GSE26763 (GSE26763_raw_gpr_design_files.tar.gz).

manufacture_protocol:
Prepare in house spotted  DNA Microarrays

PCRs and Printing

Dilution plates:

Prepare 96 well pates and label them ( eg. 1130 Dil)
Aliquot 95 µl dd water into each well (roboter '95µl verteilen')
Pipette 5µl from the copy plate into the Dilution plate (roboter 'dilution plate').
(If you do not perform immediately:
Heat for 10 min at 94°C ( PCR machine)
Spin down
Freeze away or perform PCR reaction)

PCRmix for a 96 well plate:

550µl 10x buffer (100mM Tris.HCl pH8.3, 500mM KCl)
11µl UNI-primer (1µg/µl CCCAGTCACGACGTTG)
11µl REV-primer (1µg/µl CACAGGAAACAGCTATG)
11µl 1M MgCl2 (has to be adjusted to Taq used)
44µl 25mM dNTPs
110µl Taq
1887µl dd water
2514µl 3M Betaine
5138µl total Volume (45µl per well)

PCR Reaction:

Transfer 5µl of the working dilution (see bacteria growth) to PCR-plate (MJResearch, skirted plate) containing 45µl PCRmix,

seal plate with sealing sheet (ABGene AB-0558)

Spin down

PCR program:
94°C 1min
35X 94°C 30sec
52°C 30sec
72°C 1min 30sec
72°C 5min

Load 5µl PCR product on a 1% agarose gel for quality control

Preparation for printing the PCR products:

Concentrate PCR products in a Speedvac (Determine time until no further reduction of volume is seen, in our case it is at least 4 hours when using 8 plates per batch, final volume is approximately 6-7 µl)

Add 6µl 6xSSC

Shake vigorously up to 3 hours at 4°C (we use a modified vortex,  probably mixing with pipetting robot before transfer into 384 well plates will do)

Transfer into 384 well plates

Store PCR-plates at -80°C

Spot onto Schott Nexterion A slides

Slide Blocking:
Fixation:
Put slides 30 min on 80°C heating plate and cross link with 600mJ(Schott) or 60mJ with Poly-lysine slides

Blocking:
Dissolve 1.37 g Succinic Anhydride in 90ml N-Methyl - Pyrrolidone
Add 2.5 ml N-methylimidazol (FLUKA)

Immediately pour it into a slide chamber and incubate slides for 1 hour with slight agitation

transfer slide into 0.1 % SDS for 20sec.

transfer into H2O for 20sec

Denature:
Slides are briefly washed in water (or DCE) and incubated for 4 min in a boiling water bath

After a brief rinse in 95% EtOH spin slides 4 min 1200rpm for drying

For 30 slides in a big chamber with 300 ml blocking solution:
(4,11 g SA in 270 ml NMP and 7,5 ml NMI)


title: Illumina Genome Analyzer (Schizosaccharomyces japonicus)

organism: Schizosaccharomyces japonicus


title: Illumina Genome Analyzer II (Medicago sativa)

organism: Medicago sativa


title: JCVI PFGRC DeADMAn 12K v2 array designed primarily based on strain CDC1551

city: Rockville

first: PFGRC

last: JCVI

state: MD

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Mycobacterium tuberculosis CDC1551

description: This set includes 699 oligonucleotides, has 12288 spots distributed in 48 blocks. The DeADMAn DNA microarray is a companion reagent to be used in combination with pools of M. tuberculosis genetically defined transposon knockout mutants. Please see this page for the list of knockout mutants: http://www.beiresources.org/Catalog/ItemDetails/tabid/522/Default.aspx?BEINum=NR-18958&Template=otherProducts This microarray is used to provide a simple approach for identification of genes essential for the survival of a stress condition in in vivo model systems of M. tuberculosis infection. A pool of genetically defined transposon mutants (input pool) are used to infect an animal that is subsequently subjected to a stress condition. Mutants from the input pool and those recovered from the stressed animals (output pool) are identified by amplification of the unique transposon junction sequences of each mutant. The input and output pools are labeled with different fluorescent dyes and hybridized to the DeADMAn microarray. The competitive hybridization of the two pools to the DeADMAn microarray allows for the easy detection of mutants in the input pool and missing from the output pool. For additional information on the DeADMan microarray see: Lamichhane G, Tyagi S, Bishai WR. Designer arrays for defined mutant analysis to detect genes essential for survival of Mycobacterium tuberculosis in mouse lungs. Infect Immun. 2005 Apr;73(4):2533-40

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


title: Kyushu Univ. Clostridium perfringens strain 13 DNA 7K array v1 [chromosome and extra-chromosomal plasmid]

status: Public on Jan 17 2011

city: Clayton

first: Julian

middle: I

last: Rood

state: Victoria

address: Wellington Road

department: Microbiology

country: Australia

institute: Monash University

organism: Clostridium perfringens str. 13

description: Identical to GPL7332 with the exception that genes encoded on the extra-chromosomal plasmid pCP13 are included on the array

manufacturer: Molecular Gene Technics, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.

first: Thomas

last: Hiscox

first: Jackie

middle: K

last: Cheung

first: Anjana

last: Chakravorty

first: Jocelyn

middle: M

last: Choo

first: Kaori

last: Ohtani

first: Tohru

last: Shimizu

manufacture_protocol:
2723 genes and 144 intergenic regions of strain 13 were amplified by PCR with gene-specific primers and PCR products were confirmed by gel electrophoresis
In total, 2867 probes were spotted onto poly-L-Lysine coated glass slides in twice (SD10011; Matsunami Glass Ind., Osaka, Japan) using SPBIO (Hitachi Software Engineering, Tokyo, Japan).


title: Capitalbio plant microRNA V2.0

status: Public on Jan 22 2011

city: Anyang

first: Zujun

last: Yin

state: Henan

address: 38 Huanghe Dadao, Anyang 455000, Henan, China

department: Cotton Research Institute

country: China

institute: Chinese Academy of Agricultural Sciences

organism: Viridiplantae

manufacture_protocol: as described in CapitalBio Corporation Manual


title: Agilent-023309 ISB Pyrococcus 244K 60mer tiling array

first: Sung Ho

last: Yoon

organism: Pyrococcus furiosus DSM 3638

description:
Whole genome tiling array for Pyrococcus furiosus DSM 3638
Agilent designID: 023309

first: Sung-Ho

manufacture_protocol: 60-mer probes were tiled every 16 nt. Plus extras, random control probes, and replicate probes. See manufacturer's web site at http://www.agilent.com/


title: Agilent-023308 ISB Methanococcus 244K 60mer tiling array

organism: Methanococcus maripaludis S2

description:
Whole genome tiling array for Methanococcus maripaludis S2
Agilent designID: 023308

first: J

last: Bare

first: David

manufacture_protocol: 60-mer probes were tiled every 14 nt. Plus extras, 200 random control probes, and 20x10 replicate probes. See manufacturer's web site at http://www.agilent.com/


title: UBC/Moerman C. elegans WS170 380K

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

organism: Caenorhabditis elegans

description: Wormbase version WS170

first: Mia

middle: R

last: Lowden

first: Donald

last: Moerman

first: Shawn

last: Ahmed

manufacture_protocol: See NimbleGen's website


title: CIAT Brachiaria 8k cDNA array

city: Thuwal

first: Eduardo

middle: Andres

last: Gorron Gomez

address: KAUST, Thuwal, Saudi Arabia

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

organism: Brachiaria

description: ONLY CLONES OF INTEREST HAVE BEEN SEQUENCED AND IDENTIFIED.

manufacturer: International Center for Tropical Agriculture - CIAT, Plamira Valle del Cauca, Colombia

manufacture_protocol: Clones were derived from non-susbtractive and substractive expression libraries, employing apomictc and sexual cDNA as tester and driver samples, and vice versa. The clones were amplified by PCR. 15 μl PCR product were mixed with 15 μl spotting buffer (betaine 3M, SSC 3X) using the robot Te-Shake (Tecan Group Ltda., Männedorf, Switzerland). The mix were arrayed over poly-L-lysine covered glass slides (Erie Scientific Company) using the spotting robot SPBIO (MiraiBio Inc, Alameda, CA) at a density of 8064 spots per slide. Each PCR product were spotted once in the slide. DNA was fixed onto the slide as described (Schena, 1999). Each slide was heated at 95ºC for ten seconds and was irradiated inmediately with UV at 410mJoules. The slides were incubated at 70ºC for two hours and were stored in Darkness at room temperature until hybridization.


title: Agilent-020088 Mouse 4X44K (Probe Name version)

city: San Francisco

first: Andrew

last: Jheon

state: CA

address: 513 Parnassus Ave HSE1501

institute: UCSF

organism: Mus musculus

description: Agilent mouse 4X44K (14850)

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


title: 454 GS (Medicago sativa)

last: GEO


title: Alternative Mouse Whole Genome Bioarray (CodeLink)

city: Pittsburgh

first: Joyeeta

last: Dutta-Moscato

state: PA

address: 450 Technology Drive, Suite 300

department: Surgery

institute: University of Pittsburgh

manufacture_protocol: see manufacturer's website


title: Agilent-012799 Mouse Developmental Microarray 44K (Gene name version)

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH


title: Illumina Genome Analyzer (Ascaris suum)

status: Public on Jan 29 2011

organism: Ascaris suum


title: Illumina Genome Analyzer II (Bacteria)

organism: Bacteria


title: Illumina Genome Analyzer IIx (synthetic construct)

organism: synthetic construct


title: Operon E. coli Custom 3.8K 55156017 array

status: Public on Jan 15 2011

city: Wuerzburg

first: Jaroslaw

last: Zdziarski

address: Josef-Schneider Str. 2/Bau D15

department: Institut fuer Molekulare Infektionsbiologie

institute: Universitaet Wuerzburg

organism: Escherichia coli

description: Complete genomes of six Escherichia coli strains (6 genomes and four plasmids). The number of open reading frames (ORFs) or genes represented is as follows: 4269 ORFs of non-pathogenic E. coli K-12strain MG1655, 5306 ORFs of enterohemorrhagic E. coli O157:H7 strain EDL933, 5251 ORFs of enterohemorrhagic E. coli O157:H7 strain Sakai, 5366 ORFs of uropathogenic E. coli strain CFT073, 322 ORFs of uropathogenic E. coli strain 536, 448 ORFs of uropathogenic E. coli strain UTI89, 3 genes of EHEC plasmid OSAK1, 10 genes of EHEC plasmid pO157_Sakai, 97 genes of EHEC plasmid pO157_EDL933 and genes of UPEC plasmid pUTI89. In addition, the array comprises also a number of positive and negative controls.

manufacture_protocol: The array area is 18mm wide, 54mm long, and is located 8mm from the top of the slide (barcode at bottom). Probes are spotted as single spots in 32 blogs (4 columns, 8 rows), each blog with 18 columns x 19 rows.


title: Affymetrix P putida KT2440 array

city: Hannover

first: Sarah

last: Frank

address: Carl-Neuberg-Str. 1

department: Clinic for Paediatric Pneumology and Neonatology

institute: Medical School Hannover

organism: Pseudomonas putida KT2440

manufacture_protocol: see manufacturer's web site


title: MEEBO

status: Public on Jan 14 2011

city: Jerusalem

first: naomi

last: habib

address: Givat-Ram

department: Computer Scince

country: Israel

institute: Hebrew University

manufacture_protocol: unknown


title: Mammalian miRNA Array V1.0 (CapitalBio, Beijing, China)

city: Beijing

first: Hongyan

last: Guo

address: Chengfu

department: School of Medcine

institute: Tsinghua University

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: As described in CapitalBio Corporation Manual


title: JCVI PFGRC Corona virus 3K v1 array designed primarily based on strain CV777

status: Public on Jan 13 2011

first: PFGRC

last: JCVI

organism: Betacoronavirus

description: This set includes 263 oligonucleotides, has 3456 spots distributed in 96 blocks.

manufacture_protocol: QCV, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 2725523, pen id 0, pen cycles -1, operator microarray, humidity control On, humidity set point65


title: NimbleGen Acetobacter aceti NBRC14818 4X72K array Univ. of Tokyo v1.0

status: Public on Jan 16 2011

city: Bunkyo-ku

first: Hiroyuki

last: Arai

state: Tokyo

address: Yayoi 1-1-1

department: Department of Biotechnology

country: Japan

institute: The University of Tokyo

organism: Acetobacter aceti NBRC 14818

description: NimbleGen Prokaryotic Expression array (4x72K). A gene expression design for 3,643 sequences is based on the draft genome sequence of Acetobacter aceti NBRC14818. The length of probes is 60-mer and the number of probes is 9 pairs per gene. Each probe is replicated 2 times. Probe sequences are available in the '2009-06-23_RDKK198_Aace_60mer_expr.ndf' supplementary file.

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


title: JCVI PFGRC Corona virus 3K v1 array designed primarily based on strain Tor2

organism: Gammacoronavirus


title: JCVI PFGRC Corona virus 3K v1 array designed primarily based on strain MHV-A59

organism: Alphacoronavirus


title: JCVI PFGRC Corona virus 3K v1 array designed primarily based on strain ATCC_VR-759


title: Capitalbio mammal microRNA V2.0

city: Stockholm

first: ZiMing

last: Du

address: Nobels vagen

country: Sweden

institute: Karolinska Institutet

manufacture_protocol: as described in Capital mammal microRNA V2.0 oligo array Manual


title: Phalanx Mouse & Rat miRNA OneArray (miRBase13 ID version)

city: Hsinchu Science Park

first: Phalanx

last: Biotech

state: Hsinchu

address: 6 Technology Road 5, 6th Floor

country: Taiwan

institute: Phalanx Biotech

description:
The Phalanx Mouse & Rat miRNA OneArray includes mouse and rat probes. This Platform represents only the mouse probes, annotated with miRBase 13.

Supplementary files:
GPL11415_Phalanx_MouseRat_miRNA1_arrayLayout_all.txt: The complete array layout file.
GPL11415_Phalanx_MouseRat_miRNA1_arrayLayout_mmu.txt: The array layout file for the mouse probes.

manufacture_protocol: See http://www.onearray.com/ for updated protocols.


title: JCVI PFGRC Corona virus 3K v1 array designed primarily based on strain 229E

organism: Human coronavirus 229E


title: JCVI PFGRC Corona virus 3K v1 array designed primarily based on strain BCoV-ENT


title: JCVI PFGRC Corona virus 3K v1 array designed primarily based on strain Beaudette


title: JCVI PFGRC Corona virus 3K v1 array designed primarily based on strain Purdue


title: JCVI PFGRC Aspergillus nidulans 25K v1 array designed primarily based on strain FGSC A4

organism: Aspergillus nidulans

description: This set includes 9453 oligonucleotides, has 25392 spots distributed in 48 blocks.

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


title: JCVI PFGRC Haemophilus influenzae 22K v3 array designed primarily based on strain biotype_aegyptius_F3031

organism: Haemophilus influenzae

description: This set includes 4574 oligonucleotides, has 22176 spots distributed in 48 blocks.

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


title: JCVI PFGRC Haemophilus influenzae 22K v3 array designed primarily based on strain pF3028


title: JCVI PFGRC Haemophilus influenzae 22K v3 array designed primarily based on strain HK1212


title: JCVI PFGRC Rickettsia prowazekii 9K v2 array designed primarily based on strain Wilmington

organism: Rickettsia prowazekii

description: This set includes 1391 oligonucleotides, has 9216 spots distributed in 96 blocks.

manufacture_protocol: 2QRP, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 1879974, pen id 0, pen cycles -1, operator Jon, humidity control On, humidity set point65


title: NimbleGen human 2006-02-27_HG17Tiling_Set24

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

organism: Homo sapiens

description:
Human genome build UCSC hg17 (NCBI Build 35).

Native array description files:
2006-02-27_HG17Tiling_Set24.ndf
2006-02-27_HG17Tiling_Set24.pos

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


title: JCVI PFGRC Rickettsia prowazekii 9K v2 array designed primarily based on strain Madrid_E


title: [NZ131a520662F] University of Oklahoma Health Sciences Center SPY49_NZ131 1.7K array

city: Oklahoma City

first: Jens

last: Kreth

address: 940 Stanton L. Young Blvd

department: Microbiology & Immunology

organism: Streptococcus pyogenes NZ131

first: Michael

middle: W

last: McShan

first: Joseph

last: Ferretti

manufacture_protocol: Standard Affymetrix procedures


title: CodeLink Human Whole Genome Bioarray

city: Madrid

first: Lorena

last: Sánchez-Martín

address: C/ Dr Esquerdo 46

department: Inmunología

institute: Hospital General Gregorio Marañon

last: SANCHEZ-MARTIN

first: Paloma

last: SANCHEZ-MATEOS

manufacture_protocol: CodeLink Activated Slides are designed to covalently immobilize amine-modified DNA for microarrays.It is comprised of approximately 55 000 30-mer  probes designed to conserved exons across the transcripts of targeted genes.These 55 000 probes represent well annotated, full length, and partial human gene sequences from major public databases. CodeLink Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release). Some sequences for design were derived from Incyte LifeSeq™ Gold and Foundation databases.http://www.gelifesciences.com/APTRIX/upp01077.nsf/content/codelink_site


title: JCVI PFGRC Haemophilus influenzae 22K v3 array designed primarily based on strain pF3031

city: Rockville

address: 9704 Medical Center Drive

institute: J. Craig Venter Institute


title: JCVI PFGRC Plasmodium falciparum 12K v1 array designed primarily based on strain 3D7

organism: Plasmodium falciparum

description: This set includes 5156 oligonucleotides, has 12288 spots distributed in 48 blocks.

manufacture_protocol: QPF, with arrayer LUCIDEA, mode Normal, replicates 2, repeats 1, slide_dips 75, machine cycles 1019843, pen id 10113, pen cycles -1, operator Kathy, humidity control On, humidity set point65


title: JCVI PFGRC Haemophilus influenzae 22K v3 array designed primarily based on strain R2866


title: JCVI PFGRC Haemophilus influenzae 22K v3 array designed primarily based on strain R2846


title: JCVI PFGRC Haemophilus influenzae 22K v3 array designed primarily based on strain 86-028NP


title: JCVI PFGRC Haemophilus influenzae 22K v3 array designed primarily based on strain RD_KW20


title: JCVI PFGRC Actinobacillus actinomycetemcomitans 12K v2 array designed primarily based on strain HK1651

organism: Aggregatibacter actinomycetemcomitans

description: This set includes 2303 oligonucleotides, has 12288 spots distributed in 96 blocks.

manufacture_protocol: 2QAA, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 7392081, pen id 10179, pen cycles -1, operator Susie, humidity control On, humidity set point65


title: Exiqon miRCURYTM LNA Arrays (V10.0)

status: Public on Jan 11 2011

city: NY

first: Hana

last: Totary-Jain

address: 150, St. NICHOLAS AVE

institute: Columbia University

organism: Mus musculus

manufacture_protocol: See manufacturers website, Catalog number 208100-A,208101-A,208102-A


title: Nimblegen Danio rerio Zv7 37K array

status: Public on Jan 07 2011

city: Karp 7

first: Yariv

last: Houvras

state: MA

address: 1 Blackfan Circle

institute: Childrens Hospital Boston

organism: Danio rerio

description:
071105_Zv7

Zebrafish genome Build Zv7

manufacture_protocol: See Nimblegen website.


title: SMD Print_745 Mycobacterium tuberculosis

city: Guadalajara

first: Mario

middle: A

last: Flores Valdez

state: Jalisco

address: Av. Normalistas No. 800

department: Col. Colinas de la Normal

country: Mexico

institute: Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco, A.C.

organism: Mycobacterium tuberculosis

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: Agilent/CCFFT Lactococcus lactis IL1403 8x15k v1.0 (gene name version)

city: Tallinn

first: Ranno

last: Nahku

address: Akadeemia tee 15b

country: Estonia

institute: TFTAK

organism: Lactococcus lactis subsp. lactis Il1403

description:
Steps/settings in Earray (http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/gp50660.aspx):
a. Design Wizards - Create a Microarray Design from Target Transcripts
b. Selected Method - Tm matching methodology
c. Selected Parameters:
Probe Length - 60bp
Probes per Target - 7
Probe Orientation - Sense
Design Options - Best Distribution Methodology
NO - "Design with 3' Bias" and "Allow Probes to be Trimmed"
Preferred Probe Tm - 85C
Target File Details - Upload Gene Sequence File
Note: "l.lactis.nuc" file was downloaded from the KEGG ftp site (ftp://ftp.genome.jp/pub/kegg/genes/organisms/lla/ )
Transcriptome Details - Use Target File as Transcriptome
d. 8x15K platform was used
e."Fill Microarrays" option was checked


title: SAGE:17:NlaIII:Leishmania chagasi

status: Public on Jan 10 2011

last: GEO

country: USA

organism: Leishmania chagasi

technology: SAGE NlaIII

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


title: [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array (MoEx-1_0-st-v1.na25.mm9.core+miRNA.SH.11023.mps)

first: GEO

last: admin

manufacture_protocol: see manufacturer's website


title: Agilent Yeast Microarray

city: Princeton

first: Mark

last: Hickman

state: NJ

address: Washington Road

department: Lewis-Sigler Institute of Integrative Genomics

institute: Princeton University

organism: Saccharomyces cerevisiae

description: Agilent Design ID 017566.

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


title: Prochlorococcus microarray 11K

city: Cambridge

first: Anne

last: Thompson

address: 15 Vassar Street

institute: MIT

organism:
Prochlorococcus marinus subsp. pastoris str. CCMP1986
Prochlorococcus marinus str. MIT 9313
Prochlorococcus phage P-SSM4
Tiamatvirus PSSP7


title: AB SOLiD System 3.0 (Neisseria gonorrhoeae F62)

status: Public on Jan 05 2011

organism: Neisseria gonorrhoeae F62


title: USZ/Human Toll-Like Receptor Signaling Pathway PCR Array PAHS-18A

status: Public on Jan 06 2011

city: Zurich

first: Roberto

middle: F

last: Speck

state: Zurich

address: Raemistrasse 100

department: Division of Infectious Diseases and Hospital Epidemiology

country: Switzerland

institute: University Hospital of Zurich

technology: RT-PCR

description: see http://www.sabiosciences.com/rt_pcr_product/HTML/PAHS-018A.html

first: Erika

last: Schlaepfer

manufacture_protocol: The PCR array is a set of optimized real-time PCR primer assays on 96-well plates for pathway or disease focused genes as well as appropriate RNA quality controls. The PCR array performs gene expression analysis with real-time PCR sensitivity and the multi-gene profiling capability of a microarray. Simply mix the cDNA template with the appropriate ready-to-use PCR master mix, aliquot equal volumes to each well of the same plate, and then run the real-time PCR cycling program (http://www.sabiosciences.com/rt_pcr_product/HTML/PAHS-018A.html)


title: Agilent 1 million-probe custom array from UHN/CDMC

city: Mississauga

first: Zak

last: Razak

state: Ontario

address: 3359 Mississauga Rd

institute: Canadian Drosophila Microarray Centre

organism: Drosophila melanogaster

description:
024068_D_F_20100104.xml
contains probes from agilent's GPL4149 and GPL4150, in duplicate

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


title: MiRPlants-12.0 plus 100 maize smRNAs

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

organism:
Physcomitrium patens
Pinus taeda
Gossypium hirsutum
Populus trichocarpa
Arabidopsis thaliana
Brassica napus
Glycine max
Medicago truncatula
Solanum lycopersicum
Oryza sativa
Saccharum officinarum
Sorghum bicolor
Triticum aestivum
Zea mays
Vitis vinifera
Selaginella moellendorffii

description:
LC Sciences provides a genome-wide microRNA (miRNA) expression profiling service using µParaflo® technology and proprietary probe design, which enable highly sensitive and specific direct detection of miRNAs. They have standard arrays for mature miRNA of all species available in the latest version of the Sanger miRBase database.
A proprietary µParaflo® microfluidic chip is used.   The microfluidic technology produces a uniform distribution of the sample solutions on the array and enhances binding reactions and stringency wash processes.   In situ oligonucleotide synthesis using PGA (photogenerated acid) coupled with conventional DMT chemistry means high probe quality, tight process control, and complete content flexibility.

manufacture_protocol:
The miRNA microarray was custom synthesized by LC Sciences (Houston, Texas, USA) using their protocols (Gao et al., 2004).
Gao, X., Gulari, E. and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers, 73, 579–596.


title: Agilent-021827 Human miRNA Microarray [miRNA_107_Sep09_2_105]

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description: Table corresponds to miRNA_107_Sep09_2_105 feature extraction file.


title: NCI_GREWAL_Spombe_C10_v1

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

organism: Schizosaccharomyces pombe

first: Cui

last: Bowen

manufacture_protocol: Agilent custom array preparation protocol


title: 454 GS 20 (Saccharomyces cerevisiae)


title: NimbleGen Mycobacterium smegmatis 6.7k array [100415_Msme_GP_exp]

city: Portland

first: Melissa

middle: Suzan

last: Standley

state: OR

address: 3181 SW Sam Jackson Park Rd.

institute: Oregon Health & Science University

organism: Mycolicibacterium smegmatis MC2 155

description:
NimbleGen 4X72K Custom array design name 100415_Msme_GP_exp_X4. This custom array was designed for the 6716 annotated transcripts of M. smegmatis mc2155 (NCBI accession CP000480). Each chip measures the expression level of 6,588 genes from Myobacterium smegmatis. There are five 60-mer probes per transcript and two replicates of each probe for a total of 65,880 experimental probes. The design includes random GC and other control probes.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.
design_name: 100415_Msme_GP_exp
design_id: 11849

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


title: Illumina HiSeq 2000 (Hevea brasiliensis)

organism: Hevea brasiliensis


title: Eurogentec Schizosaccharomyces pombe IGR+ORF array (J120E)

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

institute: Karolinska Inst

manufacture_protocol: Primary PCR: The PCR reactions are performed using tagged genome specific primers in the presence of genomic DNA (provided by your laboratory). We normally achieve a success rate of 93 % of PCR reactions. For the failed PCR reactions we perform three different protocols of PCR conditions, which include different MgCl2 concentrations and different Taq polymerase. We should normally get an additional 2 % working and reach a success rate of 95 % in total. We check 5 % of the total oligos by Mass Spectrometry and will re-synthesize maximum 2 % of the oligos based on a newly designed primer. We will perform the PCR reactions with the new designed oligonucleotides with the standard PCR protocol. Following this process we reach usually 97 % success rate. Secondary PCR: amplifications will be performed using a single pair of primers annealing to tag sequences introduced on primary PCR primers. These PCR amplifications will also be controlled by agarose gel electrophoresis and repeated if required reaching a minimum of 95 % success rate. The final PCR products will contain an amino group at their 5' end to promote the attachment of the predicted gene coding DNA strand to the treated glass slides.


title: Affymetrix Human Genome U133 Plus 2.0 Array [MBNI v9 Entrez Gene ID CDF]

status: Public on Jan 12 2011

city: Grand Rapids

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

organism: Homo sapiens

description: This array is identical to GPL570 but the data were analyzed with a custom CDF environment (version 9 Entrez Gene ID CDF) created by The Molecular & Behavioral Neuroscience Institute (MBNI), University of Michigan.

relation: Alternative to: GPL570 (Alternative CDF [official])

manufacture_protocol: see the Affymetrix website (www.affymetrix.com).


title: Agilent_custom_Pseudomonas sp. M18_ 8*15K

status: Public on Jan 08 2011

city: Shanghai

first: xk

last: teng

state: Shanghai

address: 151 LiBing R.d

department: technical support

institute: ShanghaiBio

organism: Pseudomonas sp. M18


title: CapitalBio 29k Arabidopsis Genome Array

status: Public on Jan 04 2011

city: Beijing

first: Zhaoliang

last: Zhang

state: Beijing

address: datun road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of sciences

organism: Arabidopsis thaliana

manufacture_protocol: as described in CapitalBio Corporation Manual


title: miRCURY LNA microRNA Array, 5th generation - hsa, mmu & rno

city: Vedbaek

first: Exiqon

last: A/S

address: Bygstubben 9

country: Denmark

institute: Exiqon A/S

organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

description:
Array covering Sanger miRBase 14.0 and Exiqon miRPlus mature miRNAs.

The platform information provided is from the time of the design.

Names, accession numbers and sequences are listed for mature miRNAs in miRBase 14.0. Some probes may target multiple miRNAs, in which case multiple miRNA names, accession numbers and sequences are listed separated by '/'

manufacture_protocol: See manufacturers website


title: Illumina Genome Analyzer (Vigna unguiculata)

status: Public on Jan 03 2011

last: GEO

organism: Vigna unguiculata


title: GenoToul/Biopuces Yeast 4K (operon-2005-12)

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

manufacture_protocol:
Oligos sold by Operon
Each well is spotted in duplicate.


title: Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray Version 13.0.0, HGU133Plus2_Hs_REFSEQ]

city: Lebanon

first: Mathieu

last: Lupien

state: NH

address: One Medical Center Drive

department: Genetics

institute: Norris Cotton Cancer Center/Dartmouth Medical School

description:
This is identical to GPL570 but a custom CDF environment was used to extract data [Brainarray Version 13.0.0, HGU133Plus2_Hs_REFSEQ]. CDF is linked below as a supplementary file.
~24k data rows because internally developed software converts the probe signal to refseq gene signal. Hence for genes with multiple probes the signal is normalized to give a single value per gene.

manufacture_protocol: see manufacturer's web site


title: VUMC MACF human 5K BAC v47

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

first: Tineke

middle: E

last: Buffart

manufacture_protocol: The platform contains approximately 5000 clones, consisting of the Sanger BAC clone set with an average resolution along the whole genome of 1.0 Mb (http://www.ensembl.org/Homo sapiens/cytoview), the OncoBac set (http://informa.bio.caltech.edu/Bac_onc.html), containing approximately 600 clones corresponding to 200 cancer-related genes, and selected clones of interest obtained from the Children's Hospital Oakland Research Institute (CHORI) (http://bacpac.chori.org/home.htm) to fill any gaps larger than 1 Mb on chromosome 6 and to have full-coverage contigs of regions on chromosomes 8, 11, 13, and 20 (previously described in Buffart et al J Pathol 2007).


title: Illumina Porcine SNP60 BeadChip (WG-410)

first: GEO

organism: Sus scrofa

technology: oligonucleotide beads

manufacture_protocol: See manufacturer's website


title: VUMC MACF human 5K BAC v55


title: NIA 15K Mouse cDNA clone set

status: Public on Jan 01 2011

city: Sydney

first: John

last: Ellis

state: NSW

address: Broadway

department: Medical & Molecular Biosciences

institute: University of Technology Sydney

organism: Mus musculus

description: Approx. 11,500 unique clones form the NIA 15K Mouse cDNA clone set

manufacture_protocol: cDNA from the clone set was spotted onto CodeLink amine binding slides (SurModics, USA) under controlled conditions (20-25ºC, 40-50% relative humidity). All microarrays were stored in the dark until use


title: TIGR Potato 10k cDNA array version 4 (condensed version)

city: East Lansing

first: Marcela

last: Carvallo

address: 310 Plant Biology bldg

department: Plant Research Laboratory

institute: Michigan State University

organism: Solanum tuberosum

manufacture_protocol: Spotted PCR amplified cDNA array on glass.  This version 4 set includes PCR products amplified from 15264 potato EST clones.  Each PCR product is duplicated on the slide.  The number of total spots including empty and controls is 32448.


title: SNU Rice Whole Genome 60K Microarray

city: Seoul

first: Ju-Seok

last: Seo

department: Dept. of Applied Biology & Chemistry

country: South Korea

institute: Seoul National University

organism: Oryza sativa

description: Oryza sativa Genome Oligo Set Version 1.0 was designed by Beijing Genomics Institute (BGI) and contain 60,727 70mer oligos representing both indica and japonica genomes. All oligos were designed from cDNAs, expreseed sequence tag (EST) sequences, predicted genes of BGI rice genome build and other public resources. Mapping to TIGR rice genome pseudommolecues release 2 is based on the BLAST results, if an oligo has greater than 97% identity to a gene sequence from TIGR pseudomolecules, the oligo represents that gene. If the oligo matches to multiple genes, only one gene ID is randomly chosen. Preference is given to a 100% match.

manufacturer: David Galbraith lab. University of Arizona

first: Yeon-Ki

last: Kim

first: Baek

middle: H

last: Nahm

manufacture_protocol: Information of the Microarray can be found at www.ggbio.com/rice60kchip.html (GreenGene Biotech). The 60 K Microarray was designed to represent all the genes in rice. In total, 60,727 oligomers were designed from gene-specific regions of both japonica and indica subsp. These include 58,417 from known and predicted genes and 66 randomized DNA. Among these, 2,310 genes were also designed as antisense oligomers. Oligomer sequences were extracted by Qiagen-Operon (Cologne, Germany) based on rice genome information from Beijing Genomics Institute (Yu et al., 2002). Oligomers were synthesized and purified by Qiagen-Operon and spotted on SuperAmine slide using facilities of the Dr. David Galbraith lab at the University of Arizona (http://ag.arizona.edu/microarray/deconvolution.html). A set of Rice 60 K Microarray is composed of 2 slides and has a total of 64,896 spot addresses. Each slide is formatted with 48 (12 x 4) blocks with addresses composed of 676 (26 x 26) spots. Blank spots (4,099) were also included for easy alignment of scanning format. Each oligomer, 70 nucleotides long and average melting temperature of 78°C, was printed in each spot address with a diameter of 100 µm.


city: St. Louis

first: Seth

middle: Daniel

last: Crosby

state: MO

address: 660 S. Euclid

institute: Washington Univeristy School of Medicine

description:
Agilent-018077 Mouse miRNA Microarray Sanger 10 Ver 1 Rev2 11/08/2007

Arrays of this design have barcodes that begin with 16018077 or 2518077.

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: UHNMAC Homo sapiens SS-H19Kv9

city: Sherbrooke

first: Jean-François

last: Beaulieu

state: Québec

address: 3001, 12ème avenue nord

department: Anatomie & biologie cellulaire

institute: Université de Sherbrooke

description: This set includes 19,200 cDNA clones from the IMAGE consortium. Single-spotted array containing 19,008 characterized and unknown human ESTs. The clone set has been sequence-verified at the Microarray Centre and the sequences can be downloaded for validation.

manufacturer: University Health Network (UHN) Microarray Center, Toronto, Canada

manufacture_protocol: As described on the UHN Microarray Centre website (www.microarrays.ca).


title: Agilent-017067 Sclerotium rolfsii 44K multiplex chip, Agilent (Tailor-made microarrays, condensed version)

city: Straubing

first: Jochen

last: Schmid

address: Schulgasse 16

department: Chair of Chemistry of Biogenic Resources

country: Germany

institute: Technische Universität München

organism: Agroathelia rolfsii

description: Full physical array layout file linked as a supplementary file, GPL11191_44K_Design.txt.gz.


title: CDMC Nimblegen Drosophila 17K v1

city: Mississauga

first: Zak

last: Razak

address: 3359 Mississauga Rd

institute: Canadian Drosophila Microarray Centre

description: combination of probes from NimbleGen Drosophila melanogaster 385K Array and CDMC oligo 14kv2 arrays


title: INSERM/LC Sciences Mammalia miRNA 3K Array [miRMammalia_14]

city: Lyon

first: Emiliano

middle: P

last: Ricci

address: 46 allée d'Italie

department: Human Virology

country: France

institute: INSERM

organism:
Ornithorhynchus anatinus
Lemur catta
Saguinus imperator
Ateles sp.
Lagothrix
Macaca mulatta
Macaca nemestrina
Symphalangus syndactylus
Gorilla gorilla
Pan paniscus
Pan troglodytes
Pongo
Homo sapiens
Canis lupus familiaris
Equus caballus
Sus scrofa
Bos taurus
Ovis aries
Cricetulus griseus
Mus musculus
Rattus norvegicus
Monodelphis domestica
Rhinopithecus bieti

last: RICCI

first: Théophile

last: OHLMANN

manufacture_protocol:
Microarray assay was performed by LC Science Company.
The microfluidic PicoArray reactor is made from silicon using standard microelectronic
fabrication procedures.  The reactor contains three topographical features: pico-
reaction chambers, fluid microchannels, and inlet/outlet through holes.  The chip
contains 128 x 31 (total 3698) individual reaction chambers, each with an internal
volume of 270 pl.  The fluid microchannels are of a tapered shape that was derived
from a fluid mechanical model to produce a uniform flow rate across all reaction
chambers.  This technology enables a high density of uniform spots.
RNA extraction and analysis protocol:
5 µg total RNA sample isolated from untreated rabbit reticulocyte lysate (Promega), was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for subsequent fluorescent dye staining. Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies)9. On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 µL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After hybridization, detection was carried out by fluorescence labeling using tag-specific Cy3 and Cy5 dyes.  Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics). Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter10 (Locally-weighted Regression) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.


title: TFRC IL1403-c2 2.5K v1.0

status: Public on Dec 15 2010

city: Fermoy

first: Vincenzo

last: Fallico

address: Moorepark

country: Ireland

institute: Teagasc Food Research Centre

organism:
Ceduovirus c2
Lactococcus lactis subsp. lactis Il1403

description: Custom-made, contains the whole genome sequences of L. lactis IL1403 (2,310 genes) and bacteriophage c2 (39 genes). 50-mer oligonucleotide probes for each gene spotted in duplicate. Control elements on each array include negative-control probes from unrelated Escherichia coli and Arabidopsis thaliana genes. Oligonucleotide probe design and microarray production were carried out by Ocimum Biosolutions Ltd. (Hyderabad, India).

first: Gerald

last: Fitzgerald

first: Paul

last: Ross

first: Olivia

last: McAuliffe

manufacture_protocol: Ocimum Biosolutions protocols


title: [Bovine] Affymetrix Bovine Genome Array [CDF: Brainarray Version 11.0.1, Bovine_Bt_REFSEQ]

city: Jouy-en-Josas

first: Nuria

last: Mach

state: Ile de France

address: Rue de Vilvert

department: Animal Genetics and Integrative Biology (GABI)

institute: INRA

organism: Bos taurus

description: This identical to GPL2112 but a custom CDF environment was used to extract data (CDF: Bovine_Bt_REFSEQ). The CDF can be found at the Web link below.

relation: Alternative to: GPL2112 (Alternative CDF [official])


title: Streptococcus mutans strain UA159 9.8K whole-genome array

city: Kansas City

first: Alexander

middle: V

last: Dmitriev

state: KS

address: 3901 Rainbow Boulevard

institute: Kansas University Medical Center

organism: Streptococcus mutans UA159

first: Indranil

last: Biswas

manufacture_protocol: Streptococcus mutans UA159 strain NimbleGen array has been synthesized using maskless array technology.


title: NimbleGen Klebsiella pneumoniae 385k version 1

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578

description:
Custom commercial, design ID 6418
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.

manufacture_protocol: Probes (60mers) were designed to the coding strand of all annotated CDS of reference strain MGH78758 prior to submission to NimbleGen for fabrication.


title: Agilent_schistosoma_8x15k_custom

status: Public on Sep 30 2010

city: Shanghai

first: xk

last: teng

address: 151 LiBing R.d

country: China

institute: ShanghaiBio

organism: Schistosoma japonicum

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


title: Lactobacillus rhamnosus GG whole genome microarray 4X44K

city: Helsinki

first: Kati

last: Laakso

address: Meijeritie 4

department: R&D

country: Finland

institute: Valio Ltd

organism: Lacticaseibacillus rhamnosus GG

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


title: Viro5AGL-60k

status: Public on Nov 01 2010

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

organism: Viruses

description: This platform includes more than 60,000 oligonucleotides for the detection and discovery of both known and novel viruses.  The sequences of ~36,000 of the viral


title: Agilent-022523 G. hirsutum (Cotton)   Oligo Microarray

status: Public on Sep 16 2010

city: shang hai

first: Wang

last: Ling

address: 780 Cailun Road

institute: OEbiotech

organism: Gossypium hirsutum

description: G. hirsutum (Cotton) Oligo Microarray

first: KIMI

last: Wang


title: Streptococcus pneumoniae D39 Multiplatform 1909k array

status: Public on Jan 15 2011

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

organism: Streptococcus pneumoniae D39

description: mixed spotted oligonucleotide/cDNA

last: de Jong

first: Siger

last: Holsappel

manufacture_protocol: Standard spotting protocol on GenpakArray21


title: JCVI PFGRC Mycobacterium tuberculosis 12K v2 array designed primarily based on strain H37Rv

status: Public on Jun 17 2010

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Mycobacterium tuberculosis

description:
This set includes 392 oligonucleotides, has 12288 spots distributed in 48 blocks. The DeADMAn DNA microarray is a companion reagent to be used in combination with pools of M. tuberculosis genetically defined transposon knockout mutants.
Please see this page for the list of knockout mutants: http://www.beiresources.org/Catalog/ItemDetails/tabid/522/Default.aspx?BEINum=NR-18958&Template=otherProducts
This microarray is used to provide a simple approach for identification of genes essential for the survival of a stress condition in in vivo model systems of M. tuberculosis infection. A pool of genetically defined transposon mutants (input pool) are used to infect an animal that is subsequently subjected to a stress condition. Mutants from the input pool and those recovered from the stressed animals (output pool) are identified by amplification of the unique transposon junction sequences of each mutant. The input and output pools are labeled with different fluorescent dyes and hybridized to the DeADMAn microarray. The competitive hybridization of the two pools to the DeADMAn microarray allows for the easy detection of mutants in the input pool and missing from the output pool.
For additional information on the DeADMan microarray see: Lamichhane G, Tyagi S, Bishai WR. Designer arrays for defined mutant analysis to detect genes essential for survival of Mycobacterium tuberculosis in mouse lungs. Infect Immun. 2005 Apr;73(4):2533-40

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


title: Agilent/CCFFT Lactococcus lactis IL1403 8x15k v1.0

status: Public on Apr 11 2010

city: Tallinn

first: Ranno

last: Nahku

address: Akadeemia tee 15b

institute: TFTAK

organism: Lactococcus lactis subsp. lactis Il1403

description:
Steps/settings in Earray (http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/gp50660.aspx):
a. Design Wizards - Create a Microarray Design from Target Transcripts
b. Selected Method - Tm matching methodology
c. Selected Parameters:
Probe Length - 60bp
Probes per Target - 7
Probe Orientation - Sense
Design Options - Best Distribution Methodology
NO - "Design with 3' Bias" and "Allow Probes to be Trimmed"
Preferred Probe Tm - 85C
Target File Details - Upload Gene Sequence File
Note: "l.lactis.nuc" file was downloaded from the KEGG ftp site (ftp://ftp.genome.jp/pub/kegg/genes/organisms/lla/ )
Transcriptome Details - Use Target File as Transcriptome
d. 8x15K platform was used
e."Fill Microarrays" option was checked


title: Clostridium acetobutylicum ATCC 824 transcriptional 44k v4

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

organism: Clostridium acetobutylicum ATCC 824

manufacture_protocol: see manufacturer's website for details


title: Affymetrix/NimbleGen Candida glabrata array [CaGl04a530005N]

city: Memphis

first: Katherine

middle: S

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

organism: Nakaseomyces glabratus

manufacture_protocol: The nucleotide sequences corresponding to 5272 C. glabrata ORFs were downloaded from the Génolevures Consortium (http://cbi.labri.fr/Genolevures/about.php, Build 2). Following the Affymetrix Design Guide, two separate probe sets for each ORF were designed, each consisting of 13 perfect match and 13 mismatch overlapping 25 base oligonucleotides targeted to the 3? 600 bp region. For ORFs < 600 bp the sequence was divided in two equal segments for subsequent design procedures. For quality control and normalization purposes, we designed two to three additional probe sets spanning the C. glabrata 18 s rRNA, TDH1 and ACT1 genes in addition to standard Affymetrix controls (BioB, C, D, cre, DAP, PHE, LYS, THR). The probe selection was performed by the Chip Design group at Affymetrix, 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. glabrata genome as well as a number of constitutively expressed genes and rRNA from other common organisms. Duplicate probesets are made to distinct regions of the ORF, thereby allowing two independent measurements of the mRNA level for that particular gene. C. glabrata custom Affymetrix NimbleExpress Arrays were manufactured by NimbleGen Systems per our specification.


title: LC_miRHuman_10.1_AUR_TaoWu

status: Public on Jun 16 2009

city: Beijing

first: Tao

middle: Paul

last: Wu

address: Datun Road 15#

department: Systems Biology

institute: Institute of Biophysics, Chinese Academy of Sciences

organism: Homo sapiens

manufacture_protocol:
uParaflo Microfluidics Chip
X. Gao, E. Gulari, X. Zhou, Biopolymers 73, 579 (Apr 5, 2004).


title: CombiMatrix 90K TomatArray 1.0

status: Public on Aug 16 2010

city: Portici (NA)

first: Antonio

last: Di Matteo

address: Via Universita' 100 - Parco Gussone - Edificio 75

department: DiSSPAPA

country: Italy

institute: University of Naples Federico II

organism: Solanum lycopersicum

description: 20,200 specific oligos (35-40mer) were designed on Tomato Gene Index Version 11 (LeGI v.11, June21, 2006) tentative consensus (TC) sequences by using the program design OligoArray 2.1 (Rouillard et al. 2003). As negative controls, nine bacterial oligonucleotides sequences provided by CombiMatrix were utilized. The 90K TomatArrayTM  1.0 was designed with four replicates of each probe randomly distributed across the array to allow measurement of the variability within the array. All the procedures provided were performed as indicated by CombiMatrix protocols available at the CombiMatrix website (www.combimatrix.com).

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

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: DTU-VET-Actinobacillus pleuropneumoniae-135K array.v1

status: Public on Oct 01 2010

city: Copenhagen

first: Kirstine

last: Klitgaard

address: Bulowsvej 27

institute: National Veterinary Institute, Technical University of Denmark

organism: Actinobacillus pleuropneumoniae

description:
native array description file: 090423_DTU_Actino_xRNA (for array no. 355074A)
native array description file: 091013_DTU_Actino_xRNA (for arrays no. 382804A, 382816A, and 431045A)

first: Carsten

last: Friis

first: Oystein

last: Angen

first: Mette

last: Boye

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


title: JCVI PFGRC Staphylococcus aureus 22K v7 array designed primarily based on strain USA300

status: Public on Jul 08 2009

organism: Staphylococcus aureus

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

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


title: TMHRI/Affy Streptococcus pyogenes array

status: Public on Aug 25 2009

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

organism: Streptococcus pyogenes

manufacture_protocol: Standard Affymetrix procedures.


title: SAMF Desulfovibrio vulgaris Hildenborough 13K oligo array version 1

status: Public on Feb 13 2008

city: Calgary

first: Sean

middle: Michael

last: Caffrey

state: Alberta

address: 2500 University Dr NW

department: Biological Scineces

country: Canada

institute: University of Calgary

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

manufacture_protocol: The designed 70-mer oligonucleotides were custom synthesized by Invitrogen (Carlsbad, CA) on an average scale of 25 pmol/oligonucleotide. They were dissolved in 3xSSC to a concentration of 40 pmol/ul and spotted in 0.7 nl quantities, using a ChipWriter Pro (BioRad, Hercules, CA) onto Corning UltraGAPS Amino-Silane 25X75 mm Coated Slides (Fisher Scientific).


title: Turkey skeletal muscle long oligonucleotide (TSKMLO) microarray

status: Public on Feb 01 2010

city: East Lansing

first: Kelly

last: Sporer

address: 3365 Anthony Hall

department: Food Science and Human Nutrition

institute: Michigan State University

organism: Meleagris gallopavo

manufacturer: Oligonucleotide design and synthesis: Invitrogen (Carlsbad, CA); Array printing: Michigan State University Research Technology Support Facility (East Lansing, MI)

first: Wen

last: Chiang

first: Robert

middle: J

last: Tempelman

first: Catherine

last: Ernst

first: Kent

middle: M

last: Reed

first: Sandra

middle: G

last: Velleman

first: Gale

last: Strasburg

manufacture_protocol:
Three skeletal muscle cDNA libraries from the developmental stages 18-day embryo, 1-day post-hatch chick, and 16-week market age bird were constructed and sequenced as in Reed et al. (2008).  Additional sequences for genes important in regulation of muscle growth, development, and extracellular matrix function were added.  Because alternative splicing has been identified as a potential mechanism in the differential regulation of the Ca2+ channel ryanodine receptor (RYR), possibly leading to downstream defects in postmortem meat quality (Chiang et al. 2004; Chiang et al. 2007), oligos were also designed to represent five different alternatively spliced products of RYR.  In total, 5809 70-mer oligonucleotides were commercially designed (Invitrogen, Carlsbad, CA).  A unique set of control probes were designed for thirty randomly chosen genes with the stipulation that the gene be greater than 1500 bases in length.  These controls consisted of: one scrambled sequence control, three “distance” controls that included oligos designed within 500, 501-1000, and 1001-1500 bases from the 3’ of the sequence, and six “mismatch” controls including 3, 5, 10, 15, 20, or 25 mismatched bases, totaling 300 control probes.
The 384 well print plates were prepared by diluting the probes in print buffer (3X SSC, 0.005% SDS) to a final concentration of 60uM. The arrays were printed on Corning UltraGAPS slides using a Genomic Solutions (GeneMachines) Omnigrid 100 spotting robot using Telechem Chipmaker 3 pins. The arrays consist of 48 subarrays (in a 4 by 12 pattern) each having a 16 by 16 grid of probe spots. Spot spacing is 250um on center and subarray (ie. pin) spacing is 4500um.  Probes were spotted in duplicate, and “blank” spots (spotting solution only) were included in each patch of the microarray.


title: [HuEx10stv2_Hs_ENSG] Affymetrix Human Exon 1.0 ST Array [Brainarray Version 11.0.1]

status: Public on Mar 04 2009

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: This platform is identical to GPL5175 but a custom CDF environment was used to extract data [Brainarray Version 11.0.1, HuEx10stv2_Hs_ENSG].

manufacture_protocol: Affymetrix standard protocol


title: RPCI Mouse 6.5K

status: Public on Jan 04 2007

city: Buffalo

first: Devin

last: McQuaid

state: NY

address: Elm and Carlton

institute: Roswell Park Cancer Institute

organism: Mus musculus

manufacture_protocol:
Isolation of BAC plasmid DNA:  BAC clone plasmid DNAs, used as templates for PCR representations are prepared using a Qiagen BioRobot 3000.  Each clone is retrieved from archival copies of the RPCI-23 BAC Resource, maintained at RPCI.  The clones are streaked to single colony, grown overnight (16-18 hours) as 1.0ml pre-cultures in 96 deep-well plates at 37 C in a New Brunswick environmental shaker, and then re-inoculated as 2ml prep-cultures in 48 deep-well plates.   After incubation, the cultures are RNase treated and prepped in the BioRobot 3000 using R.E.A.L. Prep 96 BioRobot kits (Qiagen).  The BAC DNAs are resuspended in TE and serve as templates for restriction digestion and PCR amplification.  We have found that Qiagen prepared DNA is of high quality and outperforms phenol:chloroform extraction methods for the highly sensitive restriction digestion and ligation steps.
Ligation of adapters: The adapters are ligated to the digested DNA by first annealing Mse-21 and Mse-12 primers. 1 ul of each digest (1 ng/ul), is added to 0.5 ul of 100 uM Mse-12 (TAACTAGCATGC), 0.5 ul of 100 uM Mse-21 (5’ aminolinker AGTGGGATTCCGCATGCTAGT) in a final volume of 7.5 ul using a thermalcycler (MJ Research). The mixture is incubated at 65?C for 1 min followed by ramping the temperature down to 15 C with a ramp-speed of 1.3 C per minute.  When the temperature reaches 15 C, ligation proceeds with 1 ul of 10 mM ATP, 0.5 ul One-Phor-All-Buffer-Plus (10x)  and 1 ul T4-DNA ligase (5 U/ul, Invitrogen) added to each tube and incubated at 15 C overnight.
PCR amplification:  Two rounds of amplification are required to produce enough product for array generation as described in Cowell, J. K. and N. J. Nowak. 2003. High-resolution analysis of genetic events in cancer cells using bacterial artificial chromosome arrays and comparative genome hybridization. Adv Cancer Res 90:91-125. A single BAC PCR-representation produces enough printing solution for over 4,000 arrays.	Preparation of DNA spotting solutions: PCR products (100 ul) are purified for printing by a series of ethanol precipitation steps, followed by resuspension of the pellets in 20 ul of 25% DMSO in H2O (final DNA concentration ~0.8 ug/ul) using a Qfill2 (Genetix).    The DNA solutions are rearrayed into Genetix 384-well V-bottom plates using a Hydra 96-PP liquid handling system, and stored at 4 C until printing.  We determined that DNA prepared using LM-PCR performed superiorly over other methods, including degenerate oligonucleotide primer PCR, inter Alu PCR and amplification of BAC subclones mixtures.  25% DMSO has several properties that make it an ideal solution for resuspending the amplicons.  First, it acts as a denaturant, rendering the printing solution single-stranded for optimal slide binding and subsequent hybridization.  Secondly, DMSO does not evaporate, so the printing solution volume is not affected by exposure to the environment during multiple print runs.
Array printing:  Slides are printed using a MicroGrid ll TAS arrayer (Genomic Solutions) using 10K Microspot pins at 48% relative humidity, 22?C.  We have a climate controlled, HEPA filtered room to minimize environmental changes that can affect printing.  In addition, the arrayer is supplied with HEPA filtered air to further maintain a dust-free environment. We print each BAC clone in triplicate to create an array of on amino-silanated glass slides (Schott Nexterion, Type A+).  The printed slides dry overnight, and are UV-crosslinked (350 mJ) in a Stratalinker 2400 (Stratagene).  The slides are visually inspected and stored in a dessicated environment and are hybridized without additional treatment.  Attempts at post-print processing or inclusion of pre-hybridization steps resulted in background issues that made the images difficult to analyze.  We found no indication of DNA loss from the spots at any stage of the procedure when we performed hybridization in formamide buffers at 37°C (via DAPI staining).


title: DrexelMed-Plasmodium yoelii-7K-Version 2.0

status: Public on Jan 07 2008

city: Seattle

first: Stefan

middle: H. I.

last: Kappe

state: WA

address: 307 Westlake Ave N, Suite 500

institute: Seattle Biomedical Research Institute

organism: Plasmodium yoelii

manufacturer: Center for Molecular Parasitology, Drexel University College of Medicine

first: Lawrence

middle: W

last: Bergman

first: Akhil

middle: B

last: Vaidya

first: Jamesr

last: Burns

first: Vischal

last: Nayak

first: Thomas

last: Daly

manufacture_protocol:
1.	Oligonucleotides with a concentration of 80 uM in dH20, from Illumina, Inc., were originally arrayed from 96-well plates into MJ Research 384-well flat-bottom plates.  Each well received an equal volume of 6X SSC so that each 65-mer oligo was a final concentration of 40 uM in 3X SSC.  Plates were then dried by SpeedVac, sealed and stored at 4C.
2.	One day prior to printing, oligos were rehydrated to 40uM with sterile de-ionized water, sealed with ABGene adhesive films and incubated overnight in a humid environment with continuous agitation on a flat-bed shaker.
3.	The next day, plates were centrifuged at 2K rpm for 1 min. and then stored at 4C.
4.	Each plate, as needed, was unsealed and placed onto the plate holder of a Brown Lab (Stanford) style 32-pin array printer and the oligos spotted.
5.	Following printing, each plate was re-sealed and stored at 4°C until re-dried and re-sealed as above.
6.	For subsequent printings, oligos were resuspended in 0.5ul less sterile de-ionized water to compensate for the 0.5ul removed during the previous printing.


title: [Tgondiia520372] Affymetrix Toxoplasma gondii Custom GeneChip (CDF: ToxoDB version 4)

status: Public on Sep 04 2008

city: St Louis

first: Michael

middle: Sean

last: Behnke

address: 660 S. Euclid Ave

department: Molecular Microbiology

institute: Washington University School of Medicine

organism: Toxoplasma gondii

description: Please see http://ancillary.toxodb.org/docs/Array-Tutorial.html for a complete description of the array design as well as for library files.

first: Amit

last: Bahl

first: David

last: Roos

relation: Alternative to: GPL10000 (Alternative CDF)

manufacture_protocol: Affymetrix photolithographic array - 169 format.


title: Bacillus subtilis 168 4K Oligo Array

status: Public on Oct 23 2007

first: Jan-Willem

last: Veening

institute: University of Groningen

organism: Bacillus subtilis

description:
12pins spotting with Telechem 946MP3  pins
spotsize 90-100 um

manufacture_protocol: Oligo spotted on ArrayIt Superamine slides in duplicates