title: AB SOLiD System 3.0 (Spodoptera frugiperda)

status: Public on Nov 30 2012

last: GEO

country: USA

organism: Spodoptera frugiperda

technology: high-throughput sequencing

distribution: virtual


title: [atSNPtilx520433] Arabidopsis Tiling array [TAIR9-based custom CDF, ORF version]

status: Public on Mar 01 2013

city: Austin

first: David

middle: Bryant

last: Lowry

state: TX

address: 1 University Station #C0930

department: Integrative Biology

institute: University of Texas at Austin

organism: Arabidopsis thaliana

technology: in situ oligonucleotide

description: Chip Definition File based on TAIR9 genome. The CDF file is included as a supplementary file.

distribution: custom-commercial

manufacture_protocol: see manufacturer's web site


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [MMBGX-Ensembl64]

status: Public on Jan 16 2013

city: San Francisco

first: Nevan

last: Krogan

address: 1700 4th Street

department: Cellular & Molecular Pharmacology

institute: University of California, San Francisco

organism: Homo sapiens

description:
This platform contains certain probeset groupings used for analysis with the MMBGX software platform (PMID 19854940)
http://www.bgx.org.uk/software/mmbgx.html
For data processing, the MMBGX software suite uses raw data CEL files directly as input.

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

manufacture_protocol: See manufacturer's web site


title: Agilent Krill v1.1 (Agilent Design ID: 034463)

status: Public on Jul 23 2013

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

country: Italy

institute: University of Padova

organism: Euphausia superba

description:
Arrays of this design have barcodes that begin with 16034463 or 2534463.
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.
Microarrays were synthesized in situ using the Agilent ink-jet technology with 8 x 60 K format. A total of 32,217 probes representing 32,277 E. superba transcripts were successfully obtained. So, microarray custom platform, named “Krill 1.1” (eArray Design ID: 034463), showed 29,440 duplicate probes and 2,777 single probes. Each array included default positive (1,011 probes) and negative (308 probes) controls.

first: Alberto

last: Biscontin

first: Alessandro

last: Albiero

first: Gabriele

last: Sales

first: Caterina

last: Millino

first: Gabriella

middle: M

last: Mazzotta

last: Bertolucci

first: Rodolfo

last: Costa

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


title: NimbleGen Francisella sp expression array [090630_F_tularensis_4_sp_expr]

city: San Antonio

first: Xhavit

last: Zogaj

address: One UTSA Circle

institute: UTSA

organism: Francisella

description:
090630_F_tularensis_4_sp_expr

A whole genome NibleGen microarray was developed for multiple Francisella subspecies, using shared probes for common genes as well as unique probes for subspecies-specific genes. Included were probes representing the F. novicida U112 genome, with a maximum of 6 probes/gene.

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


title: Tiedje Lab Desulfitobacterium hafniense DCB-2 oligo array

status: Public on Nov 29 2012

city: East Lansing

first: Christina

last: Harzman

state: MI

address: Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

organism: Desulfitobacterium hafniense DCB-2

technology: spotted oligonucleotide

description:
Desulfitobacterium hafniense DCB-2 (JGI ID 2351519/4083484)
spotted oligonucleotides on glass slides

distribution: non-commercial

manufacturer: Jizhong Zhou, Institute for Environmental Genomics, University of Oklahoma, Norman, OK

manufacture_protocol: as in: Rodrigues, D.F., N. Ivannova, J. Zhou, Z. He, M. Webner, J.M. Tiedje, 2008 Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach. BMC Genomics. 9:547.


title: AB 5500xl Genetic Analyzer (Aspergillus niger)

organism: Aspergillus niger


title: Goettingen_Univ_S. cerevisiae_Array-Ready Oligo Set V1.1

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

organism: Saccharomyces cerevisiae

manufacture_protocol: The array was constructed by spotting a 15µM solution of 5’ amino-C6-modified oligonucleotides in 50mM sodium phosphate pH 8.5 with a length of 70 bases on CodeLink microarray slides (SurModics, Eden Prairie, MN, USA) using a MicroGrid II microarray spotter (Zinsser Analytic, Frankfurt, Germany). Each spot contains around 1.5fmol of oligonucleotide. Oligonucleotides were covalently coupled to the slide surface and blocked using ethanolamine according to the instructions of the supplier. The array consists of 6388 probes, as provided by the Array-Ready Oligo Set V1.1 for S. cerevisiae (Eurofins). For additional information see manufacturer's website.


title: [HuEx10stv2_Hs_ENSE] Affymetrix Human Exon 1.0 ST Array [Brainarray Version 11.0.1]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: This platform is identical to GPL5175 but a custom CDF environment was used to extract data [Brainarray Version 11.0.1, HuEx10stv2_Hs_ENSG].

manufacture_protocol: Affymetrix standard protocol


title: Compugen 19K human v5.0

status: Public on Nov 28 2012

city: Darlinghurst

last: Ma

state: NSW

address: L8 Lowy Packer Building, 405 Liverpool St

department: Haematology research

country: Australia

institute: St Vincent's Hospital

manufacture_protocol:
Compugen oligos were provided as lyophilised samples.
Arrays were printed onto Corning Epoxide coated glass slides.
The oligo’s have been immobilised to the surface of each slide by baking and UV X-linking.


title: NimbleGen Custom Desulfovibrio alaskensis str. G20 4-plex [080626_Ddes_G20_EXP]

city: Berkeley

first: Morgan

middle: N

last: Price

state: CA

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

organism: Oleidesulfovibrio alaskensis G20

description:
67,194 60-mer probes with 33,414 different genic sequences in a 4-plex format
native array description file: 080626_Ddes_G20_EXP.ndf

manufacture_protocol: 60 nt probes


title: RPCI Human 6K

city: Buffalo

first: Amanda

last: Perez

state: NY

address: Elm and Carlton Streets

institute: Roswell Park Cancer Institute

technology: spotted DNA/cDNA

manufacture_protocol:
Isolation of BAC plasmid DNA: BAC clone plasmid DNAs, used as templates for PCR representations are prepared using a Qiagen BioRobot 3000. Each clone is retrieved from archival copies of the RPCI-11 BAC Resource, maintained at RPCI. The clones are streaked to single colony, grown overnight (16-18 hours) as 1.0ml pre-cultures in 96 deep-well plates at 37 C in a New Brunswick environmental shaker, and then re-inoculated as 2ml prep-cultures in 48 deep-well plates. After incubation, the cultures are RNase treated and prepped in the BioRobot 3000 using R.E.A.L. Prep 96 BioRobot kits (Qiagen). The BAC DNAs are resuspended in TE and serve as templates for restriction digestion and PCR amplification. We have found that Qiagen prepared DNA is of high quality and outperforms phenol:chloroform extraction methods for the highly sensitive restriction digestion and ligation steps.
Ligation of adapters: The adapters are ligated to the digested DNA by first annealing Mse-21 and Mse-12 primers. 1 ul of each digest (1 ng/ul), is added to 0.5 ul of 100 uM Mse-12 (TAACTAGCATGC), 0.5 ul of 100 uM Mse-21 (5’ aminolinker AGTGGGATTCCGCATGCTAGT) in a final volume of 7.5 ul using a thermalcycler (MJ Research). The mixture is incubated at 65 C for 1 min followed by ramping the temperature down to 15 C with a ramp-speed of 1.3 C per minute. When the temperature reaches 15 C, ligation proceeds with 1 ul of 10 mM ATP, 0.5 ul One-Phor-All-Buffer-Plus (10x) and 1 ul T4-DNA ligase (5 U/ul, Invitrogen) added to each tube and incubated at 15 C overnight.
PCR amplification: Two rounds of amplification are required to produce enough product for array generation as described in Cowell, J. K. and N. J. Nowak. 2003. High-resolution analysis of genetic events in cancer cells using bacterial artificial chromosome arrays and comparative genome hybridization. Adv Cancer Res 90:91-125. A single BAC PCR-representation produces enough printing solution for over 4,000 arrays. Preparation of DNA spotting solutions: PCR products (100 ul) are purified for printing by a series of ethanol precipitation steps, followed by resuspension of the pellets in 20 ul of 25% DMSO in H2O (final DNA concentration ~0.8 ug/ul) using a Qfill2 (Genetix). The DNA solutions are rearrayed into Genetix 384-well V-bottom plates using a Hydra 96-PP liquid handling system, and stored at 4 C until printing. We determined that DNA prepared using LM-PCR performed superiorly over other methods, including degenerate oligonucleotide primer PCR, inter Alu PCR and amplification of BAC subclones mixtures. 25% DMSO has several properties that make it an ideal solution for resuspending the amplicons. First, it acts as a denaturant, rendering the printing solution single-stranded for optimal slide binding and subsequent hybridization. Secondly, DMSO does not evaporate, so the printing solution volume is not affected by exposure to the environment during multiple print runs.
Array printing: Slides are printed using a MicroGrid ll TAS arrayer (Genomic Solutions) using 10K Microspot pins at 48% relative humidity, 22?C. We have a climate controlled, HEPA filtered room to minimize environmental changes that can affect printing. In addition, the arrayer is supplied with HEPA filtered air to further maintain a dust-free environment. We print each BAC clone in triplicate to create an array of on amino-silanated glass slides (Schott Nexterion, Type A+). The printed slides dry overnight, and are UV-crosslinked (350 mJ) in a Stratalinker 2400 (Stratagene). The slides are visually inspected and stored in a dessicated environment and are hybridized without additional treatment. Attempts at post-print processing or inclusion of pre-hybridization steps resulted in background issues that made the images difficult to analyze. We found no indication of DNA loss from the spots at any stage of the procedure when we performed hybridization in formamide buffers at 37°C (via DAPI staining).


title: NimbleGen Mus musculus MM8 Expression Array (12x135k)

status: Public on Dec 12 2012

city: Leicester

first: Yuri

middle: E

last: Dubrova

address: University Road

department: Genetics

country: United Kingdom

institute: University of Leicester

organism: Mus musculus

manufacture_protocol:
High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.
This platform represents two NimbleGen designs:
080925_mm8_60mer_expr
090901_mm8_60mer_expr


title: Illumina Genome Analyzer II (Brassica napus)

status: Public on Nov 26 2012

last: GEO

organism: Brassica napus


title: [HuEx10stv2_Hs_ENST] Affymetrix Human Exon 1.0 ST Array [Brainarray Version 11.0.1]


title: MAICH Horticultural genetics-Olea europaea-Kalamon v.1

status: Public on Nov 20 2012

city: Chania

first: Maria

middle: E.

last: Manioudaki

address: Makedonias 1

department: Horticultural Genetics and Biotechnology

country: Greece

institute: MAICH

organism: Olea europaea

manufacturer: Post-Genomic research laboratory of the Institute of Molecular Biology and Biotechnology in the Foundation of Research and Technology, Heraklion, Crete, Greece.

manufacture_protocol: The unique cDNAs were PCR-amplified using Taq polymerase (Minotech, Heraklion, Greece) with the primers (pDNR-F, 2: 5'-CCGCATAACTTCGTATAGC–3' and pDNR-R, 2: 5'-CATGTTCACTTACCTACTGG-3') positioned by the polylinker site. The PCR products were purified using Nucleofast 96 columns (Macherey-Nagel, Duren, Germany). Approximately 3 μg of purified PCR product was placed in 384-well printing plates (Genetix, Hampshire, UK), dried in room temperature and resuspended in printing buffer containing 450 mM NaCl, 45 mM phosphate pH 7.0, 5% [v/v] formamide and 0.01% [v/v] maltoside at a final concentration of 200 μg/μl. Printing was performed in triplicates on home-made aminosilane slides using a Packard SpotArray24 spotter with four print-tips.


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [HuEx-1_0-st-v2.r2 ENST]

city: Lisbon

first: Raquel

middle: Ferreira

last: Rodrigues

address: Av. Prof. Egas Moniz, Edifício Egas Moniz - Sala P3-A-16

country: Portugal

institute: Molecular Medicine Institute

description:
This is identical to GPL5175 but a custom CDF environment was used to extract data. The probe group file can be found below.
Annotation is based on genome build hg18

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


title: 454 GS FLX Titanium (Bos taurus)

organism: Bos taurus


title: SABiosciences RT2 miRNA PCR Array Human Cancer

status: Public on Nov 27 2012

first: Jonathan

last: Chou

address: 513 Parnassus Ave, Box 0452, HSW1301

department: Anatomy

institute: Univ of California, San Francisco

technology: RT-PCR

description:
PCR assay
SABiosciences RT2 Profiler panel of PCR assays.

manufacture_protocol: see manufacturer's website


title: Agilent-017643 Rat Microarray (017643_D_20070903)

city: Jerusalem

first: Mony

last: Shuvy

address: Ein-Karem

department: Cardiology

country: Israel

institute: Hadassah Hospital

organism: Rattus norvegicus


title: Agilent-033484 Populus 8x60K v2.0 (Probe Name version)

city: Athens

first: Chung-Jui

last: Tsai

state: GA

address: 120 Green Street

department: School of Forestry and Natural Resources

institute: University of Georgia

organism: Populus trichocarpa

description:
Populus transcriptome based on v2.2
Arrays of this design have barcodes that begin with 16033484 or 2533484.

*** 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 GPL16030.

first: Liangjiao

last: Xue

relation: Alternative to: GPL16030 (Feature Number version)


title: Agilent-029297 Human miRNA Microarray v15 (miRNA ID version)

distribution: commercial


title: Illumina Genome Analyzer IIx (Saccharum hybrid cultivar SP70-1143)

status: Public on Nov 23 2012

organism: Saccharum hybrid cultivar SP70-1143


title: Exiqon miRCURY LNA microRNA array; 7th generation; batch 208500-2, 208510; lot 35003 - hsa, mmu & rno (miRBase 19.0)

status: Public on Nov 21 2012

first: Santosh

middle: Kumar

last: Patnaik

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Human betaherpesvirus 5
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

description: The 7th generation miRCURY locked nucleic acid (LNA) oligonucleotide microarray is manufactured by Exiqon (Vedbaek, Denmark). The array has probes printed in quadruplicate as 100 um-diameter spots with 185 um inter-spot distance. Many spots on the array do not have a probe ('empty') and there are some spots that only have the Hy3 fluorescent dye ('Hy3'). Some probes on the array target multiple mature microRNAs. Some probes are species-specific; others are not. Some probes are specific for certain synthetic small RNAs used as control spike-ins in the array-use protocol provided by the array manufacturer. Some probes target non-microRNA RNAs like small nucleolar RNAs. IDs and names of probes on the array, and the miRBase (version 19.0) or proprietary Exiqon miRPlus accession numbers of mature microRNAs targeted by the probes, are provided in the data table for this Platform. The platform information here is based on the .gal array layout file for array batch numbers 208500-2 & 208510 and lot number 35003.

middle: K

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


title: Illumina Genome Analyzer IIx (Saccharum hybrid cultivar (mixed))

organism: Saccharum hybrid cultivar (mixed)


title: Agilent-020507 Rat Microarray (020507_D_F_20080612)

city: Duarte

first: jeremy

last: jones

address: 1500 E Duarte Rd

institute: City of Hope


title: Illumina HiSeq 2000 (Cucumis sativus)

organism: Cucumis sativus


title: [ATCTOBa520488] Affymetrix Custom Array - Nicotiana tabacum

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

organism: Nicotiana tabacum

manufacture_protocol: see  Affymetrix


title: AB SOLiD 4 System (Rhodococcus opacus)

status: Public on Nov 19 2012

organism: Rhodococcus opacus


title: Agilent-015764 Human Microarray (Probe Name version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Homo sapiens


title: Illumina HiSeq 2000 (Nannochloropsis oceanica)

organism: Nannochloropsis oceanica


title: Agilent-012391 Human Microarray (012391_D_F_20091216)


title: Agilent-019764 MPI_Gerberding Parhyale hawaiensis Microarray (Feature Number version)

city: Basel

first: Peter

last: Nestorov

address: Maulbeerstr. 66

country: Switzerland

institute: FMI

organism: Parhyale hawaiensis

description:
Agilent control grid: IS-15744-8-V1_8x15K_Gx_EQC_V20060608

Features are 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: Matthias

last: Gerberding


title: Streptococcus agalactiae pan microarray (GBS_2603_A909_515_1)

status: Public on Nov 18 2012

city: Baltimore

first: Julie

middle: C

last: Dunning Hotopp

address: 20 Penn St.; HSF-II; S203B

department: Institute for Genomic Sciences

institute: Univeristy of Maryland Baltimore

organism: Streptococcus agalactiae

first: Nadeeza

last: Ishmael

first: Herve

last: Tettelin

manufacture_protocol: Group B streptococcus (GBS) amplicon microarrays were prepared using DNA fragments of the annotated open reading frames (ORF) from the 2603 strain. Additional primer pairs were designed to replace unresponsive 2603 amplicons and to include A909 strain specific ORFs. PCR primer pairs were designed with Primer3 and locally developed PERL scripts. DNA fragments were amplified with these primers using a final concentration of 1X buffer, 2.5 mM MgCl2, 0.8 mM dNTP mix (Applied Biosystems, Blanchburg, NJ, USA), 1.25 U AmpliTaq DNA Polymerase (Applied Biosystems, Blanchburg, NJ, USA), 0.15 µM each primer, and 20 ng/uL DNA with denaturation at 95 oC for 5 min followed by amplification with 35 cycles at 95 oC for 45 sec, 55 oC for 45 sec, and 72 oC for 45 sec and a final elongation step at 72 oC for 10 min. Amplicons were purified using Montage 96 well SEQ plates (Millipore, Billerica, MA, USA) and spotted onto UltraGAPS aminosaline-coated glass slides (Corning, Corning, NY, USA) using 50% dimethylsulfoxide as spotting buffer. Amplicons were bound to the slides by ultraviolet cross-linking at 25,000 µJ/cm2. Printed slides were stored until use in a bench-top desiccator.


title: Streptococcus agalactiae pan microarray (GBS_2603_A909_515_4reps)


title: Affymetrix Human GeneChip GGH 3_0v1 Array

status: Public on Nov 17 2012

city: Santa Clara

first: Jason

middle: Wray

last: Hubbard

address: 3380 Central Expressway

institute: Affymetrix Inc


title: Streptococcus agalactiae pan microarray (GBS_6)


title: NimbleGen Clostridium_thermocellum_ATCC27405_Tiling_3Plex

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

organism: Acetivibrio thermocellus ATCC 27405

description:
Custom array. Design ID: 10425.
DESIGN_NAME: 090803_Ctherm_SB_EXP
SLIDE_LAYOUT_NAME: NimbleChip_HX3
The array is based on CP000568.1


title: Agilent-029908 100826_All_Pinus

status: Public on Nov 15 2012

city: Rotorua

first: Joseph

middle: Gogo

last: Dubouzet

address: 49 Sala St

department: Biotransformation

country: New Zealand

institute: Scion

organism: Pinus taeda

description:
Arrays of this design have barcodes that begin with 16029908 or 2529908.

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: Exiqon miRCURY LNA microRNA array; 7th generation; batch 208500-2, 208510; lot 35006 - hsa, mmu & rno (miRBase 19.0)

status: Public on Nov 16 2012

organism:
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Human betaherpesvirus 5
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

description: The 7th generation miRCURY locked nucleic acid (LNA) oligonucleotide microarray is manufactured by Exiqon (Vedbaek, Denmark). The array has probes printed in quadruplicate as 100 um-diameter spots with 185 um inter-spot distance. Many spots on the array do not have a probe ('empty') and there are some spots that only have the Hy3 fluorescent dye ('Hy3'). Some probes on the array target multiple mature microRNAs. Some probes are species-specific; others are not. Some probes are specific for certain synthetic small RNAs used as control spike-ins in the array-use protocol provided by the array manufacturer. Some probes target non-microRNA RNAs like small nucleolar RNAs. IDs and names of probes on the array, and the miRBase (version 19.0) or proprietary Exiqon miRPlus accession numbers of mature microRNAs targeted by the probes, are provided in the data table for this Platform. The platform information here is based on the .gal array layout file for array batch numbers 208500-2 & 208510 and lot number 35006.


title: Agilent-028803 Custom Whole Sheep Genome Oligo Microarray

city: Hangzhou

first: Aifang

last: Du

state: Zhejiang

address: Yuhangtang Road 866

department: College of Animal Sciences, Zhejiang University

country: China

institute: Institute of Preventive Veterinary Medicine

organism: Ovis aries


title: [TobArrays520623F] Affymetrix Nicotiana tabacum TobArray520623F

city: Neuchatel

first: Sam

last: Ansari

state: Neuchatel

address: Quai Jeanrenaud 5

department: Research & Development

institute: Philip Morris Products SA

description:
Custom single-channel exon array.

From the analysis and annotation of the 1,271,256 Nicotiana tabacum fasta and quality files from methyl filtered genomic survey sequences (GSS) obtained from the TGI (http://www.pngg.org/tgi/) and ~56,000 ESTs available in public databases, an exon array with 272,342 probesets was designed (four probes per exon). The array covers ~90% of the tobacco gene space.

The supplementary file 'GPL16290_TobArrays520623F.1lq.txt' includes probe sequences.

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


title: 454 GS FLX (Aquilaria sinensis)

status: Public on Nov 13 2012

last: GEO

organism: Aquilaria sinensis


title: Princeton Microarray Facility AOA Archetype Microarray BC015

city: Boston

first: Silvia

last: Newell

state: Massachusetts

address: 675 Commonwealth Ave.

institute: Boston University

organism: synthetic construct

description: single printing of AOA probes

manufacture_protocol:
1.The probe oligonucleotides are printed onto Corning Ultragaps or Erie Scientific Epoxy Silane slides using a DeRisi style arrayer (DiRisi et al., 1997) and pins from Parallel Synthesis.
2.The 70-mer oligo probes (Operon Technologies) were adjusted to a concentration of 0.05 mg ml-1 in 50% DMSO and were spotted on CMT-GAPS amino silane-coated glass slides (Corning, Corning, NY).
3. After printing, the slides were baked at 80°C for 3 h and stored in the dark at room temperature under slight vacuum in a dessicator.


title: NimbleGen Arabidopsis thaliana Whole Genome Tiling Array 385K ATH6

city: Taipei

first: Fu-Chiun

last: Hsu

address: No. 128, Sec. 2, Academia Road, Nankang

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

organism: Arabidopsis thaliana

manufacture_protocol: see NimbleGen website at http://www.nimblegen.com


title: Illumina Genome Analyzer IIx (Ovis aries)


title: "Dehalococcoides ethenogenes" strain 195 with Mixed Community Sequences [Probe Name version]

city: Ithaca

first: Cresten

last: Mansfeldt

address: 220 Hollister Hall

institute: Cornell University

organism: Dehalococcoides mccartyi 195

description: "Dehalococcoides ethenogenes" strain 195 with additional community members and luciferase. Arrays of this design have barcodes that begin with 16023019 or 2523019. Orientation:  Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent. 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.

middle: B

first: Ruth

last: Richardson

first: Annie

middle: R

last: Rowe

first: Laura

last: Hug

first: Gretchen

last: Heavner

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


title: NimbleGen Mouse 2.1M deluxe promoter array (ver. 2)

status: Public on Nov 10 2012

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

organism: Mus musculus

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: Illumina HiSeq 2000 (Chromolaena odorata)

status: Public on Nov 14 2012

organism: Chromolaena odorata


title: Agilent-029876 Haemophilus parasuis SH0165 array (Probe Name version)

city: Wuhan

first: Liu

last: yingyu

address: Hongshan district, No.1

institute: Huazhong agricultural university

organism: Glaesserella parasuis SH0165

description: Arrays of this design have barcodes that begin with 16029876 or 2529876.

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


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray ENSG Version 15]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: This is identical to GPL570 but a custom CDF environment was used to extract data [Brainarray Version 15, HGU133Plus2_Hs_ENSG].

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

manufacture_protocol: see manufacturer's protocol


title: NimbleGen_Scoe_60mer_4plex

status: Public on Nov 07 2012

city: Tsukuba

first: Behnam

last: Nazari

state: Ibaraki

address: 3-1-3 Kannondai

department: Environmental Biofunction Division

country: Japan

institute: National Institute for Agro-Environmental Sciences

organism: Streptomyces coelicolor A3(2)

description:
NimbleGen custom prokaryotic gene expression 72k_4plex array
NimbleGen design name: 2007-11-29_GFC268_Scoe_60mer_4plex
2007-11-29_GFC268_Scoe_60mer_4plex.ndf
2007-11-29_GFC268_Scoe_60mer_4plex.ngd

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


title: Illumina HiSeq 2000 (Myotis brandtii)

organism: Myotis brandtii


title: Agilent-029876 Haemophilus parasuis SH0165 array (Feature Number version)

description:
Arrays of this design have barcodes that begin with 16029876 or 2529876.

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: NimbleGen Human DNA Methylation 2.1M Deluxe Promoter Array [100929_HG19_Deluxe_Prom_Meth_HX1]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Homo sapiens

description: Build: HG19, NCBI 37


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray ENSG Version 16]

description: This is identical to GPL570 but a custom CDF environment was used to extract data [Brainarray Version 16, HGU133Plus2_Hs_ENSG].


title: NimbleGen Mouse 2.1M deluxe promoter array (ver. 3)


title: Mouse Cytokine Antibody Array 3

city: harbin

first: Huayang

last: Pan

state: heilongjiang

address: youzheng street

department: general  surgery

institute: The First Affiliated Hospital of Harbin Medical University

technology: antibody

description: RayBio® Mouse Cytokine Antibody Array 3 (8 membrane arrays) with accessories, for simultaneous detection of 62 Cytokines in 8 samples.

manufacture_protocol: see manufacturer's website; http://www.raybiotech.com/Cytokine_Antibody_array.asp


title: Agilent_017367 NISR Aspergillus oryzae 24K v.2.0

status: Public on Nov 08 2012

city: Noda City

first: Masahiro

last: Ogawa

state: Chiba

address: 399 Noda

institute: Noda Institute for Scientific Research

organism: Aspergillus oryzae RIB40

manufacture_protocol: see manufacturer's web site


title: [Rat230_2] Affymetrix Rat Genome 230 2.0 Array [CDF: Version 13.0.0, ENSG]

status: Public on Nov 06 2012

organism: Rattus norvegicus

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

June 03, 2009: annotation table updated with netaffx build 28
June 07, 2012: annotation table updated with netaffx build 32

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

manufacture_protocol:
see manufacturer's web site

The GeneChip Rat Genome 230 2.0 Array is a powerful tool for toxicology, neurobiology, and other applications using rat as a model organism.

- Provides comprehensive coverage of the transcribed rat genome on a single array
- Comprised of more than 31,000 probe sets, analyzing over 30,000 transcripts and variants from over 28,000 well-substantiated rat genes
- The publicly available draft of the rat genome and leading public rat databases were used to refine sequences and provide a higher quality of data output

All probe sets represented on the GeneChip Rat Expression Set 230 are included on the GeneChip Rat Genome 230 2.0 Array. Sequences used in the design of the GeneChip Rat Genome 230 2.0 Array were selected from GenBank, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 99, June 2002) and then refined by analysis and comparison with the publicly available draft assembly of the rat genome from the Baylor College of Medicine Human Genome Sequencing Center (June 2002).

The GeneChip Rat Genome 230 2.0 Array includes representation of the RefSeq database sequences and probe sets related to sequences and refined EST clusters previously represented on the GeneChip Rat Genome U34 Set.

Oligonucleotide probes complementary to each corresponding sequence are synthesized in situ on the arrays. Eleven pairs of oligonucleotide probes are used to measure the level of transcription of each sequence represented on the GeneChip Rat Genome 230 2.0 Array.


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [CDF: HuEx-1_0-st-v2,coreR3,A20071112,EP]

city: Aalborg

first: Maria

middle: Bro

last: Kloster

address: Sdr. Skovvej 15

department: Department of Haematology

country: Denmark

institute: Aalborg Hospital

description: Core probe intensities were summarized to gene expression levels by means of the ExonRMAPlm(, mergeGroups=TRUE) function using the customized cdf-file for core transcripts downloaded from below link

manufacture_protocol: See manufacturer's web site


title: SCPFRC Phaseolus vugaris Custom Array 74K

city: London

first: Frederic

last: Marsolais

address: 1391 Sandford Street

country: Canada

institute: Southern Crop Protection & Food Research Centre

organism: Phaseolus vulgaris

manufacturer: Plant Biotechnology Institute, National Research Council at Canada

manufacture_protocol: probes are designed on sense strand based on assembly of  current EST sequenes available in Phaseolus vulgaris using CustomArray's probe design software and  have 35-40bp long . Probes are in situ synthesized using ustomArray system .Each assemblied unigene have 1-5 different probes or duplicate probes. Probe layout was produced by ArrayRevision1.0


title: LC_MRA-1001C_miRHuman_12.0_080930 (miRNA ID version)

city: New Haven

first: Edna

last: Holman

state: CT

address: 266 Whitney Ave. KBT-442

department: Molecular, Cellular and Developmental Biology

institute: Yale University

organism:
Danio rerio
Gallus gallus
Lemur catta
Ateles sp.
Gorilla gorilla
Pan troglodytes
Homo sapiens
Bos taurus
Mus musculus
Rattus norvegicus
Monodelphis domestica

description:
LC Sciences Human miRNA Array
Based on Sanger miRBase Release 12.0
miRHuman_12.0_YU_080930
Part No.: MRA-1001C

manufacture_protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes are made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: Illumina HiSeq 2000 (Paulownia)

last: GEO

organism: Paulownia


title: Marx lab 2012 Harvard University custom Agilent 60-mer array with 15K+ features for Methylobacterium extorquens AM1

city: Cambridge

first: Sean

middle: Michael

last: Carroll

state: MA

address: Biological Laboratories, Room 3084, 16 Divinity Ave

department: Organismic and Evolutionary Biology

institute: Harvard University

organism: Methylorubrum extorquens AM1

manufacture_protocol: see manufacturer's website


title: UNIPD Grape 14K v1.0

city: Legnaro

first: Alessandro

last: Botton

state: Padova

address: Agripolis - viale dell'università 16

department: Agronomy, Food, Natural resources, Animals and Environment

institute: University of Padova

organism: Vitis vinifera

manufacture_protocol: Each of the 14,562 oligonucleotides of the Grape AROS V1.0 (Operon), harbouring a 5′ amino linker, was deposited onto glass slides (Perkin-Elmer, USA) at CRIBI (University of Padova) using GenpakARRAY 21 spotter (Genetix Inc., Massachusetts, USA) in duplicate. To facilitate image analysis reference spots have been deposited in each first line/column of each subgrid. Distance between spots was 135 μm on either axes and spot average diameter was ranging from 70 to 80 μm.


title: Nimblegen Human DNA Methylation 385K Promoter plus 11p13, 11p15 tiled regions

status: Public on Nov 05 2012

city: Bristol

first: Anthony

last: Dallosso

address: University Walk

department: School of Cellular & Molecular Medicine

institute: University of Bristol

description:
Format: 385K
Build: HG18
Probe Length: 50-75mer
Median Probe Spacing: 101bp
Promoter Upstream Tiling: 800bp
Promoter Downstream Tiling: 200bp
Designid: 5179
Designname: 2007-01-30_HG18_5189_refseq
Recommended Storage: Store arrays desiccated at room temperature.
Tiled regions: WT1 region (chr11:31440000-33360000), H19 DMR (chr11:1975000-1982000), IGF2 DMR0 (chr11:2126000-2128000).

manufacture_protocol: See www.nimblegen.com


title: UCSF HumArray 4.0

city: San Francisco

first: Xin

last: Chen

institute: UCSF

manufacture_protocol: For a detailed description on how the arrays were made please refer to: Snijders et al. Nat Genet. 2001 Nov;29(3):263-4.


title: Invitrogen Protoarray v4.0

first: Serena

middle: S

last: Kwek

address: 513 Parnassus Ave.

department: Medicine

technology: spotted peptide or protein


title: Agilent DasSarma Laboratory Halobacterium sp. NRC-1 composite array

city: Baltimore

first: Priya

last: DasSarma

address: 701 East Pratt Street, Suite 236

department: Microbiology

institute: UMB

organism: Halobacterium salinarum NRC-1

description: This Platform represents a composite of several arrays.

first: Shiladitya


title: Applied Biosystems TaqMan nuclear receptor signature 96-well fast plate

status: Public on Nov 04 2012

city: Gainesville

first: Igor

last: Ignatovich

state: FL

department: Psychiatry

institute: University of Florida

description:
The TaqMan® Array Human Nuclear Receptors 96-well Plate contains 92 assays to nuclear receptor associated genes and 4 assays to candidate endogenous control genes.
The panel of assays in the TaqMan® Array Human Nuclear Receptors 96-well Plate targets genes from nuclear receptor Subfamilies 0,1,2,3,4,5, and 6. Other nuclear receptor associated genes are also on the panel.


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [CDF: CHOP_1.0_ENTREZG]

status: Public on Nov 03 2012

city: Philadelphia

first: Zhe

last: Zhang

state: PA

address: Translational Research Lab

institute: University of Pennsylvania

description: Probe sequences were downloaded from Affymetrix web site and mapped human genome hg19. Probes having mismatch, ambiguous mapping, or overlapping to dbSNP entries were excluded. The remaining probes were grouped into NCBI Entrez genes.


title: University of Minnesota Custom miRNA microarray

status: Public on Nov 01 2012

city: Nanjing

first: Yan

last: Zeng

state: Jiangsu

address: XuanWu District, No.1 WeiGang

institute: Nanjing Agricultural University

organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

manufacturer: Biomedical Genomics Center Microarray Facility at the University of Minnesota

manufacture_protocol: A miRNA probe set was purchased from Invitrogen, which was designed based on the Sanger miRBase Sequence Database, Release 9.0.  The set contains approximately 1,140 oligonucleotides of 34 to 44 nt long as probes.  They are complementary to C. elegans, Drosophila, zebrafish, mouse, rat, and human miRNAs, and also include a number of internal and negative control probes.  The oligonucleotides were dissolved in 3 x SSC and quadruply printed on Corning® GAPSTM II coated slides  using a BioRobotics Microgrid II spotter


title: NimbleGen_Geobacter metallireducens DSM 7210-v1.0 [Design 533273]

city: Amherst

first: Tian

address: 639 North Pleasant St.

institute: University of Massachusetts

organism: Geobacter metallireducens

description:
strain : Geobacter metallireducens DSM 7210

4-plex expression for Geobacter metallireducens DSM 7210; from http://www.ncbi.nlm.nih.gov/nuccore/NC_007517 and http://www.ncbi.nlm.nih.gov/nuccore/NC_007515; 3,627 starting genes; 9 probes per target, 45-60mer probes, 3557 exemplars for 3627 genes, 3 copies of each probe on the array.

Design ID : 533273

native array description file : 100622_ZS_Gmet_CS15_expr.ndf
native array description file : 100622_ZS_Gmet_CS15_expr.ngd


title: Agilent-019701 Schizosaccharomyces pombe 8x15 expression array

status: Public on Nov 02 2012

city: Calgary

first: Gordon

last: Chua

state: Alberta

address: 2500 University Drive NW

department: Biological Sciences

institute: University of Calgary

organism: Schizosaccharomyces pombe

description: S. pombe expression

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


title: Nanostring nCounter Human microRNA Expression Platform

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

institute: IOR

manufacture_protocol: See manufacturer's website


title: Custom NimbleGen 12-plex Batrachochytrium dendrobatidis Oligo Expression Array

city: Berkeley

first: Thomas

last: Poorten

state: CA

address: 54 Mulford Hall

department: Environmental Science, Policy, and Management

institute: UC Berkeley

organism: Batrachochytrium dendrobatidis

description: We designed a NimbleGen 12-plex microarray for Bd based on the publically available Bd genomes JAM81 (B. dendrobatidis Sequencing Project, Joint Genome Institute: http://genome.jgi-psf.org/Batde5/Batde5.download.ftp.html) and JEL423 (B. dendrobatidis Sequencing Project, Broad Institute of Harvard and MIT: http://www.broadinstitute.org/annotation/genome/batrachochytrium_dendrobatidis). The microarray contained 133,254 60-mer probes representing a possible 8,896 expressed transcripts (probe sets). Probe sets were defined as all probes that mapped to a single transcript, which in turn mapped to a single gene.


title: AB 5500 Genetic Analyzer (Saccharomyces cerevisiae)

organism: Saccharomyces cerevisiae


title: miRXplore Microarray (909)

status: Public on Jun 04 2012

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec GmbH

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: The miRXplore TM Microarray is composed of 6228 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 1460 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 1460 miRNA sequences covered sequence verified miRNAs of the species human (878) mouse (682) and rat (427) as well as viral miRNAs (141) as deposited in the miRBase sequence database version 13.0. The 97 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (18 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 36 positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 13 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences.

manufacturer: Miltenyi Biotec GmbH, Bergisch Gladbach, Germany

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

manufacture_protocol: 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted four times on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides using a customized piezoelectric spotter.


title: AB 5500 Genetic Analyzer (Escherichia coli)

organism: Escherichia coli


title: [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array [CDF: Mouse4302_Mm_ENSG v13]

status: Public on Mar 22 2012

city: Corvallis

first: Stephen

last: Ramsey

state: OR

address: Dryden Hall 208A

department: Biomedical Sciences

institute: Oregon State University

organism: Mus musculus

relation: Alternative to: GPL1261 (Alternative CDF [official])

manufacture_protocol: This is identical to GPL1261 but a custom cdf environment was used to extract data. We used custom chip definition files (CDF) based on Ensembl gene annotation v13.


title: Affymetrix GeneChip Human Genome HG-U133A Custom CDF [Affy_HGU133A_CDF_ENTREZG_10]

status: Public on Feb 01 2012

city: Ann Arbor

first: Celine

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

organism: Homo sapiens

description: Human Entrez Gene custom CDF annotation version 10

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


title: Affymetrix Human Genome U133 Plus 2.0 Array [Hs133P_Hs_ENTREZG.cdf]

status: Public on Apr 13 2011

description: This array is identical to GPL570 but the data were analyzed with a custom CDF environment (Hs133P_Hs_ENTREZG.cdf).

manufacture_protocol: See the Affymetrix website (www.affymetrix.com).


title: Illumina Genome Analyzer (Sus scrofa)

status: Public on Aug 31 2009

last: GEO

organism: Sus scrofa


title: [4dehalosa520666F] Affymetrix Dehalococcoides genus 4.8K array

status: Public on Aug 18 2011

first: Patrick

last: Lee

address: 209 O'Brien Hall

department: Civil and Environmental Engineering

institute: University of California, Berkeley

organism:
Dehalococcoides mccartyi BAV1
Dehalococcoides mccartyi 195
Dehalococcoides mccartyi CBDB1
Dehalococcoides mccartyi VS

description: A microarray targeting genes from all available sequenced genomes of the Dehalococcoides genus was designed with 4305 probe sets to target 98.6% of all genes from strains 195, CBDB1, BAV1, and VS.

first: Dan

last: Cheng

first: Ping

last: Hu

first: Kimberlee

middle: A

last: West

first: Gregory

middle: J

last: Dick

first: Eoin

middle: L

last: Brodie

first: Gary

last: Andersen

middle: H

last: Zinder

first: Jianzhong

last: He

first: Lisa

last: Alvarez-Cohen

manufacture_protocol: Affymetrix Prokaryotic Sample and Array Processing protocol; 100 Format (Midi)


title: Technical Microbiology-Viable beer spoilage bacteria microarray V1

status: Public on May 23 2007

city: Bochum

first: Daniel

middle: Gilbert

last: Weber

address: Bürkle-de-la-Camp Platz 1

department: Molekulare Medizin

institute: IPA

organism:
Pectinatus frisingensis
Levilactobacillus brevis
Lacticaseibacillus casei
Loigolactobacillus coryniformis
Megasphaera cerevisiae
Pediococcus damnosus
Pectinatus cerevisiiphilus
Schleiferilactobacillus perolens
Pediococcus inopinatus

description: Each oligonucleotide species-specific probe was spotted in 70 replicate spots on the microarray. Nine single beer spoilage bacteria species were detected with the developed prototype oligonucleotide microarray and also three mixes of two different beer spoilage bacteria species.

middle: G

first: Kerstin

last: Sahm

first: Tino

last: Polen

first: Volker

middle: F

last: Wendisch

first: Garabed

last: Antranikian

manufacture_protocol: Standard glass microscope slides were coated with a poly-L-lysine solution and stored for several weeks to allow the surface to become sufficiently hydrophobic. Species-specific probes were spotted in 3x SSC onto the glass surface using a robotic printing system. For routine experiments 50 μM was used as probe concentrations. The diameter of the spots was 150 μm and the space between the centres of two spots was 205 μm allowing the preparation of seven grids each containing 70 spot replicates. To distribute the oligonucleotides more evenly, the spots were rehydrated using a 1x SSC bath at 40°C until the spots were glistening, followed by snapped-drying at 120°C using a heat block. To increase the amount of hybridisable oligonucleotides, stably attached to each spot, the nucleic acids were cross-linked by UV irradiation.


title: Exiqon miRCURY LNA microRNA array; 7th generation; batch 208500-2, 208510; lot 35004 - hsa, mmu & rno (miRBase 18.0)

status: Public on Sep 05 2012

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

state: NY

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Human betaherpesvirus 5
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

description: The 7th generation miRCURY locked nucleic acid (LNA) oligonucleotide microarray is manufactured by Exiqon (Vedbaek, Denmark). The array has probes printed in quadruplicate as 100 um-diameter spots with 185 um inter-spot distance. Many spots on the array do not have a probe ('empty') and there are some spots that only have the Hy3 fluorescent dye ('Hy3'). Some probes on the array target multiple mature microRNAs. Some probes are species-specific; others are not. Some probes are specific for certain synthetic small RNAs used as control spike-ins in the array-use protocol provided by the array manufacturer. Some probes target non-microRNA RNAs like small nucleolar RNAs. IDs and names of probes on the array, and the miRBase (version 18.0) or proprietary Exiqon miRPlus accession numbers of mature microRNAs targeted by the probes, are provided in the data table for this Platform. The platform information here is based on the .gal array layout file for array batch numbers 208500-2 & 208510 and lot number 35004.

middle: K

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


title: NimbleGen Arabidopsis thaliana 4x72K Array [080306_AT6_expr]

city: Kongens Lyngby

first: Simon

last: Rasmussen

address: Kemitorvet, Building 208

department: Department of Systems Biology

institute: Technical University of Denmark

organism: Arabidopsis thaliana

description:
Gene Expression array
Design Name: 080306_AT6_expr
Design_ID: 7225

Format: 4x72K
Source: TAIR
Build: 6.0
Probe Length: 60mer
FEAT_TYPE: transcript

The Platform data table reflects a condensed, gene-level representation of the array.

NimbleGen description files linked below:
080306_AT6_expr.ndf
080306_AT6_expr.ngd

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


title: Agilent-035430 mouse miRNA array (miRBase release 17 miRNA ID version)

status: Public on May 09 2012

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Design ID: 035430
Microarray name: Mouse_8x60K-v17

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