title: Eurogentec S. pombe ORF array (A260E)

status: Public on Mar 19 2007

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

organism: Schizosaccharomyces pombe

technology: spotted DNA/cDNA

distribution: custom-commercial

first: Tony

last: Wright

first: D

last: Talibi

first: S

middle: A

last: Hass

manufacture_protocol:
Primary PCR: The PCR reactions are performed using tagged genome specific primers in the presence of genomic DNA (provided by your laboratory). We normally achieve a success rate of 93 % of PCR reactions. For the failed PCR reactions we perform three different protocols of PCR conditions, which include different MgCl2 concentrations and different Taq polymerase. We should normally get an additional 2 % working and reach a success rate of 95 % in total. We check 5 % of the total oligos by Mass Spectrometry and will re-synthesize maximum 2 % of the oligos based on a newly designed primer. We will perform the PCR reactions with the new designed oligonucleotides with the standard PCR protocol. Following this process we reach usually 97 % success rate.
Secondary PCR: amplifications will be performed using a single pair of primers annealing to tag sequences introduced on primary PCR primers. These PCR amplifications will also be controlled by agarose gel electrophoresis and repeated if required reaching a minimum of 95 % success rate. The final PCR products will contain an amino group at their 5' end to promote the attachment of the predicted gene coding DNA strand to the treated glass slides.


title: FL002 - INDAC Drosophila melanogaster 14.5K long oligo array

status: Public on Mar 23 2007

city: Cambridge

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

organism: Drosophila melanogaster

technology: spotted oligonucleotide

description: Array mapping available at the FlyChip_long_oligonucleotide_002 (FL002) - INDAC page at the Flychip website

distribution: non-commercial

first: Steven

first: Lisa

last: Meadows

first: Richard

middle: P

last: Auburn

first: Bettina

last: Fischer

first: Gos

last: Micklem

first: Roslin

middle: R

first: Debashis

last: Rana

first: Santiago

middle: S

last: Matila

first: Peter

last: Sykacek

first: David

last: Kreil

manufacture_protocol: FL002 microarrays were printed using the Genetix Qarray2 contact-printing instrument and 48 Genetix aQu75 split-pins on FMB PowerMatrix slides. Probe DNA was dissolved in 150 mM NaPO4. Full details on Flychip website


title: PIQOR Immunology Microarray, Mouse CTID580

status: Public on Mar 31 2007

city: Cologne

first: Sebastian

last: Knoebel

address: Nattermannallee 1

country: Germany

institute: MiltenyiBiotec GmbH

organism: Mus musculus

description: The PIQOR Immunology Microarray is composed of 1076 mouse specific cDNAs. These cDNAs include for each array six house-keeping genes as positive controls. In addition four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer. Genes are spotted in quadruplicates.

distribution: commercial

first: B.

last: Gerstmayer

first: A.

last: Bosio

manufacture_protocol: Defined 200-400 bp fragments of selected cDNAs were generated by RT-PCR, cloned and sequence-verified. Amplified and purified cDNA inserts were spotted in quadruplicate on PIQOR slides using a proprietary piezoelectric spotter. The PIQOR slides were coated in a 2 step process generating a surface which covalently binds DNA molecules.


title: PIQORTM Immunology Microarray, human S (679)

city: COLOGNE

first: Frank

last: Huebel

state: NRW

address: Stoeckheimer Weg 1

department: MACS Molecular 9

institute: Miltenyi Biotec GmbH, MACS Molecular Business Unit

organism: Homo sapiens

description:
The PIQOR Immunology Microarray is composed of 1076 mouse specific cDNAs. These cDNAs include for each array six house-keeping genes as positive controls. In addition four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer, respectively. All features are spotted in quadruplicate.

The Platform data table reflects a condensed representation of the quadruplicate features.

first: Bernhard

first: Andreas


title: Human Transporter OligoChip

status: Public on May 08 2004

city: Epalinges

first: Pascale

last: Anderle

country: Switzerland

institute: ISREC

description:
Custom array chip focusing on transporters and ion channels.
Genes are represented by 70 mers.

first: Vera

last: Rakhmanova

first: Katie

last: Woodford

first: Noa

last: Zerangue

first: Wolfgang

last: Sadee


title: Codelink Mouse Whole genome array platform for TAMU CERH genomics core

city: Houston

first: Ankang

last: Li

state: TX

address: 2121 West Holcombe

department: CMDD

country: USA

institute: IBT

description: It is the same Chip as Platform GPL2897 describes. However, since the index numbers used in the result file provided by the TAMU CERH core are different from standard ID unumbers, this platform file must be used to deposit the result from this core service.


title: XC003 genome tiling array

status: Public on Mar 28 2007

first: Steve

last: Russell

first: Steven

first: Lisa

last: Meadows

first: Richard

last: Auburn

first: Bettina

first: Robert

last: White

manufacture_protocol:
Robotic spotting PCR products on FMB-cDNA slides.
Approx 3Mb of the Drosophila genome, including:
Adh region
Bithorax Complex
Antennapedia Complex
Achaete-Scute Complex
Spotting and production as described at http://www.flychip.org.uk/
Design based on arrays deposited as GEO GPL1918 and GPL3689


title: Eurogentec S. pombe ORF array (I040F)

first: Karl

last: Ekwall

first: Tony

last: Wright

first: D

last: Talibi

first: S

last: Haas


title: Danio rerio Exeter 16K V1

status: Public on Mar 22 2007

city: Exeter

first: Eduarda

middle: M

last: Santos

state: Devon

address: Prince of Wales Road

department: School of Biosciences

institute: University of Exeter

organism: Danio rerio

description: This set includes 16513 oligonucleotides, 65-70 mers, designed by Compugen based on representative Danio rerio ESTs, Compugen XEBLIB384, supplemented with custom oligonucleotides, 65-70mer, 180 representing conserved regions of putative reproductive genes and 234 genes associated with metal trafficking.

first: Peter

last: Kille

first: Victoria

last: Workman

first: Charles

last: Tyler

manufacture_protocol: Printed with SpotArray72, Perkin Elmer, with 48 SMP3 Telecam Pins and cross linked using 75% humidity overnight


title: PIQORTM Immunology Microarray, human S (616)

status: Public on Mar 21 2007

first: Frank

last: Huebel

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio


title: Eurogentec S. pombe ORF array (B130F)

first: T


title: UHN-Toronto 19K single spotted Human EST microarray v7

status: Public on Mar 02 2007

city: Navi Mumbai

first: Chandan

last: Kumar

state: Maharashtra

address: Kharghar Node

department: ACTREC

country: India

institute: Tata Memorial Center

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: CSHL S. pombe Genomic Tiling Microarray

city: Austin

first: Matthew

middle: Wayne

last: Vaughn

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

institute: University of Texas at Austin

organism: Schizosaccharomyces pombe 972h-

technology: in situ oligonucleotide

description: S. pombe genomic tiling microarray using using NimbleGen custom platform (DesignID=2005-04-18_Spombe_ChIP). The array is based on the 02-SEP-2004 version of the genome first described by Wood et al (2002).

middle: W

first: Derek

middle: B

last: Goto

first: Mikel

last: Zaratiegui

last: Martienssen


title: Kluyveromyces lactis metabolism micro-array

city: thiverval-grignon

first: serge

last: casaregola

address: 1 rue de la bretignieres

country: France

institute: INRA

organism: Kluyveromyces lactis

first: Audrey

last: Suleau

first: Serge

last: Casaregola

manufacture_protocol:
Spotting on glass slides was performed at the Biochips platform, INSA, Toulouse, France
http://biopuce.insa-toulouse.fr
Primers were designed using the ROSO software
http://pbil.univ-lyon1.fr/roso/Home.php
Primers were synthetized by Eurogentec
http://www.eurogentec.be/
The construction is described in:
Suleau et al (2005) Intraspecific gene expression variability in the yeast Kluyveromyces lactis revealed by micro-array analysis. FEMS Yeast Res.5, 595-604.


title: MVGE_TRI_RUB1

status: Public on Mar 27 2007

city: Beijing

first: Qi

last: Jin

address: Rongjing East Road 6#

country: China

institute: State Key Lab of Virus Gene Engineering

organism: Trichophyton rubrum

description: In this chip there were two fields named A and B, they described the upper and lower part(location) of the chip.Each field contains 11,232 spots.The spots in field A are same with those in field B.

manufacturer: State Key Laboratory For Molecular Virology and Genetics Engineering，Beijing

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


title: mwg-10k-6

status: Public on Mar 14 2007

city: Ciudad de Buenos Aires

first: Mariano

middle: Cesar

last: Salibe

address: Av. Patricias Argentinas 435

country: Argentina

institute: Gentron LLC

middle: C

middle: J

last: Alvarez

first: Cintia

middle: G

last: Serra

first: Daniela

last: Celi

first: Guillermo

last: Vila-Ortiz

first: Alejandra

last: Ramirez

first: Osvaldo

middle: L

last: Podhajcer

first: Fernando

last: Pitossi

manufacture_protocol: 50 mer mouse 10K oligo-set (MWG, Germany) were resuspended in 15 ul of DMSO 50% (Stock solution plates). 5 ul from each oligo of the stock solution were transferred to a 384 well plate (Whatman Inc) (Working solution plates). Oligos in the working solution plates were printed onto UltraGap Slides (Corning) using a Versarray chipwriter (Bio-Rad) with Stealth Micro Spotting quill pins (Telechem). Humidity was set at 45%, and temperature was 22-25°C. Pins were loaded in the working plate during 0.5 sec. Distance between spots was 292 um, Dwell time for printing was 0.05 sec, each oligo was spotted one time per slide. After the pins were loaded in the working plate and before printing the slides, a blotting slide was printed 5 times in order to discard the excess of oligo on the pins. After printing on slides, and before loading a new oligo, pins were washed with 3 cycles of 5 sec. wash with water, followed by 1 sec vacuum, the last vacuum time was 10 sec. After printing was completed, oligos were UV crosslinked to the slides on a CL-1000 UV crosslinker (UVP). Printed slides were stored in a dissecator


title: TIGR Staphylococcus aureus version 1 array

city: Aas

first: Solveig

last: Langsrud

address: Osloveien 1

country: Norway

institute: Matforsk, Norwegian Food Research Institute

organism: Staphylococcus aureus

description: Microarrays were constructed by The Institute for Genomic Research, Rockville, MD. They are amplicon based arrays containing all ORF's from Staphylococcus aureus COL (genbank ID CP000046), and selected ORF's from Staphylococcus aureus MW2 (genbank ID BA000033), N315 (Genbank ID BA000018) and Mu50 (Genbank ID BA000017). All genes are spotted in triplicate, including control spots (40 amplicons and 500 70-mers from A. thaliana).

manufacture_protocol: Microarrays were constructed by The Institue for Genomic Research, Rockville, MD. They are amplicon based arrays containing all ORF's from Staphylococcus aureus COL (genbank ID CP000046), and selected ORF's from Staphylococcus aureus MW2 (genbank ID BA000033), N315 (Genbank ID BA000018) and Mu50 (Genbank ID BA000017). All genes are spotted in triplicate, including control spots (40 amplicons and 500 70-mers from A. thaliana).


title: NimbleGen custom-made Bacteroides fragilis NCTC9343 array

city: Greenville

first: Charles

middle: Jeffrey

last: Smith

state: NC

address: 600 Moye Blvd.

department: Microbiology & Immunology

institute: East Carolina University

organism: Bacteroides fragilis NCTC 9343

manufacture_protocol:
Bacteroides fragilis NCTC9343 sequence using annotation supplied to us by EBI through the client.
Each probe replicated 2x on chip.
Selected 18 probe-pairs per target for 5165 target genes.  This included probe pairs for putative "small" RNAs and ribosomal RNAs that will not be published.
probes were 24 mer
This means, 18 perfect match 24mers paired with 18 24mers containing two mismatches.


title: Eurogentec S. pombe ORF array (C270F)

status: Public on Mar 18 2007

first: Karl

last: Ekwall

first: Tony

last: Wright

first: Driss

last: Talibi

first: Stefan

last: Haas


title: Galbraith Lab Maize Master Unigene Microarray

status: Public on Mar 16 2007

city: Wilmington

first: Ann

last: Stapleton

address: 601 S. College

department: Biological Sciences

institute: University of North Carolina Wilmington

organism: Zea mays

first: Carletha

last: Blanding

first: Susan

last: Simmons

first: Paula

last: Casati

first: Virginia

last: Walbot

middle: E


title: PIQOR Immunology Microarray, Mouse CTID619

first: Sebastian

last: Knoebel

first: B.

last: Gerstmayer

first: A.

last: Bosio


title: PIQORTM Immunology Microarray, human S (626)

first: Frank

last: Huebel

first: Bernhard

first: Andreas


title: mwg-10k-3

first: Mariano

last: Salibe

last: Alvarez

first: Cintia

last: Serra

first: Daniela

last: Celi

first: Guillermo

last: Vila-Ortiz

first: Alejandra

last: Ramirez

first: Osvaldo

last: Podhajcer

first: Fernando


title: mwg-10k-7

last: Pitossi


title: Populus 4.6K cDNA macroarray

status: Public on Mar 15 2007

city: Champenoux

first: Sebastien

last: Duplessis

address: INRA Centre Grand Est - Nancy

department: UMR 1136 IAM

organism: Populus trichocarpa x Populus deltoides

description: A total of 4608 features were spotted on 70 cm2 Nylon filters in 384 blocks (24 horizontal x 16 vertical, corresponding to the 384-wells plates). Within blocks of 4x4 mm, cDNA from plates 1 to 12 were respectively spotted at positions 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21 and 23 of a 5x5 grid (5 horizontal x 5 vertical). These positions are given in the 'XDotsReader ID' column of platform file. The XDotsReader ID also provide block position: vertical position, A to P; horizontal position, 1 to 24.

first: Annegret

last: Kohler

first: Francis

last: Martin

first: Sébastien

manufacture_protocol: cDNA were amplified by PCR, purified on appropriate columns, and then prepared in 12 384-wells plates including some control spots (i.e. vectors used for cDNA cloning, external control cDNA, empty positions). Spotting was processed in denaturing conditions to array single stranded cDNA molecules. Arraying was processed by Eurogentec Array Service (Sarraing, BE) in 2003 with a BioGrid arrayer (384 pins) following manufacturer protocol.


title: Carnegie Xenopus laevis 22k Micorarray v2

status: Public on Jul 08 2006

city: Bethesda

first: Biswajit

last: Das

state: MD

address: 18 Library Drive, Building 18T, Room 106

department: Laboratory of Gene Regulation and Development

institute: National Institutes of Health/National Institute of Child Health and Human Development

organism: Xenopus laevis

manufacture_protocol: see manufacturer's web site


title: mwg-10k-2


title: Human 10K-Wellcome Trust Sanger Institute

city: Oxford

first: Jiangting

last: Hu

address: Headley Way

department: NDCLS

institute: University of Oxford

manufacturer: The Wellcome Trust Sanger Institute Microarray Facility

manufacture_protocol: 10K cDNA microarray manufactured at the Microarray Facility, The Wellcome Trust Sanger Institute, Cambridge, UK


title: mwg-10k-1


title: Bacillus subtilis 168 spotted oligo array2

city: Zeist

first: Bart

last: Keijser

address: Utrechtseweg 48

country: Netherlands

institute: TNO

organism: Bacillus subtilis subsp. subtilis str. 168

description: GAPS II Corning

manufacturer: Microarray department (MAD) Amsterdam, www.microarray,nl

first: Alex

last: Ter Beek

first: Han

last: Rauwerda

last: Schuren

first: Roy

last: Montijn

first: Hans

last: van der Spek

first: Stanley

last: Brul

manufacture_protocol:
Please note, the original microarray outline can be found in the attached file. This outline was to accomodate sample values based on the average vlaues of 4 technical replica's (library was spotted in duplicate and sample was hybridized in duplicate as well).
The B.subtilus oligonucleotide libraries (Cat # BACLIB384) were obtained from Sigma-Compugen Incorporated. Technical support was supplied by LabOnWeb (http://www.labonweb.com/cgi-bin/chips/full_loader.cgi). The libraries represent in total 4128 oligos, which represent 4106 B subtilus genes, 10 controls from E.coli and the Brome mosaic virus and 12 random oligos LEADS™ clusters plus 231 controls. The oligonucelotide library was printed with a Lucidea Spotter (Amersham Pharmacia Biosciences, Piscataway, NJ, USA) on commercial UltraGAPS slides (amino-silane-coated slides, Corning 40017) and processed according to the manufacturer’s instructions.


title: Eurogentec S. pombe IGR & ORF array (I040F)

status: Public on Mar 12 2007

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

institute: Karolinska Inst

first: Michael

last: Opel

first: David

last: Lando

first: Carolina

last: Bonilla

first: Sarah

last: C. Trewick

first: Abdelhalim

last: Boukaba

first: Julian

last: Walfridsson

first: James

last: Cauwood

first: Petra

last: J.H. Werler

first: Natasha

last: Murzina

first: Antony

last: M. Carr

first: Tony

last: Kouzarides

first: Robin

last: C. Allshire

first: Enerst

last: D. Laue

manufacture_protocol: Primary PCR: The PCR reactions are performed using tagged genome specific primers in the presence of genomic DNA (provided by your laboratory). We normally achieve a success rate of 93 % of PCR reactions. For the failed PCR reactions we perform three different protocols of PCR conditions, which include different MgCl2 concentrations and different Taq polymerase. We should normally get an additional 2 % working and reach a success rate of 95 % in total. We check 5 % of the total oligos by Mass Spectrometry and will re-synthesize maximum 2 % of the oligos based on a newly designed primer. We will perform the PCR reactions with the new designed oligonucleotides with the standard PCR protocol. Following this process we reach usually 97 % success rate.


title: D. melanogaster detoxification array

status: Public on Mar 20 2007

city: Parkville

first: Lee

last: Willoughby

state: Victoria

address: 30 Flemington Road

department: Genetics

country: Australia

institute: University of Melbourne

description: The Drosophila melanogaster "detox" microarray contained the cytochrome P450, glutathione-S-transferase and esterase gene families and also incorporated both individual control genes and control dilutions, to account for the large number of "detox" genes that could have potentially been differentially regulated in response to different treatments.

first: Charles

last: Robin

first: Philip

last: Batterham

manufacture_protocol:
Fragments of the Drosophila melanogaster P450, GST, esterase and additional control genes were amplified by PCR and cloned into plasmid vectors.  DNA fragments for printing were amplified from the plasmid inserts using universal primers, which were then purified before spotting.
Three additional series of control spots were included.
  (A) Lucidea Universal Scorecard (Amersham) was included.
  (B) Digested - Drosophila melanogaster LD EST library (BDGP) was excised and digested with BglII and HindIII.  This was then serially diluted to generate a dilution series.
  (C) Pooled - PCR products from the ribosomal control genes were pooled and this was then serially diluted to generate a dilution series.
Each glass slide contained four microarrays, allowing dye swap hybridisations to be performed in the same hybridisation chamber.  Each unique feature (not the control dilution series) was duplicated four times in a four printing block arrangement.  The microarrays were printed on Corning GAPS II slides (Corning), using a Virtek SDDC2 microarrayer (Virtek Vision International Inc.).


title: Sanger Homo sapiens 4K CGH (CGH_SANGER_4K_1)

status: Public on Mar 09 2007

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: The array contains 4066 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. 3529 BACS are from the Sanger institute. 479 BACS are from the Human 32K BAC rearray of CHORI BACPAC resources. A third group of 58 BACs are from the Center for Human Genetics, University Hospital Gasthuisberg, Leuven, Belgium.  The bacs were amplified by DOP - PCR. In total the array design contains 8736 features printed in a layout of 12 meta rows, 4 meta columns, 13 rows per block and 14 columns per block.

first: Paul

last: Van Hummelen

first: Joris

last: Vermeesch

manufacture_protocol:
MicroGrid Printing Protocol
Equipment:
1. Microgrid (Genomics Solutions, UK).
2. 384 microtiter plates (X7022, Genetix)
3. 48 MicroSpot quill pins - 10K (cat# BR001489, Genomics Solutions, UK)
4. Codelink slides (cat# 30001100, GE Healthcare).
Printing 1 array of 12x4 blocks on 1 microscope slide:
1. Dissolve PCR products in 250mM Phosphate buffer, 0.00025% sarcosyl at concentrations ranging between 300 and 600 ng/ul and array in 384 microtiter plates.
2. Set spotter settings for 1 array of 12x4 blocks printed with 48 pins: column pitch = 320 um, row pitch = 320 um; Humidity 55%; 120 spots per source visit.
3. Make sure room temperature is between 20-24 degrees Celsius.
4. Place microtiter plates in the plate hotel with A1 in front left corner.
5. Place 60 to 120 slides on the slide-deck.
6. Start spotting early in the morning and stop spotting procedure at end of the day and remove pin set. Leave spotter overnight with vaccuum and humidity settings on. Continue spotting the next morning until all plates are printed.
7. After spotting, incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH, 0.1% SDS, H2O.
9. Slides can be stored for at least 6 months in a dry-cabinet.


title: Human BAC array 2-4Mb NoGap

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

institute: Queensland Facility for Advanced Bioinformatics

manufacture_protocol:
Taken directly from the manufacture website:
Spectral Genomics technology enables the manufacture of sensitive, reproducible and robust BAC clone arrays that are easily hybridized and give the right results. These arrays, available only from Spectral Genomics, make use of a patented breakthrough in the chemistry for attachment of DNA to chip substrates. This  (protected by US Patent No. 6,048,695 and foreign equivalents) allows DNA to be chemically modified for optimum adherence.


title: ConwayLab_Ecoli_6041 features_v1

status: Public on Mar 17 2007

city: Norman

first: Joe

last: Grissom

state: OK

address: 101 David L. Boren Blvd

department: Advanced Center for Genome Technology

institute: University of Oklahoma

organism: Escherichia coli

description:
Attachment = UV cross-linked
Strandedness = single
SubstrateType = glass

manufacture_protocol: E. coli oligonucleotide array spotted with Operon E.coli AROS ver 1.0 probe set for all genes from E. coli K-12 (MG1655), E. coli EDL933, and E. coli O157:H7 Sakai


title: mwg-10k-5

first: Mariano

last: Salibe

last: Alvarez

first: Cintia

last: Serra

first: Daniela

last: Celi

first: Guillermo

last: Vila-Ortiz

first: Alejandra

last: Ramirez

first: Osvaldo

last: Podhajcer

first: Fernando

last: Pitossi


title: Staphylococcus_aureus_v4_GRL

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

description: 60-mers oligonucleotide probes, in-situ synthesis on 1

first: Patrice

last: Francois

first: Yvan

last: Charbonnier

first: Antoine

last: Huyghe

first: Jacques

last: Schrenzel

first: Manuela

last: Bento

manufacture_protocol: Sure Print Technology-In situ synthesis


title: MM Burma mangrove 12K oligo array v1.0

status: Public on Mar 10 2007

city: Hachioji

first: Miyama

last: Masashi

state: Tokyo

address: Katakura 1404-1

department: School of Bionics

country: Japan

institute: Tokyo University of Technology

organism: Bruguiera gymnorhiza

first: Masashi

last: Miyama

first: Nobutaka

last: Hanagata

first: Yuichi

last: Tada

manufacture_protocol: 35-40mer Oligos are syntehsized


title: mwg-10k-1b

first: Mariano

last: Salibe

last: Alvarez


title: Pain microarray

status: Public on Mar 03 2007

city: Baltimore

first: Svetlana

middle: I

last: Novikova

address: 666 W. Baltimore st

department: Biomedical Sciences

institute: University of Maryland

organism: Rattus norvegicus

description:
Individual genes were spotted in triplicate on a standard microscope slide.  The Platform data table reflects a condensed representation of the triplicate features.
The full array layout file (GPL4733_full_layout.txt) is linked as a supplementary file to the Platform record.

first: Michael

last: Lidow

manufacture_protocol: 60-mer oligonucleotides were custom-designed TeleChem Int. Inc.


title: Riken Thermus thermophilus HB8 4K mRNA array

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

institute: RIKEN Harima Institute

organism: Thermus thermophilus HB8

first: Noriko

last: Nakagawa

first: Mariko

last: Hatakeyama

first: Ryoji

last: Masui

first: Akihiko

last: Konagaya

first: Shigeyuki

last: Yokoyama

first: Seiki

last: Kuramitsu

manufacture_protocol: Affymetrix custom array standard protocol.  Please see http://www.affymetrix.com for more information.


title: Pain microarray 3

description:
Individual genes were spotted in triplicate on a standard microscope slide.  The Platform data table reflects a condensed representation of the triplicate features.
The full array layout file (GPL4918_full_layout.txt) is linked as a supplementary file to the Platform record.

manufacture_protocol: 60-mer oligos spotted on glass slide


title: Eurogentec S. pombe IGR & ORF array (A260E)

first: Karl

last: Ekwall

organism: Schizosaccharomyces pombe

first: Micahel

last: Opel

first: David

last: Lando

first: Carolina

last: Bonilla

first: Sarah

last: C. Trewick

first: Abdelhalim

last: Boukaba

first: Julian

last: Walfridsson

first: James

last: Cauwood

first: Petra

last: J.H. Werler

first: Natasha

last: Murzina

first: Antony

last: M. Carr

first: Tony

last: Kouzarides

first: Robin

last: C. Allshire

first: Ernest

last: D. Laue


title: SBTM Microarray Laboratory Operon Rat v1.1

status: Public on Feb 23 2007

city: Temple

first: Vincent

last: VanBuren

address: 702 SW HK Dodgen Loop

department: Systems Biology and Translational Medicine

institute: Texas A&M Health Science Center

manufacturer: The SBTM Microarray Laboratory, Systems Biology, 702 SW HK Dodgen Loop, Temple, TX 76504

first: Robert

last: Jamroz

first: Reza

last: Forough

manufacture_protocol: The Array-Ready Rattus norvegicus Genome Oligo Set Version 1.1 from Operon Biotechnologies, Inc. was spotted in duplicate using a GeneMachines OmniGrid Arrayer (Arrayer manual/spotting protocol available at the Genomic Solutions website; complete genelists, annotations, and datasheets for oligos available at the Operon Biotechnologies website). Array descriptions may be found at the SBTM Microarray Laboratory website.


title: CNRS_UMR_7637/EA3508_Human_HSA21_v1

status: Public on Mar 01 2007

city: PARIS

first: Emilie

last: Aït Yahya Graison

address: 2 place jussieu

department: UFR BIOCHIMIE

institute: UNIVERSITE PARIS 7

description: Each array contained 2 matrices with 8 blocks each, in which probes were present in duplicates so that each oligonucleotide was present in four replicates on each slide. Blocks are indexed from 1 to 16 and each is constituted by 13 columns and 16 rows

first: Marie-Claude

last: Potier

first: Jean

last: Delabar

last: Ait Yahya Graison

first: Luce

last: Dauphinot

first: Geoffroy

last: Golfier

manufacture_protocol: 50-mers aminomodified oligonucleotide primers are synthesized by EuroGentec. Spotting is realized on CodeLink® activated glass slides (Amersham Biosciences) using a MicroGrid II spotter (Biorobotics)


title: SpliceExpress Human Spliceome 1.5

status: Public on Jan 17 2007

city: Berkeley

first: Jonathan

last: Bingham

state: CA

address: 733 Allston Way

institute: Jivan Biologics, Inc

first: Subha

last: Srinivasan

first: Adam

last: Siepel

manufacture_protocol: NimbleGen standard in situ synthesis using digital light projection.


title: Compugen 19K Oligo Library Spotted Arrays

status: Public on Feb 14 2007

city: Provo

first: Chin-Yo

last: Lin

state: UT

address: 753 WIDB

department: Microbiology and Molecular Biology

institute: Brigham Young University

manufacture_protocol: In-house printing


title: Edgerton Lab Candida albicans SC5314 6k array_ORF6

status: Public on Mar 05 2007

city: Buffalo

first: Wansheng

last: Li

state: NY

address: 3435 main st.

department: Oral Biology

institute: University at Buffalo

organism: Candida albicans SC5314

manufacturer: a working group funded by the National Institute of Dental and Craniofacial Research.

manufacture_protocol:
C. albicans ORFs were obtained
from assembly 6 of the C. albicans genome sequence
(http://www-sequence.stanford.edu/group/candida). ORFs encoding proteins greater than 150 aa and that started with an ATG codon were
included in the array. ORFs were sorted into two categories: those
that were unique by BLAST comparisons, and those that were likely
to represent a group of closely related genes or a gene family.
Primers to amplify each of the unique ORFs were designed using
PRIMER3 software (http://frodo.wi.mit.edu/primer3/primer3_code.
html). Primers for the gene family ORFs were designed by hand and
checked using the PRIMER3 program. Primers were designed to have
a Tm of approximately 60 uC and to amplify a region of approximately
300 bp. When possible, amplification products were targeted
to the 39 end of the coding region.
Two separate rounds of PCR were conducted with each primer pair
and C. albicans SC5314 genomic DNA as the template. PCR products
from the reactions were combined and checked for quality by
agarose gel electrophoresis. PCR products were purified using the MultiScreen-PCR 96-well filtration system (Millipore), eluted in water,
dried in a SpeedVac (ThermoLabs) and resuspended at approximately
0.1ug/ul in 3X SSC (0.45 M NaCl, 0.045 M sodium
citrate). A total of 6392 DNA samples were spotted onto SuperAmine
Substrate slides (Telechem) at Microarrays Inc. Controls included
Arabidopsis thaliana spot report genes and mammalian DNA
fragments (Stratagene), C. albicans genes of known expression profiles,
and buffer blanks.


title: Human Promoter -800+300 Set, Slide 1 of 2 G2514A Option 002 Agilent-013185

status: Public on Jan 12 2007

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Homo sapiens

description:
Location Analysis Array

Arrays of this design have barcodes that begin with 16013185 or 2513185.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

first: Chris

last: Hopkins

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


title: UHN Yeast 6.4k v2

status: Public on Mar 08 2007

city: Vienna

first: Jochen

last: Stadler

address: Dr. Bohrgasse 9

department: Department of Genetics

country: Austria

institute: MFPL, University of Vienna

organism: Saccharomyces cerevisiae

description: Grid rows-8; Grid columns-4; Rows-20; Columns-20; Spot to spot distance-200um; Spot size-100um.

manufacture_protocol: 1. Acquisition of bacterial clone set — our Yeast 6.4k clone set is derived from Research Genetics Genepairs, Detailed information about the ORFs and sequences can be found at the Saccharomyces Genome Database 2. Clone set is PCR amplified and DNA purified in working 96 well plates. 3. The purified DNA is then transferred to 384 well source plates with DNA concentration ranging from .10ug/ul to 0.25ug/ul. These are used for spotting.


title: Cattle 7,872-element cDNA

status: Public on Aug 10 2005

city: Urbana

first: Harris

last: Lewin

state: IL

address: 1201 West Gregory Drive

department: Animal Sciences

institute: University of Illinois

organism: Bos taurus

description: The 7,872 cDNAs used in this microarray were obtained from normalized and subtracted cattle placenta and spleen cDNA libraries (see Band et al., 2002 Anim. Biotechnol. 13:163-172; Everts et al., 2005 Vet. Immunol. Immunopathol. 105:235-245). Positive controls include beta actin (ACTB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and hypoxanthine phosphoribosyltransferase (HPRT). Exogenous spiking controls are the soybean genes chlorophyll ab binding protein (CAB), Rubisco small chain 1 (RBS1), and major latex protein (MSG). Negative controls are Cot1 DNA, genomic DNA, spotting buffer, poly-A, and water. All PCR products were printed in duplicate on the array.  Keywords: cDNA, cow, liver, bovine, lactation, microarray

first: Robin

last: Everts

first: Mark

last: Band

first: Lewis

middle: Z

last: Liu

first: Charu

last: Kumar

first: Lei

first: Juan

last: Loor

first: Rosane

last: Oliveira


title: Pain microarray 2

first: Svetlana

last: Novikova

description:
Individual genes were spotted in triplicate on a standard microscope slide.  The Platform data table reflects a condensed representation of the triplicate features.
The full array layout file (GPL4917_full_layout.txt) is linked as a supplementary file to the Platform record.

first: Michael

last: Lidow


title: SAGE:10:NlaIII:Brassica napus

status: Public on Mar 02 2007

last: GEO

organism: Brassica napus

technology: SAGE NlaIII

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

distribution: virtual


title: WUCGS Candida albicans 6K v1.0

city: Santa Barbara

first: Jessica

last: Sexton

address: UCSB/MCDB

institute: UCSB

organism: Candida albicans

manufacturer: Washington University Genome Sequencing Center Microarray Core Facility

middle: A

first: Victoria

last: Brown

last: Johnston

manufacture_protocol: 70mer oligonucleotides representing 6,346 of the 6,354 predicted ORFs in the annotated C. albicans genome assembly 19 were designed using an ArrayOligoSelector and were manufactured by and obtained from Illumina (San Diego, CA).  One genome equivalent of each ORF was spotted three times per slide (i.e., n = 3 for each hybridization).


title: TAGC_H.Sapiens_9K_20041223

city: angers

first: Jean-Fred

last: Fontaine

address: 4 rue Larrey

institute: INSERM

first: Frédérique

last: Savagner

first: Délphine

last: Mirebeau-Prunier

first: Patrice

last: Rodien

first: Brigitte

last: Franc

first: Rémi

last: Houlgatte

first: Yves

last: Malthièry

manufacture_protocol:
Introduction:
Nylon microarrays are a thumbnail version (of glass-slide format) of the classical macro-membranes (1-3), allowing a larger probe density compatible with pan-genomics approaches. These microarrays have been developped by Konan Peck (4). They have the advantage of an easy setup in an academic lab at very low cost, to use classical protocols of Molecular Biology, to be reusable, and to use an universal reference. Moreover, they use smaller amounts of samples without any amplification step (5): typically microarrays can be hybridized with 1 to 5µg of total RNA. Major drawbacks of this technique are a lower density of spots than other microarrays (a maximum of 15,000 spots on a glass-slide) due to indirect scanning of radioactivity, strong spots overshining, and an independent hybridization of the sample and the reference. Typically, a Nylon microarray measurement consist in one hybridization to measure the spotted amount of probes (hybridization using an oligonucleotide complementary of a vector sequence present in all PCR products), and one hybridization with the sample. Final measurement is the ratio sample/spotted amount. This measurement is necessary due to the dependency of the signal to the spotted amount of probe (5-6). One key point of this technique is to spot a large amount of probe to have a good detection (5). Nylon microarrays can also be used with other types of probes such as short or long oligonucleotides (7).
PCR:
Oligonucleotides allowing PCR amplification of clones from various IMAGE (8-9) cDNA libraries have been designed. They allow embedded PCR (LBP1A/AS and LBP2A/AS) and the measurement of spotted amounts using an internal primer (LBP3 or LBP9). It is essential that the oligonucleotide used for spotted amount measurement is not one used for PCR amplification, otherwise primer dimers occurring during PCR amplification should be measured at the same time than specific probes: measurement would be wrong.
Ten microliters of a bacterial suspension in water are added to 90µl of a PCR mix. The amplification is done by:
    * 94°C 6'
    * 40 cycles (94°C 30'', 55°C 40'', 72°C 1')
    * 72°C 10'
One microliter of PCR is deposited on 1% agarose gel. Two hundreds microliters of PCR products are evaporated at 94° in the PCR machine and resuspended in 60µl of water.
PCR product concentration should be between 150 to 300 ng/µl. Precise quantification of PCR products (if necessary) can be done directly from the gel. Methods using double-stranded DNA intercalating agents should be avoided as PCR generates double-stranded dimer of primers that are quantified at the same time. It is not necessary to purify the PCR products. PCR products showing wrong size, 2 bands or week should be discarded.
Spotting :
Precut Nylon membranes (Pall) are fixed on glass-slides in the robot using spray glue (3M). Spotting of PCR products in 384-well plates, is done using GMS417 (Affymetrix) ou BioGrid II (Matrix) robot. Spot to spot distance is 375µm, and each PCR product is spotted 4 times for greater amount spotted. Temperature is maintained at 18°C and humidity at 70% during the spotting process.
After spotting, filters are deposited (spotted side up) onto a blotting paper saturated with denaturation buffer for 2 times 10', and on a blotting paper saturated with neutralization buffer for 2 times 10'. Filters are rapidly rinsed with  2xSSC, dried in an owen at 80°C for 2H, and irradiated with short UV during 1'30''. They can be stored during years.
Oligonucleotide labelling & hybridization:
 One microliter of oligonucleotide (LBP3 or LBP9) at 1µg/µl is added to 24µl of the  oligonucleotide kinase mix. Incubate 10' at 37°C, 10' at 65°C in a waterbath, and purify on a G25 Sephadex column (Centrifuge the column for 2' at 2,500 rpm, load 100µl  of the kination reaction on top the column, centrifuge 4' at 1,000 rpm, keep the eluate), and count radioactivity.
Prehybridize membranes in the hybridization solution containing 100µg/ml heering sperm DNA denaturated (by heating 10' at 100°C and quickly cooled on ice) during  4H (10H maximum) at 42°C. Add 50.000 cpm of the labelled oligonucleotide and hybridize during 10H at 42°C. Wash with the washing solution during 10' at room temperature, and for 5' at 42°C with preheated solution. Quickly rinse filters with 2xSSC, and dry them on blotting paper. Expose dry filters onto a screen in a cassette (Raytest/Fuji) for about  8H. Scan with radioimager (Fuji Bas5000) at 50µm resolution.
Strip membranes in the heated washing solution  at 68°C in a waterbath during 3H, change solution each hour. Check for stripping by an exposure of 8H on an exposure screen. If some signal remains, try to strip the filters a second time.
Many filters can be hybridized and washed together. In this case, use larger volumes.
RNA labelling & hybridization :
  1 to 5 µg of total RNA are added to 8 µg dT25 (to saturate polyA tails), 0,3 ng spike RNA, and 13 µl of water. Incubate for 8’ at 70°C in a waterbath. Put in a dry block heater containing water at 70°C, and put the block in an owen at 42°C for 30’. Add 17 µl of labelling mix. Incubate at 42°C for 1H. Add 1µl of reverse transcriptase. Incubate one more hour at 42°C. Successively add 1µl SDS 10%, 1µL EDTA 0.5M, and 3µl NaOH 3M. Incubate 30’ at 68°C, to degrade mRNA. Incubate 15’ at room temperature. Add 10µl of Tris 1M, and 3µl of HCl 2M for neutralization. Add 2µG of dA80 and 2µg Cot1 DNA. Heat 5’ at 100°C, add 300µl of h of hybridisation buffer preheated at 65°C, and incubate for 2H30 at 65°C to saturate polyT tracks and repeats. It is not necessary to purify.
Rinse spotted membranes with 2xSSC. Pre-hybridize with 2ml of hybridisation buffer containing 100µg/ml heering sperm DNA denaturated (by heating 10' at 100°C and quickly cooled on ice) for 6H at 68°C. Remove buffer and replace by the labelled cDNA. Hybridize at 68°C for 24H to 48H in a rotating owen.
Quickly rinse membranes with hybridisation solution pre-heated at 68°C. Wash the membranes with a large volume of washing solution for 3H at 68° (Change solution each hour). Rinse with 2xSSC, and dry on blotting paper. Expose dry filters onto a screen in a cassette (Raytest/Fuji) for about 24H. Scan with radioimager (Fuji Bas5000) at 50µm resolution.
Strip membranes in the heated dehybridation solution  at 85°C in a waterbath during 5H, and quickly rinse with 2xSSC. Control stripping by an exposure of 8H on an exposure screen. If some signal remains, try to strip the filters a second time. If this protocol does not works well, repeat this after a one month delay.
References :
   1. Nguyen C, Rocha D, Granjeaud S, Baldit M, Bernard K, Naquet P, Jordan BR.. Differential gene expression in the murine thymus assayed by quantitative hybridization of arrayed cDNA clones. 1995 Genomics 29: 207–216.
   2. Zhao, N., Hashida, H., Takahashi, N., Misumi, Y. & Sakaki, Y. High-density cDNA filter analysis: a novel approach for large-scale, quantitative analysis of gene expression. 1995 Gene 156: 207–213.
   3. Piétu G, Alibert O, Guichard V, Lamy B, Bois F, Leroy E, Mariage-Samson R, Houlgatte R, Soularue P, Auffray C. Novel gene transcripts preferentially expressed in human muscles revealed by quantitative hybridization of a high density cDNA array. 1996 Genome Research  6: 492-503.
4. Chen JJ, Wu R, Yang PC, Huang JY, Sher YP, Han MH, Kao WC, Lee PJ, Chiu TF, Chang F, Chu YW, Wu CW, Peck K. Profiling expression patterns and isolating differentially expressed genes by cDNA microarray system with colorimetry detection. 1998 Genomics. 51: 313-324.
   5. Bertucci F, Bernard K, Loriod B, Chang YC, Granjeaud S, Birnbaum D, Nguyen C, Peck K, Jordan BR. Sensitivity issues in DNA array-based expression measurements and performance of nylon microarrays for small samples. 1999 Human Molecular Genetics 8: 1715 –1722.
   6. Stillman BA, Tonkinson JL. Expression microarray hybridiza


title: Human Promoter -800+300 Set, Slide 2 of 2 G2514A Option 002 Agilent-013186

last: Agilent Technologies

description:
Location Analysis Array

Arrays of this design have barcodes that begin with 16013186 or 2513186.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

first: Chris

last: Hopkins


title: Swegene Human 27K RAP (positions from file)

city: Lund

first: Johan

last: Staaf

address: Medicon Village

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

first: Ake

last: Borg

manufacture_protocol: Arrays were produced by the Swegene DNA micro array resource center at Lund University by using amplified cDNA targets from Research Genetics clones. Target amplification was performed using PCR and cDNA products were verified by agarose gel electrophoresis and purified by size-exclusion filtration. After purification, cDNA was recovered in water, adjusted to 50% DMSO and printed on amino-silane-coated glass slides (UltraGAPS from Corning) using a MicroGrid2 robot (BioRobotics) equipped with MicroSpot2500 pins (BioRobotics).


title: Pseudomonas syringae pv. tomato str. DC3000 genes

city: manhattan

first: Xiaoyan

last: Tang

email: xtang@ksu.edu, llan@ksu.edu

state: KS

address: 4702 Throckmorton

department: Plant Pathology

institute: Kansas State University

first: Lefu

last: Lan

manufacture_protocol: as described in Nimblegen Labs manual


title: NCI/Staudt human 15K v13

status: Public on Mar 30 2006

city: Bethesda

first: Louis

middle: M.

last: Staudt

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

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

first: Vu

last: Ngo

manufacture_protocol: See reference Alizadeh et al. The lymphochip: a specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes. Cold Spring Harb Symp Quant Biol. 64, 71-8 (1999).