title: Agilent-046639 Custom Salmonella Typhimurium GXP 8x15k Array designed by Genotypic Technology Pvt. Ltd. (AMADID: 046639)

status: Public on Aug 31 2015

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

technology: in situ oligonucleotide

distribution: commercial


title: Illumina MiSeq (Mus musculus molossinus)

status: Public on Aug 27 2015

last: GEO

country: USA

organism: Mus musculus molossinus

technology: high-throughput sequencing

distribution: virtual


title: Agilent-064228 qchip Hemo custom array v3

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

organism: Homo sapiens

description:
Arrays of this design have barcodes that begin with 16064228 or 2564228

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.

distribution: custom-commercial

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


title: Illumina HiSeq 2000 (Canna indica)

organism: Canna indica


title: Illumina MiSeq (Mus musculus domesticus)

organism: Mus musculus domesticus


title: SABiosciences Human Dendritic and Antigen Presenting Cell PCR assay panel (PAHS-077Z-24)

city: Piracicaba

first: Bruna

last: Benso

department: Physiological Sciences

country: Brazil

institute: UNICAMP

technology: RT-PCR

description:
PCR Array Human Inflammatory Response & Autoimmunity
SABiosciences RT² Profiler panel of PCR assays.

manufacture_protocol: see manufacturer's website


title: RayBiotech Human L493 Array, Membrane (AAH-BLM-2)

status: Public on Dec 09 2015

city: Boston

first: Ben

middle: S

last: Wittner

state: MA

address: 185 Cambridge Street

department: Cancer Center

institute: Massachusetts General Hospital

technology: antibody

description: Antibody Array (Membrane)

manufacture_protocol: Recent technological advances by RayBiotech have enabled the largest commercially available antibody array to date. With the RayBio L-Series Human Antibody Array 507 or 493, researchers can now obtain a broad, panoramic view of cytokine expression. The expression levels of 507 or 493 human proteins can be simultaneously detected, including cytokines, chemokines, adipokine, growth factors, angiogenic factors, proteases, soluble receptors, soluble adhesion molecules and other proteins in cell culture supernatants. The first step in using the Human L-507 or L-493 is to biotinylate the primary amine of the proteins in the sample. The membrane arrays are then blocked, similar to a Western blot, and the biotin-labeled sample is added onto the membrane array which is pre-printed with capture antibodies and incubated to allow for interaction of target proteins. After incubation with HRPConjugated Streptavidin, the signals can be visualized by chemiluminescence. More information can be found at http://www.raybiotech.com/files/manual/Antibody-Array/AAH-BLM-1.pdf


title: RayBiotech Human L507 Array, Membrane (AAH-BLM-1)

description: Antibody Array (Membrane)


title: Illumina HiSeq 2500 (Oncorhynchus keta)

status: Public on Aug 26 2015

organism: Oncorhynchus keta


title: Custom Vibrio cholerae Array_4K

city: Hanover

first: Salvador

last: Almagro-Moreno

state: NH

address: 112 Vail Building

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

organism: Vibrio cholerae

technology: spotted oligonucleotide

manufacture_protocol: 50-70mer oligos spotted onto Corning UltraGaps slides.


title: Illumina HiSeq 2000 (Pinus massoniana)

status: Public on Aug 24 2015

organism: Pinus massoniana


title: Illumina Genome Analyzer IIx (Chiloscyllium plagiosum)

status: Public on Aug 25 2015

organism: Chiloscyllium plagiosum


title: Illumina HiSeq 1000 (Schizosaccharomyces pombe)

organism: Schizosaccharomyces pombe


title: 100718_Scer_EXP_HX12

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

organism: Saccharomyces cerevisiae

description: Custom array

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


title: Illumina HiSeq 2500 (Macrobrachium nipponense)

organism: Macrobrachium nipponense


title: Agilent-027322 Pseudomonas putida tiling array (Feature Number version)

status: Public on Jul 07 2016

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

organism: Pseudomonas putida

description:
Custom Agilent tiling microarray.
Pseudomonas putida mt-2 metabolizes m-xylene and other aromatic compounds through the enzymes encoded by the xyl operons of the TOL plasmid pWW0 along with other chromosomally-encoded activities. This tiling array of densely overlapping oligonucleotides was designed to cover every gene involved in this process.

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


title: Full NimbleGen 090918 Vitus vinifera exp HX12, version V1 CRIBI gene names

city: Logrono

first: Jérôme

last: Grimplet

address: C/ Madre de Dios 51

institute: Instituto de Ciencias de la Vid y del Vino

organism: Vitis vinifera

description: 12-plex array with 135,000 features per subarray. Feature size: 12 um. Array is based on the V1 gene prediction by CRIBI awith corresponding ID_ref. A different version of this platform with the probe names in the ID column is assigned accession number GPL13936 and one with the former name of the gene as ID is assigned accession number GPL17894

manufacture_protocol: Standard NimbleGen manufacture protocol.


title: Illumina HiSeq 2500 (Malus domestica)

organism: Malus domestica


title: Illumina MiSeq (Pongo pygmaeus)

status: Public on Aug 20 2015

organism: Pongo pygmaeus


title: Illumina Genome Analyzer IIx (Heliothis virescens)

organism: Heliothis virescens


title: Illumina HiSeq 2500 (Aspergillus nidulans)

organism: Aspergillus nidulans


title: NIA Mouse 44K Microarray v3.0 update (Whole Genome 60-mer Oligo) [Agilent-015087]

status: Public on Aug 21 2015

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

organism: Mus musculus

description: This Platform includes updated array annotation compared to GPL6867.

distribution: non-commercial

manufacture_protocol: As described by Agilent manuals under Platform_web_link.


title: MGX NimbleGen Drosophila melanogaster 12X135K Gene Expression Array

status: Public on Aug 19 2015

city: MONTPELLIER

first: Simonelig

last: Martine

address: 141, rue de la Cardonille

department: Genetics and Development

country: France

institute: Institut de Genetique Humaine - CNRS

organism: Drosophila melanogaster

description:
Drosophila melanogaster DM5.7 build and having 60 basepair probes with target genes 16637 with 8 probes per gene ( one pair for replicates ) per each array
100718_Dmel_exp.ndf
100718_Dmel_exp.ngd


title: [MoGene-1_1-st] Affymetrix Mouse Gene 1.1 ST Array [transcript (gene) version] [CDF: mogene11st_Mm_ENTREZG_19.0.0]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: BrainArray: mogene11st_Mm_ENTREZG_19.0.0

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

manufacture_protocol: See manufacturer's web site (www.agilent.com).


title: Illumina Genome Analyzer IIx (Clostridium perfringens)

status: Public on Aug 18 2015

organism: Clostridium perfringens


title: Illumina HiSeq 2000 (Nicrophorus vespilloides)

organism: Nicrophorus vespilloides


title: Illumina MiSeq (Oryza sativa)

organism: Oryza sativa


title: Illumina HiSeq 2000 (Thermoproteus tenax)

status: Public on Aug 17 2015

organism: Thermoproteus tenax


title: PKUISB Mouse Dusp family member expression profile PCR array

city: Beijing

first: Dan

last: Lu

address: 38# Xueyuan Rd

country: China

institute: Peking University Health Science Center

description:
Dusps PCR assay panel
Applied Biosystems 7500/7500 Fast Real-Time PCR Systems


title: Illumina HiSeq 2000 (Erythranthe guttata)

organism: Erythranthe guttata


title: Invitrogen/INIA 96 qRT-PCR trout infection VHSV_NV

status: Public on Aug 14 2015

city: Madrid

first: Julio

middle: M

last: Coll

address: crt Coruna km7

department: Biotechnology

institute: INIA

organism: Oncorhynchus mykiss

description:
Expression of genes after a viral hemorrhagic septicemia virus (VHSV) challenge.

PCR assay

first: Eduardo

last: Gómez-Casado

first: Blanca

last: Chinchilla

first: Paloma

last: Encinas

manufacture_protocol: Suitable primers were selected by the NCBI Primer-BLAST utility (http://www.ncbi.nlm.nih.gov/tools/primer-blast/). q-PCR plates were manufactured by Invitrogen (Life Technologies)  (http://www.invitrogen.com/site/us/en/home.html). RT_PCR assays were performed at INIA facilities in a 7500 Fast Real-Time PCR System (Applied Biosystems).


title: CFX96 Touch Real-Time PCR Detection System #1855196

city: Hangzhou

first: Dayong

last: Li

state: Zhejiang

address: 866 Yuhangtang Rd

department: Institute of Biotechnology

institute: Zhejiang University

organism: Solanum lycopersicum

description: PCR assay


title: Bio-rad Solanum lycopersicum

description:
PCR assay
CFX96TM optics module  C1000TM thermal cycler  Bio-rad laboratories, lnc. CFX96TM Real-time system


title: BC016 Archaea Array

status: Public on Aug 15 2015

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Washington Road

department: Geosciences

institute: Princeton University

organism: Archaea

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 stored in the dark at room temperature under slight vacuum in a dessicator. They were UV irradiated before hybridization,


title: Agilent-041580 8x60K whole genome linc V1_V2 041579 (Probe name version]

status: Public on Aug 22 2015

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

institute: Berlin Institute of Health

organism: Homo sapiens

description: Mattick linc BROAD linc


title: Illumina HiSeq 2500 (Cucumis sativus)

last: GEO

organism: Cucumis sativus


title: Illumina Genome Analyzer (Ambystoma mexicanum)

status: Public on Aug 13 2015

organism: Ambystoma mexicanum


title: Illumina HiSeq 1500 (Burkholderia caribensis)

organism: Paraburkholderia caribensis


title: Illumina HiSeq 2000 (Francisella tularensis subsp. novicida U112)


title: Illumina HiSeq 2000 (Burkholderia caribensis)


title: Illumina MiSeq (Sus scrofa)

organism: Sus scrofa


title: [FRAGDIFFa520673F] Affymetrix B. fragilis NCTC 9343 and C. difficile 630 array

city: Stanford

first: Justin

middle: L

last: Sonnenburg

state: CA

address: Fairchild D315

institute: Stanford University

organism:
Bacteroides fragilis NCTC 9343
Clostridioides difficile 630

description: The GPL14584 contains reads for B. fragilis and this platform contains reads for C. difficile strain 630 in addition to B. fragilis.

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2500 (Haematococcus pluvialis)

status: Public on Aug 12 2015

organism: Haematococcus lacustris


title: Agilent_045521_wheat_5Aphysical_map_8x15k

city: Fiorenzuola d'Arda

first: Delfina

last: Barabaschi

address: Via San Protaso 302

country: Italy

institute: CRA-Genomics Research Centre

organism: Triticum aestivum

description: wheat cultivar "Chinese spring"

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


title: Illumina HiSeq 2500 (Saccharomyces mikatae)

status: Public on Aug 10 2015

organism: Saccharomyces mikatae


title: Illumina HiSeq 2000 (Sorghum bicolor)

organism: Sorghum bicolor


title: Illumina MiSeq (Pseudomonas aeruginosa PAO1)

organism: Pseudomonas aeruginosa PAO1


title: Illumina HiSeq 2500 (Saccharomyces paradoxus)

organism: Saccharomyces paradoxus


title: Illumina HiSeq 2500 (Saccharomyces kudriavzevii)

organism: Saccharomyces kudriavzevii


title: Illumina HiSeq 2000 (Rattus rattus)

status: Public on Aug 11 2015

organism: Rattus rattus


title: miRCURY LNA microRNA Array, v.10.0 - hsa, mmu & rno

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

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

manufacture_protocol: see manufacturers website


title: Illumina Genome Analyzer IIx (Pseudomonas putida)

status: Public on Aug 07 2015

organism: Pseudomonas putida


title: miRCURY LNA microRNA Array, 7th Gen [lot35006]

status: Public on Aug 06 2015

first: James

last: Donahue

address: 10 North Greene

department: Surgery

institute: University of Maryland


title: Sphingobium whole ORF oligonucleotide array

city: Vancouver

first: Hirofumi

last: Hara

state: BC

address: 2350 Health Science Mall

department: Microbilogy and Immunology

country: Canada

institute: University of British Columbia

organism: Sphingobium sp. SYK-6


title: Illumina Genome Analyzer II (Colletotrichum graminicola)

organism: Colletotrichum graminicola


title: Illumina MiSeq (Caulobacter crescentus NA1000)

organism: Caulobacter vibrioides NA1000


title: Agilent-040558

city: Clermont-Ferrand

first: william

last: tottey

address: 28 place Henry Dunant

institute: EA-CIDAM 4678

organism: human gut metagenome

description:
The GEO file is linked below as supplementary file.
040558_D_GEO_20120427.txt


title: Illumina HiSeq 2000 (Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028)


title: Agilent-034592 Arabidopsis thaliana PSC_Custom

status: Public on Aug 08 2015

city: Nara

first: Kaori

last: Sako

state: Nara

address: 3327-204, Nakamachi

department: Department of Advanced Bioscience

country: Japan

institute: Kindai University

organism: Arabidopsis thaliana

description: the probes were designed based on expressed genes and transcripts of TAIR 10 genome using previous tiling-array and RNA-seq analyses (Kawaguchi et al. 2012; Matsui et al. 2008; Okamoto et al. 2010).


title: Illumina HiSeq 2000 (soil metagenome)

organism: soil metagenome


title: Illumina HiSeq 2500 (Stenotrophomonas maltophilia K279a)

status: Public on Aug 05 2015

organism: Stenotrophomonas maltophilia K279a


title: Agilent-017566 Yeast Microarray (Probe Name version)

city: Boston

first: Fred

last: Winston

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

organism: Saccharomyces cerevisiae

description: Agilent Design ID 017566.

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


title: Illumina HiSeq 2000 (Schistosoma japonicum)

status: Public on Aug 04 2015

organism: Schistosoma japonicum


title: Illumina HiSeq 2000 (Acomys cahirinus)

organism: Acomys cahirinus


title: miRCURY LNA microRNA Array, 6th generation - hsa, mmu & rno [miRBase 18.0]

city: hang zhou

first: guifa

last: li

address: Zhejiang University School of Medicine Department of Neurobiology

department: Department of Neurobiology

institute: Zhejiang University School of Medicine

organism: synthetic construct

description:
Catalog number = 208400, 208401, 208402, 208420, 208421, 208422
LotNumberRange=34101-34101
The 6th generation of miRNA array contains more than 1891 capture probes, covering all human, mouse and rat microRNAs annotated in miRBase 16.0, as well as all viral microRNAs related to these species.
GalFileCreationDate=2011-12-08 15:12
ArrayContents_DesignedFor=miRBase 16.0
ArrayContents_CurrentNameColumn=miRBase 18.0
ArrayContents_CurrentNameColumnCoverage=Mus musculus and related vira:90.94%


title: [BovGene-1_1-st] Bovine Gene 1.1 ST Array [transcript (gene) version]

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Bos taurus

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

Platform table create dwith Affymetrix annotation file BovGene-1_1-st-v1.na34.umd3.transcript.csv:
#%create_date=Wed Apr  2 10:16:16 2014 PDT
#%chip_type=BovGene-1_1-st-v1
#%lib_set_name=BovGene-1_1-st
#%lib_set_version=v1
#%genome-version=umd3
#%genome-version-ucsc=umd3
#%genome-lifted-method=psl-map.pl
#%genome-lifted_from-version-ucsc=umd3
#%netaffx-annotation-date=2013-08-30
#%netaffx-annotation-netaffx-build=34

manufacture_protocol: See manufacturer's web site


title: CCDTM miRNA-version 5

status: Public on Aug 01 2015

first: Jiaqiang

last: Ren

institute: National Institutes of Health

organism:
Homo sapiens
Mus musculus
Rattus norvegicus
human gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus macacae

manufacturer: NIH Clinical Center, Dept. of Transfusion Medicine, Immunogenetics Section (NIH/CC/DTM)

manufacture_protocol: Oligos sythesized by Operon with 3' amine modification and purified by desalting. Oligos are adjusted to the same concentration and resuspend in 2mM phosphate buffer at 25mM oligo concentration and spotted on CodeLink(TM) Activated Slides (GE Healthcare) using an Omnigrid robotic arrayer (Genomic Solutions).


title: [miRNA-3] Affymetrix Multispecies miRNA-3 Array [CDF: miRNA30_Hs_MIRBASEF_16.0.0]

city: Barcelona

first: Mireia

last: Arnedo

state: Other

address: Casanovas, 143. CELLEX, A41

department: AIDS Unit

institute: Institut Investigacions Biomediques Agusti Pi i Sunyer (IDIBAPS)

manufacture_protocol: This is identical to GPL16384 but a custom cdf environment was used to extract data. The cdf supplementary file is linked below.


title: Agilent-019569 ECUST Subtilis 8*15K v1.0 (Probe Name version)

first: GEO

last: admin

institute: NCBI/NLM/NIH

organism: Bacillus subtilis subsp. subtilis str. 168

manufacture_protocol:
A total of 4104 B.subtilis genes were selected from the SubtiList database, of which 2230 were known.
Three probes of a length of 60mer were designed for each of the 4104 genes using Agilent eArray 5.0 program according to the manufacturer's recommendations (https://earray.chem.agilent.com/earray/). These lead to 12312 probes with prefix 'CUST_'.
Another 108 probes (of a 45mer or 46mer length) were designed for 108 B.subtilis genes with other methods and they were spotted on the array in varied replicate numbers, resulting a total of 2896 spots for such 'Bsu####' probes.
A total of 15,744 features (15,208 non-controls and 536 controls) were spotted on each grid of the microarray.
One microarray contains 8 grids of identical components.

*** A different version of this platform with the Agilent feature nubmers in the ID column is assigned accession number GPL8896.


title: Agilent-036610 Streptomyces clavuligerus  DDTS2_matrizv1

city: León

last: Liras

state: León, Spain

address: Facultad de Biología. Campus de Vegazana

department: Molecular Biology

institute: Universidad de León

organism: Streptomyces clavuligerus

description:
Arrays of this design have barcodes that begin with 16036610 or 2536610.

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: [Mouse4302_Mm_ENSG] Affymetrix GeneChip Mouse Genome 430 2.0 Array [CDF: Mouse4302_Mm_ENSG_17.0.0]

status: Public on Aug 03 2015

city: Bethesda

address: 9000 Rockville Pike

organism: Mus musculus

manufacture_protocol: This is identical to GPL1261 but a custom CDF environment was used to extract data [Brainarray Version 17, Mouse4302_Mm_ENSG_17.0.0].


title: Illumina HiSeq 2500 (Clavispora lusitaniae)

organism: Clavispora lusitaniae


title: BioMark Real-Time PCR system assay panel

city: worcester

first: yukiko

last: maeda

state: massachusetts

address: 364 Plantation Street

department: Medicine

institute: Umass Medical School

description: PCR assay panel

manufacture_protocol:
see manufacturer's website
Dynamic Array 96.96 chips


title: Illumina HiSeq 2500 (Botrytis cinerea)

status: Public on Aug 19 2015

organism: Botrytis cinerea


title: Illumina HiSeq 2000 (Clavispora lusitaniae)


title: Agilent-026000 Homo sapiens NF1_array 025961

status: Public on Jul 30 2015

city: Gdansk

first: Arkadiusz

last: Piotrowski

address: Hallera 107

department: Biology and Pharmaceutical Botany

country: Poland

institute: Medical University of Gdansk

organism: Homo sapiens

description:
NF1_copy_number_array

Arrays of this design have barcodes that begin with 16026000 or 2526000.

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-028944 human B w 20 w 27 8x60 [Feature Number version]

city: JBSA FT SAM HOUSTON

first: Phillip

middle: Dalton

last: Bowman

state: TX

address: 3698 CHAMBERS PASS STE B

department: DCR

institute: US Army Institute of Surgical Research

description:
Arrays of this design have barcodes that begin with 16028944 or 2528944.

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: Thermococcus kodakarensis microarray

status: Public on Aug 14 2013

city: Sanda

first: Ryota

last: Hidese

state: Hyogo

address: Gakuen 2-1

department: School of Science and Technology

institute: Kwansei-Gakuin University

organism: Thermococcus kodakarensis

technology: spotted DNA/cDNA

manufacture_protocol:
1. 300 bp DNA fragments were arrayed in 384-well plates.
2. Each fragment was spotted on TaKaRa microarray silide by a microarray spotter.
3. After the print run was completed, fixation treatment was performed for each array.


title: Custom 720K array (100914_HG19_IS_CGH_HX3, OID: 31268, Roche-NimbleGen Madison, WI, USA)

description: Build: hg19

manufacture_protocol: Maskless Array Synthesizer; see manufacturer's web site www.nimblegen.com


title: Candida albicans  8x15k Gene expression Microarray designed  by Genotypic Technology Private Limited (AMADID-016356)

status: Public on May 30 2013

city: Bangalore

first: Genotypic

last: technology

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

institute: Genotypic Technology

organism: Candida albicans


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [Gene Symbol Version]

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
June 03, 2009: annotation table updated with netaffx build 28
June 06, 2012: annotation table updated with netaffx build 32

manufacture_protocol:
see manufacturer's web site
Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts
All probe sets represented on the GeneChip Human Genome U133 Set are identically replicated on the GeneChip Human Genome U133 Plus 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz Golden-Path human genome database (April 2001 release).
In addition, there are 9,921 new probe sets representing approximately 6,500 new genes. These gene sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from the UniGene database (Build 159, January 25, 2003) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the NCBI human genome assembly (Build 31).


title: Agilent-025748 Corynebacterium glutamicum CGRarray

status: Public on Nov 01 2014

city: Kyoto

first: Masayuki

last: Inui

address: 9-2 Kizugawadai, Kizugawa

institute: Research institute of Innovative Technology for the Earth (RITE)

organism: Corynebacterium glutamicum R

description:
all_ORF_177bp_fragments

Arrays of this design have barcodes that begin with 16025748 or 2525748.

The ID column represents the Agilent Probe name.


title: [DroGene-1_1-st] Drosophila Gene 1.1 ST Array [transcript (gene) version]

status: Public on Jul 29 2013

organism: Drosophila melanogaster

description:
create_date=Fri Jul 19 10:25:18 2013 PDT
chip_type=DroGene-1_1-st-v1
lib_set_name=DroGene-1_1-st
lib_set_version=v1
genome-species=Drosophila melanogaster
genome-version=dm3
genome-version-ucsc=dm3
genome-version-create_date=2006-03-06
genome-lifted-method=NONE
genome-lifted_from-species=Drosophila melanogaster
genome-lifted_from-version-ucsc=dm3
netaffx-annotation-date=2013-05-05
netaffx-annotation-netaffx-build=33
netaffx-annotation-tabular-data-version=1.1
netaffx-annotation-tabular-format-version=1.1
netaffx-annotation-data-type=transcript_cluster
netaffx-annotation-docgen-method=module:affy/annotation_update/builder; exec:create-download-file.pl
netaffx-annotation-docgen-version=8487
netaffx-annotation-url-transcript=www.affymetrix.com/analysis/netaffx/gene/transcript.affx?pk=
netaffx-annotation-url-mrna=www.affymetrix.com/analysis/netaffx/gene/rna.affx?pk=


title: Affymetrix AGRONOMICS Tiling Array

status: Public on Aug 09 2011

organism: Arabidopsis thaliana

relation:
Alternative to: GPL14926
Alternative to: GPL18660
Alternative to: GPL18934
Alternative to: GPL19325
Alternative to: GPL20763

manufacture_protocol: In collaboration with Affymetrix, the European AGRON-OMICS project has developed a new array including probes representing both strands of the entire Arabidopsis genome. Performance comparison with the ATH1 array indicates that both microarrays yield data of comparable quality, but that the new tiling array yields expression information for significantly more genes, since the ATH1 array profiles only about 65% of >33.000 TAIR9 annotated genes. The AGRONOMICS1 arrays also carry all of the original ATH1 sense probes, thereby streamlining the integration with ATH1-based results.


title: Human Genome OpArray (OpHuman+samps_annot14082009)

city: Houston

first: Cecilia

middle: M.

last: Williams

state: Texas

address: 3605 Cullen Blvd

department: Center for Nuclear Receptors & Cell Signaling

institute: The University of Houston

manufacture_protocol: According to manufacturer


title: Agilent-062918 OE Human lncRNA Microarray V4.0 028004 [Probe Name version]

city: Taizhou

first: Feilin

last: Cao

address: No.150 Ximen Road

department: Department of Surgical Oncology, Taizhou Hospital,

institute: Wenzhou Medical University

description:
Arrays of this design have barcodes that begin with 16062918 or 2562918.

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: Illumina Genome Analyzer IIx (Canis lupus familiaris)

status: Public on Jun 24 2011

last: GEO

organism: Canis lupus familiaris


title: Agilent-019943 Genotypic Technology custom M tuberculosis h37Rv Whole Genome 8x15k GE Microarray [Gene Name version]

status: Public on Dec 31 2012

state: Karnataka

organism: Mycobacterium tuberculosis H37Rv

description:
This is the Gene Name version of GPL13420

Platform includes control probes.

first: Raja

middle: C

last: Mugasimangalam


title: Affymetrix S. cerevisiae TAG4 101K array

status: Public on Jun 01 2010

city: Berkeley

first: William

last: Jo

address: 119 Morgan Hall

institute: UC Berkeley

organism: Saccharomyces cerevisiae

description: Affymetrix supplied library file (GenFlex_Tag_16K_v2.cdf) contains information about probe sequences but not identity. We used this library file in conjunction with the annotations provided in the platform data table to analyze the array data.

relation:
Alternative to: GPL17030
Alternative to: GPL20845


title: Affymetrix Ambystoma mexicanum AMBY_002 20k array [CDF: AMBY_002a520748F]

status: Public on Jan 31 2012

city: Gainesville

first: James

middle: R

last: Monaghan

state: FL

address: 2033 Mowry Road

department: Biology

institute: University of Florida

organism: Ambystoma mexicanum

description:
AMBY_002a520748F
AMBY_002a520748F.cdf
Seifert_AMBY_002a520748F_probe_tab.txt

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


title: 3D-Gene Human miRNA V19_1.0.0

status: Public on Apr 25 2013

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2500 (Pan troglodytes)

status: Public on Sep 02 2014

organism: Pan troglodytes


title: NIA Mouse 44K Microarray v3.0 (Whole Genome 60-mer Oligo) [Agilent 015087]

status: Public on May 17 2008

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: The Agilent's Mouse Development Oligo Microarray 3.0 is in 4x44K HD format on a glass slide.  Each 43,451-feature microarray contains 41,999 (60-mer) probes representing all empirical and predicted mouse genes and transcripts based on NIA Mouse Gene Index. The annotation is based on NCBI Mouse RefSeq and GeneBank mRNA searches.  A set of synthetic spike-in control probes are included to control variations in target labeling and hybridization, and to provide more quantitative information on transcripts. You may login into http://lgsun.grc.nia.nih.gov/ANOVA/ for updated or previous versions of annotations.

manufacture_protocol: As descripted by Agilent manuals under Platform_web_link


title: Illumina HiSeq 2500 (Macaca mulatta)

status: Public on Aug 27 2014

organism: Macaca mulatta