title: Integrated Genomics Bacteriophage T4 2K Genome Array

status: Public on Nov 18 2005

city: Chicago

first: Yakov

middle: N.

last: Kogan

state: IL

address: 2201 W. Campbell Park Dr.

country: USA

institute: Integrated Genomics, Inc.

organism: Tequatrovirus T4

technology: spotted DNA/cDNA

description: PCR products representing T4 ORFs were spotted onto amino-silane coated glass slides from Corning (Corning, NY) using a Flexys Arrayer manufactured by Genomic Solutions, Inc. (Ann Arbor, MI). Each T4 ORF was spotted four times per slide as shown in the Supplementary file GPL3063_completeLayout.txt.

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: Custom Yeast Genomic 70-mer Oligonucleotide Microarray

status: Public on Feb 28 2005

city: Urbana

first: Kurt

middle: E

last: Kwast

address: 407 S. Goodwin Ave.

department: Molecular & Integrative Physiology

institute: University of Illinois at Urbana-Champaign

organism: Saccharomyces cerevisiae

technology: spotted oligonucleotide

description: The custom microarrays consisted of Operon’s Yeast Genomic 70-mer Oligonucleotide Set (Qiagen, Valencia, CA, v. 1.1) spotted in duplicate at a concentration of 20 mM in 150 mM sodium phosphate (pH 8.5), Arabidopsis oligonucleotide spike controls (Stratagene SpotReport, La Jolla, CA) spotted in quadruplicate, and 10 human and 10 yeast oligonucleotide negative controls spotted in duplicate.  The oligonucleotides were printed on Codelink slides (Amersham, Piscataway, NJ) by Microarrays, Inc. (Nashville, TN).  Post-print processing was conducted according to the manufacturer’s recommendations.

distribution: non-commercial

first: Liang-Chuan

last: Lai

first: Alexander

middle: L

last: Kosorukoff

first: Patricia

middle: V

last: Burke


title: Array for the Classification of CAD and DCM hearts

status: Public on Nov 15 2005

city: Trondheim

first: Vidar

last: Beisvag

address: Olav Kyrres gt 3

country: Norway

institute: Deparment of Circulation and Imaging, Norwegian University of Science and Technology

organism: Homo sapiens

description: Moleculer classification of failing hearts from coronary and myopathic patients by gene expression profiling and supervised learning

first: Per

middle: K

last: Lehre

first: Herman

last: Midelfart

first: Halfadan

last: Aas

first: Odd

last: Geiran

first: Astrid

last: Lægreid

first: Jan

last: Komorowski

first: Øyvind

last: Ellingsen


title: mwwlab yeast 70mer oligos platform 2

status: Public on Nov 28 2005

city: Albuquerque

first: Sushmita

last: Roy

state: NM

institute: Biology, University of New Mexico

description:
Spotted long oligonucleotide array on glass.
This set includes 6400 oligonucleotides

distribution: custom-commercial

first: Anthony

middle: D

last: Aragon

first: Margaret

middle: C

last: Werner-Washburne

manufacture_protocol: Commercial protocol


title: MRC Mouse array

status: Public on Nov 21 2005

city: Leicester

first: Jerry

middle: A

last: Styles

state: Leicestershire

address: Robert Kilpatrick Building, Univ. Leicester

department: Cancer Studies and Molecular Medicine

country: United Kingdom

institute: University of Leicester

organism: Mus musculus

first: Suzanne

last: Johnson

first: Douglas

middle: T

last: Gray

first: Ian

last: White

manufacture_protocol:
4000 EST clones were obtained from Research Genetics (Human known gene set)(http://www.resgen.com). The remainder were added by selection from GenBank: the actual clones were obtained from the IMAGE collections held at the MRC Human Genome Mapping Project (http:www.hgmp.mrc.ac.uk/). These clones were sequence verified prior to arraying. All of the plasmid inserts were amplified by use of a universal primer set and a standard PCR mix (ABGene) employed. The products were all electrophoresed on an agarose gel and the gel images stored for future reference.
All PCR products that failed an initial amplification or produced multiple bands were re-amplified using plasmid specific primers. The size of the insert sequence was determined from the agarose gel by comparison with ladder using MultiAnalyst software (BioRad). After PCR the reaction products were precipitated and prepared for array using the methods described by Eisen and DeRisi (DeRisi et al., 1997; Eisen et al., 1999).
Arrays were printed on poly-L-lysine coated slides and UV crosslinked and blocked prior to use (DeRisi et al., 1997; Eisen et al., 1999). The arrays were printedusing an arrayer built essentially according to the Stanford designs and can be seen at http://www.le.ac.uk/cmht/twg1/array-fp.html) The centre to centre distance of the features was 210 um and each feature was 90-100 um in diameter


title: Cornell-CGEP Tomato 13K vTOM1

status: Public on Nov 09 2005

city: Bet-Dagan

first: Carmiya

last: Bar-Or

address: Hamaccabim

department: Genomics

country: Israel

institute: ARO

organism: Solanum lycopersicum

manufacture_protocol: Twelve-thousand-eight-hundred-sixty EST clones representing ~8,500 independent tomato loci were inoculated into 384-well plates containing LB+Amp and incubated for 24-48 hrs at 37 oC. Resultant cultures were used to inoculate duplicate PCR reactions, which contained 10 mM Tris-Cl (pH 9.2), 25 mM KCl, 3.5 mM MgCl2, 0.5 mM dATP, 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dUTP, 0.04 uL Taq polymerase, 200 nM T3 primer, and 200 nM T7 primer. PCR reactions were incubated at 95 oC for 2 min, followed by 39 amplification cycles (94 oC for 20 sec, then 52 oC for 20 sec, then 72 oC for 1.5 min), and then incubated at 72 oC for 10 min. Products from duplicate 15 uL PCR reactions were combined and purified using a Genesis RSP 200 Liquid Handler (TECAN Inc., NC) and 384-well filter plates (# S384PCR10; Millipore Inc., MA). Purified products were dehydrated under vacuum, re-suspended in 12 uL of spotting buffer (3X SSC, 1.5 M betaine), and printed onto glass slides coated with g-amino-propyl-silane (25.3 X 75.5 mm, UltraGAPS; Corning Inc., NY) using a MicroGrid Pro arrayer (BioRobotics Inc., MA) with 32 MicroSpot2500 printing pins. Temperature and humidity inside the arrayer were maintained at 18-21 oC and 35-45% RH, respectively. Dwell time, spots per visit, pin wash time, and pin dry time were set at 1 second, 27 spots, 7 seconds, and 10 seconds, respectively. cDNA was fixed to the slides by treatment with 300 mJoules of UV irradiation followed by a two-hour incubation at 85oC. Array fabrication was completed with a 2 minute wash in 0.2% SDS, three rinses in Milli-Q® water, and a final rinse in 90% EtOH. EtOH was removed immediately via centrifugation (2 min at 500 rpm) and resulting microarrays were stored in a dust-free plexiglass chamber (~21oC, 0% RH).


title: Caenorhabditis elegans printU

status: Public on Jun 25 2005

city: Stanford

first: Min

last: Jiang

state: CA

institute: Stanford University

organism: Caenorhabditis elegans

manufacturer: John,,Matese; Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Room 135, Princeton, NJ, United States; (609) 258-8309; jcmatese@genomics.princeton.edu

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


title: NMC 7.7k duplicate human cDNA arrays, Ser 020617

status: Public on Nov 01 2005

first: Kristin

last: Nørsett

department: Dept of Cancer Research and Molecular Medicine

institute: Norwegian University of Science and Technology

middle: G

first: Waclaw

last: Kusnierczyk

first: Mette

last: Langaas

first: Helge

last: Waldum

first: Arne

last: Sandvik

manufacture_protocol: The 7.7k human cDNA arrays used here are part of a larger collection of 30k cDNAs purchased from Research Genetics (Huntsville, AL) (www.microarray.no). Plasmids were isolated from overnight bacterial cultures in 96-well plates and cDNA inserts amplified by PCR using M13 primers 5'-gtt gta aaa cga cgg cca gtg and 5'-cac aca gga aac agc tat g. The PCR products were precipitated with ethanol, washed and redissolved in 3x SSC (sodium dodecyl sulphate). Quality and concentration was assessed by agarose gel electrophoresis. The purified PCR products were prepared in 50% DMSO (about 50-200 ng/ l) and spotted in duplicate onto 25 x 75mm amino-silane coated CMT-GAPS glass slides (Corning, NY) using a MicroGrid II printing robot (BioRobotics; Cambridge, UK). The arrays were spotted with 8 pins and contained 4 x 8 blocks of 22 x 22 spots. The probes were fixed to the slide surface by UV irradiation. The 7.7k cDNA probes represent 7561 unique UniGene clusters, all printed in duplicates. In addition, a few in-house cDNA probes and a set of positive and negative control elements including 10 different PCR products of exogenous DNA from SpotReport™ cDNA Array Validation System (Stratagene, La Jolla, CA) were printed on the arrays. Totally, each array contained 15488 elements including duplicates and controls.


title: INSERM Homo sapiens 14K array_Liverpool

status: Public on Dec 10 2004

city: ROUEN

first: Jean

middle: Philippe

last: SALIER

address: Bvd Gambetta

department: Inserm Unit 519

country: France

institute: Faculty of Medicine and Pharmacy

description: Liverpool is a nylon array of complementary DNA (cDNA) probes for approximately 10,000 nonredundant genes expressed in embryonic, adult, and/or cancerous liver.

first: Cedric

last: Coulouarn

first: Gregory

last: Lefebvre

first: Maryvonne

last: Daveau

first: Jean-Philippe

last: Salier


title: CyanoCHIP version 2.0

status: Public on Nov 10 2005

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 2,950 DNA fragments are arrayed, which cover about 95% of total ORFs. Also DNA fragments derived from other species such as human TFR are spotted on this product as negative control spots for hybridization. These DNA fragments are arrayed at the colored area on the slide glass figure. The expression of each gene can be simultaneously analyzed through hybridization of the probes which are prepared by using total RNA obtained from Synechocysis sp. as a template. Control spots can be used to determine the background level. 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.


title: University Health Network Mouse NIA 15k M15_k3

status: Public on Nov 22 2005

city: Trieste

first: Diego

last: Vozzi

address: Via dell'Istria

department: Dipartimento di Scienze della Riproduzione

country: Italy

institute: Ospedale Burlo-Garofalo

manufacturer: Microarray Centre -University Health Network- Toronto Medical Discovery Tower- 101 College Street- Rm 9-301-  Toronto, Ontario- CANADA

manufacture_protocol:
Double-spotted array containing 15,264 sequence-verified mouse ESTs from the National Institute of Aging (NIA).
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.


title: Takara CyanoChip v.1.2

status: Public on Nov 19 2005

description: IntelliGene® Cyano CHIP Ver.1.2 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 2,891 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.


title: Rhodopseudomonas palustris whole genome microarray

city: Seattle

first: Yasuhiro

last: Oda

state: WA

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

institute: University of Washington

organism: Rhodopseudomonas palustris

manufacturer: Environmental Sciences Division, Oak Ridge National Laboratory

first: Liyou

last: Wu

first: Xiudan

last: Liu

first: Tingfen

last: Yan

first: Jizhong

last: Zhou

first: Caroline

middle: S

last: Harwood

manufacture_protocol: PCR primers for 4508 out of 4836 predicted ORFs of the Rhodopseudomonas palustris chromosome were designed using the PRIMEGENS software. Each gene was amplified 16 times in parallel 100 µl reactions in 96 well plates. All of the amplified products were pooled and purified using a Biomek F/X Automated Workstation (Beckman). All the amplified products were analyzed on 1.5% agarose gels, and were considered correct if the PCR reactions contained a single product of the expected size. Of the 4508 total predicted genes, 4350 ORFs were correctly amplified, which represents approximately 90% of the genome. Specific 50-mer oligonucleotide probes (385 ORFs) were synthesized for the genes that were not amplified. In total, the PCR amplicons and oligo probes represented 98% of the total predicted gene content of Rhodopseudomonas palustris. The purified PCR products were diluted in 50% DMSO to a minimum concentration of 50 ng/µl. Probes were then printed onto Corning UltraGAPS coated slides (Corning, Corning, NY) with a BioRobotics Microgrid II printer (Genomic Solutions, Ann Arbor, MI) as recommended by the manufacturer, and were UV cross-linked to the surfaces of slides (Statagene UV Crosslinker; Stratagene, La Jolla, CA). Each slide was printed with probes representing two copies of the genome.


title: UCSF_HumArray

status: Public on Nov 05 2005

city: San Francisco

first: Boris

last: Bastian

department: Laboratory Medicine

institute: UCSF Cancer Center

description: The arrays contain 2462 BAC clones printed as triplicate spots and are described in: Snijders AM, Nowak N, Segraves R, et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nature Genetics 2001; 29:263-264.


title: Ips_pini-midgut.1

status: Public on Oct 17 2003

city: Reno

first: Christopher

middle: Ian

last: Keeling

state: NV

address: 1664 North Virginia Street

department: Department of Biochemistry/Mail Stop 330

institute: University of Nevada, Reno

organism: Ips pini

description:
The Ips_pini-midgut.1 array is a cDNA-based glass microarray produced for Dr. Claus Tittiger's laboratory by the Nevada Genomics Center at the University of Nevada, Reno. The array features 768 spots representing 384 tentatively unique genes chosen from an Ips pini (the North American pine engraver beetle) EST project of anterior midgut tissue from juvenile hormone III treated (20 h) males (Eigenheer, A.L., MS thesis, University of Nevada, Reno 2002 & Eigenheer, A. L., et al., Gene 316:127-136, 2003).  Pheromone biosynthesis occurs de novo in this tissue.  cDNA was amplified using vector specific primers from selected clones.  PCR products were resuspended in Micro Spotting Solution Plus (Arrayit) and spotted onto SuperAmine microarray substrates (Arrayit) using a Virtek SDDC2 Microarrayer with a 2 x 4 array of SMP3 Stealth Micro Spotting pins (Arrayit) printing subarrays of 6 x 8 spots with 300 µm spacing.  Spotting was duplicated on each substrate with duplicate spots 9 mm apart.  DNA was bound to substrate by baking for 80 min at 80°C and then the spots were rehydrated, flash dried on a hot plate, and then crosslinked with 120 mJ of UV light (Stratagene UV Stratalinker 1800).  Clones were chosen to represent the longest clone of a cluster (Eigenheer, A.L., MS thesis, University of Nevada, Reno 2002).  After this platform was spotted, the ESTs were re-clustered with Virginia Bioinformatics Institute's ESTAP software using more stringent filtering (Eigenheer, A. L., et al., Gene 316:127-136, 2003).  Those spots without GenBank accession numbers were excluded from further clustering by ESTAP.
Keywords: North American pine engraver beetle; anterior midgut; juvenile hormone; pheromone biosynthesis; Coleoptera; Scolytidae

Publication reference:

Reference Type: Book Section
Authors: Tittiger, Claus; Keeling, Christopher I.; Blomquist, Gary J.
Year: 2005
Title: Some insights into the remarkable metabolism of the bark beetle midgut.
Editor: Romeo, J.T.
Book Title: Chemical ecology and phytochemistry of forest ecosystems
City: Toronto
Publisher: Elsevier
Volume: 39
Pages: 57-78
Series Title: Recent Advances in Phytochemistry

first: Claus

last: Tittiger

middle: I

first: Gary

middle: J

last: Blomquist


title: LGTCmuOLIs2

status: Public on Nov 24 2005

city: Leiden

first: Rolf

last: Turk

address: Wassenaarseweg 72

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

description: spotted olibonucleotide microarray using Sigma-Genosys oligonucleotide library


title: Human BAC to study Chromosome 21 abnormalities

status: Public on Feb 26 2004

city: Columbus

first: Nehad

last: Mohamed

state: OH

address: 420W12th Ave

department: Comperhensive Cancer Center/HCG

institute: The Ohio State University

description:
36 RPCI-11 BAC clones covering the q-arm of chromosome21 from position15.1MB(close to the centromere)to the telomeric position 46.9 MB with an average gap between clones of 800 kb (range 346-1593 kb)	In addition 23 randomly selected clones, each representing 1 of the remaining chromosomes1-20,22,X and Y"Positions of genes and BAC clones were determined according to the NCBI (http://www.ncbi.nlm.nih.gov/mapview) 59 BAC clones spotted in 4 replicas for a total 236 spots on commercial polylysine  glass slides using Promedia Arrayer (Promedia Associates,Inc,Larchmont, N.Y.)using 6 tips. (Affymetrix,Santa Clara, CA). Purified clones spotted in 50%DMSO DNA Isolation of these clones was performed from bacterial culture (250ml) using Qiagen midi kit (Qiagen, Valencia CA)
Keywords = Chromosome 21 copy number alterations

first: Claudia

last: Baldus


title: Sanger (Hurles) - Homo sapiens - 385K feature custom tiling path array - v1.0

status: Public on Nov 17 2005

city: Hinxton

first: Dan

last: Andrews

address: Wellcome Trust Genome Campus

institute: Sanger Institute

technology: in situ oligonucleotide

description: Custom fine-tiling array of 385k in situ isothermal oligonucleotide probes (Tm=76oC, 45mer - 85mer).  Array allows fine detail aCGH of 131 contiguous chromosomal regions of suspected human copy number polymorphism.

first: Donald

last: Conrad

first: Nigel

middle: P

last: Carter

first: Matthew

last: Hurles

first: Johnathon

last: Pritchard

manufacture_protocol: Maskless Array Synthesis as described in 1) Singh-Gasson et al., (1999) Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol 17:974-978 and 2) Nuwaysir et al (2002) Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res 12:1749-1755


title: Massively Parallel Signature Sequencing - MPSS (classic method)

status: Public on Nov 29 2005

city: Hayward

first: Lynx

last: Lynx

address: 25861 Industrial Blvd.

institute: Lynx Therapeutics, Inc.

technology: MPSS

description:
Sequencing from the 3' most DpnII site from mRNA using Lynx's MPSS technology.
MPSS allows a comprehensive survey of all expressed transcripts in a cell or tissue, without apriori knowledge.
This dataset was annotated using a combination of LocusLink, Unigene (build 171) and the latest human build as provided from UCSC (hg16).
Annotation Classe Table:
Virtual Signature Class    mRNA Orientation                        Poly-Adenylation Features     Position
0                          Either - Repeat Warning                 Not applicable                Not applicable
1                          Forward Strand                          Poly-A Signal, Poly-A Tail    3' most
2                          Forward Strand                          Poly-A Signal                 3' most
3                          Forward Strand                          Poly-A Tail                   3' most
4                          Forward Strand                          None                          3' most
5                          Forward Strand                          None                          Not 3' most
6                          Forward Strand                          Internal Poly-A               Not 3' most
11                         Reverse Strand                          Poly-A Signal, Poly-A Tail    5' most
12                         Reverse Strand                          Poly-A Signal                 5' most
13                         Reverse Strand                          Poly-A Tail                   5' most
14                         Reverse Strand                          None                          5' most
15                         Reverse Strand                          None                          Not 5' most
16                         Reverse Strand                          Internal Poly-A               Not 5' most
22                         Unknown                                 Poly-A Signal                 Last before signal
23                         Unknown                                 Poly-A Tail                   Last before tail
24                         Unknown                                 None                          Last in sequence
25                         Unknown                                 None                          Not last
26                         Unknown                                 Internal Poly-A               Not 3' most
1000                       Unknown- Derived from Genomic Sequence  Not applicable                Not applicable
Keywords = MPSS, mRNA sequencing, tags

distribution: virtual

first: Christian

last: Haudenschild

first: Daixing

first: Irina

last: Khrebtukova

first: Tom

last: Vasicek


title: Adelaide Microarray Facility CompuGen OligoLibrary Mouse 22k v3.0

status: Public on Nov 16 2005

city: North Adelaide

last: Wilkinson

state: South Australia

address: 72 King William Road

country: Australia

institute: Child Health Research Institute

description: 4x16 print groups, 24rows x 20 cols per print-tip group. Platform contains single copy of the CompuGen Mouse OligoLibrary v2.0 (IDs start with CGEN), plus a in house produced control plate (IDs start with AMC). This spotting layout is version 3.0, and is similar (identical) to version 1.0. The last few columns of this description also contain positions of a given spot in the previous layout (version 2.1). this was unique for the CompuGen library, but not for all control spots. The control plate spotted twice in this layout (last 16 rows of col 1 in each block), but only once in the version 2.1 layout (in the last 8 rows of col 1 in each block)).

manufacturer: Adelaide Microarray Facility, University of Adelaide, Australia

first: Ashley

last: Connolly

first: Mark

last: Van der Hoek

middle: R

manufacture_protocol: CompuGen Mouse OligoLibrary V2.0 comprising 21,991 65-mers representing 21,587 unique genes. Additional locally made control plate spotted. Spots printed onto Corning CMT-GAPS slides using a 4x16 pinhead robot. Each print head printed an array of 480 spots arranges as a 24 rows by 20 columns (23040 features per array). See www.microarray.adelaide.edu.au for printing details.


title: UHN Human 19K v7 array

city: Seibersdorf

first: René

last: Stempfer

address: Reaktorstr.

department: Life Sciences

country: Austria

institute: ARC Seibersdorf research GmbH

manufacture_protocol: cDNA microarrays are printed on CMT-GAPS slides (Corning Inc.) using high precision robotics. Contains 19008 characterized and unknown human ESTs.


title: Adelaide Microarray Facility CompuGen OligoLibrary Mouse 22k Layout v2.1

first: Christopher

description: 4x16 print groups, 24rows x 20 cols per print-tip group. Platform contains single copy of the CompuGen Mouse OligoLibrary v2.0 (IDs start with CGEN), plus a in house produced control plate (IDs start with AMC). This spotting layout is version 2.1. The last few columns of this description also contain positions of a given spot in the previous layout. this was unique for the CompuGen library, but not for all control spots. The control plate spotted twice in version 1 layout (last 16 rows of col 1 in each block), but only once in this layout, (in the last 8 rows of col 1 in each block)).


title: MCW Rattus norvegicus 2K Array Time Course 2002

city: Milwaukee

first: Mingyu

last: Liang

state: WI

address: 8701 Watertown Plank Rd.

department: Physiology

institute: Medical College of Wisconsin

organism: Rattus norvegicus

first: Baozhi

last: Yuan

first: Elizabeth

last: Rute

first: Andrew

last: Greene

first: Ai-Ping

last: Zou

first: Paulo

last: Soares

first: Gregory

last: McQuestion

first: Glenn

last: Slocum

first: Howard

last: Jacob

first: Allen

middle: W

last: Cowley Jr.

manufacture_protocol:
The custom microarrays were manufactured by the Department of Physiology at the Medical College of Wisconsin.

Total RNA was isolated from the renal medulla using the TRIzol reagent (Invitrogen/Life Technologies, Carlsbad, CA). Total RNA of 50 µg was reverse-transcribed to cDNA in a reaction primed by 2 µg of oligo-(dT)12–18. The reverse transcription reaction contained 1x RT buffer (Invitrogen/Life Technologies), 2.5 mM MgCl2, 10 mM dithiothreitol, 500 µM each of dATP, dGTP, and dCTP, 40 µM dTTP, 40 µM of either Cy3-dUTP or Cy5-dUTP (Amersham Pharmacia, Piscataway, NJ), and 7.5 U/µl SuperScript II RT enzyme (Invitrogen/Life Technologies) in a total volume of 20 µl. The reaction was performed at 39°C for 2 h with an additional 75 U of SuperScript II RT enzyme added at the middle of the reaction. After RNase H digestion, the cDNA products that had been labeled with either the Cy3 or Cy5 fluorescent dye were purified using Centri-Sep spin columns (Princeton Separations, Adelphia, NJ) and QIAquick purification columns (Qiagen, Valencia, CA). Labeled cDNAs were then concentrated using Microcon YM-30 filters (Millipore, Bedford, MA) and hybridized to a microarray at 65°C for 16 h in a hybridization solution containing mouse Cot-1 DNA, 1 µg/µl poly-dA, 1.14 µg/µl yeast tRNA, 3.4x SSC, and 0.3% SDS. Slides were washed and scanned using the ScanArray 5000 [Packard Bioscience (formerly GSI Lumonix), Meriden, CT] to quantify the fluorescent intensity of Cy3 and Cy5 in each spot. Renal medullary gene expression profiles were examined in four comparisons: SSBN13 rats on the low-salt diet compared with SS/Mcw rats on the low-salt diet; SS/Mcw rats on the high-salt diet compared with SS/Mcw rats on the low-salt diet; SSBN13 rats on the high-salt diet compared with SSBN13 rats on the low-salt diet; and SSBN13 rats on the high-salt diet compared with SS/Mcw rats on the high-salt diet. For any two samples (rats) involved in a comparison, one was labeled with Cy3 and the other was labeled with Cy5. The two samples were pooled after labeling and hybridized to a microarray. To control for dye variations, these two samples were labeled again with Cy3 and Cy5 switched between the two samples and hybridized to a second microarray. Thus 4 groups of rats with 3 rats in each group were studied, and 2 hybridizations were performed for each pair of rats, resulting in a total of 24 microarray hybridizations.
Custom-made cDNA microarrays containing cDNA probes that represented  80% of all currently known rat genes were used in the present study. The majority of these genes have some known biological functions in rats.  cDNA probes for 1,751 genes were printed on this array.
The experiment was done at 0 and 2-week time points.  For detailes, please refer to the following papers: Physiol Genomics. 2003 Feb 6;12(3):229-37 and Physiol Genomics. 2002 Feb 28;8(2):139-49


title: MCW Rattus norvegicus 2K Array Time Course 2003

first: Michael

last: Olivier

manufacture_protocol:
The custom microarrays were manufactured by the Department of Physiology at the Medical College of Wisconsin.

Total RNA was isolated from the renal medulla using the TRIzol reagent (Invitrogen/Life Technologies, Carlsbad, CA). Total RNA of 50 µg was reverse-transcribed to cDNA in a reaction primed by 2 µg of oligo-(dT)12–18. The reverse transcription reaction contained 1x RT buffer (Invitrogen/Life Technologies), 2.5 mM MgCl2, 10 mM dithiothreitol, 500 µM each of dATP, dGTP, and dCTP, 40 µM dTTP, 40 µM of either Cy3-dUTP or Cy5-dUTP (Amersham Pharmacia, Piscataway, NJ), and 7.5 U/µl SuperScript II RT enzyme (Invitrogen/Life Technologies) in a total volume of 20 µl. The reaction was performed at 39°C for 2 h with an additional 75 U of SuperScript II RT enzyme added at the middle of the reaction. After RNase H digestion, the cDNA products that had been labeled with either the Cy3 or Cy5 fluorescent dye were purified using Centri-Sep spin columns (Princeton Separations, Adelphia, NJ) and QIAquick purification columns (Qiagen, Valencia, CA). Labeled cDNAs were then concentrated using Microcon YM-30 filters (Millipore, Bedford, MA) and hybridized to a microarray at 65°C for 16 h in a hybridization solution containing mouse Cot-1 DNA, 1 µg/µl poly-dA, 1.14 µg/µl yeast tRNA, 3.4x SSC, and 0.3% SDS. Slides were washed and scanned using the ScanArray 5000 [Packard Bioscience (formerly GSI Lumonix), Meriden, CT] to quantify the fluorescent intensity of Cy3 and Cy5 in each spot. Renal medullary gene expression profiles were examined in four comparisons: SSBN13 rats on the low-salt diet compared with SS/Mcw rats on the low-salt diet; SS/Mcw rats on the high-salt diet compared with SS/Mcw rats on the low-salt diet; SSBN13 rats on the high-salt diet compared with SSBN13 rats on the low-salt diet; and SSBN13 rats on the high-salt diet compared with SS/Mcw rats on the high-salt diet. For any two samples (rats) involved in a comparison, one was labeled with Cy3 and the other was labeled with Cy5. The two samples were pooled after labeling and hybridized to a microarray. To control for dye variations, these two samples were labeled again with Cy3 and Cy5 switched between the two samples and hybridized to a second microarray. Thus 4 groups of rats with 3 rats in each group were studied, and 2 hybridizations were performed for each pair of rats, resulting in a total of 24 microarray hybridizations.

Custom-made cDNA microarrays containing cDNA probes that represented  80% of all currently known rat genes were used in the present study. The majority of these genes have some known biological functions in rats. These microarrays were constructed as we described previously with the following modifications. cDNA probes for 1,871 genes, instead of 1,751 genes, were printed on this array, which included 1,687 clones purchased from Research Genetics (Huntsville, AL), and 184 genes cloned in our department or purchased from ATCC (Manassas, VA).

The experiment was done at three time points: overnight 16 hours, 3 days and 14 days.  For detailes, please refer to the following papers: Physiol Genomics. 2003 Feb 6;12(3):229-37 and Physiol Genomics. 2002 Feb 28;8(2):139-49


title: 16S and 23S rRNA CodeLink Microarray

city: Louvain-la-Neuve

first: Laurent

last: Eyers

address: Place Croix du Sud 2/19

department: Unit of bioengineering

country: Belgium

institute: Catholic University of Louvain

organism: unidentified

description: Probes targeting the 16S and 23S rRNA of various microorganisms (mainly Bacteria).

manufacturer: University of Washington, Seattle, Civil and Environmental Engineering

first: James

last: Smoot

first: Laura

middle: M

first: Céline

last: Bugli

first: Hidetoshi

last: Urakawa

first: Zack

last: McMurry

first: Slil

last: Siripong

first: Said

last: El Fantroussi

first: Philippe

last: Lambert

first: Spyros

middle: N

last: Agathos

first: David

last: Stahl

manufacture_protocol: The CodeLink microarray contained oligonucleotide probes deposited on CodeLink slides of uniformly coated hydrophilic polymer containing amine-reactive groups (Amersham Biosciences, Buckinghamshire, UK). Oligonucleotide probes were manufactured by Argonne National Laboratory and Qiagen, Inc., and approximately 6 fmol of each probe was printed in duplicate with a SpotBot arrayer (Telechem International). Probes were covalently attached to the slide via a 3' C7 primary amine linker. Probe attachment, slide hydration, and blocking were done as described by the slide manufacturer's instructions. The design of oligonucleotide probes targeting rRNA molecules was done as described previously (El Fantroussi et al. 2003, Appl. Environ. Microbiol. 69:2377-2382). CodeLink microarrays contained 83 different perfect match oligonucleotide probes (13-25 nucleotides in length) that were complementary to universal, domain, species, and phylogenetic group specific rRNA sequences.


title: SuperArray GEArray Q Series Mouse NFkB Signaling Pathway Gene Array

status: Public on Apr 09 2004

city: Frederick

first: SuperArray

last: Bioscience Corporation

state: MD

address: Suite 101, 7320 Executive Way

institute: Technical Support

description:
Each GEArray Q Series Mouse NFkB Signaling Pathway Gene Array contains 96 genes related to NFkB mediated signal transduction. The NFkB transcription factors are implicated in the regulation of viral replication, autoimmune diseases, inflammatory responses, tumorigenesis and apoptosis. In a simple side-by-side hybridization experiment, using your RNA samples and the GEArray Q Series Mouse NFkB Signaling Pathway Gene Array kit, you can characterize the expression profile of Rel / NFkB / IkB family genes, genes responsive to NFkB signaling, and other genes involved in the NFkB signal transduction pathway.
Catalog number MM-016 (Superarray, Frederick, MD)
Platform_weblink: http://www.superarray.com/home.php


title: INSERM Homo sapiens 14K array_Liverpool2

first: Jean

last: SALIER

first: Cedric

last: Coulouarn

first: Gregory

last: Lefebvre

last: Derambure

first: Thierry

last: Lequerré

first: Maryvonne

last: Daveau

first: Jean-Philippe

last: Salier

manufacture_protocol: Liverpool2 is a spotted cDNA array for approximately 10,000 nonredundant genes expressed in embryonic, adult, and/or cancerous liver.


title: UMAS:MboI/FokI:Saccharomyces cerevisiae

status: Public on Mar 12 2004

city: New Haven

first: Kevin

last: McConnell

state: CT

address: 2 Church Street South, Suite 401

institute: Agilix Corporation

technology: other

description:
This is a virtual platform for UMAS libraries generated for Saccharomyces cerevisiae using MboI/FokI as an anchor enzyme.
Platform_anchor: MboI/FokI