title: Illumina HiSeq 1000 (Amphidinium carterae)

status: Public on Jan 31 2017

last: GEO

country: USA

organism: Amphidinium carterae

technology: high-throughput sequencing

distribution: virtual


title: Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Feature Number version; reannotated)

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

organism: Homo sapiens

technology: in situ oligonucleotide

description: Reannotation aimed to improve and update the information of array probes that interrogate long noncoding RNAs (lncRNA). The reannotation pipeline involved probe mapping to the human genome followed by filtering of probes with multiple alignments to the human genome sequence and the cross-reference of probe genomic coordinates with those from the most updated lncRNA compendia (GENCODE, Broad Institute Human lincRNA, LNCipedia, NONCODE). Details are provided in the associated publication.

distribution: custom-commercial

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


title: NimbleGen Arabidopsis thaliana Gene Expression 12x135K Array [080924_AT6_expr]

city: Singapore

first: Yifeng

last: XU

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

organism: Arabidopsis thaliana

description: BUILD: Release 6

manufacture_protocol: See manufacturer's website at http://www.nimblegen.com/


title: NanoString nCounter Rat miRNA v1.1

city: New York

first: Vasily

last: Aushev

state: NY

address: 1 Gustave Levy Pl.

department: Environmental Medicine & Public Health

institute: Icahn School of Medicine at Mount Sinai

organism: Rattus norvegicus

technology: other

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


title: NanoString nCounter Rat miRNA v1.2


title: [HuEx10st_Hs_ENSG] Affymetrix Human Exon 1.0 ST Array [Brainarray Version 21.0.0]

status: Public on Apr 21 2017

city: Horsholm

first: Peter

middle: H

last: Hagedorn

state: Danmark

address: Fremtidsvej 3

department: Research

country: Denmark

institute: Roche Innovation Center Copenhagen A/S

description: This platform is identical to GPL5175 but a custom CDF environment was used to extract data [Brainarray Version 21.0.0, HuEx10st_Hs_ENSG].

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

manufacture_protocol: Affymetrix standard protocol


title: RiboArray™ miDETECTTM Mouse Array

status: Public on Mar 01 2017

city: guangzhou

first: jiafan

last: liu

address: No. 601 West Whampoa Road, Tianhe District, guangzhou

country: China

institute: Jinan University

organism: Mus musculus

description: based on mirBase 21

distribution: commercial

manufacture_protocol: Manufacture protocol not provided.


title: Illumina Genome Analyzer II (Brassica rapa subsp. oleifera)

status: Public on Jan 25 2017

organism: Brassica rapa subsp. oleifera


title: Illumina HiSeq 3000 (Medicago truncatula)

status: Public on Jan 30 2017

organism: Medicago truncatula


title: Agilent FZ_IBG1_4plex_064191

status: Public on Aug 23 2017

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

organism:
Gluconobacter oxydans
Escherichia coli
Corynebacterium glutamicum
Bacillus subtilis subsp. subtilis str. 168

description: Corynebacterium glutamicum (NC_006958), Bacillus subtilis str. 168 (NC_000964), Gluconobacter oxydans (NC_006677, NC_006672, NC_006673, NC_006674, NC_006675, NC_006676), Escherichia coli (NC_000913)

manufacturer: Agilent Technologies (Waldbronn, Germany)

manufacture_protocol: see Agilent Technologies


title: Illumina MiSeq (Listeria weihenstephanensis)

status: Public on Jan 26 2017

organism: Paenilisteria weihenstephanensis


title: Illumina MiSeq (Phalaenopsis amabilis)

organism: Phalaenopsis amabilis


title: Illumina HiSeq 2500 (Escherichia coli B str. REL606)

organism: Escherichia coli B str. REL606


title: AB 5500xl Genetic Analyzer (Thermosynechococcus elongatus BP-1)

organism: Thermosynechococcus vestitus BP-1


title: Agilent-033839 Chr21_60k_final [Probe name version]

city: Atlanta

first: Benjamin

last: Rambo-Martin

state: Georgia

address: 1600 Clifton Road

institute: Centers for Disease Contol and Prevention

description: Arrays of this design have barcodes that begin with 16033839 or 2533839.


title: Illumina HiSeq 2000 (Prunus avium)

organism: Prunus avium


title: Illumina HiSeq 2000 (Legionella pneumophila str. Paris)

organism: Legionella pneumophila str. Paris


title: Illumina Genome Analyzer II (Brassica oleracea var. botrytis)

organism: Brassica oleracea var. botrytis


title: Illumina Genome Analyzer II (Brassica oleracea; Brassica rapa)

organism:
Brassica rapa
Brassica oleracea


title: LU-endothelial to hematopoietic transition qRT-PCR array

city: Lund

first: Carolina

last: Guibentif

country: Sweden

institute: Lund University

technology: RT-PCR

description: PCR assay

manufacture_protocol: see manufacturer's website


title: Illumina NextSeq 500 (Hypsibius dujardini)

organism: Hypsibius dujardini


title: Agilent-035953 Custom 60K Sus scrofa Array [Feature Number Version]

status: Public on Jan 27 2017

city: Lelystad

first: Marcel

last: Hulst

state: Flevoland

address: Edelhertweg 15

department: Livestock research

country: Netherlands

institute: Animal Sciences Group

organism: Sus scrofa


title: Illumina HiSeq 2000 (Nostoc punctiforme PCC 73102)

organism: Nostoc punctiforme PCC 73102


title: TaqMan OpenArray Human MicroRNA Panel

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Homo sapiens

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


title: Illumina NextSeq 500 (Oncorhynchus mykiss)

organism: Oncorhynchus mykiss


title: Illumina HiSeq 2000 (Ictidomys tridecemlineatus)

status: Public on Jan 23 2017

organism: Ictidomys tridecemlineatus


title: Illumina HiSeq 2000 (Cyanidioschyzon merolae strain 10D)

status: Public on Jan 22 2017

organism: Cyanidioschyzon merolae strain 10D


title: Illumina HiSeq 2500 (Epinephelus coioides)

organism: Epinephelus coioides


title: Illumina MiSeq (Fibrobacter succinogenes subsp. succinogenes S85)


title: Illumina HiSeq 2000 (Porphyromonas gulae)

status: Public on Jan 21 2017

organism: Porphyromonas gulae


title: Illumina HiSeq 4000 (Yarrowia lipolytica)

organism: Yarrowia lipolytica


title: Illumina HiSeq 2500 (Oncorhynchus mykiss)

status: Public on Jan 29 2017


title: Illumina HiSeq 2000 (Neodiprion lecontei)

status: Public on Jan 20 2017

organism: Neodiprion lecontei


title: Illumina HiSeq 2000 (Dufourea novaeangliae)

organism: Dufourea novaeangliae


title: Illumina HiSeq 2000 (Pisolithus microcarpus)

organism: Pisolithus microcarpus


title: Illumina HiSeq 2000 (Acanthamoeba castellanii)

organism: Acanthamoeba castellanii


title: Illumina HiSeq 2000 (Acanthamoeba castellanii; Candidatus Protochlamydia amoebophila)

organism:
Acanthamoeba castellanii
Candidatus Protochlamydia amoebophila


title: Illumina HiSeq 2000 (Matthiola incana)

status: Public on Jan 19 2017

organism: Matthiola incana


title: Illumina HiSeq 2000 (Malcolmia maritima)

organism: Malcolmia maritima


title: Aligent-047614

city: Shenyang

first: Hongyan

last: Wang

state: Liaoning Province

address: Nanjing North St. 117

department: Department of Periodontology

institute: School of Stomatology, China Medical University

organism: Porphyromonas gingivalis

manufacture_protocol: Agilent


title: [PrimeView] Affymetrix Human Gene Expression Array [Brainarray ENTREZG Version 20]

city: Wroclaw

first: Pawel

last: Karpinski

address: Marcinkowskiego 1

department: Department of Genetics

country: Poland

institute: Wroclaw Medical University

description: This is identical to GPL15207 but a custom CDF environment was used to extract data [Brainarray (version 20)].

manufacture_protocol: See details from Affymetrix.


title: Illumina HiSeq 2000 (Iberis amara)

organism: Iberis amara


title: Illumina HiSeq 2000 (Lobularia maritima)

organism: Lobularia maritima


title: Illumina HiSeq 2000 (Eruca vesicaria subsp. sativa)

organism: Eruca vesicaria subsp. sativa


title: Agilent-015906 Salmonella enterica 4x44K microarray (Feature Number version)

city: Taipei

first: Chang

last: Chieh-Hsiang

address: No. 1, Sec. 4, Roosevelt Rd

country: Taiwan

institute: National Taiwan University

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

technology: spotted oligonucleotide

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


title: Illumina NextSeq 500 (Ramazzottius varieornatus)

organism: Ramazzottius varieornatus


title: Illumina HiSeq 2000 (Aubrieta x cultorum)

organism: Aubrieta x cultorum


title: Illumina HiSeq 2000 (Erysimum cheiri)

organism: Erysimum cheiri


title: Illumina NextSeq 500 (Meiothermus ruber; Thermosynechococcus elongatus BP-1)

organism:
Meiothermus ruber
Thermosynechococcus vestitus BP-1


title: Agilent-021827 Human miRNA Microarray G4470C (miRNA ID version, miRBase v18)

organism: Homo sapiens


title: Illumina HiSeq 2500 (Potamopyrgus antipodarum)

organism: Potamopyrgus antipodarum


title: Agilent-031181 Unrestricted_Human_miRNA_V16.0_Microarray 030840 (miRBase release 18.0 miRNA ID version)

status: Public on Jan 18 2017

city: Lausanne

first: Nicolas

last: Mermod

address: Station 6, EPFL

department: Lab of Molecular Biotechnology

country: Switzerland

institute: University of Lausanne

description:
Feature Number version of this Array is GPL15018

Human and human viral miRNAs

Arrays of this design have barcodes that begin with 16031181 or 2531181.

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: Illumina HiSeq 2500 (Bos taurus indicus x Bos taurus taurus)

organism: Bos indicus x Bos taurus


title: Agilent-026578 Rat piRNA microarray (feature number version)

city: Rockville

first: Panos

last: Pan

address: 9430 Key West Avenue

institute: Arraystar Inc.

organism: Rattus norvegicus


title: [HT_HG-U133A] Affymetrix Human Genome U133A Array (custom CDF: HTHGU133A_Hs_ENTREZG.cdf version 20.0.0)

city: Boston

first: David

last: Wolski

state: MA

address: 55 Fruit Street

department: Gastrointestinal Unit

institute: Massachusetts General Hospital

description: Identical to GPL3921 but used a custom CDF

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2000 (Burkholderia multivorans)

last: GEO

organism: Burkholderia multivorans


title: Illumina HiSeq 2500 (Bos grunniens)

organism: Bos grunniens


title: Agilent-026578 Rat piRNA microarray (probe name version)


title: Arraystar Human LncRNA Pathway microarray (Metabolism)


title: Illumina MiSeq (Heligmosomoides polygyrus bakeri; Mus musculus)

status: Public on Jan 17 2017

organism:
Mus musculus
Heligmosomoides polygyrus bakeri


title: [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array (HGU133A2_Hs_ENTREZG_20.0.0)

description: Brainarray: HGU133A2_Hs_ENTREZG_20.0.0

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 2000 (Bos taurus indicus x Bos taurus taurus)


title: Illumina HiSeq 2500 (Brevibacterium linens)

status: Public on Jan 16 2017

organism: Brevibacterium linens


title: Illumina HiSeq 2500 (Mus musculus; Trichuris muris)

organism:
Mus musculus
Trichuris muris


title: GeoChip 5.0 (60k)

status: Public on Jan 12 2017

city: BEIJING

first: LINWEI

last: WU

address: NO.1 TSGINAHU UNIVERSITY

institute: TSINGHUA UNIVERSITY

organism: uncultured soil microorganism


title: Illumina HiSeq 1500 (Zea mays)

organism: Zea mays


title: Illumina HiSeq 2500 (Salmonella enterica subsp. enterica serovar Typhi)


title: Illumina HiSeq 4000 (Leucoraja erinacea)

status: Public on Jan 13 2017

organism: Leucoraja erinaceus


title: Illumina HiSeq 2500 (Solanum pennellii)

organism: Solanum pennellii


title: Illumina HiSeq 2500 (Ictidomys tridecemlineatus)

organism: Ictidomys tridecemlineatus


title: Illumina NextSeq 500 (Synechocystis sp. PCC 6803)

organism: Synechocystis sp. PCC 6803


title: Illumina HiSeq 2500 (Vibrio parahaemolyticus RIMD 2210633)

organism: Vibrio parahaemolyticus RIMD 2210633


title: Illumina HiSeq 2000 (Anopheles anthropophagus)

organism: Anopheles anthropophagus


title: [hta20_Hs_ENTREZG version 20] [HTA-2_0-st] GeneChip Human Transcriptome Array 2.0

organism: Homo sapiens

manufacture_protocol: This is identical to GPL20265  but a custom CDF environment was used to extract data [Brainarray Version 20, hta20 ]. CDF and other files can be downloaded at: (see web link below).


title: Agilent-071531 Gmaxv275_phytozomev10 G4123A [Probe Name]

status: Public on Jan 14 2017

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 411 Borlaug Hall, 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

organism: Glycine max

description:
Soybean v275 based on phytozome v10.  CGH array 1x1M probes

Arrays of this design have barcodes that begin with 16071531 or 2571531

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 4000 (Chlorocebus aethiops)

organism: Chlorocebus aethiops


title: Illumina MiSeq (Mycobacterium tuberculosis H37Rv)

status: Public on Jan 10 2017

organism: Mycobacterium tuberculosis H37Rv


title: Affymetrix ENCODE 2.0R array

city: Kumamoto

first: Ko

last: Ishihara

address: 2-2-1 Honjyo

department: Priority Organization for Innovation and Excellence

country: Japan

institute: Kumamoto University


title: 121115_Psativum_SB_expr

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

organism: Lathyrus oleraceus

description: - 2 oligo/target sequence except for the 323 miRNA which have 1 oligo/sequence - Sens: Reverse (+ Reverse and Forward sens for miRNA)-all probes are triplicate-40795 Unigen including 18 control

first: Judith

last: Burstin

first: Gregoire

last: Aubert

first: Sandrine

last: Balzergue


title: Illumina HiSeq 2500 (Phaeodactylum tricornutum CCAP 1055/1)

status: Public on Jan 09 2017

organism: Phaeodactylum tricornutum CCAP 1055/1


title: Agilent-035301 Chickpea Whole Genome 2x400K Gene Expression Custom Microarray

status: Public on Jan 07 2017

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

organism: Cicer arietinum

description: Custom Agilent Chickpea Whole Genome 2x400K Gene Expression Microarray (AMADID: 035301) designed by Genotypic Technology Private Limited


title: Illumina HiSeq 2500 (Chlorocebus aethiops)


title: SABiosciences custom panel CAPH11327E

first: Meghali

last: Goswami

address: 10 Center Drive

department: Hematology

institute: NHLBI

description:
PCR assay
SABiosciences RT² Profiler panel of PCR assays.


title: Geochip 4.0

status: Public on Jan 05 2017

city: Beijing

first: Yuguang

last: Zhang

address: Haidian

institute: Chinese Academy of Forestry

manufacturer: Institute for environmental genomics (IEG)

first: Xiao

last: Lu

first: Jing

last: Cong


title: Agilent Plasmodium falciparum 3D7 2x400K CGH microarray designed by Genotypic Technology (AMADID: G4124A_025327)

status: Public on Jan 06 2017

organism: Plasmodium falciparum 3D7


title: Illumina HiSeq 2500 (Bombus terrestris)

organism: Bombus terrestris


title: Agilent Custom Rice Gene Expression 44x44k Array (AMADID: 064815) designed by Genotypic Technology Private Limited

organism: Oryza sativa


title: Illumina HiSeq 4000 (Oryza sativa)

status: Public on Jan 31 2017


title: Agilent custom R palustris Gene Expression  8x15k Array (AMADID: 075878) by Genotypic Technology Private Ltd

organism: Rhodopseudomonas palustris


title: Illumina HiSeq 2000 (Labrus bergylta)

organism: Labrus bergylta


title: Agilent-033620 Sinica_orchid_2 [Probe name version]

first: Hsin-Hung

last: Yeh

address: No. 128, Sec. 2, Academia Road, Nankang,

department: ABRC

institute: Academia Sinica

organism: Phalaenopsis aphrodite

description:
The sequences used for probe design were collected from the Orchidstra 2.0 database (http://orchidstra2.abrc.sinica.edu.tw/orchidstra2/index.php). Totally, 42,973 probes were designed on this oligonucleotide array.

This platform describes the second version of this array referred to in the below citation.


title: Custom Agilent Chickpea Whole Genome 8x60K (AMADID: 037094) designed  by Genotypic Technology Private Limited

first: Deepti

last: Saini

first: Rohini

last: Garg

first: Vikash

middle: K

last: Singh

first: Mukesh

last: Jain

first: Raja

last: Mugasimangalam

first: Sudha

middle: N

last: Rao

first: Aiyaz

last: Mohamed


title: Illumina MiSeq (Staphylococcus aureus subsp. aureus NCTC 8325)

last: GEO


title: Illumina NextSeq 500 (Parabronema skrjabini)

organism: Parabronema skrjabini


title: Illumina HiSeq 2000 (Parabronema skrjabini)


title: Illumina NextSeq 500 (Brugia malayi)

status: Public on Jan 04 2017

organism: Brugia malayi


title: Illumina HiSeq 2500 (Streptococcus pneumoniae D39)

organism: Streptococcus pneumoniae D39


title: Agilent-026377 Candida albicans Custom Gene Expression Microarray 8x15K

organism: Candida albicans

description: Agilent Custom Candida albicans Gene Expression Microarray 8x15K (AMADID: 026377)designed by Genotypic Technology Private Limited.


title: ThermoFisher Taqman® OpenArray® Drosophila melanogaster Custom 56 Assay Plate

city: Columbia

first: Elizabeth

middle: G

last: King

state: MO

address: 105 Tucker Hall

department: Biological Sciences

institute: University of Missouri

organism: Drosophila melanogaster

description: PCR assay


title: Illumina HiSeq 2000 (Orychophragmus violaceus)

status: Public on Jan 03 2017

organism: Orychophragmus violaceus


title: Illumina HiSeq 2000 (Paenibacillus polymyxa)

organism: Paenibacillus polymyxa


title: QiaGen miScript miRNA PCR Array Mouse miRBase Profiler Product number 331223

city: Louisville

first: Huang-Ge

state: KY

address: 505 S Hancock Street

department: James Graham Brown Cancer Center

institute: University of Louisville

organism: Mus musculus


title: Illumina HiSeq 1500 (Francisella tularensis)

organism: Francisella tularensis


title: Agilent Bovine miRNA 8x60K Microarray (AMADID: 072447)

status: Public on Jan 02 2017

organism: Bos indicus


title: Illumina HiSeq 2500 (Phycomyces blakesleeanus)

organism: Phycomyces blakesleeanus


title: Klug lab - Rhodobacter sphaeroides - 15k array Version 2 (144 sRNA)

status: Public on Jan 01 2017

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

organism: Cereibacter sphaeroides 2.4.1

manufacture_protocol: The microarray contains probes against 4,304 protein-coding genes, 79 rRNA and tRNA genes, and 144 intergenic regions. Three antisense probes with a length of 60 nt were designed for each gene or intergenic region, when possible. Microarray construction was performed following the instructions of Agilent (www.chem.agilent.com).


title: Illumina HiSeq 2000 (Mesocricetus auratus)

organism: Mesocricetus auratus


title: Nanostring nCounter Human microRNA

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

institute: IOR

organism: Homo sapiens


title: Agilent-071342 LncRNA [Probe Name version]

city: Guangzhou

first: Liang

state: Guangdong

address: Xingnan Road 521

department: Translational Medicine Research Center

institute: Guangdong Women and Children Hospital

description:
Arrays of this design have barcodes that begin with 16071342 or 2571342.

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 Names.


title: 110404_MM9_BH_ChIP_HX3

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description: NCBI mouse mm9

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


title: NimbleGen Pongo pygmaeus ChIP 385k Custom Array [101112_HG17_HG18_Pongo_SP_ChIP]

city: Bologna

first: Stefania

last: Purgato

address: via Selmi 3

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

organism:
Pongo pygmaeus
Pongo abelii
Homo sapiens

description: July 2007 (WUGSC 2.0.2/ponAbe2)

manufacture_protocol: See www.nimblegen.com


title: Agilent-074336 Oryza sativa alternatively spliced transcript detecting microarray (OsASDM1, version 1)

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

organism: Oryza sativa

description: 37,868 genes are representatively annotated at IRGSP, RAP database (http://rapdb.dna.affrc.go.jp/). The 5,254 loci encode for 11,938 alternatively spliced transcripts (Table 1). Among these, the 7,502 transcripts are designed for unique exon features as indicated above. Finally, the 175,192 feature probes representing 40,139 transcripts from 44,552 are designed and designated as alternatively spliced transcripts detecting microarray (ASDM).

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


title: NimbleGen Pongo pygmaeus ChIP 385k Custom Array [080313_PP-EC-HS_GD_ChIP]

description: July 2007 (WUGSC 2.0.2/ponAbe2)


title: Agilent-031241 D. rerio 8x60k V3 Zebrafish 026437 [Genome Zv9 version]

city: Koblenz

first: Andreas

last: Schüttler

address: Am Mainzer Tor 1

department: Department Biochemistry and Ecotoxicology

institute: German Federal Institute of Hydrology

organism: Danio rerio

description:
Probes mapped to Zebrafish Genome Zv9
D. rerio (Zebrafish) Oligo Microarray V3
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.


title: Agilent-027382 Danio_Rerio_TF_V2 [Feature Number version]

city: Syracuse

first: Samantha

middle: Jane

last: England

address: 107 College Place

department: Biology

country: USA

institute: Syracuse University

description:
Arrays of this design have barcodes that begin with 16027382 or 2527382.

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: NimbleGen Treponema denticola Array [2006-07-27_TI243275_60mer; PROBE_DESIGN_ID version]

city: Chiyoda-ku

first: Kazuyuki

last: Ishihara

state: Tokyo

address: Misakicho 2-1-14

department: Microbiolgy

institute: Tokyo Dental College

organism: Treponema denticola

description:
designname=TI243275_analysis data
designid=4396
native array description file: TI243275_analysis data.ndf
Treponema denticola ATCC 35405, complete genome.


title: Agilent-071342 LncRNA [Feature number version]

last: Zhang

description:
Arrays of this design have barcodes that begin with 16071342 or 2571342.

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-037376 lincRNA PJ final

city: Gent

first: Pieter-Jan

last: Volders

address: De Pintelaan 185

country: Belgium

institute: Ghent University

description:
Arrays of this design have barcodes that begin with 16037376 or 2537376.

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-063615 P. gingivalis 8x15K v1.0

organism: Porphyromonas gingivalis

manufacturer: Hokkaido System Science Co., Ltd. (Agilent eArray)


title: Nucleic Acid Programmable Protein Arrays (NAPPA) Serous Ovarian Discovery Array - Validation Array

city: Tempe

first: Benjamin

middle: A

last: Katchman

state: AZ

address: 727 E. Tyler St.

institute: Arizona State University

technology: spotted peptide or protein

distribution: non-commercial


title: Nucleic Acid Programmable Protein Array (NAPPA) Serous Ovarian Discovery Array - GST1


title: Nucleic Acid Programmable Protein Array (NAPPA) Serous Ovarian Discovery Array - GST4


title: Nucleic Acid Programmable Protein Array (NAPPA) Serous Ovarian Discovery Array - GST2


title: Nucleic Acid Programmable Protein Array (NAPPA) Serous Ovarian Discovery Array - FLAG


title: Agilent-049002 zebrav360k026437 026437 [Probe name version]

city: Jinju

first: June-Woo

last: Park

address: 17, Jegok-gil, Munsan-eup

department: Environmental Risk Research

institute: Korea Institute of Toxicology

description:
D. rerio (Zebrafish) Oligo Microarray V3

Arrays of this design have barcodes that begin with 16049002 or 2549002.

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: Agilent-035451 0GyN 8x60k CGH array [Feature Number version]

status: Public on Jul 27 2016

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

institute: Institute for Environmental Science

description:
Agilent-035451 0GyN

Arrays of this design have barcodes that begin with 16035451 or 2535451.

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: Nucleic Acid Programmable Protein Array (NAPPA) Serous Ovarian Discovery Array - GST3


title: Agilent-034954 0GyM 4x180k CGH array [Feature Number version]

description:
Agilent-034954 0GyM

Arrays of this design have barcodes that begin with 16034954 or 2534954.

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-037371 0GyK 4x180k CGH array [Feature Number version]

description:
Agilent-037371 0GyK

Arrays of this design have barcodes that begin with 16037371 or 2537371.

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-064096 SaMW2_exp_140130_2

city: Kagoshima City

first: Kentaro

last: Oyama

address: Sakuragaoka 8-35-1

institute: Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan

organism: Staphylococcus aureus subsp. aureus MW2

description:
Arrays of this design have barcodes that begin with 16064096 or 2564096.

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: [HT_HG-U133A] Affymetrix HT Human Genome U133A Array

status: Public on Jun 26 2006

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

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® HT Human Genome U133 Array Plate Set enables researchers to perform large-scale studies by analyzing whole-genome expression for up to 96 samples at a time. The set comprises a U133A and U133B plate, measuring expression levels for more than 33,000 well-characterized genes and UniGene clusters.

Keywords = high density oligonucleotide array

relation: Alternative to: GPL18283 (Alternative CDF [AffyProbeMine])


title: Agilent-037372 0GyJ 4x180k CGH array [Feature Number version]

description:
Agilent-037372 0GyJ

Arrays of this design have barcodes that begin with 16037372 or 2537372.

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 2500 (Bacillus subtilis PY79)

status: Public on Apr 29 2015

last: GEO

organism: Bacillus subtilis PY79


title: Illumina HiSeq 2500 (Listeria monocytogenes 10403S)

status: Public on Sep 14 2015

organism: Listeria monocytogenes 10403S


title: Illumina Genome Analyzer IIx (Capra hircus)

status: Public on Feb 23 2012

organism: Capra hircus


title: Exiqon miRCURY LNA microRNA array; 7th generation REV - hsa, mmu & rno; batch 208520-22; lot 35101-35101 (miRBase 19.0)

status: Public on Aug 12 2015

city: Nanjing

first: Pengfei

last: Li

state: Jiangsu

address: NO.155 Hanzhong Road, Baixia District

department: Clinical Laboratory

institute: Jiangsu Province Hospital of TCM

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 19.0
ArrayContents_CurrentNameColumnCoverage=Homo sapiens and related vira:94.38%

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


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [CDF: hugene10st_Hs_ENSG_16.0.0]

status: Public on Sep 02 2014

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: Probe set data extracted from custom CDF (HuGene11stv1_Hs_ENSG.cdf v16.0.0). See below web link for CDF and other related files.

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


title: Agilent-027432 Syn6803_expressions454_4-3probes

status: Public on Jul 31 2012

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

institute: University of Freiburg

organism: Synechocystis sp. PCC 6803

description:
4 probes per feature on chr except for internals; otherwise 3 probes per feature; done on 454 data with new annotation

Arrays of this design have barcodes that begin with 16027432 or 2527432.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Illumina Genome Analyzer II (Escherichia coli)

status: Public on Apr 14 2010

organism: Escherichia coli


title: Fluidigm qPCR gene panel for CML analysis

city: Lund

first: Mikael

middle: Nils Erik

last: Sommarin

state: skåne

address: klinikgatan 26, BMC B12

department: Department of molecular hematology

institute: Lund university

description: PCR assay


title: HiSeq X Ten (Sus scrofa)

status: Public on Jan 12 2017

organism: Sus scrofa


title: ISB Halobacterium Spotted Microarray

status: Public on May 12 2006

city: Seattle

first: Michael

middle: Hiroshi

last: Johnson

state: WA

address: 1441 North 34th Street

department: Computational Biology

institute: Institute for Systems Biology

organism: Halobacterium salinarum NRC-1

first: Bruz

last: Marzolf

first: Nitin

last: Baliga

relation: Alternative to: GPL13682 (gene-centered version)

relation: Alternative to: GPL22925 (gene-centered version using locus tags)

manufacture_protocol:
MIAME platform type: spotted
MIAME availability: Arrays printed at ISB can be purchased, contact bmarzolf@systemsbiology.org for information.

Standard Operating Procedures for the Virtek(ESI) Spotter

*** Always remember that spotter pins are extremely fragile at the tips ***

To make spotter source plates:
1.	Total volume should be 4-8 ul
2.	Usually, DNA should be in 3X SSC and 1.5M betaine.  This can be done most accurately be putting an appropriate amount of source material in spotting plates, then drying down with the speedvac and resuspending in the final volume of 3X SSC, 1.5M betaine.

Things not to do:
1.	Move slides after printing starts ? just touching a slide can shift it and other slides enough to ruin the grid geometry.
2.	Use air to blow dust off of slides - you could move the slides
3.	Press the RED EMERGENCY button if it's not a emergency- this will turn off the spotter controller and abort the entire run
4.	Use PCR products that have been purified, then dried down and resuspended in a very small volume, this is known to cause erratic surface tension and cause spots to run together.

When starting a new print run:
1.	Allow blank slides to sit at 65% humidity for 24 hours
2.	Renew sticky mat if it's dirty
3.	Fill humidifier and turn on
4.	Pull water out of water bath, wipe out bath and fill reservoir to get bath back to correct level- IT IS EXTREMELY IMPORTANT NOT TO OVERFILL THE WATERBATH OR SONICATOR BATH, WATER SHOULD BE JUST ABOVE THE POINT WHERE CUT RUNNING UP THE PIN ENDS
5.	Place slides on the deck with label on the right-hand side.  Secure slides by using spacer glass slides held in place with the magnets at the end of the platform.
6.	Measure total X and Y distances spanned by slides, enter sizes under Calibration for Arraying->Slides
7.	Print one "dip" with no source plate to ensure that pins are hitting all slides in the same plate (slight errors in Y direction especially can really throw off grid locations.)
8.	Use the metal brace and spacer slides held by magnets to stabilize and line up the slides
9.	Stabilize humidity at approximately 65%
10.	Put blotting slide in place
To print slides:
1.	Spin down 4 source plates at 2000 rpm for one minute
2.	Put three remaining source plates (in order) at 4 C
3.	Check blotting slide for blocked pins, change slide. Remove clogged/sticking pins and try to remedy by cleaning pin and/or printhead hole.  If a pin isn't spotting on the blotter, it may just not be contacting the blotter.see if it's been spotting on actual slides.
4.	Change water bath water at beginning of run.
5.	Check level of water reservoir and sonicator bath- add water if necessary
6.	Check humidity
7.	Double-check orientation and number of source plate
8.	Press operator button
9.	Re-seal old plate and put in cold room
10.	Set timer
11.	Check old plate out, new plate in on printing checklist

When finished printing for the day:
1.	Seal all plates and place in cold room
2.	Turn off  Spotter light
3.	Turn monitor off
4.	Leave computer ON

When finished with entire printing:
1.	Allow spotter humidity to slowly drop and slides dry out.
2.	Remove slides and place into plastic Telechem slide boxes.
3.	Turn off Spotter light
4.	Turn off fan/humidifier
5.	Place boxes in desiccator at least 12 hours.
6.	Blow off slides in boxes, then bake at 85 C for 2 hours.
7.	Etch numbers and corners on slides (corners on back side), blow dry and place in desiccator ready for prehyb.

Things to do periodically:
1.	Just keep an eye on the slides themselves to see if the grids are being formed as expected

To clean a clogged pin:
1.	Remove pin by pulling out from top with a small forceps.
2.	Dip in water and blow dry with air tip, repeatedly if necessary.
3.	Make sure water reservoir is sufficiently full - low water often causes clogging.

Random experiments that we have tried and their results:

1.	Effect of Temperature and Humidity on Spot Size
Printed H-70 in 3X SSC onto Telechem Amine slides.  Temperatures chosen were 18 C, 20 C, 22 C, and humidities of 40%, 50%, 60% resulting in 9 different conditions.  Hybridization was with labeled PCR primer for 3 hours.
Results: Differences were seen in specific grids, but grid-grid variability was too high to establish a conclusive pattern.  Spots generally were most intense in a 90-100 micron diameter, then had a lighter "halo" that could extend to 130-150 microns.  It appeared that "Halo" size was often smallest at 18 C, 130-140 microns.  We decided to print at ambient temperature, generally 18-20 C.

2.	Effect of Volume and Humidity on Maximum Spots per Dip
Pooled 96 wells of purified PCR product and added SSC for a final concentration of 3X.  Then set up a plate so that 8 pins would print 1ul, another 8 would print 2ul, 4ul, 6ul, 8ul and 10ul.  This 48-pin dip was then printed 25 spots in the Y direction, across 10 plain glass slides for a total of 250 spots.  This print was done with increasing indent at 75%, 70%, 65%, 60% and 55% humidity.
Results: At 1-2ul, pins ran out of juice at 25-50 spots at all humidities.  At 4ul, 200-225 spots could be printed at 65% or higher humidity.  With 6ul or more, 250 spots could be printed at 65% or higher humidity.  Based upon this, we chose 65% humidity for all printing.

Halobacterium Flip Chips: This print is outdated
Use 24 pins (4Y by 6X), 16Y by 16X grids at 200 micron spot-spot spacing.
Plate order: 1-7, Control, Control(rotated), 7(rot), 6(rot), 5(rot), 4(rot), 3(rot), 2(rot), 1(rot)
Typical number of slides printed: 36 (strange layout used to get 2 identical "supergrids" limited to 2 columns of 18)
This layout uses the same "2 supergrid" layout as Yeast, except that there are not duplicates located directly next to each other.  Instead, after the plates have been printed normally, they are printed in reverse order and rotated, placing duplicates in a supergrid in exact opposite corners.


title: Agilent-021827 Human miRNA Microarray G4470C (Feature Number version)

status: Public on Oct 20 2011

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Human miRNA Microarray 3.0

Arrays of this design have barcodes that begin with 16021827 or 2521827.

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: GPL18509
Alternative to: GPL22949


title: Illumina HiSeq 2000 (Brassica napus)

status: Public on May 17 2012

organism: Brassica napus


title: Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Probe Name version)

status: Public on Aug 22 2008

organism: Mus musculus

description:
Designed to truly represent all known genes in the mouse genome and their resulting transcripts, Agilent's Whole Mouse Genome Oligo – 4X44K microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts. Content for this microarray was generated from leading public databases, including RefSeq, RIKEN, NIA, Ensembl, RIKEN, UCSC Goldenpath, and Unigene.

*** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL4134.


title: Agilent-070154 Rat miRNA Microarray (miRNA ID version version)

status: Public on Dec 08 2016

organism: Rattus norvegicus

description: Grid_GenomicBuild = rn4:RGSCv3.4:Nov2004


title: UMAN MI READYARRAY

status: Public on Jan 11 2017

city: Santiago

first: Leonardo

middle: Ignacio

last: Pavez

state: Santiago

address: Av Manuel Montt #948

country: Chile

institute: Universidad de Las Américas

organism: Homo sapiens


title: Illumina HiSeq 2000 (Plasmodium falciparum)

status: Public on Feb 07 2013

organism: Plasmodium falciparum