title: Illumina HiSeq 2000 (Lolium multiflorum)

status: Public on Feb 29 2016

last: GEO

country: USA

organism: Lolium multiflorum

technology: high-throughput sequencing

distribution: virtual


title: 4.8K Spotted M.tuberculosis H37Rv Microarray

status: Public on Apr 13 2016

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

organism: Mycobacterium tuberculosis H37Rv

technology: spotted oligonucleotide

distribution: non-commercial

manufacture_protocol: non provided by submitter


title: Combimatrix Apple iRIPE array [condensed MDP_ID version]

status: Public on Aug 22 2016

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

country: Italy

institute: University of Trento

organism: Malus domestica

technology: in situ oligonucleotide

description:
a custom array dedicated to fruit ripening pathways (iRIPE)

Please note that genes are reported as MDP0000xxx at https://www.rosaceae.org/gb/gbrowse/malus_x_domestica_v1.0-primary/
This ID is what was uniquely reported for the Combimatrix array. Since we started from candidate genes to design this array, any gene spotted on the array is coded with this ID.

distribution: custom-commercial

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


title: SA Biosciences RT² Profiler PCR Panel Human TGFb Signaling Targets

status: Public on Mar 10 2016

city: Pisa

first: Roberto

last: Giovannoni

address: Via Derna, 1

department: Biology

institute: University of Pisa

organism: Homo sapiens

technology: RT-PCR

description:
TGF-β and chemoresistance in CRC, 84 genes panel
SABiosciences RT² Profiler panel of PCR assays.
SA Biosciences Human TGF-β Signaling Targets RT2 array

manufacture_protocol: see manufacturer's website


title: NanoString nCounter human miRNA expression system

status: Public on Jun 30 2016

city: New York

first: Venugopalan

last: Nair

state: NY

address: 1468 Madison Avenue

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

technology: other

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


title: [LBL-Phy3b520660] Affymetrix PhyloChip G3 array 24k

status: Public on Jul 25 2016

city: San Francisco

first: Jordan

middle: Samuel

last: Mar

state: Ca

address: 513 Parnassus Ave., S-357

department: Medicine, Division of Gastroenterology

institute: University Of California, San Francisco

organism:
Bacteria
Archaea

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


title: Illumina HiSeq 2000 (Anopheles stephensi)

organism: Anopheles stephensi


title: NanoString nCounter gene expression system


title: Illumina HiSeq 2000 (Escherichia coli DH5[alpha])

organism: Escherichia coli DH5[alpha]


title: Illumina HiSeq 2000 (Escherichia coli BL21)

organism: Escherichia coli BL21


title: Illumina HiSeq 2000 (Escherichia coli W)

organism: Escherichia coli W


title: Illumina HiSeq 2500 (Tursiops truncatus)

organism: Tursiops truncatus


title: Applied Biosystems Taqman Low Density Array Human microRNA Card A+B Set v3.0

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description: PCR assay


title: Illumina HiSeq 2000 (Escherichia coli C)

organism: Escherichia coli C


title: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. W3110)


title: JPT PepStar™ Peptide Microarrays

status: Public on Feb 27 2016

city: Potsdam

first: Henry

last: Memczak

address: Karl Liebknecht Straße 24/25

country: Germany

institute: University of Potsdam

organism: unidentified influenza virus

technology: spotted peptide or protein

description: spotted synthetic peptides, glycans, proteins


title: Illumina HiSeq 1000 (Sargassum vulgare)

status: Public on Feb 26 2016

organism: Sargassum vulgare


title: Arabidopsis Oligonucleotide Microarrays Version 3.0, 70-mer oligonucleotide v2

city: saskatoon

first: daoquan

last: xiang

state: SK

address: 110 Gymnasium Place

country: Canada

institute: NRC Saskatoon

organism: Arabidopsis thaliana


title: Streptococcus pneumoniae D39 6X7K

status: Public on Feb 25 2016

city: Daejeon

first: Myung Soon

last: Kim

address: Yeusung-gu

department: R&D

country: South Korea

institute: Genomictree

organism: Streptococcus pneumoniae D39

distribution: commercial


title: NimbleGen Cynomolgus monkey CGH 4.2M Whole-Genome Tiling Array [120405_Cynomolgus5_CGH_UX1]

status: Public on Feb 24 2016

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

department: pRED

country: Switzerland

institute: Roche

organism: Macaca fascicularis

description:
whole-genome tiling array for Macaca fascicularis genome version 5.0 with 4.2 million isothermal tiling oligos with a median spacing of 598bp
Genome build information Macaca fascicularis genome version 5.0 (August 2011) described in Ebeling et al. (2011) Genome Research (PMID: 21862625)
Gene locus and gene annotation in this record is based on 120405_Cynomolgus5_CGH_UX1.gff

native array description file:
120405_Cynomolgus5_CGH_UX1.ndf
120405_Cynomolgus5_CGH_UX1.pos
120405_Cynomolgus5_CGH_UX1.gcstats.txt
120405_Cynomolgus5_CGH_UX1.gff
120405_Cynomolgus5_CGH_UX1_probe_locations.gff
120405_Cynomolgus5_CGH_UX1.ncd

DESIGN NAME: 120405_Cynomolgus5_CGH_UX1
DESIGN_ID: 568661
ORGANISM_GENOME_BUILD=cyno5
http://www.ebi.ac.uk/ena/data/view/GCA_000222185

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


title: NimbleGen 12-plex Gene Expression Array for Cynomolgus monkey (135K) [120419_Cynomolgus_v5_TH_exp]

description:
Cynomolgus monkey

NimbleGen design name: 120419_Cynomolgus_v5_TH_exp
The NimbleGen design is based on Cynomolgus genome/transcriptome version: v5 transcriptome. An expression design with 22,731 probe sets for 22,286 transcripts including transcript variants covering 18,943 genes with six 60-mer probes (PM) per probe set. The number of replicates is 1 - i.e., only one set of probes on the array. The design includes 348 probe sets for viral RNA transcripts, 3420 RANDOM_MK1 control probes for the estimation of the signal threshold, and 1536 ERCC probes for ERCC RNA Spike-In Control Mixes (Ambion/Life Technologies Catalog Numbers 4456740, 4456739).

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

Native array description file: 120419_Cynomolgus_v5_TH_exp.ndf
Native array description file: 120419_Cynomolgus_v5_TH_exp.ngd

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


title: Agilent-045741 Rice custom expression array (Probe name version)

city: Los Banos

first: Manish

middle: L

last: Raorane

state: Laguna

address: UP college campus

department: Plant Breeding, Genetics and Biotechnology

country: Philippines

institute: International Rice Research Institute

organism: Oryza sativa

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


title: TaqMan microRNA Custom Low-Density Array

city: San Giovanni Rotondo (FG)

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

description: TaqMan qRT-PCR assay


title: Illumina HiSeq 2000 (Acinetobacter venetianus RAG-1 = CIP 110063)

status: Public on Feb 22 2016


title: Illumina HiSeq 2000 (Punica granatum)

organism: Punica granatum


title: ArrayStar Human Circular RNA mircoarray V2.0

status: Public on Feb 20 2016

city: Haikou

first: Yousheng

last: Huang

state: Hainan

address: The 3rd Xueyuan Road

department: Department of pathology

country: China

institute: Hainan Medical university


title: MI_Dm_48k

city: Santiago de Chile

first: Calixto

last: Dominguez

state: Región Metropolitana

address: Zanartu 1482

department: Center for Bioinformatics and Genome Biology

country: Chile

institute: Fundación Ciencia y Vida

organism: Drosophila melanogaster

manufacture_protocol: The Drosophila melanogaster microarray set contains 14,593 long oligo probes representing 13,664 genes and 17,899 transcripts. The design directly deals with alternative splicing variants using common, partial common, or individual transcript oligos to assay gene expression. All 14,593 probes are designed from gene transcript sequences from the Gadfly release 3.1 database whole_genome_transcript_dmel_RELEASE3-1.FASTA (Berkeley Drosophila Genome Project )


title: High Density Rice Array (HDRA) Affymetrix Custom GeneChip Array

city: Ithaca

first: Susan

middle: R.

last: McCouch

address: 162 Emerson Hall

department: Plant Breeding & Genetics

institute: Cornell University

description: A High Density Rice Array (HDRA) was developed as an Affymetrix Custom GeneChip Array by the McCouch Rice Lab at Cornell University. The HDRA assays 700,000 SNPs, or approximately one SNP every 0.54 Kb across the rice genome (genome size = 380 Mb). It was designed to capture most of the haplotype variation observed in a discovery panel consisting of 16M SNPs (generated by sequencing 125 rice genomes at ~7X genome coverage) and to maximize the inclusion of non-synonymous SNPs. Six probes per SNP target were designed as 3 A-allele and 3 B-allele probes at offsets from center ranging from -6 to +6. A small fraction of SNPs have only 4 probes (2-A, 2-B). For all SNPs, the ?A? allele is the reference allele (Os-Nipponbare-Reference-IRGSP-1.0 assembly). Additionally, we designed 23,656 x 25-bp probes complimentary to invariant regions of the genome that were used to normalize systematic differences between samples. An estimated 45% of HDRA SNPs map within genes, hitting all 39,045 unique, non-TE rice gene models (MSUv7 rice genome annotation, GFF3 file, Feb. 7, 2012, http://rice.plantbiology.msu.edu/), while 55% of SNPs map to intergenic regions. Non-synonymous are found in 91% of unique, non-TE gene models, and 57% of genic SNPs are distributed within exons, 36% within introns, 5% within 5? UTRs and 2% within 3? UTRs. Of the intergenic SNPs, 40% are located in putative regulatory regions within 2 Kb of a transcriptional start site.

manufacture_protocol: see manufacturer's web site


title: 454 GS FLX Titanium (Pinus pinaster)

organism: Pinus pinaster


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

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Sus scrofa

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

Feb 24, 2016: annotation table updated with netaffx build 34

Annotations dervived from PorGene-1_0-st-v1.na34.sscr2.probeset.csv:

#%chip_type=PorGene-1_0-st-v1
#%lib_set_name=PorGene-1_0-st
#%lib_set_version=v1
#%genome-version=sscr2
#%genome-version-ucsc=sscr2
#%genome-lifted-method=psl-map.pl
#%genome-lifted_from-version-ucsc=sscr2
#%netaffx-annotation-date=2013-08-30
#%netaffx-annotation-netaffx-build=34
#%netaffx-annotation-data-type=probe_set

manufacture_protocol: See manufacturer's web site


title: Agilent-025053 Russell-Rv and CDC X3

status: Public on Feb 21 2016

first: Yancheng

last: Liu

organism: Mycobacterium tuberculosis

description:
All unique probes for H37Rv plus CDC1551 genomes.  3 probes/gene.  Includes replicate controls (Rv0001-0010c) X10.  Array filled to 100% with random additional spots from Rv genome
Arrays of this design have barcodes that begin with 16025053 or 2525053.
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 (Serratia marcescens)

last: GEO

organism: Serratia marcescens


title: Agilent-029218 Heemers AR axis PCF 2010

status: Public on Feb 19 2016

city: buffalo

first: Dan

last: Wang

address: Elm & Carlton Streets

institute: RPCI

organism: Homo sapiens

description:
AR target genes, coregulators, and some metabolism genes (Titus)

Arrays of this design have barcodes that begin with 16029218 or 2529218.

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: Invitrogen ProtoArray v4 human protein microarray lot HA20085 [Array_ID version]

city: Houston

first: Tsz-Kwong

last: Man

state: TX

address: 1102 Bates,

department: Pediatrics

institute: Baylor College of Medicine

first: Flip

last: Jansen

first: Guido

last: Jenster

first: Angelique

last: van Rijswijk

first: Wilma

last: Teubel

manufacture_protocol:
The ProtoArray® Human Protein Microarray is a high-density protein microarray containing approx. 8000 purified human proteins. Each human open reading frame (ORF) is expressed as an N-terminal GST fusion protein using a baculovirus expression system, purified from insect cells, and printed in duplicate on a nitrocellulose-coated glass slide. The human proteins spotted on the microarray are expressed in insect cells using an optimized process to maximize the production of soluble recombinant proteins.
http://www.invitrogen.com/protoarray


title: NimbleGen GeoChip v.4.2 [110902_GeoChip_JV_exp]

city: Norman

first: Jizhong

last: Zhou

state: OK

address: 101 David L Boren Blvd

department: Department of Microbiology and Plant Biology

institute: University of Oklahoma

organism:
Bacteria
Archaea
Eukaryota
Viruses

description:
Annotation based on DNA sequences in NCBI, see details in the design table
The sequences and probe information on the design file (.ndf) is patent protected and thus, is removed from this submission
designname=110902_GeoChip_JV_exp
designid=558221

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


title: Illumina Hiseq 2500 (Vanessa cardui)

organism: Vanessa cardui


title: Illumina HiSeq 2000 (Vitis labrusca x Vitis vinifera)

organism: Vitis labrusca x Vitis vinifera


title: miRCURY LNA microRNA Array, 7th generation - hsa, mmu & rno (miRBase 21; probeID version)

organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

description:
ProductNumber: 208500,208501,208502,208510,208520,208521,208522
LotNumberRange: 35109-35109
GalFileCreationDate=2014-11-13 13:30
ArrayContents_DesignedFor: miRBase 18.0
ArrayContents_CurrentNameColumn: miRBase 21.0
ArrayContents_CurrentNameColumnCoverage: Homo sapiens and related vira:75.21%

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

manufacture_protocol: See Exiqon website


title: Lactococcus lactis transfer RNA array

status: Public on Feb 18 2016

first: Paul

middle: Georg

last: Saffert

state: Brandenburg

address: Karl-Liebknecht Straße 24-25

department: Biochemistry

organism: Lactococcus lactis

manufacturer: Frauenhofer Institute for Biomedical Research (Potsdam, Germany)

manufacture_protocol:
1. Oligos were arrayed in 384 well plates with a final concentration of 10 µM in 3× SSC/0.01% SDS in a total volume of 25 µl.
2. Arrays were printed onto (3-Glycidyloxypropyl)trimethoxysilane (Sigma) activated glass slides using a contact-spotter (QArray 2, Moleculare Devices).
3. After spotting, arrays were incubated overnight at 4°C in a humidified atmosphere and subsequently dried for 30 min at 30°C.
4. Arrays were stored in a dry atmosphere at room temperature until use.


title: Illumina HiSeq 2000 (Porphyromonas gingivalis)

organism: Porphyromonas gingivalis


title: Mycroarray Pseudomonas aeruginosa PA01 array

city: Anam-Dong, Seungbuk-Ku

first: Sungeun

last: Ahn

state: Seoul

address: Anamro

department: molecular microbiology

institute: Korea university

organism: Pseudomonas aeruginosa PAO1

manufacture_protocol: ss-DNA is synthesized in situ on glass substrates functionalized with amines. The synthesis process is proprietary but uses digital micromirror mediated photolithography to generate sufficient acid locally to remove acid labile protecting groups on 5'-terminal phosphoramidite monomers where the next phosphoramidite base will be coupled. The arrays can be used to hybridize cRNA or cDNA


title: Illumina HiSeq 2500 (Boechera stricta)

organism: Boechera stricta


title: Agilent-031746 ISCA Human CGH 60K v2 (Feature Number version)

city: Newcastle upon Tyne

first: Aneta

last: Mikulasova

address: Brewery Lane

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

description:
Agilent SureDesign
G4827A-031746
International Standard Cytogenomic Array (ISCA)
Based on genome build hg19 (GRCh37).

Arrays of this design have barcodes that begin with 16031746 or 2531746.

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: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [CDF: Brainarray Version 13.0]

city: Paris Cedex 05

first: Cecile

last: Laurent

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: Probe set data extracted from custom CDF [Brainarray Version 13.0]


title: 29k Arabidopsis Genome Array

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Arabidopsis thaliana

manufacture_protocol: Oligos are arrayed in 75×25 mm chemically modified slide by SmartArrayTM (CapitalBio Corp., Beijing, China ). Slide contains 29110 of 70mer oligo DNA from The Arabidopsis thaliana Genome Oligo Set Version 3.0 (Operon) . Eleven of Arabidopsis housekeeping genes are arrayed as positive control. Hex is as spotted positive control, 50%DMSO as solvent negative control, and 8 yeast oligonucleotides as exogenous controls.


title: Affymetrix Enterococcus faecium GeneChip [PMDefcma520788F]

city: Rochester

last: Dunman

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

organism: Enterococcus faecium

manufacture_protocol: Affymetrix, Affymetrix; 11 micron; Array Format 100-3660; Part Number: 520788; Array name PMDefcm


title: HiSeq X Ten (Magnaporthe oryzae 70-15)

organism: Pyricularia oryzae 70-15


title: [GuiGene-1_0-st] Affymetrix Guinea Pig Gene 1.0 ST Array [probe set (exon) version]

status: Public on Feb 17 2016

organism: Cavia porcellus

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

#%chip_type=GuiGene-1_0-st-v1
#%lib_set_name=GuiGene-1_0-st
#%lib_set_version=v1
#%genome-species=Cavia porcellus
#%genome-version=cavpor3
#%genome-version-ucsc=cavpor3
#%genome-version-create_date=2012-03-01
#%genome-lifted-method=NONE
#%genome-lifted_from-species=Cavia porcellus
#%genome-lifted_from-version-ucsc=cavpor3
#%netaffx-annotation-date=2014-10-31
#%netaffx-annotation-netaffx-build=35
#%netaffx-annotation-data-type=probe_set


title: PacBio RS II (Schizosaccharomyces pombe)

organism: Schizosaccharomyces pombe


title: Illumina HiSeq 2000 (Setaria viridis)

organism: Setaria viridis


title: Illumina HiSeq 1000 (Ettlia oleoabundans)

organism: Ettlia oleoabundans


title: Illumina Genome Analyzer II (Metarhizium robertsii)

organism: Metarhizium robertsii


title: [GuiGene-1_0-st] Affymetrix Guinea Pig Gene 1.0 ST Array [transcript (gene) 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

#%chip_type=GuiGene-1_0-st-v1
#%lib_set_name=GuiGene-1_0-st
#%lib_set_version=v1
#%genome-species=Cavia porcellus
#%genome-version=cavpor3
#%genome-version-ucsc=cavpor3
#%genome-version-create_date=2012-03-01
#%genome-lifted-method=NONE
#%genome-lifted_from-species=Cavia porcellus
#%genome-lifted_from-version-ucsc=cavpor3
#%netaffx-annotation-date=2014-10-31
#%netaffx-annotation-netaffx-build=35
#%netaffx-annotation-data-type=transcript_cluster


title: [Axiom_GW_Hu-CHB_SNP] Affymetrix Axiom Genome-Wide CHB 1 Array Plate

organism: Homo sapiens

description:
#%create_date=2015-02-24 GMT-08:00 05:58:15
#%chip_type=Axiom_GW_Hu-CHB_SNP
#%genome-species=Homo sapiens
#%genome-version=hg19
#%genome-version-ucsc=hg19
#%genome-version-ncbi=37
#%genome-version-create_date=2009-02-00
#%mitochondrion-version=NC_012920
#%dbSNP-date=2014-10-14
#%dbSNP-version=142
#%hapmap-date=2008-01-08
#%hapmap-version=23
#%omim-date=2014-08-21
#%allele_frequency_data_reference=1KGp1_mar2012
#%netaffx-annotation-date=2015-03-01
#%netaffx-annotation-netaffx-build=35


title: Illumina HiSeq 2000 (Wolfiporia cocos)

organism: Wolfiporia cocos


title: Illumina HiSeq 2000 (Ambystoma mexicanum)

organism: Ambystoma mexicanum


title: Illumina HiSeq 2500 (Escherichia coli O104:H4)

organism: Escherichia coli O104:H4


title: Illumina MiSeq (Burkholderia pseudomallei K96243)

status: Public on Feb 16 2016

organism: Burkholderia pseudomallei K96243


title: Medicago truncatula Nimblegen array v1

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

institute: University of Verona

organism: Medicago truncatula

description: 12-plex array with 135,000 features per subarray.  Feature size: 12 um  Array is based on the Medicago Gene Index, release 11.0).

manufacture_protocol: Standard NimbleGen manufacture protocol.


title: Illumina HiSeq 2000 (Sinorhizobium fredii NGR234)

organism: Sinorhizobium fredii NGR234


title: Illumina HiSeq 2000 (Ulmus minor)

organism: Ulmus minor


title: Illumina HiSeq 2000 (Limacina inflata)

organism: Heliconoides inflatus


title: Illumina HiSeq 2500 (Brassica napus; Leptosphaeria maculans)

status: Public on Feb 09 2016

organism:
Brassica napus
Plenodomus lingam


title: AB SOLiD System 3.0 (Macaca mulatta)

status: Public on Feb 15 2016

organism: Macaca mulatta


title: Agilent-028005 Whole Genome Mouse 8x60k Array (Probe name version)

city: Bangalore

first: Genotypic

last: technology

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

institute: Genotypic Technology

organism: Mus musculus

description: Agilent Whole Genome Mouse 8x60k (AMADID: 028005)


title: Agilent-041663 Heifers Puberty Methylation Array

status: Public on Feb 10 2016

city: College Station

first: Bruna

middle: Rios Coelho

last: Alves

address: 2471 TAMU - Department of Animal Sciences

department: Animal Sciences

institute: Texas A&M University

organism: Bos taurus

description:
Arrays of this design have barcodes that begin with 16041663 or 2541663.

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).

The CHROMOSOMAL_LOCATION coordinates are based on the Baylor 4.0/bosTau4 bovine genome assembly

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: miRCURY LNA Universal RT microRNA PCR mouse and rat panel I, V2.M

status: Public on Feb 13 2016

city: Shanghai

first: Xiaoping

last: Su

address: 800 Xiangyin Road

institute: National Key Laboratory of Medical Immunology & Institute of Immunology


title: Illumina HiSeq 1500 (Candida glabrata)

last: GEO

organism: Nakaseomyces glabratus


title: Agilent-032169 Enterococcus faecalis V583

city: Villaviciosa

first: Victor

last: Ladero

state: Select if applicable

address: Paseo Rio Linares S/N

department: Technology and Biotechnology of dairy products

country: Spain

institute: IPLA-CSIC

organism: Enterococcus faecalis V583

first: Marta

last: Perez

first: Beatriz

last: del Rio

first: Begoña

last: Redruello

first: Anne

last: de jong

first: Oscar

middle: P

last: Kuipers

first: Jan

last: Kok

first: Maria

middle: C

last: Martin

last: Fernandez

first: Miguel

middle: A

last: Avarez

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


title: Exiqon miRCURY LNA microRNA array, 7th generation REV (miRBase v18.0, condensed Probe ID version)

status: Public on Feb 11 2016

city: Ghantou

first: Yang

last: Liu

state: Guangdong

address: No.22, Xingling Street, Jinping District

department: Department of Histology and Embryology

institute: Shantou University Medical College

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

manufacture_protocol: see manufacturer's website


title: Ion Torrent Proton (synthetic construct)

status: Public on Feb 08 2016

organism: synthetic construct


title: Illumina HiSeq 1500 (Gallus gallus)

organism: Gallus gallus


title: WT_Rodent_Chip_03

city: Loughborough

first: Tim

last: Giles

address: College Road

institute: University of Nottingham

organism:
Leptospira interrogans
Campylobacter jejuni
Francisella tularensis subsp. novicida
Yersinia enterocolitica
Yersinia pestis
Yersinia pseudotuberculosis
Rickettsia prowazekii
Rickettsia typhi
Bartonella quintana
Staphylococcus aureus
Mycobacterium avium
Mycobacterium tuberculosis variant bovis
Mycobacterium avium subsp. paratuberculosis
Mycobacterium tuberculosis
Mycobacterium tuberculosis variant microti
Toxoplasma gondii
Cowpox virus
Streptobacillus moniliformis
Bartonella henselae
Mycobacterium canetti
Escherichia coli O157:H7
Salmonella enterica subsp. enterica serovar Typhimurium
Francisella tularensis subsp. tularensis
Francisella tularensis subsp. holarctica
Francisella tularensis subsp. mediasiatica
Paslahepevirus balayani
Mammarenavirus choriomeningitidis
Orthohantavirus puumalaense
Orthohantavirus seoulense

manufacture_protocol: Oligonucleotides were purchased as 3′-amino-modified oligos from Metabion (Martinsried, Germany) and applied at a final concentration of 10 μM in Spotting Buffer 1 (Quantifoil Micro Tools, Jena, Germany). Arrays were spotted using a Microgrid II spotting machine (BioRobotics Inc., Cambridge, UK) according to the instructions of the manufacturer and assembled into ArrayStrips.  Each oligonucleotide probe was replicated two-fold on the array.  The average spot size was 80 μm.


title: Illumina NextSeq 500 (Streptococcus pneumoniae R6)

organism: Streptococcus pneumoniae R6


title: Illumina HiSeq 2500 (Tetrahymena thermophila CU428)

organism: Tetrahymena thermophila CU428


title: Illumina Hiseq 2500 (Escherichia coli)

organism: Escherichia coli


title: Illumina MiSeq (Pasteurella multocida)

organism: Pasteurella multocida


title: NanoString nCounter ITESM [20]

status: Public on Feb 06 2016

city: Monterrey

first: Roberto

last: Portillo Lara

state: Nuevo León

address: Ave. Eugenio Garza Sada 2501 Sur Col. Tecnológico

department: División de Biotecnología y Alimentos

country: Mexico

institute: Tecnológico de monterrey

organism: Homo sapiens

description: nCounter custom-made panel ITESM (genes associated with prostate cancer)


title: NanoString nCounter Stem cell [199]

description: nCounter Human Stem cell gene panel for 199 genes.


title: Agilent-035315 Helicoverpa virescens microarray HelioVir-V2 [Probe Name version]

city: Jena

first: Heiko

last: Vogel

address: Hans-Knoell-Strasse 8

department: Dpt. of Entomology

institute: Max Planck Institute for Chemical Ecology

organism: Heliothis virescens

description: Arrays of this design have barcodes that begin with 16035315 or 2535315.


title: Illumina NextSeq 500 (Leishmania major)

status: Public on Feb 05 2016

organism: Leishmania major


title: Illumina HiSeq 2000 (Fusarium proliferatum)

status: Public on Feb 04 2016

organism: Fusarium proliferatum


title: Agilent-019415 Custom Viral Transcript Array 1.2 [vertebrate-infecting viruses only 1.0]

first: John

last: Chiorini

state: Maryland

address: 10 Center Drive, Bldg 10, MSC1190

department: Molecular Physiology and Therapeutics Branch

institute: National Institute of Dental and Craniofacial Research, National Institutes of Health

organism: Viruses

description:
Custom Viral Array - Vert Only 1.0

This platfrom is only using the vertebrate infecting viruses from an updated version of array 019415 (GPL21032). The probe ID names from the original 019415 was updated to a more user friendly format.

relation: Alternative to: GPL21032 (Feature Number version)

manufacture_protocol:
see manufacturer's web site at http://www.agilent.com/
http://www.agilent.com/cs/library/usermanuals/Public/G4140-90040_GeneExpression_OneColor_6.9.pdf


title: NanoString nCounter GX Cancer Reference Kit [237]

description: nCounter Human Cancer Reference GX Kit for 237 genes.


title: NimbleGen Salmonella subspecies Expression Array [111201_Salm_4_subspecies_LG_exp]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Salmonella

manufacture_protocol: in situ oligonucleotide


title: Illumina HiSeq 2000 (Fusarium verticillioides 7600)

last: GEO

organism: Fusarium verticillioides 7600


title: Illumina HiSeq 2000 (Fusarium proliferatum ET1)

organism: Fusarium proliferatum ET1


title: DNA Damage Signaling Pathway PCR Array Human PAHS-029Z

city: Richmond

first: Steven

last: Grant

address: 401 College Street

institute: VCU

description:
DNA Damage Signaling Pathway PCR Array
The Human DNA Damage Signaling RT² Profiler™ PCR Array profiles the expression of 84 genes involved in DNA damage signaling pathways. The genes featured are those associated with the ATR/ATM signaling network and transcriptional targets of DNA damage response. DNA damage can result in cell cycle arrest, apoptosis, and the stabilization and repair of the cellular genome. Using real-time PCR, you can easily and reliably analyze expression of a focused panel of genes related to DNA Damage Signaling with this array.


title: [HG-U219_Hs_ENTREZG_19] Affymetrix Human Genome U219 Array [CDF: Brainarray HGU219_Hs_ENTREZG_19.0.0]

first: GEO

last: admin

state: MD

description:
This identical to GPL13667 but a custom cdf environment was used to extract data.
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/19.0.0/entrezg.asp

relation: Alternative to: GPL13667 (Alternative CDF [official])


title: MEEBO Mouse array [Gal version Euro_MOA1.1_MEEBO_B950929]

city: Barcelona

first: Yacine

last: Kharraz

state: Catalunya

address: 88 calle Aiguader

department: DCEXS

institute: University Pompeu Fabra

organism: Mus musculus

manufacture_protocol: The Mouse Exonic Evidence Based Oligonucleotide (MEEBO) array was developed by a group of researchers from Stanford and UCSF with collaborators from Rockefeller, Basel, and the Stowers Institute. The oligonucleotide set consists of 38,784 70mer probes that were designed using a transcriptome-based annotation of exonic structure for genomic loci.


title: Ion Torrent PGM (Staphylococcus carnosus)

organism: Staphylococcus carnosus


title: Ion Torrent PGM (Staphylococcus epidermidis)

organism: Staphylococcus epidermidis


title: Illumina HiSeq 2000 (Musa acuminata AAA Group)

organism: Musa acuminata AAA Group


title: Illumina HiSeq 2000 (Tetrahymena thermophila CU428)


title: Illumina HiSeq 2500 (Musa acuminata AAA Group)


title: Soil microbe GeoChip microarray

city: beijing

first: zhao

last: mengxin

address: Haidian District Zhongguancun Street

institute: tsinghua university

organism: Bacteria


title: Illumina HiSeq 2000 (Fusarium fujikuroi IMI 58289)

organism: Fusarium fujikuroi IMI 58289


title: Illumina HiSeq 2000 (Fusarium mangiferae)

organism: Fusarium mangiferae


title: Illumina HiSeq 1000 (Mycobacterium tuberculosis)

status: Public on Feb 03 2016

organism: Mycobacterium tuberculosis


title: Illumina Genome Analyzer IIx (Yersinia pestis)

organism: Yersinia pestis


title: Ion Torrent PGM (Staphylococcus aureus RF122)

status: Public on Feb 02 2016

organism: Staphylococcus aureus RF122


title: Illumina HiSeq 2000 (Corynebacterium glutamicum)

organism: Corynebacterium glutamicum


title: Illumina HiSeq 2000 (Skeletonema marinoi)

organism: Skeletonema marinoi


title: Illumina Genome Analyzer (Arthrobotrys oligospora)

status: Public on Feb 01 2016

organism: Orbilia oligospora


title: Illumina HiSeq 2500 (Escherichia coli O157:H7 str. Sakai)

organism: Escherichia coli O157:H7 str. Sakai


title: [HG-U219] Affymetrix Human Genome U219 Array [CDF: Brainarray HGU219_Hs_ENTREZG_15.1.0]

city: Beerse

first: Tine

last: Casneuf

address: Turnhoutseweg 30

department: Oncology Translational Research

country: Belgium

institute: Janssen R&D

organism: Homo sapiens

description: This identical to GPL13667 but a custom cdf environmnet was used to extract data.


title: TaqMan_IdiPAZ-Homo sapiens-64 genes

city: Madrid

first: Juan Ángel

last: Fresno Vara

state: Madrid

address: Paseo de la castellana 261

department: INGEMM

institute: Hospital La Paz

description: RT-qPCR; custom TaqMan Low Density Arrays were designed such that contained 4 reference genes, 1 mandatory control and 59 genes previously related with prognosis in hormone-receptor negative breast cancer.

manufacture_protocol: microfluidic cards with lyophilized primers and probes in each microwell (see manufacturer's website)


title: Agilent-074918 custom bovine miRNA array

city: Daejeon

first: Jinjong

last: Bong

address: Daehak-ro

institute: NEXBIO

organism: Bos taurus

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


title: Agilent-058369 Homo sapiens PD genes aug13 array

city: London

first: Christos

last: Proukakis

address: Rowland Hill Street

department: Clinical Neuroscience

institute: UCL Institute of Neurology

description:
16 PD relevant genes, filter quality >0.5, 20 kb aroud each gene (30 for NCA and park2, 50 for GBA), and 1 Mb at 10kb probe density around SNCA, park2, GBA

Arrays of this design have barcodes that begin with 16058369 or 2558369.

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: SABiosciences miRNA PCR Array Human Cell Differentiation & Development

city: Loma Linda

first: Mary

last: Kearns-Jonker

address: 25094 Daisy Ave

department: Anatomy

institute: Loma Linda University

description: PCR assay


title: NanoString Expression Assay, nCounter Prognostic AML miRNA signature

city: Toronto

first: Stanley

last: Ng

state: Ontario

address: 160 College Street

institute: Univerity of Toronto

manufacture_protocol: See manufacturer's website


title: Illumina NextSeq 500 (Equus caballus)

organism: Equus caballus


title: Illumina HiSeq 2500 (Homo sapiens x Mus musculus hybrid cell line)

status: Public on Aug 11 2014


title: NimbleGen Trichoderma reesei Whole Genome array v 1.0 [Probe-level, 090708_Tres_MS_exp]

status: Public on Mar 06 2014

city: Vienna

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

country: Austria

institute: University of Vienna

organism: Trichoderma reesei

description:
NimbleGen custom expression design for Trichoderma reesei (+4 additional control transcripts).  Picked 7 probes per gene for 9127 out of 9147 transcripts (9126 exemplars, 10 transcripts with less than 7 probes).  Total of 63836 probes.
NimbleGen design ID: 10269
NimbleGen design files linked below.

Trire2 genome database for T. reesei vs. 2.0, from which the oligonucleotides were designed (http://genome.jgi-psf.org/Trire2/Trire2.home.html)
The T. reesei nucleotide sequence and annotation data have been deposited in Genbank under accession number AAIL00000000

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


title: Agilent-035758 Human miRBASE 16.0 plus 031181

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele


title: Agilent-028383 SurePrint G3 Mouse Promoter Microarray 1x1M

status: Public on Mar 04 2013

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Mus musculus

description:
SurePrint G3 Mouse Promoter Microarray 1x1M

The ID column represents the Agilent Probe Name.


title: [ChiGene-1_1-st] Affymetrix Chicken Gene 1.1 ST Array [transcript (gene) version]

status: Public on Jan 29 2016

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Gallus gallus

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

#%chip_type=ChiGene-1_1-st-v1
#%lib_set_name=ChiGene-1_1-st
#%lib_set_version=v1
#%genome-species=Gallus gallus
#%genome-version=galgal3
#%genome-version-ucsc=galgal3
#%genome-version-create_date=2006-05-00
#%genome-lifted-method=NONE
#%genome-lifted_from-species=Gallus gallus
#%genome-lifted_from-version-ucsc=galgal3
#%netaffx-annotation-date=2013-08-30
#%netaffx-annotation-netaffx-build=34
#%netaffx-annotation-data-type=transcript_cluster

manufacture_protocol: See manufacturer's web site


title: Agilent-019415 Human and Custom Viral Transcript Array 1.2 [Feature Number version]

status: Public on Oct 14 2015

city: Bethesda

last: Chiorini

description:
Agilent 4x44k Conserved Viral Seq III Masterlist

Arrays of this design have barcodes that begin with 16019415 or 2519415.

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: GPL21413 (vertebrate-infecting viruses only)


title: NKI-Nimblegen human 135K [090527_HG18_WG_CGH_v3.1_HX12]

status: Public on Apr 15 2014

city: Amsterdam

first: Philip

last: Schouten

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
HG18
native array description file: 090527_HG18_WG_CGH_v3.1_HX12.ndf
native array description file: 090527_HG18_WG_CGH_v3.1_HX12.pos

manufacture_protocol: NimbleGen


title: NimbleGen Mouse 2.1M deluxe promoter array [100205_MM9_Promoter_MeDIP_HX1]

status: Public on Sep 01 2012

city: Edinburgh

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

first: Richard

middle: R

last: Meehan

manufacture_protocol: 2.1 million probes (50-70nt long) covering annotate promoter regions as well as CpG islands across the mouse genome (mm9 build).


title: Agilent-031025 POSTECH Arabidopsis thaliana 8x60K v1.0

status: Public on Jul 01 2012

city: Pohang

first: Hee Jung

last: Koo

address: Hyojadong San 31

institute: Pohang University of Science and Technology

organism: Arabidopsis thaliana

description: Design ID 031025

manufacture_protocol: Agilent’s SurePrint oligo manufacturing technology


title: [HT_MG-430_PM] Affymetrix HT MG-430 PM Array Plate [CDF: HTMG430PM_Mm_ENTREZG, Brainarray version 19]

last: admin

address: 9000 Rockville Pike

country: USA

institute: NCBI/NLM/NIH

description: This Platform is identical to GPL11180 but a custom CDF environment was used to extract data. The custom CDF file (from Brainarray) is based on Entrez Gene. The custom CDF is linked below as a supplementary file.

relation: Alternative to: GPL11180 (alternative CDF [official])

manufacture_protocol: See manufacturer's web site.


title: MOLMIBI_CH34_array [Agilent-034995]

status: Public on Feb 28 2013

city: Halle/Saale

first: Cornelia

last: Große

department: Faculty of Biology/Microbiology

organism: Cupriavidus metallidurans CH34

first: Frank

last: Reith

manufacture_protocol: SurePrint inkjet technology by Agilent


title: Agilent-067406 CBC lncRNA + mRNA microarray V4.0

status: Public on Jan 09 2015

city: Beijing

first: Guifeng

last: Wei

state: Beijing

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

description: Agilent SurePrint G3


title: Illumina HiSeq 4000 (Escherichia coli)

last: GEO

organism: Escherichia coli


title: NimbleGen 090918 Vitus vinifera exp HX12 [090918_Vitus_exp]

status: Public on Jul 29 2011

city: Verona

first: Alberto

last: Ferrarini

address: Strada le Grazie, 15

institute: University of Verona

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 of the 12X grape genome assembly produced by the French-Italian consortium.

A different version of this platform with the 'GENE_CALL_ID' in the ID column is assigned accession number GPL17894.

first: Paola

last: Tononi

first: Massimo

last: Delledonne

manufacture_protocol: Standard NimbleGen manufacture protocol.


title: NimbleGen Trichoderma reesei Whole Genome array v 1.0 [090708_Tres_MS_exp]

status: Public on Jan 01 2011

last: Schmoll


title: NimbleGen 090918 Vitus vinifera exp HX12 [090918_Vitus_exp; GENE_CALL_ID version]

status: Public on Nov 08 2013

city: Logrono

first: Pablo

last: Carbonell-Bejerano

state: La Rioja

address: Madre de Dios, 51

department: Instituto de las Ciencias de la Vid y del Vino

institute: CSIC

description:
12-plex array with 135,000 features per subarray.
Feature size: 12 um
Array is based on the V1 gene prediction by CRIBI of the 12X grape genome assembly produced by the French-Italian consortium.
PMID 22554261 for gene annotations for each probe

The ID column includes the GENE_CALL_ID (as identified by NimbleScan software). A different version of this platform with the probe names in the ID column is assigned accession number GPL13936


title: Agilent-041648 CMGG Human V1.1 60k [Probe Name Version]

status: Public on Sep 17 2014

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

institute: Center for Medical Genetics

description: Custom Human Microarray

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


title: Illumina NextSeq 500 (Canis lupus familiaris)

status: Public on Feb 03 2016

organism: Canis lupus familiaris


title: PfPv500 version4

city: Irvine

first: Elisabeth

last: Baum

state: CA

address: Med Surge II

institute: University of California Irvine

organism:
Plasmodium falciparum
Plasmodium vivax

description: The arrays used in this study came from a commercially available source, Antigen Discovery Inc. (Irvine, CA). It features 500 Plasmodium falciparum and 515 P. vivax ORFs spotted as in vitro rapid translation/transcription (IVTT) reactions, and some additional purified proteins, onto nitrocellulose-coated slides. Multiple spots consisting of reactions lacking plasmid templates ('no DNA' controls) are present on each array and used for data normalization. The array is called PfPv500 version4.

manufacture_protocol: Spotted IVTT reactions.


title: Macrogen Human BAC clone MacArray Karyo1440

status: Public on Jan 19 2016

city: Kanazawa

first: Kazunori

last: Kawaguchi

address: 13-1 Takara-Machi

department: Gastroenterology

country: Japan

institute: Kanazawa University

technology: spotted DNA/cDNA

description:
MacArray Karyo 1440 BAC-chip
Platform annotations based on genomic build hg18.

manufacture_protocol: See manufacturer's protocols