title: Sf301_Nimblegen_380k array

status: Public on Jun 27 2011

city: Beijing

first: Junping

last: Peng

address: No 6, Rongjing Eastern Street, BDA

country: China

institute: Chinese center for disease control and prevention

organism: Shigella flexneri 2a str. 301

technology: in situ oligonucleotide

description:
NimbleGen design name 2007-02-12_CSB_Sflexneri_tiling, design for Shigella flexneri 2a strain 301 and associated plasmid pCP301. The design includes random GC and other control probes.
The .ndf file is linked below as a supplementary file.

distribution: custom-commercial

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


title: Whole-Genome TilePath (WGTP) array

status: Public on Jun 30 2011

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

organism: Homo sapiens

technology: spotted DNA/cDNA

description: spotted large insert BAC clones

distribution: non-commercial

manufacture_protocol: see Wellcome Trust Sanger Institute's The Copy Number Variation (CNV) Project Data Index website


title: Agilent-023780 University of Nottingham 8 x 15k Onion array

status: Public on Jun 29 2011

city: Crawley

first: John

last: Hammond

state: WA

address: 35 Stirling Highway

department: School of Plant Biology

country: Australia

institute: University of Western Australia

organism: Allium cepa

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


title: [mbiAth1a520184] Mendel Arabidopsis Genome Array

city: Hayward

first: Don

middle: R

last: Maszle

state: CA

address: 3935 Point Eden Way

country: USA

institute: Mendel Biotechnology, Inc.

organism: Arabidopsis thaliana

description:
The Mendel Arabidopsis Genome Array is a custom array designed using Affymetrix GeneChip CustomExpress Array Design Guidelines. Feature size is 11 micron.  Perfect-match only probe sets are tiled, nominally  using 11 probes per transcript, and randomly distributed across the array.  Larger numbers of probes were used for certain sequences. The sequences used for probe selections are mostly based on the TAIR6 (www.arabidopsis.org) Nov 15, 2005 release of the Arabidopsis genome. Additional gene models from Mendel proprietary sequences were also used.  There are 48,972 probe sets on the array, which have been mapped to 29,543 TAIR AGI identifiers.  A number of probe sets from previous Arabidopsis arrays were also tiled.  Standard Affymetrix controls were used on the chip along with additional controls made from internal sequences.
Probe sequences unavailable due to proprietary nature.

first: Bradley

last: Sherman

first: Garry

last: Martin

first: Peter

last: Repetti

first: Hans

last: Holtan

manufacture_protocol: see manufacturer's web site


title: Affymetrix human mitochondrial array [CDF: FATMITO1a520158F]

status: Public on Oct 08 2009

city: Seattle

first: Lawrence

middle: D

last: Adams

address: 1959 NE Pacific Street

department: BNHS

institute: University of Washington

description:
Mitochondrial gene expression microarray.
FATMITO1a520158F

first: Joachim

middle: G

last: Voss

first: Adrian

last: Dobra

first: Caryn

last: Morse

first: Joseph

last: Kovacs

first: Rahgavan

last: Raju

first: Marinos

middle: C

last: Dalakas

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


title: Illumina Genome Analyzer (Equus caballus x asinus)

last: GEO

organism: Equus caballus x Equus asinus

technology: high-throughput sequencing

distribution: virtual


title: Eurogentec/CNB-CSIC Streptomyces coelicolor 17K TT-A220G

status: Public on May 03 2012

city: Campus de Cantoblanco

first: Sonia

last: Gullón

state: Madrid

address: Darwin 3

country: Spain

institute: CNB-CSIC

organism: Streptomyces coelicolor A3(2)

technology: spotted oligonucleotide

manufacture_protocol: Development and production of a full long oligo DNA MicroArray representing the complete set of S. coelicolor A3(2) genes. The 7,512 chromosome genes, the 351 SCP1 plasmid genes and the 33 SCP2 plasmid genes sequences were downloaded from the Sanger Institute website. In order to perform gene-specific primer design of long oligos with the best possible thermo dynamical features for DNA array applications, the array designer 3.0 software commercialised by Premier biosoft was acquired. 7,896 long oligos specific to the corresponding (putative) genes of S. coelicolor A3(2) of a size of 68 bases were designed and produced at the Eurogentec’s oligo production facility. A complete set of DNA array-specific controls such as positive, negative, dynamic range, spatial, normalization, hybridisation efficiency, reverse transcription efficiency and resistance genes controls were designed and produced.


title: University of Alberta Escherichia coli 19K v2.0

city: Ann Arbor

first: Dongjuan

last: Dai

state: MI

address: 109 Observatory St

department: Environmental Health Sciences

institute: University of Michigan

organism: Escherichia coli

manufacturer: University of Alberta, Department of Biological Sciences, Microarray and Proteomics Facillity

manufacture_protocol:
1. It contains 5,978 70mer oligos and a control set of 12 positive and 12 negative controls.
2. A total of 19086 spots are printed at 200 um spacing in a 4 by 4 block of sub-arrays in triplicate in each slide.
3. Oligos are dissolved to a final concentration of 18.75 uM in 150 mM NaPO4 buffer (pH 8.7) prior to printing.
4. Slides are Corning Epoxide slides.
5. Oligos represing 4,289 ORF's in Escherichia coli K12, 5,029 ORF's in O157:H7 (EDL933), and 4,836 ORF's in O157:H7 (Sakai).
6. All probes are designed within ORFs from both clones and predicted ORF's.
7. All probes are Tm nomalized to 75 (+/- 5) degree C and have a 5' amino linker.


title: Illumina Genome Analyzer (Equus asinus x caballus)

organism: Equus asinus x Equus caballus


title: Genotypic Technology designed Custom Mycobacterium tuberculosis H37Rv Whole Genome 8x15k GE (AMADID-020181)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

organism: Mycobacterium tuberculosis H37Rv

distribution: commercial

first: Mugasimangalam

last: Raja


title: Illumina Genome Analyzer (Equus asinus)

organism: Equus asinus


title: Illumina Genome Analyzer II (Aspergillus flavus)

status: Public on Jun 16 2011

organism: Aspergillus flavus


title: MWG E. coli K12 V2 Array

status: Public on Jun 25 2011

city: Rome

first: Gianni

last: Prosseda

address: via dei sardi 70

department: Biology and Biotechology C. Darwin

country: Italy

institute: Saoienza , University of Rome

manufacture_protocol:
MWG E. coli K12 V2 Array
The MWG E. coli Array contains 4,288 gene specific
oligonucleotide probes representing the complete E. coli (K12) genome. Specifications:
Total number of genes: 4,288 ORFs of E. coli strain K12
covered by 4239 oligos
Information sources: NCBI/Genbank
NC00913, U00096.1
Strand analyzed: Sense strand
Number of slides: 1
Length of probes: 50 mer
Number of oligonucleotides per gene:1
Total number of spots: 4,608
Replicated spots: 47
Production control oligos (ara): 48
Spot area: 1.8 x 1.8 cm


title: Agilent Daphnia magna 8x15k oligonucleotide array (condensed)

status: Public on Jun 23 2011

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

organism: Daphnia magna

description: This platform is similar to GPL10018. Only clones of interest have been identified with GenBank Accession Numbers.

manufacture_protocol: see manufacturer's website for details: https://earray.chem.agilent.com/earray/


title: LMT_mouse miRNA_v2 microarray

city: Bethesda

first: Jeffrey

middle: E

last: Green

state: MD

address: Rm 4054, 37 Convent Drive

institute: NCI

organism: Mus musculus

manufacture_protocol: Agilent's manufacture protocol


title: Kinexus KAM-1.2FN 800 Ab microarray

status: Public on Jun 22 2011

first: Benjamin

last: Alman

address: TMDT, 101 College Street

department: Developmental and Stem Cell Biology

institute: Hospital for Sick Children

technology: antibody

description:
Contains 800 (500 pan-specific and 300 phosphorylation-site specific) antibodies.
Most of the antibodies cross-react with mouse.

manufacturer: Kinexus Bioinformatics Corportation, Vancouver, BC, Canada


title: New Zealand White Rabbit Heart 15K cDNA array

status: Public on Jun 24 2011

city: Boston

first: James

last: McCully

state: MA

address: 77 Avenue Louis Pasteur

department: Cardiothoracic Surgery

institute: BIDMC/Harvard Medical School

organism: Oryctolagus cuniculus

description: New Zealand White Rabbit Heart; male, new born- 3 week recovery

manufacture_protocol:
cDNA Library : Isolation of  total heart (atria and ventricles)RNA:  RNA was isolated  from New Zealand rabbit (15-20 weeks; 3 to 4 kg) heart in an RNase-free environment using RNase-free lab-wear, materials and equipment according to the  procedure as described by Chomczynski and Sacchi (Anal Biochem 162:156-15). In brief tissue was pulverized under liquid nitrogen using  mortar and pestle and extracted two times in acidic guanidinium isothiocyanate-phenol-chloroform and incubated for 5 min. at room temperature to permit the complete dissociation of nucleoprotein complexes. The mixture was centrifuged at 14,000x g for 15 min. at 4oC. Following centrifugation, the aqueous phase containing the RNA was carefully removed and transferred to a new tube containing 0.5 mL isopropanol and incubated for 10 min. at room temperature to precipitate the RNA. The RNA was collected by centrifugation at 14,000x g for 20 min. at 4oC. The RNA pellet washed with 1 mL of room temperature 75%  ethanol, re-centrifuged and the RNA pellet air-dried and dissolved in DEPC-treated H2O.
POLY(A)+ RNA fractions were enriched by oligo(dT) cellulose chromatography. In brief, 1 mg of  total RNA was adjusted to 0.55 mg/mL RNA concentration in DEPC-treated H2O, and incubated for 5 min. at 650C and then chilled on ice.  The salt concentration was adjusted to 0.5M NaCl and the RNA sample mixed with 1 mL of oligo(dT) cellulose. The  suspension was  incubated for 10 min. at 37oC to allow the mRNA to bind to the oligo(dT) cellulose. The unbound RNA was eluted  and re-heated for 5 min. at 65 oC, chilled on ice and re-suspended in the oligo(dT) cellulose. The unbound RNA was washed from the column with a low salt buffer and the bound mRNA eluted from the oligo(dT) cellulose beads with 1 mL H2O (65 oC). The eluted mRNA was re-heated for 5 min. at 65 oC, chilled on ice and re-suspended in the oligo(dT) cellulose and then eluted as described above in order to further reduce any rRNA contamination. Fractions (200 uL) was collected in microfuge tubes. Positive fractions containing mRNA were determined by UV spectrophotometric analysis, pooled and the mRNA precipitated overnight, at -20oC with 50 ug/mL glycogen, 0.1 volume 7.5 M ammonium acetate and 2 volumes ethanol (-20 oC) and then collected by centrifugation  at 14,000x g for 30 min. at 4 oC. The mRNA pellet was washed twice with 75% ethanol, air-dried and dissolved in DEPC-treated H2O. The mRNA yield was determined by UV spectrophotometric analysis (260 nm) with the quality of the mRNA determined by gel electrophoresis on a 1% agarose gel containing 3% formaldehyde, 0.02 M MOPS pH 7.4 (3-[N-morpholino] propanesulfonic acid) and 0.001 M disodium EDTA (ethylenediamine tetraacetic acid) .
cDNA LIBRARY CONSTRUCTION:  cDNA libraries were constructed  using the  SuperScript Plasmid System (GibcoBRL, cat. No.18248-013) according to the manufacturer’s instructions.  The cDNAs were ligated into the plasmid vector pSPORT 1  (4,109 bp) and then transformed into DH5 competent cells (GibcoBRL, Cat. No.10643-013) according to the manufacturer’s instructions.
Estimation of cDNA library size was performed by titration of transformed  bacteria on LB-agar plates (1% bacto-tryptone, 0.5% bacto-yeast extract, 1% NaCl, 1.5% bacto-agar)containing IPTG/X-gal (0.02 ug/mL each)and ampicillin (75 ug/mL). Aliquots of cDNA libraries were stored in 7% DMSO at -80oC.
Estimation of cDNA insert size was determined by random selection of cDNA clones from IPTG/X-gal LB-agar plates containing ampicillin. In brief, single isolated cDNA clones were selected and used to inoculate 2 mL LB liquid media (1% bacto-tryptone, 0.5% bacto-yeast extract, 1% NaCl) containing ampicillin (75 ug/mL) and  incubated overnight at 500 rpm at 37oC in a New Brunswick incubator. The recombinant bacteria werre chilled on ice and the recombinant bacterial pellet collected by brief centrifugation. Plasmid cDNA was isolated by alkaline lysis using  Qiagen columns (cat. No. 12125) and the plasmid DNA precipitated with 0.6 volumes isopropanol by centrifugation at 14,000x g for 30 min. The cDNA pellet was washed twice with 70% ethanol, air-dried and dissolved in TE buffer (10 mM Tris-HCl, pH 8.0; 0.1 mM EDTA, pH 8.0). The purified plasmid cDNA was digested for 1 hour at 37oC in a reaction mixture containing a 3-fold excess of the restriction enzyme Mlu I (New England Biolabs, Cat. No. R0198S) which cleaves the unique restriction enzyme sites located at the termini of the cDNA insert distal to the  Not I and Sal I insertion sites. The digested cDNA was resolved on a 1% agarose gel in 40 mM Tris-acetate and 2 mM EDTA  (TAE) and the gel stained with ethidium bromide then photographed under UV illumination. DNA molecular weight markers (1 kb; New England Biolabs; 323-2S)  were used for estimation cDNA molecular weights.
Isolation and growth:  cDNA libraries were plated at low density  on  IPTG/X-gal LB-agar plates containing ampicillin (75 ug/mL) and  incubated overnight at 37oC.  The following day cDNA clones were selected, individually and used to inoculate individual wells in 96-well culture blocks (USA Scientific, Cat. No.7556-9600) containing 1.3 mL/well liquid LB media containing ampicillin (75ug/mL) and the plates oriented and  labeled to indicate clonal position and then sealed with Breathe–Easy sealing film (USA Scientific) and incubated overnight at 500 rpm at 37oC in a New Brunswick incubator.
Replicate plates were produced following overnight incubation by removing 100 uL samples from each well in 96-well culture blocks for the  inoculation of replicate wells in 96-well culture blocks containing 0.9 mL/well liquid LB media containing ampicillin (75 ug/mL). The replicate plates were oriented, labeled in the same manner as above, sealed with Breathe–Easy sealing film (USA Scientific) and incubated overnight at 500 rpm at 37oC in a New Brunswick incubator. Following overnight incubation replicate plates were cooled on ice and glycerol added to a  final concentration of 20 % /well and the plates sealed with  Thermowell sealers (Costar 6524) and stored at –80oC.
5’ Sequencing:  Plasmid cDNA were isolated by Qiagen Bio Robot 8000 automated nucleic acid purification and liquid handling workstation available for use by our laboratory through core facilities. Purified cDNAs were sequenced using the Applied Biosystems Taq DyeDeoxy Terminator cycle sequencing kit which utilizes a fluorescently-labeled dideoxy-nucleotide chain termination method. After cycle sequencing and clean up the DNA samples were resolved by capillary electrophoresis on an PE BIOSYS 3700 automated sequencer which translates the fluorescent signals into their corresponding base pair sequence.
Sequence  analysis of all cDNAs was performed against the non-redundant GEN Bank/ EMBL/ DDBJ nucleotide, the non-redundant Gen Bank CDS translation/ PDB/ Swiss  Prot/ PIR/ PRF peptide and the dbEST databases using the BLAST algorithm on a UNIX platform. Assignment of putative identity for cDNAs exhibiting matches to known genes required a maximum value of E=1e-25 (minimum p=10-10)and nucleotide sequence identity >95%. Prior to analysis of sequence data, sequence quality were evaluated using the accuracy assessment program  phred of the phred/phrap/consed assembly package. All sequence traces from the  ABI model sequencer werebe saved in fasta output format.
Sequence submission and storage: Sequence quality was evaluated using the accuracy assessment program  phred of the phred/phrap/consed assembly package. All sequence traces were saved in fasta output format. Sequence analysis was performed against the non-redundant GEN Bank/ EMBL/ DDBJ nucleotide, the non-redundant Gen Bank CDS translation/ PDB/ Swiss  Prot/ PIR/ PRF peptide and the dbEST databases using the BLAST algorithm on a UNIX platform . All cDNA’s were 5’ sequenced and are available under accession numbers EC618425-EC626095 and  dbEST40150263-40157933 and at www.mccull


title: Applied Biosystems human immune gene array

city: San Francisco

first: Kevin

last: Wilhelmsen

address: 513 Parnassus Ave.

department: Anesthesia

institute: University of California, San Francisco

technology: RT-PCR

description:
catalog #: 4418718
PCR assay
TaqMan fast 96-well PCR array plate

manufacture_protocol: see manufacturer's website


title: NimbleGen Human HG18 promoter 2.1M array

status: Public on Jun 17 2011

city: Ansan

first: Kim

last: Seung Jun

state: Kyunggido

address: Sangrokgu, sadong, Hanyang Univ., HBI 628

department: Genome Business

country: South Korea

institute: GenoCheck

description:
Design ID: 8567
Design name: 081229_HG18_Promoter_MeDIP_HX1
Genome build: HG18, NCBI36

Genomic regions of promoter and CpG islands (28,266 CpG islands and 475 miRNA promoters)

Native array description file: 081229_HG18_Promoter_MeDIP_HX1.ndf
Native array description file: 081229_HG18_Promoter_MeDIP_HX1.pos

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


title: GenoExplorer human microRNA array (miRBase v15)

first: Bobby

last: Yanagawa

state: ONT

address: 306-25 The Esplanade

department: Cardiac Surgery

institute: University of Toronto

description: GenoExplorer microRNA human array containing 1583 human miRNA probes (Genosensor, Tempe, AZ). Human miRNA sequences updated to miRBase V15.  Positive and negative control probes: 5S, rRNA, tRNA and U6.  For more details, see http://www.genosensorcorp.com/microRNA_chip.html.


title: Illumina Genome Analyzer IIx (Apis mellifera)

status: Public on Jun 15 2011

organism: Apis mellifera


title: Bacillus subtilis BSO8 platform

city: Ithaca

first: John

middle: D.

last: Helmann

state: NY

address: 372 Wing Hall

department: Microbiology

institute: Cornell University

organism: Bacillus subtilis

manufacture_protocol: 65mer oligo library purchased from Sigma


title: Illumina Genome Analyzer IIx (Xenopus (Silurana) tropicalis)

organism: Xenopus tropicalis


title: Illumina HiSeq 2000 (Nicotiana tabacum)

organism: Nicotiana tabacum


title: [Drosophila_2] Affymetrix Drosophila Genome 2.0 Array [CDF : Brainarray ENSEMBL Custom V12]

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Drosophila melanogaster

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

This is identical to GPL1322 but a custom CDF environment was used to extract data [Brainarray Version 12, Drosophila2_Dm_ENSG].

CDF and other files can be downloaded at:http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp

relation: Alternative to: GPL1322 (Alternative CDF[official])


title: Illumina Genome Analyzer (Magnaporthe oryzae)

organism: Pyricularia oryzae


title: Illumina Genome Analyzer IIx (Macaca mulatta)

organism: Macaca mulatta


title: Sentrix® Linkage V Panel BeadChip

status: Public on Nov 07 2011

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

organism: Homo sapiens

technology: oligonucleotide beads

description: Illumina's SNP-based Linkage IV Panel is a marker map for genetic disease studies. The panel contains over 6000 highly informative SNP markers distributed evenly  across the human genome and delivering high information optimized for linkage mapping studies.


title: Fusarium graminearum febit in situ oligonucleotide array

city: Illkirch

first: Raphael

last: Carapito

address: Bd Sébastien Brandt

country: France

institute: Ecole Supérieure de Biotechnologie de Strasbourg

organism: Fusarium graminearum

description: Geniom One, all-in-one instrument for sample loading, hybridization, washing, staining, and detection of biochips.

manufacture_protocol: DNA-Synthesis took place in the Geniom One Instrument - a benchtop device that utilizes microfluidics for light activated oligonucleotide synthesis - at febit biomed facilities (Heidelberg, Germany). One probe for each gene was synthesized on the array. Blank probes consisting of only one T were used for background correction. Probes were 50-mers.


title: 3D-Gene Human miRNA V14_1.0.1

status: Public on Jun 21 2011

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

manufacture_protocol: See manufacture's web site


title: AB SOLiD System 3.0 (Amphimedon queenslandica)

last: GEO

organism: Amphimedon queenslandica


title: Agilent_SALSIFY_Salmonella enterica subsp. enterica serovar Typhimurium_5K

city: Norwich

first: Corinne

last: Appia-Ayme

state: Norfolk

address: UEA

department: BIO

country: United Kingdom

institute: University of East Anglia

organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S


title: Agilent-026181 Fundulus heteroclitus 45K (Probe name version)

city: Charleston

first: Marion

last: Neely

state: SC

address: 331 Ft. Johnson Rd

department: NCCOS

institute: National Ocean Services

organism: Fundulus heteroclitus

description:
Arrays of this design have barcodes that begin with 16026181 or 2526181.
Orientation:
The ID column represents the Probe names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL13522.


title: ZB/SBS-NTU Plasmodium falciparum 3D7 11.0K v1.1

status: Public on Jun 08 2011

city: Singapore

first: Bernardo

middle: J

last: Foth

email: bfoth@gmx.net, ZBozdech@ntu.edu.sg

address: 60 Nanyang Drive

department: SBS

country: Singapore

institute: Nanyang Technological University

organism: Plasmodium falciparum

description: This platform is identical to platform GPL7493 except that 589 oligonucleotides have been added to the platform described here. These additional oligonucleotides represent variable genes (var, rifin) specific to strains Dd2 and HB3.

manufacture_protocol: Long oligonucleotides were selected for P. falciparum 3D7 using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P. Joachimiak, Fred E. Cohen, Brian Pulliam & Joseph L. DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biology 2003, 4:R9.


title: GenopalⓇ MICM07

city: Kodaira

first: Hirohiko

last: Hohjoh

state: Tokyo

address: 4-1-1 Ogawahigashi

institute: National Institute of Neuroscience, NCNP

manufacture_protocol: Custom-made fibrous oligonucleotide DNA microarray GenopalⓇ (Mitsubishi Rayon) with a total of 200 miRNAs which were selected from the miRBase ver9.0 database in Sanger Institute.


title: SAGE:16:NlaIII:Oncorhynchus mykiss

status: Public on Jun 06 2011

organism: Oncorhynchus mykiss

technology: SAGE NlaIII

description: This is a virtual platform for SAGE libraries generated for Oncorhynchus mykiss using NlaIII as an anchor enzyme.


title: SAGE:16:NlaIII:Danio rerio

organism: Danio rerio

description: This is a virtual platform for SAGE libraries generated for Danio rerio using NlaIII as an anchor enzyme.


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray ENSG Version 13.0.0]

status: Public on Jun 07 2011

description:
This is identical to GPL570 but a custom CDF environment was used to extract data [Brainarray Version 13.0.0, HGU133Plus2_Hs_ENSG].

CDF and other files can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/ensg.asp


title: RetroArray - a DNA chip for rapid detection and identification of retroviruses

status: Public on Jun 10 2011

city: Neuherberg

first: Michelle

last: Vincendeau

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

organism:
Macaca mulatta
Homo sapiens

manufacturer: III. Medizinische Klinik, UMM - Universitätsmedizin Mannheim, University of Heidelberg, Germany

first: Wolfgang

last: Seifarth

first: Ulf

last: Krause

first: Christine

last: Hohenadel

first: Corinna

last: Baust

first: Rüdiger

last: Hehlmann

last: Leib-Mösch

manufacture_protocol:
For preparation of DNA chips, probably any standard robotic device will provide satisfactory results. We employ an Affymetrix GMS 417 Arrayer (Affymetrix, Santa Clara, CA, USA). Corresponding pairs of 45-mer synthetic oligonucleotides are diluted to 100 mM in 3x SSC (1x SSC = 0.15 M NaCl plus 0.015 M sodium citrate) and mixed in equimolar amounts. Capture probes are spotted (three hits per dot) onto CSS-100 aldehyde-activated glass slides (TeleChem International Inc., Sunnyvale, CA, USA). Generally, to rule out local defects in the slide surface (e.g. scratches) and for hybridization reproducibility, two replicas are spotted onto the same slide. After spotting, slides are incubated in a humid chamber over night, then air dried, washed and treated with sodium borohydride (NaBH4) as recommended by the glass slide manufacturer. Slides are stored in the dark at room temperature until hybridization. For the standardized experimental flow see Seifarth et al., 2003.
Reverse transcription of RNA was performed using 1 μg total RNA with Superscript II (Roche Diagnostics) according to the manufacturer’s protocol. Reverse transcriptions were followed by an RNase H digestion step (Promega).
RetroArray hybridization is carried out according to a standardized protocol as initially described by Seifarth and coworkers [2003]. It includes the following steps:
1) Prehybridization 2) Hybridization 3) Washing 4) Drying of hybridized glass slides
In general, all handling steps involving fluorochromes are performed under dimmed light conditions, incubations are carried out in the dark. Prehybridization of glass microarrays is performed within Falcon blue cap tubes (Greiner GmbH, Nürtingen, Germany) in 6x SSC, 0.5% sodium dodecyl sulfate (SDS), 1% bovine serum albumin (DNase-free) at 50 °C for at least 4 h. Slides are then washed five times (1 min each) in bidest. water under vigorous agitation. Subsequently, slides are dried by a short centrifugation step (500x g for 1 min at 22 °C). For hybridization, a 22x22 mm glass lifter slip (Erie Scientific Co., Portsmouth, NH, USA) is taped to the microarray. Subsequently, 25 μl of the denatured (5 min at 95 °C) Cy3-labeled probe (containing 3x SSC, 0.1x SDS, 50% formamide) is applied to the small space between cover slip and microarray and sealed with Fixogum rubber cement (Marabu GmbH, Tamm, Germany). Sealed slides are incubated in a humid chamber for at least 16 h at 42 °C. Hybridized slides are then washed three times under vigorous agitation (10 min each) at 22 °C in 1x SSC, 0.5x SSC and 0.1x SSC, respectively. After a brief centrifugation step (500x g for 1 min at 22 °C), the hybridized microarrays were stored in the dark at 22 °C until evaluation by scanning.
Hybridized microarrays were scanned using an Affymetrix GMS 418 scanner (laser power setting, 100%; gain setting, 50%), and the resulting images (16-bit TIFF files) were subjected to densitometric analysis using ImaGene 4.0 software (BioDiscovery Inc.). To discriminate positive signals from background, a cut-off value of 1,200 relative fluorescence intensity units was used that corresponded to twofold overall background intensity value of the microarray. To account for the influence of RNA quality, HERV signals were normalized to the fluorescence intensity of a House keeping gene.


title: Agilent-021819 custom watermelon microarray

status: Public on Jun 09 2011

city: Beijing

first: Yong

last: Xu

address: ShuGuang Garden Middle Road 9,Haidian district

institute: National Engineering Research Center for Vegetables

organism: Citrullus lanatus

manufacture_protocol: See manufacturer's website


title: ORB Sanger15 Multispecies MIcroRNA Microarray

status: Public on Jun 14 2011

city: New York

first: Konstantinos

last: Drosatos

department: Medicine

institute: Columbia University

organism: Mus musculus

description: Multispecies platform including Human, Mouse, Rat, Macca Mulatta

manufacture_protocol: Proprietary spotting of DNA oligonucleotides containing dimer or trimer repeat of reverse complement of target sequence.


title: Agilent-016095 UNIFE_HGDMDSense_44K_V1.0

status: Public on Jun 05 2011

city: Ferrara

first: Matteo

last: Bovolenta

address: 74, Fossato di Mortara

department: Life Sciences and Biotechnology

institute: University of Ferrara

description: We tiled the entire DMD gene, in both sense and antisense directions, using the web-based Agilent eArray database, Version 4.5 (Agilent Technologies), with 60-mer oligos every 66 bp of repeat-masked genome sequence. We defined probe sets for both orientations, encompassing the DMD exons, promoters, introns, predicted MiRNA (identified by PromiRII) and conserved non-coding sequences (CNSs) identified within dystrophin introns using the VISTA programme ( http://genome.lbl.gov/vista/index.shtml). Two specific sets of probes were designed to cover, in both directions, the cDNA sequences of a group of control genes (Supplementary Table S1) identified in the Gene Expression Omnibus (GEO) database http://www.ncbi.nlm.nih.gov/geo/) and expressed equally in both normal and dystrophic muscles. Each probe set was opportunely distributed and replicated several times in order to obtain two 4x44k microarrays, referred to as DMD GEx Sense and DMD GEx Antisense, respectively, able to detect transcripts in the same and opposite directions as that of DMD gene transcription.

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


title: Agilent-024154 human hg18 45K array

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

description: This array is customized to high resolution coverage of exons for genes identified as encoding proteins included in a detailed protein interaction network for autism.

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


title: Agilent-016097 UNIFE_HGDMDAntisense_44K_V1.0

description: We tiled the entire DMD gene, in both sense and antisense directions, using the web-based Agilent eArray database, Version 4.5 (Agilent Technologies), with 60-mer oligos every 66 bp of repeat-masked genome sequence. We defined probe sets for both orientations, encompassing the DMD exons, promoters, introns, predicted MiRNA (identified by PromiRII) and conserved non-coding sequences (CNSs) identified within dystrophin introns using the VISTA programme (http://genome.lbl.gov/vista/index.shtml). Two specific sets of probes were designed to cover, in both directions, the cDNA sequences of a group of control genes (Supplementary Table S1) identified in the Gene Expression Omnibus (GEO) database http://www.ncbi.nlm.nih.gov/geo/) and expressed equally in both normal and dystrophic muscles. Each probe set was opportunely distributed and replicated several times in order to obtain two 4x44k microarrays, referred to as DMD GEx Sense and DMD GEx Antisense, respectively, able to detect transcripts in the same and opposite directions as that of DMD gene transcription.


title: Agilent-024963 UF_Wang_XAC array_8×15K_version 1.0

city: Lake Alfred

first: Yinping

last: Guo

state: FL

address: 700 Experiment station road

department: Microbiology and cell science; Citrus research and education center

institute: Xanthomonas axonopodis pv. citri

organism: Xanthomonas citri pv. citri str. 306

manufacture_protocol: see manufacturer's web site


title: Phalanx Rat OneArray® v1

city: Hsinchu Science Park

first: Phalanx

last: Biotech

state: Hsinchu

address: 6 Technology Road 5, 6th Floor

country: Taiwan

institute: Phalanx Biotech

organism: Rattus norvegicus

description:
Annotation is based on two databases:
. NCBI RefSeq release 45
. Ensembl release 60 cDNA sequences and
rattus_norvegicus_core_60_34b

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


title: The Microarray Department-University of Amsterdam Human 19K 60mer long oligo array

status: Public on Jun 04 2011

city: Genoa

first: Alberto

last: Izzotti

address: A. Pastore, 1

department: Dept. of Health Sciences

institute: University of Genoa


title: Illumina Genome Analyzer (Arabidopsis arenosa)

status: Public on Jun 02 2011

last: GEO

organism: Arabidopsis arenosa


title: Illumina Genome Analyzer (Arabidopsis arenosa x Arabidopsis thaliana)


title: Illumina Genome Analyzer (Arabidopsis suecica)

organism: Arabidopsis suecica


title: Arthropod Pathogen Microarray 1.5K v 1.0

city: San Francisco

first: Charles

last: Runckel

state: CA

department: Biochemistry

institute: UCSF

organism:
Fungi
unidentified entomopoxvirus
unidentified baculovirus
Iridovirus
Cypovirus
Birnaviridae
Luteovirus
Black beetle virus
unclassified viruses
Densovirinae
Ascovirus
Betabaculovirus
Gammabaculovirus

middle: L

last: Flenniken

first: Juan

last: Engel

first: Donald

last: Ganem

first: Raul

last: Andino

first: Joseph

last: DeRisi

manufacture_protocol: Oligos (Invitrogen) were suspended at 40 pmol/uL in 3x SSC and spotted on poly-L-lysine treated slides (Thermo) with silicon pins (~1 pL per spot).  Arrays were allowed to air-dry.  Post-processing: UV crosslinking followed by SSC/SDS shampoo wash and methylpyrrolidone wash.


title: [Bovine] Affymetrix Bovine Genome Array [CDF: BovineEndo_Ensembl57_CDF]

city: Grange

first: aideen

middle: patricia

last: killeen

state: Co. Meath

address: Dunsany

department: Animal and Bioscience Research Department

country: Ireland

institute: Teagasc

organism: Bos taurus

description: This identical to GPL2112 but a custom CDF environment was used to extract data (CDF: BovineEndo_Ensembl57).

relation: Alternative to: GPL2112 (Alternative CDF[official])


title: Phalanx Rice OneArray® v1

organism: Oryza sativa

description:
Annotation is based on three databases:
. MSU Rice Genome Annotation Project release 6.1
. BGI 93-11, 2008.10.28
. GenBank Oryza sativa Japonica Group mRNA, 2011.03.22


title: NimbleGen_UW/FPL Postia placenta MAD-698 whole genome 37K expression array version 1 (non-condensed version)

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

organism: Rhodonia placenta

description: The Platform data table reflects a non-condensed representation of the full array. The .ndf file is linked below as a supplementary file.

manufacture_protocol: proprietary maskless array in situ oligonucleotide synthesis. See http://www.nimblegen.com/


title: Agilent-017075 human hg18 promoter 800-200

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

organism: Homo sapiens

description: Custom-designed 244K promoter tiling array that contains probes covering all transcription start sites at intervals from 800 bp upstream to 200 bp downstream of all genes described in Ensembl (version 44) and within 250 bp of the ~400 microRNAs from miRBase, all at 100 bp-spacing.

manufacture_protocol: Agilent high-density ink-jet. The oligonucleotide microarray is composed of 243,504 45-60mer oligonucleotides from the Agilent's eArray ChIP probe database.


title: NimbleGen Rattus norvegicus 12×135K Array [080925_RAT _HX12_expr]

city: Hohhot

first: taodi

last: liu

address: xinhua street

institute: Inner Mongolia Medical College

description: NimbleGen design name 080925_RAT _HX12_expr,catalog number: 05543827001 Rat Gene Expression 12x135K Arrays, for 26,419 genes and there are 5 probes per gene.

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


title: ISB Halobacterium Whole Genome SpanKit Spotted Microarray v1.3

status: Public on Jun 03 2011

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

organism: Halobacterium salinarum NRC-1

manufacture_protocol:
MIAME platform type: spotted
MIAME availability: Arrays printed at ISB can be purchased, contact bmarzolf@systemsbiology.org for information.
Standard Operating Procedures for the Virtek(ESI) Spotter
*** Always remember that spotter pins are extremely fragile at the tips ***
To make spotter source plates:
1. Total volume should be 4-8 ul
2. Usually, DNA should be in 50% DMSO. This can be done most accurately be putting an appropriate amount of source material in spotting plates, then drying down with the speedvac and resuspending in the final volume of 3X SSC, 1.5M betaine.
Things not to do:
1. Move slides after printing starts ? just touching a slide can shift it and other slides enough to ruin the grid geometry.
2. Use air to blow dust off of slides - you could move the slides
3. Press the RED EMERGENCY button if it's not a emergency- this will turn off the spotter controller and abort the entire run
4. Use PCR products that have been purified, then dried down and resuspended in a very small volume, this is known to cause erratic surface tension and cause spots to run together.
When starting a new print run:
1. Allow blank slides to sit at 65% humidity for 24 hours
2. Renew sticky mat if it's dirty
3. Fill humidifier and turn on
4. Pull water out of water bath, wipe out bath and fill reservoir to get bath back to correct level- IT IS EXTREMELY IMPORTANT NOT TO OVERFILL THE WATERBATH OR SONICATOR BATH, WATER SHOULD BE JUST ABOVE THE POINT WHERE CUT RUNNING UP THE PIN ENDS
5. Place slides on the deck with label on the right-hand side. Secure slides by using spacer glass slides held in place with the magnets at the end of the platform.
6. Measure total X and Y distances spanned by slides, enter sizes under Calibration for Arraying->Slides
7. Print one dip with no source plate to ensure that pins are hitting all slides in the same plate (slight errors in Y direction especially can really throw off grid locations.)
8. Use the metal brace and spacer slides held by magnets to stabilize and line up the slides
9. Stabilize humidity at approximately 65%
10. Put blotting slide in place
To print slides:
1. Spin down 4 source plates at 2000 rpm for one minute
2. Put three remaining source plates (in order) at 4 C
3. Check blotting slide for blocked pins, change slide. Remove clogged/sticking pins and try to remedy by cleaning pin and/or printhead hole. If a pin isn't spotting on the blotter, it may just not be contacting the blotter.see if it's been spotting on actual slides.
4. Change water bath water at beginning of run.
5. Check level of water reservoir and sonicator bath- add water if necessary
6. Check humidity
7. Double-check orientation and number of source plate
8. Press operator button
9. Re-seal old plate and put in cold room
10. Set timer
11. Check old plate out, new plate in on printing checklist
When finished printing for the day:
1. Seal all plates and place in cold room
2. Turn off Spotter light
3. Turn monitor off
4. Leave computer ON
When finished with entire printing:
1. Allow spotter humidity to slowly drop and slides dry out.
2. Remove slides and place into plastic Telechem slide boxes.
3. Turn off Spotter light
4. Turn off fan/humidifier
5. Place boxes in desiccator at least 12 hours.
6. Blow off slides in boxes, then bake at 85 C for 2 hours.
7. Etch numbers and corners on slides (corners on back side), blow dry and place in desiccator ready for prehyb.
Things to do periodically:
1. Just keep an eye on the slides themselves to see if the grids are being formed as expected
To clean a clogged pin:
1. Remove pin by pulling out from top with a small forceps.
2. Dip in water and blow dry with air tip, repeatedly if necessary.
3. Make sure water reservoir is sufficiently full - low water often causes clogging.
Random experiments that we have tried and their results:
1. Effect of Temperature and Humidity on Spot Size
Printed H-70 in 3X SSC onto Telechem Amine slides. Temperatures chosen were 18 C, 20 C, 22 C, and humidities of 40%, 50%, 60% resulting in 9 different conditions. Hybridization was with labeled PCR primer for 3 hours.
Results: Differences were seen in specific grids, but grid-grid variability was too high to establish a conclusive pattern. Spots generally were most intense in a 90-100 micron diameter, then had a lighter halo that could extend to 130-150 microns. It appeared that Halo size was often smallest at 18 C, 130-140 microns. We decided to print at ambient temperature, generally 18-20 C.
2. Effect of Volume and Humidity on Maximum Spots per Dip
Pooled 96 wells of purified PCR product and added SSC for a final concentration of 3X. Then set up a plate so that 8 pins would print 1ul, another 8 would print 2ul, 4ul, 6ul, 8ul and 10ul. This 48-pin dip was then printed 25 spots in the Y direction, across 10 plain glass slides for a total of 250 spots. This print was done with increasing indent at 75%, 70%, 65%, 60% and 55% humidity.
Results: At 1-2ul, pins ran out of juice at 25-50 spots at all humidities. At 4ul, 200-225 spots could be printed at 65% or higher humidity. With 6ul or more, 250 spots could be printed at 65% or higher humidity. Based upon this, we chose 65% humidity for all printing.


title: ISB Halobacterium Spotted Microarray [gene-centered version]

description: Gene-centered version of platform GPL3739


title: UNS/UMR7138 Anemonia viridis Oligo 2K array v1

status: Public on Jun 01 2011

city: NICE

first: Cecile

last: Sabourault

address: Faculte des Sciences, Parc Valrose, BP 71

institute: University of Nice

organism: Anemonia viridis

description: The Aviridis-Oligo2K array is the first oligonucleotide microarray available for symbiotic cnidarians. It contains 60-mer oligonucleotides designed to hybridize UniSequences mostly from the sea anemone A. viridis, but also from its symbiont, the dinoflagellate Symbiodinium sp. Oligonucleotides have similar Tm, that allows homogeneous hybridization and washing conditions.

first: Philippe

last: Ganot

manufacture_protocol: 60-mer oligonucleotides were synthetized, 5' aminated, then printed on UltraGAPSII slides (Corning) using the VersArray ChipWriter Pro System (Biorad)


title: Agilent-025987 Human miRNA Microarray Release 14.0 G4471A (miRNA ID version)

city: Stockholm

first: Stefano

last: Caramuta

address: CMM L8:01, Karolinska University Hospital

department: Molecular Medicine and Surgery

country: Sweden

institute: Karolinska Institutet

description:
http://www.genomics.agilent.com/GenericA.aspx?PageType=Product&SubPageType=ProductLiterature&PageID=1533
8x15K array
Spotted 60mer oligos.


title: Nimblegen T.reesei & T.virens Trichochip-1 393K v1.0

city: Salamanca

first: Enrique

last: Monte

state: Salamanca

address: Rio Duero

department: Spanish-Portuguese Centre for Agricultural Research

institute: University of Salamanca

organism:
Trichoderma virens
Trichoderma reesei

description:
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.
SPOT_ID column:
Annotations beginning with jgi stands for the annotation made by the Joint Genome Institute for these genomes. It has the following format: jgi | <genus and species abbreviation followed by release number> | <seq id number within this sequencing project> | <gene prediction or functional annotation>.
ESTs begin with L (stands for Library) in the chip design; contigs consensus sequences begin with T (stands for Trichoderma).

manufacture_protocol: 090209_Tricho_FG_exp: The  microarray was composed of 374,824 60-mer probes designed against 14,081  EST-derived transcripts and the genomes of T. reesei (9,129 genes) and T.  virens (11,643 genes). Selected 11 probes per gene set on the final array.


title: Kolodrubetz/UTHSCSA  A. actinomycetemcomitans 72K v2.0

city: SA

first: David

last: Kolodrubetz

address: 7703 Floyd Curl Dr

department: Microbiology and Immunology

institute: UTHSCSA

description:
NimbleGen design name 080902_Aact_DK_EXP, NimbleGen design ID 8151.  An expression array for 2,116 genes from A. actinomycetemcomitans strain HK1651.   There are 11 different 60-mer probes /gene for 94% of the genes, and the entire probe set (22,537 probes) is replicated (technical replicates) three times on each array.  Each probe set is contained on a quarter of a chip and there are also 4,426 random probes per array.
native array description file: 080902_Aact_DK_EXP.ndf
native array description file: 080902_Aact_DK_EXP.ngd

manufacture_protocol: In situ oligonucleotide high-density microarray based on Maskless Array Synthesizer technology.  See manufacturer's website at http://www.nimblegen.com/.


title: Illumina Custom Prostate Cancer DASL Panel 1.5K expression beadchip

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

manufacture_protocol:
Sentrix® Array Matrix
The sophisticated Sentrix Array Matrix (SAM) platform is a fiber-optic assembly composed of 96 individual arrays arranged in an 8-by-12 format, matching the well spacing of a standard microwell plate. Each individual array in the matrix holds 1,536 different oligonucleotide probe sequences (IllumiCode sequences), in turn attached to 3-micron beads assembled into microwells at the end of the optical fiber bundle. Because the microwells outnumber probe sequences, multiple copies of each bead type are present in the array. This built-in redundancy further improves robustness and measurement precision. The SAM manufacturing process includes hybridization-based quality control for each array feature, allowing consistent production of high-quality, reproducible arrays. See manufacturer's website for more details.


title: Illumina Genome Analyzer (Glycine max; Phytophthora sojae)

last: GEO

organism:
Glycine max
Phytophthora sojae


title: Illumina Genome Analyzer (Phytophthora sojae)

organism: Phytophthora sojae


title: Illumina Custom Prostate Cancer DASL Panel miRNA

manufacture_protocol: Sentrix® Array Matrix  The sophisticated Sentrix Array Matrix (SAM) platform is a fiber-optic assembly composed of 96 individual arrays arranged in an 8-by-12 format, matching the well spacing of a standard microwell plate. Each individual array in the matrix holds 1,536 different oligonucleotide probe sequences (IllumiCode sequences), in turn attached to 3-micron beads assembled into microwells at the end of the optical fiber bundle. Because the microwells outnumber probe sequences, multiple copies of each bead type are present in the array. This built-in redundancy further improves robustness and measurement precision. The SAM manufacturing process includes hybridization-based quality control for each array feature, allowing consistent production of high-quality, reproducible arrays. See manufacturer's website for more details.


title: Agilent-026181 Fundulus heteroclitus 45K (Feature Number version)

status: Public on May 27 2011

city: Charleston

first: Marion

last: Neely

address: 331 Ft. Johnson Rd

institute: National Ocean Services

organism: Fundulus heteroclitus

description:
Arrays of this design have barcodes that begin with 16026181 or 2526181.
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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL13723.


title: UIUC Honey Bee oligo 13K v1

status: Public on May 12 2011

city: Nagoya

first: Tatsuhiko

last: Kadowaki

address: Chikusa

institute: Nagoya University

organism: Apis mellifera

manufacturer: University of Illinois Keck Center for Comparative and Functional Genomics


title: Affymetrix GeneChip Human Genome U133A 2.0 Array [CDF: Ensembl v58, Hs133Av2_Hs_ENSG]

city: Boston

first: Avrum

last: Spira

state: MA

address: 715 Albany Street, R304

department: Pulmonary and Critical Care Medicine

institute: Boston University Medical Center

description: This is identical to GPL571 but a custom CDF environment was used to extract data (CDF: Ensembl v58, Hs133Av2_Hs_ENSG).

relation: Alternative to: GPL571 (Alternative CDF [official])

manufacture_protocol: Affymetrix standard protocol


title: UIUC Bos taurus 13.2K 70-mer oligoarray (condensed)

status: Public on Oct 26 2009

city: Tjele

first: Kasey

middle: M

last: Moyes

address: Blichers Allé 20, P.O. BOX 50

department: Animal Health, Welfare, and Disease

country: Denmark

institute: University of Aarhus

description:
The 13,257 oligos used in this microarray were obtained from normalized and subtracted cattle placenta and spleen cDNA libraries and based upon the earlier cDNA array platform GPL2864 (Everts et al., 2005 Vet. Immunol. Immunopathol. 105:235-245) and subtracted cDNA libraries created from embryonic (day 36 and day 64) and extra-embryonic (day 14 to 25) tissues (NCBI libraries 15993,15993, and 17188). Positive controls include beta actin (ACTB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and hypoxanthine phosphoribosyltransferase (HPRT). Exogenous spiking controls are the soybean genes chlorophyll ab binding protein (CAB), Rubisco small chain 1 (RBS1), and major latex protein (MSG). Negative controls are Cot1 DNA, genomic DNA, spotting buffer, poly-A, and water. All 70-mer oligos were printed in duplicate on the array.  Keywords: oligo, cow, placenta, bovine, embryo, microarray
Platform GPL8776 is a condensed version of Platform GPL2853 ("UIUC Bos taurus 13.2K 70-mer oligoarray").

manufacturer: W.M. Keck Center, University of Illinois Urbana-Champaign

first: Robin

last: Everts

first: Isabelle

last: Hue

first: Olivier

last: Sandra

first: Jean-Paul

last: Renard

first: Xiuchun

last: Tian

first: Xiangzhong

last: Yang

first: Harris

middle: A

last: Lewin

manufacture_protocol: 70-mer oligos were printed in 150 mM Phosphate buffer at 20 uM concentration.


title: D. rerio_UFZ_8x15KV4

status: Public on May 13 2011

city: Leipzig

first: Wibke

last: Busch

address: Permoser Str. 15

department: Bioanalytical Ecotoxicology

institute: UFZ Helmholtz Centre for Environmental Research

organism: Danio rerio

first: Stefan

last: Scholz

manufacture_protocol: see at http://www.agilent.com


title: [olfactomw520640F] Custom Affymetrix olfactory genome tiling array

first: Eleanor

middle: Josephine

last: Clowney

department: Anatomy

organism: Mus musculus

description: GeneChip CustomExpress format 49-7875 Olfactomw520640F


title: Custom human colon-CDMR DNA methylation array (384 CpG)

city: College Park

first: Hector

last: Corrada Bravo

state: MD - Maryland

address: 3114F Biomolecular Sciences Building

department: Center for Bioinformatics and Computational Biology

institute: University of Maryland

description: Custom nucleotide-specific bead array on the Illumina GoldenGate platform to analyze 151 colon cancer-specific differentially DNA-methylated regions (cDMRs)  from Irizarry et al. (PMID 19151715).

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


title: Xenopus laevis Custom Microarray

city: Haifa

first: Itai

last: Yanai

address: Technion City

country: Israel

institute: Technion - Israel Institute of Technology

organism: Xenopus laevis

first: Leonid

last: Peshkin

first: Paul

last: Jorgensen

first: Marc

last: Kirschenr

manufacture_protocol: Standard Agilent Protocol


title: Nimblegen Human 12x135K array [090527_HG18_WG_CGH_v3.1_HX12]

status: Public on Apr 18 2010

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

description:
12x135K Arrays
Content sourced from the UCSC hg18 human genome (NCBI build 36, March 2006)
designname=090527_HG18_WG_CGH_v3.1_HX12
designid=10032

manufacture_protocol: see manufacturer's web site (http://www.nimblegen.com/)


title: Xenopus tropicalis Custom Microarray

organism: Xenopus tropicalis


status: Public on Aug 01 2010

city: Corvallis

first: Massimo

last: Bionaz

state: OR

address: 316A Withycombe Hall

department: Animal and Rangeland Sciences

institute: Oregon State University

description: The 13,257 oligos used in this microarray were obtained from normalized and subtracted cattle placenta and spleen cDNA libraries and based upon the earlier cDNA array platform GPL2864 (Everts et al., 2005 Vet. Immunol. Immunopathol. 105:235-245) and subtracted cDNA libraries created from embryonic (day 36 and day 64) and extra-embryonic (day 14 to 25) tissues (NCBI libraries 15993,15993, and 17188). Positive controls include beta actin (ACTB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and hypoxanthine phosphoribosyltransferase (HPRT). Exogenous spiking controls are the soybean genes chlorophyll ab binding protein (CAB), Rubisco small chain 1 (RBS1), and major latex protein (MSG). Negative controls are Cot1 DNA, genomic DNA, spotting buffer, poly-A, and water. All 70-mer oligos were printed in duplicate on the array.  Keywords: oligo, cow, placenta, bovine, embryo, microarray


title: NimbleGen_UW/FPL Postia placenta MAD-698 whole genome 37K expression array version 1 (condensed version)

status: Public on Jan 09 2009

city: Madison

first: Dan

last: Cullen

address: One Gifford Pinchot Dr

institute: UW/FPL

description: The Platform data table reflects a condensed representation of the full array. The .ndf file is linked below as a supplementary file.


title: NCI NimbleGen Homo sapiens HG17 Whole Genome 385K Tiling Set version 1

status: Public on May 05 2008

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: 385K element tiling array based on NCBI Build 35 of the human genome (HG17); 50-mer tiling with a median probe spacing of 6,000 bp. The NimbleGen design files (2005-03-16_HG17_WG_CGH.pos and 2005-03-16_HG17_WG_CGH.ndf) linked as supplementary files.

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


title: Agilent 16K botuarray

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

organism: Clostridium botulinum A str. ATCC 3502

manufacture_protocol: Agilent 60mer


title: Exiqon miRCURY LNA microRNA array v.9.2 Extended Version

status: Public on Dec 31 2010

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

institute: Lund University, Sweden

description:
Each Gene ID is represented four times on the array, this platform table represents the condensed version. Please see the supplementary array layout file below for complete layout.

Array represents miRBase version 9.2 with additional features.

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


title: Saccharomyces cerevisiae 6.4K array (Y6.4K), version 4

status: Public on Oct 18 2007

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

institute: Chalmers University of Technology

organism: Saccharomyces cerevisiae

first: Michael

last: Thorsen

first: Markus

last: Tamas

first: Olle

last: Nerman

manufacture_protocol: Microarrays are printed on GAPS II or UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol and are ready-to-use. Double-spotted array containing 6,240 yeast ORFs (plus control spots totalling 6.4K).


title: UIUC Bos taurus 13.2K 70-mer oligoarray

status: Public on Oct 14 2005

city: Urbana

first: Harris

last: Lewin

state: IL

address: 1201 West Gregory Drive

department: Animal Sciences

country: USA

institute: University of Illinois

organism: Bos taurus

first: Robin

last: Everts

first: Isabelle

last: Hue

first: Olivier

last: Sandra

first: Jean-Paul

last: Renard

first: Xiuchun

last: Tian

first: Xiangzhong

last: Yang

relation:
Alternative to: GPL13515
Alternative to: GPL8776
Alternative to: GPL9689


title: Agilent-028298 Embryogene Bovine 45K microarray

city: Québec City

first: Marc-André

last: Sirard

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval