title: Agilent-063245 E. coli Custom 4 X 44K array (Probe name version)

status: Public on Oct 10 2016

city: Seoul

first: Ji-Min

last: Woo

address: Ewhayeodae-gil

country: South Korea

institute: Ewha womans university

organism: Escherichia coli

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol: Microarray interrogations were performed using a custom-designed, Agilent-based microarray platform with 4 × 44 K probes per slide (E.coli_chip; Agilent Design ID:063245). Total of 3936 coding sequences of K12 and 4007 coding sequences of BL21 were obtained from NCBI Database and 1 probe was designed for each coding sequence using eArray software according to standard Agilent probe design criteria. We successfully designed 60-mer probes for 7,943  using eArray software (http://earray.chem.agilent.com/earray/) and microarrays were manufactured using Agilent Technologies (USA).


title: RPPA CORE 081913_0074 (SET 74) v.3

status: Public on Sep 30 2015

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

country: USA

institute: NIH

organism: Homo sapiens

technology: spotted peptide or protein

manufacturer: RPPA Core Facility MD Anderson Cancer Center

manufacture_protocol: see MD website


title: Illumina HiSeq 2000 (Caenorhabditis briggsae; Caenorhabditis elegans)

last: GEO

organism:
Caenorhabditis briggsae
Caenorhabditis elegans

technology: high-throughput sequencing

distribution: virtual


title: RPPA CORE 081913_0074 (SET 74) v.2

manufacture_protocol: see core facility site


title: UCSC Vc 9K VC3_gal custom array

status: Public on Jan 06 2016

city: Santa Cruz

first: Sinem

last: Beyhan

state: CA

address: 1156 High Street

department: Microbiology and Environmental Toxicology

institute: University of California, Santa Cruz

organism: Vibrio cholerae

technology: spotted oligonucleotide

distribution: non-commercial

manufacture_protocol: 70-mer oligos were transferred from microtiter plates to aminosilane-coated microscope slides using the DeRisi microarray printer at UCSC


title: Illumina HiSeq 2000 (Brucella suis 1330)

organism: Brucella suis 1330


title: Agilent-023442 Custom Mouse Array

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

organism: Mus musculus

description:
Arrays of this design have barcodes that begin with 16023442 or 2523442.

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 (Armillaria mellea)

organism: Armillaria mellea


title: Illumina HiSeq 2000 (Gastrodia elata)

organism: Gastrodia elata


title: Illumina HiSeq 2000 (Alteromonas macleodii; Prochlorococcus marinus str. NATL2A)

organism:
Alteromonas macleodii
Prochlorococcus marinus str. NATL2A


title: Agilent-029002 Human CytoSure ISCA UPD Array, 4×180K

status: Public on Sep 29 2015

city: Newcastle upon Tyne

first: Aneta

last: Mikulasova

address: Brewery Lane

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 2000 (Ciona savignyi)

organism: Ciona savignyi


title: Illumina NextSeq 500 (Drosophila suzukii)

organism: Drosophila suzukii


title: Illumina HiSeq 2000 (Ciona intestinalis)

status: Public on Sep 28 2015

organism: Ciona intestinalis


title: MassARRAY QGE

first: Adam

last: Asare

address: 7500 Old Georgetown Road, Suite 800

department: Bioinformatics Group

institute: Immune Tolerance Network

technology: RT-PCR

description:
Quantitative Gene Expression (QGE).
Gene expression analysis using a combination of competitive PCR and MALDI-TOF MS.

manufacture_protocol: See manufacturer's website (https://www.sequenom.com).


title: Illumina HiSeq 2000 (Prochlorococcus marinus str. NATL2A)

organism: Prochlorococcus marinus str. NATL2A


title: Applied Biosystems MegaPlex Kit

status: Public on Sep 24 2015

city: Fort Sam Houston

first: Jaideep

last: Banerjee

state: Texas

address: 3698 Chambers Rd, BHT-1

institute: US Army Inst of Surgical Res.

description: MegaPlex Primer Pools, Rodent Pools A

manufacture_protocol: see manufacturer's website


title: Agilent-060449 Custom Maize 4x44k Array

city: Urbana

first: Eunsoo

last: Choe

state: Illinois

address: s-306 Turner hall 1102 S. Goodwin Ave.

institute: USDA-ARS

organism: Zea mays


title: Illumina HiSeq 2000 (Petromyzon marinus)

organism: Petromyzon marinus


title: 454 GS FLX Titanium (chicken gut metagenome)

organism: chicken gut metagenome


title: 090512_Tobacco_U_VA_MT_expr 50k

status: Public on Sep 26 2015

city: Guiyan

first: Ruiyuan

last: Li

state: Guizhou

address: No. 116 Baoshanbei Road, Yuanyan District;

country: China

institute: Guizhou Normal University

organism: Nicotiana tabacum

description:
NimbleGen design name 090512_Tobacco_U_VA_MT_expr, NimbleGen design ID 2451.    Each probe is replicated 3 times.  The design includes random GC and other control probes. The .ndf is linked below as supplementary files. The .ngd file is absent because there was not a reference genome for the organism at present, but the annotation file named Tobacco_chip_annotation_July2009.txt was provided .
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.

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


title: Illumina HiSeq 1000 (Felis catus)

status: Public on Sep 21 2015

organism: Felis catus


title: Illumina HiSeq 2000 (Candida tropicalis MYA-3404)

status: Public on Sep 22 2015

organism: Candida tropicalis MYA-3404


title: Illumina Genome Analyzer II (Plecoglossus altivelis)

organism: Plecoglossus altivelis


title: Agilent custom array PATHTROUT Oncorhynchus mykiss 15K

status: Public on Sep 23 2015

city: Madrid

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

organism: Oncorhynchus mykiss

manufacture_protocol: Agilent 60-mer HD SurePrint technology (see manufacturer's web site athttp://www.agilent.com/). Custom Gene Expression Microarray, 8x15K.


title: Illumina HiSeq 1000 (Salmonella enterica subsp. enterica serovar Typhimurium str. LT2)

status: Public on Sep 18 2015


title: Illumina HiSeq 2000 (Vibrio tasmaniensis)

organism: Vibrio tasmaniensis


title: Illumina HiSeq 2500 (Larimichthys crocea)

organism: Larimichthys crocea


title: Illumina HiSeq 2000 (Blumeria graminis)

organism: Blumeria graminis


title: Agilent-035758 Human miRBASE 16.0 plus 031181 [Probe Name version]

status: Public on Oct 30 2016

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

organism: Homo sapiens

description:
contains miRBASE16.0 and selected miRNAs from miRBASE17.0. All viral miRNAs have been excluded

Arrays of this design have barcodes that begin with 16035758 or 2535758.

relation: Alternative to: GPL20095 (Feature Number version)


title: Illumina HiSeq 2500 (Strongylocentrotus purpuratus)

organism: Strongylocentrotus purpuratus


title: Illumina HiSeq 2000 (Bacillus anthracis str. Sterne)

organism: Bacillus anthracis str. Sterne


title: CanineHD BeadChip

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

organism: Canis lupus familiaris

technology: oligonucleotide beads

description: 170,000 evenly spaced and validated SNPs derived from the CanFam2.0 assembly.

distribution: commercial

manufacture_protocol: See manufacturer's website


title: Illumina HiSeq 2500 (Cyprinus carpio)

status: Public on Sep 25 2015

organism: Cyprinus carpio


title: Illumina Genome Analyzer II (Phalaenopsis aphrodite subsp. formosana)

status: Public on Sep 17 2015

organism: Phalaenopsis aphrodite subsp. formosana


title: Illumina HiSeq 2000 (Serratia sp. ZM)

status: Public on Sep 15 2015

organism: Serratia sp. ZM


title: Agilent-059516 D. vulgaris H 8x60K tiling array 030521 [Feature Number version]

city: Seattle

first: Serdar

last: Turkarslan

state: WA

address: 401 Terry Ave

institute: Institute for Systems Biology

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

description:
D. vulgaris Hildenborough tiling array with 8x60K format. Includes ncRNA, chr, mega plasmid, and extra probes per start locus. 149 bp apart probes plus 3 extra probes per start site/orf.

Arrays of this design have barcodes that begin with 16059516 or 2559516.

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: GPL20930 (Probe Name version)


title: Illumina HiSeq 2000 (Aspergillus terreus)

organism: Aspergillus terreus


title: Agilent-015933 015933_D_20070204 [Feature Number Version]

city: Tsukuba

first: Yuki

last: Nakamura

state: Ibaraki

address: 1-2 Owashi

country: Japan

institute: National Institute of Agrobiological Sciences

organism: Bombyx mori

description:
User Design

Arrays of this design have barcodes that begin with 16015933 or 2515933.

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-059516 D. vulgaris H 8x60K tiling array 030521 [Probe Name version]

description: Arrays of this design have barcodes that begin with 16059516 or 2559516.

relation: Alternative to: GPL20929 (Feature Number version)


title: Agilent-024169 P.berghei_ordered 024168

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

organism: Plasmodium berghei

description:
P.berghei  AE+QW+GEO partial

Custom whole genome Plasmodium berghei 44K array.

Arrays of this design have barcodes that begin with 16024169 or 2524169.

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 (Lotus japonicus)

organism: Lotus japonicus


title: Exiqon, miRCURY LNA microRNA array, 7th generation (hsa, mirbase 21)

city: Chicago

first: Emanuele

last: Canestrari

address: 900 S. Ashland Ave.(M/C 669)

institute: University of Illinois at Chicago

organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Saimiriine gammaherpesvirus 2
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

manufacturer: Exiqon A/S, Skelstedet 16, 2950 Vedbaek, Denmark

manufacture_protocol: See Exiqon website


title: Agilent Oryza sativa Whole Genome Rice 8x60k (AMADID: 064722) designed  by Genotypic Technology Private Limited

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: Oryza sativa


title: Illumina Genome Analyzer (Bombus terrestris)

status: Public on Sep 14 2015

organism: Bombus terrestris


title: Illumina HiSeq 2000 (Mycobacterium abscessus ATCC 19977)

organism: Mycobacteroides abscessus ATCC 19977


title: Illumina MiSeq (Mycobacterium abscessus ATCC 19977)


title: Illumina HiSeq 2500 (Cricetulus griseus)

status: Public on Sep 11 2015

organism: Cricetulus griseus


title: Ion Torrent PGM (Neisseria gonorrhoeae NCCP11945)

organism: Neisseria gonorrhoeae NCCP11945


title: [HTA-2_0] Affymetrix Human Transcriptome Array 2.0 (CDF: hta20hsensgcdf_19.0.0.cdf, version 19)

first: GEO

last: admin

institute: NCBI/NLM/NIH

organism: Homo sapiens

description: Data were extracted using hta20hsensgcdf_19.0.0.cdf.

manufacture_protocol: Standard Affymetrix Protocol


title: UIUC Honey Bee oligo 13K v1

city: Bochum

first: Henrik

last: Rudolf

address: Universitätsstr. 150

department: Medical computer science, Biometry and Epidemiology

institute: Ruhr-Universität Bochum

organism: Apis mellifera

manufacture_protocol: Honey bee oligonucleotide microarray v1 contains 28800 features, and a total of 13440 double spotted ss oligos. Oligos were synthesized by Invitrogen (San Diego, CA) and aliquoted into 384 well plates in Sodium Phosphate buffer. Final concentration of the oligos was 20 uM (micromolar). Arrays were printed on Corning UltraGAPS slides using an Omingrid 100 printing robot (Genomic Solutions, Ann Arbor Michigan) with Arrayit SMP2.5 capillary pins. Following printing slides were stored in vacuum bags purged with Argon gas.


title: Agilent-026610 Vibrio cholerae Microarray 60K (Feature Number version)

first: Jonghwan

last: Baek

address: 37 Convent Dr

institute: NIH

organism: Vibrio cholerae

description:
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 (Gorilla gorilla)

status: Public on Sep 09 2015

last: GEO

organism: Gorilla gorilla


title: Illumina HiSeq 2000 (Spinacia oleracea)

status: Public on Sep 10 2015

organism: Spinacia oleracea


title: Illumina HiSeq 2000 (Stylonychia lemnae)

organism: Stylonychia lemnae


title: Agilent-044138 ZeNo

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

organism: Danio rerio

description:
zebrafish with probes to Uniprot proteins

Arrays of this design have barcodes that begin with 16044138 or 2544138

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-021827 Human miRNA Microarray [miRBase release 14 Feature Number version]

city: Bethesda

address: 9000 Rockville Pike

description: Grid_Date: 31-Oct-2009 [miRBase release 14]

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


title: Elaeis Guineensis Tiling Microarray

city: St. Louis

first: Steve

middle: W.

last: smith

state: MO

address: 4041 Forest Park Ave

department: Bioinformatics

institute: Orion Genomics

organism: Elaeis guineensis

description:
EG5 Build
RefSeq:GCF_000442705.1
Note: Original array design was based on the early P1 build and remapped to EG5 for analysis. Genome coordinates in platform table reflect remapping to EG5.

manufacture_protocol: The microarray design was based on the E. guineensis genome (Singh, 2013, Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature 500, 335-339) and contains over 1 million 60 base probes.   Probes were selected from non-overlapping 1.5 kb windows across all scaffolds of the P1 pisifera genome build, choosing the 60mer with the lowest composite 15mer frequency count within the genome.  When compared to the publically available EG5 genome assembly (Singh, 2013, Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature 500, 335-339), 860,861 probes from the microarray match at 100% stringency (81,194 probes falling on exons and the remaining covering intronic and intergenic regions of the genome). The microarrays were manufactured by Roche NimbleGen using the HX1 platform.  Among the ~860,000 microarray probes matching the oil palm genome with 100% sequence stringency, a subset of ~460,000 uniquely mapped probes was selected to reduce noise from non-specific hybridizations.


title: Agilent-064152 Sanford_Burnum_m6A_Full

status: Public on Sep 08 2015

city: Cambridge

first: Yue

state: Massachusetts

address: 32 Vassar Street, 32-D528

institute: Massachusetts Institute of Technology

organism: Mus musculus

description:
25-mer 6bp tiling mouse genome

Arrays of this design have barcodes that begin with 16064152 or 2564152.

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-021827 Human miRNA Microarray [miRBase release 14 miRNA ID version]

description: Grid_Date: 31-Oct-2009 [corresponding to miRBase release 14]


title: RayBio® Mouse Cytokine Antibody Array G-Series 1000

city: Beijing

first: Hao

last: LI

address: No. 49, Huayuan Bei Road, Haidian District

department: Institute of Vascular Medicine

institute: Peking University Third Hospital

technology: antibody

manufacture_protocol: See manufacturer's website （http://www.raybiotech.com/files/manual/Antibody-Array/AAM-CYT-G3.pdf）


title: Agilent-015932 015932_D_20070204

status: Public on Sep 05 2015

first: Yuzuru

last: Ito

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

institute: National Institute of Advanced Industrial Science and Technology (AIST)

organism: Xenopus laevis

description:
User Design

Arrays of this design have barcodes that begin with 16015932 or 2515932.

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-048498 Pyrococcus array

city: Thuwal

first: Gregoire

last: Michoud

address: KAUST

country: Saudi Arabia

institute: KAUST

organism: Pyrococcus

description:
Arrays of this design have barcodes that begin with 16048498 or 2548498.

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

The ID column represents the Agilent Probe Name.

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

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


title: Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Gene Symbol Version; updated July 2014)

status: Public on Sep 06 2015

city: Chapel Hill

first: Richard

last: Moffitt

state: NC

address: 450 West Drive

institute: University of North Carolina

description:
This multi-pack (4X44K) formatted microarray represents a compiled view of the human genome as it is understood today. The sequence information used to design this product was derived from a broad survey of well known sources such as RefSeq, Goldenpath, Ensembl, Unigene and others. The resulting view of the human genome covers 41K unique genes and transcripts which have been verified and optimized by alignment to the human genome assembly and by Agilent's Empirical Validation process.

*** The ID column includes the updated gene symbols. The GPL4133 probes were re-annotated according to the most updated gene symbols in GPL4133-20424 (July 2014).

The 'GPL4133-20424_re-annotated.txt' contains complete annotations for all probesets.

A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL4133


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [CDF:huex10stv2_57_37b_0112.cdf]

status: Public on Sep 01 2015

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

description: This Platform is identical to GPL5175 but a custom CDF environment was used to extract data. Annotation is based on Ensembl version 57.

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


title: Illumina HiSeq 2000 (Hipposideros armiger)

organism: Hipposideros armiger


title: Illumina Genome Analyzer IIx (Asparagus officinalis)

organism: Asparagus officinalis


title: miRCURY LNA microRNA Array 7th generation - human, mouse & rat [product# 208502] (miRBase 18.0)

status: Public on Sep 03 2015

city: Madrid

first: Nerea

last: Matamala

address: Calle de Pedro Rico, 6

institute: IDIPAZ

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: The array contains probes for 1926 human miRNAs in quadruplicate, including 1894 miRNAs from miRBase Release 18.0, 25 hsa-miRPlus not included in miRBase (Exiqon proprietary) and 7 negative controls.


title: nCounter Mouse Inflammation panel V1

status: Public on Sep 04 2015

first: NanoString

last: Technologies

address: 530 Fairview Ave N  |  Suite 2000

institute: NanoString Technologies

technology: other

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


title: Nostoc punctiforme printed microarray

city: Northridge

first: Michael

middle: L.

last: Summers

state: California

address: 18111 Nordhoff St

department: Dept. of Biology

institute: California State University Northridge

organism: Nostoc punctiforme

manufacture_protocol: see website


title: Streptococcus mutans UA159 genomic tiling array mapped format

first: Tsute

last: Chen

state: MA

address: 245 First Street

department: Microbiology

institute: The Forsyth Institute

organism: Streptococcus mutans UA159

description: The probe set printed on the array consists of 385,000 unique oligonucleotide sequences. On this particular platform, all the 380k unique probes were mapped to all the matched loci of the reference genome, thus each unique probe sequence may appear multiple times due to the repeated probe sequence found in the genome.

manufacture_protocol: The probes were synthesized on the Nimblgen 385K arrays using Nimblegen's proprietary Maskless Array Synthesizer (MAS) technology.


title: Agilent-037264 mouse 400K custom CGH array

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

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


title: Illumina HiSeq 2000 (Pisum sativum)

organism: Lathyrus oleraceus


title: Agilent-039828 mouse promoter tiling

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

description:
genome build: mm9
Arrays of this design have barcodes that begin with 16039828 or 2539828.
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.
The 'GB_ACC:distance to TSS' column values are formatted as [GenBank accession number]:[distance to TSS], e.g. for "NM_001110275:112156", the probe is 112156 bases from the gene identified by GenBank accession number NM_001110275.


title: Agilent-060260 Menidia_beryllina_x3reps-V3-Sept17-2013 (Probe name version)

city: Davis

first: Ken

last: Jeffries

address: One Shields Avenue

institute: UC Davis

organism: Menidia beryllina

description:
Menidia beryllina, 14,393 independent genes, x3 probes = 43,179 probes on array, plus 1417 Agilent control. Connon lab, UC Davis, Sept 17th, 2013

Arrays of this design have barcodes that begin with 16060260 or 2560260.

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-035758 Human miRBASE 16.0 plus 031181

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

organism: Homo sapiens

description:
contains miRBASE16.0 and selected miRNAs from miRBASE17.0. All viral miRNAs have been excluded

Arrays of this design have barcodes that begin with 16035758 or 2535758.

The ID column represents the Agilent Feature Extraction feature number.

relation: Alternative to: GPL20968 (Probe name version)


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene10stv1_Mm_ENSG v.19.0.0]

first: GEO

last: admin

institute: NCBI/NLM/NIH

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

manufacture_protocol: This is identical to GPL6246 but a custom cdf environment was used to extract data. The CDF is available here: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/19.0.0/ensg.asp


title: NimbleGen_HG18 RefSeq Promoter array [080929_HG18_GC_CGH]

status: Public on Dec 31 2011

city: Bei Jing

first: Jia

last: Yu

address: Dong Dan San Tiao #5

department: Biochemistry

institute: Peking Union Medical College

description:
HG18

native array description file: 080929_HG18_GC_CGH.ndf
designid=8318

manufacture_protocol: see the NimbleGen website


title: Agilent-031189 Unrestricted_Rat_miRNA_v16.0_Microarray (Probe Name version)

status: Public on Jan 09 2015

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Rattus norvegicus

description: rat miRNAs miRbase 16.0


title: Illumina HumanHT-12 V3.0  (curated high quality probe subset, reannotated; original platform GPL6947)

status: Public on Sep 07 2015

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

manufacture_protocol: See manufacturer's web page


title: Illumina MiSeq (Pseudomonas aeruginosa)

status: Public on Sep 02 2015

last: GEO

organism: Pseudomonas aeruginosa


title: Agilent-038224 Acinetobacter baumannii v1

status: Public on Nov 14 2013

city: A CORUÑA

first: JESUS

last: ARANDA

address: AS XUBIAS

institute: CHUAC

organism: Acinetobacter baumannii ATCC 17978

description:
Arrays of this design have barcodes that begin with 16038224 or 2538224.

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: CapitalBio Corporation 35K Human Genome Array

status: Public on Apr 04 2015

city: Shanghai

first: Xin

last: Zhang

state: -- Please select an option --

address: No.180 Fenglin Road, Zhongshan Hospital

institute: Liver Cancer Institution

manufacture_protocol: as described in CapitalBio Corporation Manual


title: Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 (Gene Name version)

city: Bethesda

state: MD

address: 9000 Rockville Pike

description: *** The ID column includes the Agilent Gene Name (identifiers included in the 'GeneName' column of Agilent feature extraction files). A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL10333.

relation: Alternative to: GPL10333 (Feature number version)


title: NimbleGen Antirrhinum majus cv. Maryland True Pink_4x72k array [080125_Antirrhinum_major_expr]

status: Public on Jun 07 2012

city: West Lafayette

first: Natalia

last: Dudareva

state: Indiana

address: 625 Agriculture Mall Drive

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

organism: Antirrhinum majus

description:
MOgene design ID OID12201. An expression design for 11,959 ESTs/unigenes from Antirrhinum majus cv. Maryland True Pink with six 60-mer probes per gene.
designname: 080125_Antirrhinum_major_expr
designid: 7043

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


title: Illumina HiSeq 2500 (Symbiodinium sp. C1)

organism: Cladocopium sp. C1


title: SBI Human miRNome Sanger miRBase microRNA Profiler Set

city: Hannnover

first: Shashi

middle: Kumar

last: Gupta

address: Carl-Neuberg Strasse 1

department: IMTTS

institute: Hannover Medical School

description:
384 well plate base miRNA array with 3 plates in total.
Measurement is done by SYBR Green PCR.
miRNA ID based on Sanger miRbase v15

manufacture_protocol: see manufcaturer's website


title: Qiagen Human miRNome miScript miRNA PCR arrays (V16.0, 384-well)

city: strasbourg

first: philippe

last: georgel

address: 1 Place de l'Hopital

country: France

institute: strasbourg university

description: PCR assay

manufacture_protocol: see manufacturer's website


title: PGT- 30K Human Array v1

status: Public on Mar 24 2010

city: Nottingham

first: Patrick

middle: Jason

last: Tighe

state: Nottinghamshire

address: University Hospital

department: School of Molecular Medical Sciences

institute: The University of Nottingham

description: spotted oligonucleotides from MWG 30K sets A, B and C oligo sets

manufacturer: Post-Genomic Technologies Facility, University of Nottingham

manufacture_protocol:
The Oligoset (in Genetix 7020 polypropylene plates) was printed at 20µM concentration, in 3xSSC, 1.5M Betaine, using a Genomic solutions Microgrid II 600 Arrayer and  microspot 2500 split pins at 65% humidity. Prints were made onto Schott Nexterion A+ barcoded slides (APS coated) using 48 pins in a 4x12 array to give 48 subgrids, each of 26 columns x26 rows of possible features.  Target spot diameter was 80 micrometers.   The GE-Lifesciences Universal scorecard Oligo set were printed onto each subgrid for  QC and hybridization controls. Cy3- random 9mer-NH oligonucleotideLanding lights were printed at corners of each subgrid
Slide post-processing: Slides were then rehydrated whilst suspended upside-down in a humid chamber (80% relative humidity) for 10 minutes, followed by snap drying for 10 seconds at 120°C on a hot plate.  Slides were then baked for 3h at 80°C and stored at room temperature under dessication and vaccum untill required.  Prehybridization, each slide was washed sand blocked to remove excess oligo and block the surface by immersion in blocking solution (5xSSC 0.2%SDS 1%BSA using warm Ultra Pure Water),  Filter the blocking solutionbefore use.Block for 10 minutes with vigorous shaking or stirring of the solution..  Prepare three more wash stations, two containing Ultra Pure Water and one containing 100% Ethanol, seal the containers to prevent evaporation.  Prepare a  plate rotor on a benchtop centrifuge and set to 600rpm for two minutes.  Prepare a slide rack containing blank slides as a balance.  After the 10 minutes dunk the slides into the first wash station of Ultra Pure Water three times, the second twice then into the 100% Ethanol.  Carry this container and slides over to the centrifuge while still in the ethanol and coentrifuge to  dry. The slides should be preferably hybridized on the day of blocking, as they are not suitable for storage for more than a couple of days once blocked.


title: Illumina HumanHap550-Duov3 Genotyping BeadChip (HumanHap550-2v3_B; Name version)

description: over 555,000 tag SNP markers derived from the International HapMap Project

relation: Alternative to: GPL6982 (IlmnID version)

manufacture_protocol: See manufacturer's website


title: LC_MRA-1002-miRMouse_21

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

manufacture_protocol: mouse miRNA microarray with 100% coverage of mature mouse miRNAs listed in miRBase version 21. 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: Agilent-015421 TNPRC Macaca mulatta 4x44k Array [Probe Name version]

status: Public on Mar 18 2010

city: San Antonio

first: Deepak

last: Kaushal

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

organism:
Macaca mulatta
Homo sapiens

description: 43,803 rhesus macaque monkey probes are represented on this chip.

first: Smriti

last: Mehra

manufacture_protocol:
Synthesized using SurePrint technology. SurePrint technology allows as many as 8 arrays to reside on a single slide, allowing experiments to range from a genome-wide view to more focused studies. The current microarray was in a 4x44k format. The platform represents one out of the four sub-arrays.
For more info please see the company site: http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/pages/gp557.aspx


title: [PrimeView] Affymetrix Human Gene Expression Array [Brainarray ENSG Version 18]

status: Public on Sep 25 2015

city: Boston

first: Bose

middle: Skaria

last: Kochupurakkal

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: This is identical to GPL15207 but a custom CDF environment was used to extract data [Brainarray (version 18)]. Gene symbols for corresponding Ensembl gene IDs were gathered using Biomart.

relation: Alternative to: GPL15207 (Alternative CDF [official])

manufacture_protocol: See details from Affymetrix.


title: Illumina HumanHap550-Duov3 Genotyping BeadChip (HumanHap550-2v3_B)

status: Public on Jun 23 2008

city: San Diego

last: Illumina Inc.

state: CA

address: 9885 Towne Centre Drive

institute: Illumina Inc.


title: Illumina HumanOmni2.5-8 BeadChip

status: Public on Sep 25 2012

description: This array is based on build 37


title: Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Probe Name version)

status: Public on May 09 2008

description:
This single 44K formatted microarray represents a compiled view of the human genome as it is understood today. The sequence information used to design this product was derived from a broad survey of well known sources such as RefSeq, Goldenpath, Ensembl, Unigene and others. The resulting view of the human genome covers 41K unique genes and transcripts which have been verified and optimized by alignment to the human genome assembly and by Agilent's Empirical Validation process.

*** 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 GPL1708

relation:
Alternative to: GPL1708
Affiliated with: GPL9443