title: Agilent-018561 Hunter C. elegans Oligo Microarray 15K (v1)

status: Public on Dec 31 2011

city: Cambridge

first: Daniel

last: Schott

state: MA

address: 16 Divinity Avenue

department: Molecular and Cellular Biology

country: USA

institute: Harvard University

organism: Caenorhabditis elegans

technology: in situ oligonucleotide

distribution: custom-commercial

first: Itai

last: Yanai

manufacture_protocol: Agilent SurePrint. We used a custom microarray (Agilent) bearing 60-mer oligonucleotide spots corresponding to 15,208 C. elegans genes.  Since this is far fewer than the number of recognized genes in C. elegans, we used an arbitrary procedure to select genes for inclusion on the array.  First, we limited the genes to predicted protein-coding genes, and then we prioritized genes with 1:1 best reciprocal sequence similarity scores to annotated C. briggsae genes (Remm et al., 2001).  We selected oligonucleotide sequences corresponding to the 3’-most predicted exon that allows design of a probe that minimizes cross-hybridization with other genes.  Gene positions on the array were randomized to minimize bias due to hybridization artifacts.


title: NimbleGen Eucalyptus 386K array v.1.0.

city: Porto Alegre

first: Giancarlo

last: Pasquali

state: RS

address: Av. Bento Gonçalves, 9500 - Pr. 43.431 - Lab. 212

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

organism: Eucalyptus spp. mixed library

description: NimbleGen design name 2006-02-21_Eucalyptus_50mer, NimbleGen design ID 3112, NimbleGen Order ID 3369. Standard expression design for 21,442 ESTs from Eucalyptus spp. with nine 50-mer probes per EST.  Each probe replicated 2 times on chip (2 blocks per chip).

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


title: Agilent custom Lactobacillus brevis Microarray (complete version)

city: College Station

first: James

last: Winkler

state: TX

address: 3122 TAMU

institute: Texas A&M University

organism: Levilactobacillus brevis

description:
This is a custom 60-mer cDNA microarray designed to interrogate the transcriptional profile of Lactobacillus brevis.
Complete version of the array's replicate features. GPL10674 represents condensed array.

middle: D

first: Katy

middle: C

last: Kao

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


title: Vibrio parahaemolyticus RIMD 2210633 4x72K gene expression arrays

city: shanghai

first: Yuanxing

last: Zhang

address: 130 meilong road

department: School of Biotechnology

country: China

institute: East China University Of Science And Technology

organism: Vibrio parahaemolyticus RIMD 2210633

description: The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.

manufacture_protocol: NimbleGen design name TI223926 60mer, NimbleGen catalog number A4348-00-01.  A 1:2 expression design for 4,832 genes from Vibrio parahaemolyticus RIMD 2210633 with nighteen 60-mer probe pairs (PM/MM) per gene.  Each probe is replicated 4 times.  The design includes random GC and other control probes.


title: Viro5

city: San Francisco

first: Joseph

middle: L

last: DeRisi

state: CA

address: Byers Hall, Rm s403c, 1700 4th St.

department: Department of Biochemistry and Biophysics

institute: University of California San Francisco

organism: Viruses

technology: spotted oligonucleotide

description:
This platform includes ~17,500 oligonucleotides derived from ~2000 viral species.  These oligonucleotides include all of those from the Viro4 platform (GPL6862) as well as ~1700 additional oligonucleoties derived from virus sequences added to databases since the creation of Viro4.  This platform includes control oligonucleotides for human endogenous retroviruses, human genes, yeast intergenic sequences, and human papilloma virus sequences present in HeLa cells.
Keywords = viruses, virus detection, virus discovery

distribution: non-commercial

first: Don

last: Ganem

first: Sharon

last: Chao Wootton

first: Sarah

middle: T

last: Arron

first: Peter

last: Skewes-Cox

first: Alexander

last: Greninger

first: Charles

last: Runckel

first: Nathan

last: Yozwiak

first: Michelle

last: Dimon

middle: Y

last: Chiu

first: Amy

last: Kistler

first: Mark

last: Stenglein

manufacture_protocol: Spotted 70-mer nucleotides on glass


title: Catabolic microarray Version 2.1

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

organism: unidentified microorganism

first: Ramiro

last: Vilchez-Vargas

first: Howard

last: Junca

first: Dietmar

last: Pieper

manufacture_protocol:
1. Oligos are arrayed in Greiner 384-well flat-bottom plates. Each well contains 600 pmol of 50-mer oligo.
2. Resuspend oligos in water to 25 uM with 50mM sodium phosphate buffer pH 8


title: 090410_A_nidulans_FGSC_A4_expr_X4

status: Public on Jan 16 2012

city: Carlisle

first: Dana

middle: Jasmine

last: Wohlbach

state: PA

department: Biology

institute: Dickinson College

organism: Aspergillus nidulans FGSC A4

description: NimbleGen design name: 090410_A_nidulans_FGSC_A4_expr_X4; NimbleGen design ID: 9806.  A custom-designed four-plex genome array from Aspergillus nidulans FGSC A4.  The design includes random GC and other control probes.


title: USDA-ARS PSMRU Arcobacter butzleri V1.1

city: Albany

first: Craig

last: Parker

address: 800 Buchanan St

department: PSM

institute: USDA ARS

organism: Aliarcobacter butzleri RM4018

technology: spotted DNA/cDNA

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

manufacture_protocol:
PCR products of ORF's from Arcobacter butzleri str. RM4018  spotted on Corning barcoded UltraGAPS slides using a GeneMachine Accent printer with ChipMaker pins.
PCR products resuspended to an average concentration of 0.1-0.2 µg µl-1 in 20 µl of 50% dimethyl sulfoxide (DMSO) containing 0.3× Saline-Sodium Citrate (SSC).
Spotted on Corning barcoded UltraGAPS slides using a GeneMachine Accent printer with ChipMaker pins.
The DNA was UV cross-linked to the microarray slides with a Stratalinker at 300 mJ.


title: Agilent-015868 Mouse LMT_miRNA_v2 microarray_NCI-Frederick (Sanger miR9.0 database)

city: Frederick

first: Suhwan

last: Chang

state: MD

address: PO Box B, NCI-Frederick

institute: National Cancer Institute

organism: Mus musculus

description: Manufactured by Agilent Technologies as custom-synthesized 8 x 15 K microarrays.

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


title: Agilent-019568 Campylobacter 11168 expression array_1_Of_1

city: Norwich

first: Bruce

middle: MacKenzie

last: Pearson

state: Norfolk

address: Colney Lane

department: Food Safety

country: United Kingdom

institute: Institute of Food Research

organism: Campylobacter

description:
60mer 11168 ORF based
Arrays of this design have barcodes that begin with 16019568 or 2519568.
Orientation:
The ID column represents the Axon Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).


title: LC Human-Mouse-Rat miRNA Array

city: Chicago

first: Dauren

last: Biyashev

address: 300 E.Superior St.

institute: Northwestern University

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: Arrays are made based on µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists 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 are made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: UKM Lates calcarifer liver and spleen cDNA array

status: Public on Aug 07 2012

city: Bangi

first: Abdul Munir

last: Abdul Murad

state: Selangor

address: Jalan Universiti

department: Faculty of Science & Technology

country: Malaysia

institute: Universiti Kebangsaan Malaysia

organism: Lates calcarifer

manufacture_protocol: Using the GeneTac™G3 (Genomic Solutions™, USA) arrayer, we fabricated the in-house Asian seabass (Lates calacrifer) cDNA microarray slide, comprising 1920 probes sourced from in-house Lates calcarifer spleen and liver cDNA libraries. Putative functions encoded by these probes include immunity, stress response, metabolism, transport, transcription and translation. Negative controls, such as oligonucleotide (A)50 and several Saccharomyces cerevisiae and Escherichia coli genes, as well as positive controls, such as a serial dilution of L. calcarifer genomic DNA and pooled cDNA, were also included. PCR amplification of the clones was carried out using a pair of M13 universal primers (Forward 5’-GTAAAACGACGGCCAG-3’, Reverse 5’-GTCATAGCTGTTTCCTG-3’) under the following conditions: initial denaturation at 95oC for 2 min, followed by 30 cycles of 95oC for 30 sec, 52 oC for 30 sec and 72 oC for 2 min, and a final extension step at 72 oC for 10 min. All the amplicons were checked with agarose gel electrophoresis and subsequently purified using Montage® PCRµ96 Plate (MilliPore, USA). The amplicon was resuspended in DMSO with the final concentration of probes ranging from 150-250 μg/mL. The probes were spotted twice onto aminosilane-coated glass slides (Corning, USA). The array consists of spots arranged in 4 x 8 grids. There are 32 grids in 4 columns (meta-columns) and 8 rows (meta-rows). Each of the grids contained 11 x 11 spots generating 121 spots per grid. Each fabricated slide contained a total of 3872 spots including 32 GeneTac™G3 arrayer prefix empty spots. Each spotted slide was left overnight in the arrayer. Subsequently, the slide was crosslinked at 300 mJ of ultraviolet (UV) irradiation with HoeferTM UVC 500 Crosslinker (Amersham Biosciences, UK) and stored in humidity and light-controlled conditions until use. Quality of the slide produced was assessed by a hybridization check with a random nanomer from the SpotCheckTM  Slide QC kit (Genetix, USA).


title: MYcroarray CAT-3x15K-Streptococcus_pneumoniae_R6

status: Public on Sep 23 2012

city: Goyang

first: Jae-Jun

last: Song

state: Gyeonggi

department: Department of Otorhinolaryngology-Head & Neck Surgery

country: South Korea

institute: Dongguk University Medical center

organism: Streptococcus pneumoniae R6

manufacture_protocol: See manufacturer's web site  (http://www.mycroarray.com/technology/synthesis.html)


title: OSU_CCC v4.0 [full array layout]

city: Hong Kong

first: Hao

last: Sun

address: 306G LiHS biomedical Sciences Building

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

organism:
Homo sapiens
Mus musculus

manufacturer: Microarray Shared Resource, Comprehensive Cancer Center, The Ohio State University (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 (http://www.genomicsolutions.com ) that is fitted with a printhead and 16 SMP3 print tips from Telechem (http://www.arrayit.com). 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: FCCC Mouse 32k-OA Oligo Array Operon v.3.0.1

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

institute: Universidade de São Paulo

manufacturer: Fox Chase Cancer center Microarray facility

first: Yue-Sheng

last: Li

manufacture_protocol: The entire Operon mouse oligo set V3.0.1 was printed in 50% DMSO onto 2 Corning Ultra GAPS slides using OmniGrid 100 arrayer under 45% humidity. Each slide has about 32,000 oligonucleotides and named as Mouse 32k-OA and Mouse 32k-OB, respectively. The printed slides were UV crosslinked at 500 mJ and then blocked with succinic anhydride.


title: Recombination Detection Microarray Release I (R1.1Tiled)

status: Public on Oct 17 2012

city: St. Louis

first: Adam

middle: F

last: Allred

state: MO

address: 660 S. Euclid

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


title: SIMR Saccharomyces 23360 YOGie_2_062707

city: Kansas City

first: Chris

middle: W

last: Seidel

department: Genomics

institute: Stowers Institute

organism: Saccharomyces cerevisiae

description:
This array consists of version 1.1.1 of the Operon Yeast 70-mer Array Ready Oligo Set, supplemented with custom-designed 70-mer probes spanning the yeast genome at a resolution of approximately 450 bp.

Oligos were mapped to genome version sacCer2 (June, 2008) using Bowtie.

manufacture_protocol: Yeast Genome Array Ready Oligo Set version 1.1.1 from Operon Technologies, as well as several custom-designed 70-mer probe sets, were spotted at 40 uM in 3xSSC onto custom-made poly-L-Lysine glass slides following standard procedures using a custom-built linear servo robot (Joe Derisi, Chris Seidel).


title: Ambion 14K miRChip V1 [expanded format]

city: Los Angeles

first: Philip

middle: T.

last: Liu

address: 615 Charles E Young Drive South, 410 OHRC

department: Department of Orthopaedic Surgery

institute: University of California at Los Angeles

organism: Homo sapiens

description: Two overlapping probes were designed for each mature miRNA candidate.

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


title: CombiMatrix 4x2k human microRNA microarray miRBase 9.0

status: Public on Mar 06 2012

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

manufacture_protocol: see manufacturer's website http://www.combimatrix.com/docs/PTL012_00_4x2K_MicroRNA_Hyb_Imaging.pdf


title: Vibrio vulnificus MO6-24/O whole genome TwinChip

city: Seoul

first: Seung Min

last: Kim

address: 1 Gwanakro

institute: Seoul National University

organism: Vibrio vulnificus

manufacture_protocol: The V. vulnificus whole genome TwinChip, which has two blocks, up (upper) and dn (lower), manufactured by e-biogen (Seoul, South Korea). The slide contains 3 arrays of 15,000 features each. One array consists of a grid of 160 columns by 94 rows for a total of 15,040 spots with 40 spots reserved for internal quality control, leaving 15,000 spots available for custom probe sequences. This format is compatible with the four-chamber Agilent Technologies hybridization gasket slide.


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [v1.na30.1.mm9.probeset]

city: Riyadh

first: Kate

middle: S

last: Collison

address: Department Biological & Medical Research

country: Saudi Arabia

institute: King Faisal Specialist Hospital & Research Centre

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

#%create_date=Tue Dec  8 17:31:33 2009 PST
#%chip_type=MoGene-1_0-st-v1
#%lib_set_name=MoGene-1_0-st
#%lib_set_version=v1
#%genome-species=Mus musculus
#%genome-version=mm9
#%genome-version-ucsc=mm9
#%genome-version-ncbi=37
#%genome-version-create_date=2007-07
#%netaffx-annotation-date=2009-11-16
#%netaffx-annotation-netaffx-build=30.1
#%netaffx-annotation-tabular-data-version=1.2
#%netaffx-annotation-tabular-format-version=1.1
#%netaffx-annotation-data-type=probe_set
#%netaffx-annotation-docgen-method=module:affy/annotation_update/builder; exec:create-download-file.pl
#%netaffx-annotation-docgen-version=1.12

manufacture_protocol: See manufacturer's web site


title: SIMR Saccharomyces 16856 YOGi_P1B_062207

description:
This array consists of version 1.1.1 of the Operon Yeast 70-mer Array Ready Oligo Set, supplemented with custom-designed 70-mer probes designed to tile various portions of the yeast genome.

Oligos have been mapped to genome version sacCer2 (June, 2008) using Bowtie.


title: Agilent Human, KSHV, and EBV 44K AMADID #027774

status: Public on Dec 30 2011

city: Pittsburgh

first: Lindsay

middle: Renee

last: Dresang

address: 5117 Centre Ave, Hillman Cancer Res. Pav. 1.8

department: Cancer Virology Program

institute: University of Pittsburgh

organism:
Homo sapiens
human gammaherpesvirus 4
Human gammaherpesvirus 8

manufacture_protocol:
Refer to Agilent Technologies website for custom 4X44K array printing with Sure Print technology (www.genomics.agilent.com/GenericB.aspx?PageType=Custom&SubPageType=Custom&PageID=2011)).  This platform contains control probes for background correction and spike-in hybridization.
Tiling of KSHV, EBV, and control cellular and reporter genes were initially tiled with 60bp oligomers with 30bp overlap (straight tiling).  Major repeats were represtented once.  Initial experiments (not associated with the corresponding article) were performed to determine regions with significant background hybridization.   These regions were retiled according to Best-Tm and Best-Distribution methodologies available on the eArray website for custom microarray design (earray.chem.agilent.com).   Gaps were tolerated at <300 bp, with some exceptions as described in the methods section of the corresponding article.  All non-Agilent based probes were present in triplicate.


title: Agilent-025085 Custom Whole Genome Human 4x44k designed by Genotypic Technology Pvt. Ltd. (AMADID: 025085)

status: Public on Dec 29 2011

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

first: Raja

last: Mugasimangalam


title: Agilent v3.1 multi-species 8x15k miRNA array miRBase version 9.0 [miRNA version]

city: San Francisco

first: Andrew

last: Jheon

address: 513 Parnassus Ave HSE1501

institute: UCSF

organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus


title: Agilent-016492 three-spined stickleback 44K 60nt oligo array version 1.0

city: Palo Alto

first: Haili

last: Zhang

address: 279 Campus Dr. Beckman Center

department: Developmental Biology

institute: Stanford University

organism: Gasterosteus aculeatus

description:
Agilent customer gene expression microarray 4x44K.
Grid name 016492_D_F_20070419

manufacture_protocol: See manufacturer website (http://www.agilent.com).


title: Affymetrix GeneChip Rat Genome U34A Array [CDF: MBNI Version 13 (UniGene 183)]

city: Birmingham

first: Sarah

middle: Megan

last: Clinton

state: Alabama

address: 1720 7th Avenue South, SC 745

department: Psychiatry and Behavioral Neurobiology

institute: University of Alabama-Birmigham

organism: Rattus norvegicus

description:
UMMBNI Rat 4819 v1.0
Affymetrix, with custom cdf file from University of Michigan microarray core
This is identical to GPL85 but a custom CDF environment was used to extract data.

relation: Alternative to: GPL85 (Alternative CDF [official])

manufacture_protocol: see manufacturer's website


title: Illumina Genome Analyzer (Brassica napus)

status: Public on Dec 27 2011

last: GEO

organism: Brassica napus

technology: high-throughput sequencing

distribution: virtual


title: Genomictree human 17K cDNA microarray

city: Daejeon

first: sunwoo

last: Lee

address: 829 tamnip-dong, yuseong-gu

institute: Genomictree,Inc.

first: Sunwoo

first: Taejeong

last: Oh

manufacture_protocol: 17,075 clones of human cDNAs were purchased from Unigene Cluster. cDNAs were amplified with T7/SP6 unique primers, purified, and dissolved in spotting solution. 17K cDNA microarrays were fabricated on a silane-coated glassslide (Corning) with OmniGrid arrayer.


title: UNIPV Ceratitis capitata head and Embryo 22K v1.0

status: Public on Dec 25 2011

city: Pavia

first: Ludvik

middle: Marcus

last: Gomulski

state: PV

address: Piazza Botta 9

department: Biologia Animale

country: Italy

institute: University of Pavia

organism: Ceratitis capitata

description: Probes were designed from transcripts derived from medfly embryo and head cDNA libraries.

middle: M

first: George

last: Dimopoulos

first: Zhiyong

last: Xi

first: Giuliano

last: Gasperi

manufacture_protocol: Agilent Technologies


title: NimbleGen Arabidopsis thaliana Whole Genome Tiling Array 385K (2 of 3)

city: Vienna

first: Taku

last: Sasaki

address: Dr. Bohr-gasse 3

country: Austria

institute: Gregor Mendel Institute

organism: Arabidopsis thaliana

description:
Genome build information
2006-08-18_ATH6_ChIP_2.ndf
2006-08-18_ATH6_ChIP_2.pos

manufacture_protocol: see NimbleGen website at http://www.nimblegen.com


title: NimbleGen Arabidopsis thaliana Whole Genome Tiling Array 385K (1 of 3)

description:
Genome build information
2006-08-18_ATH6_ChIP_1.ndf
2006-08-18_ATH6_ChIP_1.pos


title: Agilent-025271 Zea mays Mais_array_v1 [Probe Name version]

status: Public on Dec 21 2011

city: Duesseldorf

first: Andrea

last: Braeutigam

address: Universitaetsstrasse 1

department: Botany

institute: Heinrich Heine University Duesseldorf

organism: Zea mays

description:
Mais array, v1, basierend auf Design 08/2009
Arrays of this design have barcodes that begin with 16025271 or 2525271.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

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


title: miRCURY LNA Human 1.5K miRNA Array Ready-To-Spot Probe Set no. 208010-A

status: Public on Dec 20 2011

city: Padova

first: Federica

last: Eduati

state: Italy

address: Via G. Gradenigo 6/B

institute: University of Padova

description: 1,500 non-blank spots with many replicate spots and 2,800 blank spots

manufacture_protocol: see manufacturer's web site


title: Illumina Genome Analyzer II (Myotis pilosus)

status: Public on Dec 19 2011

organism: Myotis pilosus


title: Illumina Genome Analyzer IIx (Glomerella graminicola)

organism: Colletotrichum graminicola


title: Illumina Genome Analyzer II (Brugia pahangi)

organism: Brugia pahangi


title: Illumina Genome Analyzer (Pyropia yezoensis)

organism: Pyropia yezoensis


title: Custom Agilent Human Chromosome 5q21 Tiling Array

city: Stanford

first: Stephanie

last: Huang

address: 269 Campus Drive, CCSR 3240

department: Pathology


title: Illumina Genome Analyzer IIx (Drosophila melanogaster x Drosophila simulans)


title: Illumina Genome Analyzer II (Chlorella variabilis)

organism: Chlorella variabilis


title: Agilent-018561 C. elegans 15k gene expression microarray

city: Haifa

first: Itai

last: Yanai

address: Technion City

country: Israel

institute: Technion - Israel Institute of Technology

organism: Caenorhabditis elegans

description: We designed a custom 15K C. elegans microarray which was then manufactured by Agilent. The 60-mer probes were determined using OligoWiz2 to target the coding region based the following factors: upon melting temperature, position along the transcript, folding potential, low-complexity in the sequence, and cross-hybridization to other coding sequences. The probes were also restricted against spanning splice junctions to avoid missing transcripts due to errors in gene structure predictions. For each gene, the best scoring probe with no significant match in other coding sequences (E-value < 0.001) was selected. This procedure yielded 16,831 gene-specific probes out of the total 20,074 genes searched. We then selected the 15,208 best scoring probes for the microarray.

first: Daniel

middle: H

last: Schott

first: Craig

middle: P

last: Hunter

manufacture_protocol: Standard Agilent oligo in situ protocol


title: 454 GS (Cymbidium ringspot virus; Nicotiana benthamiana)

organism:
Nicotiana benthamiana
Cymbidium ringspot virus


title: Illumina Genome Analyzer II (Rhizoctonia solani AG-1 IA)

organism: Rhizoctonia solani AG-1 IA


title: Applied Biosystems Taqman Array Rodent MicroRNA Cards v2.0

status: Public on Dec 23 2011

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

institute: Ludwig-Maximilians-University

organism: Mus musculus

technology: RT-PCR

description: Taqman Array A and B for miRNA from Applied Biosystems


title: NimbleGen_Rat_385K_Array

city: Paris

last: Vaiman

address: 24 rue du Faubourg St Jacques

department: Genetics and Development

country: France

institute: INSERM

manufacture_protocol: Nimblegen


title: CNIO Genomics Unit Custom Multi-Species miRNA Microarray

city: MADRID

first: Luis

last: LOMBARDIA

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Molecualr Pathology Programme

country: Spain

institute: CNIO (Spanish National Cancer Center)

organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

manufacturer: Genomics Unit. CNIO (Spanish National Cancer Research Centre). Madrid. Spain.

manufacture_protocol: NCode Multi-Species miRNA V2 probeset (Invitrogen, cat. # MIRMPS2-01) was printed on Nexterion epoxy E slides (Schott) by following manufacturer’s recommendations. The probeset contains a number of internal and negative control probes and includes 1,140 oligonucleotides that target all of the known mature miRNAs in the Sanger miRBase Sequence Database, Release 9.0 complementary to C. elegans, Drosophila, zebrafish, mouse, rat, and human miRNAs.


title: Illumina Genome Analyzer II (Escherichia coli E24377A)

last: GEO

organism: Escherichia coli O139:H28 str. E24377A


title: Austrain Institution of Technology Protein Array 642

first: Parvez

last: Syed

address: Muthgasse 11

institute: Austrian Institution of Technology

organism: Homo sapiens

technology: spotted peptide or protein

last: Weinhäusel

first: Ronald

last: Kulovics

manufacture_protocol: 642 His-tag proteins were expressed in E. coli and purified using Ni-NTA agarose. Maximum protein concentration used for spotting the microarray (SU8 Epoxy surface) was 0.5 mg/mL. Each microarray has 4 sub-arrays. Each protein was spotted in duplicates in each subarray.


title: Illumina Genome Analyzer II (Haemonchus contortus)

organism: Haemonchus contortus


title: MWG Human 1K

description:
spotted oligonucleotides with 50 bp in length
970 non-blank spots with many replicate spots and 4,560 empty spots

manufacturer: Institute for Genomics and Bioinformatics, Graz University of Technology

manufacture_protocol: Oligos were dissolved in spotting buffer consisting of 3× SSC, 1.5 M Betaine. Microarrays were produced by spotting the reporters (including spotting buffer as negative control and human genomic DNA as positive control) onto an epoxy-coated glass slide Nexterion) resulting in 33456 features on a single high density array. Oligos were fixed to the slides by baking at 42°C for 8 h at 50% relative humidity.


title: Agilent-015906 Salmonella custom oligo 4×44K microarray

city: Taipei

first: Ke-Chuan

last: Wang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Taipei medical university

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


title: UCSB/Hofmann Mytilus californianus 5K v1.0

city: Columbia

first: Sean

last: Place

state: SC

address: 715 Sumter St.

department: Biological Sciences

institute: University of South Carolina

organism: Mytilus californianus

manufacturer: Oregon State University - Center for Genome Research and Biocomputing

manufacture_protocol:
1. Samples are provided in 384-well plates with matching lids (Genetix part # X7022) at a concentration of 0.15 µg/µl for PCR products
2. Samples must be in a starting volume of 15 µl of spotting buffer (1.5M Betaine, 3xSSC for Corning UltraGaps slides)
3. cDNAs are spotted on Corning ULTRAGaps (25 mm x 75 mm) using the Biorobotics Microgrid II
4. printed slides are held in a desiccator for 24-48 hours after printing and X-linked at 225 mJ for cDNA/PCR products


title: Illumina Genome Analyzer (Naumovozyma castellii)

organism: Naumovozyma castellii


title: NimbleGen_Trichoderma_reesei_genome_version_1.2_400k_array

status: Public on Dec 22 2011

city: Espoo

first: Mikko

middle: Ilari

last: Arvas

address: Tietotie 2

department: Cell Factory

country: Finland

institute: VTT Technical Research Centre of Finland

organism: Trichoderma reesei

description:
Trichoderma reesei (Hypocrea jecorina)
NimbleGen design name 2005-09-27_Treesei_25mers Nimblegen design id 2604.  Array contains 11 25-mer probes for each open reading frame.  The design includes random GC and other control probes.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.
native array description file: 2005-09-27_Treesei_25mers.ndf
native array description file : 2005-09-27_Treesei_25mers.ngd

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


title: Illumina Genome Analyzer (Triticum durum)

country: USA

organism: Triticum turgidum subsp. durum


title: Illumina Genome Analyzer IIx (Sus scrofa)

organism: Sus scrofa


title: Agilent-015868 Human miRNA Microarray (miRBase release 9.0 Feature Number version)

status: Public on Dec 16 2011

city: Bethesda

first: Jeffrey

middle: E

last: Green

address: Rm 4054, 37 Convent Drive

institute: NCI

manufacture_protocol: See Agilent website (www.agilent.com)


title: Agilent-025771 UCSF Multi-species custom array miRNA-v3.5-8x15k

city: San Francisco

middle: J

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus

description:
miRNA microarray probe design, v3.5 (10/15/09)
Mirbase 14, hsa, mmu, dre, gga, rno, dme, cel

Total unique probe sequences:
2405(miR)+14(siRNA)+24(snRNA)+16(snoRNA)+3(tRNA)+30(spike-in)+30(mRNA)+192 = 2714

For the 2405 miRNA probes, 6 replicates were generated
For the 117 control probes, 5 replicates were generated
For the 192 mismatch probes, 1 replicate
Total UCSF probes: 15207
Agilent Controls: 536
Total probes on array: 15743  + 1 empty = 15744

NOTE: Platform ID column lists probe IDs from array design v3.5.  Core Annotation file (see design_cross_ref-5.txt below) shows relationships among the probeIDs in array designs v3.4 (Agilent-023723), v3.5 (Agilent-025771), and v3.6 (Agilent-031052).

Arrays of this design have barcodes that begin with 16025771 or 2525771.

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 HiSeq 2000 (Streptococcus thermophilus)

status: Public on Dec 15 2011

organism: Streptococcus thermophilus


title: Agilent-026693 Trypanosoma brucei 15K Microarray

city: Seattle

first: Bruz

last: Marzolf

state: WA

institute: Institute for Systems Biology

organism: Trypanosoma brucei

description:
Arrays of this design have barcodes that begin with 16026693 or 2526693.
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: GenoExplorer Human microRNA array

status: Public on Dec 14 2011

city: Philadelphia

first: Julio

last: Martin-Garcia

department: Microbiology and Immunology

institute: Drexel University College of Medicine

description: GenoExplorer MicroRNA Expression Analysis, using proprietary arrays with over 1300 miRNA probes (each in triplicate) for all described mature and most precursor human miRNA sequences (miRBase v13), in addition to multiple positive and negative control probes.

distribution: commercial

manufacture_protocol: See information at www.genosensorcorp.com/microRNA_full_kit.html


title: Illumina Genome Analyzer IIx (Enterobacteria phage lambda)

status: Public on Dec 13 2011

organism: Lambdavirus lambda


title: UZ Gent human genome-wide BAC array UG_3

city: PARIS

first: Gudrun

last: Schleiermacher

address: 26 rue d'Ulm

department: Department of Pediatric Oncology

institute: Institut Curie

description: Platform annotation is based on human genome build UCSC hg18.

manufacturer: Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium

manufacture_protocol: BAC clones were spotted.


title: Bacillus subtilis 168 Oligo Array [condensed/gene-level version]

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Bacillus subtilis

description: 12pins spotting with Telechem 946MP3  pins

manufacture_protocol: Oligo spotted on ArrayIt Superamine slides in duplicates


title: UZ Gent human genome-wide BAC array UG_2


title: Illumina Genome Analyzer IIx (Thermus thermophilus)

status: Public on Dec 09 2011

organism: Thermus thermophilus


title: Illumina Genome Analyzer IIx (Schmidtea mediterranea)

organism: Schmidtea mediterranea


title: Illumina HiSeq 2000 (Fagopyrum esculentum)

organism: Fagopyrum esculentum


title: Illumina HiSeq 2000 (Thermus thermophilus)


title: UZ Gent human genome-wide array UG_1

description:
Platform annotation is based on human genome build UCSC hg18.

Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium

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


title: PLBIO-DX2010 - IMMUNE

city: Mumbai

first: Muralidhara

last: Padigaru

state: Maharashtra

address: 1, Nirlon Compex, Off Western Express Highway

department: Translational Research

institute: Piramal Lifesciences India Limited

description: Immune signal pathways profiler

first: Debarshi

last: Chakrabarti

manufacture_protocol: A microarray chip with 283 transcripts representing key signaling genes and 17 control probes were purchased from Operon Biotechnologies (Operon, USA). Every gene was confirmed for function and sequence with the latest RefSeq genome build and represented as a unique 70-mer oligonucleotides sequence. A 40μM concentration of the oligos was achieved by dissolving the oligos with 50% DMSO solution. The MTP plates were vortexed at 150 rpm for 2 hours and spun down at 1200 rpm in a swing out rotor centrifuge. Every gene/oligo was printed with a robotic arrayer – OG100 (Genomic Solutions, Ann Arbor, USA) in duplicate for every cell on a 16-chambered aminosilane coated glass slide (Schott Nexterion, USA). The relative humidity and the temperature were maintained at 45% RH and 23°C. The printing is achieved by contact disposition of 20nL of the oligo suspension onto the glass slide with stealth microarray pins (SMP3) having an uptake capacity of 250 nL. Post printing, the slides were air dried for 6 hours in the printing environment and then cross-linked at 650 mL/sec2 with an UV cross-linker. The slides were then packed and stored under vacuum in the dark at room temperature.


title: AB SOLiD 4 System (Rattus norvegicus)

status: Public on Dec 08 2011

organism: Rattus norvegicus


title: Illumina Genome Analyzer IIx (Ambystoma mexicanum)

status: Public on Dec 12 2011

organism: Ambystoma mexicanum


title: Agilent-029152 Unrestricted Mouse miRNA v15.0 Microarray 028772 (miRBase release 15.0 miRNA ID version)

status: Public on Dec 07 2011

city: ATLANTA

first: Tuoqi

last: Wu

state: GA

address: 1510 Clifton Rd, Room G211

institute: Emory University

organism: Mus musculus


title: Illumina Genome Analyzer (Penicillium decumbens)

organism: Penicillium decumbens


title: Illumina Genome Analyzer IIx (Human herpesvirus 6B)

status: Public on Dec 06 2011

organism: Human betaherpesvirus 6B


title: AB SOLiD System 3.0 (Porphyromonas gingivalis)

organism: Porphyromonas gingivalis


title: NimbleGen Human 385K Gallagher Erythroid Array v2.0

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

organism: Homo sapiens

description: HG18, NCBI36

manufacture_protocol: See www.nimblegen.com.


title: PFGRC Streptococcus sanguinis SK36 oligo array version 1

city: Tianjin

first: Lei

last: Chen

address: 92 Weijin Rd

institute: Tianjin University

organism: Streptococcus sanguinis

manufacturer: Pathogen Functional Genomics Resource Center

manufacture_protocol: Detailed protocols can be found at: http://pfgrc.jcvi.org/index.php/microarray/protocols.html


title: Panorama Mouse Microarray

city: Ishikari

first: Arisa

last: Shibuya

state: Hokkaido

address: 777-13, Nishi-1, Shin-ko

department: Custom Prodcuts Division

country: Japan

institute: SIGMA Aldrich Japan K.K.


title: Illumina HiSeq 2000 (Anolis carolinensis)

last: GEO

organism: Anolis carolinensis


title: Utz lab histone protein and peptide array

status: Public on Dec 02 2011

city: Oberlin

first: Jordan

last: Price

state: OH

address: 119 Woodland St

institute: Oberlin College

organism:
Gallus gallus
Homo sapiens
Bos taurus

manufacture_protocol: Proteins (Immunovision, Springdale, AR) were printed at 0.2mg/ml and peptides (Yale Keck Facility, New Haven CT) were printed at 0.4mg/ml on nitrocellulose FAST slides (Whatman, Piscataway, NJ) in replicates of six using a BioRad VersArray robot and ChipWriter Pro software (Bio Rad, Hercules, CA).


title: Illumina HiSeq 2000 (Vitis amurensis)

status: Public on Dec 05 2011

organism: Vitis amurensis


title: Intel array v2

description:
Photolithographic synthesis of peptides on silicon substrate
Array patterning by photolithography and amino acid coupling. For wafer-scale array patterning, we used spin coater (Brewer Science, Rolla, MO) to apply a photosensitive imaging solution containing a photoacid generator and a sensitizer in propylene glycol methyl ether acetate (PGMEA, Sigma). In a class-10,000 clean room, we mounted wafers on a computer-controlled X-Y stage (Newport Corporation, Irvine, CA) and patterned array features by exposing selected areas of the wafer to UV light though a virtual mask with a digital exposure tool modified from a DLP device (Texas Instruments, Dallas, TX). At each coupling step, we treated UV-exposed wafers with coupling solution: [t-BOC amino acid of interest (Novabiochem, San Diego, CA), hydroxybenzotriazole (HOBt, CPC Scientific, Sunnyvale, CA), and N,N’-diisopropylcarbodiimide (DIC, CPC Scientific) dissolved in N-Methyl-2-pyrrolidone (NMP, Sigma) with a final concentration of 0.1 M each] for 30 min at room temperature (RT). After a brief rinse in N,N-dimethyl formamide (DMF, Sigma), we transferred wafers into capping solution (5% Ac2O in DMF). We then washed the wafers extensively in DMF and 2-propanol (IPA, Sigma) in preparation for the subsequent photolithography step.

manufacture_protocol: Wafer derivatization and linker attachment. We derivatized blank six-inch silicon wafers (Silicon Valley Microelectronics, Santa Clara, CA) by thermal oxidation followed by salination via immersion in a 0.5% v/v mixture of 3-aminopropyltriethoxysilane (Sigma-Aldrich, St. Louis, MO) in 95% ethyl alcohol (EtOH, Sigma) for 30 min at RT. We then cured wafers at 100 °C for 1 h under ultrapure and ultradry N2 (Airgas, Sacramento, CA) to crosslink silane groups to each other and to the silicon surface. Following salination, we added a PEG6 linker to the wafer surface to facilitate addition of custom peptides.


title: Intel array v1

description: Photolithographic synthesis of peptides on silicon substrate


title: RITEmmg_Cglutamicum_3K_ver.1.0

city: Kyoto

first: Masayuki

last: Inui

address: 9-2 Kizugawadai, Kizugawa

institute: Research institute of Innovative Technology for the Earth (RITE)

organism: Corynebacterium glutamicum

manufacture_protocol: PCR primers (20-mers) were designed to amplify the full-length coding DNA segments of 3080 predicted ORFs based on the annotation of the complete C. glutamicum R genome sequence (NC_009342). Amino-terminus primers amplified 20 bp downstream from the initiation codon, which was included. Carboxy-terminus primers amplified 20 bp upstream from the termination codon, which also was included. The ORF-specific double-stranded DNA fragments were produced by standard PCR amplification methods, as described above, with genomic DNA of C. glutamicum R as template and the above primer sets. Each PCR product was analysed routinely by agarose gel electrophoresis to ensure its size and purity. When PCR products of the expected size or purity were not obtained, modification of PCR conditions, redesign of primer pairs, or purification of DNA fragments from gels were attempted. As a result, a library of 3076 single PCR products was obtained that contained 99.9 % of a total of 3080 predicted ORFs present in the C. glutamicum R genome. PCR products were purified by a PCR96 Cleanup kit (Millipore), desiccated and resuspended in Solution-T (Takara Bio). The PCR products thus obtained were printed in duplicate at two separate positions onto a 1x3 inch (2.5x7.5 cm approx.) Takara slide glass TX704 (Takara Bio) using an arraying robot. The DNA microarrays were rehydrated in a humidity chamber at 37 °C for 1 h. They were subsequently exposed to UV light at an energy setting of 60 mJ cm–2 in a UV cross-linker, and soaked in 0.2 % SDS for 2 min at room temperature. After being washed twice with ultrapure water, the slides were immersed in a succinic anhydride solution for 20 min at room temperature, and placed in boiling water for 2 min. The slides were then immersed in 100 % ethanol for 1 min and dried by centrifugation at 185 g for 2 min. Spotting quality was assessed by checking as controls the configuration and concentration of non-specific stained DNA spots on the DNA microarrays. In addition, 12 spots each of human transferrin receptor (1 kb), E. coli plasmid pUC19 and {lambda}DNA were printed onto the slides as negative controls for DNA hybridization.


title: Exiqon miRCURY LNA microRNA Array 5th generation (DesignedFor miRBase 14.0, CurrentVersion miRBase 16.0)

state: MD

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

manufacture_protocol: See manufacturer's website.


title: NimbleGen 090807 H. erato tile and expr HX12 V1.0

city: San Juan

first: Riccardo

last: Papa

address: Avenida Barbosa

department: Biology

country: Puerto Rico

institute: University of Puerto Rico

organism: Heliconius erato petiverana

description: This array contains probes covering three genomic intervals, the CR, the DLOCUS and the HERA CINN. In this array there are also ~8000 genes represented.  The data that this study refers to is the DLOCUS, which is the genomic interval linked to the red polymorphism in Heliconius erato butterflies.

manufacturer: Roche NimbleGen Inc., Madison, Wisconsin, United States

manufacture_protocol: see manufacturer's website


title: MRA-1001_miRHuman_16 ( LC science)

status: Public on Dec 10 2011

city: Detroit

first: Fazlul

middle: H.

last: Sarkar

state: MI

address: 4100 John R

institute: Wayne State University School of Medicine

manufacture_protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). 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.


title: Agilent-028745 PFreudenreichii15K

status: Public on Dec 01 2011

city: Fermoy

first: Marion

last: Dalmasso

address: Moorepark

department: Food Safety

country: Ireland

institute: Teagasc

organism: Propionibacterium freudenreichii

description:
PFreudenreichii 15K Thierry

Arrays of this design have barcodes that begin with 16028745 or 2528745.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

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


title: febit biomed miRBase Human array

city: Hannover

first: Sya

last: Ukena

address: Carl-Neuberg-Strasse 1

country: Germany

institute: Hannover Medical School

manufacture_protocol:
MicroRNAs (miRNAs) are endogenous, non-coding RNAs that play a fundamental role in gene regulation and have critical functions across various biological processes. Pairing to mRNAs of protein-coding genes, they direct posttranscriptional repression by altering the stability or translational efficiency of their target mRNAs.
Recent studies indicate that miRNAs are involved in the development of human malignancies, suggesting that they represent a promising new class of cancer biomarkers. Identifying miRNAs involved in specific cancers could provide useful diagnostic information, allow disease classification and reveal potential treatment targets.
MPEA: On-Chip Labeling for Highest Sensitivity
Enzymatic labeling assay requires minimal sample amount
In addition to the standard hybridization of pre-labeled RNA, the microfluidic Geniom Biochip enables a highly sensitive enzymatic labeling protocol.
MPEA benefits
* Higher sensitivity and specificity
* miRNA hybridization without preceding treatment like enrichment, PCR -based amplification or labeling eliminates potential bias
* High discriminatory power
* Minimal amount of sample RNA needed (more than or equal 20 ng total RNA)
* Easy to use protocol for Geniom RT Analyzer
The unique Microfluidic Primer Extension Assay (MPEA) uses unlabeled miRNAs for hybridization. In a second step, Klenow fragment of DNA polymerase I is added directly into the channels of the microfluidic chip, where the specific elongation of the bound miRNAs takes place.
The method combines the specificity of a hybridization assay with the discriminatory power of an enzymatic extension and reduces the required sample amount to a minimum.


title: Agilent-016938 MIT/Laub-Caulobacter-44k-v1.0

city: Boston

first: Mark

last: Umbarger

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

organism: Caulobacter vibrioides CB15

description:
Caulobacter chip including 400 bp upstream and 200 bp downstream of every gene

Arrays of this design have barcodes that begin with 16016938 or 2516938.

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: Agilent-020719 Human OBS Barcode Array Version2

city: Huntsvilee

first: Kruti

last: Patel

state: AL

address: 601 Genome Way, Suite 2100

institute: Thermo Fisher Scientific


title: Agilent-022442 Saccharomyces cerevisiae genotyping v1

city: Princeton

first: Noorossadat

last: Torabi

state: NJ

address: 110 Carl Icahn Lab

department: Molecular Biology

institute: Princeton University

organism: Saccharomyces cerevisiae

description:
Arrays of this design have barcodes that begin with 16022442 or 2522442
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
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).


title: TaqMan qRT-PCR Homo sapiens Low-Density Array

city: La Jolla

first: Sara

last: Weis

state: CA

address: 3855 Health Sciences Drive #0803

institute: Univ of California San Diego

description: TaqMan® Gene Signature Array Configuration - Human Angiogenesis Array


title: Nimblegen 12-plex 135K full genome mouse custom NKI array [091016_MM9_RK_CGH_HX12]

city: Amsterdam

first: Rinske

last: Drost

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

description:
CGH design for whole mouse genome (mm9; NCBI Build 37).
SLIDE_LAYOUT_NAME: NimbleChip_HX12.
mm9_whole_genome_probes_18500bp_spacing.
designname: 091016_MM9_RK_CGH.
designid:10801.

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


title: Nimblegen Human 390K HG17 Custom Array

city: Gaithersburg

first: Peter

last: Johansson

state: Maryland

address: 8717 Grovemont Circle

department: Pediatric Oncology Branch

institute: National Cancer Institute

description:
NimbleGen arrays were synthesized using maskless array technology. A digital light projector (DLP1) was used to selectively deprotect features where new DNA bases are to be added. The DLP is 768 column x 1204 rows (XVGA). There were in total 389,119 elements on the array we used, of which 2,954 were controls and remaining 386,165 were measurement elements.
The genome build was HG17.


title: SMD Print_661

city: Stanford

first: Minnie

last: Sarwal

address: 703 Welch Road

department: Pediatric Nephrology

institute: Stanford University

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_843


title: SMD Print_948 Homo sapiens

status: Public on Jun 04 2010

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité


title: SMD Print_885 Homo sapiens


title: [Canine_2] Affymetrix Canine Genome 2.0 Array

status: Public on May 09 2006

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Canis lupus familiaris

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

The GeneChip® Canine Genome 2.0 Array enables researchers to simultaneously interrogate 18,000 C. familiaris mRNA/EST-based transcripts and over 20,000 non-redundant predicted genes.

Sequence information for this array includes content from Canis familiaris UniGene Build #11 (April, 2005), GenBank® mRNAs up to April 15, 2005, as well as the BROADD1 gene predictions from the boxer dog genome, downloaded from EBI on May 9, 2005.

manufacture_protocol: see manufacturer's web site


title: SMD Print_677 Homo sapiens


title: Human protoarray KSP gal file HA20034

status: Public on Dec 01 2009

city: Durham

first: Matthew

last: Foster

state: NC

address: Box 2612 Research Dr.

department: Medicine

institute: Duke University

manufacture_protocol: GST-tagged human proteins and control spotted in duplicate on glass slides


title: SMD Print_771 Homo sapiens


title: 454 GS 20 (Homo sapiens)

status: Public on Sep 11 2009

last: GEO


title: SMD Print_621 Homo sapiens


title: Agilent-019159 Rat miRNA Microarray (miRBase release 9.2 miRNA ID version)

status: Public on Apr 22 2010

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Rattus norvegicus

description: Rat miRNA Microarray 1.0


title: Azoarcus sp. BH72 Array

city: Bremen

first: Barbara

last: Reinhold-Hurek

department: Microbe-Plant-Interactions

institute: University Bremen

organism: Azoarcus olearius

manufacturer: Eurofins MWG GmbH and Transcriptomic facility of CeBiTec University Bielefeld

manufacture_protocol: The Azoarcus microarray was designed by spotting gene-specific 70mer oligonucleotides (manufactured by Eurofins MWG GmbH) in quadruplicates onto epoxy-coated glass slides representing 3992 predicted protein-coding genes of Azoarcus sp. Strain BH72. Each oligonucleotide (40 µM) was spotted in 1.5 M betaine/450 mM sodium chloride/45 mM sodium citrate (pH 7).


title: Agilent-022830 RIKEN_AT_sORF0902

status: Public on Nov 30 2011

city: Iizuka

first: Kousuke

last: Hanada

state: Fukuoka

address: 680-4 Kawazu

department: Department of Bioscience and Bioinformatics

institute: Kyushu Institute Technology

organism: Arabidopsis thaliana

description:
This microarray targets 34546 mRNA-like transcripts inclusing 26254 annotated coding genes (TAIR8), 6,946 coding sORFs identified at Hanada et al (Genome Research 2007 17:632-640) and 1,346 novel transcripts verified by full length cDNAs. This microarray will be useful for scientists studying gene activity associated with various plant organ functions, stages of growth, and biotic and abiotic stresses.

Arrays of this design have barcodes that begin with 16022830 or 2522830.

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: Agilent-023576 Helicoverpa armigera V3 44K

status: Public on Oct 20 2011

city: Stockholm

first: Maria de la Paz

last: Celorio-Mancera

address: Svante Arrheniusväg 18 B

department: Zoology

country: Sweden

institute: Stockholm University

organism: Helicoverpa armigera

description:
Arrays of this design have barcodes that begin with 16023576 or 2523576.

The ID column represents the Agilent Probe name.


title: Applied_Biosystems_Taqman_miRNA_Expression Assays_B (Mouse)

status: Public on May 13 2009

city: San Antonio

first: Jonathan

middle: Adam

last: Gelfond

state: TX

address: Mail Code 7933, 7703 Floyd Curl

department: Epidemiology & Biostatistics

institute: UT Health Science Ctr San Antonio

organism: Mus musculus

description: TaqMan microRNA Array B from Applied Biosystems

middle: A

first: Yongxin

last: Chen


title: Applied_Biosystems_Taqman_miRNA_Expression Assays_A (Mouse)

description: Taqman Array A for miRNA from Applied Biosystems


title: Rosetta/Merck Mouse 44k 1.0 microarray

status: Public on Apr 18 2006

city: Seattle

first: Amit

middle: V

last: Kulkarni

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description:
Oligonucleotide array on glass.
Contains 60-mer probes (60-mer).

first: John

last: Castle


title: Agilent-016436 Human miRNA Microarray 1.0 G4472A (miRNA ID version)

status: Public on Aug 24 2009

organism: Homo sapiens

description:
Human miRNA Microarrays, 8x15K, version 1 (G4472A)

This platform is based on the GeneView file produced by Agilent's feature extraction software.