title: Agilent-025055 Salmonid 44k (Probe Name Version)

status: Public on Aug 31 2014

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

country: France

institute: Institut National de la Recherche Agronomique

organism: Salmo salar

technology: in situ oligonucleotide

description: Arrays of this design have barcodes that begin with 16025055 or 2525055.

distribution: custom-commercial

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


title: Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (condensed Probe Name version)

status: Public on Oct 28 2014

city: GIF SUR YVETTE

first: Adrien

last: Georges

address: CEA/SACLAY

institute: CNRS

organism: Mus musculus

manufacture_protocol: see Agilent


title: EcoArray Fathead Minnow 8 x 15K Microarray v1.0

city: Laval

first: Jennifer

last: Arstikaitis

state: Quebec

address: 531, boulevard des Prairies

department: Toxicology/Cellular and Molecular Biology

country: Canada

institute: INRS-Institut Armand Frappier Universite du Quebec

organism: Pimephales promelas

description: This microarray contains 60-mer probes for 15,208 fathead minnow sequences.  Because there are eight arrays per slide, this is the most economical array.  This microarray is 100% ANNOTATED.  Genes included on this array matched the Nonredundant database with an evalue <E-05, or the Nucleotide database with evalue <E-06.  All duplicate accession numbers were removed.  The genes are part of a wide variety of biological pathways and processes including: reproduction, cell communication, metabolism, homeostasis, and others.  This array is perfect for those researchers who do not want to worry about “no hits.”

first: Barbara

middle: J

last: Carter

first: Patrick

middle: M

last: Larkin

manufacture_protocol: EcoArray selected Agilent Technologies as the manufacturer of our microarrays for environmental toxicology.  Agilent Technologies is a leading supplier of genomics and proteomics products.  Using their SurePrint inkjet deposition of in situ synthesized 60-mer oligonucleotides, all microarrays are manufactured on superior quality 1” x 3” (24.2 mm x 76.2 mm) treated glass slides for overall excellent performance.  See their website for details: http://www.agilent.com.


title: Fluidigm Human adipose tissue markers analysis

status: Public on Nov 27 2014

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

institute: INSERM

organism: Homo sapiens

technology: RT-PCR

description: Fluidigm PCR assay

distribution: non-commercial

manufacture_protocol: The 222 transcripts were selected from previous published and unpublished Agilent Human 4x44k microarray analyses of human subcutaneous adipose tissue biopsies performed on limited number of individuals as described in Viguerie N et al (Plos Genetics 2012, 8: e1002959). These genes encode proteins involved in various pathways including metabolism (43% of the transcripts), immune response (20%), cell differentiation and proliferation (9%), cell and tissue structure (7%), transport (5%), signal transduction (3%) and response to stress (1.3%). The list of genes extracted from the previous microarray data analysis includes 89 genes previously shown as markers of subcutaneous adipose tissue from obese insulin resistant individuals with metabolic syndrome, 44 genes described as markers of subcutaneous adipose tissue from lean individuals, 39 markers of weight changes after caloric restriction, 40 genes selected from previous caloric restriction induced weight loss studies, and 18 unpublished predictors of weight change to distinguish between those individuals that will regain weight after calorie restriction.


title: Breakthrough Human 17K 2.1.2

status: Public on Aug 30 2014

city: London

first: Richard

middle: Dafydd

last: Williams

address: 30 Guilford Street

department: Developmental Biology and Cancer

country: United Kingdom

institute: UCL Institute of Child Health

technology: spotted DNA/cDNA

manufacturer: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, UK

manufacture_protocol: IMAGE clones in bacterial glycerol stocks were acquired from the CRUK DNA microarray facility at the Institute of Cancer Research, Sutton, UK, and from MRC Geneservice, Cambridge, UK. Clones were PCR-amplified using YieldAce DNA Polymerase (Stratagene) and primers: KIMF (GAGCGGATAACAATTTCACACAG) and KIMR (GTTTTCCCAGTCACGACG) for ampicillin resistant clones, or PM001a (GTCGACGTTAGAACGCGGCTAC) and PM002a (GGGTTAAATTCCCGGGTACTGC) for chloramphenicol resistant clones. PCR products were purified using the Montage 96-well purification plate system (Millipore). Purified DNA was mixed with equal volumes of 2x Microarray Spotting Solution (Genetix), and printed on FMB cDNA slides (Full Moon Biosystems) using a Lucidea ArraySpotter (Amersham). ). The array was laid out in 24 blocks (2 columns, 12 rows). Each block contained 748 features (17 rows, 44 columns, Pitch 190 micrometre). [Adapted from A. Grigoriadis, ArrayExpress A-MEXP-347].


title: Illumina HiSeq 2000 (Frankia sp. CcI3)

status: Public on Aug 29 2014

last: GEO

country: USA

organism: Frankia casuarinae

technology: high-throughput sequencing

distribution: virtual


title: Breakthrough Human 32K v5

manufacture_protocol: DNA from the 32K human BAC re-array set, a tiling path collection of BACs covering the entire human genome, was obtained from Pieter de Jong at the Children's Hospital Oakland Research Institute (CHORI). DNA was amplified by Genomiphi version 1 according to the manufacturer’s instructions. Following amplification, the DNA collection was randomized for spotting. DNA was mixed with an equal volume of 2x Microarray Spotting Solution (Genetix) and printed on UltraGaps APS coated microarray slides (Corning) using a Genetix QArray 2 spotter. The slides were printed with 48 blocks per array (4 columns, 12 rows) with a layout of 714 features per block (14 columns, 51 rows orange-pack pattern), a total of 34272 features with a nominal size of 110-120 micrometres. After printing, DNA was fixed to the slide using UV cross-linking using 200mJ with a Stratalinker (Stratagene). Slides were then stored in a desiccating cabinet before use.


title: OPERON Human 70-mer

status: Public on Aug 28 2014

city: Estado de Mexico

first: Rubi

last: Viedma

state: Estado de Mexico

address: Av. de los Barrios 1, Los Reyes Ixtacala,  Tlalnepantla,

department: bioquimica

country: Mexico

institute: unam

technology: spotted oligonucleotide


title: Exiqon miRCURY LNA microRNA array; 7th generation - hsa, mmu & rno (miRBase 18.0)

status: Public on Aug 27 2014

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

description:
ProductDate=March 2012
ProductNumber=208520,208521,208522
LotNumberRange=35101-35101
ArrayContents_DesignedFor=miRBase 18.0
ArrayContents_CurrentNameColumn=miRBase 18.0
ArrayContents_CurrentNameColumnCoverage=Homo sapiens and related vira:99.95%


title: [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [MoEx10stv1_Mm_REFSEQ.cdf]

city: Stanford

first: Agnes

last: Lim

state: CA

address: 265 Campus Drive

department: Developmental Biology

institute: Stanford University

description: This is identical to GPL6096 but a custom MoEx10stv1_Mm_REFSEQ.cdf environment was used to extract data.

relation: Alternative to: GPL6096 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site


title: Agilent-037053 FUB Vibrio parahaemolyticus 15K array v1 (Feature number version)

city: Berlin

first: Stephan

last: Huehn

address: Koenigsweg 69

country: Germany

institute: Freie Universität Berlin

organism: Vibrio parahaemolyticus RIMD 2210633


title: SurePrint G3 Rat GE 8x60K Microarray Toxplus ver.1 [Probe Name Version]

city: Kitakatsushika-gun

first: Hiroshi

last: Matsumoto

state: Saitama

address: 1600 Shimotakano, Sugito-machi

country: Japan

institute: Chemicals Evaluation and Research Institute, Japan

organism: Rattus norvegicus

description: custom rat array


title: Illumina NextSeq 500 (Drosophila yakuba)

organism: Drosophila yakuba


title: Illumina HiSeq 2000 (Salvia miltiorrhiza)

status: Public on Aug 26 2014

organism: Salvia miltiorrhiza


title: Illumina Genome Analyzer II (Manihot esculenta subsp. flabellifolia)

organism: Manihot esculenta subsp. flabellifolia


title: Illumina HiSeq 2000 (Manihot esculenta subsp. flabellifolia)


title: [AMEDS_expr] Custom Affymetrix Amycolatopsis mediterranei S699 10k chip

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

organism: Amycolatopsis mediterranei S699

manufacture_protocol: in situ oligonucleotide synthesis (see manufacturer's web site)


title: PacBio RS (Homo sapiens)


title: Illumina HiSeq 2000 (Triticum turgidum subsp. durum)

status: Public on Aug 22 2014

organism: Triticum turgidum subsp. durum


title: [MoGene-1_1-st] Affymetrix Mouse Gene 1.1 ST Array [transcript (gene) version] [CDF: MoGene11stv1_Mm_ENTREZG_14.1.0]

description: Brainarray:  MoGene11stv1_Mm_ENTREZG.cdf

relation: Alternative to: GPL11533 (Alternative CDF [official])


title: Qiagen/SA Biosciences (PAMM-011A)

city: Galveston

first: Istvan

last: Boldogh

state: Texas

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

description: PCR assay

manufacture_protocol: see manufacturer's website


title: NimbleGen Arabidopsis thaliana 4x72K Array [ATH6_60mer_expr]

status: Public on Aug 25 2014

city: Hong Kong

first: Boon Leong

address: 5N01, Kaddorie Biological Sciences Building, the University of Hong Kong, Pokafulam Road

department: School of Biological Sciences

country: Hong Kong

institute: The University of Hong Kong

organism: Arabidopsis thaliana

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


title: Ion Torrent PGM (Mycobacterium smegmatis)

status: Public on Aug 21 2014

organism: Mycolicibacterium smegmatis


title: IBMT Kpneumoniae alanine scan

city: Potsdam

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

department: Bioanalytics and Biosensorics

institute: Fraunhofer Institute for Cell Therapy and Immunology

organism: Klebsiella pneumoniae

technology: spotted peptide or protein

description: K. pneumoniae KPN_00459 and KPN_00363 protein

manufacture_protocol: Pepstar peptide microarrays (JPT)


title: Ion Torrent PGM (Mycobacterium phage Kampy; Mycobacterium smegmatis)

organism:
Mycolicibacterium smegmatis
Mycobacterium phage Kampy


title: Illumina HiSeq 2000 (Burkholderia gladioli)

status: Public on Aug 18 2014

organism: Burkholderia gladioli


title: ENS SGDB Trichoderma reesei Tr20_Transcript_1

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

institute: École normale supérieure

organism: Trichoderma reesei

description:
Trichoderma reesei Tiling array. One probe has been design every 140 base every other strand in known or putative transcript regions.
The probe design has been done according to T. reesei v2.0 genome assembly from the DOE JGI available here: http://genome.jgi-psf.org/Trire2/Trire2.home.html

The probe ID is a code to fing genome localisation of each probe: Scaffold_Start_Strand
The first number next to ensTrB_ prefix indicates the scaffold number
The second number is the start position of the probe
The third number is the strand FWD or REV

The gene ID and transcript ID are JGI genome browser IDs.

last: Le Crom

first: Laurent

last: Jourdren

manufacture_protocol: In situ oligonucleotide synthesis of 60mer custom oligos. See manufacturer's web site at http://www.agilent.com/.


title: Agilent-041035 EA587 Genotypic S.pombe CoC Microarray

status: Public on Aug 19 2014

city: New York

first: Songtao

last: Jia

state: NY

address: 1114, Fairchild center

institute: Columbia University

organism: Schizosaccharomyces pombe

description:
Arrays of this design have barcodes that begin with 16041035 or 2541035.

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 Probe Name.

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: University of Iowa/Graff-Homo sapiens-48.48-v1_Fluidigm

city: Iowa City

first: Joel

last: Graff

state: IA

address: 400 EMRB

department: Internal Medicine

institute: University of Iowa

organism: Homo sapiens

description: PCR assay using custom collection of TaqMan Assays

manufacture_protocol: See manufacturer's website


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: mogene10st_Mm_ENTREZG_18.0.0]

organism: Mus musculus

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

manufacture_protocol: This is identical to GPL6246 but a custom cdf environment was used to extract data. The cdf can be found at the link below.


title: Illumina HiSeq 2000 (Serratia sp. SCBI)

organism: Serratia sp. SCBI


title: Illumina MiSeq (Sulfolobus solfataricus)

status: Public on Aug 16 2014

organism: Saccharolobus solfataricus


title: Illumina HiSeq 2000 (Mnemiopsis leidyi)

organism: Mnemiopsis leidyi


title: Illumina HiSeq 2000 (Daphnia pulex)

organism: Daphnia pulex


title: NimbleGen Human miRNA Tiling Microarray

city: Wuhan

first: Xing-Xing

last: He

state: Hubei

address: 1095# Jie-Fang Avenue

department: Institute of Liver and Gastrointestinal Diseases

country: China

institute: Tongji Hospital

description:
HG18
It is a 385k array containing 541 miRNAs (all miRNAs in miRBase10.1) regions and 2700 CpG Islands regions (CpG islands located in regions from 150kb upstream to 150kb downstream of pre-miRNAs or from 100kb upstream to 100kb downstream of host genes). If a miRNA locates in the intergenic region, the miRNA region is from about 50kb upstream to 10kb downstream of the pre-miRNA. If a miRNA locates in a host gene, the miRNA region is from about 20kb upstream of the host gene’s transcription start site (TSS) to the end of host gene.
DESIGN_ID: 8318
native array description file:
NimbleGen_Human_miRNA_Tiling_Microarray.ndf
NimbleGen_Human_miRNA_Tiling_Microarray.pos

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


title: Targeted array-based proteomics [RPPA-Longterm-BT474]

status: Public on Aug 13 2014

city: Heidelberg

first: Ulrike

last: Korf

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

institute: German Cancer Research Center

description: reverse phase protein array (RPPA/RPA), lysate array

manufacturer: Division of Molecular Genome Analysis, B050, German Cancer Research Center

manufacture_protocol: Arrays were prepared on nitrocellulose-coated glass (Grace Biolabs) slides by using a solid-pin arrayer (Aushon 2470) with 180 µm pins.


title: [HG-U219] Affymetrix Human Genome U219 Array [CDF: Brainarray HGU219_Hs_ENTREZG_15.1.0]

status: Public on Aug 20 2014

description: This identical to GPL13667 but a custom cdf environment was used to extract data.


title: Targeted array-based proteomics [RPPA-Shortterm-SKBR3]


title: Targeted array-based proteomics [RPPA-Shortterm-BT474]


title: TaqMan Array Human Immune Response, Fast 96-well Plate

city: São José do Rio Preto

first: Érika

middle: Cristina

last: Pavarino

state: São Paulo

address: Avenida Brigadeiro Faria Lima, nº 5416 - UPGEM/Bloco U-6

department: Departamento de Biologia Molecular

country: Brazil

institute: Faculdade de Medicina de São José do Rio Preto (FAMERP)

description:
PCR assay
The TaqMan® Array Human Immune Response 96-well Plate contains 92 assays to immune response associated genes and 4 assays to candidate endogenous control genes.


title: Illumina HiSeq 1500 (Arabidopsis thaliana)

last: GEO


title: Illumina HiSeq 2500 (Cryptococcus neoformans)

organism: Cryptococcus neoformans


title: LC Sciences Homo sapiens LC_MRA-1001B2_miRHuman_20

status: Public on Aug 12 2014

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

distribution: commercial

manufacture_protocol: human miRNA microarray with 100% coverage of mature human miRNAs listed in miRBase version 20. Arrays are made based 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://miRBase.org) 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: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [custom CDF: hugene10stv1_74_030.cdf]

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

description:
Probe set data extracted from custom CDF:
hugene10stv1_74_030.cdf

For transcript probe set definition a custom CDF package was used, that was based on a complete re-alignment of the Exon microarray oligo-probes and annotation to Ensembl version 74.

relation: Alternative to: GPL6244 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: SABiosciences Human Wnt signaling pathway RT² Profiler™ PCR Array (PAHS-043Z)

city: Minneapolis

first: susanta

middle: k

last: hui

state: MN

address: 420 Delaware Street SE

department: Therapeutic Radiology

institute: University of Minnesota

description:
catalog number: PAHS-043Z
Human Wnt pathway PCR array panel
SABiosciences RT² Profiler panel of PCR assays.


title: AB SOLiD 4 System (Toxoplasma gondii)

status: Public on Aug 11 2014

organism: Toxoplasma gondii


title: Illumina MiSeq (Listeria monocytogenes EGD-e)

organism: Listeria monocytogenes EGD-e


title: Agilent Popular 8X60K oligo array

city: Suwon

first: seokyung

last: yoon

address: Onjeong-ro

country: South Korea

institute: KFRI

organism: Populus alba x Populus glandulosa

manufacture_protocol: see manufacturer website


title: Agilent-040666 Guinea Pig Array v1.2 (Feature Number version)

status: Public on Aug 10 2014

city: Liverpool

first: Peter

last: Davidsen

state: Merseyside

address: Crown Street

institute: University of Liverpool

organism: Cavia porcellus

description:
Guinea Pig Array based on RNA-seq and Cavia porcellus 3 genome. Probes with FF_0 have been confirmed. FF_1-4 are untested with 1 and 2 being specific for the sequence, 3 and 4 are sequences for genes were no specific sequence could be found.

Arrays of this design have barcodes that begin with 16040666 or 2540666.

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: Illumina HiSeq 2500 (Listeria monocytogenes EGD-e)


title: Illumina HiSeq 2000 (Neurospora tetrasperma)

status: Public on Aug 08 2014

organism: Neurospora tetrasperma


title: CAT-30K-Acinetobacter_baumannii_ATCC-17978

status: Public on Aug 09 2014

city: seoul

first: BORA

last: SHIN

state: 성북구 안암로

institute: Korea university

organism: Acinetobacter baumannii ATCC 17978

manufacture_protocol: see manufacture website


title: Illumina HiSeq 2000 (Neurospora discreta)

organism: Neurospora discreta


title: WUSTL Mouse 39K MEEBO Oligo Array

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

manufacturer: Genome Sequencing Center Microarray Facility

manufacture_protocol: MEEBO oligos were obtained from Illumina (San Diego, CA). Oligos were dissolved at 20uM in 3xSSC with 750mM betaine, then printed onto Corning epoxysilane slides using a custom built array printer with Telechem 75um Stealth pins.


title: Illumina MiSeq (Gallus gallus)

organism: Gallus gallus


title: Ion Torrent PGM (Arabidopsis thaliana)

status: Public on Aug 07 2014

organism: Arabidopsis thaliana


title: Applied Biosystems Human Taqman MicroRNA Array v3.0

city: Atlanta

first: Dong

last: Liu

state: GA

address: 720 Westview Drive, SW

department: Cardiovascular Research Institute

institute: Morehouse School of Medicine

description: qRT-PCR TaqMan Low-Density Array

manufacture_protocol: see manufacturer's website: http://www.appliedbiosystems.com/


title: Mouse Genome-Wide SpliceArray microarrays on the Affymetrix platform

city: Frederick

first: Masahiko

last: Ajiro

address: 1050 Boyles St Bldg 539 Rm 153

institute: National Cancer Institute

manufacture_protocol: Probes are designed for exonic regions and splice-junction of mouse genes.


title: Agilent-046066 Unrestricted Rat miRNA V19.0 (miRNA ID version)

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Rattus norvegicus


title: Illumina HiSeq 2000 (Morus alba var. atropurpurea)

status: Public on Aug 05 2014

organism: Morus alba var. atropurpurea


title: Agilent-038678 Candida dubliniensis CD36 tiling array (Probe name version)

status: Public on Aug 06 2014

city: Dublin

first: Gary

middle: P.

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

organism: Candida dubliniensis

description:
Tiling array of C. dubliniensis CD36
Agilent Sure Print 4x180K Array
175,758 unique 60mer probes, spaced at 20 bp intervals
Arrays of this design have barcodes that begin with 16038678 or 2538678.

manufacture_protocol:
See manufacturer's web site at http://www.agilent.com/
See http://www.chem.agilent.com/en-US/Products/Instruments/dnamicroarrays/Pages/gp557.aspx


title: 454 GS FLX (Malus domestica)

organism: Malus domestica


title: Agilent Vvulnificus SS microarray V2.0

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: Vibrio vulnificus

description: Agilent Vvulnificus SS microarray V2.0


title: NimbleGen Maize high-density big-block Array [111208_Zmay_B73_GH_CGH]

city: Tallahassee

first: Daniel

last: Vera

state: FL

address: 319 Stadium Drive

department: Biological Science

institute: Florida State University

organism: Zea mays

description:
B73v2 (AGP_v2, maizesequence.org)
Zea Mays L. B73 cultivar
Designname: 111208_Zmay_B73_GH_CGH
Designid: 563161

manufacture_protocol: Isothermal 49-74 bp probes derived from the B73v2 geome assembly (AGP_v2)  at ~18 bp spacing surrounding 3kb of 389 TSSs from the Classical Maize Genes


title: Yeast_WG

city: Tsuruoka

first: Douglas

middle: Brian

last: Murray

state: Yamagata

address: Nipponkoku 403-1, Daihouji

institute: Institute for Advanced Biosciences

organism: Saccharomyces cerevisiae

description: Genome build: sacCer3, 2011_02_03, R64-1-1

manufacturer: NimbleGen for Genome Research Facility, NASA Ames Research Center

manufacture_protocol: Maskless Array Synthesizer (MAS); see manufacturer's website


title: NimbleGen Maize high-density TSS Array [1102014_MaizeB73TSS_JD_CGH]

description:
B73v2 (AGP_v2, maizesequence.org)
Zea Mays L. B73 cultivar
Designname: 1102014_MaizeB73TSS_JD_CGH
Designid: 548611


title: 454 GS FLX Titanium (Calluna vulgaris)

organism: Calluna vulgaris


title: Illumina Genome Analyzer (Spodoptera frugiperda)

status: Public on Aug 04 2014

organism: Spodoptera frugiperda


title: Illumina HiSeq 2000 (Nicotiana benthamiana)

organism: Nicotiana benthamiana


title: Illumina HiSeq 2000 (Pestalotiopsis fici W106-1)

organism: Pestalotiopsis fici W106-1


title: D. melanogaster expression Kim 1.0 (annotation v2)

city: San Francisco

first: Charlie

last: Kim

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

organism: Drosophila melanogaster

manufacture_protocol: In situ oligonucleotide synthesis


title: Illumina Genome Analyzer IIx (Litomosoides sigmodontis)

status: Public on Aug 01 2014

organism: Litomosoides sigmodontis


title: 300033 CodeLink™ Mouse Whole Genome Bioarray

city: Bryan

first: Rajesh

middle: C

last: Miranda

address: MREB, 8447 Riverside Parkway

department: Neuroscience

institute: Texas A&M HSC

organism: Mus musculus


title: Exiqon Human miRCURY LNA Universal RT miRNA PCR Human Serum/Plasma focus panel (V3.R)

state: MD

organism: Homo sapiens

description: PCR assay

manufacture_protocol: see manufacturer's website


title: Agilent-038200 Clostridium difficile Clos_diff630

status: Public on Aug 02 2014

city: Leiden

first: Jeroen

last: Corver

address: Albinusdreef 2

department: Medical Microbiology

country: Netherlands

institute: LUMC

organism: Clostridioides difficile


title: Agilent-028434 Custom Gene Expression Microarray for Paeonia suffruticosa (Probe Name version)

city: Qingdao

first: Shu-Peng

last: Gai

state: Shandong Province

address: Changcheng Road 700

department: College of Life Science

institute: Qingdao Agricultural University

organism: Paeonia suffruticosa


title: miRCURY LNA microRNA Array, v.11.0 - hsa, mmu & rno [miRBase 11.0]

city: chongqing

first: guo

middle: zhen

last: zhao

address: Cancer Institute of PLA, Xinqiao Hospital, Third Military Medical University, Chongqing, China

organism:
Mus musculus
Murid betaherpesvirus 1
Murid gammaherpesvirus 4

description:
ProductNumber=208200-A,208201-A,208202-A
LotNumberRange=31019-31019

ArrayContents_DesignedFor=miRBase 11.0
ArrayContents_CurrentNameColumn=miRBase 11.0
ArrayContents_CurrentNameColumnCoverage=Mus musculus and related vira:99.85%

manufacture_protocol: See manufacturers website (www.exiqon.com),


title: Arraystar Human LncRNA microarray V2.1 (Agilent_039809 custom Probe Name version)

city: Rockville

first: Panos

last: Pan

address: 9430 Key West Avenue

institute: Arraystar Inc.


title: Agilent-038166 cbc_human_miR18.0

city: Beijing

first: Jiagen

last: Li

address: 17 Panjiayuannanli Chaoyang District

institute: Cancer Institute, CAMS

description:
Arrays of this design have barcodes that begin with 16038166 or 2538166.
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.


title: NimbleGen 100505_KI_Gordonia_KTR9_expr_HX12

status: Public on Feb 05 2013

city: Vicksburg

first: Dawn

middle: E

last: Hancock

state: Mississippi

address: 3909 Halls Ferry Road

department: Engineer Research and Development Center

institute: DEPARTMENT OF DEFENSE Army Corps of Engineers

organism: Gordonia sp. KTR9

description:
NimbleGen design name 100505_KI_Gordonia_KTR9_expr_HX12
NimbleGen DESIGN_ID: 11957
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: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.


title: NIZO food research Lactococcus lactis MG1363 60-mer array

city: Ede

first: Annereinou

last: Dijkstra

address: Kernhemseweg 2

institute: NIZO food research

organism: Lactococcus lactis


title: Agilent-054261 026652AsQuintuplicatesOn180k_new [Feature Number version]

status: Public on Jul 31 2014

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover

description:
This Microarray represents a refined version of the Whole Human Genome Oligo Microarray 4x44K v2 (Design ID 026652, Agilent Technologies), called '026652AsQuintuplicatesOn4x180k' (design ID 054261) developed in the Research Core Unit Transcriptomics of Hannover Medical School. Microarray design was defined at Agilent's eArray portal using a 4x180k design format for mRNA expression as template. All non-control probes of design ID 026652 have been selected to be printed five times onto one 180k Microarray (on-chip quintuplicates). Control probes required for proper Feature Extraction software algorithms were determined and placed automatically by eArray using recommended default settings.

all non-control probes of design 026652 (human 4x44k V2) were printed as quintuplicates as 4x180k format

Arrays of this design have barcodes that begin with 16054261 or 2554261.

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.

relation: Alternative to: GPL19034 (Probe name version)


title: Agilent-053869 Clostridium acetobutylicum DSM 1731 and Arthrobacte sp. CGMCC 3584 8X15K array [Probe Name Version]

city: shanghai

first: qian

last: jin

address: libing road

institute: MSP

organism:
Arthrobacter sp.
Clostridium acetobutylicum DSM 1731

description:
Arrays of this design have barcodes that begin with 16042658 or 2542658.

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 probe name.

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-042658 Clostridium acetobutylicum ATCC 824 and Arthrobacte sp. CGMCC 3584 8X15K array [Probe Name Version]

organism:
Clostridium acetobutylicum
Arthrobacter sp.

description:
Arrays of this design have barcodes that begin with 16042658 or 2542658.

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 probe name.

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: [FRAGDIFFa520673F] Affymetrix Bacteroides fragilis NCTC 9343 array

status: Public on Sep 30 2012

city: Davis

first: Bart

middle: C.

last: Weimer

state: CA

address: 1 Shields Ave

department: Population Health and Reproduction

institute: University of California, Davis

organism: Bacteroides fragilis NCTC 9343

description: The GPL19121 contains reads for C. difficile strain 630 in addition to B. fragilis.


title: Agilent-023349 HSV Histone mapping

city: Philadelphia

first: Nigel

last: Fraser

state: PA

address: 3101 Walnut St

department: Dept. of Microbiology

institute: Upenn

organism: Human alphaherpesvirus 1


title: LUNDNIH_Mouse_37K_2

status: Public on Mar 16 2005

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

description: Mouse cDNA 37K

first: Göran

last: Karlsson

first: Yingchun

last: Liu

first: Marie-Jose

last: Goumans

first: Jonas

last: Larsson

first: Ju-Seog

last: Lee

first: Snorri

middle: S

last: Thorgeirsson

first: Stefan


title: miRCURY LNA microRNA Array, v. 9.2, all organisms

status: Public on Dec 19 2008

city: Vedbaek

first: Exiqon

last: A/S

address: Bygstubben 9

country: Denmark

institute: Exiqon A/S

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

description:
Array covering Sanger miRBase 12.0 and Exiqon miRPlus mature miRNAs.
The platform information provided is from the time of the design.
Names, accession numbers and sequences are listed for mature miRNAs in miRBase 12.0. Some probes may target multiple miRNAs, in which case multiple miRNA names, accession numbers and sequences are listed separated by '/'

manufacture_protocol: See manufacturers website


title: LUNDNIH_Mouse_37K_1

description: Mouse cDNA 37K


title: Phalanx Human OneArray

status: Public on Dec 07 2007

city: Hsinchu Science Park

first: Phalanx

middle: Biotech

last: Group Inc.

state: Hsinchu

address: 6 Technology Road 5, 6th Floor

department: Bioinformatics

country: Taiwan

institute: Phalanx Biotech

description:
Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1080 control probes, spotted onto glass slides using a proprietary non-contact printing method. Detection probes are annotated against the human genome and grouped into the following categories:
Group 1 - gene specific: exon
Group 2 - intron hit
Group 3 - intergenic
Group 4 - multi-gene hits
Group 5 - no hit to genome
Group 6 - >200 hits to genome

relation: Alternative to: GPL13287 (Alternative annotation [HOA5 release 1.0])

relation: Alternative to: GPL19137 (Alternative annotation [HOA6 1.0])

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