title: Illumina HiSeq 2000 (Moraxella catarrhalis O35E)

status: Public on Apr 30 2013

last: GEO

country: USA

organism: Moraxella catarrhalis O35E

technology: high-throughput sequencing

distribution: virtual


title: Illumina HiSeq 2000 (Notophthalmus viridescens)

organism: Notophthalmus viridescens


title: HD2.3X_REV

status: Public on Jun 29 2013

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

organism: Arabidopsis thaliana

technology: in situ oligonucleotide

description: Tiling array HD2.3X. ChIP-chip design of Arabidopsis 7.0 whole genome, with 175 bp spacing.  This design is a refinement of AT7v2 with 3 chambers of 711320 spots on a single slide and all oligo are in REVERSE design.

distribution: custom-commercial

first: Sandrine

last: Balzergue


title: Affymetrix custom maize microarray

status: Public on Jul 15 2013

city: Gent

first: boris

last: parizot

address: Technologiepark 927

country: Belgium

institute: VIB Department of Plant Systems Biology

organism: Zea mays

distribution: non-commercial

manufacture_protocol: Affymetrix


title: Brucella abortus bv. 1 str. 9-941 2K genes 8x15K Gene Expression Array

city: Shanghai

first: Mingxing

last: Tian

address: NO.518, Ziyue Road, Minhang District

country: China

institute: Shanghai Veterinary Research Institute

organism: Brucella abortus bv. 1 str. 9-941

manufacture_protocol: see manufacturer's website


title: Illumina Genome Analyzer II (Miniopterus schreibersii)

status: Public on Apr 26 2013

organism: Miniopterus schreibersii


title: Illumina Genome Analyzer (Acropora millepora)

status: Public on Apr 25 2013

organism: Acropora millepora


title: Illumina HiSeq 2000 (Streptomyces coelicolor A3(2))

organism: Streptomyces coelicolor A3(2)


title: Illumina Genome Analyzer IIx (Ipomoea batatas)

status: Public on Apr 29 2013

organism: Ipomoea batatas


title: Ion Torrent PGM (Trypanosoma brucei brucei)

organism: Trypanosoma brucei brucei


title: Illumina HiSeq 1000 (Caenorhabditis elegans)

organism: Caenorhabditis elegans


title: Illumina Genome Analyzer IIx (Saccharomyces cerevisiae x Saccharomyces bayanus)


title: Illumina Genome Analyzer (Oryzias latipes)

status: Public on Apr 24 2013

organism: Oryzias latipes


title: Illumina Genome Analyzer IIx (Saccharomyces cerevisiae x Saccharomyces mikatae)


title: Illumina Genome Analyzer (Trypanosoma brucei brucei)


title: miRCURY LNA microRNA Array, v.11.0 covering miRBASE version 14.0 at the Sanger Institute

status: Public on Apr 27 2013

city: Krakow

first: Klaudia

last: Skrzypek

address: ul. Gronostajowa 7

department: Department of Medical Biotechnology

country: Poland

institute: Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University

organism: Homo sapiens

technology: spotted oligonucleotide

manufacture_protocol: See manufacturers website


title: Custom NimbleGen 16S Microbial OTU Consensus Array

city: Madison

first: Andrew

last: Corcoran

state: Wisconsin

address: 1415 Engineering Drive

department: Civil and Environmental

institute: UW-Madison

organism: synthetic construct

description:
NimbleGen design name 090611_Unk_SY_EXP, NimbleGen design ID 22598.
Based on consensus sequences for 16S OTUs

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


title: Illumina Genome Analyzer IIx (Saccharomyces cerevisiae x Saccharomyces paradoxus)


title: FDMC Populus euphratica cDNA microarray slide

city: Oulu

first: Suvi

middle: Tuulia

last: Sutela

department: Biology

country: Finland

institute: University of Oulu

organism: Populus euphratica

description: The creation of P. euphratica EST collection is described in Brosché et al. (Genome Biol. 6 (2005) R101). The PCR-amplified fragments originated from EST were spotted on Schott Nexterion E type epoxy-coated slides. The array consists of 3 replicates (4 x 2 arrays per replicate), spacing between replicates spots 8464. The grid of spots is 190 um x 190 um, and one subarray consists of 46 x 23 spots. The grid between subarrays is 9 mm x 4.5 mm.


title: Illumina HiSeq 2000 (Oryzias latipes)


title: Illumina MiSeq (Caulobacter crescentus CB15)

organism: Caulobacter vibrioides CB15


title: AB SOLiD 4 System (Bifidobacterium longum)

status: Public on Apr 28 2013

organism: Bifidobacterium longum


title: Illumina Genome Analyzer Iix (Bactrocera dorsalis)

status: Public on Apr 23 2013

organism: Bactrocera dorsalis


title: Illumina HiSeq 2000 (Pseudomonas putida KT2440)

organism: Pseudomonas putida KT2440


title: Illumina MiSeq (Solanum melongena)

organism: Solanum virginianum


title: Illumina HiSeq 2000 (Nematostella vectensis)

organism: Nematostella vectensis


title: [HGU133 Plus2_hs_EntrezG] Affymetrix GeneChip Human Genome 133 Plus 2.0 Array [Brainarray Version 10]

status: Public on Apr 22 2013

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: This is identical to GPL570 but a custom CDF environment was used to extract data [Brainarray Version 10, hgu133plus2hsentrezg]. CDF and other files can be downloaded at: (see web link below).

relation: Alternative to: GPL570 (Alternative CDF [official])


title: Illumina MiSeq (Ascaris suum)

organism: Ascaris suum


title: Illumina Genome Analyzer IIx (Mycobacterium avium)

organism: Mycobacterium avium


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

organism: Brassica carinata x Brassica rapa


title: Illumina HiSeq 2000 (Pinctada martensi)

organism: Pinctada imbricata


title: Illumina HiSeq 2000 (Felis catus)

organism: Felis catus


title: Illumina HiSeq 2000 (Salmonella enterica subsp. enterica serovar Enteritidis)


title: Illumina Genome Analyzer IIx (Chlamydomonas moewusii)

status: Public on Apr 19 2013

organism: Chlamydomonas moewusii


title: Illumina HiSeq 2000 (Plutella xylostella)

organism: Plutella xylostella


title: Agilent-021876 Populus 4x44K [gene-level]

status: Public on Apr 20 2013

city: Umeå

first: Nathaniel

middle: Robert

last: Street

address: Umeå Plant Science Centre

department: Plant Physiology

country: Sweden

institute: Umeå University

organism: Populus trichocarpa

description: whole-genome expression array

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


title: Affymetrix Human Exon 1.0 ST Array, Ensembl transcript probe sets [exon.pmcdf]

status: Public on Apr 17 2013

city: Fairfax

first: Michael

last: Ryan

state: VA

address: 11781 Lee Jackson Hwy, Ste 320

institute: In Silico Solutions

organism: Homo sapiens

description: Probe-level data extracted from a Bioconductor chip definition 'exon.pmcdf' file.

manufacture_protocol: see manufacturer's web site


title: NimbleGen Trypanosoma brucei Strain 927 Oligonucleotide Expression Array [120828_Tbrucei927_RS_exp]

status: Public on Apr 18 2013

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

organism: Trypanosoma brucei brucei TREU927

description:
DESIGN_NAME: 120828_Tbrucei927_RS_exp
DESIGN_ID: 574071

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


title: Agilent-031266 Mouse miRNA v16.0 8X15k Microarray

city: Beijing

first: Peng

last: Li

address: Dongda street 20# Fengtai District

department: Department of Infectious Disease Control

institute: Institute of Disease Control and Prevention

organism: Mus musculus

description:
Mouse miRBase 16.0

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

The ID column represents the Agilent Probe Name.


title: Illumina HiSeq 2000 (Boehmeria nivea)

organism: Boehmeria nivea


title: Affymetrix S. cerevisiae TAG4 101K array [GenFlex_Tag_16K_v2]

city: Logroño

first: Ramon

last: Gonzalez

address: C. Madre de Dios, 51

department: Instituto de Ciencias de la Vid y del Vino

country: Spain

institute: Consejo Superior de Investigaciones Científicas

organism: Saccharomyces cerevisiae

description: Preprocessed data format after extraction from raw data file for Affymetrix TAG4 S. cerevisiae array. Original array platform design can be found as raw data file and in submission GPL8633.

manufacture_protocol: In situ synthesis (Affymetrix)


title: AFGC 15K cDNA array

status: Public on Apr 15 2013

city: Taipei

first: Cheng-En

last: Chen

address: No.1, Sec.4, Roosevelt Road.

country: Taiwan

institute: National Taiwan University

organism: Arabidopsis thaliana

technology: spotted DNA/cDNA

manufacturer: DNA Microarray Facility, Institute of Plant and Microbial Biology, Academia Sinica.

manufacture_protocol: The DNA elements for the DNA microarrays were amplified as part of the Arabidopsis Functional Genomics Consortium (AFGC). The DNA solutions were printed on CMT-GAPS2-coated glass slides (Corning, http://www.corning.com/) with use of the OmniGrid 100 microarrayer (GeneMachines; http://www.genomicsolutions.com). After printing, slides were baked at 80 C for 6 h and blocked (0.1 mg ml)1 BSA, 3· SSC, 0.1% SDS) before hybridization.


title: Applied Biosystems Taqman Low Density Array Human microRNA Card B

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

technology: RT-PCR

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


title: Illumina Genome Analyzer (Streptomyces coelicolor A3(2))

organism: Streptomyces coelicolor A3(2)


title: Illumina Genome Analyzer IIx (Fusarium fujikuroi)

status: Public on Apr 12 2013

organism: Fusarium fujikuroi


title: Agilent-039363 Schizosaccharomyces pombe 44K oligo array Ozan_C10S

status: Public on Apr 21 2013

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

organism: Schizosaccharomyces pombe

description:
Regions of meiotic islands and ura4 locus were added to the original C10B design.  The regions were demarcated by Ozan, and array was designed by Sameet

Arrays of this design have barcodes that begin with 16039363 or 2539363.

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: Febit L. monocytogenes EGD-e DNA Micorarray

city: Zurich

first: Carolina

last: Arguedas-Villa

state: Zurich

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

organism: Listeria monocytogenes EGD-e

manufacture_protocol:
Febit´s Geniom® RT Analyzer was used for automated processing of biochips, hybridization, washing and detection of signals. One probe for each gene of L. monocytogenes EGD-e was synthesized on array.
Whole processing including sample labelling, washing and detection was done by febit GmbH.
Febit used MessageAmpTMII-Biotin Enhanced RNA kit (Ambion) for labelling of RNA for mRNA expression analysis.


title: OspC Protein Microarray

city: Irvine

first: Elisabeth

last: Baum

state: CA

address: Med Surge II

institute: University of California Irvine

organism: Borreliella burgdorferi

technology: spotted peptide or protein

manufacture_protocol: Primers used for amplifying full-length ospC alleles had sequences corresponding to positions 16903 through 16925 (Forward) and 17529 through 17558 (Reverse) of cp26 of the B31 strain. For amplification of subcloning targets for protein expression the Forward primer eliminated the signal peptide and 4 different Reverse primers  (to accommodate 3’ end nucleotide polymorphisms amongst ospC alleles), corresponding to nucleotide positions 614 through 633 were used. Sequence-verified clones of full-length ospC alleles were subcloned into a pXT7 expression vector containing an amino-terminal 10X-Histidine (His) fusion tag. Plasmids were transformed into E. coli BL21(DE3)pLysS (Promega, Madison, WI) for protein expression in Terrific Broth (MP Biomedicals, Solon, OH) induced with IPTG (RPI, Mt. Prospect, IL), lysed and  centrifuged. Cleared bacterial lysate was incubated with Ni-coupled magnetic beads (MagneHis kit, Promega, Madison, WI). Purified recombinant proteins were eluted from beads and sample purity was estimated by densitometry of coomassie-blue stained protein bands on sodium dodecyl sulfate-polyacrylamide (SDS-PAGE) gels; protein concentration was determined by BCA Protein Assay kit (Pierce, Rockford, IL). Purified recombinant-OspC proteins were printed on nitrocellulose-coated glass FAST slides (Whatman, Piscataway, NJ) using an Omnigrid 100 apparatus (Digilab, Holliston, MA), in duplicate spots and 2 different amounts of approximately 10 pg and 30 pg of protein per spot. Protein storage buffer alone was printed on the array to serve as a background signal control.


title: Illumina HiSeq 2000 (Aedes albopictus)

last: GEO

organism: Aedes albopictus


title: miRCURY LNA microRNA Array, 6th generation - mmu and related vira, miRBase 17.0

city: Vedbaek

first: Jorg

last: Krummheuer

address: Bygstubben 9

country: Denmark

institute: Exiqon A/S

organism:
Mus musculus
Murid betaherpesvirus 1
Murid gammaherpesvirus 4

distribution: commercial

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

manufacture_protocol: See Exiqon website


title: Thermotoga maritima MSB8 Tmar_Design_v4

city: La Jolla

first: Haythem

last: Latif

state: California

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive

institute: University of California San Diego

organism: Thermotoga maritima MSB8

description: NimbleGen tiling array for Thermotoga maritima.


title: [HG-U133A] Affymetrix Human Genome U133A Array [hgu133ahsentrezg.cdf]

city: Ann Arbor

first: Andy

middle: W

last: Lin

state: MI

address: 205 Zina Pitcher Place

department: MBNI

institute: University of Michigan

description: Identical to GPL96 but used a custom CDF

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


title: Illumina HiSeq 2000 (Escherichia coli O157:H7 str. Sakai)

status: Public on Apr 16 2013

organism: Escherichia coli O157:H7 str. Sakai


title: Illumina Genome Analyzer IIx (Escherichia coli O157:H7 str. Sakai)


title: Agilent-029854 T. pseudonana gene-specific microarray

city: Seattle

first: Justin

last: Ashworth

address: 401 Terry Ave N

institute: Institute for Systems Biology

organism: Thalassiosira pseudonana

manufacture_protocol: Agilent custom oligonucleotide array (60mer, 4x180k format), sense-stranded


title: NimbleGen Enterococcus faecalis OG1RF 12x135K version1

city: Milwaukee

first: Dusanka

last: Vesic

address: 8701 Watertown Plank Road

department: Microbiology and Molecular Genetics

institute: Medical College of Wisconsin

organism: Enterococcus faecalis OG1RF

description:
NimbleGen design  ID OID33524.  ORF-based expression design for 2,477 genes from Enterococcus faecalis OG1RF (derived from annotation via RAST - Aziz et. al. 2008. BMC 9:75 , as described by Frank et al (2012) Infect. Immun. 80:539) with eighteen 24-mer probe pairs (PM/MM) per gene.  Each probe is replicated 3 times.  The design includes random GC and other control probes.
The ORF sequences used in design of this microarray were derived from a custom annotation of the E. faecalis OG1RF genome by RAST (Aziz et al 2008. BMC 9:75), as previously described by Frank et al (2012 Infect. Immun.  80:539), which was performed before the publicly available OG1RF annotation was completed. As a result of this RAST annotation, each ORF identified was assigned a unique RAST feature ID (see the OG1RF RAST output file provided). These ORFs were queried by BLAST against the E. faecalis V583 genome to identify the best hits (EFnnnn locus identifiers), which was the identifier that was subsequently used when assigning names to the array probes. If no clear hit was identified in the E. faecalis V583 genome by BLAST, the RAST-annotated ORFs were given arbitrary OG1RFnnnn identifiers, which were used when assigning names to the array probes.


title: Illumina HiSeq 2000 (Trypanosoma brucei)

organism: Trypanosoma brucei


title: Homo sapiens 390K tiling v1 prostate_8q24

status: Public on Apr 11 2013

city: Reykjavik

first: Sigrun

middle: Helga

last: Lund

address: Dunhagi 3

country: Iceland

institute: University of Iceland

organism: Homo sapiens

manufacture_protocol: see NimbleGen website


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

first: Tao

last: Peng

state: WA

address: 1100 Fairview Ave N/FHCRC/E5-110

department: Medicine

institute: University of Washington

technology: oligonucleotide beads

description: This platform is the gene-centered version of the original GPL6883 platform.


title: Exiqon miRCURY LNA microRNA Human panel V1.R [miRBase v13]

city: Gif Sur Yvette Cedex

first: Guillaume

last: PINNA

address: Bat. 144 - Point courrier n° 22 - CEA SACLAY

institute: CEA

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


title: PICME Poplar 30K

city: Tunis

first: Wassim

last: Azri

address: Campus universitaire

country: Tunisia

institute: Biology

organism:
Populus trichocarpa x Populus deltoides
Populus tremula x Populus alba

manufacturer: Austrian Research Centers GmbH - ARC, PICME

manufacture_protocol: Spotting buffer: 3xSSC+ 1,5MBetain; Spotting plate setting: Biozym 10µl; Arrayer Hardware: GeneMachines Omnigrid II; Arrayer Software: OmniGrid Gridder 2.2.13; Humidity: 40%; Dipping time in sec: 1.


title: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)


title: MUG homo sapiens 8 v KAM 1.2

status: Public on Apr 09 2013

city: Graz

first: Rokhsareh

last: Rohban

address: Stiftingtalstrasse 24

country: Austria

institute: Medical University Graz

technology: antibody

manufacturer: Kinexus Bioinformatics Corp., Vancouver, Canada, (www.kinexus.ca)

manufacture_protocol: The Kinex™ using the KAM-1.2 chip analyzes two samples in a double field array side by side at a time. It   uses approximately 500 pan-specific antibodies (for protein expression) and more than 300 phospho-site-specific antibodies (for  phosphorylation) in duplicate for a minimum number of 248 different phospho-sites, 193 protein kinases, 24 protein phosphatases  and 150 regulatory subunits of proteins involved in cell signalling mediating cell proliferation, migration and apoptosis.


title: Homo sapiens 390K tiling v3 prostate_8q24

description: The whole region is tiled with 50 nt probes at 20 nt interval, every probe is repeated 10 times. Some of the probes are repeated 100 times, as well as random probes, probes from MYC and probes from housekeeping genes. Unfortunately unavailable, but the probeset is attached.


title: Homo sapiens 390K tiling v2 prostate_8q24


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

description:
The Whole-Genome DASL® Assay enables sensitive, reproducible, cost-effective gene expression profiling of low-abundance and partially degraded RNA, such as that found in formalin-fixed, paraffin-embedded (FFPE) samples. Over 24,000 targets can be analyzed at once. The Whole-Genome DASL Assay combines the proven DASL (cDNA-mediated Annealing, Selection, and Ligation) Assay and the HumanRef-8 Expression BeadChip currently used in Illumina’s Direct Hybridization Expression Assays to create an accurate, easy-to-use, higher multiplex assay. Each BeadChip contains eight arrays for simultaneous processing of eight samples. Chosen targets provide genome-wide transcriptional coverage of well-characterized National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq Build 36.2, Release 22) genes.

This platform is the gene-centered version of the original GPL platform GPL8432.


title: Illumina HiSeq 2000 (Streptomyces avermitilis)

organism: Streptomyces avermitilis


title: Agilent-035655 Mouse miRNA_v17

city: Munich

first: Karin

last: Weber

address: Veterinärstr. 13

department: Medizinische Kleintierklinik

institute: Zentrum für klinische Tiermedizin

organism: Mus musculus

description:
Mus musculus miRNAs MiRBase v17 (Agilent

Arrays of this design have barcodes that begin with 16035655 or 2535655.

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: IBMT Campylobacter jejuni epitope mapping (1 of 2)

status: Public on Apr 06 2013

city: Potsdam

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

department: Bioanalytics and Biosensorics

institute: Fraunhofer Institute for Cell Therapy and Immunology

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

description: Spotted peptides.

manufacture_protocol: Pepstar peptide microarrays (JPT).


title: Exiqon microRNA Ready-to-Use PCR, Human panel I+II, V2.M

city: Vancouver

first: Sara

last: MacLellan

state: British Columbia

address: 675 West 10 Ave

institute: BC Cancer Research Centre

description:
PCR Assay
miRCURY LNA™ Universal RT microRNA PCR, 4x Human panel I and 4x Human panel II in 384well PCR plates, one reaction each of 742 human microRNAs and 6 reference genes. For use with ABI 7900HT and other instruments.

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2000 (Streptomyces venezuelae)

organism: Streptomyces venezuelae


title: IBMT Campylobacter jejuni NCTC 11168 full-length 22 immunogenicity (3 of 3)

description:
Spotted fusion proteins.
Overexpressing E. coli (Acella).
Full-length proteins were attached using a specific HaloTag to their corresponding ligand surface, HaloLink.

manufacturer: Platform Halolink Arrays (Promega), spotting performed at IBMT.

manufacture_protocol: Spotting was performed with a Qarray2 (Genetix).


title: IBMT Campylobacter jejuni NCTC 11168 full-length 22 immunogenicity (1 of 3)


title: IBMT Campylobacter jejuni NCTC 11168 full-length 22 immunogenicity (2 of 3)


title: Agilent-020087 human whole genome 4x44K (Probe Name version)

status: Public on Apr 08 2013

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Human whole genome array from Agilent catalogue
Arrays of this design have barcodes that begin with 16020087 or 2520087

*** 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 GPL15287

relation: Alternative to: GPL15287 (Feature Number version)


title: IBMT Campylobacter jejuni alanine scan

description:
Spotted peptides.
Campylobacter jejuni NCTC 11168 cj0669 protein.

manufacture_protocol: Pepstar peptide microarrays (JPT)


title: Illumina Genome Analyzer IIx (Verticillium dahliae)

status: Public on Apr 10 2013

organism: Verticillium dahliae


title: NuGO array (mouse) NuGO_Mm1a520177 [NuGOMm1a520177_Mm_ENTREZG_15.1.0]

city: Nuthetal

first: Gunnar

last: Loh

address: Arthur-Scheunert-Allee 114-116

department: Gastrointestinal Microbiology

institute: German Institute of Human Nutrition

description:
custom CDF alternative to GPL7440
nugomm1a520177mmentrezg custom cdf
This array has been designed by NuGO and manufactured by Affymetrix.
NuGO is a European Union-funded Network of Excellence, the full title of which is 'The European Nutrigenomics Organisation: linking genomics, nutrition and health research'. This array contains aproximately 24.000 probesets, relevant to nutrigenomics studies.
More info:
http://www.nugo.org
http://blog.bigcat.unimaas.nl/~martijn/NuGO/index.html

manufacture_protocol: See manufacturer's web site


title: IBMT Campylobacter jejuni NCTC 11168 1.5k protein screening array (4 of 4)

description:
Spotted fusion proteins.
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.
Fusion proteins were spotted and coupled to the microarray surface for one hour at room temperature with 70% humidity.


title: IBMT Campylobacter jejuni NCTC 11168 1.5k protein screening array (3 of 4)


title: IBMT Campylobacter jejuni NCTC 11168 1.5k protein screening array (2 of 4)


title: Illumina HiSeq 2000 (Streptomyces coelicolor)

organism: Streptomyces coelicolor


title: IBMT Campylobacter jejuni NCTC 11168 1.5k protein screening array (1 of 4)


title: SMD Print_1520 CAT07R4 Saccharomyces cerevisiae

status: Public on Apr 05 2013

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism: Saccharomyces cerevisiae

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine

manufacture_protocol: Material is transferred from microtiter plate wells to the slide surface by an automated print head


title: SMD Print_1333 ACATR1 Saccharomyces cerevisiae


title: Illumina HiSeq 2000 (Mesorhizobium sp. STM 4661)

last: GEO

organism: Mesorhizobium sp. STM 4661


title: SMD Print_1590 CAT07L2 Saccharomyces cerevisiae


title: SMD Print_1699 Saccharomyces cerevisiae


title: LNJHSY Human cleft lip/palate SNP Array

city: shenyang

first: lu

last: yongping

address: huanggu strict puhe street

institute: key lab of liaoning province family planning research institution

manufacturer: Liaoning Province Family Planning Research Institution

manufacture_protocol:
Twenty four oligonucleotide tags function as probe capture on the glass slide were obtained from www.genome.wi.mit.edu, These tags were modified with 3'-amino and synthesized by Nanjing genescript biological technology CO, LTD.
Tags suspended at a concentration of 30uM in 0.3M carbonate buffer PH 8.0, were spotted with two replicate on the slides using a Nano-Plotter 2.1 arrayer (GeSiM Germany) at a rate of ten hits per spot, in a humidified chamber(60% relative humidity).
After spotting, the microarrays were incubated at room temperature overnight in a humid chamber, and then broiled at 60C for 1 hour. Microarrays were rinsed in dH2O and dried. Reverse complements of the tags were called com-tags. Each allele-specific primer was composed by a com-tag at the forward and an allele-specific primer sequence backward. For each SNP, two allele-specific primers were designed, which were match with the two alleles of SNPs respectively. In addition, a com-tag labeled with cy3 was synthesized to act as a positive control.
Multiplex PCR was amplified with the Multiplex PCR Assay Kit (Takara) in 20uL [Multiplex PCR mix2 10uL, Multiplex PCR mix1 0.2uL, 0.2uM primers, 50ng DNA]. In order to remove excess dNTPs and primers, a mix was added into 10ul PCR product, containing 2 units of shrimp alkaline phosphatase (Takara) and 4 units EXO I(Takara) with incubation at 37°C for 30 min followed by 96°C for 10 min. 10ul of treated PCR products was added to 5ul ASPE mix containing 1×Thermopol reaction buffer, 80M of each dATP, dGTP, dTTP (Takara), 40uM Cy3-dCTP (GE), 0.2 unit of a vent exo- DNA polymerase(New England Biolabs), 25nM allele-specific primers.The extension conditions were as follows: an initial 3min at 94°C, 35 cycles of 94°C for 30 second, 60°C for 30 second 72°C for 1 min, and final extension at 72°C for 5minutes. To prepare Cy3 labeled single strand products, 10ul allele-specific extension products were added 10ul mix containing 1.33×SSC, 0.067% SSC, 0.033mg/ml salmon sperm DNA, and 50nM Cy3-labeled com-tag. The mix was denatured at 94°C for 10 min and cooled 5 min on ice. Hybridization was then performed using this hybridization solution in a hybridization chamber at 60°C for 2 hours. Hybridization was followed by two washes in 2×SSC/0.1%SDS (preheated to 50°C) for 5min, proceeded by washing in 0.2×SSC/0.1%SDS for 1 min, then rinsed in dH2O and dried by centrifugation 3 min at 500 r.p.m. Microarrays were scanned at 100-?m resolution, using GenePix 4000B scanner (Axon instruments, USA), the TIFF images were imported into GenePix 6.0 software (Axon Instruments, USA).


title: cGRASP 16K Salmonid Array

city: St John's

first: Tiago

last: Hori

state: NL

address: 0 Marine Lab Rd

department: Ocean Sciences Centre

institute: Memorial University of Newfoundland

organism:
Osmerus mordax
Oncorhynchus mykiss
Salmo salar
Coregonus clupeaformis
Oncorhynchus tshawytscha

manufacture_protocol: Clones were amplified by PCR from plasmids, PCR products were cleaned and ressuspended in printing buffer and printed in the array.


title: IBMT Campylobacter jejuni epitope mapping (2 of 2)

description: Spotted peptides.


title: Agilent-021783 custom human 244K microarray

status: Public on Apr 04 2013

city: Cambridge

first: Weng Khong

last: Lim

state: Cambridgeshire

address: Tennis Court Road

country: United Kingdom

institute: Cambridge Systems Biology Centre

description:
in situ synthesis process prints 60-mer length oligonucleotide probes, base-by-base, from digital sequence files.
annotation in the GEO formatted Agilent file is hg19 while this analysis and Platform record used hg18.

manufacture_protocol: manufactured using a proprietary non-contact industrial inkjet printing process, in which oligo monomers are deposited uniformly onto specially-prepared glass slides


title: Illumina Genome Analyzer II (Solanum pennellii)

country: USA

organism: Solanum pennellii


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

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

institute: Cancer Research Center (CiC-IBMCC)

description:
The probes were mapped to GENE LOCi by the CDF built by GATExplorer
http://bioinfow.dep.usal.es/xgate/principal.php
http://bioinfow.dep.usal.es/xgate/mapping/mapping.php

The CDF file is designed to install as 'R' package;
'genemapperhumangene1.0cdf_3.0.tar.gz' available at:
http://bioinfow.dep.usal.es/xgate/mapping/mapping.php?content=rprogram

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


title: GeneTrack Human 35K oligonucleotide microarray

city: Bucheon-si

first: Seung-Woo

last: Shin

state: Gyeonggi-do

address: 1174 Jung-dong, Wonmi-gu

department: Genome research Center for Allergy and Respiratory Diseases

country: South Korea

institute: Soon Chun Hyang University hospital


title: Illumina Genome Analyzer II (Solanum habrochaites)

organism: Solanum habrochaites


title: AB SOLiD System 3.0 (Enterococcus faecalis)

organism: Enterococcus faecalis


title: Illumina Genome Analyzer II (Solanum pimpinellifolium)

organism: Solanum pimpinellifolium


title: Affymetrix EUTOM3 tomato exon array [CDF: EUTOM3_exon]

city: Wageningen

first: Ruud

middle: A

last: de Maagd

address: PO Box 619

country: Netherlands

institute: Plant Resarch International

organism: Solanum lycopersicum

description:
The identifiers in the platform data table are for cDNA models which are publicly accessible at: http://solgenomics.net/

supplementary file: eutom3gene_v2_aprobes.cdf
supplementary file: probes_tab.txt

manufacture_protocol: The included cdf file was build by mapping the 1,055,953 Affymetrix probes on the tomato genome (assembly 2.4) and then matched with the iTAG annotation v.2.3. The included probes_tab file contains the probe sequences and mapping to the iTAG v2.3 cDNA exons.


title: NimbleGen Rat CpG Island Plus RefSeq Promoter 720k array [100718_RN34_CpG_Refseq_Prom_MeDIP]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Rattus norvegicus

description:
DESIGN_NAME: 100718_RN34_CpG_Refseq_Prom_MeDIP
DESIGN_ID: 535623
SLIDE_LAYOUT_NAME: NimbleChip_HX3


title: Agilent-021636

status: Public on Apr 02 2013

city: Atlanta

first: Karen

middle: E

last: Hermetz

state: GA

address: 1518 Clifton Rd

institute: Emory University School of Medicine

organism: Homo sapiens

description:
chr11-17:5Mb of p and q arms

Arrays of this design have barcodes that begin with 16021636 or 2521636.

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: Agilent-032629

description:
Arrays of this design have barcodes that begin with 16032629 or 2532629.

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-021637

description:
chr18-X:5Mb of p and q arms

Arrays of this design have barcodes that begin with 16021637 or 2521637.

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-019783

description:
Z9pAND20pXBackbone

Arrays of this design have barcodes that begin with 16019783 or 2519783.

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-032630

description:
Arrays of this design have barcodes that begin with 16032630 or 2532630.

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-027687

description:
Arrays of this design have barcodes that begin with 16027687 or 2527687.

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-029464

description:
Arrays of this design have barcodes that begin with 16029464 or 2529464.

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-021635

description:
chr6-10:5Mb of p and q arms

Arrays of this design have barcodes that begin with 16021635 or 2521635.

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-027686

description:
Arrays of this design have barcodes that begin with 16027686 or 2527686.

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-027688

description:
Arrays of this design have barcodes that begin with 16027688 or 2527688.

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-023978

description:
Arrays of this design have barcodes that begin with 16023978 or 2523978.

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-018181

description:
Arrays of this design have barcodes that begin with 16018181 or 2518181.

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-015749 Rat ToxArrayIII ver.2 44Kx4 array

city: Kitakatsushika-gun

first: Hiroshi

last: Matsumoto

state: Saitama

address: 1600 Shimotakano, Sugito-machi

country: Japan

institute: Chemicals Evaluation and Research Institute, Japan

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


title: Source MDx Precision Profiles_Human

city: New York

first: Matthew

last: Galsky

address: 1 Gustave L Levy Place

institute: Mount Sinai School of Medicine

description:
PCR assay
Applied Biosystem’s TaqMan® Universal PCR Master Mix (catalog number: 4304437) and Source MDx® proprietary primer-probe sets (Precision Profiles™)


title: UKD Gastroenterologie Mus musculus oligo array

status: Public on Apr 01 2013

city: Düsseldorf

first: Thor

last: Gehrmann

address: Moorenstrasse 5

department: Klinik für Gastroenterologie

institute: Universitätsklinikum Düsseldorf

manufacture_protocol: 280 mouse oligonucleotide probes and 4 negative controls were designed using OligoWiz and synthesized from Operon (Cologne, Germany). The probes are 70-mers with an average Tm = 79°C and 5’-amino group with a C6 spacer. They were dissolved in Genetix Micro Array Spotting Solution (Genetix, New Milton, UK) to a final concentration of 50 pmol / µl and were printed as four replicates on each slide with a QArray 2 (Genetix, New Milton, UK) at 55% relative humidity and room temperature on Corning UltraGAPS (Corning, Lowell MA, USA). The amino-modified probes were covalently bound to the surface by UV crosslinking (600 mJ) according to the protocol from Corning. The quality of the printing process was proofed with test hybridization using SpotCheck (Genetix, New Milton, UK).


title: Illumina HiSeq 2000 (Mesorhizobium metallidurans STM 2683)

organism: Mesorhizobium metallidurans STM 2683


title: Illumina HiSeq 2000 (Drosophila melanogaster; Saccharomyces cerevisiae)

organism:
Saccharomyces cerevisiae
Drosophila melanogaster


title: Illumina HiSeq 2000 (Synechococcus elongatus PCC 7942)

organism: Synechococcus elongatus PCC 7942 = FACHB-805


title: NRC Human 49k HEEBO

city: Montreal

first: Andre

last: Nantel

address: 6100 Royalmount

department: Biotechnology Research Institute

institute: National Research Council of Canada

manufacturer: National Research Council of Canada - Montreal

manufacture_protocol:
Oligonucleotides of the HEEBO Genome Set were acquired from Invitrogen (http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Nucleic-Acid-Amplification-and-Expression-Profiling/Oligonucleotide-Design/HEEBO-and-MEEBO-Genome-Sets.html).
Oligonucleotides 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: NimbleGen Nasonia vitripennis 1.0 Whole-genome Tiling Array Set (2 of 4) [080222_Nvit1_JC_ChIP_HX1]

status: Public on Mar 18 2013

city: Augusta

first: Justin

last: Choi

address: 1410 Laney Walker Blvd.

department: Cancer Center

institute: Georgia Regents University

organism: Nasonia vitripennis

description:
This is a Jewel Wasp (Nasonia vitripennis) whole-genome tiling array set (2 of 4) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen. The array is based on assembly Nvit_1.0.

Native array description file: 080222_Nvit1_JC_ChIP_HX1_2.ndf
Native array description file: 080222_Nvit1_JC_ChIP_HX1_2.pos
Native array description file: 080222_Nvit1_JC_ChIP_HX1_2.ncd

The GenBank and RefSeq accessions.version for the scaffolds in the .pos file are available in the supplementary file 'GPL16801_accessions_for_array_set.txt'.

first: John

middle: K

last: Colbourne

first: Jeong

middle: H

first: Jack

last: Werren

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


title: NimbleGen Nicotiana benthamiana expression array [110121_N_benthamiana_60mer_exp]

status: Public on Jan 17 2013

city: Braamfontein

first: Chrissie

last: Rey

state: Johannesburg, Gauteng

address: 1 Jan Smuts Avenue

department: School of Molecular and Cell Biology

country: South Africa

institute: University of the Witswatersrand

organism: Nicotiana benthamiana


title: NimbleGen Nasonia vitripennis 1.0 Whole-genome Tiling Array Set (1 of 4) [080222_Nvit1_JC_ChIP_HX1]

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

Native array description file: 080222_Nvit1_JC_ChIP_HX1_1.ndf
Native array description file: 080222_Nvit1_JC_ChIP_HX1_1.pos
Native array description file: 080222_Nvit1_JC_ChIP_HX1_1.ncd

The GenBank and RefSeq accessions.version for the scaffolds in the .pos file are available in the supplementary file 'GPL16800_accessions_for_array_set.txt'.


title: Illumina Genome Analyzer II (Cynopterus sphinx)

status: Public on Sep 19 2012

last: GEO

organism: Cynopterus sphinx


title: Agilent-019788 Ambystoma mexicanum 44k_v3_20080327

status: Public on Jan 01 2013

city: Dresden

first: Dunja

last: Knapp

address: Fetscherstraße 105

institute: DFG-Center for Regenerative Therapies Dresden

organism: Ambystoma mexicanum

description:
Arrays of this design have barcodes that begin with 16019788 or 2519788.
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.

first: Herbert

last: Schulz

first: Cynthia

last: Rascon

first: Michael

last: Volkmer

first: Juliane

last: Scholz

first: Eugen

last: Nacu

first: Mu

last: Le

first: Sergey

last: Novozhilov

first: Akira

last: Tazaki

first: Stephanie

last: Protze

first: Tina

last: Jakob

first: Norbert

last: Huebner

first: Bianca

last: Haberman

first: Elly

middle: M

last: Tanaka


title: Agilent-021634

first: Karen

last: Hermetz

department: Human Genetics

description:
chr1-5: 5Mb of p and q arms

Arrays of this design have barcodes that begin with 16021634 or 2521634.

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: Homarus americanus 15K array v2.1

status: Public on Mar 27 2013

city: Charlottetown

first: Fraser

last: Clark

state: PEI

address: 550 University Ave

department: Pathology and Microbiology

institute: University of Prince Edward Island

organism: Homarus americanus

description:
The ID column represents the feature numbers (UID).

A different version of this platform with the oligo IDs in the ID column is assigned accession number GPL16931

manufacturer: Vancouver Prostate Centre DNA Microarray Facility


title: Chipscreen Human microRNA V1.0

city: Guangzhou

first: Xu

last: Chen

state: Guangdong

address: 107. W. Yanjiang Road

department: Department of Urology

country: China

institute: Sun Yat-sen Memorial Hospital

manufacturer: Chipscreen (Chipscreen Biosciences, Ltd., Shenzhen, China)


title: Agilent-039889 MosFish_array

city: Gainesville

first: Erica

middle: Karin

last: Brockmeier

state: FL

address: 2187 Mowry Road

institute: University of Florida

organism: Gambusia holbrooki

description:
Arrays of this design have barcodes that begin with 16039889 or 2539889.

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: Ciona intestinalis 135k x 12plex microarray

status: Public on Nov 01 2011

city: Onnna, Kunigami

first: Takeshi

last: Kawashima

state: Okinawa

institute: Okinawa Institute of Science and Technology

organism: Ciona intestinalis

description: 106,285 probes from KH gene models 2008 and UniGene clusters. NimbleGen OID: 33645.

first: H

last: Matsumae

first: M

last: Hamada

first: T

first: N

last: Satoh


title: Agilent-020087 human whole genome 4x44K (Feature Number version)

status: Public on Mar 06 2012

city: Santa Clara

first: Akshay

last: Zawar

address: 5301 Stevens Creek Blvd

institute: Agilent Technologies

description:
Human whole genome array from Agilent catalogue
Arrays of this design have barcodes that begin with 16020087 or 2520087
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: GPL16981 (Probe Name version)


title: Agilent TIFN Lactobacillus bulgaricus arrays, TB1_8, Version 1

status: Public on Mar 22 2013

city: Brabrand

first: Sander

last: Sieuwerts

address: rørdrumvej 2

department: Arla Scientific Innovation Centre

institute: Arla Foods

organism: Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365

manufacture_protocol: The oligomers were designed using the algorithm described in Appl Environ Microbiol 73:1753-1765. Spotting the probes was performed according to Agilent's standards


title: Agilent-030589 Enchytraeus albidus Gene Expression Array 8x15k

status: Public on Apr 01 2012

city: Aveiro

first: Sara

last: Novais

address: Campus de Santiago, Department of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

organism: Enchytraeus albidus

description:
E.albidus_1035probes_SSHmet+SSHpest+norm

Arrays of this design have barcodes that begin with 16030589 or 2530589.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Illumina Genome Analyzer II (Ascaris suum)

status: Public on Jan 29 2011

last: GEO

organism: Ascaris suum


title: Illumina HiSeq 2000 (Musca domestica)

status: Public on Jul 13 2012

organism: Musca domestica


title: Illumina Custom Huamn Prostate Cancer DASL Panel 1.5K

city: San Diego

first: Yi

last: Zhang

address: 9640 Towne Centre Drive, Suite 200

institute: bioTheranostics


title: MIT Agilent Caulobacter 45K Array

status: Public on Dec 01 2010

city: Cambridge

first: Michael

last: Laub

state: MA

address: 31 Ames St.

institute: MIT

organism: Caulobacter vibrioides CB15

manufacture_protocol: standard Agilent spotted oligonucleotide arraying


title: UW-Madison Escherichia coli K-12 MG1655 tiling array (YD Design)

status: Public on Jun 21 2009

city: Madison

first: Jason

middle: Matthew

last: Peters

address: 1550 Linden Drive

department: Biochemistry

institute: UW-Madison

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

first: Rachel

last: Mooney

first: Pei-Fen

last: Kuan

first: Jennifer

middle: L

last: Rowland

first: Sunduz

last: Keles

first: Robert

middle: C

last: Landick

manufacture_protocol: Nimblegen maskless oligonucleotide synthesized array that tiles the E. coli K-12 genome with Tm matched probes that alternate strands at a length of 42bp or greater with ~12bp spacing.


title: NCI Glycoarray-204

city: Frederick

first: Christopher

last: Campbell

state: MD

address: 376 Boyles Street

institute: NCI

organism:
Quercus alba
Gossypium hirsutum
Rhodotorula
Pandalus borealis
Gallus gallus
Homo sapiens
Bos taurus
Ovis aries
Mus musculus
Megathura crenulata
Bothrops moojeni
Frangula alnus
Senegalia senegal
Pachymenia carnosa
Dermestes lardarius

description:
Spotted glycoproteins and neoglycoproteins
Each slide contains 16 identical array containing 204 components printed in duplicate (408 features total)

manufacturer: National Cancer Institute, Chemical Glycobiology Section

manufacture_protocol: Glycoproteins and neoglycoproteins spotted onto epoxide functionalized glass slides (ArrayIt SME2) using a MicroGrid II arrayer.


title: [Ce25b_MR] Affymetrix C. elegans Tiling 1.0R Array

status: Public on Jul 20 2007

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Caenorhabditis elegans

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

The GeneChip C. elegans Tiling 1.0R Array is designed for identifying novel transcripts or mapping sites of protein/DNA interaction in chromatin immunoprecipitation (ChIP) experiments, or other Caenorhabditis elegans whole-genome experiments. The C. elegans 1.0R Array is a single array comprised of over 3.2 million perfect match/mismatch probe pairs tiled through the complete non-repetitive Caenorhabditis elegans genome. Sequences used in the design of the C. elegans Tiling 1.0R Array were selected from the WormBase web site, www.wormbase.org, release WS140, March 26, 2005.

Probes are tiled at an average resolution of 25 base pair, as measured from the central position of adjacent 25-mer oligos.

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

manufacture_protocol: see manufacturer's web site


title: NCI Glycoarray-220

organism:
Quercus alba
Gossypium hirsutum
Medicago sativa
Rhodotorula
Pandalus borealis
Gallus gallus
Homo sapiens
Bos taurus
Ovis aries
Mus musculus
Megathura crenulata
Bothrops moojeni
Frangula alnus
Senegalia senegal
Pachymenia carnosa
Dermestes lardarius

description:
Spotted glycoproteins and neoglycoproteins
Each slide contains 16 identical array containing 220 components printed in duplicate (440 features total)


title: EcoArray 8 x 15K Daphnia magna Microarray v1.0

status: Public on Sep 27 2008

city: Alachua

first: Barbara

middle: Joan

last: Carter

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

organism: Daphnia magna

description:
Our Daphnia microarray was constructed by first assembling sequence from publicly held accessible databases1 to identify non-overlapping, unique sequences (singlets and contigs). Homology searches (Blast) were performed on these sequences in order to provide annotation (gene name) and ontology (gene function) information where present. A total of 4,936 contigs were assembled. Probes, 60- bases in length, were designed using Agilent’s web-based E-Array program. The content of our Daphnia microarray is located on our web site and contains 4936 contigs of which:
• 2,255 are annotated and represented by one probe for the forward strand.
• 247 are annotated and represented by one reverse complement for the probe.
• 2,434 are un-annotated and represented by one sense and one antisense probe.
Thus, we designed a total of 7,370 probes; each spotted twice on the array.

middle: J

manufacture_protocol: These microarrays are manufactured for EcoArray by Agilent Technologies, Inc. in an “8-pack” (8 individual 15K arrays per slide) format, which allows for maximum information at lowest cost. Each of the arrays on the slide may be hybridized with a unique sample. Probes are synthesized in situ using Agilent’s inkjet based “SurePrint” technology. These arrays are manufactured on superior quality 1” x 3” (24.2 mm x 76.2 mm) treated glass slides for overall excellent performance. This process minimizes variability across each production lot (batch to batch) and provides the highest consistency in slide-to-slide comparisons. See website for details: http://www.agilent.com


title: Illumina HiSeq 2000 (Ascaris suum)

status: Public on Jun 04 2012


title: Agilent-021924 SurePrint G3 Human CGH Microarray 8x60K (Feature Number version)

status: Public on Mar 10 2010

city: Palo Alto

last: Agilent Technologies

organism: Homo sapiens

description:
SurePrint G3 Human CGH Microarray 8x60K

Arrays of this design have barcodes that begin with 16021924 or 2521924.

Data table annotations based on build hg18:NCBI36:Mar2006.

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: GRASP 16K version 2

status: Public on Aug 05 2005

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

institute: The University of Victoria

organism:
Osmerus mordax
Oncorhynchus mykiss
Salmo salar
Coregonus clupeaformis
Oncorhynchus tshawytscha

description:
The microarrays have a 4-by-12 metagrid layout with 19 X19 spot subgrid, each spot having an approximate diameter and pitch of 100 um and 0.20 mm, respectively. A 280 bp GFP (green fluorescent protein) cDNA was amplified from a GFP clone (Clontech) using the primers (5'-GAAACATTCTTGGACACAAATTGG-3') and (5'-GCAGCTGTTACAAACTCAAGAAGG-3') and printed in each subgrid corner to assist in gridding. Six exogenous genome (Arabidopsis) cDNAs were amplified from the following clones kindly provided by The Arabidopsis Information Resource:  rubisco activase [GenBank:T41667], protochlorophyllide reductase precursor [GenBank:R30630], chlorophyll a/b-binding protein CP29 [GenBank:N65746], PSII oxygen-evolving complex protein 2 [GenBank:H36167], tonoplast intrinsic protein root-specific RB7 [GenBank:AA067532] and ferredoxin (2Fe_2S) precursor [GenBank:W43249] and spotted in quadruplicate on each microarray. Also, a ubiquitin normalizer serially diluted (50 pg, 5 pg, 500 fg, 50 fg, 5 fg, 0.05 fg and 0.005 fg) was applied to the array. Spot morphology was assessed by visual inspection, SYBR® Green 1
(Molecular Probes) staining or hybridization with labeled non-specific probe.

manufacturer: The Prostate Centre at Vancouver General Hospital, Gene Array Facility

first: Kristian

middle: R

last: von Schalburg

first: Matthew

last: Rise

first: Glenn

last: Cooper

first: Gordon

middle: D

last: Brown

first: Ross

last: Gibbs

first: Jong

last: Leong

first: Colleen

last: Nelson

first: Jeff

last: Zeznik

first: Bob

last: Shukin

first: Bruce

last: Dangerfield

first: Stephane

last: Le Bihan

first: William

last: Davidson

first: Alan

last: Wardroper

manufacture_protocol:
Clones were robotically rearrayed from daughter glycerol stock 384-well plates into 96-well plates pre-filled with 7% glycerol in LB + ampicillin, incubated overnight at 37°C, and checked for uniform optical density. Plasmid inserts were PCR amplified in a Tetrad PTC-200 thermocycler (MJ Research) using 1 ul overnight culture, 0.2 mM M13/pUC forward primer (5'-CCCAGTCACGACGTTGTAAAACG-3'), 0.2 mM M13/pUC reverse primer (5'-AGCGGATAACAATTTCACACAGG-3'), 2 mM MgCl2, 10 mM Tris-HCl, 50 mM KCl, 250 mM dNTPs, 1U AmpliTaq (Perkin Elmer), and nuclease-free H2O (Gibco) to 100 ul. PCR conditions were: 2 min for 95°C; then 35 cycles of 95°C for 30 sec, 60°C for 45 sec, 72°C for 3 min; followed by 72°C for 7 min. Five ul of each PCR product were run on a 1% agarose gel to assess yield and quality. PCR products were robotically cleaned (Qiagen) and consolidated into 384-well plates, lyophilized by speed-Vac, and resuspended in 20 ul 3X SSC. Each purified PCR product concentration was determined and diluted to give a final concentration of 400ng/uL.
All cDNAs were printed as single spots on EZ Rays aminosilane slides (Matrix/Apogent Discoveries) with the Biorobotics Microgrid II microarray printer (Genomic Solutions). Microspot™ 10K quill pins (Biorobotics) in a 48 pin tool were used to deposit approximately 0.5 nl (0.2 ng cDNA) per spot onto the slide. The slides were crosslinked in a UV Stratalinker 2400 (Stratagene) at 300 mJ.


title: NuGO array (mouse) NuGO_Mm1a520177

status: Public on Oct 15 2008

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

organism: Mus musculus

description:
This array has been designed by NuGO and manufactured by Affymetrix.
NuGO is a European Union-funded Network of Excellence, the full title of which is 'The European Nutrigenomics Organisation: linking genomics, nutrition and health research'. This array contains aproximately 24.000 probesets, relevant to nutrigenomics studies.
More info:
http://www.nugo.org
http://blog.bigcat.unimaas.nl/~martijn/NuGO/index.html

first: Martijn

last: van Iersel

first: Patrick

last: Koks

first: Ruan

last: Elliott

first: Philippe

last: Rocca-Serra

relation:
Alternative to: GPL7441
Alternative to: GPL16983

manufacture_protocol: See manufacturer's web site