title: UHN SS-Human 19Kv7

status: Public on Dec 31 2005

city: Buenos Aires

first: Michele

last: Bianchini

address: Cramer 1180

department: Centro de Investigaciones Oncologicas

country: Argentina

institute: Instituto Alexander Fleming

organism: Homo sapiens

technology: spotted DNA/cDNA

distribution: commercial

manufacturer: The Microarray Centre (UHN) Ontario, Canada

manufacture_protocol: Microarrays are printed on UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol and are ready-to-use. Single-spotted array containing 19,008 characterized and unknown human ESTs. The clone set has been sequence-verified at the Microarray Centre After printing, the slides are subjected to processing and performance testing based on true labelling, hybridization and scanning procedures. To ensure quality performance of microarrays, printed slides that are less than 95% perfect (in printing fidelity and spot integrity) are not released to users.


title: NIAID - Mtaa

status: Public on Mar 29 2003

city: Bethesda

first: Michael

last: Wilson

state: MD

address: 50 South Drive, Room 5509

department: Division of Intramural Research

country: USA

organism: Mycobacterium tuberculosis

technology: spotted oligonucleotide

description:
Printing by NIAID / Microarray Research Facility
Surface type: non-adsorptive, polylysine-coated glass
Attachment: covalent, (UV-treated polylysine)
Array description: The custom microarrays are manufactured by the Microarray Research Facility of the National Institute of Allergy and Infectious Diseases (NIH/NIAID). Microarrays are printed with an Omnigrid robotic arrayer by GeneMachines (http://www.genemachines.com) that is fitted with a printhead and 16 SMP5 print tips from Telechem (http://www.arrayit.com). The M. tuberculosis microarray (Mtaa) probe set is based on 70mer oligonucleotides from Qiagen's Tuberculosis Genome Oligo Set V1 (http://oligos.qiagen.com/arrays/omad.php). Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in 4XSSC print buffer at a normalized 25 micromolar concentration. The Mtaa microarray spot densities are 250 microns(center-to-center). The microarrays are printed on poly-L-lysine coated slides and post-processed according to the procedures on the Stanford website: http://cmgm.stanford.edu/pbrown/protocols/index.html

distribution: non-commercial


title: GRASP salmonid 16,006-gene microarray

city: Milwaukee

first: Matthew

middle: Lawrence

last: Rise

state: WI

address: 600 E. Greenfield Ave.

department: Great Lakes WATER Institute

institute: University of Wisconsin - Milwaukee

organism: Salmo salar

manufacturer: GRASP (Genomic Research on Atlantic Salmon Project)

first: Kristian

middle: R

last: von Schalburg

middle: L

first: Glenn

middle: A

last: Cooper

first: Gordon

middle: D

last: Brown

first: A

last: Gibbs

first: Colleen

middle: C

last: Nelson

first: William

middle: S

last: Davidson

first: Ben

middle: F

last: Koop

manufacture_protocol:
Gene selection
Microarray fabrication is described in detail in von Schalburg et al. 2005 (BMC Genomics  6:126).  Selection criteria for unique Atlantic salmon (AS) and rainbow trout (RT) cDNAs for inclusion on the 16K microarray were as follows: ESTs (cDNA fragments) were assembled into contiguous sequences (contigs) by PHRAP under stringent clustering parameters (minimum score: 100; repeat stringency: 0.99). Contig consensus sequences and singleton sequences were aligned with non-redundant GenBank nucleotide and amino acid sequence databases using BLASTN and BLASTX, respectively. Threshold for a significant BLAST hit was set at E=1e-15.

It was determined that a cluster must contain at least one "usable" sequence, where "usable" was a) the sequence must be 3' (with high probability; containing polyA signal or having been sequenced with an oligo-dT primer or being at the 3’-end of a contig, with orientation determined by a strong hit against a protein in GenBank’s non-redundant protein database); b) be a sequence stretch containing more than 400 bp and c) the sequence must be at least 95% similar to the consensus of the contig.

It was also determined that if a cluster was a singleton or singleton-equivalent (where all sequences were from the same plate or library thus not providing sufficient evidence for non-chimera status), then the cluster selection was reinforced either by a) a significant BLAST hit, E<1e-15 (BLASTN or BLASTX), or b) it having 94% (or more) identity with a homolog (either paralog or ortholog) covering at least 400 nucleotides. If the cluster was a non-singleton, it was determined that it must be a) one "block" having no regions in the interior of the contig covered by only one sequence (to decrease probability of chimeras) and b) of high enough overall quality (with an overall score > 95% positions without conflicts, weighted by number of sequences which support the consensus) and c) have few leading and trailing singleton positions (no more than 25%), since such positions make it a de facto singleton.

Approximately 3,500 additional sequences were selected with the following criteria: a) no chosen cluster could have 94% or more identity with another chosen cluster (for 400bp) and b) tentative consensus sequences (TC) identified by TIGR (http://www.tigr.org/) could be included. By these criteria, approximately 1000 clones were picked indiscriminately from both normalized AS and RT cDNA libraries, 800 clones were selected from suppression subtracted hybridization libraries, and 700 sequences were added from requests of potential array users. Additionally, 949 non-overlapping sequences (856 AS, 93 RT) from clones included in the preliminary 3,557-gene chip (plus one T cell receptor beta) were selected. Finally, approximately 500 immune-specific genes were also chosen to bring the total number of genes represented on the chip to 16,006. In the 16,006 cDNA features there are 13,421 AS, 2,576 RT, 4 chinook salmon, 3 rainbow smelt and 2 lake whitefish representatives.

Gene Identification
EST contigs were built using cDNAs on the array as reference and all ESTs currently in the GRASP database. Subsequent to microarray fabrication, the consensus sequences were screened for repeats using a custom salmonid repeat database with RepeatMasker. Masked consensus sequences were compared to GenBank databases.

Microarray fabrication
Clones were robotically rearrayed from daughter glycerol stock 384-well plates into 96-well plates pre-filled with 7% glycerol in LB + ampicillin, incubated overnight at 37°C, and checked for uniform optical density. Plasmid inserts were PCR amplified in a Tetrad PTC-200 thermocycler (MJ Research) using 1 ul overnight culture, 0.2 mM M13/pUC forward primer (5'-CCCAGTCACGACGTTGTAAAACG-3'), 0.2 mM M13/pUC reverse primer (5'-AGCGGATAACAATTTCACACAGG-3'), 2 mM MgCl2, 10 mM Tris-HCl, 50 mM KCl, 250 mM dNTPs, 1U AmpliTaq (Perkin Elmer), and nuclease-free H2O (Gibco) to 100 ul. PCR conditions were: 2 min for 95°C; then 35 cycles of 95°C for 30 sec, 60°C for 45 sec, 72°C for 3 min; followed by 72°C for 7 min. Five ul of each PCR product were run on a 1% agarose gel to assess yield and quality. PCR products were robotically cleaned (Qiagen) and consolidated into 384-well plates, lyophilized by speed-Vac, and resuspended in 20 ul 3X SSC. Each purified PCR product concentration was determined and diluted to give a final concentration of 400ng/uL.

All cDNAs were printed as single spots on EZ Rays aminosilane slides (Matrix/Apogent Discoveries) with the Biorobotics Microgrid II microarray printer (Genomic Solutions). Microspot™ 10K quill pins (Biorobotics) in a 48 pin tool were used to deposit approximately 0.5 nl (0.2 ng cDNA) per spot onto the slide. The slides were crosslinked in a UV Stratalinker 2400 (Stratagene) at 300 mJ. The resulting microarrays have a 4-by-12 metagrid layout with 19 X19 spot subgrid, each spot having an approximate diameter and pitch of 100 um and 0.20 mm, respectively. A 280 bp GFP (green fluorescent protein) cDNA was amplified from a GFP clone (Clontech) using the primers (5'-GAAACATTCTTGGACACAAATTGG-3') and (5'-GCAGCTGTTACAAACTCAAGAAGG-3') and printed in each subgrid corner to assist in gridding.

Six exogenous genome (Arabidopsis) cDNAs were amplified from the following clones kindly provided by The Arabidopsis Information Resource:  rubisco activase [GenBank:T41667], protochlorophyllide reductase precursor [GenBank:R30630], chlorophyll a/b-binding protein CP29 [GenBank:N65746], PSII oxygen-evolving complex protein 2 [GenBank:H36167], tonoplast intrinsic protein root-specific RB7 [GenBank:AA067532] and ferredoxin (2Fe_2S) precursor [GenBank:W43249]. The Arabidopsis cDNAs were spotted in quadruplicate on each microarray and used for thresholding (determining number of transcripts present). Also, a ubiquitin normalizer serially diluted (50 pg, 5 pg, 500 fg, 50 fg, 5 fg, 0.05 fg and 0.005 fg) was applied to the array. Spot morphology was assessed by visual inspection, SYBR® Green 1 (Molecular Probes) staining or hybridization with labeled non-specific probe. To check clone tracking, 47 high quality sequences were obtained from randomly-selected wells of the cleaned, consolidated 384-well plates used for microarray printing. Each tracked clone had BLAST identifiers matching gene IDs predicted from the re-array spreadsheet, indicating highly accurate clone tracking throughout the process of microarray fabrication.


title: Proteins in mitochondrial, chromatin, and soluble fractions of Myc-induced apoptosis in Rat1 fibroblasts

status: Public on Dec 20 2005

city: San Antonio

first: Yuzuru

last: Shiio

state: TX

address: 8403 Floyd Curl Dr.

department: CCRI

institute: UTHSCSA

organism: Rattus norvegicus

technology: MS

description: Proteins identified in mitochondrial, chromatin, and soluble fractions of Rat1_Myc and Rat1_vector cells 12 hours after serum deprivation which induces apoptosis.

distribution: virtual


title: Acyrthosiphon pisum + Buchnera aphidicola dual genome array

city: Tucson

first: Nancy

last: Moran

state: AZ

address: Biosciences West, Room 310, 1041 E. Lowell St.,  The University of Arizona

department: Ecology and Evolutionary Biology

institute: University of Arizona

organism:
Buchnera aphidicola
Acyrthosiphon pisum

description:
Dual-genome microarray for the pea aphid, Acyrthosiphon pisum, and its obligate bacterial symbiont, Buchnera aphidicola

The platform table is condensed to show each GENE on the array. The full array table, showing all spots, is linked as a supplementary file (see download link below).

first: David

last: Stern

first: Alex

first: Helen

middle: E

last: Dunbar

first: Gregory

middle: K

last: Davis

first: Wayne

middle: B

last: Hunter

manufacture_protocol: Genes were arranged in duplicate spots on slides, with Buchnera genes grouped into the first and second of 24 subarrays.  In addition to spot duplication, the entire set was printed twice on each slide.


title: IMB Atlantic salmon cDNA microarray

status: Public on Dec 30 2005

city: Halifax

first: Jason

last: Williams

state: Nova Scotia

address: 1411 Oxford Street

department: Institute for Marine Biosciences

country: Canada

institute: National Research Council

description: Corning GAPS II

manufacturer: Institute for Marine Biosciences/Biotechnology Research Institute

first: Susan

last: Douglas

last: Ewart

first: Stephen

last: Tsoi

first: Daniel

last: Tessier

first: Tracey

last: Rigby

manufacture_protocol: Inserts from 4104 cDNAs were amplified by PCR, purified, resuspended in distilled water and spotted in duplicate on Gap II glass slides in 50% DMSO using a Virtek SDDC-2 ChipWriter at the National Research Council Biotechnology Research Institute. Two-fold dilutions of a plasmid encoding chlorophyll synthetase G4 from Arabidopsis thaliana were included at the bottom of each sub-array to serve as internal controls. The resulting array of 8,208 spots was printed twice  on each slide, giving a total of 16,416 spots.


title: VUMC MACF human 30K oligo v30

status: Public on Dec 19 2005

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description:
- oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions
- oligonucleotides were mapped by Ensembl to the NCBI35 version of the human genome
- all plates were printed once (no replicate spots)

first: Paul

last: van den IJssel

first: Bauke

last: Ylstra

manufacture_protocol: The Human Release 2.0 oligonucleotide library, containing 60-mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). The oligonucleotides were dissolved at 10 uM concentration in 50 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink™ slides (Amersham Biosciences), using an SA-72 microarrayer (Perkin Elmer) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). After printing slides were processed and blocked prior to use according to the manufacturer’s protocol.


title: VUMC MACF human 30K oligo v31

description:
- oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions
- oligonucleotides were mapped by Ensembl to the NCBI35 version of the human genome
- from a total of 76 384-well plates in the library plate 15 was not printed in this platform
- all other plates were printed once (no replicate spots)

manufacture_protocol: The Human Release 2.0 oligonucleotide library, containing 60-mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). The oligonucleotides were dissolved at 10 uM concentration in 50 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink™ slides (Amersham Biosciences), using an OmniGrid® 100 microarrayer (Genomic Solutions, Ann Arbor, MI, USA) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). After printing slides were processed and blocked prior to use according to the manufacturer’s protocol.


title: Human TReg Chip

status: Public on Dec 26 2005

city: Braunschweig

first: Susanne

last: Pfoertner

address: Mascheroder Weg 1

country: Germany

manufacturer: German Research Centre for Biotechnology (GBF), Array Facility

manufacture_protocol: Amino-modified 50-mer oligonucleotides are printed onto CodeLink activated slides (Amersham) using a MicroGrid TAS II spotter.


title: SAGE:10:NlaIII:Leishmania donovani

status: Public on Dec 14 2005

last: GEO

organism: Leishmania donovani

technology: SAGE NlaIII

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


title: Zf_16.5K_oligo_COMP_v3Apx

status: Public on Dec 16 2005

city: Singapore

first: Siew Hong

last: Lam

address: 14 Science Drive 4

department: Biological Sciences

country: Singapore

institute: National University of Singapore

organism: Danio rerio

description:
This set includes 16416 oligo probes (60 mers) designed by Compugen-Sigma.
Spotted long oligonucleotide array on glass

first: Lance

last: Miller

manufacture_protocol: See GISMADB homepage


title: VUMC MACF human 30K oligo v36

description:
- oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions
- oligonucleotides were mapped by Ensembl to the NCBI35 version of the human genome
- from a total of 76 384-well plates in the library plates 10 and 11 were printed twice (in duplicate)
- all other plates were printed once (no replicate spots)

manufacture_protocol: The Human Release 2.0 oligonucleotide library, containing 60-mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). The oligonucleotides were dissolved at 10 μM concentration in 50 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink™ slides (Amersham Biosciences), using an OmniGrid® 100 microarrayer (Genomic Solutions, Ann Arbor, MI, USA) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). After printing slides were processed and blocked prior to use according to the manufacturer’s protocol.


title: SA72-9_Mouse_151003

status: Public on Dec 21 2005

organism: Mus musculus

description: Mouse 21K oligo array (65-mer oligo’s)


title: VUMC MACF mouse 22K v9

description:
- oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions
- oligonucleotides were mapped by Ensembl to the NCBIm33 version of the mouse genome
- all plates were printed once (no replicate spots)

manufacture_protocol: The Mouse 8K and Mouse 14K extension oligonucleotide libraries, containing 65-mer oligonucleotides representing 21825 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). The oligonucleotides were dissolved at 10 μM concentration in 150 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink™ slides (Amersham Biosciences), using an SA-72 microarrayer (Perkin Elmer) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). After printing slides were processed and blocked prior to use according to the manufacturer’s protocol.


title: GIS MEGS Hs 28K COMP v1

manufacturer: GIS Microarray and Expression Genomics Lab (Genome Institute of Singapore)

first: Dhinoth

last: Bhangarusamy

first: Lanc

manufacture_protocol: The Human Release 2.0 oligonucleotide library, containing 60-mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys. The oligonucleotides were dissolved at 10 uM concentration and single spotted onto GAPS slides (Corning), using a home built microarrayer.


title: VUMC_Mouse_19122002

description: This array contains 7524 oligonucleotides of 65 bp in length that were spotted in duplicate, representing 7230 separate mouse genes from the Compugen Mouse Oligo Library version 1.0.


title: VUMC MACF human 30K oligo v42

description:
- oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions
- oligonucleotides were mapped by Ensembl to the NCBI35 version of the human genome
- from a total of 76 384-well plates in the library plates 12 and 13 were printed twice (in duplicate)
- all other plates were printed once (no replicate spots)


title: DaphniaArray

city: Okazaki

first: Hajime

last: Watanabe

state: Aichi

address: 5-1, Higashiyama

department: Center for Integrative Bioscience

country: Japan

institute: National Institutes of Natural Sciences

organism: Daphnia magna

manufacturer: Development of Daphnia magna DNA microarray for the evaluation of toxicity in environmental chemicals

first: Eri

last: Takahashi

first: Shigeto

last: Oda

first: Norihisa

last: Tatarazako

first: Taisen

last: Iguchi

manufacture_protocol:
Based on EST database of daphnia magna (Daphniabase, http://daphnia.nibb.ac.jp), 178 genes were selected for DNA microarray.  Genes were selected based on their annotations.  Genes that have similarities to other genes related to detoxification and metabolism were mainly selected.  Other EST genes were randomly selected from the database.
An oligonucleotid corresponding to each gene was designed so that it did not have similarities to other sequences in the database.  Then the oligonucleotids were synthesized and spotted onto Geneslide (Toyokohan, Tokyo, Japan), whose surface is coated with carbon that facilitates covalent linkage of DNA.  Spotting was performed by manufacturer (NGK Insulators, Nagoya, Japan) by ink-jet printer.


title: DNA Chip Consortium Mouse Microarray v2.0

city: Sakyo-ku, Kyoto-shi

first: Akihiro

last: Matsunaga

state: Kyoto

address: Yoshida-konoe-cho

department: Medicine

institute: Kyoto University

description: The oligonucleotide microarray is composed of 21987 of 65 mer oligonucleotides from the Sigma Geneosys oligo DNA library.  Oligonucleotides were printed by Hitachi Software Engineering.

manufacture_protocol: Total RNA is extracted using TRI Reagent (Sigma) and amplified with AminoAllyl MessageAmp aRNA Amplification Kit (Ambion) according to the manufacturer’s protocol.  The amino allyl aRNA is labeled by coupling reaction with NHS ester fluorescent dye, Cy3 or Cy5.  Each labeled aRNA sample is diluted with 5 × Fragmentation Buffer (DNA Chip Consortium) and fragmented by boiling at 94 ºC for 15 min after.  Hybridization mixture is prepared using labeled and fragmented aRNA at 0.4 μg/μl in 5 × SSC, 0.5% SDS, 4 × Denhardt’s solution, and 20% hibridization solution (DNA Chip Consortium).  The hybridization mixture is denatured at 95 ºC for 2 min and then mixed with salmon sperm DNA at 100 µg/ml (Sigma) and 10% Formamide.  The mixture is hybridized for 16 hr at 60 ºC in a hybridization oven.  After hybridization, the microarray is washed with solution I (2 × SSC, 0.1% SDS), solution II (2 × SSC), and solution III (1 × SSC) for each 5 min at 30ºC.  After washing, the microarray is scanned.


title: Affymetrix ENCODE Tiling Array - ANTISENSE - NCBI build 35

status: Public on Dec 13 2005

city: Santa Clara

first: Thomas

last: Gingeras

state: CA

address: 3380 Central Expressway

institute: Affymetrix, Inc.

technology: in situ oligonucleotide

description:
21bp resolution oligonucleotide tiling array.
Annotation in this record based on NCBI build 35.

distribution: custom-commercial

manufacture_protocol: See manufacturer's web site


title: Galbraith Laboratory Arabidopsis thaliana Operon Long Oligonucleotide Microarray version 3.0 (ATv303.03.Z)

status: Public on Dec 24 2005

first: David

middle: William

last: Galbraith

address: 303 Forbes Building

department: Plant Sciences and Bio5 Institute

organism: Arabidopsis thaliana

description: This oligonucleotide array is produced from the Operon Version 3.0 Array-Ready Oligo set (AROS), which comprises 29,110 70-mer oligonucleotides representing 26,173 protein-coding genes, and 28,964 protein-encoding gene transcripts, and 87 microRNA gene precursors.  AROS design is based on ATH1 release 5.0 of the TIGR Arabidopsis genome annotation database, and Release 4.0 of the miRNA Registry at the Sanger Institute.  Various additional elements are printed as controls.  Microarrays can be ordered from the Galbraith laboratory. This platform represents slides ATv303.03.001-ATv303.03.300 (http://www.ag.arizona.edu/microarray).

manufacturer: The Galbraith Lab, University of Arizona

middle: W

manufacture_protocol: GeneMachines Omnigrid 300


title: Ramaciotti Centre 10k combined Rat Oligo

status: Public on Dec 15 2005

city: Melbourne

first: Maria

last: Schache

country: Australia

institute: St Vincents Institute

description: Compugen and Operon oligo sets


title: Lobster1

status: Public on Dec 08 2005

city: Lexington

first: Timothy

last: McClintock

state: KY

address: 800 Rose Street

department: Department of Physiology

institute: University of Kentucky

organism: Homarus americanus

description: Clones spotted in duplicate. Duplicates have the same numeric part of ID in the table (for example 125 and 125b).

manufacturer: Department of Physiology and MicroArray Core Facility, University of Kentucky, Lexington.

first: Kristen

last: Day

manufacture_protocol: cDNA microarray that consisted of five subarrays was designed. We generated two of the sub-arrays, each with 1,152 clones spotted in duplicate. A common set of 96 clones, consisting of positive and negative control sequences, was spotted on each sub-array.  Each cloned cDNA insert was amplified by PCR and spotted on nylon membranes using an Affymetrix 417 Arrayer according to protocols supplied by Dr. Kevin Becker (Tanaka et al., 2000; Barrett et al., 2001).  Arrays were hybridized against 33P-labeled cDNA produced by oligo-dT priming of reverse transcription using the RadPrime DNA labeling kit (Invitrogen).  Hybridization was done in quadruplicate at 50˚C in 50 ml tubes in a hybridization oven as described in Barrett et al. (2001).  Washing wash done twice in 2x SSC and 0.1% SDS for 10 min and twice in 1x SSC and 0.1%SDS for 15 min at room temperature.  Signals from hybridized arrays were quantified using a STORM phosphorimaging device running ImageQuant software (Molecular Dynamics, Sunnyvale, CA).  ImageQuant,was used to segment each spot and calculate the volume signal intensity for each.


title: GRASP salmonid array, 16k v. 1.0, March 2004

status: Public on Dec 09 2005

city: West Lafayette

first: Krista

last: Nichols

state: IN

address: 915 W State Street

institute: Purdue University

organism:
Oncorhynchus mykiss
Salmo salar

description:
16k salmonid cDNA microarray from GRASP
including features primarily from Atlantic salmon and rainbow trout

manufacturer: Genomic Research on Atlantic Salmon Project

manufacture_protocol:
details on the manufacture and testing of the 16k v. 1.0 array may be found in:

von Schalburg KR, Rise ML, Cooper GA, Brown GD, Gibbs RA, Nelson CC, Davidson WS, Koop BF.  2005.  Fish and chips:  various methodologies demonstrate utility of a 16,006-gene salmonid microarray.  BMC Genomics 6: 126

additional information may be found on the GRASP website:  http://web.uvic.ca/cbr/grasp/


title: University of Cologne Dictyostelium discoideum 15K

status: Public on Dec 25 2005

city: Cologne

first: Ludwig

last: Eichinger

address: Joseph-Stelzmann-Strasse 52

institute: Institute for Biochemistry 1

organism: Dictyostelium discoideum

manufacturer: Institute for Biochemistry I, University of Cologne

manufacture_protocol: The current Dictyostelium DNA microarray carries approximately 5,400 non-redundant ESTs from the Dictyostelium cDNA project, 9,000 partial gene sequences from the Dictyostelium genome project, partial sequences of 450 known genes and appropriate positive and negative controls


title: Lobster2

description: Clones spotted in duplicate. Duplicates have the same numeric part of ID in the table (for example 2225 and 2225b).

manufacture_protocol: cDNA microarray that consisted of five subarrays was  designed. We generated two of the sub-arrays, each with 1,152 clones spotted in duplicate. A common set of 96 clones, consisting of positive and negative control sequences, was spotted on each sub-array. Each cloned cDNA insert was amplified by PCR and spotted on nylon membranes using an Affymetrix 417 Arrayer according to protocols supplied by Dr. Kevin Becker (Tanaka et al., 2000; Barrett et al., 2001). Arrays were hybridized against 33P-labeled cDNA produced by oligo-dT priming of reverse transcription using the RadPrime DNA labeling kit (Invitrogen). Hybridization was done in quadruplicate at 50˚C in 50 ml tubes in a hybridization oven as described in Barrett et al. (2001). Washing wash done twice in 2x SSC and 0.1% SDS for 10 min and twice in 1x SSC and 0.1%SDS for 15 min at room temperature. Signals from hybridized arrays were quantified using a STORM phosphorimaging device running ImageQuant software (Molecular Dynamics, Sunnyvale, CA). ImageQuant,was used to segment each spot and calculate the volume signal intensity for each.


title: rikDACFxMboI

status: Public on Dec 12 2005

city: Geneva 4

first: Ulrich

middle: K.

last: Laemmli

address: 30, quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

organism: Saccharomyces cerevisiae

description: chromosome VI tiling array

manufacture_protocol: see manufacturer's website


title: intestine-spleen combined array

status: Public on Dec 05 2005

city: Lelystad

first: Saskia

middle: van

last: Hemert

address: PO box 65

institute: Animal Sciences Group

organism: Gallus gallus

manufacture_protocol: van Hemert, S., B. H. Ebbelaar, M. A. Smits, and J. M. J. Rebel. 2003. Generation of EST and microarray resources for functional genomic studies on chicken intestinal health. Anim. Biotechnol. 14:133-143.


title: NIA Homo sapiens 1.1k v1.0 Neuroarray

status: Public on Dec 02 2005

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

manufacturer: David Donovan, Kevin Becker and Tanya Barrett, NIA, Baltimore

manufacture_protocol:
The NIA Neuroarray has previously been described (1-4), http://www.grc.nia.nih.gov/branches/rrb/dna/dna.htm). 1152 human cDNAs and EST representing various factors such as transcription factors, neuronal cell adhesion molecules, kinases, proteases and oncogenes. were spotted onto nylon membranes in duplicate. NIA Neuroarrays were interrogated in triplicate with C or D SON targets as described (1).

1. Ghorbel, M.T., Sharman, G., Leroux, M., Barrett, T., Donovan, D.M., Becker, K.G., and Murphy, D. (2003) Microarray analysis reveals interleukin-6 as a novel secretory product of the hypothalamo-neurohypophyseal system. J. Biol. Chem. 278, 19280-19285

2. Barrett, T., Cheadle, C., Wood, W.B., Teichberg, D., Donovan, D.M., Freed, W.J., Becker K.G., and Vawter, M.P. (2001) Restor. Neurol. Neurosci. 18, 127-135

3. Vawter, M.P., Barrett, T., Cheadle, C., Sokolov, B.P., Wood, W.H., Donovan, D.M., Webster, M., Freed, W.J., and Becker, K.G. (2001) Brain Res..Bull. 55, 641-650

4. Vawter, M.P., Crook, J.M., Hyde, T.M., Kleinman, J.E., Weinberger, D.R., Becker, K.G., and Freed, W.J. (2002) Microarray analysis of gene expression in the prefrontal cortex in schizophrenia: a preliminary study. Schizophr. Res. 58, 11-20


title: Incyte Human UniGEM V2.40

status: Public on Dec 11 2005

city: BOSTON

first: Kuan-Chun

last: Huang

state: MA

address: 221 Longwood Ave. BLI-431

department: OB-GYN

institute: Brigham and Women's Hospital

description:
The Incyte Human UniGEM V2.40  gene expression microarray contained 9,160 elememts/9,128 unique human cDNA genes and ESTs. 132 elements of conrol spots. The clones are derived from Incyte’s set of sequence-verified cDNA clones and represent unique human genes identified in NCBI’s UniGene database
Keywords = high density cDNA microarray

first: Samuel

last: Mok

first: Shu-Wing

last: Ng


title: UCHSC_Mouse_NIA15K

city: Aurora

first: Erik

middle: James

last: MacLaren

state: CO

address: Mail Stop 8303, P.O. Box 6511

department: Pharmacology

institute: University of Colorado at Denver and Health Sciences Center

description:
The National Institute of Aging Mouse 15K clone set was obtained from the
Vanderbilt Microarray Shared Resource. Approximately 15,000 unique cDNA
clones were derived from 52,374 ESTs from pre- and perimplantation embryos,
E12.5 female gonad/mesonephros, and newborn ovary. Of the clones represented, 50%
may be novel. There are 11,853 Unigene clusters represented and the set has been sequence verified. The average insert size is 1.5kb. For more information about the set
go to http://lgsun.grc.nia.nih.gov/cDNA/15k.html .

manufacturer: University of Colorado Health Sciences Center Gene Expression Core Facility

middle: J

first: Brian

last: Soriano

first: Jeanette

last: Gaydos

first: James

middle: M

last: Sikela

manufacture_protocol:
Plasmid DNAs were isolated from the 15K clone set using a high throughput Qiagen BioRobot 8000. Qiagen Plasmid prep reagents, and filter plates were used to extract and dispense the plasmid DNA into 96 well microtiter plates. The plasmids were assayed by gel electrophoresis for purity. A small random sampling of plasmids was done, and the inserts sequence verified by BLAST analysis. Plasmid inserts were amplified using universal primers, and an MJ Research Tetrad Thermocycler. The PCR products were purified using Millipore MultiScreen PCR plates. The PCR products were assayed by gel electrophoresis for purity and size. The PCR product set was very accurate, and clean. Occasionally, errors were found, and PCR products were re-amplified from the original clone set, or a replacement clone was ordered from Vanderbilt. The purified PCR products were dried down in a SC250DDA Speedvac Concentrator, and resuspended for distribution into 384 well microtiter plates for printing. Control PCR products including housekeeping gene, B-Actin, and several
Arabidopsis genes were plated.  The PCR products and controls were resuspended in 3X SSC and printed with a GeneMachines OmniGrid 100 Arrayer onto Poly-L-Lysine coated microscope slides. The slides were blocked with succinic anhydride in 1-Methyl-2-Pyrrolidinone, and stored in a dessicator until hybridized.


title: GeneXp BioGrid_poplar maturation

status: Public on Dec 31 2005

city: Corvallis

first: Jingyi

last: Li

state: OR

institute: Oregon State University

organism: Populus

description:
Single channel oligonucletide array for comparing gene expression among 16 tissue types to explore maturation and flowering in poplar
Keywords = poplar maturation

first: Olga

last: Shevchenko

first: Steve

middle: H

last: Strauss

first: Amy

last: Brunner


title: Sanger Pilot Study V1

status: Public on Dec 01 2005

city: Geneva

first: Emmanouil

middle: T

last: Dermitzakis

address: 1 Rue Michel-Servet

department: Department of Genetic Medicine and Development

institute: University of Geneva Medical School

technology: oligonucleotide beads

description: The array contains 630 protein coding genes of all RefSeq genes in the ENCODE regions, all RefSeq genes on human chromosome 21 and all RefSeq and manually curated genes from a 10Mb region at 20q12-13.2.  The array is composed of 3 micron features with an average feature redundancy of 30-fold.  All features are quality controlled by a sequential hybridization process called array decoding.  Each gene represented on the array contains 2 or more unique probes that are fully screened, full-length 50-mers.

first: Barbara

last: Stranger

first: Matthew

last: Forrest

first: Andrew

middle: G

last: Clark

first: Samual

last: Deutsch

first: Robert

last: Lyle

first: Sarah

last: Hunt

first: Brenda

last: Kahl

first: Stylianos

last: Antonarakis

first: Simon

last: Tavare

first: Panagiotis

last: Deloukas


title: MRC Mouse Known Gene Oligo Array

city: Leicester

first: Jerry

middle: A

last: Styles

state: Leicestershire

address: Robert Kilpatrick Building, Univ. Leicester

department: Cancer Studies and Molecular Medicine

institute: University of Leicester

first: Suzanne

last: Johnson

first: Douglas

last: Gray

first: Ian

last: White

manufacture_protocol: Not known


title: Human oligo splicing array

status: Public on Dec 30 2005

city: Duarte

first: Ren-Jing

last: Lin

address: 1500 E. Duarte Rd.

department: Molecular Biology

institute: Beckman Research Institute

description: This set includes 2641 oligonucleotides, mostly 40-mers, designed to detect splice variants for 64 human genes

first: Manuel

last: Ares Jr.

first: Lily

last: Shiue

first: Chunxia

last: Li

first: Ren-Jang

manufacture_protocol: as described in Brown's lab


title: Keck Glycine max 18kA cDNA Prints101-108

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

organism: Glycine max

description: see Vodkin et al., BMC Genomics 5:73 (2004) for details of cDNAs represented and Thibaud-Nissan, et al., Plant Physiol 132: 118-136 (2003); and Zabala and Vodkin, Plant Cell 17: 2619-2632 (2005) for use of cDNA arrays in soybean

manufacturer: Vodkin laboratory, University of Illinois and W.M. Keck Center, University of Illinois

middle: O

first: Delkin

last: Gonzalez

first: Jigyasa

last: Tuteja

first: Gracia

last: Zabala

first: Steve

last: Clough

first: Anupama

last: Khanna

first: Martina

last: Stromvik

last: Jones

first: Al

last: Bari

first: Mark

last: Band

first: George

last: Gong

first: Lei

last: Liu

manufacture_protocol: amplified cDNAs printed with Genemachines Omnigrid


title: Yeast Splicing Chip v62

status: Public on Oct 20 2005

city: Santa Cruz

first: Roland

last: Nagel

address: Sinsheimer Labs

department: Biology

institute: UCSC

description:
Yeast Splicing Chip v62
This is an oligonucleotide microarray designed to measure splicing and expression in yeast. Each intron containing gene has 3 features (Splice Junction, Intron, Exon2). The SJ oligo symmetrically spans the splice junction with 20nt on each side. The SJ, Int, and Ex2 oligos are custom designed 40-mers. The array also contains the Operon Yeast Genome 70-mer Set. All of the SJ, Int, and Ex2 oligos are printed 4 times, the Operon 70-mers are printed twice each.
Keywords = Splicing and Expression

manufacture_protocol: spotted oligonucleotide


title: VUMC MACF human 30K oligo v44

status: Public on Dec 19 2005

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

institute: Vrije Universiteit Medical Center

organism: Homo sapiens

description:
- oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions
- oligonucleotides were mapped by Ensembl to the NCBI35 version of the human genome
- from a total of 76 384-well plates in the library plates 14 and 15 were printed twice (in duplicate)
- all other plates were printed once (no replicate spots)

first: Paul

last: van den IJssel

first: Bauke

last: Ylstra

manufacture_protocol: The Human Release 2.0 oligonucleotide library, containing 60-mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). The oligonucleotides were dissolved at 10 μM concentration in 50 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink™ slides (Amersham Biosciences), using an OmniGrid® 100 microarrayer (Genomic Solutions, Ann Arbor, MI, USA) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). After printing slides were processed and blocked prior to use according to the manufacturer’s protocol.


title: MRC Human Known Gene Oligo Array

status: Public on Nov 11 2005

first: Jerry

last: Styles

first: Suzanne

last: Johnson

first: Douglas

last: Gray

first: Ian

last: White


title: NIEHS Human Operon Oligo/ToxChip Hybrid V 1.0

status: Public on Nov 02 2005

city: RTP

first: Pierre

middle: Robert

last: Bushel

state: NC

department: Biostatistics and Computational Biology Branch

institute: NIEHS

technology: mixed spotted oligonucleotide/cDNA

description:
This array was developed in-house at NIEHS, and used for gene expression profiling experiments. A complete listing of the genes on this chip is available at the following Web site: http://dir.niehs.nih.gov/microarray/chips.htm
Oligos for spotting were purchased from the Operon Human Genome Oligo Set V1.1 and cDNAs were prepared according to DeRisi et al., 1996, Nat. Genet. 14, 457-460. The PCR products from the cDNAs and the oligos were spotted onto poly-L-lysine-coated glass slides using a modified, robotic DNA arrayer (Beecher Instruments, Bethesda MD).

first: Jeffrey

last: Tucker

middle: R

first: Richard

middle: S

last: Paules


title: UR_TWT_version 1.0

city: Marseille

first: nicolas

last: crapoulet

address: 27 BD J. Moulin

country: France

institute: Unité des Rickettsies (CNRS-UMR 6020)

organism: Tropheryma whipplei

manufacturer: Unité des Rickettsies CNRS UMR 6020 and Institut de Pharmacologie Moléculaire et Cellulaire UMR 6097 CNRS/UNSA

first: Nicolas

last: Crapoulet

first: Patricia

last: Renesto

first: Pascal

last: Barbry

first: Didier

last: Raoult

manufacture_protocol:
T. whipplei whole-genome microarray construction. 1,608 PCR primers were designed in order to amplify by PCR 804 annoted ORFs representing about 99.5% of T. whipplei genome {Raoult, 2003 26 /id}. The 0.5% remaining genes can not be targeted because their sequences share repeated regions impairing the design of specific probes.
The following criteria were used to identify optimal forward and reverse primers to generate PCR products specific to each of the selected ORFs: (i) primers were highly specific for T. whipplei genome; (ii) length of amplicons were roughly 260 bp; (iii) amplicons were highly specific for their corresponding genes; (iv) each primer contained 20 to 25 bases and annealing temperature of primers was ~60°C; (v) each primer contained an additional sequence in 5’-area specific for the forward and the reverse primer. These universal sequences added were used for a second round of amplification. The sequences of primers used are listed in Table S1.
ORF-specific fragments were amplified using T. whipplei DNA as template and under following conditions: 40 cycles including 20 sec. denaturation at 95°C, 30 sec. annealing at 60°C, and 30 sec. extension at 72°C, along with an initial 5 min. denaturation at 95°C and a final extension reaction at 72°C for 5 min. Following amplification, PCR products were visualized by ethidium bromide staining after migration in a 2% agarose gel. Purified amplicons (QIAquick 96-well purification kit ; QIAGEN, Courtaboeuf, France) were sequenced (3100 Genetic Analyzer, Applied Biosystems, Courtaboeuf, France) to check for the identity of amplified samples and processed in a second PCR run by using universal primers.
Amplified DNA fragments resuspended in 50% DMSO solution were printed in quadruplicate onto Nexterion® Slide A+ (SCHOTT AG, Mainz, Germany) by using a SDDC-2 (Bio-Rad, Marnes-la-Coquette, France). A set of 23 artificial genes that serve as analytical controls to validate, filter, and normalize microarray data contained in Universal ScoreCard™ kit (AMERSHAM BIOSCIENCES, Orsay, France) was also printed onto glass slides. The spotted slides were crosslinked by using a UV Stratalinker (Stratagene, La Jolla, CA, USA) each at a total energy of 250 mJ, and then were stored in a dry environment at room temperature.


title: Ovita Ovine 20K Array

city: Dunedin

first: Orla

middle: Mary

last: Keane

state: Otago

address: 710 Cumberland St

department: Animal Genomics

country: New Zealand

institute: AgResearch

organism: Ovis aries

description: This array contains spotted PCR products from an ovine EST collection. Included are housekeeping genes, water blanks (negative PCR) and no DNA blanks (to estimate carryover)

first: Robert

last: Bower

first: Theresa

last: Wilson

first: Dianne

middle: L

last: Hyndman

first: Alan

middle: F

last: McCulloch

first: Allan

last: Crawford

manufacture_protocol: Ovine EST inserts were amplified in 96 well plates using the universal primers SP6 and T7 in 50 ul reactions (1.5 mM MgCl2, 2 mM each dNTP, 45 pmol primers and 2.5 units AB Red Hot Taq polymerase). The reactions were denatured at 94 degrees C for 3 minutes then cycled 36 times at 94C for 45 sec, 55C for 45 sec and 72C for 60 sec. Finally products were extended at 72C for 5 min. The PCR products were verified by agarose gel electrophoresis, precipitated and resuspended in printing solution. An ovine microarray consisting of 19,968 spots was printed onto poly-L-lysine coated glass slides using an ESI array robot with 32 split pinheads depositing 0.6 nl with a 100 um spot size. After printing the slides were UV irradiated to cross-link the DNA to the polylysine coating.


title: NIEHS Human Operon Oligo/ToxChip Hybrid V 2.0

description:
This array was developed in-house at NIEHS, and used for gene expression profiling experiments. A complete listing of the genes on this chip is available at the following Web site: http://dir.niehs.nih.gov/microarray/chips.htm
Oligos for spotting were purchased from the Operon Human Genome Oligo Set V1.1 and cDNAs were prepared according to DeRisi et al., 1996, Nat. Genet. 14, 457-460. The  PCR products from the cDNAs and the oligos were spotted onto poly-L-lysine-coated glass slides using a modified, robotic DNA arrayer (Beecher Instruments, Bethesda MD).


title: LAFUGA Cattle subtr lib 18ET v1.0

status: Public on Dec 07 2005

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

institute: University of Zurich

organism: Bos taurus

manufacturer: Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians University of Munich

manufacture_protocol:
Pretreatment of Animals and Collection of Endometrial Tissue Samples for the production of subtracted cDNA libraries:
The estrous cycle of five monozygotic twin pairs (Simmental cows, non-lactating), generated by embryo splitting, which had given birth to an average of one or two calves previously, was synchronized by a single intramuscular injection of 500 µg Cloprostenol (Estrumate®; Essex Tierarznei, München, Germany) at diestrus. Animals were observed for sexual behavior (i.e. toleration, sweating, vaginal mucus) to determine standing heat, which occurred around 60 h after Estrumate® injection. Seven days after standing heat, two in vitro produced bovine blastocysts (day 7 after in vitro fertilization) in 200 µl culture medium were transferred into the ipsilateral uterine horn of one twin of each pair. In vitro production of embryos was performed as described previously (Stojkovic M. 1999) with minor modifications. The corresponding twin served as a control and received a sham-transfer of the same amount of transfer medium without embryos. On Day 18 of pregnancy, or of the estrous cycle, respectively, the animals were slaughtered. Blood samples for determination of serum progesterone levels were taken just before slaughter. All animals displayed high progesterone values (mean 3.7 ng/ml), which did not differ significantly between both groups, indicating the presence of an endocrinologically active corpus luteum. The uterine horns were opened longitudinally with a scissors and intercaruncular endometrial tissue samples from defined uterine regions (for further details see Bauersachs S. et al. 2005) were dissected using a scalpel. Pregnancy was confirmed by the presence of an apparently normal conceptus in the uterine lumen. Tissue samples of the endometrium were transferred into tubes containing 4 ml of RNAlater™ (Ambion, Huntigton, UK) within 20 minutes after slaughter, stored overnight at 4°C and then at -20°C until further processing. For gene expression analyses only those tissues samples of pregnant animals, which had been in contact with an embryo were used, i.e. the middle and caudal sections of the uterine horn ipsilateral to the ovary bearing the corpus luteum. From control animals, endometrial samples from the same uterine sections were analyzed. All experiments with animals were carried out with permission from the local veterinary authorities.
Generation of Subtracted cDNA Libraries:
One twin pair was selected for the preparation of a subtracted library enriched for cDNAs of genes up-regulated due to the presence of a conceptus during the pre-implantation period. Total RNA was isolated using Trizol™ reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer's recommendations. Quality of total RNA was checked by agarose gel electrophoresis and quantity was determined by spectrometry. The first subtracted library was generated using the Suppression Subtractive Hybridization (SSH) method (Diatchenko et al. 1996) and was done as reported previously (Bauersachs S. et al. 2003; Bauersachs S. et al. 2004) with a minor modification: at the second step of subtractive hybridization no driver cDNA was added. A second library was constructed using a purchased subtracted cDNA (vertis AG, Freising, Germany). Subtraction was performed as previously described (Ros B. et al 2004) using the same RNA samples as used for construction of the SSH library.
Preparation of cDNA arrays:
4,608 cDNA clones were randomly picked from the two subtracted libraries (SSH library: 3072, vertis library: 1536) and grown overnight at 37 °C in 100 µl LB medium in 96-well microtiter plates. Bacterial suspensions were diluted 20-fold in TE buffer (pH 8.0), incubated at 96 °C for 10 min, and stored at -20 °C. PCR amplification of the cDNA insertions was performed in 20 µl in 96-well cycle plates and contained 1 µl diluted bacterial cells, PCR buffer (peQLab, Erlangen, Germany), 200 pmol/µl dNTPs, 0.3 pmol/µl of the respective primers (modified T3 and T7 primers), and 1 U Taq DNA polymerase (peQLab). All PCR products were analyzed by 0.8 % agarose gel electrophoresis showing that more than 95 % of the PCR reactions yielded defined PCR products. 15 µl of PCR reactions were transferred to 384-well microtiter plates (ABgene) containing 15 µl 2-fold spotting buffer (40 mmol/l Tris-HCl pH 8, 2 M NaCl, 2 mmol/l EDTA, bromophenol blue). 1,536 PCR products were spotted onto nylon membranes (Nytran Supercharge, Schleicher & Schuell, Dassel Germany) on an area of 20 x 50 mm using an Omnigrid Accent microarrayer (GeneMachines, San Carlos, California, USA) and solid pins (SSP015, diameter 0.015 inches; Telechem International, Sunnyvale, California, USA). Spotting was done 6 times for each PCR product on the same position for sufficient and equal application. 25 arrays were produced simultaneously. The cDNAs were denatured on the arrays by incubation on filter paper (Schleicher & Schuell) soaked with 0.5 N NaOH for 20 min at room temperature. DNA was fixed by baking at 80 °C for 30 min and UV cross-linking (120 mJ/cm2, XL-1500 UV Crosslinker, Spectronics Corp., New York, USA). A set of three arrays were produced (A, B, C) whereas arrays A and B contained the cDNA clones of the SSH library and array C contained the clones of the vertis library.


title: VUMC MACF human 19K oligo v5

first: Daoud

last: Sie

department: Pathology

description:
- oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions
- oligonucleotides were mapped by Compugen to the July 2003 Freeze of the human genome
- all plates were printed once (no replicate spots)

first: Paul

last: van den IJssel

first: Bauke

last: Ylstra

manufacture_protocol: The Human Release 1.0 oligonucleotide library, containing 18861 60-mer oligonucleotides representing 17260 unique genes as designed by Compugen (San Jose, CA, USA) was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). The oligonucleotides were dissolved at 10 µM concentration in 150 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink slides (Amersham Biosciences) using an SA-72 microarrayer (Perkin Elmer) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). After printing slides were processed and blocked prior to use according to the manufacturer’s protocol.


title: MRC Human Known Gene Oligo Array Print B

first: Jerry

last: Styles

first: Suzanne

last: Johnson

first: Douglas

last: Gray

first: Ian

last: White


title: Affymetrix ENCODE Tiling Array - SENSE

status: Public on Jun 16 2005

city: Santa Clara

first: Thomas

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

description:
21 bp resolution oligonucleotide tiling array - sense strand
Keywords = synthetic, oligonucleotide, tiling array


title: 18O Isotopic Labeling of Plasma Membrane

status: Public on Jun 21 2005

city: Madison

first: Michael

last: Sussman

state: WI

address: 425 Henry Mall

department: Biotechnology Center

institute: University of Wisconsin

description: An isotopic labeling experiment designed to identifiy plasma membrane proteins.  Fractions from a two-phase partitioning experiment are labeled using natural abundance or 18O enriched water to compare the PM enriched fraction to the PM-depleted microsomal fraction.

first: Clark

last: Nelson

first: Adrian

middle: D

last: Hegeman

first: Amy

middle: C

last: Harms


title: NIAID - Mta[a,b,c]

status: Public on Aug 10 2004

city: Bethesda

last: Wilson

state: MD

address: 50 South Drive, Room 5509

department: Division of Intramural Research

organism: Mycobacterium tuberculosis

description:
Printing by NIAID / Microarray Research Facility
Surface type: non-adsorptive, polylysine-coated glass
Attachment: covalent, (UV-treated polylysine)
Array description: The custom microarrays are manufactured by the Microarray Research Facility of the National Institute of Allergy and Infectious Diseases (NIH/NIAID). Microarrays are printed with an Omnigrid robotic arrayer by GeneMachines (http://www.genemachines.com) that is fitted with a printhead and 16 SMP5 print tips from Telechem (http://www.arrayit.com). The M. tuberculosis microarray (Mtaa) probe set is based on 70mer oligonucleotides from Qiagen's Tuberculosis Genome Oligo Set V1 (http://oligos.qiagen.com/arrays/omad.php). Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in 4XSSC print buffer at a normalized 25 micromolar concentration. The Mtaa microarray spot densities are 250 microns(center-to-center). The microarrays are printed on poly-L-lysine coated slides and post-processed according to the procedures on the Stanford website: http://cmgm.stanford.edu/pbrown/protocols/index.html


title: NIAID - Mmbf

status: Public on Mar 03 2004

description:
Printing by NIAID / Microarray Research Facility
Surface type: non-adsorptive, epoxy-coated glass
Attachment: covalent
Array description: The custom microarrays are manufactured by the Microarray Research Facility of the National Institute of Allergy and Infectious Diseases (NIH/NIAID). Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions (http://www.genomicsolutions.com ) that is fitted with a printhead and 48 SMP3 print tips from Telechem (http://www.arrayit.com ). The mouse microarray (Mmbf) probe set is based on 70mer oligonucleotides from Qiagen's Mouse Genome Oligo Set V2.0 (http://oligos.qiagen.com/arrays/omad.php ).  A comprehensive gene list is also available at http://madb.niaid.nih.gov/
Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved to a normalized 25 micromolar concentration in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauroylsarcosine).  The Mmbf microarray spot densities are 210 microns (center-to-center).  The microarrays are printed on MWG Epoxy Slides (MWG Biotech Inc., # 1150-000000) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: Affymetrix ENCODE Tiling Array - ANTISENSE - NCBIv34

status: Public on Jan 31 2005

description:
21bp resolution oligonucleotide tiling array.
Annotation in this record based on NCBI build 34.


title: NIAID - Mmbe

description:
Printing by NIAID / Microarray Research Facility
Surface type: non-adsorptive, epoxy-coated glass
Attachment: covalent
Array description: The custom microarrays are manufactured by the Microarray Research Facility of the National Institute of Allergy and Infectious Diseases (NIH/NIAID). Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions (http://www.genomicsolutions.com ) that is fitted with a printhead and 48 SMP3 print tips from Telechem (http://www.arrayit.com ). The mouse microarray (Mmbe) probe set is based on 70mer oligonucleotides from Qiagen's Mouse Genome Oligo Set V2.0 (http://oligos.qiagen.com/arrays/omad.php ).  A comprehensive gene list is also available at http://madb.niaid.nih.gov/
Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved to a normalized 25 micromolar concentration in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauroylsarcosine).  The Mmbe microarray spot densities are 210 microns (center-to-center).  The microarrays are printed on MWG Epoxy Slides (MWG Biotech Inc., # 1150-000000) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: NIAID - Mmbb

description:
Printing by NIAID / Microarray Research Facility
Surface type: non-adsorptive, epoxy-coated glass
Attachment: covalent
Array description: The custom microarrays are manufactured by the Microarray Research Facility of the National Institute of Allergy and Infectious Diseases (NIH/NIAID). Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions (http://www.genomicsolutions.com ) that is fitted with a printhead and 32 SMP3 print tips from Telechem (http://www.arrayit.com ). The mouse microarray (Mmbb) probe set is based on 70mer oligonucleotides from Qiagen's Mouse Genome Oligo Set V2.0 (http://oligos.qiagen.com/arrays/omad.php ).  A comprehensive gene list is also available at http://madb.niaid.nih.gov/
Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved to a normalized 25 micromolar concentration in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauroylsarcosine).  The Mmbb microarray spot densities are 180 microns (center-to-center).  The microarrays are printed on MWG Epoxy Slides (MWG Biotech Inc., # 1150-000000) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: NIAID - Hsbc

description:
Printing by NIAID / Microarray Research Facility
Surface type: non-adsorptive, epoxy-coated glass
Attachment: covalent
Array description: The custom microarrays are manufactured by the Microarray Research Facility of the National Institute of Allergy and Infectious Diseases (NIH/NIAID). Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions (http://www.genomicsolutions.com ) that is fitted with a printhead and 48 SMP3 print tips from Telechem (http://www.arrayit.com ). The human microarray (Hsbc) probe set is based on a subset of the library of 70mer oligonucleotides from Qiagen's Human Genome Oligo Set V2.0 ( http://oligos.qiagen.com/arrays/omad.php ).  A comprehensive gene list is also available at http://madb.niaid.nih.gov/
Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved to a normalized 25 micromolar concentration in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauroylsarcosine).  The Hsbc microarray spot densities are 205 microns (center-to-center).  The microarrays are printed on MWG Epoxy Slides (MWG Biotech Inc., # 1150-000000) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: Ontario Cancer Institute full-genome S. cerevisiae ORF array

status: Public on Nov 25 2002

city: Boston

first: Haley

last: Hieronymus

address: 1 Jimmy Fund Way SM922

institute: Harvard Medical School and Dana-Farber Cancer Institute

description: Full-genome S. cerevisiae ORF microarray spotted with all 6240 ORFs plus control spots totals to 6.4k by the Microarray Centre at the Ontario Cancer Institute, University Health Network of the University of Toronto.


title: ACRF microarray consortium human 8k array

city: Parkville

first: Ken

last: Simpson

state: Victoria

address: 1G Royal Parade

department: Genetics and Bioinformatics

institute: The Walter and Eliza Hall Institute

description:
H8K210302, barcodes 1719-1774
Spotted
Corning GAPS-II Amino silane Slides
25x75mm Slides
18432 dots
Custom made with human 1K at end
Reporter Type: PCR products of cDNA clones, Double stranded
Primer  sequence used to amplify human 8K clone set plates 1-75, and Anthea's 1K human plates:
Reverse 5'gtgagcggataacaatttcacacaggaaacagc3'
Forward 5'ctgcaaggcgattaagttgggtaac 3'
Primer sequence used to amplify human 8K clone set plates 76-78:
Reverse 5'cacaggaaacagctatgacca3'
Forward 5'acggccagtgccagcttat3'
cDNA Clone set from Research Genetics, Alabama, USA
Human 8K clone set obtained Nov 2001, Housed at AGRF, Melbourne Australia
Anthea's 2 plates leukemia subset of human 40K clone set obtained Sep 2000, housed at AGRF, Melbourne Australia.
Amplification Protocol: (Human 8K only)
0.2mM dNTP, 25 pmols each primer, 2.5 units HotStar Qiagen TAQ, 1X HotStar buffer, and 1ul straight clone culture in 100ul reactions.
95C for 15min; 7 cycles of 94C for 30s; 72C for 1min (-1C every cycle); 72C for 2min; 23 cycles of 94C for 30s; 65C for 1min; 72C for 2min; final elongation 72C for 5min; 4C 2min.
Amplification Protocol: (Anthea's plates)
95C for 15min; 38 cycles of 94C for 30s; 60C for 45s; 72C for 3.5min; final elongation 72C for 5min; 4C 2min.
Millipore PCR plate purification, gel analysis, aliquot into 384 well plates by robot (A1,A2,B1,B2).
Resuspended in water for 4 days in fridge, then added an equal amount of DMSO.
Printing concentration was ~250 ng/ul in 50% DMSO, 6ul total.
Post Processing: UV crosslinked 70mj; baked 2hrs at 80C; stored dessicated.
Feature Information:
~150um diameter
Covalent and ionic attachment.
Control Elements on the array:
Human 8K control plate version 1, 6ul 50%DMSO
Printing Buffer and blank wells for pin washing controls
Various dilutions of geographic control (concentrated mix of all PCR products in that library set) for concentration, normalisation and positive controls.
Various mouse, human and yeast 'housekeeping genes'.
Poly A, pGEM, Human Cot1 DNA, Mouse Cot1 DNA, salmon sperm are all spotted to assess sufficient blocking of repetitive elements which if not properly blocked can give rise to non-specific annealing.
Printed controls for future spiked (exogenous) applications (yeast intergenic) SP2, SP3; present negative controls
RT efficacy controls based on yeast intergenic RT1-7, again for future, presently negative controls.


title: Takara CyanoChip v.2.0

city: Gif sur yvette CEDEX

first: Franck

last: Chauvat

department: DSV/DBJC

institute: CEA Saclay

organism: Synechocystis sp. PCC 6803

description: IntelliGene® Cyano CHIP Ver.2.0 is a product which is arrayed and immobilized with the DNA fragments of ORF (Open Reading Frame) derived from Synechocystis sp. PCC6803, a photosynthetic gram-negative bacterium on a slide glass. Approximately 2,954 DNA fragments are arrayed. Further detailed information about ORF name, Genetic symbol and Gene name in Array list can be obtained from CyanoBase (http://www.kazusa.or.jp/cyano/ index.html) in Kazusa DNA Research Institute.

manufacture_protocol: see manufacturer's web site