title: TUAT Magnetospirillum magneticum AMB-1 5K whole genome DNA microarray

status: Public on Jan 01 2006

city: Koganei

first: Tadashi

last: Matsunaga

state: Tokyo

department: Biotechnology

country: Japan

institute: Tokyo University of Agriculture and Technology

organism: Paramagnetospirillum magneticum AMB-1

technology: spotted oligonucleotide

distribution: non-commercial

first: Takeyuki

last: SUZUKI

first: Yoshiko

last: OKAMURA

first: Ronie

middle: J

last: CALUGAY

first: Haruko

last: TAKEYAMA

last: MATSUNAGA

manufacture_protocol: Each sequence was determined and synthesized from the 60-mer minimal homology region to other ORF sequences analyzed with BLAST program.  The amino-activated oligonucleotides (40 pmol) were printed onto TaKaRa-Hubble Slide Glass coated with active ester (TaKaRa Bio Inc., Japan) using the Affymetrix 417/427 arrayer (Affymetrix, Santa Clara, CA).  The microarray slides were stored in light shaded desiccators until use.


title: SHFK

status: Public on Jan 27 2006

city: Stanford

first: Markus

last: Bredel

state: CA

country: USA

institute: Stanford University School of Medicine

organism: Homo sapiens

technology: spotted DNA/cDNA

description:
Support: glass
Coating: unknown_surface_type
Manufacturer: Joan,,Hebert; SFGF, 2255, CCSR, Stanford, Ca, USA, 94025; 650-736-0075; jhebert@genome.Stanford.edu
Technology: other


title: UHN Yeast  6.4kv3.48

status: Public on Jan 25 2006

city: Rehovot

first: Naama

last: Barkai

address: P.O box 26

country: Israel

institute: Weizmann Institute

organism: Saccharomyces cerevisiae

description: Grid rows-12; Grid columns-4; Rows-17; Columns-17; Spot to spot distance-200um; Spot size-100um.

manufacturer: University Health Network Clinical Genomics Centre Microarray Centre

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 http://www.yeastgenome.org/  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: UMC Yeast 16k1.2

description: Grid rows-12; Grid columns-4; Rows-18; Columns-18;

manufacturer: University Medical Centre Utrecht, Holstege Laboratory

manufacture_protocol: Glass arrays spotted with oligonucleotides (70 nucleotides in length). Each gene in the yeast genome was represented by two points on the array. In addition the array included 2894 control spots (3xSSC buffer, empty and other external controls).


title: UHN Yeast 6.4kv4

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 http://www.yeastgenome.org/  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: SHFA

description:
Coating : unknown_surface_type
Support : glass
Manufacturer : Joan,,Hebert; SFGF, 2255, CCSR, Stanford, Ca, USA, 94025; 650-736-0075; jhebert@genome.Stanford.edu
Technology : other


title: Affymetrix Schizosaccharomyces pombe 23K Tiling Array

status: Public on Jan 12 2006

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

organism: Schizosaccharomyces pombe

technology: in situ oligonucleotide

description: Affymetrix High-density genome tiling array for S.pombe chromosome 2 and 3 (Left arm). 11X25bp oligo-nucleotide were set for every 250bp in average.

distribution: custom-commercial

first: Y

last: Katou

first: T

last: Itoh

first: J

last: Nakayama

first: K

last: Shirahige

manufacture_protocol: see manufacturer's web site


title: ares_ucsc_mouse_59198_affyMouseA

status: Public on Jan 19 2006

city: Santa Cruz

first: Charles

last: Sugnet

address: Sinsheimer Labs

department: MCD

institute: UC Santa Cruz

organism: Mus musculus

middle: W

first: Manny

last: Ares

manufacture_protocol: Affymetrix Standard Protocol


title: FHCRC chicken 13K

status: Public on Jan 21 2006

city: Ames

first: Susan

last: Lamont

state: IA

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

organism: Gallus gallus

description:
Background
The application of microarray technology to functional genomic analysis in the chicken has been limited by the lack of arrays containing large numbers of genes.

Results
We have produced cDNA arrays using chicken EST collections generated by BBSRC, University of Delaware and the Fred Hutchinson Cancer Research Center. From a total of 363,838 chicken ESTs representing 24 different adult or embryonic tissues, a set of 11,447 non-redundant ESTs were selected and added to an existing collection of clones (4,162) from immune tissues and a chicken bursal cell line (DT40). Quality control analysis indicates there are 13,007 useable features on the array, including 160 control spots. The array provides broad coverage of mRNAs expressed in many tissues; in addition, clones with expression unique to various tissues can be detected.

Conclusions
A chicken multi-tissue cDNA microarray with 13,007 features is now available to academic researchers from genomics@fhcrc.org. Sequence information for all features on the array is in GenBank, and clones can be readily obtained. Targeted users include researchers in comparative and developmental biology, immunology, vaccine and agricultural technology. These arrays will be an important resource for the entire research community using the chicken as a model.

distribution: commercial

first: Joan

last: Burnside

first: Paul

last: Neiman

first: Jianshan

last: Tang

first: Ryan

last: Basom

first: Richard

last: Talbot

first: Mark

last: Aronszajn

first: David

last: Burt

first: Jeff

last: Delrow

manufacture_protocol: BBSRC and UD clones were shipped to the FHCRC core genomics lab. Information on the libraries joined to produce this collection is available at individual web sites and previous publications. Microarrays were constructed using modified protocols of those discussed by De Risi et al. Individual PCR products were verified as unique via gel electrophoresis and purified using the Millipore Multiscreen-PCR filtration system. Purified PCR products were mechanically "spotted" in 3X SSC (1X = 150 mM sodium chloride, 15 mM sodium citrate, pH 7.0) onto poly-lysine coated microscope slides using a GeneMachines OmniGrid high-precision robotic gridder (Genomics Solutions, Ann Arbor, MI). The array layout consists of 32 blocks in a 4 × 8 configuration and each PCR product is represented once on the array. In addition, each array sub-grid (i.e., "block") contains spots representing 4 different Arabidopsis genes (negative controls) and 1 spot consisting of sheared chicken (white leghorn) genomic DNA.


title: Yeast ORF array Bauer Center for Genomics Research Harvard University, Cavalieri Lab

city: Florence

first: Duccio

last: Cavalieri

address: Viale Pieraccini 6

department: Department of Pharmacology

country: Italy

institute: University of Florence

description: The complete set of open reading frames of the S. cerevisiae genome were obtained from Research Genetics (Huntsville, Ala.) and amplified by PCR

manufacturer: Produced and printed at the Bauer Center for Genomics Research, Harvard University

manufacture_protocol: Refer to Townsend, Cavalieri and Hartl 2003


title: UHN Yeast 6.4k1v2

first: Naama

last: Barkai

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


title: NIEHS Human ToxChip v1.0

status: Public on Jan 15 2006

city: DURHAM

first: Cynthia

last: Innes

state: NC

address: 111 ALEXANDER DR

department: NCT

institute: NIEHS

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
cDNA microarray chips were prepared according to DeRisi et al., 1996, Nat. Genet. 14, 457-460. The spotted cDNAs were derived from a collection of sequence-verified clones that covered the 3` end of the gene and ranged in size from 500 to 2000 base pairs (Research Genetics). M13 primers were used to amplify insert cDNAs from purified plasmid DNA in a 100 5l polymerase chain reaction (PCR) mixture. A sample of the PCR products (10 microliters) was separated on 2% agarose gels to ensure quality of the amplifications. The remaining PCR products were purified by ethanol precipitation, resuspended in spotting buffer and spotted onto poly-L-lysine-coated glass slides using a modified, robotic DNA arrayer (Beecher Instruments, Bethesda MD).

first: Emile

last: Nuwaysir

last: Afshari


title: KLA-1

status: Public on Jan 06 2006

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism: Austrofundulus limnaeus

manufacturer: Janos,,Demeter; Dept. Genetics, CCSR 2255, Stanford, CA, USA, 94305; 726-0075; jdemeter@genome.stanford.edu

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


title: UHN Yeast 6.4kv2


title: BFK 20 DNA microarray

status: Public on Jan 13 2006

city: Bratislava 45

first: Tomas

last: Majtan

address: Dubravska cesta 21

department: Department of Molecular Genomics

country: Slovakia

institute: Institute of Molecular Biology SAS

organism: Corynebacterium phage BFK20

first: Jozef

last: Timko

first: Gabriela

last: Bukovska

manufacture_protocol: Probes were PCR amplified using gene-specific primers. Double stranded PCR products were purified using QIAquick PCR Purification Kit (QIAGEN), eluted into the sterile water, quantified spectrophotometrically and lyophilized. Probe DNA was subsequently dissolved in 50 % DMSO as spoting solution in 200 ng/ul. The 12 ul was tranfered into 384-well spoting microplate and spotted in 4 replicates onto GAPS slides (CORNING) using PixSys5500 microarrayer (CARTESIAN TECHNOLOGIES) equipped with CMP4 Micro Spotting pin (TELECHEM INTERNATIONAL). Spoting conditions included 22°C temperature and 47% humidity. Slides were dried overnight and crosslinked by UV irradiation at 250 mJ.


title: Pathogen Chip

city: Bethesda

first: Concepcion

last: Conejero-Goldberg

state: MD

address: 8901 Wisconsin Avenue

institute: Stanley Medical Research Institute

organism: Viruses

description: Synthetic long oligonucleotide probes spotted in duplicate on glass. The platform includes 567 oligonucleotides derived from specific viruses. Viral oligonucleotides were designed based on open reading frames from highly conserved and heterogenic regions within viral families. Viral genes reflecting different stages of infection were also included, to potentially define the stage of viral infection. The platform also includes 17 oligonucleotides from parasites, 11 oligonucleotides from bacterial species and 120 oligonucleotides from housekeeping human genes.

first: Ena

last: Wang

first: Chuli

last: Yi

first: Terry

middle: E

last: Goldberg

first: Lorraine

last: Jones-Brando

first: Francesco

middle: M

last: Marincola

first: Maree

last: Webster

first: Fuller

last: Torrey

manufacture_protocol: Synthetic oligonucleotide probes (Operon-QIAGEN, Stanford, CA) were solubilized in 3X SSC at a concentration of 50 pmol/ml and spotted in duplicate on each Poly-L-Lysine coated glass slide (http://nciarray.nci.nih.gov/reference/NCIReference.shtml). Each array was configured in 4 x 20 x 20 format and post processed using standard procedures (http://nciarray.nci.nih.gov/reference/NCIReference.shtml).


title: NIEHS Human ToxChip v2.0

first: E

first: C


title: SAM1.1

status: Public on Jul 31 2005

first: Patrick

middle: S.

last: Schnable

address: 2035B Roy J Carver Co-Lab

organism: Zea mays

manufacturer: Schnable Laboratory at Iowa State University(ISU)

middle: S

manufacture_protocol: The ISU microarray facility have generated a maize gene chip that contains 19,200 spotted cDNA inserts. In this chip there are two fileds, which were called Field A and Field B seperately. In Field A there are 8(meta row total)x4(meta column total)x20(row total)x20(column total)=12800 spots, and 4(meta row total)x4(meta column total)x20(row total)x20(column total)=6400 spots in field B.


title: Chromosome coordinates of yeast oligo microarray (Agilent G4140A)

status: Public on Jan 30 2006

city: Seattle

first: Bonita

last: Brewer

state: WA

department: Genome Sciences

institute: University of Washington

description: this submission gives chromosome coordinate information for the oligos on Agilent's Yeast Oligo Microarray (G4140A).

manufacture_protocol: see manufacturer's website


title: SRC Human Compugen 19K

city: St Lucia

first: Sean

last: Grimmond

state: QLD

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute of Molecular Bioscience, Uni of QLD

manufacture_protocol: Compugen oligos (Catalog# HUMLIB96) were provided as lyophilised samples. Arrays were printed in NaPO4 buffer (pH 7.2).  See http://microarray.imb.uq.edu.au for details


title: UCSF GS Operon Mouse v.2 Oligo Array

status: Public on Jan 10 2006

city: San Francisco

first: Michael

middle: E.

last: Salazar

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

manufacture_protocol: MGuide / ArrayMaker


title: DKFZ/Operon Human Oligo Set v2.1

city: Heidelberg

first: Olaf

last: Thuerigen

address: Im Neuenheimer Feld 280

department: Molecular Genetics (B060)

country: Germany

institute: German Cancer Research Center

description:
Spotted long oligonucleotide array produced using the Operon Human Genome Oligo Set Version 2.1 (21,329 70mer oligonucleotides, based on build #147 of the Human UniGene database).
Keywords = spotted
Keywords = human
Keywords = long oligonucleotide
Keywords = oligo
Keywords = 70mer
Keywords = Operon

first: Grischa

last: Toedt

first: Heidi

last: Kramer

first: Meinhard

last: Hahn

first: Peter

last: Lichter

manufacture_protocol: 70mer oligonucleotides were diluted at 40 µM in FBNC buffer (G. Wrobel et al., Nucleic Acids Res 31 e67, 2003) and spotted as array duplicates using epoxy-silane coated glass slides (Schott Nexterion) and stainless steel split pins (SMP3, Telechem) at 20°C and 40% rH. Slides were dried (60' @ 60°C) and DNA was UV-crosslinked with 240 mJ/cm2 @ 254 nm. Slides were stored, sealed airtight and dry, at 4°C.


title: QIMR Human 4.5k v30

status: Public on Jan 20 2006

city: Brisbane

first: Glen

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

institute: QIMR Berghofer Medical Research Insitute

manufacture_protocol: The microarrays were made of the Research Genetics GF211 sequence verified set (4,032 genes) plus clones contributed by users. The microarrays were spotted in duplicate on the same slide, and contained various positive and negative controls to enable labelling and hybridisation quality control. The microarrays were printed using the GMS-417 Arrayer.


title: custom made Agilent 8.4K array

city: Amsterdam

first: Floor

last: Stam

address: de Boelelaan 1087

department: Institute for Neurosciences

country: Netherlands

institute: Vrije Universiteit

organism: Rattus norvegicus

description:
This array was created in 2001 and was designed to contain:
*all unigene clusters containing at least 1 mRNA sequence (~4500)
*ESTs overrepresented in libraries derived from neuronal tissues
*ESTs present in rat DRG libraries

first: Joost

last: Verhaagen

first: August

middle: B

last: Smit

manufacture_protocol: 60-mer oligo's are synthesized in situ on glass slides


title: Emericella nidulans EST-based chip primary data

status: Public on Jan 05 2006

city: Debrecen

first: Istvan

last: Pocsi

address: Egyetem tér 1.

department: Dept.of Microbiology and Biotechnology

country: Hungary

institute: University of Debrecen

organism: Aspergillus nidulans

description: Double printed Emericella nidulans chips containing 3533 unique EST sequences in 4352 spots.

first: Marton

last: Miskei

first: Zsolt

last: Karanyi

first: Tamas

last: Emri

first: Patricia

last: Ayoubi

first: Tunde

last: Pusztahelyi

first: Gyorgy

last: Balla

first: Rolf

middle: A

last: Prade


title: UCSF 7Mm Mouse v.2 Oligo Array

first: Michael

last: Salazar


title: Emericella nidulans EST-based chip normalized data