title: [HuEx-1_0-st_v2] Affymetrix Human Exon 1.0 ST v2 Array [CDF: Brainarray Version 14.1.0, HuEx10stv2_Hs_ENTREZG]

status: Public on Jul 09 2013

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

country: Germany

institute: University of Münster

organism: Homo sapiens

technology: in situ oligonucleotide

description: Probe set data extracted from custom CDF [Brainarray Version 14.1, HuEx10stv2_Hs_ENTREZG]

distribution: custom-commercial

manufacture_protocol: See manufacturer's web site


title: Agilent-022499 Ciona intestinalis 244k Microarray

status: Public on Oct 29 2013

city: Kyoto

first: Yutaka

last: Satou

state: Kyoto

address: Kitashirakawa Oiwake-tyo, Sakyo-ku

department: Department of zoology, Graduate School of Science

country: Japan

institute: Kyoto University

organism: Ciona intestinalis

description:
Agilent-022499 Expression244k200901

Arrays of this design have barcodes that begin with 16022499 or 2522499.

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: Operon Array-Ready 29K Oligo Sets for the Pig Genome Version 1.0 and the Pig Genome Oligo Extension Set Version 1.0

status: Public on Apr 16 2013

city: Lelystad

first: Marcel

last: Hulst

state: Flevoland

address: Edelhertweg 15

department: Livestock research

country: Netherlands

institute: Animal Sciences Group

organism: Sus scrofa

technology: spotted oligonucleotide

description: Zhao SH, Recknor J, Lunney JK, Nettleton D, Kuhar D, Orley S, Tuggle CK: Validation of a first-generation long-oligonucleotide microarray for transcriptional profiling in the pig.Zhao SH, Recknor J, Lunney JK, Nettleton D, Kuhar D, Orley S, Tuggle CK., Genomics. 2005 Nov;86(5):618-25.

manufacture_protocol: Oligonucleotides were printed in duplicate on epoxide slides by operon. Operon probes are designed from The TIGR Gene Index Database SsGI Release 5.0 released 10/1/02. The Oligo set contains 10,665 70mer probes representing 10,665 Sus scrofa gene sequences with a hit to a known human, mouse, or pig transcript and some sequences containing a 3' expressed sequence tag. The Pig Genome Oligo Extension Set Version 1.0 contains 2,632 70mer probes representing 2632 Sus scrofa gene sequences with at least one 3' EST.


title: NimbleGen Mouse 2.1M tiling (MM9_Deluxe_Prom_ChIP_HX1)

status: Public on Apr 19 2013

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

organism: Mus musculus

description: Promoter tiling array using NimbleGen platform. Mouse MM9 build. Probe length 50-75bp isothermal. -8kb/+3kb around promoters.


title: UCSF/Sil lab-Histoplasma capsulatum-G186Aorfs1

status: Public on Apr 09 2013

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

organism: Histoplasma capsulatum

description: 70mer probes were designed by Array Oligo Selector (Genome Biol. 4:R9) for the Histoplasma capsulatum G186AR predicted gene set from the Genome Sequencing Center at Washington University.  One probe was designed for each "high confidence" gene, and two probes were designed for each "low confidence" gene.

distribution: non-commercial

first: Catherine

middle: K

last: Foo

first: Diane

middle: O

last: Inglis

first: Anita

last: Sil

manufacture_protocol: Spotted using DeRisi arrayer in Center for Advanced Technology, Genentech Hall, Mission Bay.  70-mer oligonucleotides representing each predicted gene are resuspended in 3XSSC and spotted on poly-lysine slides purchased from Erie Scientific.


title: Agilent-027134 Ciona intestinalis 44kx4 Microarray

description:
Agilent_Array_027134_D_GEO_20100130.txt

Arrays of this design have barcodes that begin with 16027134 or 2527134.

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: MSU/McDermott_Cmerolae_12x135K_v1.0

status: Public on Mar 31 2013

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

organism: Cyanidioschyzon merolae

description:
NimbleGen design name: 110204_Cmerolae_DS_exp_HX12; order # 32590.
Native array description file: 110204_Cmerolae_DS_exp_HX12.ndf
Native array description file: 110204_Cmerolae_DS_exp_HX12.ngd

Design includes 6,699 genes from two ecologically relevant isolates originating from Dragon Spring (CCMEE isolate 5508) and Lemonade Creek (CCMEE isolate 5578), sequences from the C. merolae strain 10D reference genome, and coding regions identified in two cDNA pyrosequencing libraries derived from Dragon Spring Cyanidiales mat material.

A set of five 60-mer probes represent each gene (for nearly all genes). Each probe is replicated in four distinct blocks on the array. The design includes random GC and other control probes.

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


title: Agilent customized Chicken CGH Microarray 4x180K

first: Hideaki

last: Abe

address: 2-24 Tanaka-Sekiden-cho, Sakyo

department: Wildlife Research Center

organism: Gallus gallus

manufacture_protocol: genome assembly: galGal3:v2.1:May2006


title: Customized Yarrowia lipolytica array

status: Public on Mar 30 2013

city: Wilmington

first: Seung-Pyo

last: Hong

state: DE

address: Experimental Station, E328/B47B

department: BCS&E

institute: DuPont Central Research and Development

organism: Yarrowia lipolytica

description:
Standard expression design for Y. lipolytica sequences provided by customer.  Each probe replicated 4x on chip.  Design includes random GC probes.
re-layout of NimbleGen design_id 4687 (NimbleGen design name 2006-11-20_Y_lipolytica_60mer)
native array description file: 081113_Y_lipolytica_expr.ndf
native array description file: 081113_Y_lipolytica_expr.ngd


title: Whole Genome Equine Array

city: College Station

first: Priyanka

last: Kachroo

address: University Drive

institute: Texas A&M University

organism: Equus caballus

manufacture_protocol:
1. 15ul of 3X saline-sodium citrate (SSC) buffer to each well of the 300pM oligonucleotide set to make a 20uM oligonucleotide solution
2. Transfer to an orbital shaker for 1 hour at room temperature with speed of 100rpm. At the end of 1 hour, oligos are ready to be printed
3. The Texas A&M equine oligoarrays were printed on GAPS coated glass (Corning) with  aminosinale surface chemistry using using Telechem Type SMP3 printing pins
4. Printing of the array was done by maintaining 30% realtive humidity and by using 48-pin in the print-head, redipping pins after every 50 slides
5. Slides were then maintained at 80 degree temperature for 2 hours to complete the printing process. The slides were sealed and stored at room temperature in absence of light and moisture.


title: JCVI_PFGRC_Campylobacter jejuni version 3_NCTC11168

status: Public on Mar 29 2013

city: Ames

first: Zuo-Wei

last: Wu

state: IA

address: 1113 Veterinary Medicine Bldg

institute: Iowa state university

organism: Campylobacter jejuni

description: This set includes the probes only for strain NCTC11168.

manufacture_protocol: see manufacturer's web site http://pfgrc.jcvi.org/index.php/microarray.html


title: Aedes aegypti whole genome array

city: New Haven

first: Tonya

middle: M

last: Colpitts

state: CT

address: 300 Cedar St, TAC S410

department: Internal Medicine, Section of Infectious Diseases

institute: Yale University School of Medicine

organism: Aedes aegypti

description:
ORF array of the aedes aegypti genome
native array description file:  aaegypti_60mer_probes_rank4.filter
native array description file:  OID14431.ngd

manufacture_protocol: High-density DNA array with X4 build. See manufacturer's website at http://www.nimblegen.com/.


title: LinkGenomics Whole Genome DNA Microarray

city: Houston

first: Takahiro

last: Kogawa

state: TX

address: 1515 Holcomb Blvd

department: Breast Medical

institute: MD Anderson

technology: spotted DNA/cDNA

manufacture_protocol: Whole Genome DNA Microarray was created with complete coverage of the human genome using 12310 individually amplified bacterial artificial chromosomes (BAC) clones. All BAC clones were cultured from a single colony and validated by PCR amplification using clone specific primers that were designed in-house. Extracted BAC DNAs were BstYI restricted and amplified by ligation-mediated PCR. The products were printed on glass slides with an inkjet-type spotter.


title: MBPL human 30k P10

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

manufacture_protocol: Arrayer obtained from Dr. Patrick O. Brown MGuide II and ArrayMarker program version 2.3.2 (Dr. Joseph DeRisi, university of California, San Francisco) with 48 spotting pins (TeleChem).We control printing condition in temperature 28~29°C and Humidity about 37~48%, and printing on September 2009. cDNA clones were purchased from Incyte Genomics and 7334 sequence-verified clones were amplified by PCR.We purified these 7334 clones by isopropanol precipitation and used 3× saline-sodium citrate (SSC) as spotting solution. cDNA spotted on GAPS II coated slides (Corning Incorporated) coating of pure gamma amino propylsilane.


title: Illumina Genome Analyzer II (Salmo trutta)

last: GEO

organism: Salmo trutta

technology: high-throughput sequencing

distribution: virtual


title: Illumina HiSeq 2000 (Hirudo medicinalis)

status: Public on Mar 28 2013

organism: Hirudo medicinalis


title: MBPL human 30k P9

manufacture_protocol: Arrayer obtained from Dr. Patrick O. Brown MGuide II and ArrayMarker program version 2.3.2 (Dr. Joseph DeRisi, university of California, San Francisco) with 48 spotting pins (TeleChem).We control printing condition in temperature 25~26°C and Humidity about 49~51%, and printing on January 2009. cDNA clones were purchased from Incyte Genomics and 7334 sequence-verified clones were amplified by PCR.We purified these 7334 clones by isopropanol precipitation and used 3× saline-sodium citrate (SSC) as spotting solution. cDNA spotted on GAPS II coated slides (Corning Incorporated) coating of pure gamma amino propylsilane.


title: HMS/MLB_Cbf1Tye7_44k_validation

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

organism: Saccharomyces cerevisiae

manufacture_protocol: In situ oligosynthesized array with proprietary synthetic sequences that target Cbf1 and Tye7 putative binding sites in genomic context, with 0 to 4 mutations.


title: HMS/MLB_Cbf1Tye7_44k

manufacture_protocol: In situ oligosynthesized array with proprietary synthetic sequences that target Cbf1 and Tye7 putative binding sites in genomic context.


title: Agilent-029238 KSHV tiling microarray

city: Emeryville

first: Henry

middle: H

address: 4560 Horton Street

department: Infectious Diseases Group

institute: Novartis Institutes for BioMedical Research

organism:
Homo sapiens
Human herpesvirus 8 strain rKSHV.219

description: KSHV tiling microarray AMADID: 029238

manufacture_protocol: Standard Agilent printing methods. 60-mer tiling oligonucleotides. Offset = 20 nts from both strands of the KSHV genome (GQ994935.1). Platform contains both KSHV and human probes, all of which are used in the LOWESS normalization protocol. Platform contains standard Agilent controls probes, including probes that detect spike-in control transcripts.


title: Illumina HiSeq 2000 (Brassica oleracea var. capitata)

organism: Brassica oleracea var. capitata


title: Agilent-013282 Human Genome CGH Microarray (Feature number version) [ALT to GPL2897 minus400]

status: Public on Mar 26 2013

city: Heidelberg

first: Thomas

last: Wolf

address: Im Neuenheimer Feld 580

institute: DKFZ


title: Agilent-022755 momNIFTS10 (probe version)

status: Public on Mar 27 2013

city: Shizuoka

first: Hiroshi

last: Fujii

state: Shizuoka

address: 485-6 Okitsunakacho, Shimizu

department: Division of Citrus Research

institute: Institute of Fruit Tree Science, NARO

organism: Prunus persica

description:
Momo 091030

Arrays of this design have barcodes that begin with 16022755 or 2522755.

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: NimbleGen Tomato ITAG2 gene promoters 720K array

city: Tsukuba

first: Yasuhiro

last: Ito

state: Ibaraki

address: 2-1-12 Kannondai

department: Food Biotechnology Division

institute: National Food Research Institute

organism: Solanum lycopersicum

description:
Tomato genome sequence build SL2.31 provided by the Tomato Genome Consortium and a gene prediction model (ITAG2) provided by the International Tomato Annotation Group (ITAG) (http://solgenomics.net/organism/Solanum_lycopersicum/genome)
Probes (52-70 mers tiled throughout non-repetitive sequences at a median spacing of 80 bp) were designed from the 2-kb upstream (putative promoter) regions of the predicted genes.

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


title: GE Healthcare/Amersham Biosciences CodeLink™   Mouse Whole Genome Bioarray

status: Public on Sep 29 2005

city: Tempe

first: Randall

last: Lockner

state: AZ

address: 7700 S River Parkway

department: Bioinformatics

institute: GE Healthcare Life Sciences

description:
Mice exhibit high similarity to many human biological pathways, making it a key model system for human physiological and toxicological studies in drug discovery applications. The probe sequences, representing well annotated, full length and partial mouse gene sequences, were designed based on sequences selected from the NCBI UniGene build #139, RefSeq database (April 1, 2004 release) and dbEST database (July 31, 2004 release).Well-annotated mRNA or coding sequences were chosen to ensure usefulness for a large range of applications in basic research, biotechnology, and drug development. Each sequence was carefully screened to ensure high-quality, specific probe design, and to reduce redundancy of gene targets. All of the probes designed to these sequences were functionally tested, and over 97% were functionally validated against 14 mouse tissues to ensure best representation of the gene and biologically relevant results.
For flexibility and data preservation, CodeLink Mouse Whole Genome Bioarrays are compatible with lower density CodeLink mouse bioarrays. This means that existing data from CodeLink UniSet Mouse 20K Bioarrays can be continuously used in future studies along with newly generated data from CodeLink Mouse Whole Genome Bioarrays.

CodeLink users can submit data to GEO by exporting tab-delimited text files from the CodeLink software. The "Feature_id" header will need to be renamed to "ID_REF", and the "Normalized_intensity" header to "VALUE" before uploading the exported tables.

In addition, users are encouraged to include additional raw data columns in their data uploads. These additional columns do not need to be renamed.

distribution: commercial


title: Illumina Genome Analyzer II (Dictyostelium discoideum AX4)

organism: Dictyostelium discoideum AX4


title: [U133AAofAv2] Affymetrix GeneChip HT-HG_U133A Early Access Array

status: Public on Jan 05 2007

city: Minato-ku

first: Kenta

last: Shibuya

state: Tokyo

institute: Affymetrix Japan

organism: Homo sapiens

description: HT-HG_U133A (early access version) high-throughput array (Affy part number 520276)

manufacture_protocol: see manufacturer's web site


title: Illumina Genome Analyzer IIx (Capsella grandiflora)

organism: Capsella grandiflora


title: Illumina Genome Analyzer IIx (Capsella rubella)

organism: Capsella rubella


title: Illumina HiSeq 2000 (Capsella grandiflora)


title: Illumina Genome Analyzer IIx (Alishewanella agri)

organism: Alishewanella agri


title: Illumina Genome Analyzer IIx (Alishewanella aestuarii)

organism: Alishewanella aestuarii


title: Illumina Genome Analyzer IIx (Alishewanella jeotgali)

organism: Alishewanella jeotgali


title: Illumina Genome Analyzer IIx (Arabidopsis thaliana x Arabidopsis arenosa)


title: Illumina Genome Analyzer IIx (Neisseria gonorrhoeae F62)

status: Public on Mar 23 2013

organism: Neisseria gonorrhoeae F62


title: Custom miRCURY LNA microRNA Array ready-to-spot probe sets V7.1

city: Sinjuku-ku

first: Masami

last: Tanaka

address: Sinjuku 6-1-1

institute: Tokyo Medical University

organism: Mus musculus

description: based on mirBase v7.1

manufacturer: Hokkaido System Science Co.,Ltd. (consigned from Exiqon A/S)

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


title: Illumina HiSeq 2000 (Salmonella enterica subsp. enterica serovar Typhimurium str. LT2)


title: Derived from GPL9460 - Applied Biosystems Human TaqMan Low Density Array (TLDA, v1.0)

status: Public on Mar 22 2013

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

technology: RT-PCR

description: Microfluidic 384-well TaqMan real time RT-PCR platform version 1.0

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2000 (Arabidopsis arenosa)

organism: Arabidopsis arenosa


title: Escherichia coli whole-genome tiling array (2 x 105K) [Feature number version]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Escherichia coli

manufacture_protocol: Agilent customer-designed arrays


title: Illumina HiSeq 2500 (Apis mellifera carnica)

status: Public on Mar 21 2013

organism: Apis mellifera carnica


title: Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Gene ID version)

city: Paris

first: Danièle

last: Lacasa

address: 15 rue de l'Ecole de Médecine

country: France

institute: INSERM

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


title: 2006-07-18 Scerevisiae ChIP Stefan Jentsch MPI Biochemistry S.cerevisiae 385K Tiling Array Version 1

city: Martinsried/Munich

first: Jörg

last: Renkawitz

address: Am Klopferspitz 18

department: Molecular Cell Biology

institute: Max Planck Institute of Biochemistry

organism: Saccharomyces cerevisiae

description:
S.cerevisiae S288C (see e.g. SGD (http://www.yeastgenome.org/))
2006-07-18_Scerevisiae_ChIP_Stefan Jentsch MPI Biochemistry S.cerevisiae 385K Tiling Array 2006-07-18_Scerevisiae_ChIP_Stefan Jentsch MPI Biochemistry S.cerevisiae 385K Tiling Array Version 1.ndf
2006-07-18_Scerevisiae_ChIP_Stefan Jentsch MPI Biochemistry S.cerevisiae 385K Tiling Array Version 1.pos


title: Agilent-024568 Escherichia coli whole-genome tiling array (2 x 105K) [Probe name version]


title: NCode Human miRNA Microarray V3

city: Albuquerque

first: shannon

last: bruse

state: New Mexico

address: 2425 ridgecrest drive SE

institute: lovelace respiratory research institute


title: 100304 Scer2 MS Chip Stefan Jentsch MPI Biochemistry S.cerevisiae 135K Tiling Array Version 2

description:
S.cerevisiae S288C (see e.g. SGD (http://www.yeastgenome.org/))
100304_Scer2_MS_Chip_Stefan Jentsch MPI Biochemistry S.cerevisiae 135K Tiling Array Version 2.ndf
100304_Scer2_MS_Chip_Stefan Jentsch MPI Biochemistry S.cerevisiae 135K Tiling Array Version 2.pos


title: Custom Salmonella Typhimurium Gene Expression 8x15k designed by Genotypic Technology Pvt. Ltd. (AMADID: 017809)

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: Salmonella enterica subsp. enterica serovar Typhimurium


title: Salmonella enterica serovar Typhimurium SL1344 4X72K Custom arrays

city: Dublin

first: Shane

last: Dillon

address: Trinity College

department: Department of Microbiology

country: Ireland

institute: Moyne Institute of Preventive Medicine

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

description: The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are submitted 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: NimbleGen S. cerevisiae Gene Expression (12x135K) (probe-level)

status: Public on Mar 20 2013

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.


title: LC Sciences Pig miRNA array LC_MRA-1013_miRPig_16 [miRNA ID version]

city: Houston

first: Christoph

last: Eicken

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism: Sus scrofa

description:
MRA-1013_miRPig_16 (miRNA ID version)
Pig miRNA microarray with 100% coverage of unique mature miRNAs listed in miRBase version 16.
Reporter BioSequence Type = ss_oligo
Reporter BioSequence Polymer Type = DNA

manufacture_protocol: 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: SABiosciences Human Cell Cycle PCR assay panel [PAHS-020Z]

status: Public on Mar 19 2013

city: Chicago

first: Ilya

last: Ulasov

address: 5841 S Maryland ave SBRO J339

institute: University of Chicago

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


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array (Brainarray CustomCDF, HGU133Plus2_Hs_UG_Version 12.cdf)

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

institute: University Heidelberg

manufacture_protocol: Affymetrix standard protocol


title: Renji Hospital ABI Human TaqMan® MicroRNA Assays V2.0

city: Shanghai

last: Shen

address: 145 Shan Dong Middle Road

department: Department of Rheumatology

country: China

institute: Renji Hospital, JiaoTong University School of Medicine

manufacture_protocol: See manufacturer's website (http://www.appliedbiosystems.com/).


title: Applied Biosystems TaqMan Array Human MicroRNA A+B Cards Set v3.0

city: Hong Kong

first: Yujuan

last: Dong

address: Ngan Shing Street

department: Surgery

country: Hong Kong

institute: The Chinese University of Hong Kong

description: PCR assay


title: Agilent-020382 Human Custom Microarray 44k (Feature Number version)

city: Heidelberg

first: Thomas

last: Wolf

address: Im Neuenheimer Feld 580

institute: DKFZ


title: Agilent-028639 RTIQ Oncorhynchus mykiss

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

organism: Oncorhynchus mykiss

description:
rainbow trout chip

Arrays of this design have barcodes that begin with 16028639 or 2528639.

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 IIx (Streptococcus pyogenes)

last: GEO

organism: Streptococcus pyogenes


title: Agilent-024616 ISCA human array 4X180K v2 (Feature Number version)

status: Public on Mar 16 2013

city: Rochester

first: Ganesh

last: Boora

state: MN

address: 200 First Street

institute: Mayo Clinic

organism: Homo sapiens

description:
Agilent-024616 ISCA human 180K v2 7-16-09
ISCA; International Standard Cytogenomic Array

Arrays of this design have barcodes that begin with 16024616 or 2524616.

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: 454 GS FLX Titanium (Mus musculus)


title: Illumina HiSeq 2000 (Botryotinia fuckeliana)

organism: Botrytis cinerea


title: Illumina HiSeq 2000 (Shewanella sp. MR-4)

organism: Shewanella sp. MR-4


title: Illumina HiSeq 2000 (Shewanella loihica PV-4)

organism: Shewanella loihica PV-4


title: Illumina HiSeq 2000 (Shewanella putrefaciens CN-32)

organism: Shewanella putrefaciens CN-32


title: Illumina HiSeq 2000 (Shewanella sp. ANA-3)

organism: Shewanella sp. ANA-3


title: Illumina HiSeq 2000 (Shewanella sp. MR-7)

organism: Shewanella sp. MR-7


title: Illumina HiSeq 2000 (Shewanella oneidensis MR-1)

organism: Shewanella oneidensis MR-1


title: Solanum lycopersicum Custom 4x180K Array designed by Genotypic Technology Private  Limited. (AMADID:043310)

organism: Solanum lycopersicum


title: Custom NimbleGen Shewanella oneidensis MR-1 Tiling  v2 [NimbleGen_MR1_2005K_1]

status: Public on Mar 18 2013

city: Berkeley

first: Wenjun

last: Shao

address: 2151 Berkeley Way

department: Molecular and Cell Biology

institute: University of California

description:
NC_004347 and NC_004349
100318_Shew_one_MR1_JK_EXP_HX1.ndf

manufacture_protocol: see NimbleGen website


title: Illumina Genome Analyzer II (Xenorhabdus nematophila)

organism: Xenorhabdus nematophila


title: PacBio RS (Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992)

status: Public on Mar 14 2013


title: Illumina HiSeq 2000 (Solanum pimpinellifolium)

organism: Solanum pimpinellifolium


title: AB SOLiD 4 System (Entamoeba invadens)

status: Public on Mar 13 2013

organism: Entamoeba invadens


title: Illumina HiSeq 2000 (Shewanella sp. W3-18-1)

organism: Shewanella sp. W3-18-1


title: Illumina HiSeq 2000 (Shewanella amazonensis SB2B)

organism: Shewanella amazonensis SB2B


title: Illumina Genome Analyzer II (Candida albicans)

organism: Candida albicans


title: Illumina Genome Analyzer IIx (Plasmodium falciparum)

organism: Plasmodium falciparum


title: NimbleGen Nasonia vitripennis 1.0 Whole-genome Tiling Array Set (3 of 4) [080222_Nvit1_JC_ChIP_HX1]

city: Augusta

first: Justin

last: Choi

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

institute: Georgia Regents University

organism: Nasonia vitripennis

description:
This is a Jewel Wasp (Nasonia vitripennis) whole-genome tiling array set (3 of 4) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen. The array is based on assembly Nvit_1.0.

Native array description file: 080222_Nvit1_JC_ChIP_HX1_3.ndf
Native array description file: 080222_Nvit1_JC_ChIP_HX1_3.pos
Native array description file: 080222_Nvit1_JC_ChIP_HX1_3.ncd

The GenBank and RefSeq accessions.version for the scaffolds in the .pos file are available in the supplementary file 'GPL16802_accessions_for_array_set.txt'.

first: John

last: Colbourne

first: Jeong

first: Jack

last: Werren


title: NimbleGen Nasonia vitripennis 1.0 Whole-genome Tiling Array Set (4 of 4) [080222_Nvit1_JC_ChIP_HX1]

description:
This is a Jewel Wasp (Nasonia vitripennis) whole-genome tiling array set (4 of 4) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen. The array is based on assembly Nvit_1.0.

Native array description file: 080222_Nvit1_JC_ChIP_HX1_4.ndf
Native array description file: 080222_Nvit1_JC_ChIP_HX1_4.pos
Native array description file: 080222_Nvit1_JC_ChIP_HX1_4.ncd

The GenBank and RefSeq accessions.version for the scaffolds in the .pos file are available in the supplementary file 'GPL16803_accessions_for_array_set.txt'.


title: Agilent Vvulnificus SS microarray V1.0

status: Public on Mar 12 2013

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

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


title: [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [custom CDF: moex10stv1_52_37e_0111genes.cdf], transcript(gene) version

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

organism: Mus musculus

description:
Probe set data extracted from custom CDF:
moex10stv1_52_37e_0111genes.cdf
The CDF was based on a complete re-alignment of oligonucleotide probes to the genome and transcriptome (Ensembl 52, ASTD 1.1; further information on http://bioinfo.i-med.ac.at).

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

manufacture_protocol: See manufacturer's web site


title: Oligo GEArray for Human Endothelial Biology

city: Tokyo

first: Hidekata

last: Yasuoka

address: 35 Shinanomachi, Shinjuku

department: Internal Medicine

institute: Keio University School of Med

organism: Homo sapiens

manufacture_protocol: See manufaturer's website


title: Agilent TurbotV2_SSFN microarray2013

organism: Scophthalmus maximus


title: Oligo GEArray for Human Chemokine & Receptors


title: Human MDR resistance in cancer qRT-PCR array

city: Bethesda

first: Robert

last: Robey

address: 37 Convent Drive Rm 2112

institute: NCI

description: TaqMan-based qRT-PCR assay


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENSG version 13.0.0]

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: Probe set data extracted from custom CDF (HuGene10stv1_Hs_ENSG.cdf v13.0.0). See below web link for CDF and other related files.

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


title: Human 70-mer oligonucleotide microarray

city: Jinan

first: Ji

last: Ma

state: Shandong

address: West Wen Hua Road 107

department: Department of Hematology

institute: Qilu Hospital, Shandong University

manufacture_protocol: A human genome 70-mer oligonucleotide microarray was obtained from CapitalBio Corporation (Beijing, China) Briefly, a human genome oligonucleotide set (version 4.0) consisting of 5’ amino acid-modified 70-mer probes and representing 25,100 well-characterized Homo sapiens genes was purchased from Operon. Then Oligonucleotides were dissolved in EasyArrayTM spotting solution (CapitalBio Corp) , and printed on PolymerSlide, in which the surface is covered by a thin layer of aldehyde group modified three-dimensional polymer chain (CapitalBio Corp.).


title: Illumina HiSeq 2000 (Capsicum annuum var. glabriusculum)

organism: Capsicum annuum var. glabriusculum


title: Illumina Genome Analyzer IIx (Oryza coarctata)

status: Public on Mar 06 2013

organism: Oryza coarctata


title: Illumina Genome Analyzer (Streptococcus pneumoniae TIGR4)

status: Public on Mar 07 2013

organism: Streptococcus pneumoniae TIGR4


title: Illumina HiSeq 2000 (Methanopyrus kandleri AV19)

status: Public on Mar 08 2013

organism: Methanopyrus kandleri AV19


title: Miltenyi PIQOR(TM) Human antisense Ubiquitin-PS Microarray

status: Public on Mar 09 2013

city: Cologne

first: Kerstin

last: Brinkmann

address: Joseph-Stelzmann-Str. 9

department: IMMIH2, Geb. 37

institute: University Hospital Cologne


title: SABiosciences  TGFβ/BMP Signaling Pathway PCR array

status: Public on Mar 02 2013

city: Rome

first: fiorella

last: ciaffoni

state: Italy

address: Viale Regina Elena 299

department: Cellular Biology and Neurosciences

institute: Istituto Superiore di Sanità

description:
TGFβ/BMP Signaling Pathway PCR arrayPCR assay
SABiosciences RT² Profiler panel of PCR assays.


title: Agilent Seabass SS microarray V2.0

organism: Dicentrarchus labrax


title: SHOU miRNA Fishes 1K

status: Public on Mar 10 2013

first: Yuanshuai

last: Fu

address: Hu-Cheng-Huan Road

institute: Shanghai Ocean University

organism: Paralichthys olivaceus

manufacture_protocol: 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://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: Illumina HiSeq 2000 (Escherichia coli O157:H7)

status: Public on Mar 04 2013

organism: Escherichia coli O157:H7


title: JCVI Synechococcus sp. WH 8102 19K v2.0 [gene-centered version]

status: Public on Mar 01 2013

city: Sydney

first: Sasha

last: Tetu

state: NSW

address: North Ryde

department: CMBS

country: Australia

institute: Macquarie University

organism: Parasynechococcus marenigrum WH 8102

technology: mixed spotted oligonucleotide/cDNA

description: This is the gene/ORF-centered version of Plaform GPL7449

manufacture_protocol: Primers were designed to yield 2142 PCR amplicons of approximately 800 base pairs, and 70-mer oligonucleotides were designed for another 389 genes that were less than 200 base pairs in length or could not be amplified by PCR.  PCR amplicons and oligonucleotides were suspended in 50% DMSO and spotted onto Corning UltraGAPS slides using an Intelligent Automation Systems arrayer.  Each gene is represented six times on the array.  Negative controls include 50% DMSO / 50% DI water and air.  A mixture of PCR amplicons, Arabidopsis spike-in controls, and Arabidopsis 70-mer oligonucleotides were used as positive controls.  Slides were air dried for at least 30 minutes after printing.  DNA was irreversibly cross-linked to the slides with 250 mJ/cm^2 UV energy by using a Stratagene Stratalinker.  Slides were stored at room temperature in a dessicator.


title: Illumina HiSeq 2000 (Capsicum chinense)

organism: Capsicum chinense


title: Illumina Genome Analyzer II (Escherichia coli BL21(DE3))

organism: Escherichia coli BL21(DE3)


title: Agilent-022364 Oryzias latipes array (Feature Number version)

status: Public on Mar 05 2013

city: Durham

first: Hilary

last: Miller

address: LSRC Science Drive Rm A305

institute: Duke University

organism: Oryzias latipes

description:
Agilent-022364 Olat_15207genes_1208 array
Grid_Name: 022364_D_F_20081216

Arrays of this design have barcodes that begin with 16022364 or 2522364.

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 (Physcomitrella patens subsp. patens)

last: GEO

organism: Physcomitrium patens


title: Illumina HiSeq 2000 (Caragana korshinskii)

organism: Caragana korshinskii


title: [HT_HG-U133A] Affymetrix HT Human Genome U133A Array [custom CDF: ENTREZ brainarray v. 14]

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description:
alternate CDF for GPL3921
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.


title: Princeton Microarray Facility AOA Archetype Microarray BC014

city: Boston

first: Silvia

last: Newell

state: Massachusetts

address: 675 Commonwealth Ave.

institute: Boston University

organism: synthetic construct

description: AOA probes printed in triplicate

manufacture_protocol:
1.The probe oligonucleotides are printed onto Corning Ultragaps or Erie Scientific Epoxy Silane slides using a DeRisi style arrayer (DiRisi et al., 1997) and pins from Parallel Synthesis.
2.The 70-mer oligo probes (Operon Technologies) were adjusted to a concentration of 0.05 mg ml-1 in 50% DMSO and were spotted on CMT-GAPS amino silane-coated glass slides (Corning, Corning, NY).
3. After printing, the slides were baked at 80°C for 3 h and stored in the dark at room temperature under slight vacuum in a dessicator.


title: NimbleGen Mus musculus 2.1M 2007-09-21_MM8_Deluxe_Promoter_HX1 tiling design

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

organism: Mus musculus

description: Promoter tiling array using NimbleGen platform. Mouse MM8 build. Probe length 50-75bp isothermal. Tiled regions are 8200bp upstream and 3000bp downstream of 5 prime ends of genes as annotated in MM8.


title: NimbleGen Brucella melitensis 16M Gene Expression Array [BMEL-00001-X]

city: Madison

first: Erik

last: Petersen

address: 1656 Linden Dr.

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

organism: Brucella melitensis bv. 1 str. 16M

description: NimbleGen design name BMEL-00001-X.  The 3198 ORFs of B. melitensis are represented by seventeen 24-mer probe pairs (PM/MM) per gene.


title: JCVI Synechococcus sp. CC9311 21k v1.0 [gene-centered version]

organism: Synechococcus sp. CC9311

description: This is the gene/ORF-centered version of Plaform GPL7622

manufacture_protocol: Unique 70-mer oligonucleotides were designed for 2892 genes of the Pseudomonas fluorescens Pf-5 genome. Oligonucleotides were suspended in 50% DMSO and spotted onto Corning UltraGAPS slides using an Intelligent Automation Systems arrayer. Each gene is represented six times on the array. Negative controls include 50% DMSO / 50% DI water and air. Arabidopsis spike-in controls and Arabidopsis 70-mer oligonucleotides were used as positive controls. Slides were air dried for at least 30 minutes after printing. DNA was irreversibly cross-linked to the slides with 250 mJ/cm^2 UV energy by using a Stratagene Stratalinker. Slides were stored at room temperature in a dessicator.


title: Agilent-037908 Sider C. elegans 60K

city: Cambridge

first: Xicotencatl

last: Gracida

address: 52 Oxford St.

institute: Harvard University

organism: Caenorhabditis elegans


title: Illumina HiSeq 2000 (Fragaria vesca)

organism: Fragaria vesca


title: Illumina HiSeq 2000 (Toxoplasma gondii)

status: Public on Mar 11 2013

organism: Toxoplasma gondii


title: Soybean 1.3 Million CGH microarray

city: Saint Paul

last: Stupar

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

organism: Glycine max

description:
Tiling array designed from the Glycine max genome (assembly version 1.01).  This genome version is deposited at DDBJ/EMBL/GenBank under the accession number ACUP01000000.
Whole-genome tiling array with a median length of approximately 500 bp between adjacent probes
110718_Gmax_Williams82_RS_CGH.ndf
110718_Gmax_Williams82_RS_CGH.pos

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


title: Agilent-037970 Listeria monocytogenes EGD-e [Probe Name version]

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

organism: Listeria monocytogenes EGD-e

description:
Arrays of this design have barcodes that begin with 16037970 or 2537970.

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.


title: [HT_HG-U133B] Affymetrix HT Human Genome U133B Array [custom CDF: ENTREZ brainarray v. 14]

organism: Homo sapiens

description:
alternate CDF for GPL9197
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.

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2000 (Apostichopus japonicus)

organism: Apostichopus japonicus


title: Candida albicans ENS oligo array version 1.0 [Full array version]

city: New Delhi

first: Rajendra

last: Prasad

state: Delhi

address: New Mehrauli Road

department: School of Life Sciences

institute: Jawaharlal Nehru University

organism: Candida albicans

manufacture_protocol:
1.Oligos are arrayed in Greiner 384-well flat-bottom plates. Each well contains 600 pmol of 70-mer oligo.
2. Resuspend oligos in Corning buffer to 20 uM and rearray 10 µL into 384-well, Genetix polystyrene V-bottom plates (cat# X6004).
3. Shake plates near maximum rotational speed on flat-bed shaker for 1 minute.
4. Centrifuge plates at 2000 rpm for 3 minutes.
5. Print oligonucleotides in duplicate on corning ultragaps II slides, using a Biorobotics spotting device and 16 pins.
6. Fix DNA on slides using UV treatment (1200 mJ default set up in a stratalinker device)


title: NanoString nCounter mRNA Human Cancer Reference Kit

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

technology: other


title: Plasmodium falciparum Custom 244k Array designed by Genotypic Technology Pvt. Ltd. & Prof.Ashis K Das  (AMADID:019056)

status: Public on Jan 10 2013

city: Bangalore

first: Genotypic

last: technology

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

institute: Genotypic Technology

organism: Plasmodium falciparum 3D7

first: Das

last: Ashis

first: M

middle: C

last: Raja


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZG_15.1.0]

status: Public on Jan 18 2013

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: Brainarray: HuGene10stv1_Hs_ENTREZG_15.1.0

relation: Alternative to: GPL6244 (Alternative CDF)


title: Illumina Genome Analyzer II (Sinocyclocheilus anophthalmus)

status: Public on Aug 29 2012

organism: Sinocyclocheilus anophthalmus


title: Illumina HiSeq 2000 (Pseudopodoces humilis)

organism: Pseudopodoces humilis


title: Illumina HiSeq 2000 (Sinocyclocheilus angustiporus)

organism: Sinocyclocheilus angustiporus


title: Agilent-021750 Schmidtea mediterranea 45K Smed_WI_expression_chip_Reddien_v2 015536 (Feature Number version)

status: Public on Nov 28 2011

first: Mansi

last: Srivastava

address: 9 Cambridge Center

institute: Whitehead Institutue

organism: Schmidtea mediterranea

description:
Arrays of this design have barcodes that begin with 16021750 or 2521750.

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 2000 (Sinocyclocheilus anophthalmus)


title: Custom Human ABC transporter gene RT-PCR assays

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

description:
Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
qPCR was performed in RotorGene 6000 produced by Corbett Research (Sydney, Australia)

manufacture_protocol: Custom made-to-order or pre-designed TaqMan assays were used with protocol recommended by the producer (Life Technologies Corp., Carlsbad, CA, USA)


title: Illumina Genome Analyzer II (Sinocyclocheilus angustiporus)


title: AB SOLiD 4 System (Trichoderma reesei)

status: Public on Feb 25 2013

organism: Trichoderma reesei


title: [Blactisa520677F] Custom Affymetrix Bifidobacteria Genome Array [gene-level]

status: Public on Feb 20 2013

city: Logan

first: Taylor

middle: S

last: Oberg

state: UT

address: 8700 Old Main

department: NDFS

institute: Utah State University

organism: Bifidobacterium animalis subsp. lactis


title: Affymetrix Maize Genome Array [CDF:SYNG007a520046]

city: Guelph

first: Gregory

last: Downs

address: 50 Stone Road E

country: Canada

institute: University of Guelph

organism: Zea mays

description:
custom microarray with 82,661 probe-sets and 1,322,551 probes.

The microarray platform was annotated by determining homology between probe sequences and the cDNA sequences for predicted transcripts from the filtered gene set of the 4a.53 release of the B73 genome using BLAST

annotations as described in http://dx.doi.org/10.1104/pp.112.213231

The identifiers (in the CLONE_ID column) are gene model IDs from the public maize genome sequencing project:
http://maizesequence.org
http://maizegdb.org/

SYNG007a520046.cdf


title: Agilent-039659 hs_miR_18_addvirus 038169

city: Nanjing

first: Huibo

last: Wang

state: Jiangsu

address: 300# Guangzhou Rd.

department: Department of Neurosurgery

institute: First Affiliated Hospital of Nanjing Medical University

description:
Arrays of this design have barcodes that begin with 16039659 or 2539659.

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: Plasmodium Vivax Custom 244k Array designed by Genotypic Technology Pvt. Ltd. & Prof.Ashis K Das (AMADID:019103)

status: Public on Jan 12 2013

organism: Plasmodium vivax


title: Illumina HiSeq 2000 (Capsicum annuum)

status: Public on Oct 17 2012

last: GEO

organism: Capsicum annuum


title: Agilent Human gut metagenome array

city: Clermont-Ferrand

first: Nicolas

last: Parisot

address: 28 place Henri Dunant

institute: EA 4678 CIDAM

organism: human gut metagenome

description:
Human gut microbiota
Agilent-030618 and Agilent-040558 design IDs.
Human Gut chip "HuGChip": A phylogenetic microarray targeting 66 families described in the human gut microbiota.


title: AB SOLiD 4 System (Arabidopsis thaliana)

status: Public on Sep 21 2011

organism: Arabidopsis thaliana


title: Illumina HiSeq 2000 (Candida dubliniensis)

organism: Candida dubliniensis


title: Phalanx Yeast OneArray® v1

status: Public on Jun 15 2011

city: Hsinchu Science Park

first: Phalanx

last: Biotech

state: Hsinchu

address: 6 Technology Road 5, 6th Floor

institute: Phalanx Biotech

organism: Saccharomyces cerevisiae

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


title: Applied Biosystems TaqMan Array Human MicroRNA Cards (A+B Card Set v3)

status: Public on Apr 27 2012

city: Jena

first: Udo

middle: R.

last: Markert

address: Bachstraße 18

department: Department of Obstetrics

country: Germany

institute: Universitätsklinikum Jena

organism: Homo sapiens

description: The TaqMan® Array Human MicroRNA Card Set v3.0 is a two card set containing a total of 384 TaqMan® MicroRNA Assays per card

manufacture_protocol: see manufacturer's website


title: NimbleGen S. cerevisiae Gene Expression (12x135K) (gene-level)

status: Public on May 04 2011

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

country: USA

institute: NimbleGen Systems, Inc.

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


title: Agilent-031181 Unrestricted_Human_miRNA_V16.0_Microarray 030840 (miRBase release 14.0 miRNA ID version)

status: Public on Dec 15 2011

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

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.

relation: Alternative to: GPL16770 (miRNA ID version)


title: Agilent-030860 Salmon Immunity and Quality 15k custom array_SIQ6

status: Public on Jan 29 2013

city: aas

first: Fabian

last: Grammes

address: Arboretvn. 2

department: CIGENE

institute: Norwegian University of Life Sciences

organism:
Oncorhynchus mykiss
Salmo salar


title: Agilent-028679 SurePrint G3 Human Exon 4x180K Microarray (Probe Name Version)

status: Public on Sep 08 2011

description:
Human4x180KExon

Arrays of this design have barcodes that begin with 16028679 or 2528679.

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: OSU-CCC Human and Mouse MicroRNA Microarray Version 4.0

status: Public on Aug 01 2012

city: Bethesda

first: Aaron

last: Schetter

state: MD

address: 37 Convent Drive, Building 37, Room 3050

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

organism:
Homo sapiens
Mus musculus

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

relation:
Alternative to: GPL14184
Alternative to: GPL16744

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: Illumina Genome Analyzer IIx (Gallus gallus)

status: Public on Jul 01 2011

organism: Gallus gallus


title: Escherichia coli whole-genome tiling array (2 x 105K)

status: Public on Jun 15 2010

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

organism: Escherichia coli

description: The Platform data table reflects a condensed representation of the array's replicate features. The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.

relation:
Alternative to: GPL16858
Alternative to: GPL16859

manufacture_protocol: Agilent customer-designed arrays


title: Illumina HumanRef-8 v3.0 [gene-centered version]

status: Public on Jul 26 2010

city: Heidelberg

first: Lukas

last: Chavez

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

technology: oligonucleotide beads

description:
The HumanRef-8 v3.0 Expression BeadChip features up-to-date content derived from the National Center for Biotechnology Information Reference Sequence (NCBI RefSeq) database (Build 36.2, Release 22).
Please use the GEO Data Submission Report Plug-in v1.0 for Gene Expression which may be downloaded from https://icom.illumina.com/icom/software.ilmn?id=234 to format the normalized and raw data. These should be submitted as part of a GEOarchive. Instructions for assembling a GEOarchive may be found at http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html
This platform is the gene-centered version of the original GPL6883 platform.


title: Phalanx Mouse OneArray® v2

status: Public on Jun 14 2011

country: Taiwan

organism: Mus musculus

description:
Annotation is based on two databases:
. NCBI RefSeq release 45
. Ensembl release 60 cDNA sequences and
mus_musculus_core_61_37n annotations


title: Illumina HumanMethylation450 BeadChip [UBC enhanced annotation v1.0]

status: Public on Mar 04 2013

city: Vancouver

first: Magda

last: Price

institute: University of British Columbia

manufacture_protocol: See manufacturer's website


title: Agilent-030687 Oryctolagus cuniculus kyushu_matsuo_custom [Probe Name version]

status: Public on Mar 06 2013

city: Fukuoka

first: Satoshi

last: Matsuo

address: 3-1-1, Maidashi, Higashi-ku

country: Japan

institute: Graduate School of Medical Sciences, Kyushu University

organism: Oryctolagus cuniculus

description:
Arrays of this design have barcodes that begin with 16030687 or 2530687.

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-031181 Unrestricted_Human_miRNA_V16.0_Microarray 030840 (Probe Name version)

status: Public on Jan 24 2012

description:
Human and human viral miRNAs.

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

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


title: A-UMCU-Y16k-1.3

status: Public on Nov 20 2010

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

manufacturer: Holstege Lab, UMC Utrecht, The Netherlands

first: dik

last: van Leenen

first: Marian

last: Groot Koerkamp

first: Philip

last: Lijnzaad

first: Linda

last: Bakker

first: Erik

last: Sluiters

first: Sander

last: van Hooff

first: Frank

last: Holstege

manufacture_protocol:
1. Oligos are resuspended and adjusted to 10µM in 150mM phosphatebuffer, pH8.5 in Genetix 384-wells plates
2. Array production is done using a Biorobotics MicroGridII spotter located in a low dust cleanroom (ISO7/ downflow ISO5) at 18C, at 48% humidity
3. Slide postprocessing is carried out according to CodeLink protocol: Printed slides are kept at 20C, 75% humidity for 24 hours
4. Residual reactive groups are blocked using pre-warmed blocking solution (50 mM ethanolamine, 0.1 M Tris (pH 9) at 50C for 30 min; slides are rinsed thoroughly with milliQ water; slides are washed with 4x SSC, 0.1% SDS (pre-warmed to 50C) for 30 min at 50C on a shaker
5. Slides are rinsed with milliQ water, centrifuged to dry and stored dessicated at room temperature.