title: Qiagen miScript miRNA PCR Array Human miFinder 384HC

status: Public on Mar 09 2016

city: scottsdale

first: qinqin

last: xu

state: arizona

address: 13400 E shea blvd

country: USA

institute: mayo clinic arizona

organism: Homo sapiens

technology: RT-PCR

description: PCR assay

distribution: virtual


title: Applied Biosystems TaqMan TLDA 64-Breast cancer associated-gene panel

status: Public on Sep 30 2014

city: San Francisco

first: Mark

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

description:
We selected 64 genes from previously published data focused on QPCR analyses of CTCs. Included in the list are clinically relevant genes, stem cell and epithelial-mesenchymal transition (EMT) markers, and highly expressed genes in breast and prostate cancers. We also included EPCAM and PTPRC (encodes CD45) to measure the expression of these markers specific for epithelial cells and leukocytes, respectively. Also, included are 6 candidate reference genes for data normalization.
We designed a custom Taqman® Low Density Array (TLDA, Applied Biosystems) microfluidic card (384-well format) containing two sets of 64 Taqman® gene expression assays printed in triplicate.

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2000 (Pinus pinaster)

last: GEO

organism: Pinus pinaster

technology: high-throughput sequencing


title: Culex quinquefasciatus

city: Notre Dame

first: David

middle: W

last: Severson

state: IN

address: 44 Galvin Life Sciences

department: Biological Sciences

institute: University of Notre Dame

organism: Culex quinquefasciatus

technology: in situ oligonucleotide

description: NimbleGen design name 110120_Cmosq_BH_exp, NimbleGen design ID 547751. A 12-plex 135K feature expression design (Expr12x135K) for 18,692 protein coding genes from Culex quinquefasciatus based on the CpipJ1.2 geneset in Vectorbase using an average of 3 60-mer probes per transcript, with each transcript/probe duplicated on the array. Probes representing 124 non-coding RNAs were also included on the array. The design includes random GC and other control probes.

distribution: custom-commercial

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


title: Agilent SurePrint G3 CBC lncRNA+mRNA microarray V2.0 (condensed version)

city: HANGZHOU

first: wang

last: jianguo

state: ZHEJIANG

address: 79 Qingchun Road

department: Department of Surgery, First Affiliated Hospital, Zhejiang University School of Medicine

country: China

institute: zhejiang university

technology: spotted oligonucleotide

description: A different version of this platform is assigned accession number GPL18581


title: UNC PerouLab 244K Custom Human Array version 6

status: Public on Jun 06 2015

city: HOUSTON

first: Eric

middle: C.

last: Chang

state: TX

address: ONE BAYLOR PLZ

department: BREAST CENTER

institute: BAYLOR COLLEGE OF MEDICINE

manufacture_protocol: Agilent Technology (see manufacturer's website)


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] custom

city: Shinjuku-ku

first: Kumiko

last: Saeki

state: Tokyo

address: 1-21-1 Toyama

department: Department of disease control

country: Japan

institute: National Center for Global Health and Medicine

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

distribution: commercial

manufacture_protocol: See manufacturer's web site


title: CAT-3x20K-Pseudomonas_aeruginosa_PAO1-gene-layout-C3

city: Kermanshah

first: Hossein

last: Fallahi

state: Kermanshah

address: Bagh-e-Abrisham

department: Biology

country: Iran

institute: Razi University

organism: Pseudomonas aeruginosa PAO1

manufacture_protocol: As indicated on the manufacturer's website, array format 3x20K, number of unique probes per arry 5545, number of replicates per probe 3, The manufacturer do not spot presynthesized oligonucleotides. They directly synthesize them on a microscope slide. Their synthesis is using the robust phosphoramidite chemistry refined since the 1970's for commercial oligonucleotide synthesis. In standard oligonucleotide synthesis, the terminal acid-labile protective group of a growing oligomer is removed by a treatment with a strong acid. The only modification they have introduced in their process is the usage of a photo-generated acid. At a given synthesis cycle, each spot that needs to be deprotected is exposed to light in the presence of a photogenerated acid precursor, leading to local acid production and cleavage of the terminal protective group. Only the deprotected spots will be able to react with a new monomer. By so doing,they can synthesize tens of thousands oligonucleotides in parallel on the same microarray substrate. The advantage of using the phosphoramidite chemistry is that they can synthesize oligonucleotides at a reduced cost compared to other chemistries while maintainingtheir stepwise yield well above 99%. The probe lengths were between 45 and 47 nucleotides and the spacer has a length equivalent to a 15-mer sequence.


title: Illumina Genome Analyzer II (Fusarium verticillioides)

status: Public on Sep 29 2014

organism: Fusarium verticillioides


title: Illumina Genome Analyzer II (Fusarium graminearum)

organism: Fusarium graminearum


title: Agilent-057895 Vibrio parahaemolyticus RIMD 2210633 8X15K array [Probe Name Version]

city: shanghai

first: qian

last: jin

address: libing road

institute: MSP

organism: Vibrio parahaemolyticus RIMD 2210633

description:
Arrays of this design have barcodes that begin with 16057895 or 2557895.

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."

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


title: Agilent-050292 Saccharum 8X60K array [Probe Name Version]

organism: Saccharum

description:
Arrays of this design have barcodes that begin with 16050292 or 2550292.

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: UNC-SCHISLER Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F [gene-level]

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

organism: Mus musculus

description: Gene Level Experiment - 7.6K genes - Acsl1H-/-

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


title: Applied Biosystems TaqMan Gene Expression Assays (human)

city: Leioa

first: Jose Ramon

last: Bilbao

state: Outside the US or Canada

address: Bº Sarriena

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

manufacture_protocol: see manufacturer's web site


title: Nimblegen Human HG19_HELP array [100128_HG19_MKF_HELP_ChIP]

city: Dallas

first: Duojia

last: Pan

state: Texas

address: 6001 Forest Park

department: Physiology

institute: UT Southwestern Medical Center

description:
designname=100128_HG19_MKF_HELP_ChIP
Array based on the human genome (hg19) release.
Condensed on SEQ_ID of .pos file.

manufacture_protocol: See manufacturer's website.


title: NimbleGen_Cryptomeria japonica_72K [120720_RDKK342_Leaf_exp]

status: Public on Sep 28 2014

city: Hitachi

first: Mine

last: Nose

state: Ibaraki

address: 3809-1 Ishi, Juo

institute: Forest Tree Breeding Center

organism: Cryptomeria japonica

description:
design_name: 120720_RDKK342_Leaf_exp_X4.
design_id: 573161

The platform data table is based on the ndf file.

native array description file: 120720_RDKK342_Leaf_exp.ndf
native array description file: 120720_RDKK342_Leaf_exp.ngd


title: Agilent-020745 4x44K Maize Oligo Microarray

status: Public on Sep 27 2014

city: Urrbrae

first: Darren

last: Plett

state: South Australia

address: Hartley Grove Road

department: ACPFG

country: Australia

institute: University of Adelaide

organism: Zea mays


title: SABiosciences  TGFβ/BMP Signaling Pathway PCR array PAHS-035ZA

city: Rome

first: fiorella

last: ciaffoni

state: Italy

address: Viale Regina Elena 299

department: Cellular Biology and Neurosciences

country: Italy

institute: Istituto Superiore di Sanità

description:
Human TGFbeta/BMP Signaling Pathway PCR array
SABiosciences RT² Profiler panel of PCR assays.


title: M1, M3, M18 GAS Array

status: Public on Apr 06 2005

city: College Park

first: Kevin

middle: S

last: McIver

state: MD

address: 3124 Biociences Research Bldg. (413)

department: Cell Biology and Molecular Genetics

institute: University of Maryland, College Park

organism: Streptococcus pyogenes

description: oligonucleotide array containing unique ORFs rom M1, M3 and M18 Streptococcus pyogenes

distribution: non-commercial

first: Deborah

middle: A

last: Ribardo


title: NimbleGen E. coli MG1655 72K x 4 array v1.0

status: Public on Sep 25 2014

city: Ames

first: Hui-Hsien

last: Chou

state: IA

address: 503 Science II

department: Genetics, Development and Cell Biology

institute: Iowa State University

organism: Escherichia coli str. K-12 substr. MG1655

description:
NimbleGen design name 120920_Eco_MG1655_HC_expr, NimbleGen design ID 574821.  Expression design for 67,435 probes from E. Coli MG1655.  Each probe has 2 biological replications.  The design includes 2,000 spike control probes from hygromycin.

The Platform data table reflects a condensed representation of the expression array's replicate (PROBE_ID shown as ID_REF) features.  The .ndf and .ncd files are linked below as supplementary files.


title: Illumina HiSeq 2000 (Homo sapiens; Salmonella enterica)

status: Public on Sep 24 2014

organism:
Homo sapiens
Salmonella enterica


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

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism:
Homo sapiens
Human alphaherpesvirus 1
Human betaherpesvirus 5
Lymphocryptovirus
Human immunodeficiency virus 1
Betapolyomavirus macacae

description:
LotNumberRange: 31049-31049

ArrayContents_DesignedFor=miRBase 11.0
ArrayContents_CurrentNameColumn=miRBase 11.0
ArrayContents_CurrentNameColumnCoverage=Homo sapiens and related vira:99.46%
http://www.exiqon.com/SEEEMS/26.asp

manufacture_protocol: See manufacturers website


title: Illumina HiSeq 2000 (Salmonella enterica)

last: GEO

organism: Salmonella enterica


title: NimbleGen Agrobacterium tumefaciens C58 72K x 4 array v1.0

organism: Agrobacterium fabrum str. C58

description:
NimbleGen design name 120920_Atum_C58_HC_expr, NimbleGen design ID 574811.  Expression design for 71,498 probes from 4 chromosomes of Agrobacterium tumefaciens C58.  Each probe has 2 biological replications.  The design includes 1,000 spike control probes from hygromycin.

The Platform data table reflects a condensed representation of the expression array's replicate (PROBE_ID shown as ID_REF) features.  The .ndf and .ncd files are linked below as supplementary files.


title: [ZebGene-1_0-st] Zebrafish Gene 1.0 ST Array [probe set (exon) version]

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Danio rerio

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

HuGene-2_0-st-v1.na34.hg19.probeset.csv

#%chip_type=ZebGene-1_0-st-v1
#%lib_set_name=ZebGene-1_0-st
#%lib_set_version=v1
#%genome-version=zv9
#%genome-version-ucsc=zv9
#%genome-lifted-method=NONE
#%genome-lifted_from-version-ucsc=zv9
#%netaffx-annotation-date=2013-08-30
#%netaffx-annotation-netaffx-build=34
#%netaffx-annotation-data-type=probe_set


title: Illumina HiSeq 2500 (Gossypium hirsutum)

organism: Gossypium hirsutum


title: Illumina HiSeq 2000 (Brassica rapa x Brassica nigra)

organism: Brassica rapa x Brassica nigra


title: Illumina HiSeq 2000 (Camellia sinensis)

organism: Camellia sinensis


title: Agilent-027114 Genotypic Technology designed Custom Human Whole Genome 8x60k Microarray [Feature Number Version]

status: Public on Sep 23 2014

city: navi mumbai

first: Srikanta

last: Basu

state: Maharashtra

address: Kharghar, sector 22

department: Sorab's Lab

country: India

institute: TMC-ACTREC

organism: Homo sapiens


title: Illumina HiSeq 2000 (Candida glabrata)

status: Public on Sep 22 2014

organism: Nakaseomyces glabratus


title: Illumina HiSeq 2000 (Nicotiana attenuata)

status: Public on Sep 19 2014

organism: Nicotiana attenuata


title: Agilent-031538 Canis familiaris Cfa_custom_20101122 021193

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

organism: Canis lupus familiaris

description:
Canine custom array

Arrays of this design have barcodes that begin with 16031538 or 2531538.

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 (Xanthomonas oryzae pv. oryzae KACC 10331)


title: NimbleGen Mus musculus 385K Array [2006_08_03_MM8_60mer_expr]

status: Public on Sep 20 2014

city: Madison

first: Igor

last: Slukvin

state: WI

address: 1220 Capitol Court

department: Department of Pathology and Laboratory Medicine

institute: University of Wisconsin

organism: Mus musculus

description: The .ndf and .ngd files are linked below as supplementary files.

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


title: NimbleGen Mouse Deluxe Promoter Array [100718_MM9_Deluxe_Prom_ChIP_HX1]

status: Public on Sep 18 2014

city: Toronto

first: Eric

middle: J

last: Chater-Diehl

state: ON

address: 686 Bay St.

country: Canada

institute: SickKids Research Institute

description: design id: 100718_MM9_Deluxe_Prom_ChIP_HX1

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


title: Agilent-020575 Staphylococcus xylosus array

city: Saint-Genès Champanelle

first: Sabine

last: Leroy

address: Clermont-Ferrand Theix Research Center

department: MICA

country: France

institute: INRA

organism: Staphylococcus xylosus

description:
Staphylococcus xylosus C2a complete genome micro array.

Arrays of this design have barcodes that begin with 16020575 or 2520575.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Illumina HiSeq 2000 (Helicoverpa armigera)

status: Public on Sep 17 2014

organism: Helicoverpa armigera


title: Illumina HiSeq 2000 (Influenza A virus (A/Perth/16/2009(H3N2)))


title: Illumina HiSeq 2000 (Influenza A virus (A/Udorn/307/1972(H3N2)))


title: Illumina HiSeq 2000 (Influenza A virus (A/Brisbane/10/2007(H3N2)))


title: NRC-BRI C. albicans expression microarray V2.0

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

institute: CHU Québec

organism: Candida albicans

manufacturer: National Research Council Canada - Biotechnology Research Institute

manufacture_protocol: Probe design was done using a sliding window of 70 bp moved from the 3' -> 5' end of the target sequence. Self-annealing was calculated at each position as well as the GC count. A pre-computed cumulative mask of all the significant alignments found in the genome was made to favour regions that are unique for each genomic region. Oligos were resuspended at 22 µM concentration in 50% DMSO and spotted on Corning Ultragaps slides with a BioRad ChipWriter Pro microarray spotter equipped with 48 SMP3 pins (Telechem ArrayIt). UV crosslinking (600 mJ) was performed in a Stratagene UV Stratalinker.


title: Illumina HiSeq 2000 (Diospyros lotus)

status: Public on Sep 12 2014

organism: Diospyros lotus


title: Illumina HiSeq 2500 (Diospyros lotus)


title: Agilent-049625 Bos taurus_miRNA [Probe Name Version]

status: Public on Sep 15 2014

city: Warsaw

first: Zofia

last: Wicik

state: mazovia

address: Pawinskiego 5

department: Department of Human Epigenetics

country: Poland

institute: Mossakowski Medical Research Center

organism: Bos taurus

description:
Arrays of this design have barcodes that begin with 16049625 or 2549625.

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


title: Illumina Genome Analyzer II (Frankia)

organism: Frankia


title: [HTA-2_0] Affymetrix Human Transcriptome Array 2.0 (CDF: hta20hsensgcdf_18.0.0.cdf, version 18)

status: Public on Sep 16 2014

description: Data were extracted using hta20hsensgcdf_18.0.0.cdf.

relation: Alternative to: GPL17585 (Alternative CDF [official])

manufacture_protocol: Standard Affymetrix Protocol


title: PFGRC Burkholderia mallei/pseudomallei 5.8k oligo microarray version 2

city: Maung

first: THANATCHAPORN

last: BARTPHO

state: Khon Kaen

address: 123 Mitthaphap

department: Microbiology

country: Thailand

institute: Meliodosis Research Center, Faculty of Medicine, Khon Kaen University

organism:
Burkholderia mallei
Burkholderia pseudomallei

description: spotted ss-oligonucleotide (70 mers)

manufacturer: Pathogen Functional Genomics Resource Center (PFGRC) at the JCVI


title: [HG-U219] Affymetrix Human Genome U219 Array (ENSG Brainarray CDF Version 17.1.0)

description: CDF downloaded from: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17.1.0/ensg.asp


title: Illumina HiSeq 2000 (Burkholderia cenocepacia)

status: Public on Sep 11 2014

organism: Burkholderia cenocepacia


title: Illumina HiSeq 2000 (Mantella betsileo)

organism: Mantella betsileo


title: Affymetrix GeneChip Human Genome U133 Array Set HG-U133 Plus2 based on a custom CDF (GeneAnnot version 2.2.0)

status: Public on Sep 10 2014

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

description: Affymetrix HG-U133 Plus2 microarrays analysed with custom chip definition files based on the GeneAnnot database. For further information, see Ferrari F, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli GA, Bicciato S.: Novel definition files for human GeneChips based on GeneAnnot. BMC Bioinformatics. 2007 Nov 15;8(1):446 We used Version 2.2.0 of custom CDF files and R packages based on GeneAnnot version 2.0 and GeneCards version 3.04, available online at http://www.xlab.unimo.it/GA_CDF/


title: LC Sciences MRA-1002_miRMouse_17 (miRNA_ID version)

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

description: Mouse miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 17

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: miRCURY LNA microRNA Array, 7th generation - hsa, mmu & rno (miRBase 19.0)

city: Takatsuki City

first: Masutani

last: Ryota

state: Osaka

address: Daigaku-machi

department: clinical central laboratory

institute: osaka medical college hospital

organism:
Homo sapiens
Mus musculus
Rattus norvegicus


title: GeoChip 3.0 for Bacteria, Archaea, Eukaryota and Viruses

city: Chengdu

first: Junpeng

last: Rui

state: Sichuan

address: No. 9 Section 4, Renmin Nan Road

institute: Chengdu Institute of Biology, Chinese Academy of Sciences

organism: Bacteria

description: Soil microbes


title: Invitrogen ProtoArray v5.0 (HA20252)

technology: spotted peptide or protein


title: [HG-U133B] Affymetrix Human Genome U133B Array [Custom Brainarray v16 ENTREZG CDF]

description: Identical to GPL97 but used a custom CDF

manufacture_protocol: see the Affymetrix website


title: AB SOLiD 3 Plus System (Mus musculus)


title: [HG-U133A] Affymetrix Human Genome U133A Array [Custom Brainarray v18 ENTREZG CDF]

description: Identical to GPL96 but used a custom CDF


title: Illumina HiSeq 2000 (Pyronema omphalodes CBS 100304)

status: Public on Sep 09 2014

organism: Pyronema omphalodes CBS 100304


title: Agilent-047562 Danio rerio 15K custom array zfin2.2

city: Madrid

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

institute: INIA

organism: Danio rerio

manufacture_protocol: see manufacturer's web site www.chem.agilent.com


title: Illumina HiSeq 2000 (Plasmodium vivax)

organism: Plasmodium vivax


title: Agilent-041017 Embryogene Bovine 45K microarray with drosophila controls v.2.1 [EMBV_Droso_V2.1]

city: Quebec

last: Fournier

state: Quebec

address: 2325 Rue de l'Universite

department: Departement des sciences animales

institute: Universite Laval

description:
Embryogene Bovine 45K microarray with drosophila controls

Arrays of this design have barcodes that begin with 16041017 or 2541017.

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-015062 Mouse Dev Gene Expression Microarray (Probe name version)

last: admin

description:
Design Format = 4 X 44K
Build Version = mm9:NCBI37:Jul2007


title: Illumina HiSeq 2500 (Apis mellifera)

last: GEO

organism: Apis mellifera


title: NimbleGen Zymomonas mobilis 8b 100907_Z_mobilis_expr_tiling_HX12

status: Public on Sep 08 2014

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

organism: Zymomonas mobilis

manufacture_protocol:
high-density tiling array
a new NimbleGen high-density 12-plex microarray was designed to investigate all the coding region (CDS) and intergenic regions containing 146K features for both expression and tiling arrays covering both the genome and five plasmids as well as genes (talB, tktA, araBAD and xylAB) engineered into Z. mobilis for xylose and arabinose metabolism.


title: TaqMan OpenArray Human MicroRNA Panel (4461104; 'miRNA_ID+assay ID' verion)

city: Baltimore

first: Ashwin

last: Balagopal

address: 855 North Wolf Street, Rangos Building Room 520

department: Medicine

institute: Johns Hopkins Univ. School of Medicine

organism: Homo sapiens

description: The GPL17837 contains ID followed by pool designation.

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


title: Illumina Genome Analyzer IIx (Papio anubis)

organism: Papio anubis


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: GATExplorer_Ensembl v57]

city: Valladolid

first: Thomas

last: Schimmang

address: Sanz y Fores 3

institute: CSIC

organism: Mus musculus

description:
The probes were mapped to GENE LOCi by the CDF built by GATExplorer v3.0
http://bioinfow.dep.usal.es/xgate/mapping/mapping.php
The CDF file is designed to install as 'R' package;
genemappermousegene1.0cdf_3.0.tar' available at:
http://bioinfow.dep.usal.es/xgate/mapping/mapping.php?content=rprogram

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


title: Exiqon miRCURY LNA microRNA Array (miRBASE 14.0, lot numbers 31015 and 31078)  [condensed ProbeID version]

city: Lexington

first: Steven

middle: Ray

last: Presnell

state: KY

address: 800 Rose St.

department: Pathology, Medicine

institute: University of Kentucky

description:
miRCURY™ locked-nucleic acid microarray (Version 11.0; Exiqon; Vedbaek, Denmark) consisting of control probes, mismatch probes, and 1769 capture probes complementary to human, mouse, rat, and viral sequences from the miRBase v.14.0 release
human, mouse, rat, and viral


title: Illumina HiSeq 2000 (Isatis tinctoria)

status: Public on Sep 04 2014

organism: Isatis tinctoria


title: Human 4K miRNA LC_MRA-1001_miRHuman_14 [miRNA_ID version]

status: Public on Sep 05 2014

description: Human miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 14

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 (Taeniopygia guttata)

status: Public on Sep 03 2014

organism: Taeniopygia guttata


title: Illumina MiSeq (Malus domestica)

organism: Malus domestica


title: Agilent Atlantic Halibut 027262_D_F_20100210 NIVA_HH_44K_Array_TV2_290210

city: Oslo

first: Knut Erik

last: Tollefsen

address: Gaustadallèen 21

country: Norway

institute: Norwegian Institute for Water Research (NIVA)

organism: Hippoglossus hippoglossus

manufacture_protocol: Agilent SureDesign, see https://earray.chem.agilent.com/


title: M1, M3, M18 GAS Array

city: College Park

first: Yoann

last: Le Breton

state: Maryland

address: 3217 Bioscience Research Building (413)

institute: University of Maryland

organism: Streptococcus pyogenes

description: oligonucleotide array containing unique ORFs rom M1, M3 and M18 Streptococcus pyogenes

manufacture_protocol: Not provided


title: Illumina HiSeq 1000 (Bos taurus)

status: Public on Sep 02 2014

organism: Bos taurus


title: Illumina HiSeq 2000 (Nasonia giraulti)

organism: Nasonia giraulti


title: Agilent-045382 UGSF flax 45K v1.0

city: Villeneuve d'Ascq

first: Chantreau

last: Maxime

state: Nord

address: Université de lille 1

institute: Université de Lille 1

organism: Linum usitatissimum

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


title: Agilent-016579 Nelson Whole Mouse Genome Microarray 4x44K [Probe Name version]

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center


title: [MoGene-1_1-st] Affymetrix Mouse Gene 1.1 ST Array [transcript (gene) version] [CDF: MoGene11stv1_Mm_ENTREZG_15.1.0]

city: Bethesda

first: GEO

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

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

manufacture_protocol: This array is identical to GPL11533 but a custom, remapped CDF environment is used to extract data. This is version 15.1.0 of the remapped CDF.


title: Agilent-028727 SurePrint G3 Mouse Exon 2x400K Microarray [Probe Name version]

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

description:
Mouse2x400KExon

Arrays of this design have barcodes that begin with 16028727 or 2528727.

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 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: 020940_IRD_RHIZO-CASUARINA-15K-V1.0

status: Public on Sep 01 2014

city: MONTPELLIER CDX 5

first: Valérie

last: HOCHER

address: 911 av. Agropolis BP64501

department: DIADE

institute: IRD

organism: Casuarina glauca

manufacturer: IMAXIO - Biopôle Clermont-Limagne- 63360 Saint-Beauzire, France- Tél: +33 (0)4 73 64 43 90 – Contact : V. VIDAL. This platform is Certified Service Provider by AGILENT.

manufacture_protocol: Agilent protocol


title: GenopalⓇ MICH07

city: Kodaira

first: Hirohiko

last: Hohjoh

state: Tokyo

address: 4-1-1 Ogawahigashi

institute: National Institute of Neuroscience, NCNP

manufacture_protocol:
Custom-made fibrous oligonucleotide DNA microarray GenopalⓇ (Mitsubishi Rayon) for a total of 200 miRNAs which were selected from the miRBase ver9.0 database in Sanger Institute.
All oligonucleotide capture probes, including those for negative controls, were designed to have approximately the same annealing temperature (Tm).
Genopal DNA microarray was made as follows: Plastic hollow fibers, in which oligonucleotide capture probes were chemically bonded to hydrophilic gels, were bundled in an orderly arrangement, hardened with resin to form a block (12 rows × 19 columns) and then sliced into thin chips. Finally, three thin chips were set into a holder together.


title: [MoGene-1_1-st] Affymetrix Mouse Gene 1.1 ST Array [transcript (gene) version] [CDF: mogene11st_Mm_ENTREZG_17.0.0]

description: Brainarray:  mogene11st_Mm_ENTREZG_17.0.0

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 2500 (Capra hircus)

organism: Capra hircus


title: [Rat230_2] Affymetrix Rat Genome 230 2.0 Array [CDF: Rat2302_Rn_ENTREZG_18.0.0]

organism: Rattus norvegicus

relation: Alternative to: GPL1355 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site.


title: Rice 135k tiling V2 array

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

organism: Oryza sativa

description:
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf file is linked below as supplementary files.
Rice_135k_tiling_V2.ndf
Rice_135k_tiling_V2.ncd

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


title: NimbleGen Vitis vinifera array [090918_Vitus_exp]

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

organism: Vitis vinifera

description:
145868 probes/chamber.Several different probes/Gene.

designid=10646
designname=090918_Vitus_exp

native array description file: 090918_Vitus_exp.ngd
native array description file: 090918_Vitus_exp.ndf

A different version of this platform with the probe ids in the ID column is assigned accession number GPL17460


title: Zhong Mouse pre-implantation development PCR assay panel (96 genes)

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

description:
DELTAgene™ Assays
na

manufacture_protocol: see manufacturer's website


title: PHRI-UMNDJ-CAG Bacillis subtilis 4.1K V1.0 [full layout version]

city: Hannover

first: Kürsad

last: Turgay

address: Schneiderberg 50

department: Institut für Mikrobiologie

country: Germany

institute: Leibniz Universität Hannover

organism: Bacillus subtilis

description: gene-condensed version is GPL16693

manufacturer: The Center for Applied Genomics at the Public Health Research Insitute of UMDNJ

manufacture_protocol: Oligonucleotides 65mer long from the B. Subtilis OligoLibrary by Compugen and Sigma-Genosys set were spotted using a Genemachines omnigrid arrayer at a concentration of 25uM in 3x SSC onto glass slides coated with Poly-L-Lysine.


title: SA Biosciences DNA damage signaling PCR Array

city: Cambridge

first: Kelly

middle: Louise

last: Gray

state: Cambs

address: Addenbrookes Hospital, Hills Road

country: United Kingdom

institute: University of Cambridge

organism: Homo sapiens

description:
DNA damage signalling PCCR array panel
RT² Profiler™ PCR Array System


title: Duke/RG_MycMax_Max

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

country: USA

institute: Duke University

organism: synthetic construct

manufacture_protocol: In situ oligosynthesized array with synthetic sequences that cover all possible 10-mers


title: Agilent-029660 eohaus_mod_44k_v3  array (Probe name version)

city: Moncton

first: Paula

last: Jackman

state: NB

address: 443 University ave

institute: Environment Canada

organism: Eohaustorius estuarius

description:
Arrays of this design have barcodes that begin with 16029660 or 2529660.

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

The ID column represents the Agilent Probe Names.

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: MAD_MM_v1_Nimble_e_135

city: Amsterdam

first: Oskar

last: Bruning

address: Science Park 904

department: SILS

country: Netherlands

institute: University of Amsterdam

organism: Mus musculus

description: NimbleGen custom oligonucleotide Mus musculus 12x135K microarray that covers approx. 44,000 genes and contains 2 different 60mers per gene.

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


title: Agilent-025293 Mouse Whole Genome 4x44k Microarray (Probe Name version)

city: New Delhi

first: Kanury

middle: VS

last: Rao

state: Delhi

address: Aruna Asaf Ali Marg

institute: ICGEB

description: Agilent Custom Mouse Whole Genome 4x44k Array designed by Genotypic Technology Private Limited (AMADID: 25293)


title: Agilent-035953 Sus scrofa Array

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

institute: Wageningen UR

organism: Sus scrofa


title: Agilent-026873 Spodoptera frugiperda SpodoArray (Probe Name version)

status: Public on Aug 26 2014

city: 6th of october

first: Tamer

middle: Zaki

last: Salem

state: Giza

address: Shiekh Zayed

department: Biomedical sciences

country: Egypt

institute: Zewail city of science and technology

organism: Spodoptera frugiperda

description:
Probes were designed from EST records in Spodobase (http://bioweb.ensam.inra.fr/spodobase/).

Arrays of this design have barcodes that begin with 16026873 or 2526873.

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


title: Illumina MiSeq (Escherichia coli BW25113)

status: Public on Jul 25 2014

last: GEO

organism: Escherichia coli BW25113


title: NanoString nCounter Human miRNA assay (v1.1)

city: Columbus

first: Alessandra

last: Drusco

state: Ohio

address: 460 W 12th Ave

institute: The Ohio State University

technology: other

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


title: Illumina HiSeq 2000 (Pseudomonas chlororaphis subsp. aureofaciens 30-84)

status: Public on Mar 18 2013


title: Phalanx Human OneArray [Annotation HOA6 release 1.0]

status: Public on Aug 28 2014

last: admin

description:
Annotation is based on two databases:
- NCBI RefSeq release 51
- Ensembl release 65 cDNA sequences and homo_sapiens_core_68_37f annotations

Long oligonucleotide probes (~60-mers) were engineered using specific lengths to match melting temperatures for superior hybridization performance.

Each array contains 32679 total probes (31741 content probes and 938 control probes)

Probes are classified into three groups based on the number of genes can be hit in the databases. The number of probes for each group is as follows.
Group 1 - one gene hit 26926
Group 4 - multi-gene hits 1473
Group 5 - no hit 322

relation: Alternative to: GPL6254 (Alternative annotation [official])

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


title: GeoChip 3.0

status: Public on Oct 30 2013

city: Beijing

first: Zhao

last: Mengxin

address: Haidian District, Zhongguancun Street

country: China

institute: Tsinghua University

organism: Bacteria

description: Soil microbes


title: Agilent-019159 Rat miRNA Microarray 8 X 15K (Probe Name version)

status: Public on Jul 22 2014

last: Agilent Technologies


title: Agilent-026873 Spodoptera frugiperda SpodoArray (Feature Number version)

description:
Probes were designed from EST records in Spodobase (http://bioweb.ensam.inra.fr/spodobase/).

Arrays of this design have barcodes that begin with 16026873 or 2526873.

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: [HTMG430PM_Mm_ENTREZG] Affymetrix HT MG-430 PM Array Plate [Brainarray Version 14]

status: Public on Jun 20 2013

city: Bethesda

institute: NCBI/NLM/NIH


title: [HG-U133A] Affymetrix Human Genome U133A Array [Custom Brainarray v16 ENTREZG CDF]

status: Public on Feb 28 2014

city: Boston

first: Vijay

middle: G

last: Sankaran

state: MA

address: 300 Longwood Avenue

institute: Boston Children's Hospital

description: Identical to GPL96 but used a custom CDF

relation: Alternative to: GPL96 (Alternative CDF [official])

manufacture_protocol: see the Affymetrix website


title: [Dm35b_MF] Affymetrix Drosophila Tiling 1.0F Array

status: Public on Jan 07 2011

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Drosophila melanogaster

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

This is the first generation of the Drosophila 1.0F Tiling Arrays. The Drosophila Tiling 1.0F Array uses 25-mer oligonucleotide probes, spaced evenly across the Drosophila genome at intervals of approximately 35 base pairs as measured from the center of a probe to the center position of the adjacent probe. Repetitive sequences were eliminated from the design using RepeatMasker software.

BPMAP and other files can be downloaded from the Affymetrix Web site below.

manufacture_protocol: see manufacturer's web site


title: Agilent-019883 Actinobacillus pleuropneumoniae expression array

status: Public on Nov 08 2011

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

institute: Huazhong Agricultural University

organism: Actinobacillus pleuropneumoniae

manufacture_protocol: Sure Print technology (Proprietary, Agilent)


title: Agilent-022097 Actinobacillus pleuropneumoniae expression array

status: Public on Mar 31 2010


title: BIOTEC P. falciparum 8448 features

status: Public on Jul 09 2011

city: Pathumthani

first: Philip

middle: James

last: Shaw

state: Pathumthani

address: 113 Phahonyothin Road

department: National Center for Genetic Engineering and Biotechnology

institute: National Science and Technology Development Agency

organism: Plasmodium falciparum

description: Plasmodium falciparum coding specific 70mer oligonucleotides designed by ArrayOligoSelector

manufacturer: DeRisi laboratory, University of California San Francisco

first: Kanyanan

last: Kritsiriwuthinan

first: Sastra

last: Chaotheing

first: Chayaphat

last: Wongsombat

first: Porntip

last: Chavalitshewinkoon-Petmitr

first: Sumalee

last: Kamchonwongpaisan

first: Jennifer

last: Shock

first: Joseph

last: DeRisi

manufacture_protocol: The oligonucleotides were printed on polylysine-coated slides using a new generation, ultra fast, linear servo driven DeRisi microarrayer as described at http://derisilab.ucsf.edu


title: [HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [HuGene11stv1_Hs_ENSG version 14.1.0]

status: Public on Apr 05 2013

first: GEO

address: 9000 Rockville Pike

description: Probe set data extracted from custom CDF (HuGene11stv1_Hs_ENSG.cdf v14.1.0). See below web link for CDF and other related files.

relation: Alternative to: GPL11532 (Alternative CDF[official])


title: MRA-1002_miRMouse_17

status: Public on Jul 12 2011

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

description: Mouse miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 17

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: Agilent-016579 Nelson Whole Mouse Genome Microarray 4x44K

status: Public on Sep 15 2010

city: Seattle

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

institute: Fred Hutchinson Cancer Center

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


title: Human 4K miRNA LC_MRA-1001_miRHuman_14

status: Public on Nov 13 2009

description: Human miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 14

relation: Alternative to: GPL19157 (miRNA_ID version)

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: Agilent-014879 Whole Rat Genome Microarray 4x44K G4131F (Probe Name version)

status: Public on Oct 08 2008

city: Palo Alto

institute: Agilent Technologies

description:
With a focus on well known rat genes and homologues to human and mouse genes with useful annotation, Agilent's Whole Rat Genome Oligo – 4X44K microarray provides researchers with a new tool for modeling human biology in the rat model organism. For researchers, this means they now have access to a microarray made up of relevant content that has been empirically validated by Agilent.

*** 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 GPL4135.


title: NimbleGen/INRA-CNRS-UEVE Arabidopsis thaliana expression array [111220_Athal_SB_exp]

status: Public on Sep 10 2014

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

organism: Arabidopsis thaliana