title: Illumina Genome Analyzer II (Populus trichocarpa)

status: Public on Apr 29 2011

last: GEO

country: USA

organism: Populus trichocarpa

technology: high-throughput sequencing

distribution: virtual


title: Illumina Genome Analyzer II (Persea americana)

organism: Persea americana


title: Micor-CRIBI Mouse 13K Oligo Array (Operon v1.1)

status: Public on Apr 27 2011

city: Roma

first: Federica

last: Moschella

address: Viale Regina Elena 299

department: Cell Biology and Neurosciences

country: Italy

institute: Istituto Superiore di Sanità

organism: Mus musculus

technology: spotted oligonucleotide

distribution: custom-commercial

manufacture_protocol: This set consists of 13,443 70mer oligonucleotides (Operon version 1.1) designed on Mouse Unigene clusters, mainly in the 3'-terminal region. Each oligonucleotide is spotted by our robotic station Biorobotics Microgrid II, in two replicates on a MICROMAX glass slide SuperChip I (Cat No MPS696) provided by PerkinElmer Life Sciences Inc. The deposition is qualitatively assessed by a scan of the spotted slide at 10 micron resolution, using a GSI Lumonics scanner and a protocol that allows the detection of spotted features through the salts derived from the dried solution in which oligonucleotides are dissolved. Microarray slides that meet the quality standards, are washed as recommended by the supplier and the glass slides are stored, ready for use, in the dark under deep vacuum. Click below to see images of the array and detailed description of the spotting geometry, with the necessary parameters for analysis.


title: Illumina Genome Analyzer II (Picea abies)

organism: Picea abies


title: Illumina Genome Analyzer II (Hordeum vulgare)

organism: Hordeum vulgare


title: Illumina Genome Analyzer II (Musa acuminata)

organism: Musa acuminata


title: Illumina Genome Analyzer II (Gossypium arboreum)

organism: Gossypium arboreum


title: Illumina Genome Analyzer II (Marsilea quadrifolia)

organism: Marsilea quadrifolia


title: Illumina Genome Analyzer II (Mimulus guttatus)

organism: Erythranthe guttata


title: Illumina Genome Analyzer II (Ginkgo biloba)

organism: Ginkgo biloba


title: Illumina Genome Analyzer II (Cucurbita maxima)

organism: Cucurbita maxima


title: Illumina Genome Analyzer II (Panicum virgatum)

organism: Panicum virgatum


title: NimbleGen custom Human HG18 144-gene region Array

status: Public on Apr 28 2011

city: Beijing

first: Jun

last: Wu

address: No.7 Beitucheng West Road

country: China

institute: Beijing Institue of Genomics, Chinese Academy of Science

organism: Homo sapiens

technology: in situ oligonucleotide

description:
native array description file: 2007-10-25_HG18_QW_ChIP.ndf
native array description file: 2007-10-25_HG18_QW_ChIP.pos
Genome build information: HG18, build36
~48,824 Kb of genomic sequences spanning the entire genomic loci of 144 genes and their flanking intergenic regions were examined in the ChIP-on-chip analysis. The custom array contains 381,882 probes with a median probe spacing 110 bp.

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


title: Illumina Genome Analyzer II (Nuphar advena)

organism: Nuphar advena


title: [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array [Custom CDF: TAIR-8v11]

status: Public on Apr 21 2011

city: Vienna

first: Gudrun

last: Boehmdorfer

address: Dr. Bohr-Gasse 3

country: Austria

institute: GMI – Gregor Mendel Institute of Molecular Plant Biology

organism: Arabidopsis thaliana

description: CDF file was created using "aroma" tools tools avaialbale at: http://www.aroma-project.org/node/40

relation: Alternative to: GPL198 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: NimbleGen custom Mouse 17K TSS array

description:
native array description file: 090120_MM8_JW_promoter.ndf
native array description file: 090120_MM8_JW_promoter.pos
Genome build information: MM8, build36
We designed a custom array containing -1Kb/+3.5kb of the TSS, to capture binding information representing ~17,000 NCBI reference genes


title: Agilent-026161 ZV81M

status: Public on Dec 26 2011

city: Boston

first: Charles

last: Lee

state: MA

address: 221 Longwood Ave., EBRC-422

department: Pathology

institute: Brigham and Women's Hospital/Harvard Medical School

organism: Danio rerio

description:
ZV8 1M

Arrays of this design have barcodes that begin with 16026161 or 2526161.

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.

distribution: commercial

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


title: Agilent-022689 Custom BCM-Beaudet Human 1M Exon Autism Array

status: Public on Apr 30 2011

city: Houston

first: Patricia

middle: Borges

last: Celestino

state: TX

address: One Baylor Plaza, T613

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description:
Custom Agilent 1M CGH array that was designed to cover exons of 97% of all RefSeq genes in the genome, based on hg18 build.

Arrays of this design have barcodes that begin with 16022689 or 2522689.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Illumina Genome Analyzer II (Nicotiana tabacum)

organism: Nicotiana tabacum


title: BMR Mouse 32K Chip

city: Noda

first: Ryo

last: Abe

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biological Sciences

country: Japan

institute: Tokyo University of Science

manufacture_protocol: Operon Mus musculus AROS ver 3.0 probe (32,000 probe) were spotted on glass. Details can be found at the manufacturer’s website (http://www.biomatrix.co.jp/eng/index.html).


title: WiCell HG18 WG CGH 12x135K v3.1 HX12

city: Madison

first: Melodee

last: Patterson

state: WI

address: 510 Charmany Dr Ste 58 & 59

institute: WiCell

first: Karen

last: Montgomery

manufacture_protocol: Single array CGH design for whole human genome (hg18; NCBI Build 36). Probes selected from hg18_tiling database. Isothermal probes target Tm of 78C. Interval spacing: 12,524 bp (median). See www.Nimblegen.com for more details.


title: Illumina Genome Analyzer II (Cycas rumphii)

organism: Cycas rumphii


title: Carcinus maenas oligo microarray

status: Public on Oct 09 2011

city: Winnipeg

first: Sandra

last: Fehsenfeld

state: MB

address: 509 Buller Building, 45 Chancellors Circle

department: Biological Science

country: Canada

institute: University of Manitoba

organism: Carcinus maenas

description: Contig IDs (CMX) according to Towle DW, Henry RP, Terwilliger NB: Microarray-detected cahnges in gene expression in gills of green crabs (Carcinus maenas) upon dilution of environmental salinity. Comp.Biochem. Physiol.D 2010, in press.

distribution: non-commercial

manufacturer: designed as described in: Towle DW, Henry RP, Terwilliger NB: Microarray-detected changes in gene expression in gills of green crabs (Carcinus maenas) upon dilution of environmental salinity. Comparative Biochemistry and Physiology, Part D, in press.

manufacture_protocol:
1. Oligonucleotide design: Array Designer 4 software, based on the sequences of the ESTs (50mers)
2. Oligonucleotide synthesizing: Integrated DNA Technologies, provided in 384-well plates at a concentration of 250 μmol l-1
3. Microarray printing: to 17 μl of Pronto Universal Spotting Solution (Corning) in a 384-well plate, dispense 3 μl of oligonucleotide solution
4. adjust OmniGrid Accent [equipped with silica spotting pins (Parallel Synthesis Technologies 116 Inc.]) arrayer: set density and spot pattern desired; chamber humidity to 62-64% silica spotting pins (Parallel Synthesis Technologies  116 Inc.
5. place 384-well plates containing diluted oligos into position
6. place slides into the chamber and wait for humindity to stabilize for 30min, then start printing protocol
7. after printing, dry slides in a vacuum desiccator overnight, then cross-link in a UV Stratalinker (Stratagene) at a setting of 6000 x 100 μJ


title: Agilent Custom Rattus norvegicus miRNA microarray

city: Suita

first: yoshito

last: hayashi

state: Osaka

address: 2-2 Yamadaoka

department: Department of Gastroenterology and Hepatology

institute: Osaka University Graduate School of Medicine

organism: Rattus norvegicus

manufacturer: Hokkaido System Science Co.,Ltd. and Agilent Technologies

manufacture_protocol: Agilent SurePrint Technology, see manufacture`sweb site at http://www.agilent.com/


title: Agilent-021827 Human miRNA Microarray Rel12.0, v3.0, 8x15k array (Feature Number version)

city: Budapest

first: Zsófia

last: Tömböl

address: Szentkirályi u. 46.

department: 2nd Department of Medicine

country: Hungary

institute: Semmelweis University

description: Design ID: 021827.


title: Dicentrarchus labrax oligonucleotide-microarray (LOQ)

status: Public on Apr 23 2011

city: Chile

first: Sebastian

last: Boltana

state: Bio BIO

address: Edmundo Larenas s/n, Barrio Universitario. Biotechnology Center

department: Oceanografia

country: Chile

institute: Universidad de Concepcion

organism: Dicentrarchus labrax

description: Oligonucleotide probes were used to construct a high-density seabass microarray based on the Agilent 4 × 44 K design format (http://www.agilent.com/), which covers 13,199 unique transcripts of Dicentrarchus labrax. Oligonucleotides, 60-mer plus a “linker”, are synthesized directly on glass slides using the Agilent’s SurePrint Tecnology; oligo design was carried out by Agilent. This microarray includes 6275 annotated transcripts, each with x3 specific probes, and 4516 ESTs with 1 probe/target sequence.

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


title: Exiqon miRNA array [DesignedForVersion: miRBase ver.9.2, CurrentVersion: miRBase ver.10.0] condensed version

status: Public on Apr 22 2011

city: Lodz

first: Marcin

middle: P

last: Mycko

address: Kopcinskiego 22

department: Department of Neurology

country: Poland

institute: Medical University of Lodz

organism: Mus musculus

manufacture_protocol: See manufacturer's website: http://www.exiqon.com/array


title: Rosetta custom human 23K array

status: Public on Apr 25 2011

city: West Point

first: Michael

last: Nebozhyn

state: PA

address: Mail Stop WP53B-120, 770 Sumneytown Pike, Building 53, P.O. Box 4

department: GpGx/Computational System biology

institute: Merck, Inc

description: Oligonucleotide array on glass. Contains 60mer probes designed against 23,000+ human genes arrayed on Agilent ink-jet arrays.

manufacture_protocol: see manufacturer's website


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene10stv1_Mm_ENTREZG_13]

status: Public on Apr 13 2011

city: Copenhagen

first: Kristine

last: Williams

address: Ole Maaløes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

relation: Alternative to: GPL6246 (Alternative CDF [official])

manufacture_protocol:
see manufacturer's web site
This is identical to GPL6246 but a custom cdf environment was used to extract data. ANNOTATION: chip library files are provided as supplementary files below, and can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp as Package name mogene10stv1mmentrezg. vers13 july 6 2010.


title: Ocimum Biosolutions E.coli O157 OciChip (alternative version)

city: Fargo

first: Birgit

middle: Magdalene

last: Pruess

state: North Dakota

address: 1523 Centennial Blvd.

department: Veterinary and Microbiological Sciences

institute: North Dakota State University

organism: Escherichia coli O157:H7

relation: Alternative to: GPL10291 (original version)


title: Illumina Genome Analyzer II (Citrus sinensis)

status: Public on Apr 20 2011

last: GEO

organism: Citrus sinensis


title: Illumina Genome Analyzer (Sclerotinia sclerotiorum)

organism: Sclerotinia sclerotiorum


title: Illumina Genome Analyzer II (Aristolochia fimbriata)

organism: Aristolochia fimbriata


title: Illumina Genome Analyzer II (Capsicum annuum)

organism: Capsicum annuum


title: Illumina Genome Analyzer II (Chara corallina)

organism: Chara corallina


title: Stanford Affymetrix Caulobacter crescentus 16.7K CauloHi1 (alternative CDF)

city: Stanford

first: Leticia

last: Britos

state: CA

address: 279 Campus Dr.

institute: Stanford University

organism: Caulobacter vibrioides

manufacture_protocol: This is a custom commercial array designed by Affymetrix and the Harley McAdams and Lucy Shapiro Labs at Stanford University using the Caulobacter crescentus strain CB15 genome annotation of 2001 (Proc Natl Acad Sci USA. 98:4136-4141).  The construction of this Affymetrix GeneChip has been described by McGrath et. al., 2007. Nat Biotechnol. 25:584-592.


title: Illumina Genome Analyzer II (Carica papaya)

organism: Carica papaya


title: Illumina Genome Analyzer II (Amborella trichopoda)

organism: Amborella trichopoda


title: SuperArray Oligo GEArray® Notch Signaling Pathway oligoarray Array

city: Hangzhou

first: Jiang

last: Hong

state: Zhe Jiang

address: Yuhangtang Road,NO.388

department: life science

institute: Zhejiang University


title: Illumina Genome Analyzer II (Drosophila mauritiana)

status: Public on Apr 15 2011

organism: Drosophila mauritiana


title: Illumina Genome Analyzer IIx (Taxus wallichiana var. chinensis)

organism: Taxus chinensis


title: Hemorrhagic Fever Microarray Release I (V2.10HF)

status: Public on Apr 19 2011

city: St. Louis

first: Adam

middle: F

last: Allred

state: MO

address: 660 S. Euclid

institute: Washington University in St. Louis, School of Medicine

organism:
Flaviviridae
Filoviridae
Arenaviridae
Peribunyaviridae

technology: spotted DNA/cDNA


title: [INDEL01m520678F] Affymetrix human INDEL genotyping array

city: Baltimore

first: Scott

middle: E.

last: Devine

state: MD

address: 801 W. Baltimore Street

institute: Institute for Genome Sciences

organism: Homo sapiens

description: Custom array.

middle: E

manufacture_protocol: See manufacturer's website (www.affymetrix.com).


title: GreenGene/Operon Rice 60K Oligo Array

city: Suwon

first: Myoung Ryoul

last: Park

address: 126 Suin-ro

country: South Korea

institute: National Institute of Crop Science

organism: Oryza sativa

first: Myoung-Ryoul

first: So-Hyeon

last: Beak

first: Song-Joong

last: Yun

manufacture_protocol: The 60K 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. 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 × 4) blocks with addresses composed of 676 (26 × 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℃, was printed in each spot address with a diameter of 100 ㎛.


title: Illumina Genome Analyzer II (Drosophila sechellia x Drosophila mauritiana)


title: TaqMan Array Mouse Stem Cell Pluripotency Card

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

technology: other

description: The TaqMan® Mouse Stem Cell Pluripotency Array is an efficient, easy-to-use micro fluidic card for the characterization of undifferentiated stem cells or their differentiated derivatives. This gene signature panel contains mouse orthologs of well-defined human markers for pluripotency plus 6 endogenous controls. The format of the TaqMan Array allows for 1-4 replicates to be run in parallel per array.


title: 454 GS (Cucumis melo)

organism: Cucumis melo


title: Affymetrix Yeast Genome 2.0 Array (Yeast2_ENTREZG.cdf)

status: Public on Apr 18 2011

city: Cold Spring Harbor

first: Bruce

last: Stillman

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

organism: Saccharomyces cerevisiae

relation: Alternative to: GPL2529 (Alternative CDF [official])


title: SCCWRP-Vulpe Longjaw Mudsucker 15K v1.0.

city: Berkeley

first: Don

last: Pham

address: 238 Morgan Hall

institute: University of California, Berkeley

organism: Gillichthys mirabilis


title: SMD Print_1256 lc-53a Homo sapiens

status: Public on Apr 14 2011

first: Patrick

middle: O

last: Brown

address: Beckman Center b439

department: Department of biochemistry

institute: Stanford university school of medicine

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine

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


title: SMD Print_1110 LC-49 Homo sapiens


title: SMD Print_1046 LC-48 Homo sapiens


title: Conway Institute Candida parapsilosis 5834 v1.1

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

organism: Candida parapsilosis

description:
The Cpag_IDs can be downloaded as a .zip file from the Broad institute page at the following link:

http://www.broadinstitute.org/annotation/genome/lodderomyces_elongisporus/MultiDownloads.html

manufacture_protocol: Oligonucleotides were designed from an in-house annotation of the C.parapsilosis genome sequence (http://www.sanger.ac.uk/sequencing/Candida/parapsilosis/) using eArray from Agilent Technology. Each of 5834 open reading frames is represented by two oligonucleotides probes. Mitochondrial genes are indicated by the prefix cpmt. Controls from Arabidopsis thaliana were included. The probes were used to generate custom microarrays in a 4x44 K format with a randomized layout.


title: Illumina MouseWG-6 v2.0 expression beadchip (Gene view)

city: Berlin

first: Torben

last: Redmer

address: Robert-Roessle Str. 10

department: Signaling in embryonic stem cells

country: Germany

institute: Max-Delbrueck-Center (MDC)

organism: Mus musculus

technology: oligonucleotide beads

description: The MouseWG-6 v2.0 Expression BeadChip offer the most up-to-date content for whole-genome expression profiling in the mouse. Featuring content derived from the National Center for Biotechnology Information Reference Sequence (NCBI RefSeq) database (Build 36, Release 22).


title: Illumina Genome Analyzer (Capsella bursa-pastoris)

organism: Capsella bursa-pastoris


title: Lawrence Livermore Microbial Detection Array version 2 subarray B

city: Livermore

first: Kevin

last: McLoughlin

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

organism: synthetic construct

description: Array design is described in Gardner S, Jaing CJ, McLoughlin KS, Slezak TR, 'A Microbial Detection Array (MDA) for Viral and Bacterial Detection', submitted to BMC Genomics, 2010. ThIS platform is a subarray of a larger design with 388K features; this 61K subarray focuses on human bacterial and viral pathogens (a special NDF file IS USED to identify the data from this subarray only).


title: WUSTL Cryptococcus neoformans 11K oligo array

city: Vancouver

first: Won Hee

last: Jung

state: British Columbia

address: 2185 East Mall

department: Michael Smith Laboratories

institute: University of British Columbia

organism: Cryptococcus neoformans

manufacturer: The Genome Sequencing Center (GSC) at Washington University

manufacture_protocol: see manufacturer's web site at http://genomeold.wustl.edu/home.cgi


title: whole-genome oligonucleotide array for Acidithiobacillus ferrooxidans ATCC 23270

city: changsha

first: xueduan

last: liu

address: lushan south road

institute: central south university

description: spotted 50-mer-based oligonucleotide


title: Species Specific Phosphorylation Array

city: Winnipeg

first: Neeloffer

last: Mookherjee

address: 799-JBRC, 715 McDermot Ave

department: Internal Medicine

institute: University of Manitoba

organism:
Bos taurus
Ovis aries

technology: spotted peptide or protein

description:
JPT Peptide Technologies applies its unique PepStar™ peptide microarray platform to generate customized peptide microarrays on glass slides for biomarker discovery, immuno monitoring and detection and validation of protein interactions. In addition, PepStar™ technology also enables characterization of enzyme target families such as kinases, phosphatases and proteases as well as methyl, glycosyl, acetyl transferases and lysine deacetylases.
Peptides are immobilized on glass slides via a flexible linker. Chemoselective coupling generates microarrays of directed and covalently attached peptides. Multiple identical copies of peptide microarrays can be prepared at unmatched prices and turnaround times. Incubation can be performed manually or automated and read-out is performed via fluorescence. This results in low backgrounds and high sensitivity.

first: Emily

last: Turner-Brannen

first: Ka-Yee

last: Choi

first: Ryan

last: Arsenault

first: Hani

last: El-Gabalawy

last: Napper

manufacture_protocol:
Peptide derivatives (50 nmol) were dissolved in 25 μL of printing solution (70% DMSO, 25% 0.2 M sodium acetate pH 4.5, 5 % glycerol; by
vol.) and transferred into 384-well microtiterplates. Two droplets of 0.5 nL peptide solution were deposited per spot on aldehyde functionalized glass slides using the non-contact printer Nanoplotter of GESIM (Großerkmannsdorf, Germany) equipped with 8 piezoelectric NanoTips
(GESIM, Großerkmannsdorf, Germany). Printed peptide microarrays were kept at room temperature for 5 hours, washed with deionised water, quenched for 1 hour with 50% aqueous hydroxylamine, washed extensively with water followed by ethanol, and dried under a stream of nitrogen. Each block of 300 peptides was printed in triplicate on each slide. The final physical dimensions of the array were 19.5 X 19.5 mm with each peptide spot having a diameter of ~350 μm and peptide spots being 750 μm apart.


title: Agilent-019465 The Genome Sequencing Center (GSC) at Washington University Cryptococcus neoformans 14K array

city: Incheon

first: Jaehyuk

address: 119 Academy-ro

institute: Inceon National Univ

organism: Cryptococcus neoformans H99

manufacture_protocol: Agilent Technologies: see manufacturer's web site


title: Roche NimbleGen_Custom designed R. microplus_12x135K HD2 array

status: Public on Apr 12 2011

city: PULLMAN

first: Ricardo

middle: Francisco

last: Mercado-Curiel

state: WA

address: BUSTAD 402

department: College Of Veterinary Medicine

institute: Washington State University

organism:
Rhipicephalus microplus
Anaplasma marginale str. St. Maries

description: NimbleGen design name 090120_Amar_Bmic_RFMC, NimbleGen design ID 19181. A Roche NimbleGen high-density gene expression microarray custom designed for 14,447 genes based on the expressed sequence tag (EST) database, B. microplus Gene Index Version 2 (BmiGI V2) for R. microplus. Eight 60-mer probe per gene; each probe is replicated 1 time. The design includes random GC and other control probes.

first: RICARDO

last: MERCADO-CURIEL

first: GUY

middle: H

last: PALMER

first: FELIX

middle: D

last: GUERRERO

first: KELLY

middle: A

last: BRAYTON

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


title: Mussel Immunochip 1.0

city: Padova

first: Laura

last: Varotto

address: via U. Bassi 58/3

department: Biology Department

institute: University of Padova

organism: Mytilus galloprovincialis

manufacturer: Department of Biology and C.R.I.B.I. (University of Padova)

first: Umberto

last: Rosani

first: Filippo

last: Bernante

first: Stefano

last: Cagnin

first: Gerolamo

last: Lanfranchi

first: Alberto

last: Pallavicini

first: Paola

last: Venier

manufacture_protocol:
Immunochip 1.0 includes 1820 spotted oligonucleotides representing putative immune-related transcripts of M. galloprovincialis. The probe ID also indicates the related transcript sequence available at http://mussel.cribi.unipd.it. For instance, MGO_00175 relates to MGC00175 in Mytibase, a dynamic knowledgebase of expressed mussel sequences described in BMC Genomics 2009 Feb 9;10:72. Probes were designed with OligoArray 2.1. Additional 38 oligonucleotides, with no virtual hybridization against the whole mussel EST collection, were similarly prepared from human sequences.
The probe set was arranged and deposited twice (BioRobotics MicroGrid II, Digilab, Genomic Solutions) on derivatized glass slides (MICROMAX Glass Slides: SuperChip I, Perkin-Elmer) at 50% relative humidity. Each array is organized in 16 subarrays and contains 4x1820 mussel probes, 652 unrelated probes in multiple replicates and 112 alignment spots. Probe fixation on slide was performed with a UV cross linker (Stratagene). Slides were rinsed once in 1% SDS, 3× SSC for 1 min at room temperature, twice in distilled water for 5 min at room temperature and than dried in a laminar flux chamber.


title: Nimblegen_Custom_Chloroethene_array_V01

city: AUBIERE

first: Peyret

last: Pierre

address: 24, avenue des landais

country: France

institute: CNRS - Blaise Pascal University

description: The Platform data table reflects a condensed representation of the expression array's replicates (SEQ_ID) features. The design includes 3392 probes targeting 21 genes involved in chlorinated solvent biodegradation pathways.


title: OSU-CCC custom miRNA Array Homo sapiens

status: Public on Apr 10 2011

first: Dido

last: Lenze

address: Hindenburgdamm 30

department: Pathologie, Campus Benjamin Franklin

institute: Charité-Universitätsmedizin Berlin

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

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


title: Agilent chicken CGH array

city: Columbus

first: Yanqiang

last: Wang

state: Ohio

address: 12th w street

institute: The Ohio State University

organism: Gallus gallus

description:
Agilent design ID 031112.
Platform is based on chicken genome build WUGSC 2.1/galGal3.

manufacture_protocol: See the manufacturer's website (www.agilent.com).


title: Agilent-015347 Regeneron Custom Whole Genome Oligo - mouse v1.0

city: Tarrytown

first: Ivan

middle: B

last: Lobov

address: 777 Old Saw Mill River Road,

department: Regeneron Pharmaceuticals

institute: Regeneron Pharmaceuticals

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


title: IRD_RHIZO-ALNUS-15K-V1.0

status: Public on Apr 11 2011

city: Villeurbanne Cedex

first: Nicole

last: ALLOISIO

address: 43 bd du 11 Novembre 1917

institute: CNRS / Univ Lyon 1

organism: Alnus glutinosa

manufacturer: IMAXIO - Biopôle Clermont-Limagne- 63360 Saint-Beauzire, France- Tél: +33 (0)4 73 64 43 90 – Contact : V. VIDAL. This platform is Certified Service Provider by AGILENT.

manufacture_protocol: Agilent protocol


title: Wuerzburg Neisseria meningitidis 14.6K (Feature)

status: Public on Apr 09 2011

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

institute: University of Wuerzburg

organism: Neisseria meningitidis

manufacturer: Institute für Hygiene und Mikrobiologie, Universität Würzburg

first: Roland

last: Schwarz

first: Biju

last: Joseph

first: Gabriele

last: Gerlach

first: Kathrin

last: Engelhard

first: Mathias

last: Frosch

first: Tobias

last: Müller

first: Christoph

last: Schoen

manufacture_protocol: The oligonucleotides were synthesized by Operon technologies(Germany) and were spotted on Nexterion E epoxy silane coated slides using an OmniGrid scanner after resuspension in the recomended buffers. The sequence of the oligonucleotides on the slides are similar to Platform GPL8787


title: Illumina Genome Analyzer II (Oryza glaberrima)

status: Public on Apr 05 2011

last: GEO

organism: Oryza glaberrima


title: WUSTL_TIGR Listeria monocytogenes spotted 70-mer oligonucletoide array

city: Chicago

first: Jess

last: Leber

state: IL

address: 920 E. 58th Street CLSC 615

department: Microbiology

institute: The University of Chicago

organism:
Listeria monocytogenes EGD-e
Listeria monocytogenes serotype 4b str. F2365
Listeria monocytogenes serotype 1/2a str. F6854
Listeria monocytogenes serotype 4b str. H7858

description: TIGR PFGRC 70-mer oligonucleotides

manufacture_protocol: printed on Corning UltraGap slides


title: AB SOLiD System (Arabidopsis thaliana)

organism: Arabidopsis thaliana


title: UCSF_PARK_Human BAC Array3.2Kuf

status: Public on Apr 01 2011

city: San Francisco

first: Mark

last: Magbanua

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

organism: Homo sapiens

description:
Annotations based on human genome sequence hg17.
UCSF_PARK_HumArray3.2Kuf
The clonepos file contains information on all the clones.
The spotclone file maps the identifiers to the location on the subarray.

manufacture_protocol: For a detailed description on how the arrays were made please refer to: Snijders et al. Nat Genet. 2001 Nov;29(3):263-4.


title: Affymetrix GeneChip Universal 70K Tag Array (MIP_Tag_70K_SAPE_CN.1sq)

status: Public on Apr 02 2011

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: library files available from Affymetrix

manufacture_protocol: Standard Affymetrix photolithography protocol


title: A-UMCU-HS44K-1.0

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

manufacturer: Holstege Lab, UMC Utrecht, The Netherlands

first: Dik

last: van Leenen

first: Marian

last: Groot Koerkamp

first: Philip

last: Lijnzaad

first: Linda

last: Bakker

first: Erik

last: Sluiters

first: Sander

last: van Hooff

first: Frank

last: Holstege

manufacture_protocol: 1. Slides are obtained from a commercial provider (Agilent) and reannotated using blat to obtain the latest gene annotations from ensembl.


title: Illumina Genome Analyzer II (Lactuca sativa)

organism: Lactuca sativa


title: Ocimum Biosolutions E.coli O157 OciChip (alternative version)

city: Seoul

first: Jinki

last: Yeom

address: Anam-Dong, Sungbuk-Gu

department: Life Science

institute: Korea University

organism: Escherichia coli

description: original version of this platform is GPL10291

manufacture_protocol: E.coli O157 OcichipTM consists of 6336 spots printed on Corning® epoxy coated glass slides using Omnigrid (Gene Machines). Chip has been printed using 4x8 SMP4 pins on 75.5x 25.5x1.3 mm microarray glass slides with a spot area of 18 x36 cm. The origin offset values were 0 for X direction and 10000 for Y direction. The dot to dot distance is 240 mm; distance between subarrays is 150 mm and no of dots per array is 11x18=198. Oligos were printed using spotting buffer A from Ocimum Biosolution at 50% humidity and temperature at 22°C. The time taken by the robotic gridder to print was 16 hrs. Each probe was checked for its performance by standard QC process followed at Ocimum Biosolutions. Printed slides were stored in a light-tight box in a bench-top dessicator, with desiccant and were kept at 4°C until they were used for hybridization.


title: μParaflo™ MicroRNA microarray Assay

city: Guangzhou

first: chen

last: wen

address: 74 Zhongshan Road 2

department: Department of Toxicology

institute: Sun Yat-sen University

first: Wen

last: Chen

first: Qing

last: Wang

first: Daochuan

last: Li

manufacture_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 2 to 5 μg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from 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 later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments. Hybridization was performed overnight on a μParaflo™ microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). 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/) or other RNA (control or customer defined 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 used 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 filter (Locally-weighted Regression) (2). For two color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.


title: Exiqon custom Mus musculus miRNA array [DesignedForVersion: miRBase ver.9.2, CurrentVersion: miRBase ver.10.0]

organism: Mus musculus

manufacture_protocol:
See manufacturer's website: http://www.exiqon.com/array
miRBase_DesignedForVersion=miRBase ver. 9.2
miRBase_CurrentVersion=miRBase ver. 10.0


title: DiFazio_poplar_60mer_JGI_V1.1

city: Oak Ridge

first: David

middle: J

last: Weston

state: TN

department: Environmental Sciences Division

institute: David Weston

organism: Populus trichocarpa

description: This array has probes designed from gene models taken from the Joint Genome Institute Populus trichocarpa genome sequence, as well as probes designed using aspen ESTs.

manufacture_protocol: Propriety in situ oligonucleotide synthesis


title: Agilent-020940 Casuarina glauca Oligo Microarray (8 x 15K) V1.0 (Probe Name version)

city: MONTPELLIER CDX 5

first: Valérie

last: HOCHER

address: 911 av. Agropolis BP64501

department: DIADE

institute: IRD

organism: Casuarina glauca

description:
IRD_RHIZO-CASUARINA-15K-V1.0

Based on 14327 annotated unigenes for C. glauca, 60mers probes were designed using eArray software (1 probe per unigene) and custom 8 x 15K Oligo Microarrays were manufactured by Agilent.


title: Yeast Splicing/Expression Chip v6.2-6.3

city: Santa Cruz

first: Lily

last: Shiue

address: 1156 High Street

department: MCD Biology

institute: UCSC

organism: Saccharomyces cerevisiae

description:
This is an oligonucleotide microarray designed to measure splicing and expression in yeast. Each intron containing gene has 3 features (Splice Junction, Intron, Exon2). The SJ oligo symmetrically spans the splice junction with 20nt on each side. The SJ, Int, and Ex2 oligos are custom designed 40-mers. The array also contains the Operon Yeast Genome 70-mer Set. All of the SJ, Int, and Ex2 oligos are printed 4 times, the Operon 70-mers are printed twice each.
Keywords = Splicing and Expression
Supplementary files: GAL files representing 2 different print layouts.

first: Roland

last: Nagel

first: Tiffani

last: Quan

first: Lisa

last: Trevino

first: Grant

last: Hartzog

first: Manuel

last: Ares

manufacture_protocol:
DeRisi style arrayer;
Printed on CodeLink slides;
5' amine modified oligonucleotides were printed in phosphate buffer onto CodeLink slides;
Slides were processed to remove unbound oligo.


title: EBT_UA_Enchytraeus albidus_version2

status: Public on Dec 28 2010

city: Aveiro

first: Sara

last: Novais

address: Campus de Santiago, Department of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

organism: Enchytraeus albidus

description: Platform is based on a non-model organism, so information is unavailable for some of the genes from this library. Of the 480 genes, 348 have been sequenced and are listed in the Platform table with the respective accession number from GenBank.

manufacturer: Laboratory for Ecophysiology, Biochemisty and Toxicology, University of Antwerp; CESAM & University of Aveiro

first: Mónica

last: Amorim

first: Amadeu

last: Soares

first: Wim

last: De Coen

manufacture_protocol: The microarray is composed of a normalised cDNA library that followed the protocol of Shagin (Shagin et al., 2002). A pooled RNA sample - containing RNA aliquots from the individuals exposed to all the different exposure conditions - was used for the construction of the normalized cDNA library. The exposures included different concentrations of two chemical compounds and different soil types. In general, the differentially expressed genes were ligated in a TA-vector system using the pGEM-T easy vector (Promega, USA). Escherichia coli competent cells (JM109, Promega) were transformed through heat shock. Clones were amplified with vector specific primers (T7 and SP6 primers, Promega) and purified by an exosap reaction. In preparation for spotting, cDNA-inserts of the clones were, amplified using adaptor specific primers (nested primers, Clontech), purified by Montage PCR Plate (Millipore, USA) and loaded into 384-well plates (Genetix, UK) in 50% dimethylsulfoxide at ~150 ng/µl. A MicroGrid Compact spotter (Biorobotics) was used to spot each clone in triplicate onto aminosilane coated glass slides (Generoma microarray slides; Asper Biotech, Estonia). In addition, a set of artificial genes control genes (Lucidea Universal Scorecard, Amersham Biosciences, UK) was spotted in 20 replicates spread over each array: 10 calibration controls, 8 ratio controls and 2 negative controls. After rehydration and drying, the slides were fixated by UV-radiation at 300mJ (UV Stratalinker 2400; Stratagene, USA).


title: Turbot-USCMicroarray2.0

city: Lugo

first: Adrian

middle: Millan

last: Perez

state: Lugo

address: Facultad Veterinaria, Campus Universitario Pabellon IV 2 superior

department: Acuigen

country: Spain

institute: Universidad Santiago Compostela

organism: Scophthalmus maximus

manufacture_protocol: In situ oligo sinthesys


title: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S 0.3K

status: Public on Dec 07 2010

city: Rockville

first: John

last: Braisted

address: 9704 Medical Center Dr

department: PFGRC

country: USA

institute: J Craig Venter Institute

technology: RT-PCR

first: Marcus

last: Jones

first: Qiang

last: Sun

first: Tatiana

last: Dracheva


title: A-UMCU-M44K-1.0

first: Patrick

last: Kemmeren

first: Dik

last: van Leenen

first: Marian

last: Groot Koerkamp

first: Philip

last: Lijnzaad

first: Linda

last: Bakker

first: Erik

last: Sluiters

first: Sander

last: van Hooff

first: Frank

last: Holstege


title: BWH Comstock Bacteroides fragilis 9343 385k array

status: Public on Aug 06 2010

city: Boston

first: Michael

last: Coyne

state: MA

address: 181 Longwood Avenue

department: Medicine

institute: Brigham & Women's Hospital

organism: Bacteroides fragilis NCTC 9343

description: Roche NimbleGen design name 2006-07-27_TI272559_60mer, design ID 4433.  Catalog design for 4,231 genes from Bacteroides fragilis NCTC 9343 and associated plasmid pBF9343 with eighteen 60-mer probes per gene. Each probe is replicated 5 times and the probes are randomly distributed over the surface of the array. Unused features have been filled with randomly generated probes of comparable GC content.  The Platform data table reflects a condensed representation of the expression array's replicate features. The .ndf and .ngd files are linked below as supplementary files.

first: Laurie

last: Comstock

first: Maria

last: Chatzidaki-Livanis

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


title: Agilent-021782 Custom Staphylococcus aureus V6 Array

status: Public on Jan 01 2011

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: Staphylococcus aureus

description:
Staphylococcus aureus 564
Staphylococcus aureus UAMS-1
Staphylococcus aureus Newman
Staphylococcus aureus SA113

first: Antoine

last: Huyghe

first: Adrien

last: Fischer

first: Patrice

last: Francois

first: Jacques

last: Schrenzel

manufacture_protocol: In situ synthesis (SurePrint Technology)


title: Alternative Human Exon 1.0 ST Array [custom CDF: huex10stv2_52_36n_0110-bin.cdf]

status: Public on May 07 2010

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description: Probe set data extracted from custom CDF [huex10stv2_52_36n_0110-bin.cdf]

relation: Alternative to: GPL5175 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: UBC Moerman Caenorhabditis elegans WG 2006

status: Public on Dec 17 2009

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

institute: University of British Columbia

organism: Caenorhabditis elegans

description: Wormbase version WS139

first: Jason

middle: S

last: Maydan

first: Adam

last: Lorch

first: Mark

middle: L

last: Edgley

first: Donald

middle: G

last: Moerman

manufacture_protocol: See NimbleGen's website.


title: Maize Pioneer Hi-Bred 105K mRNA Microarray

status: Public on Sep 02 2010

city: Johnston

first: Kevin

middle: Robert

last: Hayes

state: IA

address: 7200 NW 62nd Ave

institute: Pioneer Hi-Bred International

organism: Zea mays

description: The Agilent “105K” microarray chip was designed for maize genomic and transcript sequences in an effort to cover most maize genes with at least one 60-mer oligonucleotide probe.  A pool of about 1.4 million public and private ESTs was consulted, derived from diverse tissues and treatments. The majority of the sequences was derived from the B73 genotype, but there were other genotypes represented.  A higher quality subset of 1.1 million ESTs was used to generate a transitory transcript assembly of about 66K transcript sequences of average length 1.0 kb.  At least one 60-mer oligo was designed for nearly all of these transcripts, but at times more than one oligo was designed per transcript.  In an effort to identify other genes, or perhaps parts of genes, not represented in the 66K transcript set, and to fill out the array, various BLAST analyses were conducted against the then (in fall 2006) available public B73 genomic sequences, namely B73 BACs in GenBank and the AZM5 GSS Assembly dataset produced by TIGR.  The resulting array design is believed to encompass most maize genes at least once, but there are certainly genes missing, others represented more than once, and sequence errors or genotypic variation in the dataset, or oligos designed to straddling intron-exon junctions, or to chimeric junctions inherent in ESTs and their assemblies, that may deter some oligos from functioning against a B73-specific transcript sample.  Subsequent efforts to estimate the number of unique genes in this microarray suggest about 45,000 genes.  This “105K” format Agilent microarray consists of 103,685 oligos designed to maize genic sequences. The balance of the space on the “105K” microarray (105,073 total oligos) was reserved for technical and internal hybridization controls.

middle: R

first: Carl

last: Simmons

first: Bin

last: Hu

manufacture_protocol:
Produced by:
Agilent Technologies Inc.
5301 Stevens Creek Blvd
Santa Clara CA 95051
United States


title: VCU S. sanguinis 12.2k v1.0

status: Public on Dec 01 2009

city: Richmond

first: Alejandro

last: Rodriguez

state: VA

address: 521 North 11th Street

department: Dentistry

institute: Virginia Commonwealth University

organism: Streptococcus sanguinis SK36

description: Elements on the array are arranged in blocks. There are 8 columns and 12 rows of blocks. Each block contains 8 columns and 16 rows of printed oligonucleotides. There are four technical replicates of each gene printed on the slide. The dimension of the slide is 25 x 75mm.

manufacturer: Pathogen Functional Genomics Resource Center

middle: M

first: Jill

last: Callahan

first: Paul

last: Fawcett

first: Todd

last: Kitten

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


title: Ocimum Biosolutions E.coli O157 OciChip

status: Public on Apr 07 2010

city: Hyderabad

first: Ocimum

last: Biosolutions

email: govind.a@ocimumbio.com, sandhya.p@ocimumbio.com, hazira.b@ocimumbio.com, anwaruddin.m@ocimumbio.com

state: Andhra Pradesh

address: Banjara Hills Road No., 1 VI Floor Reliance Classic

department: Bioinformatics

country: India

institute: Ocimum Biosolutions

description: epoxide

first: Govind

last: Rao

first: Rashmi

last: Sharma

first: Sandya

middle: P

last: Kiran

first: Hazira

last: Begum

relation: Alternative to: GPL13358 (alternative version)

relation: Alternative to: GPL13448 (alternative version)

manufacture_protocol: E.coli O157 OcichipTM  consists of 6336 spots printed on Corning® epoxy coated glass slides using Omnigrid (Gene Machines). Chip has been printed using 4x8 SMP4 pins on 75.5x 25.5x1.3 mm microarray glass slides with a spot area of 18 x36 cm. The origin offset values were 0 for X direction and 10000 for Y direction. The dot to dot distance is 240 mm; distance between subarrays is 150 mm and no of dots per array is 11x18=198. Oligos were printed using spotting buffer A from Ocimum Biosolution at 50% humidity and temperature at 22°C. The time taken by the robotic gridder to print was 16 hrs. Each probe was checked for its performance by standard QC process followed at Ocimum Biosolutions. Printed slides were stored in a light-tight box in a bench-top dessicator, with desiccant and were kept at 4°C until they were used for hybridization.


title: MSU Dworkin Drosophila melanogaster wing 1400 V1

city: East Lansing

first: Ian

last: Dworkin

state: MI

address: 203 Natural Science Bldg. Michigan State University

department: Zoology

institute: Michigan State University

organism: Drosophila melanogaster

description: The custom Drosophila melanogaster BeadChip contains 16 arrays on a single BeadChip, each with 1400 probes derived from 1000 Drosophila melanogaster genes in the National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) and UniGene databases. The goal of this focused platform was to represent a majority of the expressed genes in the wing imaginal disc of Drosophila (plus some negative control genes).

manufacture_protocol: see manufacturer's website


title: UniversityofOregon Dmelanogaster CustomAgilent44K

status: Public on Apr 23 2009

city: Eugene

first: Michael

last: Miller

state: OR

address: 1229 University of Oregon

department: Institute of Molecular Biology

institute: University of Oregon

first: Chris

middle: Q

last: Doe

manufacture_protocol: We used the Agilent (Palo Alto, CA) eArray platform to design a custom D. melanogaster oligonucleotide microarray representing 14,141 unique genes from the Flybase release 5.4 genome.  Briefly, we downloaded the dmel-all-transcript-r5.4.fasta file from Flybase which contains the sequences of every predicted transcript from genome release 5.4.  We used eArray to design two 60 bp oligo probes with a 3' bias for each transcript.  We removed duplicate probes and ordered microarrays with the remaining probe set.


title: Tavazoie Vora Escherichia coli Affy tiling 2009

status: Public on Sep 01 2009

city: Princeton

first: yirchung

last: Liu

state: NJ

address: 220 Carl Icahn Laboratory

department: Molecular Biology

institute: Princeton University

description: The oligonucleotides were based on NC_000913.2.

first: Tiffany

last: Vora

first: Alison

middle: K

last: Hottes

first: Saeed

last: Tavazoie

manufacture_protocol: We designed an Affymetrix tiling array for the MG1655 E. coli genome, containing probes that cover the entire genome at a resolution of 4 bp between steps; however, the steps alternate strand coverage, so there is an 8 bp step between probes on the same strand. There are a total of 2.47 million probes on the array, of which 2,300,160 directly enter analysis as E. coli probe pairs. The Affymetrix system pairs each 25-mer perfect match genomic sequence with a corresponding 25-mer that has a mismatch in the 13th position. The mismatch probe is intended as a cross-hybridization control. In addition to the E. coli sequences, 33,996 probe pairs are sequence-specific controls against other genomes, including B. subtilis, lambda phage, and A. thaliana. The tiling array (Ecoli_Tab520346F) is a standard-sized 200 μL-volume microarray with 5 micron features.


title: NimbleGen Porphyromonas gingivalis Streptococcus mutans 080319_BK_mixed_bact_expr

city: Rostock

first: Sylvio

last: Redanz

state: Mecklenburg Vorpommern

address: Schillingallee 70

department: Institute of microbiology, virology and hygiene

institute: hospital university rostock

organism:
Streptococcus mutans UA159
Porphyromonas gingivalis W83

description:
385K-format: 3 replicates of up to 13 probes per gene, 60-mer oligonucleotides, 3510 randomized sequence probes.

The array includes probes for Porphyromonas gingivalis W83, Fusobacterium nucleatum DSMZ 25586, Streptococcus sanguinis SK36, Actinobacillus actinomycetemcomitans HK1651, and Streptococcus mutans UA159. The probes for all of these organisms are represented in the supplemental files 'GPL10873_080319_BK_mixed_bact_expr.ndf' and 'GPL10873_080319_BK_mixed_bact_expr.ngd'. However, the Platform table includes probes only for Porphyromonas gingivalis W83 and Streptococcus mutans.

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


title: Madhani Saccharomyces cerevisiae tiling 16429

status: Public on May 01 2009

city: San Francisco

first: Hiten

last: Madhani

state: CA

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description: Design based on September 13, 2000 genome.

last: Hartley

manufacture_protocol: Custom-synthesized oligos were spotted across 32 print blocks onto poly-l-lysine slides using a custom-built arrayer.


title: Affymetrix GeneChip Universal 70K Tag Array

status: Public on Jan 23 2009

city: Santa Clara

first: Yuker

last: Wang

address: 3380 Central Expressway

institute: Affymetrix

description: This array should be used together with the MIP (Molecular Inversion Probes) technology

manufacture_protocol: Standard Affymetrix photolithography protocol


title: Washington University/Genome Sequencing Center C. elegans 23K

status: Public on Oct 31 2009

city: St. Louis

first: C

middle: Michael

last: Crowder

state: MO

address: 660 S. Euclid Ave Campus Box 8054

department: Anesthesiology

institute: Washington University in St. Louis

manufacturer: Genome Sequencing Center, Washington University in St. Louis


title: NCGR Human RefSeq 7 08

status: Public on Nov 12 2008

city: Santa Fe

first: Stephen

last: Kingsmore

state: NM

address: 2935 Rodeo Park Drive East

institute: National Center for Genome Resources

description:
Refseq Transcript Set.
Sequencing-by-synthesis: Cerebellum samples were sequenced using Illumina Genome Analyzers with modifications for mRNA samples (Lister et al., 2008; Morin et al., 2008)(Mortazavi et al., 2008): Following quality assessment using a Bioanalyzer 2100 (Agilent Inc., Santa Clara, CA; Table 1), poly A+ RNA was isolated from 5 – 10 μg total RNA by two rounds of oligo-dT selection (Invitrogen Inc., Santa Clara, CA).   mRNA was annealed to high concentrations of random hexamers and reverse transcribed.  Following second strand synthesis, end repair, and A-tailing, adapters complementary to sequencing primers were ligated to cDNA fragment ends.  Resultant cDNA libraries were size fractionated on agarose gels, 200 bp fragments excised, and amplified by 15 cycles of polymerase chain reaction.  Following quality assessment using a Bioanalyzer 2100, single-stranded cDNA-adapter fragments were randomly annealed to the surface of a flow cell in a cluster station (Illumina Inc., San Diego, CA) via primers complementary to the adapters and incubated under conditions fostering annealing of the ends of cDNA-adapter fragments to adjacent complementary primers.  Primers with annealed cDNA-adapter fragments were extended with DNA polymerase and unlabelled dNTPs in a solid-phase “bridge amplification”.  Resultant double-stranded products were denatured, yielding 2 single stranded fragments.  The latter steps were repeated for 35 cycles, generating ~40 million clusters of clonal amplicons.  Subsequently, 32 – 36 cycles of sequencing-by-synthesis chemistry were performed in Illumina Genome Analyzer instruments with 4 dNTPs featuring cleavable dyes and reversible terminators.  Following each base extension, 4 images (one for each nucleotide) are taken upon laser excitation.  Incorporation of the next base occurred after removal of the blocked 3’ terminus and fluorescent tag of the previously incorporated nucleotide.
Read Alignment-based gene expression profiling: Reads were aligned to the human genome and RefSeq transcript databases (Pruitt et al., 2005) using the algorithm GMAP (Wu and Watanabe, 2005) and the software system Alpheus (Sugarbaker et al., 2008), with adjustments for short SBS reads (oligomer overlap interval = 3nt, identities > 34/36 or 94%). Only the highest scoring alignment(s) was retained. Reads with a single best alignment or with equally good alignments to alternative transcripts of the same gene were considered uniquely aligned.  Aligned read frequencies (per million aligned reads) were calculated for each sample and gene using Alpheus (Sugarbaker et al., 2008).
Statistical Analysis:  Array hybridization signals and read frequencies were log10 transformed prior to evaluation of inter-sample differences.  Overlayed kernel density estimates, univariate distribution results, Mahalanobis distances, correlation coefficients of pairwise sample comparisons, unsupervised principal component analysis (by Pearson product-moment correlation) and Ward hierarchical clustering of Pearson product-moment correlations of read frequencies were performed with JMP Genomics, Version 3.2 (SAS Institute, Cary, NC). Decomposition of principal components of variance of array signals and read frequencies, FDR corrected analysis of variance (with inclusion of the non-diagnosis components of variance discussed above as fixed effects) and chi squared comparisons of GO annotations were also performed with JMP Genomics, Version 3.2. Patient, sample, and experimental parameters examined to quantify sources of variability in measurements were age, alignment percentage, brain pH, cause of death, cluster station, diagnosis, library creator, number of reads, post-mortem interval, psychotropic medication, race, read length, read quality score, RNA isolation date, RNA integrity number, sample storage duration, sequencing instrument and year sequenced.

middle: F

first: Greg

last: May

first: Ryan

last: Kim

first: Joann

last: Mudge

first: Jenny

last: van Velkinburgh

first: Ray

last: Langley


title: sciTracer Staphylococcus aureus N315 Scienion2004

status: Public on Oct 22 2008

city: Bonn

first: Peter

last: Sass

state: NRW

address: Sigmund-Freud-Straße 25

department: Institute for Microbiology (IMMIP)

institute: University of Bonn

organism: Staphylococcus aureus subsp. aureus N315

manufacture_protocol: The sciTRACER S. aureus contains 2338 PCR products from all 2593 ORFs in the annotated genome (Ref ID: NC_002745), arranged in unique and second sequences: since the ORFs sizes range from 51 bp (e.g.: 13700427) up to 2kb (e.g.: 13701232), additional second PCR products have been developed. As unique sequences, 2333 PCR products and as second sequences, 333 PCR products are immobilized from which 5 are not in the group of unique gene fragments. All unique products cover 90 % of all ORFs. All PCR fragments are purified, concentration normalized, dissolved in spotting solution and spotted robotically onto modified glass slides. They are represented twice (duplicates) on each array. Controls are usually spotted in the last row of each subarray block forming the control area and comprising controls for spiking and endogenous controls. The SCIENION control set consists of positive, negative and multifunctional elements. All references/controls are spotted in a special pattern enabling functional monitoring of the entire experimental process. The glass slides are processed and ready for hybridization reaction. For easy correlation of gene names to their spot position on the slide the “Spot Identification Pattern-Table” (gal-file) is available. Information source: The genes represented on sciTRACER S. aureus are selected from order requests derived from the University of Würzburg, Infectious Biology Group (Head: Prof. Dr. Jörg Hacker) at the Institut für Molekulare Infektionsbiologie. Generation of sequences: 1. The PCR fragments derive mostly from regions at the last 500 nt from the 3’ end and have an average size of 355 bps. In case that the predicted ORF displayed a size unsuitable for appropriate amplicon generation, the primer design was extended towards flanking regions in order to cover the desired ORF. 2. All selected sequences are designed to provide the highest specificity and display minimal similarity to other mRNA and DNA sequences within the specified host genome. 3. In order to obtain strong and comparable sensitivity and signal specificity, all fragments are designed to feature similar lengths, comparable G/C-contents and optimized melting temperatures. 4. Based on algorithmic and manual revisions of the predicted sequences, the designed PCR fragments are well suited for the generation of highly reliable gene expression data. Quality controls: All sequences are validated in silico and approved by size control and sequence verification. The spot morphology is checked by automated optical control and hybridization of labeled RNA or SyBRGreenI® assay. Functional tests are performed by complex hybridization with labeled reference RNA for each batch. Source Organism: Staphylococcus aureus N 315 (NC_002745, contig BA000018) Microarray mapping: Each SCIENION microarray consists of two regions: the hybridizing region and the identifier region. The identifier region carries a sticker showing the name of the product, the date of production, batch number and the ID of the array. This region also serves to grasp the slide. The DNA microarray is in the center of the hybridizing region. Spot distance and feature size: The spot distance (center to center) is 375 µm. The array size is approximately 54 mm x 18 mm (height x broadness). Each array consists of 48 blocks and each block comprises 12 x 11 spots. These blocks are separated by a blank line and display a defined order. to Product description: The sciTRACER S. aureus contains 2338 PCR products from all 2593 ORFs in the annotated genome (Ref ID: NC_002745), arranged in unique and second sequences: since the ORFs sizes range from 51 bp (e.g.: 13700427) up to 2kb (e.g.: 13701232), additional second PCR products have been developed. As unique sequences, 2333 PCR products and as second sequences, 333 PCR products are immobilized from which 5 are not in the group of unique gene fragments. All unique products cover 90 % of all ORFs. All PCR fragments are purified, concentration normalized, dissolved in spotting solution and spotted robotically onto modified glass slides. They are represented twice (duplicates) on each array. Controls are usually spotted in the last row of each subarray block forming the control area and comprising controls for spiking and endogenous controls. The SCIENION control set consists of positive, negative and multifunctional elements. All references/controls are spotted in a special pattern enabling functional monitoring of the entire experimental process. The glass slides are processed and ready for hybridization reaction. For easy correlation of gene names to their spot position on the slide the “Spot Identification Pattern-Table” (gal-file) is available. Information source: The genes represented on sciTRACER S. aureus are selected from order requests derived from the University of Würzburg, Infectious Biology Group (Head: Prof. Dr. Jörg Hacker) at the Institut für Molekulare Infektionsbiologie. Generation of sequences: 1. The PCR fragments derive mostly from regions at the last 500 nt from the 3’ end and have an average size of 355 bps. In case that the predicted ORF displayed a size unsuitable for appropriate amplicon generation, the primer design was extended towards flanking regions in order to cover the desired ORF. 2. All selected sequences are designed to provide the highest specificity and display minimal similarity to other mRNA and DNA sequences within the specified host genome. 3. In order to obtain strong and comparable sensitivity and signal specificity, all fragments are designed to feature similar lengths, comparable G/C-contents and optimized melting temperatures. 4. Based on algorithmic and manual revisions of the predicted sequences, the designed PCR fragments are well suited for the generation of highly reliable gene expression data. Quality controls: All sequences are validated in silico and approved by size control and sequence verification. The spot morphology is checked by automated optical control and hybridization of labeled RNA or SyBRGreenI® assay. Functional tests are performed by complex hybridization with labeled reference RNA for each batch. Source Organism: Staphylococcus aureus N 315 (NC_002745, contig BA000018) Microarray mapping: Each SCIENION microarray consists of two regions: the hybridizing region and the identifier region. The identifier region carries a sticker showing the name of the product, the date of production, batch number and the ID of the array. This region also serves to grasp the slide. The DNA microarray is in the center of the hybridizing region. Spot distance and feature size: The spot distance (center to center) is 375 µm. The array size is approximately 54 mm x 18 mm (height x broadness). Each array consists of 48 blocks and each block comprises 12 x 11 spots. These blocks are separated by a blank line and display a defined order.


title: UNC Celegans 2.1mil HX1 (C elegans ChIP HX1)

status: Public on Nov 21 2008

city: Chapel Hill

first: Christina

last: Whittle

state: NC

address: 406 Fordham Hall, CB#3280

institute: University of North Carolina-Chapel Hill

description:
C. elegans whole genome tiling array at 50bp resolution, 2.1 million features per array
Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR,Cerrina F. Maskless fabrication of light-directed oligonuc
leotide microarrays using a digital micromirror array. Nat Biotechnol. 1999 Oct;17(10):974-8. PMID: 10504697

first: Jason

last: Lieb

first: Leo

last: Iniguez


title: NMSU OConnell Bean DroughtArray 1700 V1.0

status: Public on Feb 01 2008

city: Las Cruces

first: Mary

middle: Anne

last: O'Connell

address: MSC 3Q, PO Box 30003

department: Plant and Environmental Sciences

institute: New Mexico State University

organism:
Phaseolus vulgaris
Phaseolus acutifolius

first: Laura

last: Rodriguez-Uribe

first: Sandra

last: Micheletto

first: Ricardo

last: Hernandez

first: Richard

last: Richins

first: Jeanne

last: Curry

manufacture_protocol:
cDNAs were amplified from P. acutifolius root cDNA library of drought stressed plants, from P. vulgaris root cDNA library of drought stressed plants, and from P. acutifolius leaf cDNA library.  M13 forward/reverse primers used.  cDNAs precipitated, resuspended in 1X ArrayIt Micro Spotting Solution, and spotted onto Corning GAPS slides using a GeneMachines OMNI/GRID spotter.  Slides were uv crosslinked and baked.

SUBMITTER_CITATION: Micheletto S, Rodriguez-Uribe L, Hernandez R, Richins RD, Curry J, O?Connell MA. (2007) Comparative Transcript Profiling in Roots of Phaseolus acutifolius and P. vulgaris Under Water Deficit Stress. Plant Sci 173:510-520. doi:10.1016/j.plantsci.2007.08.003


title: Custom Illumina Sentrix Human Cancer Genes

status: Public on Apr 10 2008

city: Rockville

first: Andrew

middle: W

last: Bergen

state: MD

address: 6120 Executive Blvd

department: Cancer Epidemiology & Genetics

institute: NCI/NIH

organism: Homo sapiens

description: This custom Illumina Sentrix® Array Matrix-96 microarray contains 50mer probes targeting 697 genes relevant to cancer research. Candidate gene content for the custom array was developed by a voting scheme based on other "cancer gene" lists available on the World Wide Web on November 6, 2003.  Eleven lists were assembled from a variety of academic, industrial and government sources and a list of all genes present on all lists was assembled with the genes ranked according to frequency of occurrence.  Any gene appearing ≥ four lists was included in the array design. We designed the custom microarray using transcript sequences from NCBI RefSeq build 34.3. Sequences overlapping SNPs as defined in dbSNP build 121 and SNP500Cancer were avoided.

first: Andrea

last: Baccarelli

first: Timothy

last: McDaniel

first: Kenneth

last: Kuhn

first: Ruth

last: Pfeiffer

first: Jerry

last: Kakol

first: Patrick

last: Bender

first: Kevin

last: Jacobs

first: Bernice

last: Packer

last: Chanock

first: Meredith

last: Yeager

manufacture_protocol: Sentrix Array


title: NCSU_chicken_JS1 (96 oligos)

status: Public on Jan 31 2008

city: Raleigh

first: Jean

middle: Eduardo

last: de Oliveira

address: 2711 Founders Dr

department: Poultry Science

institute: North Carolina State University

organism: Gallus gallus

middle: E

first: Shelly

last: Druyan

first: Chris

last: Ashwell

manufacture_protocol:
1.70-mer oligos synthetized by Operon Biothechnologies Inc. Oligos were resuspended in Tris buffer; 250 µM of each oligo was added to a well of a 384-well plate and dried.
2. Oligos were resuspended in Universal Spotting Solution (Corning, Inc)
3. Seal plates with Corning seals.
4. Shake plate at mid speed on plate vortexer for 1 minute.
5. Remove seal and place plate on appropriate place on VersArray ChipWriter array printer.
6. Place UltraGaps Amino-Silane Coated Slides on appropriate place on array printer
7. Run pin clean-up steps 5 times before start printing (using 1 pin)
8. Start printing run
9. Turn-off printer once run is completed
10. Take plate from printer, seal it with Corning seal and store it at -20C
11. Let slides dry on printer for 24h
12. Crosslink slides on UV over set to 6000 x 100 µJ/cm2, store slides on secator


title: Chlamydomonas reinhardtii Version_2 Microarray

status: Public on Oct 28 2008

city: Bielefeld

first: Anh Vu

last: Nguyen

address: G2-154, CEBITEC, Universitaetsstr. 27

department: Cell and Molecular Biology

institute: Bielefeld University

organism: Chlamydomonas reinhardtii

first: Anh

middle: V

first: Jen

last: Rupprecht

first: Skye

last: Thomas-Hall

first: Ben

last: Hankamer

first: Olaf

last: Kruse

first: Peer

last: Schenk

manufacture_protocol:
Reference
Eberhard et al. (2002) Generation of an oligonucleotide array for analysis of gene expression in Chlamydomonas reinhardtii. Curr Genet (2006) 49: 106–124


title: BCM/Shaulsky Dictyostelium accent 16K v1.0

status: Public on Jun 18 2007

city: Houston

first: Nancy

last: Van Driessche

state: TX

address: One Baylor Plaza

institute: Baylor college of medicine

organism: Dictyostelium discoideum

description: •	General array design:  Glass slides were coated with 3-Glycidoxypropyltrimethoxysilane (Aldrich).  Target DNA was printed on the activated glass slides on 200 µm centers with a GeneMachines OmniGrid Accent robot with Chipmaker II pins (Tele-chem Intl.).  The full ‘Accent” array has 22x24 targets (total 8,488 targets) targets as described in supplemental table 5 (see supplemental file ‘6_arrayMap2(table5).xls’).

manufacture_protocol:
Array Design:
•	The source of the reporter molecules: 5,655 cDNA clones were from the Dictyostelium cDNA project; 987 extra cDNA clones were selected from a low redundancy screen of a lambda library and a plasmid library of late developmental stage, vegetative and early developmental stage of AX4 cells, respectively; 647 genomic DNA clones were selected as long open reading frames that matched published protein sequences; and 96 clones were from miscellaneous sources.  Sequences were compared to public databases and annotated 4.  The degree of redundancy is less than 15%.  The control targets that were made from the Dictyostelium ribosomal 17S RNA gene, histone H1, actin8 and mhcK as well some yeast genes and ‘no DNA’ controls.
•	The method of reporter preparation:  DNA targets were amplified from plasmids by PCR with common oligonucleotides and their size verified by gel electrophoresis.  PCR products were purified by precipitation with 50% isopropyl alcohol 0.3 M sodium acetate pH5.2, washed once with 70% ethanol, dissolved in water and adjusted to 800 mM sodium chloride 200 mM sodium phosphate pH10.5.
•	The spotting protocols used, including the array substrate, the spotting buffer, and any post-printing processing, including cross-linking:  Glass slides (Gold Seal Products, VWR) were washed by sonication in acetone for 10 minutes, rinsed twice in distilled water, immersed in 1 N NaOH for 10 minutes, washed in distilled water, and immersed for 3 minutes in 3% (v/v) 3-Glycidoxypropyltrimethoxysilane (Aldrich) made in 95% ethanol/acetic acid pH 5.0.  The slides were washed in 100% ethanol, dried with nitrogen gas and baked for at least 2 hrs at 100°C.  Target DNA in 800 mM sodium chloride 200 mM sodium phosphate pH10.5 solution was printed on the activated glass slides. Arrays were stored desiccated in the dark.
•	Any additional treatment performed prior to hybridization: The arrays were treated with hot water for 1 min at 100°C for target denaturation prior to hybridization.


title: NimbleGen MM8 Mouse Promoter plus CpG Island 374K Tiling Array

status: Public on Jul 18 2008

city: Indianapolis

first: GUOHUA

last: WANG

state: IN

address: 410 West 10th Street, Suite 5000

department: Medicine

institute: Indiana University Center for Computational Biology and Bioinformatics

organism: Mus musculus

description:
Source: UCSC
Build: MM8
Probe Length: 50-75mer
Promoter Upstream Tiling (bp): 1300
Promoter Downstream Tiling (bp): 500

first: Guohua

last: Wang

manufacture_protocol: See www.nimblegen.com


title: sciTracer Staphylococcus aureus N315 Scienion2005

first: Peter

last: Sass

manufacture_protocol:
Product description:
The sciTRACER S. aureus contains 2338 PCR products from all 2593 ORFs in the annotated genome (Ref ID: NC_002745), arranged in unique and second sequences: since the ORFs sizes range from 51 bp (e.g.: 13700427) up to 2kb (e.g.: 13701232), additional second PCR products have been developed. As unique sequences, 2333 PCR products and as second sequences, 333 PCR products are immobilized from which 5 are not in the group of unique gene fragments. All unique products cover 90 % of all ORFs. All PCR fragments are purified, concentration normalized, dissolved in spotting solution and spotted robotically onto modified glass slides. They are represented twice (duplicates) on each array. Controls are usually spotted in the last row of each subarray block forming the control area and comprising controls for spiking and endogenous controls.
The SCIENION control set consists of positive, negative and multifunctional elements. All references/controls are spotted in a special pattern enabling functional monitoring of the entire experimental process. The glass slides are processed and ready for hybridization reaction. For easy correlation of gene names to their spot position on the slide the “Spot Identification Pattern-Table” (gal-file) is available.
Information source:
The genes represented on sciTRACER S. aureus are selected from order requests derived from the University of Würzburg, Infectious Biology Group (Head: Prof. Dr. Jörg Hacker) at the Institut für Molekulare Infektionsbiologie.
Generation of sequences:
1. The PCR fragments derive mostly from regions at the last 500 nt from the 3’ end and have an average size of 355 bps. In case that the predicted ORF displayed a size unsuitable for appropriate amplicon generation, the primer design was extended towards flanking regions in order to cover the desired ORF.
2. All selected sequences are designed to provide the highest specificity and display minimal similarity to other mRNA and DNA sequences within the specified host genome.
3. In order to obtain strong and comparable sensitivity and signal specificity, all fragments are designed to feature similar lengths, comparable G/C-contents and optimized melting temperatures.
4. Based on algorithmic and manual revisions of the predicted sequences, the designed PCR fragments are well suited for the generation of highly reliable gene expression data.
Quality controls:
All sequences are validated in silico and approved by size control and sequence verification. The spot morphology is checked by automated optical control and hybridization of labeled RNA or SyBRGreenI® assay. Functional tests are performed by complex hybridization with labeled reference RNA for each batch.
Source Organism:
Staphylococcus aureus N 315 (NC_002745, contig BA000018)
Microarray mapping:
Each SCIENION microarray consists of two regions: the hybridizing region and the identifier region. The identifier region carries a sticker showing the name of the product, the date of production, batch number and the ID of the array. This region also serves to grasp the slide. The DNA microarray is in the center of the hybridizing region. Spot distance and feature size: The spot distance (center to center) is 375 µm. The array size is approximately 54 mm x 18 mm (height x broadness). Each array consists of 48 blocks and each block comprises 12 x 11 spots. These blocks are separated by a blank line and display a defined order.


title: Agilent-014791 Human CpG Island ChIP-on-Chip Microarray 244K (G4492A) (Probe Name version)

status: Public on Dec 07 2009

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Human CpG Island Chip-on-Chip Set 244K

The ID column represents the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL4126.

relation:
Alternative to: GPL4126
Alternative to: GPL13349

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


title: Custom Vibrio fischeri GeneChip Array (Affymetrix)

status: Public on Jun 01 2007

city: Vancouver

first: L. Caetano

middle: M.

last: Antunes

department: Michael Smith Laboratories

institute: The University of British Columbia

organism: Aliivibrio fischeri

first: Luis

first: Amy

last: Schaefer

first: Everett

last: Greenberg

manufacture_protocol: Custom GeneChips (11 uM feature size) representing >99% of the annotated open reading frames in the V. fischeri ES114 genome, as well as 125 intergenic regions greater than 150 bp, were constructed by Affymetrix Inc. (Santa Clara, CA). GeneChips were designed as described by the manufacturer in their GeneChip Custom Express Array Design Guide (www.affymetrix.com) except that, due to the low GC content of V. fischeri DNA, 16 probe pair sets (25-bp oligonucleotide probe length) were used per gene sequence. Poly-A control sequences of dap, lys, phe, and trp from Bacillus subtilis were also included.


title: NCSU_chicken_JS2 (312 oligos)

first: Jean

last: de Oliveira

description:
Due to array printer configuration, 320 wells were spoted but only 312 actually contained oligo material. The remaining 8 wells had only spoting solution. These wells were annotated as NA and were excluded from statistical analysis. Each well was spotted 3 times (side-by-side) in the same grid, and
grids were replicated 4 times on each slide; so each gene was spotted a total of 12 times per array (3840). According to experimental design and to increase statistical power, the 3 side-by side spots were averaged so reducing the total number of data rows from 3840 to 1280.

first: Shelly

manufacture_protocol:
1.A 384 well plate with the 70-mer oligos was synthetized by Operon Biothechnologies Inc.
2. Oligos were resuspended in Universal Spotting Solution (Corning, Inc)
3. Seal plates with Corning seals.
4. Shake plate at mid speed on plate vortexer for 1 minute.
5. Remove seal and place plate on appropriate place on VersArray ChipWriter array printer.
6. Place UltraGaps Amino-Silane Coated Slides on appropriate place on array printer
7. Run pin clean-up steps 5 times before start printing (using 4 pins)
8. Start printing run
9. Turn-off printer once run is completed
10. Take plate from printer, seal it with Corning seal and store it at -20C
11. Let slides dry on printer for 24h
12. Crosslink slides on UV over set to 6000 x 100 µJ/cm2, store slides on secator


title: UCSF Cancer Center HumArray3.2

status: Public on Jan 06 2009

first: Antoine

last: Snijders

address: 2340 Sutter Street

department: Cancer Research Institute

institute: University of California San Francisco

description: Human BAC array. Two spot-to-clone data files linked below as supplementary files.

manufacture_protocol: For a detailed description on how the arrays were made please refer to: Snijders et al. Nat Genet. 2001 Nov;29(3):263-4.


title: Stanford Caulobacter crescentus printing Y

status: Public on Dec 08 2005

first: Alison

last: Hottes

address: 220 Carl Icahn Lab Washington Road

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

organism: Caulobacter vibrioides

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

first: Harley

middle: H

last: McAdams

first: Maliwan

last: Meewan

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

Arrays use the same oligos as those in Platform GPL1076.


title: Stanford Caulobacter crescentus printing Z

manufacture_protocol: The microarrays for this study were printed using the GeneMachines Omnigrid Microarrayer with Telechem 16-pin ArrayIt Stealth MicroSpotting Pins.  Oligo sequences were chosen to satisfy the following criteria:  be a unique sequence in the genome, be located near the 5’ end of the gene, approximately 100 base pairs downstream of the predicted start codon, have similar melting temperatures, and have minimal predicted secondary structure formation.  The oligos were modified at the 5’ end with a six-carbon spacer followed by a primary amino group and diluted to 20µM for printing. Aldehydesilane coated slides (Schott Nexterion-slide AL)  and QMT Spotting Solution I (Quantifoil) were used.  Arrays use the same oligos as those in Platform GPL1076.


title: GSF/IEG mouse 21K array (+RZPD)

status: Public on May 01 2007

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description: GSF/IEG mouse 21K (additionally RZPD)

manufacturer: IEG, Gene regulation and Expression Profiling Group

first: Marion

last: Horsch

first: Johannes

last: Beckers

manufacture_protocol: PCR amplification of cDNA clones, purification of PCR product using 96-well filter plates, 3x SSC as spotting buffer. spotting robot: Microgrid II


title: UCT Brombacher lab Mus MEEBO 40K version1

status: Public on Sep 12 2007

city: Cape Town

first: Anita

last: Schwegmann

state: Western Cape

address: Institute for Infectious Diseases and Molecular Medicine, UCT medical School, Anzio Rd, Observatory

department: Division of Infectious Immunology

country: South Africa

institute: Institute for Infectious Diseases and Molecular Medicine, University of Cape Town

description:
The MEEBO (Mouse Exonic Evidence Based Oligonucleotide) Set contains a collection of oligo probes, largely derived from constitutively expressed exons, allowing interrogation of almost 25,000 mouse genes. The set was designed to enable study of mouse transcription patterns and, as
broadly as possible, alternative splicing. An exon-centric design was selected to allow the differentiation of constitutively expressed versus alternatively expressed exons. This design also supports comparative genome hybridization (CGH) analysis. In addition to the exon-centric probes, the set contains an extensive assortment of controls that facilitate accurate evaluation of expression results.
The MEEBO Set contains 38,467 70mer oligonucleotide probes with an amino modification on the 5’ end. Probes are provided at a final yield of 200pmol each, and delivered in 101 384-well microarray print plates (Genetix model X7020). Probes are Tm normalized, and are designed to minimize cross-hybridization and secondary structure.

manufacturer: Capar Microarray Facility, University of Cape Town, South Africa

first: Reto

last: Guler

first: Antony

middle: J

last: Cutler

first: Berenice

last: Arendse

first: William

last: Horsnell

first: Alexandra

last: Flemming

first: Andreas

last: Kottmann

first: Gregory

last: Ryan

first: Winston

last: Hide

first: Michael

last: Leitges

first: Cathal

last: Seoighe

first: Frank

last: Brombacher

manufacture_protocol:
Platform type: spot printed
Slide surface: Gamma Amino Propyl Silane (GAPS)
Slide dimensions: 25 x 75mm
Spot diameter: 100um from 10K pin set
Spot attachment: ionic during to printing then covalent attachment via UV-crosslinking and baking
Printer: MicroGridII, BioRobotics
Software: TAS, BioRobotics
Printing solution: 50% DMSO
Drying after printing: 12 hour minimum, room temp.
UV crosslinking: 120mJ
Baking: 2hour 80°C


title: UBEC Array3

status: Public on Jan 07 2006

city: Birmingham

first: Chrystala

last: Constantinidou

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

organism: Escherichia coli

manufacturer: UBEC, School of Biosciences, University of Birmingham, Birmingham, UK

first: Jon

middle: L

last: Hobman

first: Charles

last: Penn

first: Mala

last: Patel

middle: C

last: Jones

manufacture_protocol: The 70-mer oligonucleotide array was constructed, containing 6112 oligonucleotides that sampled chromosomal genes identified in the genome sequences of E. coli strains K-12 MG1655, O157:H7 VT2 Sakai, and O157:H7 EDL933 and plasmid genes from the two genome-sequenced O157:H7 strains (the Operon Array Ready E. coli Oligonucleotide™ set 1.0, Qiagen- Operon, Hilden, Germany). 12 positive and 12 negative control oligonucleotides were also included. The oligonucleotides were resuspended in Corning Pronto! buffer and printed on to Corning UltraGAPS™ slides (Corning B.V Life Sciences, Schiphol-Rijk, Netherlands ) using a Biorobotics Microgrid TAS array printer. Amersham Lucidea  Universal Scorecard™ controls (GE Healthcare, Little Chalfont, UK) were printed in each subarray. Slides were desiccated under vacuum for 48 hours and then U.V. cross-linked with a dose of 600mJ using a Stratalinker (Stratagene limited, U.K.). Slides were stored under desiccating conditions in the dark until use


title: ABI Rat Genome Survey Microarray

status: Public on Jan 13 2006

first: chunlin

last: xiao

address: 45 West Gude Drive

institute: Applied Biosystem

organism: Rattus norvegicus

description: See manufacturer's web site

manufacture_protocol: See manufacturer's web site


title: CDMC_Drosophila_12k1

status: Public on Oct 01 2004

city: Mississauga

first: Zak

last: Razak

state: ON

address: 3359 Mississauga Road

department: Zoology Department

country: Canada

institute: University of Toronto

description:
The 12k1 platform is a primarily cDNA-based glass microarray. The array features 11,018 Berkeley Drosophila Genome Project cDNAs, 297 NIH Testis cDNAs (Andrews et al., 2000) and 432 gene sequences that were amplified from genomic DNA.  Approximately 10,500 unique genes are represented by the above, corresponding to roughly 78% of the predicted genes in Drosophila melanogaster (FlyBase annotation release 3.2).  This array is produced by the Canadian Drosophila Microarray Centre located at the University of Toronto.  It is available for distribution to academic labs.

The 12k1 arrays are printed on CMT-UltraGAPS substrates (Corning Inc, Acton, MA) using a SpotArray 72 microarrayer (Perkin Elmer, Boston, MA).  There are 26880 spots and 768 blanks on each array in a 12 row by 4 column arrangement of blocks.  Each block contains 560 spots and 16 blanks arrayed in a 24 row by 24 column grid.  The blanks occupy positions 9 through 24 of the 24th row.  The blocks are spaced at 4500 micron intervals and the spot-to-spot distance is 180 microns.  The nominal spot diameter is 125 microns.  Printing conditions and post-print treatments are as described earlier (Neal et al., 2003).
Keywords = CDMC
Keywords = Drosophila
Keywords = microarray
Keywords = cDNA

first: Jianming

last: Pei

first: Huafen

last: Li

first: Scott

last: Neal

first: J

middle: T

last: Westwood


title: RT^2 Profiler PCR Array Mouse Angiogenesis (PAMM-024A)

status: Public on Apr 01 2009

city: Beijing

first: Huan

last: Meng

address: Mailbox 918, Yuquan Road 19

country: China

institute: Lab of Bioeffects of Nanosized Materials, Institute of High Energy Physics

description: We synthesize a novel nanoparticle with functional surface coating, which inhibits tumor growth without detectable cytotoxicities by suppress angiogenesis in the tumor mass. Quantitative counting RTPCR-array analysis was used to evalute the pro-angiogenic factor(s) on mRNA level.

first: Gengmei

last: Xing

first: Yuliang

last: Zhao

first: Chengcheng

last: Zhang

first: Zhen

last: Chen

first: Ning

first: Hui

last: Yuan

first: Feng

first: Chunying

first: Hao

last: Lei

first: Xuxia

last: Wang

first: Xingjie

last: Liang