title: GSC C.elegans 22.5K jan04

status: Public on Dec 01 2007

city: Novato

first: Gawain

last: McColl

state: CA

address: 8001 Redwood Blvd

country: USA

institute: Buck Institute for Age Research

organism: Caenorhabditis elegans

technology: spotted oligonucleotide

distribution: non-commercial

manufacturer: Genome Sequencing Center, University of Washington School of Medicine


title: Gallus gallus 3k multi-sample microarray platform

status: Public on Dec 29 2007

city: Blacksburg

first: Huifeng

last: Li

state: VA

address: 3570 Litton Reaves Hall

department: Animal and Poultry Sciences

institute: Virginia Tech

organism: Gallus gallus

manufacturer: MOA Laboratory of Animal Genetics and Breeding, Collage of Animal Science and Technology, China Agriculture University, Beijing, People’s Republic of China, 100094.

first: Ning

last: Yang

manufacture_protocol: Oligonucleotide probes were synthesized by a company(Sanbiotech, Beijing) and purified by using QIAquick PCR Purification kit (Qiagen, Chatsworth, CA).  After checked on a 1% agarose gel, probes were dissolved in 15µl spotting buffer (50% DMSO) at final concentration of 0.5 ug/ul.  Using SpotBot™ microarrayer (Telechem international Inc, CA), these probes were printed in duplicate on ExprexionsTM slide (GenExprex Corp, NY).  Each slide contains 3072 spots within 48 blocks which contain the same 20 genes and controls at 23°C and 50% humidity.  After being spotted, the slides were snap dried in an 80°C oven for 30 seconds, cross-linked with UV light at 600 mJ in a UVP CL-1000 cross-linker (UVP Inc, Upland, CA), and stored at room temperature.


title: TIGR PFGRC Vibrio cholerae 19K v2 array designed primarily based on strain El Tor N16961 (condensed table)

status: Public on Dec 31 2007

city: Atlanta

first: Jorge

middle: Antonio

last: Benitez

state: GA

address: 720 Westview Dr., SW

department: Microbiology

institute: Morehouse School of Medicine

organism: Vibrio cholerae

description:
This set includes 3811 oligonucleotides, has 19008 spots distributed in 96 blocks.
This array is the same as GPL4353. The data table is condensed since the normalized data in the Sample data tables condenses the replicates..

manufacture_protocol: 2QVC, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 5885507, pen id 0, pen cycles -1, operator Jon, humidity control On, humidity set point65


title: INRA Sus scrofa 4K

city: Castanet-Tolosan Cedex

first: Agnes

last: Bonnet

address: Chemin de Borde-Rouge  BP 52627

country: France

institute: INRA

organism: Sus scrofa

technology: spotted DNA/cDNA

description: spotting 12*12 microgrid in two fields

manufacture_protocol: as described in Institute Labs manual


title: NLI_SSC_11.5K_cDNA_V1

status: Public on Dec 17 2007

city: Beijing

first: Jin

last: Zhang

address: 2#, Yuanmingyuan West Road

country: China

institute: China Agricultural University

first: Wei

last: Guo

middle: W

first: Xue

middle: M

last: Deng

first: Xiao

middle: X

last: Hu

manufacture_protocol: Plasmid inserts were amplified by PCR using T3 (5’-GTA AAACGACGGCCAGT-3’) and T7 (5’-CAGGAAACAG CTATGAC-3’) flanking vector primers in 50ul volume reactions. Amplifications were performed in a thermal cycler (PE Amp9700, Perkin-Elmer, USA). PCR reaction mixes contained 5ul 10×Taq polymerase buffer solution, 50 pmol of each primer, 4ul 10 mM dNTPs, and 1 U Taq polymerase. An initial 5 min denaturation at 95oC was followed by 35 cycles of 1 min denaturation at 95oC, 1 min annealing at 55oC and 1 min elongation at 72oC. The reaction ended with an additional incubation of 5 min at 72oC. PCR products were analyzed on 1.0% agarose gels. Samples containing multiple bands or weak products were reamplified. PCR products were precipitated with isopropanol and redissolved in 50% dimethyl sulphoxide (DMSO). A commercial OmniGridTM microarrayer (Genomic Instrumentation Services, Inc, San Carlos, CA) was employed to print all spots on Telechem Superamine slides (Arrayit, Sunnyvale, CA) and to verify reproducibility each spot was arrayed three replicates. Control samples included the expressed pig genes encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ribosomal protein L24 (RPL24), eukaryotic translation elongation factor 1 alpha 1 (EEF1A1), glutathione peroxidase 1 (GPX1), and peptidylprolyl isomerase A (cyclophilin A) (PPIA). Additional, control samples including three different Arabidopsis thaliana DNA fragments (GenBank accession numbers AC004146, AC007661 and U09332) and 12 spots of DMSO were also arrayed. The centre-to-centre distance between two adjacent spots was 225 m. After printing, the slides were baked for 1 h at 80oC and stored dry at room temperature until use.


title: Rainbow trout custom 8.8k microarray

city: Nantes

first: Daniel

last: BARON

state: Loire-Atlantique (44)

address: 30 Bd Jean Monnet

department: UMR1064 - Centre de Recherche en Transplantation & Immunologie

institute: Institut national de la santé et de la recherche médicale-INSERM

organism: Oncorhynchus mykiss

last: Baron

first: Jérome

last: Montfort

first: Rémi

last: Houlgatte

manufacture_protocol: DNA Microarray construction : Gene expression analyses were carried out using home-made Nylon microarrays using a previously described technology [10441335]. These microarrays were built using as templates cDNA clones provided by the INRA-AGENAE program [16887034]. All these clones were PCR-amplified at the INRA Resources Centre for Animal Genomics (CRB GADIE, Jouy en Josas, France) using primers designed on the plasmid sequences flanking the cDNA inserts (M13RP1 5’- GTGGAATTGTGAGCGGATAAC and M13RP2 5’-GCAAGGCGATTAAGTTGGG). PCR amplifications (35 rounds) were carried out in 100μl of 1X buffer containing 25 mM MgCl2, 250 μM dNTP, 100μM each primer, and 2.5 Units of Taq polymerase (Promega, Madison, WI). For each cDNA clone, two amplification products were pooled, desiccated and resuspended in 50 μl of distilled water. They were then spotted as previously described [10445855] onto Hybond-N+ 2x7 cm2 membranes (Amersham Pharmacia Biotech, Cleveland, OH, USA) stuck to glass slides using a 8-pin print head (Pin-and-Ring™ technology) on the GMS 417™ (Affymetrix, MWG-Biotech, Ebersberg, Germany). Spotted DNA was then denatured and UV– cross-linked onto nylon filters. All membranes used in this study were made at the same time and under the same condition.


title: Yeast 70mer oligoset

status: Public on Dec 27 2007

city: Albuquerque

first: Sushmita

last: Roy

state: NM

institute: Biology, University of New Mexico

organism: Saccharomyces cerevisiae

first: Anthony

middle: D

last: Aragon

first: Margaret

middle: C

last: Werner-Washburne

manufacture_protocol: Oligos resuspended in 3X SSC, stored at -20 C. Prior to printing plates were thawed and shaken at 4 C. Plates were spun and placed on the microarray plate holders with well A1 at the upper left corner.


title: NHGRI Homo sapiens 6K

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

organism: Homo sapiens

manufacture_protocol: This cDNA microarray comprises ~6,700 genes printed in the Microarray Core of the National Human Genome Research Institute (NHGRI)/NIH. These cDNA microarrays were generated by PCR amplification from cDNA clones obtained from the sequence verified IMAGE clone selection from Research Genetics (Invitrogen corporation, Inc). The gene description of these clones was based on the Unigene database, build #199. Annotations were updated using the Array Clone Information Database (PMID: 14962935). A detailed description of array manufacturing protocols can be found at the Microarray Project website at NHGRI


title: USDA-ARS PSMRU Campylobacter jejuni version 8

status: Public on Dec 28 2007

city: Albany

first: Craig

middle: T

last: Parker

address: 800 Buchanan St

department: PSM

institute: USDA ARS

organism: Campylobacter jejuni

description:
A microarray with features corresponding to almost all ORFs in the Campylobacter jejuni strains NCTC 11168 genome, unique ORFs from RM1221; ORFs from LOS classes A, B, D, E, F, G, H and M; ORFs from capsular biosynthesis loci for HS1, HS19, HS23:36, and HS41; ORFs from pVIR (spots in duplicate).
Blocks per array:16
Columns per block:18
Rows per block:18
Corning barcoded UltraGAPS slides

manufacturer: Produce Safety and Microbiology, USDA-ARS, Albany CA

manufacture_protocol: PCR product array of ORF's from Campylobacter jejuni strains NCTC 11168, RM1221, RM1047, 81-176, RM1048, RM1050, RM3193 (260.94), RM1045, RM1555, 43446. PCR products resuspended in resuspended to an average concentration of 0.1-0.2 µg µl-1 in 20 µl of 50% dimethyl sulfoxide (DMSO) containing 0.3× Saline-Sodium Citrate (SSC). Spotted on Corning barcoded UltraGAPS slides using a GeneMachine Accent printer with ChipMaker pins.


title: USDA-ARS PSMRU Campylobacter jejuni version 2

description:
A microarray with features corresponding to almost all ORFs in the Campylobacter jejuni strains NCTC 11168 genome, unique ORFs from RM1221, ORFs from LOS classes A, B, D, E, F, and H (spots in duplicate).
Blocks per array:16
Columns per block:18
Rows per block:18
Corning barcoded UltraGAPS slides


title: NCI Human 454 Platform 2795K

status: Public on Dec 21 2007

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

technology: other

distribution: virtual

manufacture_protocol: not applicable


title: UHN Yeast 6.4kv6

status: Public on Dec 22 2007

city: Rehovot

first: Naama

last: Barkai

address: P.O box 26

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute of Science

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: INRA-BDR Bovine D14 Embryo 1K

status: Public on Dec 20 2007

city: Jouy en Josas

first: Isabelle

last: Hue

address: Domaine de Vilvert

department: PHASE

organism: Bos taurus

description: (8cmx12cm, Amersham Biosciences) 5x5 pattern

manufacturer: INRA/UMR Biologie du Developpement et Reproduction

first: Severine

last: Degrelle

first: Francois

last: Piumi

manufacture_protocol: cDNA inserts from the bcai arrayed library (bcai library indexed in TIGR as #FJB and in NCBI as "15979") were amplified by PCR using the flanking primers used to construct this SMART-amplified library (PCRp1 primers from the Cap Finder cDNA kit, Clontech). After a short run on a 2.5% agarose gel, the probes were selected (size >= 500pb), spotted and fixed (UV light, 1 min, 1200J, twice) onto nylon N+ membranes (8cmx12cm, Amersham Biosciences) with a 5x5 pattern (BioRobotics). The whole array represents 1920 probes but the biological core of the array (1K array) represents only 987 informative probes (1097 sequences submitted to the EBI deprived of the 110 mitochondrial sequences).


title: AresLabUCSC_Mouse_24K_MuSpliceV1

city: Los Angeles

first: Douglas

last: Black

address: 675 Charles E Young Dr S

department: MIMG

institute: UCLA

organism: Mus musculus

first: Manuel

last: Ares

first: Lily

last: Shiue

first: John-Paul

last: Donohue

first: Roland

last: Nagel

first: Leslie

last: Grate

first: Christina

last: Zheng

middle: L

first: Peter

last: Stoilov

first: Geetanjali

last: Chawla

first: Ji-Ann

last: Lee

manufacture_protocol:
Oligonucleotide and microarray design have been described previously (Clark et al., 2002; Srinivasan et al., 2005). To chose exons whose regulation was likely to be functionally significant, we used exons from 5 datasets: (i) Exons identified from the literature that exhibit neuron-specific or muscle-specific regulation, or have partially characterized mechanisms of regulation; (ii) Exons derived from genes coding for known splicing factors or protein kinases involved in splicing where EST, phylogenetic, and other evidence supports a role for these exons in regulating protein expression by coupling to NMD (similar to PTB exon 11); (iii) Exons in genes associated with cancer and tumor development, whose splicing is thought to have important functional effects on the encoded proteins; (iv) Exons derived from the MAASE database of alternative splicing (Zheng et al., 2005). These exons affect proteins that have well described functions in the Swiss-prot database; (v) a subset of the exons identified by Sugnet (Sugnet et al., 2004) as showing conserved regulation between human and mouse. The exon sets were combined, filtered for redundancies and used to build models for the corresponding transcripts. Oligonucleotide probes for the exon-exon junctions from skipped and included isoforms were designed, along with probes for sequence within the alternative exon itself and within adjacent constitutive exons.
Oligonucleotides were spotted in duplicate. Briefly, 5' amino-linker containing oligonucleotides at 33uM in print buffer (150 mM NaPO4, 6.25% Na2SO4, 0.0005% SDS) were printed and covalently attached to Codelink slides (GE). Printing was done on a linear servo-driven robotic contact pin printer essentially as described by the DeRisi lab at UCSF (http://derisilab.ucsf.edu/arraymaker.shtml). Coupling and post-processing of slides were described previously (Clark et al., 2002).
Clark, T. A., Sugnet, C. W., and Ares, M., Jr. (2002). Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296, 907-910.
Srinivasan, K., Shiue, L., Hayes, J. D., Centers, R., Fitzwater, S., Loewen, R., Edmondson, L. R., Bryant, J., Smith, M., Rommelfanger, C., et al. (2005). Detection and measurement of alternative splicing using splicing-sensitive microarrays. Methods 37, 345-359.
Sugnet, C. W., Kent, W. J., Ares, M., Jr., and Haussler, D. (2004). Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac Symp Biocomput, 66-77.
Zheng, C. L., Kwon, Y. S., Li, H. R., Zhang, K., Coutinho-Mansfield, G., Yang, C., Nair, T. M., Gribskov, M., and Fu, X. D. (2005). MAASE: an alternative splicing database designed for supporting splicing microarray applications. Rna 11, 1767-1776.


title: miMAX microRNA Array

first: maocheng

last: yang

address: 10 Center Drive

department: NCI

institute: National Institutes of Health

organism:
Caenorhabditis elegans
Drosophila melanogaster
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol:
Dimer probes complementary to mature (or abridged) miRNA sequences were printed on glass slided as reference below.
Loyal A. Goff, Maocheng Yang, Roberts C. Getts, Richard W. Padgett, Ronald P. Hart. (2005) Rational probe optimization and enhanced detection strategy for microRNAs using microarrays. RNA Biology 2(3): 93-100


title: Homo Sapiens ENCODE 244k Array

city: Cambridge

first: Elizabeth

last: Herbolsheimer

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

description: Specific Arrays for Spike in Control testing

first: Scott

last: McCuine


title: Macaca fascicularis GeneChip

status: Public on Dec 18 2007

city: Ibaraki

first: Naoki

last: Osada

state: Osaka

address: 7-6-8 Saito-Asagi

department: Division of Biomedical Research Resources

country: Japan

institute: National Institute of Biomedical Innovation

organism: Macaca fascicularis

technology: in situ oligonucleotide

description: Macaca fascicularis GeneChip CDF file is linked as a supplementary file at the foot of this record.

distribution: custom-commercial

first: Katsuyuki

last: Hashimoto

first: Yosuke

last: Kameoka

first: Keiji

last: Terao

first: Jun

last: Kusuda

first: Ichirou

last: Takahashi

manufacture_protocol: The array was made using the standard Affymetrix GeneChip protocol. Oligo DNA probes are designed using information from Macaca fascicularis cDNA libraries that are derived from the brain, liver, and testis.


title: USDA_Fverticillioides_15K_v1

city: Peoria

first: Robert

last: Butchko

state: IL

address: 1815 N. University St.

institute: U.S. Dept. of Agriculture

organism: Fusarium verticillioides

middle: H

last: Proctor

first: Daren

last: Brown

middle: A

first: Charles

middle: P

last: Woloshuk

manufacture_protocol: Maskless Array Synthesizer (MAS) technology


title: Micro-CRIBI Mouse 29K Oligo Array (Operon V1.1)

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

distribution: commercial

manufacturer: Microcribi - Microarray Service (CRIBI - University of Padova)

first: Stefano

last: Cagnin

first: Beniamina

last: Pacchioni

first: Caterina

last: Millino

first: Barbara

last: Celegato

first: Cristiano

last: De Pittà

first: Lucia

last: Tombolan

first: Camilla

last: Bean

first: Chiara

last: Romualdi

manufacture_protocol: This set consists of 13,443 70mer oligonucleotides (Operon version 1.1) designed on Mouse Unigene clusters, mainly in the 3'-terminal region. Each oligonucleotide is spotted by our robotic station Biorobotics Microgrid II, in two replicates on a MICROMAX glass slide SuperChip I (Cat No MPS696) provided by PerkinElmer Life Sciences Inc. The deposition is qualitatively assessed by a scan of the spotted slide at 10 micron resolution, using a GSI Lumonics scanner and a protocol that allows the detection of spotted features through the salts derived from the dried solution in which oligonucleotides are dissolved. Microarray slides that meet the quality standards, are washed as recommended by the supplier and the glass slides are stored, ready for use, in the dark under deep vacuum. Click below to see images of the array and detailed description of the spotting geometry, with the necessary parameters for analysis.


title: Yeast 70mer oligoset by4742

first: Sushmita

last: Roy

first: Anthony

last: Aragon

first: Margaret

last: Werner-Washburne


title: JCVI PFGRC Staphylococcus aureus 22K v6 array designed primarily based on strain MRSA252

status: Public on Dec 13 2007

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Staphylococcus aureus

description: This set includes 4440 oligonucleotides, has 22176 spots distributed in 48 blocks.

manufacture_protocol: 6QSA, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Plasmodium Sal-1 18K v1 array designed primarily based on strain Sal-1

organism: Plasmodium vivax Sal-1

description: This set includes 16120 oligonucleotides, has 18240 spots distributed in 48 blocks.

manufacture_protocol: 2QPV, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Haemophilus influenzae 32K vt1 array designed primarily based on strain HK1212

organism: Haemophilus influenzae

description: This set includes 4574 oligonucleotides, has 32448 spots distributed in 48 blocks.

manufacture_protocol: T1QHI, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Streptococcus mutans 10K v2.1 array designed primarily based on strain UA159

organism: Streptococcus mutans

description: This set includes 1948 oligonucleotides, has 10752 spots distributed in 96 blocks.

manufacture_protocol: 2QSM, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 6075497, pen id 10185, pen cycles -1, operator cs, humidity control On, humidity set point65


title: JCVI PFGRC Neisseria gonorrhoeae 23K v3 array designed primarily based on strain MC58

organism: Neisseria gonorrhoeae

description: This set includes 5383 oligonucleotides, has 23232 spots distributed in 48 blocks.

manufacture_protocol: 3QNG, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Salmonella typhimurium 25K v5 array designed primarily based on strain LT2 (SGSC1412)

organism: Salmonella enterica subsp. enterica serovar Typhimurium

description: This set includes 5459 oligonucleotides, has 25392 spots distributed in 48 blocks.

manufacture_protocol: 5QST, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: NCI Human Solexa Platform 14814K

first: Sean

last: Davis


title: USDA-ARS PSMRU Campylobacter jejuni version 5

status: Public on Dec 19 2007

first: Craig

last: Parker

description:
A microarray with features corresponding to almost all ORFs in the Campylobacter jejuni strains NCTC 11168 genome, unique ORFs from RM1221, ORFs from LOS classes A, B, D, E, F, G, H and M , ORFs from capsular biosynthesis loci for HS1, HS19, HS23:36, and HS41 (spots in duplicate).
Blocks per array:16
Columns per block:18
Rows per block:18
Corning barcoded UltraGAPS slides


title: LC-49

city: Stanford

first: Stephen

last: Popper

department: Division of Infectious Diseases, Dept. of Medicine

institute: Stanford University

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


title: NimbleGen Homo sapiens HG18 promoter 2 of 2

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
Source: UCSC
Build: HG18, NCBI 36
Probe Length: 50-75mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16um x 16um
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)

manufacture_protocol: see manufacturer's web site


title: NimbleGen Homo sapiens HG18 promoter 1 of 2

description:
Source: UCSC
Build: HG18, NCBI 36
Probe Length: 50-75mer
Median Probe Spacing: 100bp
Probes per Array: 385,000
Feature Size: 16um x 1um
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)


title: LC-42


title: CEA - DSV/IRCM/LEFG : Mouse 24k oligo v1.0

status: Public on Dec 15 2007

city: Evry

first: Olivier

last: ALIBERT

address: 2 rue Gaston Crémieux

department: IRCM

institute: CEA

first: Amelie

last: Robert

first: Peggy

last: Maltere

first: Simon

last: Tendil

manufacture_protocol: Chip contains 25344 features (probes and controls): 24109 oligonucleotides from mouse RNG/MRC collection (Le Brigand K et all, An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. Nucleic Acids Res. 2006 Jul 19;34(12)). Oligos printed in phosphate buffer with MicroGridII (BioRobotics).


title: JCVI PFGRC Listeria monocytogenes 21K v3 array designed primarily based on strain 4b F2365

organism: Listeria monocytogenes

description: This set includes 6322 oligonucleotides, has 21168 spots distributed in 48 blocks.

manufacture_protocol: 3QLM, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Escherichia coli 6k oligo microarray

city: Vancouver

first: Mickael

last: Le Gac

address: University Boulevard

country: Canada

institute: University of British Columbia

organism: Escherichia coli

manufacturer: Microarray Facility, Prostate Centre at Vancouver General Hospital

first: Melanie

last: Bertrand

first: Minghui

last: Yang

first: Michelle

last: Brazas

first: Robert

middle: E

last: Hancock

first: Michael

last: Doebeli

manufacture_protocol: Oligonucleotides were resuspended in 384 well flat-bottom plates (Nunc, New York, USA) to a concentration of 30 μM in 3X SSC (600 pmol of oligo into a volume of 20 μl 3X SSC).  Arrays were printed on EZ-Rays aminosilane slides (Matrix Technologies, Hudson, NH, USA) with the Biorobotics Microgrid II microarray printer (Genomic Solutions, Ann Harbor, Michigan, USA). Microspot 10K quill pins (Biorobotics, Cambridge, UK) in a 48-pin tool were used to deposit 0.5 nL (0.1 ng cDNA) per spot onto the slide. The resulting microarrays have a 12 x12 subgrid layout with 144 features per subgrid, each spot having approximate diameter and pitch of 90 µm and 300µm, respectively. A 280-bp GFP (green fluorescent protein) cDNA was amplified from a GFP clone (BD Biosciences, Mountain View, CA, USA) by using the primers (5’-GAAACATTCTTGGACACAAATTGG-3’) and (5’-GCAGCTGTTACAAACTCAAGAAGG -3’), and printed in subgrid corners to assist in placing on the grid. The slides were crosslinked in a UV Stratalinker 2400 (Stratagene, La Jolla, CA, USA) at 300mJ. All slides are inspected manually to identify any major printing issues. One slide every 20 to 30 slides was hybridized with labeled random 9-mer oligonucleotide (SpotQC, Integrated DNA Technologies, Coraville, IA, USA) or SYBR Green 1 (Invitrogen, Carlsbad, Ca, USA) staining and scanned using ScanArray Express scanner (Perkin Elmer, Wellesley, MA, USA). Presence/absence, shape, signal intensity vs. background, diameter and DNA binding site capability were measured for each spot on the slide using files generated by Imagene software (BioDiscovery Inc., El Secundo, CA, USA). Position and description of flagged spots (spots absent or thought to be unusable during post hybridization analysis) as well as dust, sub-grid defects and other noticed irregularities are recorded. All information collected from all slides controlled for each batch was combined into a report.


title: JCVI PFGRC Staphylococcus aureus 22K v4.1 array designed primarily based on strain N315

description: This set includes 4531 oligonucleotides, has 22080 spots distributed in 96 blocks.

manufacture_protocol: 4QSA, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 1785606, pen id 0, pen cycles -1, operator Jon, humidity control On, humidity set point65


title: JCVI PFGRC Staphylococcus aureus 22K v6 array designed primarily based on strain MW2


title: JCVI PFGRC Staphylococcus aureus 22K v6 array designed primarily based on strain COL


title: JCVI PFGRC Staphylococcus aureus 22K v6 array designed primarily based on strain Mu50


title: JCVI PFGRC Staphylococcus aureus 22K v6 array designed primarily based on strain N315


title: JCVI PFGRC Staphylococcus aureus 22K v6 array designed primarily based on strain MSSA476


title: JCVI PFGRC Trypanosoma brucei 19K v3 array designed primarily based on strain TREU927

organism: Trypanosoma brucei

description: This set includes 8375 oligonucleotides, has 19200 spots distributed in 48 blocks.

manufacture_protocol: 3QTB, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Mycobacterium tuberculosis 22K v4 array designed primarily based on strain CDC1551

organism: Mycobacterium tuberculosis

description: This set includes 4742 oligonucleotides, has 22176 spots distributed in 48 blocks.

manufacture_protocol: 4QMT, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Helicobacter pylori 10K v1 array designed primarily based on strain J99

organism: Helicobacter pylori

description: This set includes 2571 oligonucleotides, has 10800 spots distributed in 72 blocks.

manufacture_protocol: QHP, with arrayer LUCIDEA, mode Normal, replicates 3, repeats 1, slide_dips 50, machine cycles 1867390, pen id 180, pen cycles -1, operator ROBIN, humidity control On, humidity set point65


title: JCVI PFGRC Mycobacterium smegmatis 14K v1 array designed primarily based on strain MC2 155

organism: Mycolicibacterium smegmatis

description: This set includes 6158 oligonucleotides, has 14688 spots distributed in 48 blocks.

manufacture_protocol: QMS, with arrayer LUCIDEA, mode Normal, replicates 2, repeats 1, slide_dips -1, machine cycles 3096582, pen id 10186, pen cycles -1, operator MICROARRAY, humidity control On, humidity set point65


title: SAGE:17:NlaIII:Rhipicephalus microplus

last: GEO

organism: Rhipicephalus microplus

technology: SAGE NlaIII

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


title: JCVI PFGRC Salmonella typhimurium 25K v5 array designed primarily based on strain Ty2


title: JCVI PFGRC Porphyromonas gingivalis 10K v1.1 array designed primarily based on strain W83

organism: Porphyromonas gingivalis

description: This set includes 1903 oligonucleotides, has 10752 spots distributed in 96 blocks.

manufacture_protocol: QPG, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 1065790, pen id 186, pen cycles -1, operator Robin, humidity control On, humidity set point65


title: JCVI PFGRC Salmonella typhimurium 25K v5 array designed primarily based on strain CT18


title: EJH Mcat Oligo-DNA Microarray 2

status: Public on Dec 07 2007

city: Dallas

first: Eric

middle: J

last: Hansen

state: TX

address: 5323 Harry Hines Boulevard

institute: University of Texas Southwestern Medical Center

organism: Moraxella catarrhalis

first: Wei

last: Wang

first: Rob

last: Blick

manufacture_protocol: The oligonucleotides were synthesized by Qiagen and spotted in triplicate on Corning UltraGapII slides


title: JCVI PFGRC Neisseria gonorrhoeae 23K v3 array designed primarily based on strain Z2491

first: PFGRC

last: JCVI


title: IU/UNH/DU Daphnia pulex Generation 2.4 (3.1K)

city: Bloomington

first: Joseph

middle: R

last: Shaw

state: IN

address: 1315 E. Tenth Street

department: The School of Public and Environmental Affairs

institute: Indiana University

organism: Daphnia pulex

description: This is a condensed platfom of the full array which was printed with duplicate spots side-by-side, and consisted of 24 blocks of 18 rows and 17 columns each.

manufacturer: Indiana University - The Center for Genomics and Bioinformatics

first: John

middle: K

last: Colbourne

manufacture_protocol:
cDNA libraries were constructed as described in Colbourne et al. (BMC Genomics 2007, 8). From each library, 384 samples were PCR amplified from plasmids purified using the PerfectPrep kit (Eppendorf) and sequenced using BigDye (ABI; v.2) on an ABI 3730 sequencer. These samples served as a random sample for quality control in further analysis. Remaining samples (3,168 in all) were PCR amplified from colony picks of transformed bacterial cells. Template was generated by growing colonies in 1.2 ml of 2X YT and 0.005 % chloramphenicol in 96-deepwell plates for 24 hours at 37 °C. Reactions were run in 100 μl containing: 1X Taq buffer (Eppendorf), 0.2 mM dNTPs, 0.2 microM primers (Fwd. 5'-GTGTAAAACGACGGCCAGTAG 3’ and Rev. 5'-AAACAGCTATGACCATGTTCAC 3’), 5 U Taq (Eppendorf), and 5 microliters fresh bacterial growth or 2 microliters purified plasmid. Quality of PCR amplifications was verified by gel electrophoresis, and number and size of bands was recorded using Kodak’s 1D imaging software (v.3.6). Concentration of samples was determined by 96-well microplate spectrophotometer (Molecular Devices SpectraMax 190) and adjusted to 50-200 ng/microliter for printing.
A Genemachines Omnigrid 100 was used to print the D. pulex cDNA on GapsII aminosilane slides (Corning). The cDNA was printed in 3X SSC and 1.5 M Betaine buffer and deposited with Stealth Micro-Spotting Pins (Telechem) at 20 °C and 65 % humidity. The cDNA was fixed to the microarray slides by baking at 85 °C for 3 hours. Slides were processed by agitating in 0.2 % SDS for 5 min. and in HPLC-grade water, 5 min at 21 °C, followed by 2 min in 95 °C water, rinsing briefly in ice-cold 100 % isopropanol, and centrifuging at 500 x g for 5 min. Five types of negative controls were printed, including printing buffer, failed PCR reaction with template DNA but no primers, ORFs from Arabidopsis and lambda phage, and bacterial PCR spikes (Ambion). Positive controls of D. pulex genes were printed next to printing buffer to insure no carryover, and included cytochrome c (subunits I, II, and III), cytochrome b, actin, and ferritin.


title: JCVI PFGRC Mycobacterium smegmatis 22K v3 array designed primarily based on strain MC2 155

description: This set includes 6158 oligonucleotides, has 22176 spots distributed in 48 blocks.

manufacture_protocol: 3QMS, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Neisseria gonorrhoeae 23K v3 array designed primarily based on strain FA 1090


title: JCVI PFGRC Francisella tularensis 12K v2 array designed primarily based on strain F6168

organism: Francisella tularensis

description: This set includes 2294 oligonucleotides, has 12288 spots distributed in 96 blocks.

manufacture_protocol: 2QFT, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 868990, pen id 10179, pen cycles -1, operator bj_sp, humidity control On, humidity set point65


title: SBC Human 16K cDNA Microarray

status: Public on Dec 12 2007

city: Shanghai

first: Huasheng

last: Xiao

address: No.151,Libing Rd.,Zhangjiang Hi-Tech Park,Pudong

department: Department of Genechip

institute: Shanghai Biochip Co., Ltd.

organism: Homo sapiens

first: J

last: Zhou

first: Z

last: Zhu

last: Han

first: X

last: Gu

first: Q

first: Y

last: Chen

last: Zhang

first: H

manufacture_protocol: The cDNA fragments of selected genes were amplified by PCR and the final concentration is ranged from 200 ng/μl to 250 ng/μl. The cDNA fragments were spotted on poly-lysine coated slides by using OmniGrid 100 spotter and cross linked in 400 mJ UV. Keep temperature(room temperature: around 20℃) and the humidity(50%-55%).


title: VMSR Mus musculus MEEBO 38.5K v1.0

city: Nashville

first: Braden

last: Boone

state: TN

address: 465 21st Ave South

department: Vanderbilt Microarray Shared Resource

institute: Vanderbilt University

organism: Mus musculus

description: Full genome M. musculus array containing all oligonucleotides from the MEEBO mouse genome set (http://mmc.ucsf.edu/Meebo.html).

manufacture_protocol: Microarrays were produced by Microarrays Incorporated (www.microarrays.com) utilizing custom, high precision robotics and amine-coated glass slides from Genexprex


title: QArray Oligo OL19kA Prints 0301-0307

status: Public on Dec 05 2007

city: Urbana

first: Lila

middle: O.

last: Vodkin

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

organism: Glycine max

manufacturer: Vodkin laboratory, University of Illinois

middle: O

first: Delkin

last: Gonzalez

manufacture_protocol: spotted on Corning GAPS II glass slides


title: JCVI PFGRC Burkholderia mallei 22K v2 array designed primarily based on strain GB8 horse 4

organism:
Burkholderia mallei
Burkholderia pseudomallei

description: This set includes 9826 oligonucleotides, has 22176 spots distributed in 48 blocks.

manufacture_protocol: 2QBM, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Clostridum botulinum 8K v1 array designed primarily based on strain Hall strain A

organism: Clostridium botulinum

description: This set includes 3617 oligonucleotides, has 8448 spots distributed in 48 blocks.

manufacture_protocol: QCB, with arrayer LUCIDEA


title: JCVI PFGRC Francisella tularensis 12K v2 array designed primarily based on strain LVS


title: JCVI PFGRC Francisella tularensis 12K v2 array designed primarily based on strain Schu 4


title: JCVI PFGRC Burkholderia mallei 22K v2 array designed primarily based on strain K96243


title: JCVI PFGRC Streptococcus pyogenes 21K v1 array designed primarily based on strain MGAS2096

organism: Streptococcus pyogenes

description: This set includes 9395 oligonucleotides, has 21168 spots distributed in 48 blocks.

manufacture_protocol: QSY, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Burkholderia mallei 22K v2 array designed primarily based on strain 1710b


title: JCVI PFGRC Streptococcus pyogenes 21K v1 array designed primarily based on strain MGAS10750


title: JCVI PFGRC Streptococcus pyogenes 21K v1 array designed primarily based on strain MGAS9429


title: JCVI PFGRC Streptococcus pyogenes 21K v1 array designed primarily based on strain MGAS10270


title: JCVI PFGRC Burkholderia mallei 22K v2 array designed primarily based on strain ATCC 23344


title: JCVI PFGRC Streptococcus pyogenes 21K v1 array designed primarily based on strain MGAS6180


title: JCVI PFGRC Yersinia pestis 25K v3 array designed primarily based on strain CO92

organism: Yersinia pestis

description: This set includes 4826 oligonucleotides, has 25392 spots distributed in 48 blocks.

manufacture_protocol: 3QYP, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Streptococcus pyogenes 21K v1 array designed primarily based on strain MGAS5005


title: JCVI PFGRC Yersinia pestis 25K v3 array designed primarily based on strain KIM


title: Kraus_lab Human custom PCR-based spotted microarray

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
There are two replicate regions ('Upper' and 'Lower') on the same microarray slide.  The Platform data table reflects a condensed representation of the array's replicate features.  The exact details of the microarray design have been published and can be found here: http://mcb.asm.org/cgi/content/full/27/14/5090?view=long&pmid=17515612 and here: http://mbg.cornell.edu/cals/mbg/research/kraus-lab/sm.cfm#kinnis
The .gal file is linked below as a Supplementary file.

first: Miltiadis

last: Kininis

first: Benjamin

middle: S

first: Adam

middle: G

last: Diehl

first: Gary

last: Isaacs

first: Tong

last: Siepel

first: Andrew

last: Clark

first: William

manufacture_protocol: Spotting of PCR products on glass slides


title: JCVI PFGRC Streptococcus sanguinis 12K v1 array designed primarily based on strain SK36

first: PFGRC

last: JCVI

organism: Streptococcus sanguinis

description: This set includes 2273 oligonucleotides, has 12288 spots distributed in 96 blocks.

manufacture_protocol: QSS, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 830590, pen id 179, pen cycles -1, operator cs, humidity control On, humidity set point65


title: JCVI PFGRC Streptococcus pyogenes 21K v1 array designed primarily based on strain SF370


title: Agilent 244k ENCODE custom tiling array

first: David

middle: Scott

last: Johnson

address: 300 Pasteur Drive

department: Genetics

description: Human genome build 35

manufacture_protocol: see the manufacturer's website


title: JCVI PFGRC Helicobacter pylori 10K v1 array designed primarily based on strain 26695

manufacture_protocol: QHP, with arrayer LUCIDEA, mode Normal, replicates 3, repeats 1, slide_dips 50, machine cycles 1867390, pen id 180, pen cycles -1, operator ROBIN, humidity control On, humidity set point65


title: JCVI PFGRC Streptococcus pyogenes 21K v1 array designed primarily based on strain MGAS8232


title: JHMI_GGG_Mouse_24K_v1

city: Baltimore

first: Gregory

last: Germino

address: 720 Rutland Ave., room 958

department: Medicine, Division of Nephrology

institute: Johns Hopkins School of Medicine

technology: oligonucleotide beads

description: Researchers can profile eight samples per MouseRef-8 BeadChip and approximately 24,000 well-annotated RefSeq transcripts per sample.

first: Klaus

last: Piontek

first: Luis

middle: F

last: Menezes

first: Miguel

last: Garcia-Gonzalez

last: Huso

manufacture_protocol: Available from the Manufacturer (http://www.illumina.com)


title: MIT/SharpLab Mouse ES cell 454 2007

status: Public on Oct 31 2007

first: J. Mauro

last: Calabrese

address: 40 Ames Street

department: Biology

institute: MIT

description: High throughput sequencing of mouse embryonic stem cell short RNAs, 16-30nt fraction.  Libraries were made from J1 ES cells before and 5 days after demethylation with 5-aza-deoxycytidine, and from Dicer-conditional ES cell lines before and after deletion of Dicer's floxed region.  Adaptor ligation required 5' monophosphates and 3' hyrdoxyls.

first: Amy

last: Seila

first: Gene

middle: W

last: Yeo

first: Phillip

last: Sharp


title: EJH Mcat Oligo-DNA Microarray

first: Eric

last: Hansen

department: Microbiology

first: Wei

last: Wang

first: Rob

last: Blick

manufacture_protocol: The oligonucleotides were synthesized by Qiagen and spotted in duplicate on Corning UltraGapII slides


title: UGAmamlab_Silicibacter_pomeroyi_DSS-3_8k_v1.0

status: Public on Dec 09 2007

city: Athens

first: Shulei

last: Sun

address: Department of Marine Science

department: Marine Science

institute: UGA

organism: Ruegeria pomeroyi DSS-3

first: Helmut

last: Buergmann

first: Erinn

last: Howard

first: Wenying

last: Ye

first: Feng

first: Sarah

last: Napierala

first: MaryAnn

last: Moran

manufacture_protocol: Hybridization protocol for Customarray 12K microarrays by COMBIMATRIX


title: UTSW Homo sapiens 1.6K subtelomeric genes

city: Dallad

first: zhenjun

last: Lou

department: Cell Biology

institute: The University of Texas Southwestern Medical Center at Dallas

manufacturer: Microaaray facility, UT Southwestern Medical Center at Dallas

first: Zhenjun

first: Jerry

last: Shay

first: Woodring

last: Wright

first: Quan

last: Li

manufacture_protocol:
Spotted array
nucleotides on glass slides


title: UW Lidstrom Methylobacterium extorquens AM1 11K v1.0

city: Seattle

first: Jonathan

middle: A.

last: Miller

state: WA

address: 616 NE Northlake Place

institute: University of Washington

organism: Methylorubrum extorquens AM1

description: Platform annotation based on June 2002 annotation (genome sequencing done by Integrated Genomics, http://www.integratedgenomics.com/genomereleases.html)

first: Mary

last: Lidstrom

first: Yoko

last: Okubo

first: Dhileep

last: Sivam

first: Charlie

last: Nelson

first: Chris

last: Hopkins

manufacture_protocol: Agilent uses a non-contact in situ standard phosphoramidite chemistry synthesis process to print 60-mer oligonucleotide probes.


title: Hunstman Cancer Institute/University of Utah Mouse a/b cDNA Array

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

description: This platform consists of two slides (mA and mB) with approximately 9000 clones from the NIH/NIA 15K and 7.5K mouse cDNA clone sets on each slide.

manufacturer: Hunstman Cancer Institute/University of Utah Microarray Core Facility

first: Brian

last: Dalley

manufacture_protocol: Amplified clones from the NIH/NIA 15k and 7.5k mouse cDNA clone sets were spotted on Corning Ultra-GAPS glass slides using an Amersham Biosciences Lucidea spotter. Each clone is printed in duplicate.


title: Human microRNA 1K array version 1.0

first: Tsung-Cheng

last: Chang

address: 733 N. Broadway

institute: Johns Hopkins University School of Medicine

organism:
Caenorhabditis elegans
Homo sapiens
Human betaherpesvirus 5
human gammaherpesvirus 4
Murid gammaherpesvirus 4
Human gammaherpesvirus 8

first: Joshua

middle: T

last: Mendell

first: David

last: Valle

first: Dane

last: Witmer

manufacture_protocol: Combimatrix CustomArray™ uses a specially modified “CMOS” semiconductor to direct the molecular assembly of a specific sequence of DNA bases in response to a digital command. Each feature on the array (a microelectrode) is digitally addressed to selectively generate acid, by means of an electrochemical reaction which, in-turn, controls the detritylation reaction during phosphoramidite synthesis. A software program is used to control the microelectrodes, and thus, the detritylation pattern applied on the chip during synthesis.


title: Mouse microRNA 1K array version 1.0

organism:
Caenorhabditis elegans
Mus musculus
Human betaherpesvirus 5
human gammaherpesvirus 4
Murid gammaherpesvirus 4
Human gammaherpesvirus 8


title: VC-oligos

status: Public on Aug 16 2007

last: Stanford Microarray Database

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism: Vibrio cholerae

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


title: WashU_St_Louis_GCAT_yeast_04-05

status: Public on Dec 03 2007

city: Davidson

first: Laurie

last: Heyer

state: NC

address: 209 Ridge Rd, Box 6959

department: Mathematics

institute: Davidson College

organism: Saccharomyces cerevisiae

first: Todd

last: Eckdahl

first: Adam

middle: D

last: Brown

first: Steven

middle: N

last: Hart

first: Kelly

last: Malloy

first: Martha

last: Shott

first: Gloria

last: Yiu

first: Laura

middle: L

last: Mays Hoopes

manufacture_protocol: 70mer oligos printed on epoxy slides. Oligos were based on sequencing of S268C wild type, prepared by Operon.


title: ISB Halobacterium Whole Genome SpanKit Spotted Microarray v1.2

status: Public on Jan 17 2007

first: Bruz

last: Marzolf

institute: Institute for Systems Biology

organism: Halobacterium salinarum NRC-1

first: Marc

last: Facciotti

first: Nitin

last: Baliga

manufacture_protocol:
MIAME platform type: spotted
MIAME availability: Arrays printed at ISB can be purchased, contact bmarzolf@systemsbiology.org for information.
Standard Operating Procedures for the Virtek(ESI) Spotter
*** Always remember that spotter pins are extremely fragile at the tips ***
To make spotter source plates:
1.	Total volume should be 4-8 ul
2.	"Usually, DNA should be in 50% DMSO.  This can be done most accurately be putting an appropriate amount of source material in spotting plates, then drying down with the speedvac and resuspending in the final volume of 3X SSC, 1.5M betaine."
Things not to do:
1.	Move slides after printing starts ? just touching a slide can shift it and other slides enough to ruin the grid geometry.
2.	Use air to blow dust off of slides - you could move the slides
3.	Press the RED EMERGENCY button if it's not a emergency- this will turn off the spotter controller and abort the entire run
4.	"Use PCR products that have been purified, then dried down and resuspended in a very small volume, this is known to cause erratic surface tension and cause spots to run together."
When starting a new print run:
1.	Allow blank slides to sit at 65% humidity for 24 hours
2.	Renew sticky mat if it's dirty
3.	Fill humidifier and turn on
4.	"Pull water out of water bath, wipe out bath and fill reservoir to get bath back to correct level- IT IS EXTREMELY IMPORTANT NOT TO OVERFILL THE WATERBATH OR SONICATOR BATH, WATER SHOULD BE JUST ABOVE THE POINT WHERE CUT RUNNING UP THE PIN ENDS"
5.	Place slides on the deck with label on the right-hand side.  Secure slides by using spacer glass slides held in place with the magnets at the end of the platform.
6.	"Measure total X and Y distances spanned by slides, enter sizes under Calibration for Arraying->Slides"
7.	"Print one ""dip"" with no source plate to ensure that pins are hitting all slides in the same plate (slight errors in Y direction especially can really throw off grid locations.)"
8.	Use the metal brace and spacer slides held by magnets to stabilize and line up the slides
9.	Stabilize humidity at approximately 65%
10.	Put blotting slide in place
To print slides:
1.	Spin down 4 source plates at 2000 rpm for one minute
2.	Put three remaining source plates (in order) at 4 C
3.	"Check blotting slide for blocked pins, change slide. Remove clogged/sticking pins and try to remedy by cleaning pin and/or printhead hole.  If a pin isn't spotting on the blotter, it may just not be contacting the blotter.see if it's been spotting on actual slides."
4.	Change water bath water at beginning of run.
5.	Check level of water reservoir and sonicator bath- add water if necessary
6.	Check humidity
7.	Double-check orientation and number of source plate
8.	Press operator button
9.	Re-seal old plate and put in cold room
10.	Set timer
11.	"Check old plate out, new plate in on printing checklist"
When finished printing for the day:
1.	Seal all plates and place in cold room
2.	Turn off  Spotter light
3.	Turn monitor off
4.	Leave computer ON
When finished with entire printing:
1.	Allow spotter humidity to slowly drop and slides dry out.
2.	Remove slides and place into plastic Telechem slide boxes.
3.	Turn off Spotter light
4.	Turn off fan/humidifier
5.	Place boxes in desiccator at least 12 hours.
6.	"Blow off slides in boxes, then bake at 85 C for 2 hours."
7.	"Etch numbers and corners on slides (corners on back side), blow dry and place in desiccator ready for prehyb."
Things to do periodically:
1.	Just keep an eye on the slides themselves to see if the grids are being formed as expected
To clean a clogged pin:
1.	Remove pin by pulling out from top with a small forceps.
2.	"Dip in water and blow dry with air tip, repeatedly if necessary."
3.	Make sure water reservoir is sufficiently full - low water often causes clogging.
Random experiments that we have tried and their results:
1.	Effect of Temperature and Humidity on Spot Size
Printed H-70 in 3X SSC onto Telechem Amine slides.  Temperatures chosen were 18 C, 20 C, 22 C, and humidities of 40%, 50%, 60% resulting in 9 different conditions.  Hybridization was with labeled PCR primer for 3 hours.
Results: Differences were seen in specific grids, but grid-grid variability was too high to establish a conclusive pattern.  Spots generally were most intense in a 90-100 micron diameter, then had a lighter "halo" that could extend to 130-150 microns.  It appeared that "Halo" size was often smallest at 18 C, 130-140 microns.  We decided to print at ambient temperature, generally 18-20 C.
2.	Effect of Volume and Humidity on Maximum Spots per Dip
Pooled 96 wells of purified PCR product and added SSC for a final concentration of 3X.  Then set up a plate so that 8 pins would print 1ul, another 8 would print 2ul, 4ul, 6ul, 8ul and 10ul.  This 48-pin dip was then printed 25 spots in the Y direction, across 10 plain glass slides for a total of 250 spots.  This print was done with increasing indent at 75%, 70%, 65%, 60% and 55% humidity.
Results: At 1-2ul, pins ran out of juice at 25-50 spots at all humidities.  At 4ul, 200-225 spots could be printed at 65% or higher humidity.  With 6ul or more, 250 spots could be printed at 65% or higher humidity.  Based upon this, we chose 65% humidity for all printing.


title: STv7S_MMCC

status: Public on Feb 06 2007

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

organism: Salmonella enterica

first: Steffen

last: Porwollik

first: Carlos

last: Santiviago

first: Pui

last: Cheng

first: Xiao-Qin

last: Xia

manufacture_protocol: Custom made Salmonella array


title: JCVI PFGRC Streptococcus pyogenes 21K v1 array designed primarily based on strain MGAS10394

status: Public on Dec 01 2007

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

manufacture_protocol: QSY, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Streptococcus pyogenes 21K v1 array designed primarily based on strain SSI-1


title: JCVI PFGRC Streptococcus pyogenes 21K v1 array designed primarily based on strain MGAS315


title: Saccharomyces cerevisiae RSC Specific 22K 8pack

first: Timothy

last: Parnell

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute

description: The RSC specific 22K 8pack array is a customized miniature genomic tiling microarray designed for the analysis of chromatin structure in mutants defective for RSC (Remodels Structure of Chromatin) function. The array represents 218 specific loci from the Saccharomyces cerevisiae genome. These loci include 99 highly occupied targets, 43 non-occupied loci, 54 loci containing Pol III genes, and 22 other loci of interest. Each locus consists of 60mer oligonucleotides spanning an intergenic region of interest and a portion of the flanking ORFs with a mean resolution of 110 bp. The oligo probes were selected from Agilent Technologies’ Yeast Whole Genome ChIP-on-chip Microarray (Platform GPL3737). Additional probes were designed to increase tiling resolution; these are identified with Spot_ID prefix of SC_TJP. The array is based on the 8 pack 22K array format. Each array consists of 1900 spots. The Agilent Design ID is 014377.

first: Brad

last: Cairns

manufacture_protocol: see manufacturer's web site


title: ISB Halobacterium Whole Genome SpanKit Spotted Microarray v1.0


title: Combimatrix Schistosoma mansoni Tenative Consensus Expression Array v1.0

status: Public on Jun 19 2007

city: San Francisco

first: Steve

last: Miller

address: 1600 Divisadero St, Room B-232, Box 1613

department: Laboratory Medicine

institute: University of California, San Francisco

organism: Schistosoma mansoni

description: Schistosoma mansoni Gene Index Tenative Consensus sequences (http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=s_mansoni) were selected for oligonucleotide uniqueness and acceptable metling temperature.  Oligonucleotides were synthesized directly on Combimatrix CustomArray 12K slides using a CustomArray Synthesizer (Combimatrix, Mukiltea, WA) following manufacturer instructions.

first: Emmitt

last: Jolly

first: James

middle: H

last: McKerrow

manufacture_protocol: Combimatrix CustomArray 12K


title: Agilent_custom_Human_C3A_10K

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

organism: Homo sapiens

description: A custom array containing 60-mer oligonucleotides to monitor 5,130 well characterized human transcripts that are chemical responsive in the C3A hepatoma cell line.

first: Wim

last: De Coen

first: Paul

last: Van Hummelen

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


title: Cerevisiae Operon Ybox and Aros UCSF

city: Berkeley

first: Jesse

middle: C

last: Patterson

address: 528 Barker Hall

department: Dept of Molecular and Cell Biology

institute: UC-Berkeley

manufacturer: Oligos from Operon, Printed at the Center for Advanced Technology UCSF

first: Patrick

last: Westfall

first: Raymond

middle: E

last: Chen

first: Jeremy

last: Thorner

manufacture_protocol: Single stranded 70mer oligos printed onto poly-lysine coated slides according to the protocol found at: http://cat.ucsf.edu/resources/printManual_v2.2.pdf


title: Eurogentec-Scerevisiae-Array

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

institute: INRA

technology: mixed spotted oligonucleotide/cDNA

manufacture_protocol:
* 5803 yeast ORFs spotted in duplicate on glass slide
* 68 control genes
* Also available:
- Set of primer pairs for PCR
- Set of aminated PCR products
- Mix of specific oligos for RT reaction
- Optimized hybridization
Construction of S. cerevisiae MicroArray
Comparative genome analysis of 6213 predicted Saccharomyces cerevisiae open reading frame (ORF) products with 13 yeast genome sequence related species proposed the elimination of 612 predicted ORFs that are not real genes (A. Malpertuy et al, FEBS Letters, Volume 487, 22 December 2000). The study identified the presence of 50 new genes.
Specific pair of primers was designed by Pasteur Institute, Paris to amplify all 5803 ORFs non-spurious coding sequences. The primers were selected carefully to amplify only a specific region of each ORF.
Universal sequences of 15 bases were incorporated on the 5' of each specific forward and reverse primer.
The two-step PCR method has been employed to generate 5' amino-modified PCR for covalent attachment to the aldehyde-coated support.
All the amplicons have an average length of 300 bp and they were controlled systematically by electrophoresis on agarose gels.
Spotting design
The yeast 5803 ORFs MicroArray is composed of 32 subgrids, which follow a pattern of 8 metarows and 4 metacolumns. Each subgrid contains 20 columns and 21 rows with a dot spacing of 200 µm. Probes are spotted as closed duplicates. In order to provide a friendly environment, the first subgrid row on each array metarow contains all the normalization controls, which include the controls with serial dilution of the Renilla LuxA cDNA PCR product. In addition to this control, four serial dilutions of the sonicated yeast S288c genomic DNA are also located in the corner subgrids of the MicroArray.
MicroArray content
To determine the background values, the stringency of the hybridization and washing conditions we add the following probes to the MicroArray:
1- Three E. coli genes showing no homology with yeast ORFs (aceF, kdtA and tufA),
2- Ten yeast intergenic regions
3- Three orthologous genes from Schizosaccharomyces pombe Leu1, His1 and Ura4 and printing buffer are spotted on the MicroArray (negative controls).
Marker genes are also present onto the MicroArray in order to follow the expression of genes of interest (Schistosoma mansoni 28 kDa glutathione S-transferase, Aequorea victoria green-fluorescent protein GFP, TAP fusion tag, human c-myc tag, LexA DNA binding domain , Pho4 DNA binding domain, b-galactosidase LacZ 5'- and 3'- encoding regions) or the genetic background of a KanMX-modified strain.
Finally, two sets of oligonucleotides cover the large genes YKL182w (6.153 kbp, 11 oligonucleotides), and YLR310c (4.567 kbp, 9 oligonucleotides) to allow the user to monitor the efficiency of the reverse transcription reaction.
Quality control
* The S. cerevisiae MicroArrays are certified to generate high quality data.
* All printed slides are previously selected for coating uniformity and low intrinsic background.
* The MicroArrays are visually inspected for spotting quality (doughnuts), uniformity, integrity and for perfect alignment of spots and grids.
* From each batch of printed MicroArrays, three are randomly chosen for further quality control. We use the Terminal Transferase reaction to assess the amount of DNA covalently attached to the slides. Finally, we perform a real hybridization using labeled cDNA from heat-shock cultured cells.
Packaging


title: UTTH_Mouse/P.bergheiANKA_44K_v1.0

status: Public on Nov 24 2006

city: Toronto

first: Fiona

last: Lovegrove

state: ON

address: 1 King's College Circle, MSB Rm 7318

department: Institute of Medical Science

institute: University of Toronto

organism:
Plasmodium berghei
Mus musculus

first: Lourdes

last: Pena-Castillo

first: Naveed

last: Mohammad

middle: R

last: Hughes

first: Kevin

last: Kain

manufacture_protocol: In situ oligosynthesized


title: NimbleGen Human HG17 60mer expression 381K array

status: Public on Oct 21 2007

city: Madison

first: Melodee

address: 510 Charmany Dr Ste 58 & 59

institute: WiCell

manufacture_protocol: Standard NimbleGen maskless array synthesis for standard 60-mer hg17 gene expression array


title: Riken Mouse 4K miRNA array M8.2

status: Public on Oct 01 2007

city: Kobe

first: Anthony

middle: CF

last: Perry

state: Hyogo-ken

address: 2-2-3 Minatojima-minamimachi

department: Center for Developmental Biology

institute: RIKEN

organism: Mus musculus

manufacture_protocol: as described in RIKEN Center for Developmental Biology manual


title: Riken Mouse 4K miRNA array M8.0


title: Array designs: Whole Genome

status: Public on Nov 18 2006

city: Vancouver

first: Donald

last: Moerman

state: British Columbia

address: 301 - 2185 East Mall

department: Michael Smith Laboratories

institute: University of British Columbia

organism: Caenorhabditis elegans

manufacture_protocol:
see NimbleGen website at http://www.nimblegen.com
50-mers oligos were used.


title: Array designs: Chromosomes X and II


title: Affymetrix Drosophila Melanogaster Antisense Tiling Array

status: Public on Aug 04 2006

city: Santa Clara

first: Thomas

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

organism: Drosophila melanogaster

description:
35bp Resolution Oligonucleotide Tiling Array
Annotation in this record is based on BDGP Release 4, Apr 2004 version
Keywords: synthetic, oligonucleotide, tiling array

manufacture_protocol: See manufacturer's website.


title: Riken Mouse 4K miRNA array M8.1


title: VUMC MACF Mouse 38K oligo v64

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: - oligonucleotides were mapped by using the file MEEBO_track from UCSF

first: Thijs

last: Krugers

last: van den IJssel

first: Bauke

last: Ylstra

first: Alan

last: Mrsic

manufacture_protocol: The Oligator "MEEBO" Mouse Genome Set, containing 70-mer oligonucleotides representing 35302 unique genes as produced by Illumina (San Diego, CA, USA). The oligonucleotides were dissolved at 10 μM concentration in 50 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink™ slides (Amersham Biosciences), using an OmniGrid® 100 microarrayer (Genomic Solutions, Ann Arbor, MI, USA) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). After printing slides were processed and blocked prior to use according to the manufacturer’s protocol.


title: Riken Mouse 4K miRNA array version 2.0

status: Public on Sep 06 2006

description: This set includes 3296 oligonucleotides


title: WCFS Lactobacillus plantarum 15K 60-mer array, Version 3, our ID LPAG3_8

status: Public on Sep 20 2007

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

institute: Vrije Universiteit Amsterdam

organism: Lactiplantibacillus plantarum WCFS1

description: This array contains 60-mer probes that are designed for L. plantarum strain WCFS1. The sequence of this organism is present in public databases, Acc. Nr. AL935263.

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


title: piRNA sequences in mouse

status: Public on Jul 03 2006

city: Waltham

first: Nelson

last: Lau

address: 415 South St MS029

department: Biology

institute: Brandeis University

description: Sequences were analyzed and annotated for matches to the mouse genome. See Supplemental Online Materials from Lau et al. Science. 2006 Jun 15; [Epub ahead of print] PMID: 16778019 for detailed protocol on data processing.

first: Anita

last: Seto

first: Jinkuk

last: Kim

first: Satomi

last: Kuramochi-Miyagawa

first: Toru

last: Nakano

first: David

middle: P

last: Bartel

first: Robert

last: Kingston

manufacture_protocol: We constructed a cDNA library from small RNAs purified from Q column fractions of testes extracts. Briefly, gel-purified small RNAs from the column fractions were ligated with adaptor oligos on both 3' and 5' ends of the small RNAs. Reverse-transcription and PCR amplification was then performed on the ligated small RNAs to yield a cDNA library. This cDNA library was finally converted by PCR into a single-stranded DNA library compatible for coupling to beads on the 454 Life Sciences Genome Sequencer 20 System. Reads and sequences of the small RNAs were processed from linker sequences, examined for matches to the mouse genome, and tallied.


title: Arabidopsis whole genome tiling array ver1.0

status: Public on Dec 14 2006

city: New Haven

first: Kun

last: He

state: CT

address: 165 Prospect

department: Molecular, Cellular & Developmental Biology

institute: Yale University

organism: Arabidopsis thaliana

description:
Oligo nucleotides 60mer in length are designed to represent single strand of the nonrepetitive DNA of the arabidopsis genome.
The probes were selected from the Jan 22, 2004 TIGR release ver5.0  Arabdiopsis genome data

first: Jungeun

last: Lee

first: Viktor

last: Stolc

first: Ilha

first: Xingwang

last: Deng

manufacture_protocol: Microarrays containing these oligos are synthesized on glass with Expedite DNA synthesizers (Applied Biosystems, Foster City, CA) in conjunction with Maskless Array Synthesis units (NimbleGen Systems, Madison, WI).


title: Hutch_HP_2006

status: Public on Aug 09 2007

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

institute: Stanford Microarray Database (SMD)

organism: Helicobacter pylori

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: STv6_MMCC

status: Public on May 24 2006

first: Michael

last: McClelland

address: 132 Med Surge I

institute: University of California, Irvine

description: purified PCR products amplified from Salmonella genomes spotted in 50% DMSO

first: Steffen

last: Porwollik

first: Carlos

last: Santiviago

first: Pui

last: Cheng


title: UCSF Cancer Center HumArray2.0

status: Public on Mar 16 2007

first: Antoine

last: Snijders

address: 2340 Sutter Street

department: Cancer Research Institute

institute: University of California San Francisco

manufacture_protocol: For a detailed description on how the arrays were made please refer to: Snijders et al. Nat Genet. 2001 Nov;29(3):263-4.


title: STv7bS_MMCC

first: Xiao-Qin

last: Xia

manufacture_protocol: Custom made Salmonella array


title: UCSF Cancer Center HumArray1.14


title: BCCRC Lam SMRT array 32k_1.2

status: Public on Feb 17 2006

first: Ashleen

last: Shadeo

state: BC

address: 675 west 10th Ave

institute: British Columbia Cancer Research Center

description: A tiling resolution array of 32,433 overlapping BAC clones spanning the human genome (NOTE: this is the same clone-set as the "BCCRC Lam SMRT array 32k" except that clones with insufficient annotation data have been removed; genome coverage remains the same).


title: Syn-2

status: Public on Jan 19 2006

organism: Synechocystis sp. PCC 6803


title: ISB Halobacterium Whole Genome SpanKit Spotted Microarray v1.1

status: Public on Jan 17 2007

city: Seattle

first: Bruz

last: Marzolf

institute: Institute for Systems Biology

first: Marc

last: Facciotti

first: Nitin

last: Baliga

manufacture_protocol:
MIAME platform type: spotted
MIAME availability: Arrays printed at ISB can be purchased, contact bmarzolf@systemsbiology.org for information.
Standard Operating Procedures for the Virtek(ESI) Spotter
*** Always remember that spotter pins are extremely fragile at the tips ***
To make spotter source plates:
1.	Total volume should be 4-8 ul
2.	"Usually, DNA should be in 50% DMSO.  This can be done most accurately be putting an appropriate amount of source material in spotting plates, then drying down with the speedvac and resuspending in the final volume of 3X SSC, 1.5M betaine."
Things not to do:
1.	Move slides after printing starts ? just touching a slide can shift it and other slides enough to ruin the grid geometry.
2.	Use air to blow dust off of slides - you could move the slides
3.	Press the RED EMERGENCY button if it's not a emergency- this will turn off the spotter controller and abort the entire run
4.	"Use PCR products that have been purified, then dried down and resuspended in a very small volume, this is known to cause erratic surface tension and cause spots to run together."
When starting a new print run:
1.	Allow blank slides to sit at 65% humidity for 24 hours
2.	Renew sticky mat if it's dirty
3.	Fill humidifier and turn on
4.	"Pull water out of water bath, wipe out bath and fill reservoir to get bath back to correct level- IT IS EXTREMELY IMPORTANT NOT TO OVERFILL THE WATERBATH OR SONICATOR BATH, WATER SHOULD BE JUST ABOVE THE POINT WHERE CUT RUNNING UP THE PIN ENDS"
5.	Place slides on the deck with label on the right-hand side.  Secure slides by using spacer glass slides held in place with the magnets at the end of the platform.
6.	"Measure total X and Y distances spanned by slides, enter sizes under Calibration for Arraying->Slides"
7.	"Print one ""dip"" with no source plate to ensure that pins are hitting all slides in the same plate (slight errors in Y direction especially can really throw off grid locations.)"
8.	Use the metal brace and spacer slides held by magnets to stabilize and line up the slides
9.	Stabilize humidity at approximately 65%
10.	Put blotting slide in place
To print slides:
1.	Spin down 4 source plates at 2000 rpm for one minute
2.	Put three remaining source plates (in order) at 4 C
3.	"Check blotting slide for blocked pins, change slide. Remove clogged/sticking pins and try to remedy by cleaning pin and/or printhead hole.  If a pin isn't spotting on the blotter, it may just not be contacting the blotter.see if it's been spotting on actual slides."
4.	Change water bath water at beginning of run.
5.	Check level of water reservoir and sonicator bath- add water if necessary
6.	Check humidity
7.	Double-check orientation and number of source plate
8.	Press operator button
9.	Re-seal old plate and put in cold room
10.	Set timer
11.	"Check old plate out, new plate in on printing checklist"
When finished printing for the day:
1.	Seal all plates and place in cold room
2.	Turn off  Spotter light
3.	Turn monitor off
4.	Leave computer ON
When finished with entire printing:
1.	Allow spotter humidity to slowly drop and slides dry out.
2.	Remove slides and place into plastic Telechem slide boxes.
3.	Turn off Spotter light
4.	Turn off fan/humidifier
5.	Place boxes in desiccator at least 12 hours.
6.	"Blow off slides in boxes, then bake at 85 C for 2 hours."
7.	"Etch numbers and corners on slides (corners on back side), blow dry and place in desiccator ready for prehyb."
Things to do periodically:
1.	Just keep an eye on the slides themselves to see if the grids are being formed as expected
To clean a clogged pin:
1.	Remove pin by pulling out from top with a small forceps.
2.	"Dip in water and blow dry with air tip, repeatedly if necessary."
3.	Make sure water reservoir is sufficiently full - low water often causes clogging.
Random experiments that we have tried and their results:
1.	Effect of Temperature and Humidity on Spot Size
Printed H-70 in 3X SSC onto Telechem Amine slides.  Temperatures chosen were 18 C, 20 C, 22 C, and humidities of 40%, 50%, 60% resulting in 9 different conditions.  Hybridization was with labeled PCR primer for 3 hours.
Results: Differences were seen in specific grids, but grid-grid variability was too high to establish a conclusive pattern.  Spots generally were most intense in a 90-100 micron diameter, then had a lighter "halo" that could extend to 130-150 microns.  It appeared that "Halo" size was often smallest at 18 C, 130-140 microns.  We decided to print at ambient temperature, generally 18-20 C.
2.	Effect of Volume and Humidity on Maximum Spots per Dip
Pooled 96 wells of purified PCR product and added SSC for a final concentration of 3X.  Then set up a plate so that 8 pins would print 1ul, another 8 would print 2ul, 4ul, 6ul, 8ul and 10ul.  This 48-pin dip was then printed 25 spots in the Y direction, across 10 plain glass slides for a total of 250 spots.  This print was done with increasing indent at 75%, 70%, 65%, 60% and 55% humidity.
Results: At 1-2ul, pins ran out of juice at 25-50 spots at all humidities.  At 4ul, 200-225 spots could be printed at 65% or higher humidity.  With 6ul or more, 250 spots could be printed at 65% or higher humidity.  Based upon this, we chose 65% humidity for all printing.


title: CE_printS

status: Public on Dec 20 2005

first: Florencia

last: Pauli

address: 279 Campus Drive

department: Developmental Biology

institute: Stanford University

description:
Coating = unknown_surface_type
Support = glass
Platform_manufacturer: John,,Matese; Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Room 135, Princeton, NJ, United States; (609) 258-8309; jcmatese@genomics.princeton.edu
Platform_technology: other


title: STREP-7

status: Public on Feb 02 2006

department: Stanford University, School of Medicine

organism: Streptomyces coelicolor

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


title: STM062602

status: Public on Aug 24 2005

organism: Salmonella enterica subsp. enterica serovar Typhimurium

manufacturer: Tina,,Boussard; School of Medicine, Department of Genetics, Stanford, CA, United States, 94305; 650-736-0077; boussard@genome.stanford.edu


title: NKI-CMF Mus musculus 6k BAC Array

status: Public on Sep 16 2005

first: Daoud

last: Sie

address: Plesmanlaan 161

institute: Dutch Cancer Institute

description: CodeLink Activated Slides from Amersham Biosciences are used as support for the arrays. The slides are coated with a hydrophilic polymer containing N-hydroxysuccinimide (NHS) ester reactive groups and designed to minimize nonspecific binding.

manufacturer: Central Microarray Facility, NKI Amsterdam

first: Ron

last: Kerkhoven

first: Jos

last: Jonkers

first: Mike

last: Heimerikx

first: Wim

last: Brugman

first: Arno

last: Velds

manufacture_protocol: As described in Chung et al., Genome Research, 2004, vol.14, 188-196


title: HP_Hutcharray_6-03

status: Public on Aug 26 2005

last: Stanford Microarray Database

manufacturer: Jeremy,,Gollub; CCSR 2255, Stanford, California  94305; 650-736-0075; jgollub@genome.stanford.edu


title: SSH-PCR SON-C-D array

status: Public on Dec 02 2005

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

organism: Rattus norvegicus

manufacturer: Mohamed Ghorbel, Greig Sharman, Charles Hindmarch, Kevin Becker, Tanya Barrett and David Murphy

first: Mohamed

last: Ghorbel

first: Greig

last: Sharman

first: Charles

last: Hindmarch

first: Kevin

last: Becker

first: Tanya

last: Barrett

manufacture_protocol:
Generation of SON subtracted cDNA libraries - We generated two subtracted libraries enriched for sequences in either control (C) or dehydrated (D) SON total RNA using the SSH-PCR technique (PCR-Select cDNA Subtraction Kit, BD Biosciences Clontech, Oxford, UK) Total RNA was extracted from pools of 10 -12 SON from either C or D animals using TRIzol (Invitrogen, Paisley, UK). Full-length double stranded cDNA, synthesised using the SMART kit (BD Bioscences Clontech, Oxford, UK), was digested with Rsa I to generate short, blunt-ended fragments optimal for adapter ligation and subtraction. The cDNA in which the specific transcripts are to be found is termed the “tester”, with the reference cDNA being the “driver”. Aliquots of both the C and D cDNAs were then ligated to either of two different adapters (1 or 2R) to generate tester populations (C1, C2R, D1 and D2R). To enrich for differentially expressed sequences present in either C or D SON mRNA populations, two sequential hybridisation reactions were performed. In the first hybridisation, an excess of driver cDNA was added to each tester. Following denaturation, the samples were allowed to anneal for 8 hours at 68 C. As annealing is faster for more abundant mRNA species, due to second order hybridisation kinetics, remaining single stranded tester molecules are enriched for low abundance sand differentially expressed sequences. The two samples from the first hybridisation were then mixed in the presence of fresh denatured driver cDNA and incubated overnight at 68C. This further enriches for differentially expressed sequences through the generation of double-stranded tester molecules with different single-stranded adaptor sequences on each end. Following dilution, hybridisation mixes were subjected to PCR (Advantage PCR Kit, BD Bioscences Clontech, Oxford, UK) which firstly fills in the adapter ends, creating binding sites for primer annealing. Only molecules with two different primer annealing sites are exponentially amplified. A subsequent nested PCR step further reduced background and enriched for differentially expressed sequences.PCR products were then cloned into pT-Adv Vector (Advantage PCR Cloning Kit, BD Bioscences Clontech, Oxford, UK) to produce two subtracted libraries enriched in differentially expressed cDNAs. Optimal ligation efficiency was obtained using <1 day old PCR product with a 1:1 vector:insert ratio. The reaction was incubated overnight at 14 C. The pT-Adv vector contains a single 3' T-overhang that is promiscuous in ligating all PCR products.  It also contains flanking M13 forward and reverse primer sites with the whole vector being resistant to kanamycin and ampicillin with a lacZ gene allowing simple blue / white visual identification for positive recombinant clones. Ligation mixes were transformed into TOP10F' E. coli competent cells using a modified heat shock method. White colonies representing true recombinants were picked from each plate, amplified and stored at -80 C.

Microarray analysis of the cDNA libraries generated by SSH - The putative differentially expressed clones were arrayed on a nylon matrix (27) to generate the SON-C-D array. cDNA inserts were amplified in a 96-well plate format using PCR. The PCR products were checked by gel electrophoresis the transferred to 96-well 'V' bottom plates, ethanol precipitated and air dried overnight.  Pellets were resuspended in 40ml of 1xTE with 0.1M of NaOH added to immediately prior to arraying in order to denature the samples. Nytran+ supercharge (Schleicher and Schuel BioScience, Dassel, Germany) nylon membrane was coated with Krylon repositional adhesive (Schleicher and Schuel BioScience, Dassel, Germany) and cut to the correct size, trimming the edges with a razor and wearing gloves at all times.  The membrane units were placed into the arrayer, with enough to fill the entire plate.  This allowed 42 microscope slide size areas to be printed. Printing of the cDNA microarray was performed using an Affymetrix 417 (Affymetrix, Santa Clara, USA) arrayer.  This machine is capable of arraying 1152 spots in duplicate, producing 42 identical arrays in 8h of continuous printing. cDNA was spotted using a 300mm pin and spot spacing of 665mm centre to centre in 16 identical 12x12 grids.  After spotting, membranes were individually numbered before UV-cross-linking twice using a Stratalinker 2400 (BD Bioscences Clontech, Oxford, UK) at 120mJ/cm2.  As a quality control measure, arrays were inspected by sight, removed and baked at 70 C for 1-2h before being stored at -20 C in heat-sealed plastic bags.
Separate microarrays were probed three times using independently generated target from either C or D SON. For each replicate, SONs from 12 rats, micro-dissected from 1-2 mm coronal slices, were pooled for RNA extraction. Radiolabelled target was generated from 3-10mg of total SON RNA (from either C or D rats) template. [±-33P] CTP was incorporated into cDNA using Superscript II reverse transcriptase (Invitrogen, Paisley, Scotland) and10-20-mer poly(dT) primer (Invitrogen, Paisley, Scotland). Arrays were placed DNA side inwards into 50ml disposable Falcon tubes and washed with 50ml of 2xSSC.  After draining of SSC and removal of air bubbles, membranes were pre-hybridised for 4h at 50 C with 4.0ml Microhyb (Invitrogen, Paisley, Scotland) containing 10ml of 1mg/ml human Cot 1 DNA and 10ml of 8mg/ml poly(dA) both denatured at 95 C for 5min prior to use.  The labelled target was denatured for 5min at 95 C, then added to the 4.0ml pre-hybridisation solution and allowed to hybridise to the probe at 50 C for 12-18h. Washing of the membranes was performed in 50ml 2xSSC 1.0% (v/v) SDS at 50 C, followed by 2x15min washes in 2xSSC 0.1% (v/v) SDS at 50oC.  Moist membranes were aligned on a plastic plate, wrapped tightly in plastic and exposed to phosphorimager screens for 1-3 days.  Spot intensities were captured into ImageQuant software (Amersham Biosciences, Little Chalfont, UK) by scanning screens at 50mm resolution on a phosphorimager (STORM; Amersham Biosciences, Little Chalfont, UK).


title: CAGE-Xylella USP - v.1

status: Public on Dec 22 2005

first: Tie

last: Koide

address: 1441 N 34th street

organism: Xylella fastidiosa

description:
DNA Microarray Construction. PCR primers were designed to amplify unique internal fragments of 200-1000 bp of each predicted CDS described in the annotated genome sequence of X. fastidiosa strain 9a5c (http://aeg.lbi.ic.unicamp.br/xf). Primers (18-23mers) with equivalent predicted melting temperature were designed with the use of a perl program that ran PRIMER3 (http://www-genome.wi.mit.edu/genome_software/other/primer3.html) for the complete CDS list, automatically testing many parameter settings and also guaranteeing that primers hybridized only to a single genome location. Oligonucleotides were synthesized by MWG and Operon Technologies. Genomic or cosmid DNA, obtained in the X. fastidiosa genome sequencing project (Simpson et al. 2000), were used as template in the first round of PCR amplification, and 200-fold-diluted PCR products were used as templates for PCR reamplification to increase product concentration when necessary. The reactions were done in 96-well plates. The mixture in each well contained 100 ng of DNA, 0.5 U of Biolase Taq polymerase (Bioline), 0.2 mM of each dNTP (Invitrogen), 1.5 mM MgCl2 and the primers at 0.5 uM, in a total volume of 100 ul. A 5min denaturing step at 95oC was applied, followed by 40 cycles of 95oC for 45s, 50oC for 30s, 72oC for 1min and a final step at 72oC for 10min. 4 ul of each PCR reaction were checked for product size and concentration by electrophoresis in 1.2% agarose gels. The amplicons were then purified with 96-well MultiScreen purification plates (Millipore) and an equal volume of dimethyl sulfoxide was added to the purified products (~100 ng/ul final concentration). Generation III DNA spotter (Amersham Biosciences) was used to array the samples onto coated type-7 glass slides (Amersham Biosciences). After deposition, the probes were crosslinked to the slides by applying 50 mJ of UV light and the slides were stored desiccated at ~10% relative humidity at room temperature until use.
Keywords = xylella fastidiosa
Keywords = genomotyping
Keywords = DNA microarray
Keywords = comparative genomics

first: Paulo

middle: A

last: Zaini


title: ScoKao_03-05-20

status: Public on Jul 12 2005


title: Sp4000

status: Public on Aug 03 2005

organism: Streptococcus pneumoniae


title: 6k-array, version 3/4.

status: Public on Jul 31 2005

city: Heidelberg

first: Frank

last: Mendrzyk

country: Germany

institute: German Cancer Research Center (DKFZ)

description:
Whole-genome BAC-array. Isolated BAC-DNA was amplified by two-step DOP-PCR. PCR products were dissolved in 3xSSC, 1.5M betaine and spotted as triplicates on epoxysilane-coated slides.
Keywords = Matrix-CGH
Keywords = array-CGH

first: Bernhard

last: Radlwimmer

first: Peter

last: Lichter


title: Array designs: Chromosome II

status: Public on Nov 18 2006

first: Donald

last: Moerman


title: Riken Mouse 4K miRNA array version 3.0

status: Public on Sep 06 2006

first: Anthony

last: Perry

description: This set includes 3493 oligonucleotides


title: Riken Mouse 4K miRNA array version 1.0

description: This set includes 3218 oligonucleotides


title: STREP-2

status: Public on Jul 23 2005


title: USDA Bovine 60mer 344k Array (oligo layout)

status: Public on May 05 2006

city: Beltsville

first: Robert

last: Li

state: MD

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

organism: Bos taurus

description: There are 85235 distinct 60mer oligonucleotides on the array representing ~45383 unique bovine sequences/genes (4 identical spots/features for each 60 oligo).

middle: V

last: Capuco

first: Curt

last: Van Tassell

first: Tad

middle: S

last: Sonstegard

first: Erin

last: Connor

first: Louis

last: Gasbarre

manufacture_protocol: in situ synthesis


title: IS5KO_NonMotile_platform

status: Public on Jun 02 2005

city: Saint Paul

first: Betsy

last: Martinez-Vaz

state: MN

address: 1479 Gortner Ave

department: Biochemistry , Molecular Biology and Biophysics

institute: University of Minnesota

organism: Escherichia coli

description:
This is a platform containing the names and ID for the arrays used in the experiments to compare the level of expression of the sample with IS5 deletion (upstream of flhDC) and the non motile isolate
Keywords = IS
Keywords = mapping
Keywords = DNA
Keywords = arrays
Keywords = nonmotile

middle: M

first: Yang

last: Xie

first: Wei

last: Pan

first: Arkady

middle: B

last: Khodursky


title: FHCRC Human BAC v1.0

status: Public on Mar 18 2005

first: Ryan

last: Basom

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

description: FHCRC Human BAC


title: FHCRC Mouse BAC v1.0

description: FHCRC Mouse BAC v1.0


title: BCCRC Lam SMRTr array

status: Public on Feb 22 2006

city: Bethesda

first: William

middle: Wallace

last: Lockwood

address: 50 South Drive

institute: National Human Genome Research Institute

description:
A tiling resolution array of 26, 928 overlapping BAC clones spanning the human genome
Keywords = SMRTr tiling array

first: Cathie

last: Garnis

middle: W

first: Wan

last: Lam


title: RMRG array

status: Public on Jan 17 2004

city: Cambridge

first: Cristin

last: Print

institute: Cambridge University

description: Cambridge university RMRG nylon filter gene array

first: Walmsley

last: Sarah

first: Print

middle: G

last: Cristin


title: Arabidopsis Whole Genome Tiling Array 1-rc-2

status: Public on Aug 20 2003

city: Palo Alto

first: Curtis

middle: J

last: Palm

address: 855 California Ave

institute: Stanford Genome Technology Center

description:
This Affymetrix array tiles the Arabidopsis genome end to end using in situ synthesized 25 bp oligonucleotides. The January 2002 version of the Arabidopsis genome sequence was used to make these chips and the position coordinates in the table refer to this version of the sequence.  Six chips were required to tile one strand of the genome.  This chip tiles the opposite strand of the sequence of Chromosome 1 (GenBank accession # NC_003070.2  GI:18426880) from base 19,658,476 to base 30,080,809 (end) and Chromosome 2 (GenBank accession # NC_003071.1  GI:15224037) from base 1 to base 9,108,425.
Position coordinates in table refer to the accession(s) listed above and are the same for each pair of forward (chip WGA 1-2) and opposite strand oligos (this chip WGA 1-rc-2), so the position listed in the table is the position of base 25 (5-prime to three-prime) of the opposite strand oligo.

Features that have no sequence information represent positioning grids/checkerboards or random sequence controls.

first: Athanasios

last: Theologis

first: Joseph

last: Ecker

first: Ronald

last: Davis


title: CE_printR

status: Public on Dec 20 2005

first: Florencia

last: Pauli


title: Arabidopsis Whole Genome Tiling Array 1-6

description:
This Affymetrix array tiles the Arabidopsis genome end to end using in situ synthesized 25 bp oligonucleotides. The January 2002 version of the Arabidopsis genome sequence was used to make these chips and the position coordinates in the table refer to this version of the sequence.  Six chips were required to tile one strand of the genome.  This chip tiles the forward strand of the sequence of Chromosome 5 (GenBank accession # NC_003076.2  GI:18426882) from base 6,932,926 to base 26,689,408 (end).
Position coordinates in table refer to the accession(s) listed above and are the same for each pair of forward (this chip, WGA 1-6) and opposite strand oligos (chip WGA 1-rc-6), so the position listed in the table is the position of base 25 (5-prime to three-prime) of the opposite strand oligo.

Features that have no sequence information represent positioning grids/checkerboards or random sequence controls.


title: CE_printT


title: STREP-6

status: Public on Feb 02 2006

last: Stanford Microarray Database


title: Arabidopsis Whole Genome Tiling Array 1-4

description:
This Affymetrix array tiles the Arabidopsis genome end to end using in situ synthesized 25 bp oligonucleotides. The January 2002 version of the Arabidopsis genome sequence was used to make these chips and the position coordinates in the table refer to this version of the sequence.  Six chips were required to tile one strand of the genome.  This chip tiles the forward strand of the sequence of Chromosome 3 (GenBank accession # NC_003074.2  GI:18426881) from base 8,826,801 to base 23,465,812 (end) and Chromosome 4 (GenBank accession # NC_003075.1  GI:15233324) from base 1 to base 5,087,400.
Position coordinates in table refer to the accession(s) listed above and are the same for each pair of forward (this chip, WGA 1-4) and opposite strand oligos (chip WGA 1-rc-4), so the position listed in the table is the position of base 25 (5-prime to three-prime) of the opposite strand oligo.

Features that have no sequence information represent positioning grids/checkerboards or random sequence controls.


title: Old_Affy_Bs

status: Public on Aug 16 2005

organism: Bacillus subtilis

manufacturer: Gavin,,Sherlock; School of Medicine, Department of Genetics, Stanford, CA, United States, 94305; 650-498-6012; sherlock@genome.stanford.edu


title: ScoKao_02-08-14


title: Arabidopsis Whole Genome Tiling Array 1-2

description:
This Affymetrix array tiles the Arabidopsis genome end to end using in situ synthesized 25 bp oligonucleotides. The January 2002 version of the Arabidopsis genome sequence was used to make these chips and the position coordinates in the table refer to this version of the sequence.  Six chips were required to tile one strand of the genome.  This chip tiles the forward strand of the sequence of Chromosome 1 (GenBank accession # NC_003070.2  GI:18426880) from base 19,658,476 to base 30,080,809 (end) and Chromosome 2 (GenBank accession # NC_003071.1  GI:15224037) from base 1 to base 9,108,425.
Position coordinates in table refer to the accession(s) listed above and are the same for each pair of forward (this chip, WGA 1-2) and opposite strand oligos ( chip WGA 1-rc-2), so the position listed in the table is the position of base 25 (5-prime to three-prime) of the opposite strand oligo.

Features that have no sequence information represent positioning grids/checkerboards or random sequence controls.


title: Arabidopsis Pilot Genome Tiling Array 1C

description:
This set of Affymetrix array tiles 5 Mb the Arabidopsis genome with a 12 bp overlap
using in situ synthesized 25 bp oligonucleotides.
Perfect match and central position mismatch probes were made for these arrays.
The position coordinates in the table refer to the begining of the 2.5 Mb chromosomal fragment that was tiled on the array.
This chip tiles the first half (1.25 MB) of both strands of the 2.5 Mb sequence of Chromosome 2 that was chosen for these pilot arrays.

Features that have no sequence information represent positioning grids/checkerboards or random sequence controls.

first: George

last: Karlin-Neumann


title: Home-made salmonella inducing cDNA array

status: Public on Jul 02 2005

city: Atlanta

first: Hui

last: Zeng

state: GA

address: 1600 Clifton Rd. MS:G16

department: Influenza Branch

institute: Centers for disease control

organism: Homo sapiens

first: Andrew

last: Neish

first: Adam

last: Carlson

first: Yanwen

last: Guo

manufacture_protocol: Human cDNA library were from Research Genetics Inc.  Target cDNAs were amplified from selected clones by PCR.  PCR products were purified and spotted onto glass slides.


title: CAGE-Xylella USP - v.2

status: Public on Dec 22 2004

first: Tie

last: Koide

first: Paulo

last: Zaini


title: Arabidopsis Pilot Genome Tiling Array 1A

description:
This set of Affymetrix array tiles 5 Mb the Arabidopsis genome with a 12 bp overlap
using in situ synthesized 25 bp oligonucleotides.
Perfect match and central position mismatch probes were made for these arrays.
The position coordinates in the table refer to the begining of the 2.5 Mb chromosomal fragment that was tiled on the array.
This chip tiles the first half (1.25 MB) of both strands of the 2.5 Mb sequence of Chromosome 1 that was chosen for these pilot arrays.

Features that have no sequence information represent positioning grids/checkerboards or random sequence controls.


title: Sigma Genosys Panorama Mycobacterium tuberculosis Gene Array

status: Public on Dec 20 2002

city: The Woodlands

last: Sigma-Genosys

address: 1442 Lake Front Circle

institute: Sigma-Genosys

organism: Mycobacterium tuberculosis

description: The Panorama Mycobacterium tuberculosis Gene Array contains 3,875 PCR-amplified open reading frames from strain H37Rv. The entire genome contains 3,918 putative ORFs. However, extensive homology in the remaining ORFs renders analysis of these ORFs redundant. PCR products have been designed to be less than 500 bp in length and in most part have been designed to represent a region of the ORF that has as little homology to other ORFs as possible.  The gene arrays are 8 cm x 24 cm in size and contain equal mass of all the genes.

manufacture_protocol: see manufacturer's web site


title: FHCRC Yeast Intergenic v1.0

first: Ryan

last: Basom

organism: Saccharomyces cerevisiae

description: 6518 feature spotted array comprised mainly of yeast intergenic regions (6438 + 80 control spots.)  Yeast intergenic regions were PCR amplified from genomic DNA using primer pairs obtained from Research Genetics (Huntsville, Alabama).


title: Sigma Genosys Panorama Helicobacter pylori Gene Array

description: The Panorama Helicobacter pylori Gene Array contains 1,681 PCR-amplified open reading frames (ORFs), representing all putative H. pylori strain 26695 protein-coding genes (1,590 genes) and 91 protein-coding genes of H. pylori strain J99 that are unique to this strain. For the majority of ORFs, the PCR products have been designed to represent a region of the ORF that has as little homology to other ORFs as possible. The gene arrays are 8 cm x 12 cm in size and contain equal mass of all the genes.


title: Arabidopsis Whole Genome Tiling Array 1-rc-6

description:
This Affymetrix array tiles the Arabidopsis genome end to end using in situ synthesized 25 bp oligonucleotides. The January 2002 version of the Arabidopsis genome sequence was used to make these chips and the position coordinates in the table refer to this version of the sequence.  Six chips were required to tile one strand of the genome.  This chip tiles the opposite strand of the sequence of Chromosome 5 (GenBank accession # NC_003076.2  GI:18426882) from base 6,932,926 to base 26,689,408 (end).
Position coordinates in table refer to the accession(s) listed above and are the same for each pair of forward  (chip WGA 1-6) and opposite strand oligos (this chip, WGA 1-rc-6), so the position listed in the table is the position of base 25 (5-prime to three-prime) of the opposite strand oligo.

Features that have no sequence information represent positioning grids/checkerboards or random sequence controls.


title: Arabidopsis Whole Genome Tiling Array 1-rc-5

description:
This Affymetrix array tiles the Arabidopsis genome end to end using in situ synthesized 25 bp oligonucleotides. The January 2002 version of the Arabidopsis genome sequence was used to make these chips and the position coordinates in the table refer to this version of the sequence.  Six chips were required to tile one strand of the genome.  This chip tiles the opposite strand of the sequence of Chromosome 4 (GenBank accession # NC_003075.1  GI:15233324) from base 5,087,401 to base 17,549,528 (end) and Chromosome 5 (GenBank accession # NC_003076.2  GI:18426882) from base 1 to base 6,932,925.
Position coordinates in table refer to the accession(s) listed above and are the same for each pair of forward (chip WGA 1-5) and opposite strand oligos (this chip, WGA 1-rc-5), so the position listed in the table is the position of base 25 (5-prime to three-prime) of the opposite strand oligo.

Features that have no sequence information represent positioning grids/checkerboards or random sequence controls.


title: Arabidopsis Whole Genome Tiling Array 1-rc-3

description:
This Affymetrix array tiles the Arabidopsis genome end to end using in situ synthesized 25 bp oligonucleotides. The January 2002 version of the Arabidopsis genome sequence was used to make these chips and the position coordinates in the table refer to this version of the sequence.  Six chips were required to tile one strand of the genome.  This chip tiles the opposite strand of the sequence of Chromosome 2 (GenBank accession # NC_003071.1  GI:15224037) from base 9,108,426 to base 19,643,621 (end) and Chromosome 3 (GenBank accession # NC_003074.2  GI:18426881) from base 1 to base 8,826,800.
Position coordinates in table refer to the accession(s) listed above and are the same for each pair of forward (chip, WGA 1-3) and opposite strand oligos (this chip WGA 1-rc-3), so the position listed in the table is the position of base 25 (5-prime to three-prime) of the opposite strand oligo.

Features that have no sequence information represent positioning grids/checkerboards or random sequence controls.