title: Stanford Denko EOS Human 35K Genechip v1.1

status: Public on Mar 07 2006

city: Stanford

first: Nicholas

last: Denko

state: CA

address: Rm 1245 269 campus dr

department: Radiation Oncology

country: USA

institute: Stanford University

organism: Homo sapiens

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol: see manufacturer's website


title: Chicken_Neuroendocrine_System_5K

status: Public on Dec 11 2004

city: College Park

first: Tom

middle: Eric

last: Porter

state: MD

address: Building #142

department: Animal and Avian Sciences

institute: University of Maryland

organism: Gallus gallus

technology: spotted DNA/cDNA

description:
Spotted amplified cDNA array on glass.  Produced with cDNA clones expressed in the chicken neuroendocrine system.  Tissues used to produced the cDNA library included the hypothalamus, anterior pituitary gland, and pineal gland.
7200 spots
Keywords = spotted
Keywords = cDNA

distribution: non-commercial

middle: E

first: L

last: Ellestad

first: M

last: Muchow

first: S

middle: A

last: Jenkins

first: W

last: Carre

first: Larry

last: Cogburn


title: Caltech 16K cDNA Mouse Array

status: Public on Mar 06 2003

city: Pasadena

first: Sangdun

last: Choi

address: 1200 E. California Blvd

department: Biology

institute: California Institute of Technology

organism: Mus musculus

description:
The 16K mouse cDNAs probes used in this microarray were designed using sequence information gathered from RIKEN FANTOM cDNA library.
Probes can be 0.5 to 3 kb in length where about 60% of the probes represent full length transcripts.
The PCR products were inkjet-printed on the array by Agilent Technologies (Palo Alto, CA).


title: UHN Yeast 6.4kv6

status: Public on Mar 31 2006

city: Rehovot

first: Naama

last: Barkai

address: Hertzel

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute of Science

organism: Saccharomyces cerevisiae

description: Grid rows-12; Grid columns-4; Rows-20; Columns-20; Grid to grid distance-4500um; 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. We use high precision robots that can use up to 48 pins or print heads.   The Y6.4kv6 slides are printed using 48 pins and we use UltraGAPS ™ slides (Corning Inc.).  We are able to print up to 120 slides in each batch and batches that result in greater than 95% printing fidelity are selected for post printing quality control tests.


title: GF100 GeneFilters

status: Public on Aug 05 2002

city: Copenhagen Valby

first: Kjeld

last: Olesen

address: Gamle Carlsberg Vej 10

country: Denmark

institute: Carlsberg Research Laboratory

description:
Research Genetics GF100 GeneFilters
based on corrected annotation database
gf100_final_data_071201

first: Troels

last: Felding

first: Claes

last: Gjermansen

first: Jorgen

last: Hansen


title: COGEME Saccharomyces cerevisiae ORF array

status: Public on Aug 15 2003

city: Manchester

first: Dawn

last: Jones

country: United Kingdom

institute: UMIST

description:
Comparison of the transcriptomes of Saccharomyces cerevisiae wild type FY23 and a PDE2 deletion mutant DJ28.

FY23 (Winston et al. 1995) was used as the reference wild-type strain and as the host for the deletion of PDE2 (Guldener et al. 1996; Wach et al. 1994).SFH-PCR mediated replacement (Guldener et al. 1996; Wach et al. 1994) of PDE2 was carried out in FY23 by transforming a KanMX4 cassette amplified from pFA6a-KanMX4.  Cells were pelleted by centrifugation, frozen in liquid nitrogen and stored at –80oC until RNA was prepared (Hauser et al. 1998).  Frozen cells were transferred to a pre-cooled Teflon vessel containing a 7mm tungsten carbide bead and placed into a Micro-Dismembrator (B.  Braun Biotech).  Total RNA was extracted using TriZOL reagent (Invitrogen) according to the manufacturer’s instructions.  Single-stranded nucleic acids were precipitated with LiCl and resuspended in DEPC-treated water before synthesis and labelling of cDNA (Hegde et al. 2000).  Unincorporated fluorescent nucleotides were removed by purification with GFX columns (Amersham Pharmacia).  Labelling efficiency was assessed by visualisation on a Storm 860 phosphoimager (Amersham) following agarose gel electrophoresis.   Microarrays based on PCR products of all S. cerevisiae open reading frames were manufactured in-house in the Transcriptome Resource Facility of the Consortium for the functional Genomics of Microbial Eukaryotes (COGEME).  The differentially labelled samples were hybridised to the array slides overnight at 42oC before being washed as follows: once in 2xSSC, 0.1 % SDS (w/v) for 15min; once in 1xSSC, 0.2% SDS (w/v) for 8min; 0.1xSSC, 0.1% SDS (w/v) for 5min.  All washes were carried out in Coplin jars in the dark at room temperature with agitation.  The slides were dried by centrifugation at 3000rpm.  The hybridised arrays were scanned with a GenePix 4000A scanner (Axon Instruments).  Artefacts were removed after visual inspection of the spots and the intensity of fluorescence adjusted to the medians.   To minimise the intrinsic variability involved in this technique ten microarray slides were used for the experiment.  Half of the slides involved reciprocal dye labelling, allowing compensation for the differences in preferential incorporation of the two fluorescent labels.  The labelling will be detailed in the sample.
Keywords = PDE2, Ras/cAMP pathway

middle: L


title: Khodursky Lab E. coli B 4290 ORFs Microarray

status: Public on Mar 06 2006

city: Princeton

first: Dipen

last: Sangurdekar

state: NJ

address: 132 Carl Icahn laboratory, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

organism: Escherichia coli

description:
A microarray with 4405 spot features.
Tip Configuration: Standard 16-tip

middle: P

first: Friedrich

last: Srienc

first: Arkady

middle: B

last: Khodursky

manufacture_protocol: 4290 amplified ORFs from primer pairs (from Sigma Genosys) were printed onto glass slides using a 16 tip robotic printer from 384-well microwell plates


title: Cerebellargenexp

status: Public on Apr 18 2001

city: Wako-shi

first: Yoshihiro

last: Kagami

state: Saitama

address: 2-1 Hirosawa

country: Japan

institute: RIKEN Brain Science Institute

description:
The Affymetrix GeneChip Mu11K was used to analyze the gene expression profile in developing mouse cerebellum (two GeneChips per E18, P7, P14, P21, and P56) to assist in the understanding of the genetic basis of cerebellar development in mice.  The analysis showed 81.6% (10,321/12,654) of the genes represented on the GeneChip were expressed in the postnatal cerebellum, and among those, 8.7% (897/10,321) were differentially expressed with more than a two-fold change in their maximum and minimum expression levels during the developmental time course.  All of these 897 differentially expressed genes were listed in this platform.  The explanation of gene function classification is as follows:  CGDD (cellular growth, differentiation, and death), CLAM (carbohydrate, lipid, and amino acid metabolism), CSC (cell structure and communication), IMTN (intra/intercellular molecular transport and neurotransmission), NNM (nucleotide and nucleic acid metabolism), ST (signal transduction), and TTPM (transcription, translation, and protein modification).
Keywords = cerebellum, postnatal development, high-density oligonucleotide array


title: UHN Mouse 15K array, rearranged

city: London

first: Ann

last: Chambers

state: Ontario

address: 790 Commissioner's Road E

department: Victoria research labs

country: Canada

institute: London Regional Cancer program

description: This array is the same as the UHN mouse 15K array (GEO platform number GPL519), with the Grid-row, grid-column, row and column rearranged to coincide with the output from the quantification software (Arrayvision 6.0) that was used on the samples. For a more complete description of this array, see http://www.microarrays.ca/support/glists.html

first: Robert

last: Gros

first: Qingming

last: Ding

first: Chorazyczewski

last: Jozef

first: Joseph

last: Andrews

first: J. Geoffrey

last: Pickering

last: Hegele

first: Ross

middle: D

last: Feldman


title: Qiagen Rat Oligonucleotide Array

status: Public on Jun 06 2003

city: Tucson

first: Niranjan

last: Maitra

state: AZ

address: 1501 North Campbell Avenue

department: Sarver Heart Center

institute: University of Arizona

organism: Rattus norvegicus

technology: spotted oligonucleotide

description:
Rat genome oligo set comprises 4273 UniGene clones
Keywords = Unigene Oligo Nucleotide Array


title: UCSF_Gross_Ecoli_v18.txt

city: San Francisco

first: Virgil

middle: Arthur

last: Rhodius

address: Genentech Hall, 600 16th Street

department: Microbiology and Immunology

institute: UCSF

description:
A microarray with 6400 spot features.
Tip configuration: Standard 16-tip steel pin
Columns per Sector: 20
Rows per Sector: 20
Column spacing: 210 um
Row spacing: 210 um

manufacture_protocol: PCR products for 4110 ORFs representing 95.8% of the Escherichia coli K12 MG1655 ORFs were prepared according to Richmond et al (1999; Nucleic Acids Res. 27:3821-35). The products were spotted onto glass slides to make DNA arrays as described in MGUIDE at http://cmgm.stanford.edu/pbrown/mguide/index.html and protocols on http://www.microarrays.org/


title: Institute of Food Research Salmonella typhimurium LT2 6k array

status: Public on Mar 28 2006

city: Norwich

first: Arthur

last: Thompson

state: Norfolk

address: Colney Lane

department: Food Safety Science

institute: Institute of Food Research

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

first: Sacha

last: Lucchini

first: Jay

last: Hinton

manufacture_protocol: PCR product array of whole ORF's from S. Typhimurium LT2. For description of PCR amplification and printing procedures see Clements et al., (2002) PNAS 99(13): 8784-8789.


title: SrcMalaria (Scripps/GNF 2002 affymetrix chip)

status: Public on Mar 24 2006

city: Riverside

first: Karine

middle: Gaelle

last: Le Roch

address: 900 University Avenue

department: Department of Cell Biology & Neuroscience

institute: University of California

organism: Plasmodium falciparum

manufacture_protocol: In situ oligonucleotides


title: Nitrosomonas europaea, whole genome microarray

status: Public on Mar 23 2006

first: Lisa

middle: Yael

last: Stein

address: Geology 2207, 900 Univ. Ave.

department: Environ. Sciences

organism: Nitrosomonas europaea

manufacturer: Jizhong Zhou - Oak Ridge National Laboratories

first: Catherine

middle: M

last: Cho

first: Tingfen

last: Yan

first: Xueduan

last: Liu

first: Liyou

last: Wu

first: Jizhong

last: Zhou

middle: Y

manufacture_protocol: Construction of whole open reading frame (ORF) microarrays for N. europaea was done by generating gene-specific fragments (<75% homology) by PCR using individually designed primer sets using PRIMEGENS software. All amplified products (8-16 reactions per primer set x 100 μl) were pooled together and purified using a robot (Biomek F/X Automated Workstation; Beckman). The range of product sizes was 100-1200 bp with most between 500-600 bp. Of the 2603 total predicted genes, 2318 ORFs were correctly amplified and specific 50-mer oligonucleotide probes (74 ORFs) were synthesized for the remainder, representing 96.8% of the total predicted gene content of N. europaea. Diluted PCR products (50 ng μl-1) were spotted onto CMT-GAPS slides (Corning, Corning, NY) using a BioRobotics Microgrid II microarrayer (Genomic Solutions, Ann Arbor, MI).


status: Public on Aug 01 2005

city: Belmont

first: Ting Ting

last: Zhang

state: MA

address: 115 Millman st

department: Mclean Hospital

institute: Harvard University

manufacture_protocol: The Qiagen/Operon version 2.0 mouse oligonucleotide library, comprised of oligonucleotides (70-mers) representing 16,443 unique mouse genes, was printed on poly-L-lysine-coated glass slides. The library also included sets of positive and negative controls that were used for quality control purposes. Oligonucleotides were prepared in sets of 384-well plates at a concentration of 40 <E6>M. Arrays were prepared using a custom-built array printer equipped with Majer MicroQuill-2000 split tip pins with a capacity of 255 slides per print run. The printed arrays were numbered sequentially during each run and tracked by a unique identification number. After completion of printing and air drying of the arrays, all slides were washed in 0.2% SDS to remove excess oligonucleotide followed by a brief rinse in 70% ethanol. Slides selected from throughout the run were tested for correct printing by nonspecific hybridization of Cy3-labeled, random 9-mers.


title: Adelaide Microarray Facility CompuGen OligoLibrary Mouse 22k Hybrid of v1.0 and v2.1

status: Public on Mar 20 2006

city: North Adelaide

first: Christopher

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. this experiment covered two print runs with print run 1 layout used for slides AMC0374 - AMC0472 and print run 2 layout was used for slides AMC1000+. The layout was changes between print runs requiring remapping of run 1 spot positions to run 2 spot positions. For the CompuGen OligoLibrary, and the last 8 rows of column 1 this was a simple remapping. However for run 1, the Adelaide control plate was spotted twice and for run 1 it was spotted once. Thus spots in print run 2, rows 9-16 of col 1, are hybrids. In run 1 these were housekeeping genes or other controls, but in run 2 their equivalent spot was always buffer. In this platform description these are indicated by Hybrid in ID name.

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: NimbleGen 60mer Arabidopsis array

status: Public on Jul 07 2004

city: Tsukuba

first: Kyoko

last: Matsui

department: Gene Function Research Center

institute: National Institute of Advanced Industrial Science and Technology (AIST)

organism: Arabidopsis thaliana

description: NimbleGen oligonucleotide Arabidopsis microarray that covers approx. 28,000 genes and contains 6 different 60mers per gene.

first: Masaru

last: Ohme-Takagi


title: RIKILT Human Oligo Array

status: Public on Aug 07 2005

city: Wageningen

first: Jaap

last: Keijer

address: Bornsesteeg 45

country: Netherlands

institute: RIKILT Institute of Food Safety

manufacture_protocol:
The 10K MWG human oligoset together with additional 50-mer oligo probes involved in energy metabolism were in-house printed on GAP II coated slides (Corning), using the Microgrid II arrayer (BioRobotics Ltd, Cambridge, UK). After printing, microarrays were allowed to dry at room temperature. The oligo arrays were rehydrated and immobilized by UV cross-linking (120 MJ of UV energy). The microarray slides were then prewashed in the following order to reduce background; 20 minutes at 55C with 2x SSC/0.2% SDS, 5 minutes at room temperature (RT) with 0.2x SSC and 3 minutes at RT with demineralized water. Slides were dried by 2 minutes of centrifugation (2000 rpm).
Spotbuffer: 5* SSC
Concentration Oligo's: 700pmol/14 microliter


title: Ontario Cancer Institute Yeast 6.4K array (Y6.4k_v4 OCI)

city: Toronto

first: Tzvi

last: Aviv

address: 600 University

institute: Lunenfeld institute


title: Ontario Cancer Institute Yeast 6.4K array (Y6.4k_v2 OCI)


title: NKI-AVL Homo sapiens 18K cDNA microarray

status: Public on Mar 21 2006

city: Amsterdam

first: Bas

last: Kreike

address: Plesmanlaan 121

department: Radiotherapy

institute: Netherlands Cancer Institute

first: ron

last: kerkhoven

first: mike

last: heimerikx

manufacture_protocol:
he human cDNA arrays we print contain a part of the sequence verified Invitrogen cDNA library of 45K. We selected the genes that are named as well as added a collection of ESTs to print on the array.
This means that approximately 11000 sequences belong to named genes of which around 7000 are unique. The arrays consist of 19600 features printed in a 20x20 subarray layout using 48 Biorobotic 2500-microspot pins and are commonly referred to as our 18K human cDNA arrays. We are printing purified PCR products that vary in length from 200 to 4000 bp. All PCRs have been checked on gel.


title: Leishmania major whole-genome 60-mer DNA oligonucleotide microarray

status: Public on Mar 10 2006

city: West Lafayette

first: Timothy

last: Holzer

state: IN

address: 175 S. University St.

department: Biochemistry

institute: Purdue University

organism: Leishmania major

description: This platform supports 11 60-mer DNA oligonucleotide probes synthesized twice on each slide for 8160 (98%) of the Leishmania major Friedlin genes annotated at www.genedb.org. Refer to: Timothy R. Holzer, W.R. McMaster, James D. Forney. “Expression profiling by whole-genome interspecies microarray hybridization reveals differential gene expression in procyclic promastigotes, lesion-derived amastigotes, and axenic amastigotes in Leishmania mexicana.” Molecular and Biochemical Parasitology 146 (2): 198-218. Apr, 2006.

first: James

last: Forney

manufacture_protocol: Refer to: S. Singh-Gasson, R.D. Green and Y. Yue et al., Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array, Nat Biotechnol 17, pp. 974–978, 1999.


title: OHU16K (old)

city: Zürich

first: Keith

middle: S

last: Hoek

address: private

country: Switzerland

institute: Currently unaffilliated

description: Human OHU16K (old) array is created from the first 16K Operon set - 70 mer oligos. The array is in 32 pin conformation with 24 columns and 22 rows and only 4 spots on the 23rd row.

manufacture_protocol: Unknown but very similar to platform GPL989 which is the latest version available from the W.M. Keck Foundation Biotechnology Resource Laboratory.


title: Spotted cDNA array from Lily pollen

city: Siena

first: Cecilia

last: Del Casino

address: Via Mattioli 4

department: Scienze Ambientali "G.Sarfatti"

country: Italy

institute: Università di Siena

organism: Lilium longiflorum

description: approximately 1500 clones from a pollen cDNA library spotted on a glass array

first: Antonella

last: Autino


title: MPSS [DpnII: Mus musculus] signature list

status: Public on Oct 26 2004

city: Hayward

first: Daixing

last: Zhou

address: 25861 Industrial Blvd

department: Bioinformatics

institute: Solexa

technology: MPSS

description:
MPSS signatures detected in Lynx mouse transcriptome analysis experiment.

To generate a complete, annotated mouse signature database, we extracted all the possible signatures (“virtual signatures”) from the mouse genome sequence (NCBI build 33) and the mouse UniGene sequences (UniGene build #145).  Each virtual signature is ranked based on its position and orientation in the original sequence. The annotation for that sequence is then assigned to the signature and the resulting signature database is used to annotate the data from the experiments, using our “TopHit” algorithm.

Virtual Signature Class| mRNA Orientation| Poly-Adenelation| 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 3' 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

distribution: virtual

first: Tom

last: Vasicek

first: Irina

last: Khrebtukova


title: Mm-FDA-OperonV2

status: Public on Mar 11 2006

city: Bethesda

first: Amy

middle: Xiaoyun

last: Yang

address: 8800 Rockville Pike

department: Division of Celular and Gene Therapies

institute: CBER, FDA

manufacture_protocol: The mouse genome oligonucleotide probe set contains 16,896 optimized 70mers (plus controls) obtained from Operon (http://www.operon.com/). The oligonucleotide probes were purchased in 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in 4XSSC print buffer at a concentration of 20-30 uM. The microarray is composed of 32 blocks and one spot is printed per probe per slide. The spot size is 100 micron and spot distance is 185 microns (center-to-center). The microarrays were printed on Gold Seal micro slides (Cat #3010) coated with poly-L-lysine and post-processed according to Operon's protocol.


title: NimbleGen hg17 Human 1.5 Kb MinPromoter array

status: Public on Mar 03 2006

city: Calgary

first: Mark

last: Bieda

state: AB

address: 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

description: Average of 15 probes/promoter. Most promoters have 15 probes, but in particular, some bidirectional promoters have ~30. Note that spacing and overlap of probes is highly variable.

middle: C

first: Shally

last: Xu

first: Peggy

last: Farnham

first: Roland

last: Green

manufacture_protocol: oligos fabricated on array


title: custom mouse IMAGE GEM1 8.734K

city: Manchester

first: Ralph

last: Andre

address: Michael Smith Building, Oxford Road

department: Faculty of Life Sciences

institute: University of Manchester

manufacture_protocol: custom-built; Betts et al., Toxicology 185: 103-117


title: Galbraith Laboratory Operon Long Oligonucleotide Microarray version 3.0 (ATv304.01.Z)

status: Public on Mar 08 2006

city: Tucson

first: David

middle: William

last: Galbraith

address: 303 Forbes Building

department: Plant Sciences and Bio5 Institute

institute: University of Arizona

description: This oligonucleotide array is produced from the Operon Version 3.0 Array-Ready Oligo set (AROS), which comprises 29,110 70-mer oligonucleotides representing 26,173 protein-coding genes, and 28,964 protein-encoding gene transcripts, and 87 microRNA gene precursors.  AROS design is based on ATH1 release 5.0 of the TIGR Arabidopsis genome annotation database, and Release 4.0 of the miRNA Registry at the Sanger Institute.  Various additional elements are printed as controls.  Microarrays can be ordered from the Galbraith laboratory. This platform represents slides ATv304.01.001-ATv304.01.300 (http://www.ag.arizona.edu/microarray).

manufacturer: The Galbraith Lab, University of Arizona

middle: W

manufacture_protocol: GeneMachines Omnigrid 300


title: VIMSS Desulfovibrio vulgaris Hildenborough

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

manufacture_protocol: Oligonucleotide probes were spotted onto SuperAmine glass slides using a PixSys 5500 robotic printer.  Each probe had two replicates on a single slide.  After printing, the oligonucleotide probes were fixed onto the slides by UV cross-linking.  See He, Z., Wu, L., Li, X., Fields, M., and Zhou, J. 2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.


title: Galbraith Laboratory Operon Long Oligonucleotide Microarray version 3.0 (ATv304.02.Z)

description: This oligonucleotide array is produced from the Operon Version 3.0 Array-Ready Oligo set (AROS), which comprises 29,110 70-mer oligonucleotides representing 26,173 protein-coding genes, and 28,964 protein-encoding gene transcripts, and 87 microRNA gene precursors.  AROS design is based on ATH1 release 5.0 of the TIGR Arabidopsis genome annotation database, and Release 4.0 of the miRNA Registry at the Sanger Institute.  Various additional elements are printed as controls.  Microarrays can be ordered from the Galbraith laboratory. This platform represents slides ATv304.02.001-ATv304.02.300 (http://www.ag.arizona.edu/microarray).


title: Sanger Institute M. musculus array, Mver1.1.1

status: Public on Mar 12 2006

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

manufacture_protocol: 1. Inoculate media (200 ul/well of L-broth supplemented with 7.5% glycerol and 50 ug/ml ampicillin) in 96-well microtitre plates (Falcon, 353072) with bacterial clones. Incubate for 16 hours at 37C. These cultures will represent the working copy of the clones from which all subsequent manipulations are performed. 2. Perform a 1:10 dilution of the bacterial cultures by removing 20 ul from each well and add into 180 ul of sterile ddH20 in a new microtitre plate. Store the remaining working copy plates at -70C. The dilutions can now be used immediately or stored at -20C. 3. For each plate of clones to be PCR amplified, set up PCR reactions in 96-well thin-walled thermowell plates (Costar, 6511) by mixing the following on ice: 15 ul of 1:10 bacterial culture dilution, 6 ul of 10x PCR buffer (500 mM KCl, 50 mM Tris pH 8.5, 25 mM MgCl2), 3 ul of dNTPs (10 mM dATP, dTTP, dCTP, dGTP), 1.5 ul of 5'-aminolink primer 1 (sense, 200 ng/ul), 1.5 ul of primer 2 (antisense, 200 ng/ul), 0.375 ul of Taq polymerase (5 U/ul, Perkin Elmer-Cetus), and 32.625 ul of sterile ddH20 (total volume = 60.0 ul). 4. Place PCR reactions in thermocycler and incubate for 10 min at 95C, and follow with the program - 95C for 1 min; 60C [1] for 1.5 min; 72C for 7 min - for 30 cycles. Finish with a 10 min incubation at 72C. 5. Analyse 2 ul of PCR products [2] on 2.5% agarose 1x TBE slab gels. 6. Transfer PCR products to Multiscreen filter plates (Millipore, MAGVN2250) and add 15 ul of 4x spotting buffer (1 M sodium phosphate buffer pH 8.5, 0.001% sarkosyl) to each PCR reaction. Filter by centrifugation at 2000 rpm for 10 min into 96-well plates (Falcon, 353077). Samples are now ready to array or can be stored at -20C. Notes: [1] Annealing temp may vary depending on the primer pairs used. [2] The PCR products should be at a final concentration of between 100-200 ng/ul.


title: CATMA version 2

status: Public on Mar 17 2006

middle: de

last: Jong

address: Kruislaan 318

institute: University of Amsterdam

manufacturer: Utrecht University - Molecular Genetics Group

manufacture_protocol:
Production of the Complete Arabidopsis Transcriptome MicroArray (CATMA)

CATMA (Complete Arabidopsis Transcriptome MicroArray) is a spotted microarray of Arabidopsis thaliana gene specific tags (GSTs). Production took place in a cooperative effort of 12 European research groups [1]. Each group produced part of the 21120 Gene Specific Tags (GSTs), while spotting took place at each individual laboratory. Using a high-resolution spotter enabeled our group to produce all CATMA GSTs on one slide.
GST and primer design

CATMA consists of 21120 GSTs. In order to design these GSTs, a proprietary gene annotation of the Arabidopsis nuclear genome was made with EuGene software [2]. For each annotated gene, a specific region in the first exon was selected and for that region a specific primer pair was designed. Each primer carries a gene-specific 3-prime domain and a 5-prime extension which allowed re-amplification using a small set of extension primers. GST selection and primer design were performed with SPADS software [3].
Amplification

Where possible GSTs were amplified from a collection of IGF[4] and TAMU[5] BAC DNAs. Genomic Col-0 DNA was used if this proved to be impossible. The PCR products were examined by agarose gel electrophoresis, and were only accepted if a single clear band of the correct size was observed. Moreover the sequences of a random selection of BAC-amplified GSTs and in addition all GSTs amplified from genomic DNA were determined. Of 1400 GSTs checked, no incorrect sequences were found. All GSTs were purified, quantified and normalised to 200 ng / µl before spotting.
Spotting

The GSTs are spotted on GAPSII glass slides (Corning) with 48 pins (type 10K) using a MicroGrid II TAS spotter (BioRobotics). A spot size of less than 100 micrometer, and a spot distance of 100 micrometer allows for a total number of 30.000 spots on each slide. Spotting quality is ensured by sampled analysis of deposited buffer salt chrystals, ethidium bromide staining and test hybridisations.
Batch-wise processing

To track the quality of each slide, bar codes are used to administer the spotting runs, and the manufacturers production batch. This provides the ability to quickly recognise series of slides with spotting defects and even the ability to recall certain groups of slides.
Conclusion

The CATMA microarray consists of GSTs that are based on modern gene annotation software which provide a minimal level of sequence overlap. Production of the slides takes place under stringent conditions ensuring high quality and reproducability over a wide range of experiments.

remarks

   1. The general homepage with the contributing groups can be found at www.catma.org
   2. Schiex, T, Moisan, A, and Rouzé, P (2001), EUGENE: An Eukaryotic Gene Finder That Combines Several Sources of Evidence, Lecture Notes in Computer Sciences 2066: 111-125
   3. SPADS is available on the internet: genoplante-info.infobiogen.fr/spads/
   4. Mozo T, Fischer S, Shizuya H, Altmann T (1998) Construction and characterization of the IGF Arabidopsis BAC library, Molecular and General Genetics 258(5):562-70
   5. TAMU BAC DNA: hbz.tamu.edu/bac.html


title: Amersham Biosciences CodeLink Uniset Rat I Bioarray

first: Peter

last: Yuen

address: 10 Center Drive, Room 3N108

department: NIDDK

institute: NIH

description: ~10 000 rat genes, one specific, prescreened 30-mer probe per gene, functionally validated

first: Sang-Kyung

last: Jo

first: Robert

middle: A

last: Star


title: Li UCSF yeast 14062 v1.0

city: San Francisco

first: Joachim

middle: J

last: Li

address: 600 16th Street S376

department: Microbiology and Immunology

institute: University of California, San Francisco

first: Richard

last: Morreale

first: Brian

first: Bilge

last: Ozaydin

first: Joseph

middle: L

last: Derisi

manufacture_protocol:
PCR products representing ORF and intergenic yeast genomic sequences were amplified.  Products were spotted on poly-L-lysine coated glass slides using a linear servo arrayer from the DeRisi Lab at UCSF.

Blast analysis of oligos sequences was used to determine the position of the final PCR product. Those oligo pairs which Blast analysis indicated could not generate a product or generated more than one product given the flag –1.  In cases where no product was found the fields Chr, Start and End have been left empty.  In cases where multiple products were found values in the fields Chr, Start and End correspond to the first product identified.

For all elements (except mitochondrial) the sequence of the PCR product was determined using the positions determined above.  Blast analysis of the PCR products was used to determine how repetitive each product was.  Elements that had products that were too repetitive were given a flag of –2.  The sequence of these products is listed.

Elements with flags of –1 or –2 were removed from all datasets prior to analysis.

Lamda DNA spots were not included in analysis.


title: UCSF 9Mm Mouse v.2 Oligo Array

status: Public on Mar 22 2006

first: Agnes

last: Paquet

address: 1550 Fourth Street, RM 545

description:
Arrays were printed on aldehyde coated slides (Erie Scientific)
http://www.eriemicroarray.com/substrates/aldehyde.aspx

manufacturer: UCSF Shared Microarray Facility, http://www.arrays.ucsf.edu

first: Andrea

last: Barczak

last: Erle

manufacture_protocol:
Operon Mouse V2 70mer oligonucleotide set.
http://www.operon.com/arrays/omad.php?
Oligos were resuspended in 3XSSC and printed at a concentration of 40um on an in-house Stanford style arrayer http://cmgm.stanford.edu/pbrown/mguide/index.html


title: SAM2.0

status: Public on Jul 01 2005

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

organism: Zea mays

manufacturer: Schnable Laboratory at Iowa State University(ISU)

manufacture_protocol: The ISU microarray facility has generated a maize gene chip that contains 14,080 spotted cDNA inserts.


title: Cotton Ovule cDNA MicroArray ghA

status: Public on Nov 03 2005

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

institute: CSIRO Plant Industry

organism: Gossypium hirsutum

description: 10584 spot Cotton Ovule cDNA MicroArray

first: Yingru

last: Wu

first: Iain

last: Iain

manufacture_protocol: The cotton ovule cDNA microarray comprised a total of 10,410 PCR amplified inserts from cDNA clones. The PCR amplified inserts were purified using ethanol, sodium acetate precipitation. The PCR amplicons were re-suspended in 10 micro liters of 50% DMSO. Quality control of the amplified products was done by separation on agarose gels containing EtBr. Spotting was performed using a VersArray ChipWriter Pro (BioRad) arrayer equipped with 24 Stealth Micro Spotting Pins SMP 3 (Telechem International Inc.). Samples were spotted onto CMT-GAPS II™ coated microarray slides (Corning). Post-printing slide processing was performed by baking the slides at 80 oC for 3 hours.


title: DEL-MAR 14K Integrated Systems

status: Public on Dec 09 2004

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

description:
Spotted amplified cDNA array on glass. 19200 spot corresponding to 14053 different genes.
liver / fat / muscle / pituitary / hypothalamus / pineal / testis / ovary / oviduct / Oligo

first: Tom

middle: E

last: Porter

first: Laura

last: Ellestad

first: Xiaofei

last: Wang

first: Wilfrid

last: Carré


title: OMM16K

status: Public on Feb 25 2004

city: New Haven

first: E. Janet

last: Hager

state: CT

address: 300 George Street, Suite 2110

department: W.M. Keck Foundation Biotechnology Resource Laboratory

institute: Yale University School of Medicine

description: Mouse OMM16K cDNA array is created from a set of 16K Operon 70 mer oligos. The array is in 32 pin conformation. It has 24 columns and 22 complete rows and a partial 23rd row.

first: Janet

manufacture_protocol: proprietary


title: SAM1.0

manufacture_protocol: The ISU microarray facility have generated a maize gene chip that contains 19,200 spotted cDNA inserts.


title: KI Schizosaccharomyces pombe 23K tiling array

status: Public on Mar 01 2006

city: Gothenburg

first: Claes

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

organism: Schizosaccharomyces pombe

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.

manufacture_protocol: see manufacturer's web site


title: Atlas Plastic Human 12k Microarray

status: Public on Mar 02 2006

city: Grosshansdorf

first: Olaf

last: Holz

address: Woehrendamm 80

country: Germany

institute: KH Grosshansdorf

manufacture_protocol:
Comercial Array
Details www.bdbiosciences.com/clontech


title: NASA Ames Research Center yeast 360K whole genome tiling

city: Moffett Field

first: Waraporn

last: Tongprasit

institute: NASA Ames Research Center

description: GenBank accession numbers: NC_001133-NC_001148, NC_001224

manufacturer: Genome Research Facility, NASA Ames Research Center

first: Manoj

middle: P

last: Samanta

first: Himanshu

last: Sethi

first: Chen-shan

last: Chin

first: Viktor

last: Stolc

manufacture_protocol: Maskless Array Synthesizer (MAS)


title: 11K_VJF-ARRAY

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

description:
Quality Control of the probes: Aliquots of each PCR product is analyzed for quality by UV measurement and agarose gel electrophoresis (< 2%) with ethidium bromide staining. Sample amplification is considered to have failed when multiple bands, unexpected product size or low integrity is observed. A low A260:A280 ratio is indicative of a low purity of the PCR product and may be associated with alcohol, detergent and protein contaminations, resulting in a high absorbance at 235 nm and 320 nm. These products were flagged out and specifically re-amplified. A re-sequencing step was randomly performed for 689 clones distributed across the plates, in order to identify any manipulation errors and to allow refinement of the annotations. Representative PCR products were quantified using PicoGreen dyes (Molecular Probes, USA) in a fluorescent assay measuring double-strand DNA concentration according to the manufacturer’s instruction. Samples with quantity under 4 pmol, a threshold for our microarrays, are considered to have failed, were flagged out and then re-amplified.

Microarray printing design: The 11K_VJF-array contains 8388 clones from the Mammalian Gene collection (MGC, IMAGE Consortium). This collection, namely IRAL, seeks to identify and sequence a representative full open reading frame clone for each human gene. A complementary cDNA IMAGE clone collection containing 1126 more clones were selected to represent a cancer targeted-set. Both Amersham Biosciences Lucidea™ Universal Scorecard™ and Lucidea™ Microarray ScoreCard v1.1, control clones are also present on this array.

Thus, the 11K_VJF-array consists in a 23,040 spots array (n = 2), including 9,514 spots of cDNA clones (83 %), from which 9,160 non redundant clones, then 432 technical control fragments (4 %) and 1,574 blank spots (13 %).

Arrays printed on this device contain four meta-columns and twelve meta-rows, thus there are 48 grids in total, each grid containing 22 rows and 22 columns. Duplicate spots are placed in the same relative position in two separate meta-columns i.e. meta-column 2 is a replicate of meta-column 1 and meta-column 4 is a replicate of meta-column 3. Overall array dimensions are 53 mm length and 18 mm width. Spot size of each element is around 170 µm in diameter and spot centers are 185 µm apart.

first: Esther

last: Graudens

first: Virginie

last: Boulanger

first: Eric

last: Eveno

first: Régine

last: Mariage-Samson

first: Christine

last: Couillault

first: Cindy

last: Mollard

first: Guilaine

last: Grémy

first: Malika

last: Lajémi

first: Xavier

last: Barlet

first: Patrick

last: Zaborski

first: Charles

last: Auffray

manufacture_protocol:
Probes synthesis: The cDNA clone inserts were PCR amplified twice using vector-specific primers (The PCR primers M13: 5’-GTAAAACGACGGCCAGT-3’ and M13 reverse: 5’-AACAGCTATGACCATG-3’ were used for amplification of cDNA inserts in pOTB7 and pDNR-LIB plasmids. The PCR primers T3: 5’-AATTAACCCTCACTAAAGGG-3’ and T7: 5’-GTAATACGACTCACTATAGGGG-3’ were used for amplification of cDNA inserts in Bluescript® SK- plasmids). PCR products were cleaned up by filtration using robotics stations (Multiscreen™ PCR, Millipore, USA; BioRobot 8000, Qiagen, Germany) and eluted in water.
Quality checked PCR (size, purity, sequence) were pooled, then dried down. A total of 4 pmol of each product were re-suspended into 384-well plates and were combined 1:1 with DMSO to reach the printing criteria.

Printing: Amino-modified mirrored glass slides (type 7star) were printed using the high speed robotics with the 4th generation Lucidea™ array spotter (Amersham Biosciences, USA). During the spotting process, environmental conditions [Clean environment, controlled humidity (~ 65%) and temperature (~ 22°C)] were strictly controlled. DNA adhesion to the glass was achieved by irradiation in the Hoefer model UVC500 illuminator (Hoefer, USA) with energy output of 10e6 µJ/cm². Quality of the spotting was checked by prescanning the slides. Microarrays were routinely stored in opaque plastic slide boxes at room temperature (no more than 6 months).


title: SAM1.1a

status: Public on Jan 12 2006

last: Schnable

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: Single HHV-4 ViruChip

status: Public on Mar 19 2005

city: Tokyo

first: Junko

middle: H

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

institute: Tokyo Medical University

organism: human gammaherpesvirus 4

description:
The ViruChip HHV-4(Celonex, Inc., Edmonton, Canada), the Epstein-Barr virus (EBV) DNA chip is made up of triplicate spots of 60-mer oligonucleotide specific probes for each EBV transcription unit. Human genes (Tubilin, G3PDH, Action, and ribo-S9) were included in order to standardize the amount of applied cDNA and to normalize the signals between samples and references. HIV genes were also printed to exclude non-specific hybridization.
Keywords = EBV


title: UD_Liver_3.2K

status: Public on Dec 11 2004

first: Larry

last: Cogburn

description:
Spotted amplified cDNA array on nylon membrane (8 x 12 cm).
3456 spots
Keywords = spotted
Keywords = cDNA

first: Wilfrid

last: Carre

first: Xiaofei

last: Wang


title: UD 7.4K Metabolic/Somatic Systems

status: Public on Dec 10 2004

description:
Spotted amplified cDNA array on glass.
7680 spots corresponding to 7435 genes from Liver and Adipose tissue.

last: Carré


title: Whole Genome Array L. acidophilus NCFM

status: Public on Aug 09 2005

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

state: NC

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

organism: Lactobacillus acidophilus

description: The microarray contains 97.4 % of the annotated genes of L. acidophilus NCFM

first: Maria

last: Azcarate-Peril

first: Olivia

last: McAuliffe

last: Altermann

first: Sonja

last: Lick

first: William

middle: M

last: Russell


title: Maize cDNA Generation II Version C

status: Public on Jun 01 2005

description: The ISU microarray facility have generated a maize gene chip that contains 12,160 spotted cDNA inserts. These cDNA clones were obtained from NSF Plant Genome EST projects led by Ginny Walbot and Pat Schnable.