title: Monsanto-rice-454-smallRNAs-high throughput sequencing

status: Public on Nov 23 2008

city: Saint Louis

first: Sara

middle: Elizabeth

last: Heisel

state: MO

address: 800 North Lindbergh

department: Biotechnology

country: USA

institute: Monsanto

organism: Oryza sativa

technology: in situ oligonucleotide

description: intrument model: 454 GS FLX

distribution: virtual


title: Okayama University rat Nimblegen custom tiling array

status: Public on Nov 27 2008

city: Okayama

first: Mary Miyaji-Yamaguchi

state: Okayama

address: 2-5-1 Shikata-cho

department: Department of Neurogenomics

country: Japan

institute: Okayama University

organism: Rattus norvegicus

description: The rat genomic sequence was based on the Version 3.1 (RN3) that was released by the Atlas group at  Baylor Human Genome Sequencing Center (HGSC) as part of the Rat Genome Sequencing Consortium. The array probes, 50-75mer oligos, were tiled with 100 bp-intervals along 7 selected genomic regions (about 79 Mb in total), each containing at least one gene that is controled by toposomerase IIbeta in neuronal differentiation.

distribution: custom-commercial

first: Kuniaki

last: Sano

first: Mary

last: Miyaji-Yamaguchi

first: Kimiko

middle: M

last: Tsutsui

first: Ken

manufacture_protocol: per Nimblegen protocol


title: NimbleGen Systems Human HG17 Chromosome19 386K Array1 version1

city: Milan

first: Myriam

last: Alcalay

address: Via Adamello 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

organism: Homo sapiens

manufacture_protocol: NGS_HG17_Chr19.Array contains ~360,000 isothermal probes (from 50 to 60 bp long) contiguously tiled along chromosome 19.  Non-repetitive sequences of the whole chr.19 available from UCSC Hg.17 were used for the probe design. Sequence tiled at a 49bp spacing.  Probe design: Isothermal, target Tm=76C


title: NimbleGen Systems Human HG17 Promoter 386K Array1 version 1

status: Public on Nov 28 2008

manufacture_protocol: Contents of the 2 array set: 27,434 regions of expected promoter activity representing 75,227 annotated transcripts (Array 1: Chromosomes 1-10, ENr112 ENCODE region; Array 2: Chromosomes 11-22,X and Y, unmapped genes, and ENr112, ENm010), Probe spacing: 110 bp minimum spacing, Minimum region size: 5,000 bp, Probe design: Isothermal, target Tm=76C


title: Neurospora crassa LGVII 44K tiling array

status: Public on Nov 30 2008

city: Eugene

first: Zachary

middle: A

last: Lewis

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

organism: Neurospora crassa

description: each slide contains 4 x 44K subarrays

first: Nicholas

last: Stiffler

first: Eric

middle: U

last: Selker

manufacture_protocol: Uploaded oligo sequences for custom array synthesis


title: Identification of targets of the protein disulfide reductase thioredoxin

status: Public on Nov 20 2008

city: Kgs Lyngby

first: Per

last: Hagglund

address: Soltofts plads

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

organism: Hordeum vulgare

technology: MS


title: GenAu mouse chr17 2588

status: Public on Nov 24 2008

city: Vienna

first: Florian

last: Pauler

state: Vienna

address: Dr Bohrgasse 9/4

country: Austria

institute: CeMM

organism: Mus musculus

description: single copy regions of mouse chr.17 (3021656bp-92867493bp) with custom repeat masking

first: Mathew

last: Sloane

first: Denise

middle: P

last: Barlow

manufacture_protocol: as described in www.nimblegen.com


title: IPMC - microRNA v7

status: Public on Nov 25 2008

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

technology: spotted oligonucleotide

distribution: non-commercial

first: Bernard

last: Mari

first: Pascal

last: Barbry

manufacture_protocol: Spotted microarray


title: Human oligo array from MWG version cancerochips

status: Public on Nov 21 2008

city: Nantes

first: Raluca

last: TEUSAN

address: 1, rue gaston veil

institute: INSERM U915

first: Catherine

last: Chevalier

first: Isabelle

last: Guisle

manufacture_protocol: spotted on the  Amersham Lucidea spotter. Epoxyslide.


title: NimbleGen Homo sapiens HG17 promoter 1 of 2

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description: Build: HG17, NCBI 35

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: RSMAS Crawford Fundulus 384 cDNA [condensed array version]

city: Miami

first: Cinda

last: Scott

state: FL

address: 4600 Rickenbacker Cswy

department: Marine Biology and Fisheries

institute: University of Miami

organism: Fundulus heteroclitus

technology: spotted DNA/cDNA

manufacturer: Crawford Laboratory- University of Miami

first: Jeff

last: VanWye

first: Danielle

last: McDonald

first: Douglas

middle: L

last: Crawford

manufacture_protocol: The 384 F. heteroclitus cDNA microarrays were printed using 55 control genes and 329 cDNAs which encode essential proteins for cellular metabolism.  Microarrays were created by printing cDNAs amplified with amine-linked primers onto 3-D Link Activated Slides.  All printed cDNAs were re-sequenced from the same source used for printing.


title: Siberian hamster hypothalamic 4K array

status: Public on Nov 29 2008

city: Aberdeen

first: Gill

last: Campbell

address: Greenburn Road

department: Rowett Institute of  Nutrition and Health

country: United Kingdom

institute: University of Aberdeen

organism: Phodopus sungorus

description: The array has been printed in 48 blocks (4 columns and 12 rows), each block contains 255 features; 17 columns with 5 rows in triplicate at 0.25mm spacing.  Mixed Arabidopsis thaliana cDNAs have been printed as landmarks in the outer corners of the 4 corner blocks. Individual and mixed A. thaliana cDNAs have also been printed within the array.

manufacture_protocol: This array has been made from a subtracted cDNA library of Siberian hamster hypothalamic tissue. Transcripts expressed in liver and kidney were subtracted from hypothalamic mRNA.   A total of 5000 individual colonies were picked from the library using a robotic colony picker and these were amplified by PCR using Rsa1 and Rsa2 primers. Approximately 4000 clones containing single inserts of 250 to 1000bp sizes were identified and used for the array. Clones have been saved as glycerol stocks.


title: Placental 5K array

manufacture_protocol: This array has been made from a placental gene expression library in lampda zap. The initial library was made from a 30 week placenta (male). The library was grown with one round of amplification and colonies collected using a robotic colony picker. cDNA was generated by PCR using T3 and T7 primers. Clones have been saved as glycerol stocks.


title: Human Genome U133 A 2.0 Custom CDF Version 9

city: Atlanta

first: Troy

middle: D

last: Querec

state: GA

address: 954 Gatewood Rd

department: Emory Vaccine Rearch Center

institute: Emory University

relation: Alternative to: GPL96 (Alternative CDF [official])


title: NimbleGen Systems Human HG17 Promoter 367K Array2 version 1

first: Myriam

last: Alcalay


title: CSIRO Cane Toad 5.5k cDNA array

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

organism: Rhinella marina

description: 5472 spot cane toad array

first: Damien

middle: C

last: Halliday

first: Gavin

last: Kennedy

manufacture_protocol: A toadlet cDNA library was constructed with the plasmid pCMVSport6 and gene fragments PCR amplified using M13/pUC forward and reverse primers. PCR products from 5000 randomly selected clones were precipitated (sodium acetate/ethanol) and resuspended with ddH2O:DMSO (Dimethyl Sulfoxide, Sigma) in preparation for spotting. Microarray slides were printed using a VersArray ChipWriter Pro microarray robotic system (CSIRO Plant Industry).


title: Human Genome U133 Plus 2.0 Custom CDF Version 9

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


title: GenAu mouse chr17 1734

first: Florian

last: Pauler

first: Mathew

last: Sloane

first: Denise

last: Barlow


title: NimbleGen Homo sapiens HG17 promoter 2 of 2

description: Build: HG17, NCBI 35


title: NimbleGen 1.5 kb mouse promoter ChIP-chip (version 2005-03-31_MM5_min_promoter)

status: Public on Nov 26 2008

city: Boston

first: Philipp

last: Oberdoerffer

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description:
NimbleGen Design information: Mouse minimal set of promoters, from build mm5 for 26,275 target regions
Design name: 2005-03-31_MM5_min_promoter
OID3293
NimbleGen .ndf and .ngd description files linked below as supplementary files.
Individual probe sequences and their positional information within the target chromosome can be found in the PROBE_SEQUENCE and PROBE_ID columns, respectively, of the.ndf file.


title: GenAu mouse chr17 2356


title: INSERM/UEVE Homo sapiens 5.5K CGH-Integragen5508

status: Public on Nov 19 2008

city: Evry cedex

first: Anselme

middle: Louis

last: Perrier

address: 5 rue desbrueres

department: I-Stem, AFM

institute: INSERM/UEVE UMR 861,

manufacture_protocol:
IntegraChip genome-wide BAC arrays of 4,898 BAC clones (600-kb median spacing) were hybridized by the manufacturer, IntegraGen (Evry, France). The genomic positions of all clones on the array have been determined by BAC end sequencing.
A genomic DNA labeling kit (Enzo, Farmingdale, NY) was used to label the sample DNA with Cy5 or with Cy3. The labeled products were purified with QiaQuick polymerase chain reaction (PCR) purification kits (Qiagen, Valencia, CA). After addition of tRNA (48 mg) plus a quantity of human Cot DNA (Invitrogen, Carlsbad, CA) equal to 50 times the mass of the labeled DNAs, the resulting products were concentrated by vacuum centrifugation, resuspended in 43 mL of hybridization solution (Ambion, Austin, TX) and deposited on the array under a coverslip. Hybridization in a sealed chamber (Corning Life Sciences, Acton, MA) was for 66 hours at 55_C, and then washed. Slides were scanned (Agilent Technologies, Santa Clara, CA), data were extracted with GenePix 6 (Axon InstrumentseMolecular Devices, Sunnyvale, CA), and copy number analysis was performed with GenoCensus (IntegraGen), which includes block Loess normalization.


title: Arabidopsis thaliana 8.4k 70-mer spotted oligoprobes

city: Bethesda

first: Misook

last: Ha

state: MD

address: NIH

institute: National Heart Lung Blood Institute

organism: Arabidopsis thaliana

first: Jianlin

last: Wang

first: Lu

last: Tian

first: Hyeon-Se

last: Lee

first: Ning

middle: E

last: Wei

first: Hongmei

last: Jiang

first: Brian

last: Watson

manufacture_protocol: This oligonucleotide array is produced from the Operon Version 1.0 Array-Ready Oligo set (AROS). The 70-mer oligo was designed from the 3'-end of 26,090 annotated genes. Every 70-mer oligo is spotted once on each slide.


title: UNESP Xylella fastidiosa array version 1

city: Berlin

first: Tiago

last: Lopes

address: Robert Rossle Strasse, 10

country: Germany

institute: Max-Delbruck Center for Molecular Medicine

organism: Xylella fastidiosa

manufacturer: Sao Paulo State University (UNESP) Jaboticabal Campus. Laboratory of Biochemistry of microorganisms and plants (LBMP).

manufacture_protocol: The amplified products were suspended in 50% v/v DMSO in a final concentration of 100 to 300 ng/microliter and arranged in duplicate at a distance of 250 micrometer in glass slides treated with aminosilane (Corning). The printing of the microarrays was done by a robot model GMS 417 Arrayer (Affymetrix Inc.). After printing, the DNAs were re-hydrated (42 degrees C for 10 s), dried (70 degrees C for 1 min) and fixed in a UV camera cross-link (1300 x 100 microJ cm2). The slides were kept at 70 degrees C for 2 h and then stored at room temperature under vacuum. Genetically distant negative controls were also included in this array, consisting of human genes (pHUM1 and pHUM7) and plant genes (707050B11 - Rubisco), as well as synthetic controls from various species (human, mouse, Arabidopsis spp., Archaeabacteria and E. coli) obtained by the Lucidea Universal ScoreCard kit (Amersham Biosciences).


title: INSERM/UEVE Homo sapiens 5.9K CGH-Integragen5878


title: Bacillus subtilis WGS2 platform

city: Cambridge

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

address: 31 Ames Street, 68-530

department: Biology

institute: MIT

organism: Bacillus subtilis

first: Lyle

last: Simmons

first: Alexi

last: Goranov

first: Graham

last: Walker

manufacture_protocol:
See description in:
Britton RA, Eichenberger P, Gonzalez-Pastor JE, Fawcett P, Monson R, Losick R, Grossman AD.
Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis.
J Bacteriol. 2002 Sep;184(17):4881-90.


title: Arabidopsis thaliana 11.2k 70-mer spotted oligoprobes

description: 11199 probes were detected to be differentially expressed between leaves of Arabidopsis thaliana and Arabidopsis arenosa

first: Andreas

last: Madlung

first: Thoman

last: Osborn

first: R

middle: W

last: Doerge

first: Luca

last: Comai

first: Z

middle: J

last: Chen


title: INSERM/UEVE Homo sapiens 5.1K CGH-Integragen 3

first: Anselme

last: Perrier


title: RSMAS Crawford Fundulus 384 cDNA [full array version]

first: Cinda

last: Scott

manufacture_protocol: Microarrays were printed using 329 cDNAs which encode essential proteins for cellular metabolism.   All ESTs with enzyme commission numbers or associated with central metabolic pathways from a F. heteroclitus EST collection of over 42,000 expressed sequences were included on the array.   These cDNAs were amplified with amine-linked primers and printed on 3-D Link Activated slides (Surmodics Inc., Eden Prairie, MN) at the University of Miami core microarray facility.


title: INSERM/UEVE Homo sapiens 5.7K CGH-Integragen

description: IntegraChip genome-wide BAC arrays of 4,898 BAC clones (600-kb median spacing)


title: Arabidopsis thaliana 9.9k 70-mer spotted oligoprobes

first: Misook

last: Ha

first: Jianlin

last: Wang

first: Lu

last: Tian

first: Thomas


title: NimbleGen HG18 Tiling Set Array 5 of 38

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 5 Array 5 of 38 chr2 71,983,425 150,976,181

first: Tibor

last: Rauch

first: Gerd

last: Pfeifer

manufacture_protocol: see NimbleGen website


title: NimbleGen HG18 Tiling Set Array 4 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 4 Array 4 of 38 chr2 166,819 71,983,140


title: OGT_Ecoli_22000_v1.0

city: Richardson

first: Stephen

last: Spiro

state: TX

address: 800 W Campbell Road

department: Molecular and Cell Biology

institute: University of Texas at Dallas

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

first: Diane

last: Bodenmiller

first: Mike

last: Humphrys

manufacture_protocol: OGT microarrays consist of 22,000 sixty nucleotide long oligonucleotide probes designed to hybridise throughout the E.coli genomic DNA. The microarrays are synthesised on a glass slide using an in-situ ink jet printer ensuring high quality arrays. These are designed to be used in two colour experiments i.e. one sample is labelled with one fluorescent dye (Cy3) and another sample is labelled with another fluorescent dye (Cy5). These arrays can also be used to compare two E.coli genomic DNAs for the presence of large deletions.


title: NimbleGen HG18 Tiling Set Array 3 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 3 Array 3 of 38 chr1 175,050,895 247,197,901


title: NimbleGen HG18 Tiling Set Array 8 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 8 Array 8 of 38 chr3 53,043,153 130,523,638


title: NimbleGen HG18 Tiling Set Array 2 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 2 Array 2 of 38 chr1 77,833,918 175,048,429


title: NimbleGen HG18 Tiling Set Array 1 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 1 Array 1 of 38 chr1 1,644 77,833,868


title: NimbleGen HG18 Tiling Set Array 7 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 7 Array 7 of 38 chr2 221,986,912 242,751,051


title: CRC-OHS Porphyromonas gingivalis W83 1977v2

city: Parkville

first: Helen

last: Mitchell

address: 720 Swanston St

department: School of Dental Science

institute: The University of Melbourne

organism: Porphyromonas gingivalis

manufacturer: Oligonucleotide probes synthesised by Geneworks (Illumina Oligator), Microarrays printed by The Australian Genome Research Facility

first: Stuart

middle: G

last: Dashper

first: Nada

last: Slakeski

first: Steven

last: Cleal

first: Eric

last: Reynolds

manufacture_protocol: Microarrays consist of 1,977 60-mer oligonucleotides based on the >1,990 predicted open reading frames of P. gingivalis W83 (RefSeq Acc No NC_002950.2).  Additional probes based on predicted protein coding regions found in the Los Alamos National Laboratory Oralgen project (www.oralgen.lanl.gov) and probes for normalisation and validation are also included.  The full complement of probes are printed three times onto each microarray slide.


title: NimbleGen HG18 Tiling Set Array 21 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 21 Array 21 of 38 chr8 139,834,778 146,273,006
chr8 random 2,645 943,766


title: NimbleGen HG18 Tiling Set Array 20 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 20 Array 20 of 38 chr8 64,735,105 139,834,728


title: NimbleGen HG18 Tiling Set Array 6 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 6 Array 6 of 38 chr2 150,976,231 221,986,862


title: NimbleGen HG18 Tiling Set Array 16 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 16 Array 16 of 38 chr6 93,424,310 165,905,673


title: NimbleGen HG18 Tiling Set Array 17 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 17 Array 17 of 38 chr6 165,905,853 170,896,928
chr6 random 723 1,875,488


title: NimbleGen HG18 Tiling Set Array 13 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 13 Array 13 of 38 chr5 43,102,682 120,977,621


title: NimbleGen HG18 Tiling Set Array 15 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 15 Array 15 of 38 chr6 14,400,108 93,424,260


title: NimbleGen HG18 Tiling Set Array 9 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 9 Array 9 of 38 chr3 130,523,688 199,446,729
chr3 random 1,180 749,171


title: NimbleGen HG18 Tiling Set Array 12 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 12 Array 12 of 38 chr4 162,580,158 191,260,272
chr4 random 1 842,645
chr5 64,882 43,102,632


title: NimbleGen HG18 Tiling Set Array 18 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 18 Array 18 of 38 chr7 71,893,499 146,115,149


title: NimbleGen HG18 Tiling Set Array 11 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 11 Array 11 of 38 chr4 86,895,741 162,579,935


title: NimbleGen HG18 Tiling Set Array 10 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 10 Array 10 of 38 chr4 5,907,836 86,895,691


title: NimbleGen HG18 Tiling Set Array 37 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 37 Array 37 of 38 chr22 39,529,878 49,590,841
chr22 random 1 257,295
chrX 447 85,044,437


title: NimbleGen HG18 Tiling Set Array 35 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 35 Array 35 of 38 chr19 19,529,928 63,805,962
chr19 random 8,246 301,805


title: NimbleGen HG18 Tiling Set Array 38 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 38 Array 38 of 38 chrM 1 16,477
chrX 85,044,487 154,911,115
chrX random 1 1,718,128
chrY 447 57,770,315


title: NimbleGen HG18 Tiling Set Array 36 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 36 Array 36 of 38 chr20 50,138,864 62,432,160
chr21 9,882,592 46,941,530
chr21 random 1,024 1,679,609
chr22 14,430,066 39,529,828


title: NimbleGen HG18 Tiling Set Array 19 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 19 Array 19 of 38 chr7 146,115,199 158,821,243
chr7 random 66 547,244


title: NimbleGen HG18 Tiling Set Array 34 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 34 Array 34 of 38 chr18 22,940,045 76,116,085
chr18 random 1 4,250


title: NimbleGen HG18 Tiling Set Array 33 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 33 Array 33 of 38 chr17 28,580,086 78,654,701
chr17 random 1 2,617,362


title: NimbleGen HG18 Tiling Set Array 31 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 31 Array 31 of 38 chr15 58,530,439 100,336,874
chr15 random 1 784,326


title: NimbleGen HG18 Tiling Set Array 32 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 32 Array 32 of 38 chr16 32,788,379 88,820,540
chr16 random 485 105,474


title: NimbleGen HG18 Tiling Set Array 30 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 30 Array 30 of 38 chr14 72,700,808 106,360,511


title: NimbleGen HG18 Tiling Set Array 29 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 29 Array 29 of 38 chr13 95,001,817 114,127,886
chr13 random 1 186,280


title: NimbleGen HG18 Tiling Set Array 26 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 26 Array 26 of 38 chr11 117,278,030 134,450,373


title: NimbleGen HG18 Tiling Set Array 27 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 27 Array 27 of 38 chr12 58,836,844 132,289,483


title: NimbleGen HG18 Tiling Set Array 28 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
HG18Tiling Set 28 Array 28 of 38 chr13 22,163,047 95,001,767


title: NimbleGen HG18 Tiling Set Array 14 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 14 Array 14 of 38 chr5 120,977,671 180,836,772
chr5 random 700 141,287


title: NimbleGen HG18 Tiling Set Array 25 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 25 Array 25 of 38 chr11 35,341,452 117,277,977


title: NimbleGen HG18 Tiling Set Array 23 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 23 Array 23 of 38 chr10 19,977,040 99,783,066


title: NimbleGen HG18 Tiling Set Array 24 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 24 Array 24 of 38 chr10 99,783,524 135,370,851
chr10 random 899 113,241
chr11 50,001 35,341,402


title: NimbleGen HG18 Tiling Set Array 22 of 38

description:
Source: UCSC
Build: HG18
Probe Length: 50mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
HG18Tiling Set 22 Array 22 of 38 chr10 50,001 19,976,990
chr9 87,382,347 140,272,350
chr9 random 1,524 1,146,418


title: JCVI PFGRC Treponema denticola 13K v2 array designed primarily based on strain ATCC 35405

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Treponema denticola

description: This set includes 2744 oligonucleotides, has 13824 spots distributed in 96 blocks.

manufacture_protocol: 2QTD, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 7449021, pen id 10189, pen cycles -1, operator Kathy, humidity control On, humidity set point65


title: JCVI PFGRC Plasmodium falciparum 25K v3 array designed primarily based on strain 3D7

organism: Plasmodium falciparum

description: This set includes 5193 oligonucleotides, has 25392 spots distributed in 48 blocks.

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


title: JCVI PFGRC Francisella tularensis 15K v3 array designed primarily based on strain LVS

organism: Francisella tularensis

description: This set includes 2294 oligonucleotides, has 15552 spots distributed in 48 blocks.

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


title: JCVI PFGRC Francisella tularensis 15K v3 array designed primarily based on strain Schu_4


title: JCVI PFGRC Streptococcus sanguinis 15K v2 array designed primarily based on strain SK36

organism: Streptococcus sanguinis

description: This set includes 2273 oligonucleotides, has 15552 spots distributed in 48 blocks.

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


title: JCVI PFGRC Francisella tularensis 15K v3 array designed primarily based on strain F6168


title: Plasmodium falciparum Rathod Lab 8096

status: Public on Nov 15 2008

city: Seattle

first: Pradipsinh

middle: K

last: Rathod

state: WA

address: Campus Box 351700

department: Chemistry

institute: University of Washington

manufacturer: Rathod Lab, University of Washington, USA

first: Napawan

last: Ponmee

first: Lei

last: Jiang

manufacture_protocol: Arrays printed using poly-lysine slides and 70-mer oligonucleotides (60 µM solutions in 3xSSC). P. falciparum 70-mer oligo-microarray contained malarial elements representing the entire genome (Operon, version 1.1) and in-house elements representing folate and nucleotide biosynthesis genes, designed by ArrayOligoSelector. This set has 8096 spots distributed in 16 array blocks.


title: S. pombe IGR & ORF array (test)

status: Public on Nov 14 2008

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

organism: Schizosaccharomyces pombe

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.


title: Eurogentec S. pombe IGR & ORF array (sp280202)


title: JCVI PFGRC Pseudomonas aeruginosa 25K v2 array designed primarily based on strain PAO1

status: Public on Nov 13 2008

organism: Pseudomonas aeruginosa

description: This set includes 5552 oligonucleotides, has 25392 spots distributed in 48 blocks.

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


title: Rhodococcus sp. RHA1 13.8K MERH03-S1-0004

city: Houston

first: Jacques

last: Mathieu

department: Civil and Environmental Engineering

institute: Rice University

organism: Rhodococcus jostii RHA1

manufacturer: The Microarray Facility of the Prostate Centre at Vancouver General Hospital

first: Shawn

last: Anderson

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


title: HUGHES_Toronto_44K_v1.0

city: Calgary

first: Gordon

last: Chua

state: Alberta

address: 2500 University Drive, N.W.

department: Biological Sciences

country: Canada

institute: University of Calgary

organism: Saccharomyces cerevisiae

first: Timothy

middle: R

last: Hughes

first: Fred

last: Winston

first: Vanessa

last: Cheung

manufacture_protocol: Agilent SurePrint Technology


title: Leishmania major Friedlin v5.1 Forward Tiling Microarray

status: Public on Nov 11 2008

first: Sean

last: Thomas

address: WTC East #600, 2211 Elliott Ave

department: Genome Sciences

organism: Leishmania major

first: Peter

last: Myler

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


title: JCVI PFGRC Candida albicans 23K v2 array designed primarily based on strain SC5314

organism: Candida albicans

description: This set includes 7001 oligonucleotides, has 23232 spots distributed in 48 blocks.

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


title: JCVI PFGRC Giardia lamblia 20K v1 array designed primarily based on strain WB_C6

organism: Giardia duodenalis

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

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


title: MacLeod custom equine cartilage cDNA microarray

status: Public on Nov 09 2008

city: Lexington

first: Michael

middle: J.

last: Mienaltowski

email: M.Mski@uky.edu, mmienalt@health.usf.edu

state: KY

address: 108 Gluck Equine Research Center

department: Veterinary Science

institute: University of Kentucky

organism: Equus caballus

description: The 9,322 cDNAs spotted on this microarray were obtained from a normalized and subtracted cDNA library generated from the total RNA of articular cartilage from a 15-month old equine Thoroughbred gelding.   In addition, cDNAs from 28 plasmids used within the lab were spotted; 2 plasmids have been submitted to GenBank.  Positive control spots include Elongation Factor Tu (EFTu) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Negative control spots are the soybean genes chlorophyll ab binding protein (CAB - SPOT_ID: ABbinding) and Rubisco small chain 1 (RBS1 - SPOT_ID: Rubisco). Other spots might be identified as empty of buffer.   Keywords: cDNA, equine, articular cartilage, microarray

manufacturer: W.M. Keck Center, University of Illinois Urbana-Champaign

first: James

middle: N

last: MacLeod

first: Mark

last: Band

first: Qi

last: Sun

first: Stephen

last: Coleman

first: Naoki

last: Miura

manufacture_protocol: The cDNAs were spotted in 3x SSC buffer supplemented with 1.5 M betaine


title: Plasmodium falciparum Rathod Lab 8832

first: Pradipsinh

last: Rathod

first: Napawan

last: Ponmee

manufacture_protocol: Arrays printed using poly-lysine slides and 70-mer oligonucleotides (60 µM solutions in 3xSSC). P. falciparum 70-mer oligo-microarray contained malarial elements representing the entire genome (Operon, version 1.1) and in-house elements representing folate and nucleotide biosynthesis genes, designed by ArrayOligoSelector. This set has 8832 spots distributed in 16 array blocks.


title: JCVI PFGRC Treponema denticola 13K v3 array designed primarily based on strain ATCC 35405

first: PFGRC

last: JCVI

description: This set includes 2744 oligonucleotides, has 13872 spots distributed in 48 blocks.

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


title: PICME Poplar 15K Series 1

city: Seibersdorf

first: Dieter

last: Kopecky

address: Campus Seibersdorf

department: Biogenetics/Natural Resources

institute: Austrian Research Centers GmbH - ARC

organism:
Populus trichocarpa x Populus deltoides
Populus tremula x Populus alba

description:
This platform represents all slides of the two series 1_1_1 and 1_2_2, which are fully identical in their properties except the lot number.
PICME Poplar 15K 1_1_1 uses lot number: 14204000B
PICME Poplar 15K 1_2_2 uses lot number: 19404000B
Support: Corning GAPS II; Coating: Gamma Amino Propyl Silane
Number of spots: 15.488
Number of pins/blocks: 32
Spottdistance in µm: 200
Recurrances spots/slide: 2
Number of spots vertical: 22
Number of spots horinzontal: 22
Vertical offset of first block in µm: 1200
Horizontal offset of first block in µm: 3150

manufacturer: Austrian Research Centers GmbH - ARC, PICME

first: F

last: Martin

first: J

last: Leple

first: S

last: Fluch

manufacture_protocol:
Spottingbuffer: 3xSSC+ 1,5MBetain
Spottingplate setting: Biozym 384
Arrayer Hardware: GeneMachines Omnigrid II
Arrayer Software: OmniGrid Gridder 2.2.13
Humidity: 40%
Dipping time in sec: 1


title: Print_529

status: Public on Nov 06 2008

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism: Caenorhabditis elegans

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: Print_528


title: Univ Wuerzburg Blochmannia floridanus 564 v1.0

status: Public on Nov 10 2008

city: Wuerzburg

first: Sascha

last: Stoll

address: Biozentrum am Hubland

department: Dpt. of Microbiology

institute: University of Wuerzburg

organism: Candidatus Blochmanniella floridana

description: whole genome DNA macroarray

first: Heike

last: Feldhaar

first: Roy

last: Gross

manufacture_protocol: Gene-specific PCR primer pairs were designed and synthesized by MWG Biotech (Ebersberg, Germany) based on the Bl. floridanus genome sequence (RefSeq accession no NC_005061.1) to yield products of approximately 500 bp. We amplified 564 genes in duplicate 50 µl reactions, omitting the genes for most non-coding RNAs and several ribosomal subunit proteins. Reactions contained 1x PCR buffer with 1.5 mM MgCl2, 0.2 mM dNTPs, 0.8 µM each primer, 1.25 units Taq polymerase (Molzym, Bremen, Germany) and 4 ng of purified Bl. floridanus genomic DNA. Products were checked by agarose gel electrophoresis for correct size and purity. The DNA concentration of each product was measured photometrically and DNA was diluted to 100 ng/µl in sterile distilled water. PCR products were spotted in duplicate (approx. 30 ng DNA per spot) on 7x11 cm nylon filters together with an external control PCR product from a kanamycin resistance gene (neo) as the central spot of each 3x3 spot group (Eickhoff et al., 1999) as well as a PCR reaction without primers and template as a negative control at the German Resource Center for Genome Research (Berlin, Germany).


title: Zebrafish Oligonucleotide Library (Compugen)

status: Public on Nov 08 2008

city: Eugene

last: Miller

address: 1229 University of Oregon

department: Institute of Molecular Biology

institute: University of Oregon

organism: Danio rerio

description: This set of zebrafish oligonucleotides was designed by Compugen and synthesized by Sigma-Genosys. The set consists of 16,399 65-mer oligonucleotides representing 16,228 gene clusters and 171 control elements. Compugen and Sigma-Genosys no longer sell or support this product. Sequences are not for commercial use, copyright reserved to Compugen 2002.

first: John

middle: F

last: Rawls

manufacture_protocol: For each gene, one 65-mer oligonucleotide probe was designed from the 3' region of the sequence. Each probe was selected from a sequence segment that is common to a maximum number of splice-variants predicted for each gene.


title: Affymetrix NimbleExpress; Pseudmonas syringae DC3000

city: Ithaca

first: Philip

middle: Alan

last: Bronstein

state: NY

address: Cornell University Plant Science Building RM334

department: Plant Microbe Interaction Research Unit

institute: USDA-ARS

organism: Pseudomonas syringae pv. tomato str. DC3000

manufacture_protocol: see Affymetrix's web site


title: Porcine oligonucleotide microarray version 4 (POM4) (Condensed version)

city: Frederiksberg

first: Jayda

last: Siggers

state: C

address: Roligehdsvej 30

department: Human Nutrition

institute: University of Copenhagen

organism: Sus scrofa

manufacturer: National Veterinary Institute, DTU, Denmark

first: Shila

last: Mortensen

first: Kerstin

last: Skovgaard

first: Peter

last: M. H. Heegaard

manufacture_protocol:
1. This microarray is holding 384 different 60-70mer oligonucleotide probes representing more than 200 different immune related porcine genes and 8 synthetic array control oligonucleotide probes (ArrayControl)
2. The porcine target sequences used for oligo design were obtained from public databases (NCBI, National Center for Biotechnology Information, GenBank (http://www.ncbi.nlm.nih.gov/) and the Gene Index Project (http://compbio.dfci.harvard.edu/tgi/tgipage.html)
3. Probes were designed using Oligowiz (http://www.cbs.dtu.dk/services/OligoWiz2/)
4. Probes were synthesized at DNA Technology A/S (Århus, Denmark)
5. Probes were diluted to 50uM in 50% DMSO while array controls were diluted to 30uM in 50% DMSO
6. Probes were spottet on Corning UltraGAPS Coated Slides using a VersArray Chip Writer Pro, software version 2.1.1., equipped with 8 SMP3 pins (TeleChem International, Inc)
7. Oligonucleotides were spottet in tripilcate in 8 sub-arrays each holding 10 x 15 spots, these 8 sub-arrays were repeated 3 times vertically on the slide.
8. After printing , slides were dried, UV cross-linked and stored in a vacuum desiccator at room temperature until use.
9. Prior to hybridization the slides were pre-hybridized according to manufactures protecol


title: NimbleGen mouse mm7 ENCODE tiling array (385k)

status: Public on Nov 05 2008

city: Madison

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Mus musculus

description: Design number: 2006-02-17_MM7_ENCODE_ChIP

manufacture_protocol: Mouse genome tiling arrays covering ENCODE regions


title: GRL Rickettsia conorii str. Malish 7 5k array

status: Public on Nov 07 2008

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

organism: Rickettsia conorii str. Malish 7

description: Oligonucleotide set of 5,098 probes resulting to a final coverage of 97% for ORFs and 32% for inter-ORFs (considering a length > 40bp) of R.conorii strain Malish 7.

first: Patricia

last: Renesto

first: Clarisse

last: Rovery

first: Patrice

last: François

first: Quentin

last: Leroy

first: Antoine

last: Huyghe

first: Wenjun

last: Li

first: Hubert

last: Lepidi

first: Jacques

last: Schrenzel

first: Didier

last: Raoult

manufacture_protocol: Sure Print Technology-In situ synthesis


title: Switchgear Genomics - mouse - DNA methylation array

status: Public on Nov 04 2008

city: Boston

first: Alexey

last: Fedulov

address: 75 Francis St.

department: Brigham and Women's Hospital

institute: Harvard Medical School

manufacture_protocol: The position information relies in February 2006 mouse genome assembly. According to UCSC the data for this were obtained from the Build 36 essentially complete assembly by NCBI and the Mouse Genome Sequencing Consortium.


title: Print_1220

last: Stanford Microarray Database


title: Agilent-015963 Mouse Promoter tiling array

city: New York

first: Brian

last: Dynlacht

department: Cancer Institute

institute: NYU Medical Center

first: Chris

last: van Oevelen

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


title: Salk-Yeo-Solexa-ES,NP,NE cells

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Drive, Room 3114

department: SCRM

institute: UCSD

organism: Homo sapiens

technology: other

manufacture_protocol: high throughput sequencing


title: Zea mays 1x44K Agilent array - designed by Walbot Lab

status: Public on Nov 01 2008

first: John

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

organism: Zea mays

manufacture_protocol: 43K 60-mer oligo probes were designed from the TIGR maize contigs and synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry on glass slides.


title: NimbleGen human (hg17) ENCODE tiling array

last: Nimblegen Systems

manufacture_protocol: human genome tiling arrays covering ENCODE regions


title: CEA Saccharomyces cerevisiae 6k Whole Genome Microarray

first: Nicolas

last: Robine

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

first: Waka

last: Lin

first: Valerie

last: Borde

first: Alain

last: Nicolas

manufacture_protocol: Array contains 6152 features, corresponding to every ORF of the yeast Saccharomyces cerevisiae.


title: GenoToul/biopuces operon_yeast22x22b

city: Braga

first: Pedro

middle: M. R.

last: Guimaraes

address: Campus de Gualtar

department: Department of Biological Engineering

country: Portugal

institute: University of Minho - CEB

description: Dendrislides are prepared according to Trevisiol et al. 2003, New J. Chem. 27, 1713-1719

first: P

first: V

last: Le Berre

first: S

last: Sokol

first: J

last: Francois

manufacture_protocol:
Oligos sold by Operon 70-mer NH2 modified, put in phosphate buffer 0.3 M, pH 9 at 20 µM
spotted on dendrislide (Le Berre et al. Nucleic Acids Research, 2003, Vol. 31, No. 16 e88).
Robot is ChipWriterPro (Biorad) with 4x8 pins each pin has spotted a block of 22x22 spots.
Each well is spotted in duplicate.


title: Hubrecht Institute Zebrafish Zili- and Ziwi-interacting small RNAs (454 GS FLX system)

status: Public on Nov 03 2008

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

technology: MPSS

last: Houwing

first: E

first: R

last: Ketting

manufacture_protocol: small RNA deep sequencing


title: NimbleGen Saccharomyces cerevisiae Whole Genome Tiling Array (385K)

status: Public on Oct 31 2008

first: Inc

description: Chromosome mappings based on Oct 2003 UCSC genome release.


title: CombiMatrix_Influenza A_12,000_design 5200

city: Mukilteo

first: Michael

middle: Joseph

last: Lodes

address: 6500 Harbour Heights Pkwy, Suite 303

department: Assay Development

institute: CombiMatrix Corp

organism: Influenza A virus

description: Semiconductor based array with in situ synthesized oligonucleotides that can be used with electrochemical detection.

first: David

middle: S

last: Boyle

first: Brandon

middle: T

last: Leader

first: Elizabeth

last: Wieman

first: Paul

last: Swenson

first: Dominic

last: Suciu

first: Robin

last: Liu

first: Jinxin

last: Hu

manufacture_protocol:
The custom oligonucleotide microarray is synthesized on a semiconductor using an electrochemical synthesis process. Each oligonucleotide probe (spot) is synthesized on a platinum electrode that is independently controlled by the synthesizer’s computer. Synthesis is based on established phosphoramidite chemistry and occurs at thousands of sites simultaneously according to a computer algorithm that activates only specified electrodes. Since physical photolithographic masks, mechanical micromirrors, or inkjet technologies are not involved in the process, all probes can be easily changed without extra time or cost.
The oligonucleotides are synthesized in a proprietary porous reaction layer that coats the surface of the semiconductor, and acts to covalently attach the oligonucleotide to the surface of the chip.
Influenza A subtypes H1-15 and N1 - 9


title: SAGE:10:NlaIII:Leishmania major

status: Public on Feb 07 2008

last: GEO

technology: SAGE NlaIII

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


title: Operon Mouse 3.0.1 Cincinnati University

status: Public on Oct 29 2008

city: Madrid

first: Luis

middle: A.

last: Lopez-Fernandez

address: Dr. Esquerdo 46

department: Pharmacy

country: Spain

institute: Hospital General Universitario Gregorio Marañon

description: The 70-mer oligonucleotides are spotted at 22oC and 65-85% relative humidity at ~100 μm center-spacing using a high-speed robotic machine (OmniGrid-100 model; GeneMachines; San Carlos, CA) using Stealth pins (SMP3 pins) from Telechem (Sunnyvale, CA) mounted in a 48-pin head. Spot volumes are 0.5 nl and spot diameters are 75-85 μm.

manufacturer: Genomics and Microarray Laboratory, University of Cincinnati

middle: A

first: Pedro

middle: P

last: Lopez-Casas

first: Jesus

last: del Mazo


title: PICME Pine 24K Series 1

status: Public on Mar 22 2008

first: Dieter

last: Kopecky

institute: Austrian Research Centers GmbH - ARC

organism: Pinus pinaster

description:
Material generated by INRA - UMR BIOGECO.
This platform represents all slides of the Series 1, which are fully identical in their properties except the lot number.
PICME Pine 24K 1_1 uses lot number: 35506000
Support: Corning GAPS II; Coating: Gamma Amino Propyl Silane
Number of spots: 23.808
Number of pins/blocks: 48
Spottdistance in µm: 190
Recurrances spots/slide: 2
Number of spots vertical: 22
Number of spots horinzontal: 23
Vertical offset of first block in µm: 1250
Horizontal offset of first block in µm: 3150

first: Silvia

last: Fluch

first: Christophe

last: Plomion

first: Philippe

last: Chaumeil

manufacture_protocol:
Spottingbuffer: 3xSSC+ 1,5MBetain
Spottingplate setting: Biozym 10µl
Arrayer Hardware: GeneMachines Omnigrid II
Arrayer Software: OmniGrid Gridder 2.2.13
Humidity: 50%
Dipping time in sec: 1


title: University of Idaho_Fortunato_homo-HHV5_2240

status: Public on Oct 18 2008

city: Moscow

first: Holger

last: Hannemann

state: ID

department: MMBB

institute: University of Idaho

organism:
Homo sapiens
Human betaherpesvirus 5

last: Fortunato

first: Kyle

last: Rosenke

first: John

last: O'Dowd

manufacture_protocol:
see Combimatrix:
www.combimatrix.com


title: Print_530

last: Stanford Microarray Database

institute: Stanford Microarray Database (SMD)

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


title: PICME Poplar 28K 4_1/4_3

status: Public on Oct 27 2007

department: Biogenetics/Natural Resources

organism:
Populus trichocarpa x Populus deltoides
Populus euphratica
Populus tremula x Populus alba

description:
This platform represents all slides of the earlier Series 4, i.e. 4_1_4 and 4_3_2, which are fully identical in their properties except the lot number (Series 4_2_5 differs from this series and a separate platform exists).
PICME Poplar 28K 4_1_4 uses lot number: 13705000B
PICME Poplar 30K 4_3_2 uses lot number: 19505000B
Support: Corning GAPS II; Coating: Gamma Amino Propyl Silane
Number of spots: 27.648
Number of pins/blocks: 48
Spottdistance in µm: 180
Recurrances spots/slide: 1
Number of spots vertical: 24
Number of spots horinzontal: 24
Vertical offset of first block in µm: 1200
Horizontal offset of first block in µm: 3150

first: F

last: Martin

first: J

middle: C

last: Leple

last: Kangasjarvi

first: S

manufacture_protocol:
Spottingbuffer: 3xSSC+ 1,5MBetain
Spottingplate setting: Biozym 10µl
Arrayer Hardware: GeneMachines Omnigrid II
Arrayer Software: OmniGrid Gridder 2.2.13
Humidity: 40%
Dipping time in sec: 1


title: PICME Sweetpotato 13K Series 1

status: Public on Feb 22 2008

organism: Ipomoea batatas

description:
Material generated by Centro Internacional de la Papa - CIP.
This platform represents all slides of the Series 1, which are fully identical in their properties except the lot number.
PICME Sweetpotatoe 13K 1_1 uses lot number: 24806000
Support: Corning GAPS II; Coating: Gamma Amino Propyl Silane
Number of spots: 26.496
Number of pins/blocks: 48
Spottdistance in µm: 180
Recurrances spots/slide: 2
Number of spots vertical: 24
Number of spots horinzontal: 23
Vertical offset of first block in µm: 1200
Horizontal offset of first block in µm: 3150


title: Campylobacter jejuni 6.5K whole-ORF array v1.0

status: Public on Sep 10 2008

city: East Lansing

first: Linda

middle: S.

last: Mansfield

state: MI

address: 181 Food Safety Bldg.

department: Microbiology and Molecular Genetics

institute: Michigan State University

organism: Campylobacter jejuni

manufacturer: Michigan State University Research Technology Support Facility

first: Anne

middle: E

last: Plovanich-Jones

first: Jodi

last: Parrish

first: Russell

middle: L

last: Finley

first: Dave

last: Wilson

first: Tom

last: Whittam

last: Dewitt

first: Julia

last: Bell

first: Jeff

last: Landgraf

first: Jenna

last: Gettings

first: Jessica

last: St. Charles

last: Jerome

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


title: PICME Poplar 30K Series 2

city: Seibersdorf

first: Dieter

last: Kopecky

address: Campus Seibersdorf

description:
This platform represents all slides of Series 2, i.e. 2_1_3 and 2_2_3, which are fully identical in their properties except the lot number.
PICME Poplar 30K 2_1_3 uses lot number: 14204000B
PICME Poplar 30K 2_2_3 uses lot numbers: 24704000B; 27404000B; 25204000B
Support: Corning GAPS II; Coating: Gamma Amino Propyl Silane
Number of spots: 29.952
Number of pins/blocks: 48
Spottdistance in µm: 180
Recurrances spots/slide: 2
Number of spots vertical: 25
Number of spots horinzontal: 25
Vertical offset of first block in µm: 1200
Horizontal offset of first block in µm: 3150

last: Fluch


title: PICME Poplar 28K Series 4_4/4_5

description:
This platform represents all slides of the later Series 4, i.e. 4_4 and 4_5, which are fully identical in their properties except the lot number.
PICME Poplar 28K 4_4 uses lot numbers: 34705000B; 01606000B
PICME Poplar 30K 4_5 uses lot number: 23706000
Support: Corning GAPS II; Coating: Gamma Amino Propyl Silane
Number of spots: 27.264
Number of pins/blocks: 48
Spottdistance in µm: 170
Recurrances spots/slide: 1
Number of spots vertical: 24
Number of spots horinzontal: 24
Vertical offset of first block in µm: 1200
Horizontal offset of first block in µm: 3150

last: Martin


title: SAGE:10:Sau3A:Homo sapiens

status: Public on Jan 04 2001

last: GEO

technology: SAGE Sau3A


title: SAGE:10:NlaIII:Bos taurus

status: Public on Dec 04 2002

organism: Bos taurus


title: SAGE:10:NlaIII:Danio rerio

status: Public on Nov 28 2005

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


title: SAGE:17:NlaIII:Mus musculus

status: Public on Jul 15 2004

description:
This is a virtual platform for longSAGE 17 libraries generated for Mus musculus using NlaIII as an anchor enzyme.
Platform_anchor: NlaIII


title: SAGE:17:NlaIII:Homo sapiens

status: Public on Oct 07 2004

description:
This is a virtual platform for longSAGE 17 libraries generated for Homo sapiens using NlaIII as an anchor enzyme.
Platform_anchor: NlaIII


title: PICME Poplar 28K Series 3

description:
This platform represents all slides of Series 3, i.e. 3_1_4, 3_1_5 and 3_2_1, which are fully identical in their properties.
Lot number: 10205000B
Support: Corning GAPS II; Coating: Gamma Amino Propyl Silane
Number of spots: 27.648
Number of pins/blocks: 48
Spottdistance in µm: 180
Recurrances spots/slide: 1
Number of spots vertical: 24
Number of spots horinzontal: 24
Vertical offset of first block in µm: 1200
Horizontal offset of first block in µm: 3150

last: Leple

last: Kangasjarvi


title: SAGE:10:Sau3A:Mus musculus

status: Public on Aug 14 2003


title: SAGE:10:NlaIII:Mus musculus

status: Public on Jun 04 2001