title: Affymetrix GeneChip Human Tiling 2.0R Array Set_Array 7of7 (NCBI Build 36)

status: Public on May 28 2009

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

organism: Homo sapiens

technology: in situ oligonucleotide

description: Sequences used in the design of this Human Tiling 2.0R Array Set were based on NCBI human genome assembly hg18 (Build 36).

distribution: custom-commercial

manufacture_protocol: See manufacturer's web site


title: UCM-Medina-Mfaveolata-1310-v2

status: Public on May 31 2009

city: San Francisco

first: Michael

last: DeSalvo

state: CA

department: Department of Anesthesia

country: USA

institute: UC San Francisco

organism: Orbicella faveolata

technology: spotted DNA/cDNA

distribution: non-commercial

manufacturer: University of California, San Francisco, Center for Advanced Technology

first: Jodi

middle: A

last: Schwarz

first: Monica

last: Medina

first: Christian

middle: R

last: Voolstra

first: Shinichi

last: Sunagawa


title: Kyoto Univ. 3D-Gene Human miRNA Oligo chip v11.0

status: Public on May 14 2009

city: Kyoto

first: Akira

last: Myomoto

address: Yoshida-Shimoadachi

institute: Kyoto Univ.

technology: spotted oligonucleotide

description: In “3D-Gene” Human/Mouse miRNA, sense strand oligonucleotides have been spotted on the high performance DNA chip substrate “3D-Gene.” These nucleotides on one “3D-Gene” chip can detect 850 types of human, 610 types of mice, and -350 types of rat miRNAs selected from database mirBase release 11.0. This high performance DNA chip substrate “3D-Gene” was uniquely developed by Toray Industries Inc. Toray uses unique technologies involving the creation of a substrate with characteristic morphology and agitation method using microbeads during reaction, and gene immobilization by molecular control at a nano level. In addition to high reproducibility and quantitative results, ultra high sensitivity has been actualized (0.1 atto-mol = 10-19 mol). This value corresponds to the expression level of 1 copy per 104 cells.

first: F

last: Sato

first: S

last: Tsuchiya

first: K

last: Terasawa

first: G

last: Tsujimoto


title: PBI-NRC_Brassica 10K V1.0

city: Saskatoon

first: Jitao

last: Zou

state: Saskatchewan

address: 110 Gymnasium Place

country: Canada

institute: Plant Biotechnology Institute, National Research Council Canada

organism: Brassica napus

description: A set of 10,642 PCR primer pairs were designed and corresponding amplicons were produced for preparation of a targeted seed cDNA microarray. cDNA amplicons were printed on Corning UltraGAPS slides with the Chipwriter Pro microarray printer (Bio-Rad). The microarray consists of 12 row × 4 column sub-arrays, and each sub-array has 23 row × 22 column (506) spots. Spots were printed in duplicate side-by-side by columns, and the total number of spots on the microarray is 24288, of which 22,656 spots are cDNA probes. Controls are printed at the beginning and the end of each sub-array. The distance between spot is 185 µm and the spot diameter is 145 µm.

manufacturer: Biotechnology Research Institute, National Research Council Canada

first: Daoquan

last: Xiang

first: Raju

last: Datla

first: Fengling

last: Li

first: Adrian

last: Cutler

first: Meghna

last: Malik

first: Joan

middle: E

last: Krochko

first: Nirmala

last: Sharma

first: Pierre

last: Fobert

first: Fawzy

last: Georges

first: Gopalan

last: Selvaraj

first: Ed

last: Tsang

first: Darrin

last: Klassen

first: Chushin

last: Koh

first: Jean-Sebastien

last: Deneault

first: Andre

last: Nantel

first: Jacek

last: Nowak

first: Wilf

last: Keller

first: Faouzi

last: Bekkaoui

manufacture_protocol:
Protocol for cDNA array fabrication
1)	Amplify the insertions with a GeneAmp PCR System 9700 (Applied Biosystems, ABI) using AmpliTaq (ABI);
2)	Purify the PCR products using the Biomek FX (Bechman/Coulter) and check the quality through agrose gel electrophoresis;
3)	Amplicons were consolidated into 384-well plates, lyophilized, and resuspended in 10 µl of 50% DMSO to a final concentration of 250 ng/µl.
4)	The Stratagene SpotReport Alien cDNA Array Validation kit and an in-house Candida albicans ECE1 gene (L17087) were ready in a dilution series. The buffer/blank control was 50% DMSO;
5)	Printing the microarray on Corning UltraGAPSTM slides using the VersArray ChipwriterTM Pro microarray printer (Bio-Rad). SMP3 Microspot quill pins (TeleChem) in a 48-pin tool to deposit ~7 nL per spot onto the slide;


title: PFGRC Streptococcus pneumoniae Version 1

status: Public on May 29 2009

city: Galveston

first: Utpal

last: Pandya

state: TX

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch

organism:
Streptococcus pneumoniae TIGR4
Streptococcus pneumoniae R6
Streptococcus pneumoniae G54

description:
Microarray Version: 1
Number of Grids: 96
Element Type: Amplicon
Surface Coating: Aminosilane
Oligonucleotides Designed: 2249
Replicate Oligo Printings: 4x
Controls: 0 Arabidopsis thaliana 70mers; 40 Arabidopsis thaliana amplicons

manufacture_protocol: see: Hendriksen et al. 2006


title: Affymetrix GeneChip Human Tiling 2.0R Array Set_Array 1of7 (NCBI Build 36)

first: Katsuhiko

last: Shirahige


title: Nimblegen 385k tiling array 081031_RDI_UK_Bsubtilis_FT

city: Newcastle upon Tyne

first: Stephan

last: Gruber

address: Framlignton Place

department: ICaMB

country: United Kingdom

institute: Newcastle University

organism: Bacillus subtilis

manufacture_protocol: Nimblegen protocol


title: AQUAFIRST_seabream_18K_Ver1

status: Public on May 30 2009

city: Galway

first: Michael

middle: Taylor

last: Cairns

address: University Road

department: MRI

country: Ireland

institute: NUI Galway

organism: Sparus aurata

manufacturer: Richard Reinhardt, MPI Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin-Dahlem, Germany

first: michael

middle: t

last: cairns

first: grace

last: davey

first: josep

last: calduch-giner

first: jaume

last: pérez-sánchez

first: benoit

last: houeix

first: anita

last: talbot

first: richard

last: reinhardt

first: svante

last: winberg

first: per-ove

last: linquist

manufacture_protocol: This array was constructed from a combination of SSH libraries created within AQUAFIRST and libraries within the Marine Genomics project. Two experiments were carried out within AQUAFIRST - one on confinement and one on parasite infection. All AQUAFIRST SSH libraries relate to these experiments. Libraries were made from liver, head kidney, gill and brain for confinment and from head kidney and intestine for pathogen exposure. All clones were sequenced and analysed along with the Marine Genomics clones to select best representation.


title: Custom microRNA microarray Design 4343

status: Public on May 22 2009

city: Baltimore

first: Joshua

middle: T

last: Mendell

state: MD

address: 733 N. Broadway, BRB 471

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

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: MPIMG Homo sapiens 105K Transloc4 array

status: Public on May 27 2009

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

institute: MPIMG

description: Customized 105k oligonucleotide array covering chromosomal regions chr1: 107,172,477-106,477,206; chr11: 45,907,446-46,099,561; chr9: 115,000,001-137,000,000; chr11: 46,359,782-46,817,878; chr9: 125,159,337-125,335,217; chr12: 43,415,572-43,558,584; chr7: 6,792,884-7,087,324 and chr19: 17,687,000-17,706,702 with an average probe spacing of 300bp. Chromosome coordinates are given according to HG18 (NCBI Build 36). Oligo design was done by means of eArray (Aglilent) using the Similarity Score and TM filter.

manufacture_protocol: SurePrint technology from Agilent


title: Listeria monocytogenes (EGDe) macroarray

city: Porto

first: Didier

last: Cabanes

state: Porto

address: rua do Campo Alegre, 823

country: Portugal

institute: IBMC

organism: Listeria monocytogenes EGD-e

first: Eliane

last: Milohanic

first: Philippe

last: Glaser

first: Jean-Yves

last: Coppée

first: Lionel

last: Frangeul

first: Yolanda

last: Vega

first: José

last: Vázquez-Boland

first: Frank

last: Kunst

first: Pascale

last: Cossart

first: Carmen

last: Buchrieser

manufacture_protocol:
The macroarrays were constructed by Milohanic et al (Mol Microbiol 2003. 47: 1613-1625). Whole-genome arrays were constructed by amplifying 500-bp-long PCR products specific for each gene using open reading frame (ORF)-specific primers. Ninety-nine per cent (2816 ORFs) of the 2853 predicted ORFs of the L. monocytogenes EGDe genome were amplified successfully.
For macroarray preparation, nylon membranes were soaked in 10 mM TE, pH 7.6. Spot blots of ORF-specific PCR products and controls were printed using a Qpix robot. Immediately after spot deposition, membranes were neutralized for 15 min in 0.5 M NaOH, 1.5 M NaCl, washed three times with distilled water and stored wet at -20°C until use.


title: Custom mouse (mm8) imprinting tiling array

status: Public on May 26 2009

first: Andrew

middle: P.

last: Feinberg

address: 855 N. Wolfe Street

department: Center for Epigenetics and Department of Medicine

institute: Johns Hopkins University

organism: Mus musculus

manufacture_protocol: Mouse genome tiling arrays containing imprinted regions


title: PFGRC Streptococcus pneumoniae Version 2

first: Utpal

last: Pandya

description:
Microarray Version: 2
Number of Grids: 96
Element Type: Amplicon
Surface Coating: Aminosilane
Oligonucleotides Designed: 2694
Replicate Oligo Printings: 4x
Controls: 500 Arabidopsis thaliana 70mers; 40 Arabidopsis thaliana amplicons


title: Agilent-021974 Syn_PCC6803_transcriptome

status: Public on May 20 2009

city: Freiburg

first: Bjoern

last: Voss

address: Schänzlestr. 1

department: Institute of Biology III

institute: University of Freiburg

organism: Synechocystis sp. PCC 6803

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


title: CCF Human ISG v.1.3.2

city: Bethesda

first: Michelle

last: Holko

address: 45 Center Dr

department: NCBI

institute: GEO

description: Array contains 810 unique putative ISGs, 85 housekeeping genes, and 4 bacterial control genes.

manufacturer: Bryan RG Williams lab, Cleveland Clinic Foundation

first: Bryan

last: Williams

manufacture_protocol: ISG cDNA microarray was generated from a list of ISGs compiled from previous array experiments in our laboratory and others. Housekeeping genes and bacterial control genes were also included for standardization or normalization purposes. cDNA for genes was obtained, and arrays were printed as previously reported in Frevel MA, Bakheet T, Silva AM, Hissong JG, Khabar KS, Williams BR. p38 mitogen-activated protein kinase-dependent and-independent signaling of mRNA stability of AU-rich element-containing transcripts. Mol. Cell. Biol. 2003;23:425–436, and Sledz CA, Williams BR. RNA interference and double-stranded-RNA-activated pathways. Biochem. Soc. Trans. 2004;32:952–956.


title: modEncode_Caenorhabditis elegans_2M tiling aray

status: Public on May 15 2009

city: Chapel Hill

first: Everett

last: Zhou

state: NC

address: 1000 Manning Dr.

institute: UNC

organism: Caenorhabditis elegans

description:
modEncode_CE_chip
Native NimbleGen files (ndf, pos) are linked below as supplementary files.

first: Susan

last: Strome

first: Jason

last: Lieb

manufacture_protocol: Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR,Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol. 1999 Oct;17(10):974-8. PMID: 10504697


title: MSU Bos taurus BLO 8400

city: Guelph

first: John

middle: Henry

last: Doelman

state: Ontario

address: 50 Stone Road East

department: Animal and Poultry Science

institute: University of Guelph

organism: Bos taurus

manufacture_protocol: Oligos designed and synthesized by Operon (http://www.operon.com/).  Complete annotation on the gene spots available via the GeneLink database (http://cafg.msu.edu). The Operon Bovine AROS Version 1.1 contains 8329 70-mer oligonucleotide probes representing 8329 genes from bovine genome. Each probe contains an amino linker at its 5' end. Gene sequences used for probe design are obtained from TIGR Cattle Gene Index Release 11 (http://www.tigr.org/tigr-scripts/tgi/T_index.cgi?species=cattle) and GenBank.


title: UTSW-Ambion mirVana Probe Set custom array

city: Houston

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: The Platform data table reflects a condensed representation of the array's replicate features.  The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.

manufacturer: University of Texas Southwest Medical Center Microarray Core Facility

manufacture_protocol:
The oligo set consisted of the mirVana miRNA Probe Set, a collection of amine-modified DNA oligonucleotides targeting a comprehensive selection of human, mouse, and rat miRNAs from miRBase, purchased from Ambion.
The probes in the mirVana miRNA Probe Set are 42-46 nucleotides (nt) long and consist of an 18-24 nt segment that targets a specific known human, mouse, or rat miRNA, plus spacer and attachment sequences for coupling to the surface of the microarray slide.
The oligo set was printed on SCHOTT Nexterion Slide E microarray slides with 6 replicated spots for each probe.


title: Affymetrix GeneChip Human Tiling 2.0R Array Set_Array 3of7 (NCBI Build 36)

first: Katsuhiko

last: Shirahige


title: LC_MRA-1003_miRRat_13.0_090309

status: Public on May 19 2009

first: Christoph

last: Eicken

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism: Rattus norvegicus

description: Rat miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 13.0

distribution: commercial

manufacture_protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes are made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: Nimblegen Mouse MM8 Promoter Array

city: Dallas

first: guanghua

last: xiao

address: 5323 Harry Hines Blvd

department: Psychiatry

institute: University of Texas Southwestern Medical Center

description:
Design name: 2006-07-18_MM8_RefSeq_promoter

NimbleGen .ndf and .pos description files are linked below as supplementary files.
Individual probe sequences can be found in the PROBE_SEQUENCE column of the.ndf file.

manufacture_protocol: See www.nimblegen.com.


title: LC_MRA-1003_miRRat_11.0_080411

description: Rat miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 11.0


title: 2004_02_03_Hogenhout_24mer

status: Public on May 21 2009

city: Wooster

first: Esther

last: van der Knaap

state: OH

address: 1680 Madison Ave.

department: Horticulture and crop science

institute: The Ohio State University

organism: Solanum lycopersicum

description:
2004_02_03_Hogenhout platform was custom-designed oligoarray manufactured by Nimblegen (Nimblegen Systems Inc. http://www.nimblegen.com) based on TIGR (now Computational Biology and Functional Genomics Laboratory: http://compbio.dfci.harvard.edu/tgi/) tomato Tentative Contigs sequences (release 9). It consists of 15270 Tentaive Clsuters (TC) corresponding to 7600 different clusters (transcripts) and each TC was represented by 12 pairs of perfect and mismatch probes of 24-mers.
The .ndf and .ngd files are linked below as supplementary files.

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.


title: Texas A&M Brucella melitensis 8K

city: College Station

first: Leslie

middle: Garry

last: Adams

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

organism: Brucella melitensis

manufacturer: Western Regional Center of Excellence (WRCE) Pathogen Expression Core (Arizona State University)

first: Stephen

last: Johnston

first: Mitchell

last: McGee

first: Rhonda

last: Friedberg

manufacture_protocol: A set of unique 70-base oligonucleotides representing 3,227 ORFs of B. melitensis strain 16M and unique / divergent genes from B. abortus and B. suis were designed at the Pathogen Expression Core and purchased from Sigma-Genosys (The Woodland, TX). Oligonucleotides were suspended in 3X SSC (Ambion) at the final concentration of 40 uM before robotic arraying in triplicate onto ultraGAPS coated glass slides (Corning) using a Spotarray 72 microarray printer (Perkin Elmer, Downer’s Grove, ILL). Printed slides were steamed and UV cross-linked and stored in a desiccators until use.


title: CCF Human ISG v.1.3.1

description: Array contains 758 unique putative ISGs, 85 housekeeping genes, and 4 bacterial control genes.


title: Wolbachia pipientis wMel microarray

status: Public on May 11 2009

first: Julie

middle: C

last: Dunning Hotopp

address: 20 Penn St.; HSF-II; S203B

department: Institute for Genomic Sciences

institute: Univeristy of Maryland Baltimore

organism: Wolbachia pipientis

first: Nadeeza

last: Ishmael

last: Werren

first: Herve

last: Tettelin

manufacture_protocol: A wMel microarray was constructed which represents 95% of the unique ORFs. Primers were designed from the unique predicted genes annotated in wMel. In order to obtain pure amplicons devoid of background amplification of host genes, all amplicons were produced, where possible, from two separate clones from the wMel genome sequencing project. Genes in physical gaps where a sequencing clone was not available were amplified directly from genomic DNA from D. melanogaster infected with wMel. Amplicons (50-1000 bp) were produced using AmpliTaq (Applied Biosystems), purified using filtration plates (Millipore), and analyzed on agarose gels. The purified amplicons were diluted 1:1 with DMSO, spotted in quadruplicate onto Corning UltraGap slides with a Lucidea printing robot (GE Healthcare), and irradiated with ultraviolet light.


title: Kyoto Univ. EXIQON miRCURY LNA microRNA Array kit v10.0 - human, mouse & rat

status: Public on May 13 2009

first: Akira

last: Myomoto

address: Yoshida-Shimoadachi

institute: Kyoto Univ.

first: F

last: Sato

first: S

last: Tsuchiya

first: K

last: Terasawa

first: G

last: Tsujimoto

manufacture_protocol: miRCURY LNA microRNA Arrays consist of control probes, mismatch probes, and 1154 capture probes, perfectly matched probes for all miRNAs in human, mouse, rat and their related viruses in miRBase Release 10.0. Arrays also contain a number of proprietary miRPlus sequences not yet in miRBase.


title: Kyoto Univ. Ambion mirVana Bioarrays v9.2

manufacture_protocol: Manufactured for Ambion by Applied Microarrays, Inc., mirVana miRNA Bioarrays are produced using the CodeLink 3-D Gel Matrix slide surface. This provides an aqueous environment that holds the probe away from the surface of the slide, allowing maximum interaction between probe and target.


title: Affymetrix GeneChip Human Tiling 2.0R Array Set_Array 6of7 (NCBI Build 36)

city: Bunkyo-ku

last: Shirahige

address: 1-1-1 Yayoi

institute: The University of Tokyo

manufacture_protocol: See manufacturer's web site


title: Affymetrix GeneChip Human Tiling 2.0R Array Set_Array 4of7 (NCBI Build 36)


title: OSU-CCC/miRNACHIPv2

status: Public on May 07 2009

city: Genoa

first: Alberto

last: Izzotti

address: A. Pastore, 1

department: Dept. of Health Sciences

country: Italy

institute: University of Genoa

organism:
Arabidopsis thaliana
Homo sapiens
Mus musculus

manufacture_protocol: Forty-mer 5' amine modified C6 oligos were resuspended in 50 mM phosphate buffer pH 8 at a 20 mM concentration. The individual oligo-probe was printed in quadruplicate on Amersham Code link activated slides under 45% humidity by Gene Machine OmniGrid 100 Microarrayer. The spot diameter was 100 µm and the distance from center to center was 200 µm the printed miRNA microarray were covalently bound by overnight coupling under 70% humidity.


title: Kyoto Univ Agilent Human miRNA Microarray, Version 2

city: Kyoto

organism: Homo sapiens

description: Agilent design ID 019118. miRNA probes were designed using Sanger miRBase, release 10.1.

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


title: Affymetrix GeneChip Human Tiling 2.0R Array Set_Array 2of7 (NCBI Build 36)

first: Katsuhiko

department: Research Center for Epigenetic Disease


title: Human custom chip-on-chip 2x105k tiling microarray AMADID: 018053

status: Public on May 10 2009

city: Regensburg

first: Christian

last: Schmidl

address: Franz-Josef-Strauss-Allee 11

institute: Rengensburg Center for Interventional Immunology

first: Michael

last: Rehli

manufacture_protocol: Agilent SurePrint technology, see manufacturer's website at http://www.agilent.com/


title: Complete shotgun genomic Leishmania infantum DNA microarrays

city: MADRID

first: PEDRO

middle: JOSÉ

last: ALCOLEA ALCOLEA

address: Ramiro de Maeztu, 9

department: CENTRO DE INVESTIGACIONES BIOLÓGICAS

country: Spain

organism: Leishmania infantum

description: epoxy

manufacturer: CENTRO DE INVESTIGACIONES BIOLÓGICAS-CONSEJO SUPERIOR DE INVESTIGACIONES CIENTÍFICAS (CIB-CSIC)/CENTRO DE ASTROBIOLOGÍA-INSTITUTO NACIONAL DE TÉCNICA AEROESPACIAL "ESTEBAN TERRADAS"/CSICO

first: Pedro

middle: J

last: Alcolea

first: Ana

last: Alonso

first: Alicia

last: Sánchez-Gorostiaga

first: Mercedes

last: Moreno-Paz

first: Manuel

last: Gómez

first: Irene

last: Ramos

first: Víctor

last: Parro

first: Vicente

last: Larraga

manufacture_protocol: Leishmania parasites were grown in RPMI 1640 supplemented with glutamine, 10% heat inactivated foetal bovine serum and antibiotics. A complete shotgun genomic library of Leishmania infantum (32,6Mbp) was constructed by digesting genomic DNA with Sau3AI restriction enzyme. After digestion, fragments ranging from 2 to 10 Kb were separated by ultracentrifugation through a 10-40% sucrose gradient. pUC18 vector was digested with BamHI, thus yielding compatible blunt-ended fragments, that were ligated with the purified set of inserts with T4-DNA ligase. Finally, DH10B electrocompetent E. coli cells were transformed. The efficiency of this L. infantum shotgun DNA library was 95%.We picked 29952 colonies, incubated them overnight and performed alkaline lysis at 95ºC during 3 min. Lysates were centrifuged during 3 minutes and 1ul supernatant was used to amplify each insert with Expand Long Template PCR system (Roche). 83% of reactions were positive and average insert size was approximately 4 Kb. Then, we purified inserts with a 96-well plate DNA purification kit (Telechem Intl.), dried samples, resuspended in Microspotting solution plus (Telechem) and finally reorganized samples into 384-well plates, using a liquid handling machine (eppendorf). Finally, arrays were spotted with MicroGrid II TAS arrayer.


title: Univ of Miss. Frog virus 3 (family Iridoviridae) array

status: Public on May 01 2009

city: Silver Spring

first: Sai

middle: P

last: Majji

address: 503 Robert Grant Avenue

department: Malaria

institute: Naval Medical Research Center

organism: Frog virus 3

first: Venkata

last: Thodima

first: Robert

last: Sample

first: Dexter

last: Whitley

first: Youping

last: Deng

first: Jinghe

last: Mao

first: Gregory

last: Chinchar

manufacture_protocol:
1. Array robot type: MI's robot is a custom design and is not commercially available
2. Printing Type: Contact printing
3. Deposition Methodology: MI uses ceramic capillary printing pins.
4. Buffer type: 150mM NaPO4, pH 8.0,
5. Substrate type: Corning UltraGAP


title: Affymetrix GeneChip Human Tiling 2.0R Array Set_Array 5of7 (NCBI Build 36)

status: Public on May 28 2009

first: Katsuhiko

last: Shirahige


title: Stanford University/Stevens Lab Paracoccidioides brasiliensis 12K v1.0

status: Public on May 08 2009

city: San Jose

first: Jomar

middle: Patrício

last: Monteiro

address: 2260 Clove Drive

department: Division of Infectious Diseases and Geographic Medicine

institute: Stanford University

organism: Paracoccidioides brasiliensis

first: Karl

middle: V

last: Clemons

first: Laurence

middle: F

last: Mirels

first: John

last: Coller

first: Thomas

middle: D

last: Wu

first: Jata

last: Shankar

first: Catalina

last: Lopes

first: David

last: Stevens

manufacture_protocol:
Library construction:
	Genomic DNA was sheared hydrodynamically into ~1.5 Kb fragments using a HydroShear® apparatus (Genomic Solutions, Ann Arbor, MI) as previously described (Oefner et al., 1996; Thorstenson et al., 1998).  Adequacy of DNA shearing was assessed by 1.5% agarose gel electrophoresis and visualized by UV after ethidium bromide staining.  Sheared DNA was used as inserts for the genomic library.
	The genomic library was assembled using the λ ZAP II phage as vector (λ ZAP II Predigested EcoRI/CIAP-treated Vector Kit, Stratagene, La Jolla, CA) and a modification of the linker-adaptor strategy described by Thorstenson et al. (Thorstenson et al., 1998) (also see: http://www-sequence.stanford.edu/protocols/library.html).  The sequence of the linker oligo is 5'pAATTGTTTG3'. The sequences of the oligos used to assemble the adaptor are 5'pTGAGTCACCAAAC3' and 5'pGTGACTCA3'.
Phage Insert and Control Gene Amplifications:
	Individual DNA inserts in the phage were amplified using PCR as follows: phage capsids were denatured at 70 degrees C for 5 minutes to release viral DNA.  DNA inserts were amplified using Platinum® PCR Supermix 96 (Invitrogen Life Technologies, Carlsbad, CA) with primers complementary to the vector (primer SK: 5’cgctctagaactagtggatc3’ and primer KS: 5’tcgaggtcgacggtatc3’) following the manufacturer’s instructions.
	Thirty-four genes from P. brasiliensis were selected for inclusion as known controls on the array.  Genes were chosen based on known or expected expression patterns in M, or Y or during form transition from M to Y.  Template sequences were obtained from GenBank and primer pairs were designed for each gene using Primer 3 software considering an amplicon size of ~1 Kb (Rozen & Skaletsky, 2000).  Nine primer pairs were designed from regulatory gene sequences provided by Dr. Adrian R. Walmsley (Univ. of Durham, UK).
	All amplified fragments were electrophoresed through 1.0% agarose gels for 12 minutes using an E-Gel® 96 High-Throughput Agarose Electrophoresis System (Invitrogen), and photographed.  Amplicon lengths were estimated using 1 Kb Plus DNA Ladder (Invitrogen).  Amplicons were purified using Nucleofast® 96 PCR Clean-up Kit (BD Biosciences, San Jose, CA).
Microarray construction:
	Purified PCR products from the cloned fragments and controls were spotted onto aminosilane coated glass slides (UltraGAPSTM Slides, Corning Inc. Life Sciences, Acton, MA) using custom built robots at the Stanford Microarray Core Facility (www.microarray.org).
References:
Oefner, P. J., Hunicke-Smith, S. P., Chiang, L., Dietrich, F., Mulligan, J. & Davis, R. W. (1996). Efficient random subcloning of DNA sheared in a recirculating point-sink flow system. Nucleic Acids Res 24, 3879-3886.
Thorstenson, Y. R., Hunicke-Smith, S. P., Oefner, P. J. & Davis, R. W. (1998). An automated hydrodynamic process for controlled, unbiased DNA shearing. Genome Res 8, 848-855.
Rozen, S. & Skaletsky, H. (2000). Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132, 365-386.


title: Biomedical Genomics Center Microarray Facility Custom Multi-Species miRNA Microarray

status: Public on May 04 2009

city: Minneapolis

first: Xiaoxiao

last: Zhang

address: 312 Church St. SE

institute: University of Minnesota

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

manufacturer: Biomedical Genomics Center Microarray Facility at the University of Minnesota

manufacture_protocol: A microRNA probe set was purchased from Invitrogen (NCode™ Multi-Species miRNA Microarray Probe Set V2, #MIRMPS2-01), which was designed based on the Sanger miRBase Sequence Database, Release 9.0.  The set contains approximately 1,140 oligonucleotides of 34 to 44 nt long as probes.  They are complementary to C. elegans, Drosophila, zebrafish, mouse, rat, and human miRNAs, and also include a number of internal and negative control probes.  The oligonucleotides were dissolved in 3 x SSC and quadruply printed on Corning® GAPSTM II coated slides  using a BioRobotics Microgrid II spotter


title: FBG_EUC_2608_v1.1

status: Public on May 12 2009

city: Pretoria

first: Owen

middle: Luke

last: Solomon

state: Gauteng

address: Lab 6-20, Agricultural Building, University of Pretoria, Lynwood Rd

department: Genetics

country: South Africa

institute: University of Pretoria

organism:
Eucalyptus grandis
Eucalyptus tereticornis

middle: L

first: Alexander

middle: A

last: Myburg

manufacture_protocol:
The cDNA microarray comprises 2608 ESTs, with four replicates. 555 ESTs represent the UniGene set derived from the sequencing of a cDNA library from Eucalyptus grandis differentiating xylem generated by the Forest Biotechnology Group at NCSU (egx prefix). The remaining 2053 ESTs are from four libraries from Eucalyptus grandis leaf and root tissue and two libraries from Eucalyptus tereticornis flower tissues, kindly made available by DuPont (Scott Tingey, DuPont Crop Genetics, Newark, DE). These ESTs were selected from a collection of approximately 13,000 sequences, based on their putative function in the biogenesis of cell walls, biogenesis of the cytoskeleton, biosynthesis of phenylpropanoids, protein targeting, c-compound and carbohydrate metabolism, cell growth, signal transduction, protein transport, energy metabolism and other functions potentially associated to wood formation. The cDNA clones were amplified by PCR, purified (Millipore 96-well Multiscreen filter plates) and the quality of the amplification evaluated using agarose gels. Preparations with multiple bands and low quality amplified cDNAs were eliminated and repeated. After dilution in 50% DMSO, cDNAs were printed in duplicate on aminosilane-coated glass slides (Corning) using an Affymetrix 417 Spotter. This array is a condensed version.
Keywords = Eucalyptus xylem


title: SMD Print_1548 Saccharomyces cerevisiae

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

organism: Saccharomyces cerevisiae

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine

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


title: SIU Streptococcus pyogenes 5K

city: Carbondale

first: KyuHong

last: Cho

state: IL

address: 1125 Lincoln Dr. Room 131

department: Microbiology

institute: Southern Illinois University Carbondale

organism: Streptococcus pyogenes

manufacturer: The microarray core facility in Washington University

first: Michael

last: Caparon

first: Wess

last: Warren

first: Seth

last: Crosby

manufacture_protocol:
An antisense oligonucleotide array based on the published
genome of S. pyogenes SF370 (Ferretti et al., 2001) was
made at the Microarray Core Facility in the Genome-
Sequencing Center at Washington University (GSC, http://
genome.wustl.edu/groups/microarray/main_page/). A single
60–80 mer oligonucleotide was designed to hybridize to the
putative transcripts from each annotated open reading frame
using ‘TOP’ software that was created at the GSC. To reduce
complexity, probes for rRNA, tRNA  genes were not included. The oligonucleotides
were synthesized by Illumina and were deposited onto
a MWG epoxy microarray slide by custom Linear Servo
Arrayer so that each slide included triplicates spots for each
probe. Quality of the array was validated by hybridization with
a Cyanine 5-labelled random nonamer (Hybchecker, Sigma)
to ensure that the frequency of missed spots were less than
1.0% and by self-self hybridization using a single RNA sample
to generate Cyanine 3- and Cyanine 5-labelled cDNAs, which were then co-hybridized on the slide. Slide
batches were rejected if the average ratio of hybridization
differed significantly from 1.0.


title: Cyanidioschyzon merolae cell cycle

city: Toshima-ku

first: Takayuki

last: Fujiwara

department: Life Science

institute: Rikkyo University

organism: Cyanidioschyzon merolae

manufacturer: Rikkyo University, Research Information Center of Extremophile (RICE)

first: Osami

last: Misumi

first: Kousuke

last: Tashiro

first: Keiji

last: Nishida

first: Fumi

last: Yagisawa

first: Yamato

last: Yoshida

first: Masaki

first: Toshiyuki

last: Mori

last: Sakajiri

last: Hashimoto

first: Haruko

last: Kuroiwa

first: Tsuneyoshi

manufacture_protocol: Based on the annotated C. meroae genome, we ordered synthesis of the ORF-specific oligonucleotides for Sigam Genosys and searched a unique 50-mer sequence for each of the 4586 ORFs coding protein gene (>96% of the ORFs in the nucleus genome). In brief, 50-mer sequences were first selected from ORF sequences based on a set of criteria that included Tm of 75 ± 10 degrees Celsius. 98% of the ORFs-specific oligonucleotides were selected among 1.5 kb from the 3′ end of the ORF.  All the oligonucleotiodes were synthesized (Sigma Genosys) and spotted onto poly-lysine–coated glass slides by using a spotting machine. Spotted glass slides were post-processed according to Brown lab’s protocol (http://cmgm.stanford.edu/pbrown/) and used directly in hybridization or stored at room temperature in a dry cabinet for later use.


title: Lewis-Sigler Institute Saccharomyces 13K [20071114MD_PMC]

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

description: SBSC print, a multi-organism print.

manufacturer: Lewis-Sigler Institute Microarray Facility

manufacture_protocol:
The following parameters were used to manufacture the printed array named "20071114MD_PMC"
Printer:	Arrayer 250A
Array Configuration: (columns X rows)	48 sectors ( 4 X 12 spotted) Standard 48 tip
Spot Columns per Sector:	16
Spot Rows per Sector:	17
Column Spacing:	235
Row Spacing:	240
Plate Orientation:	rotated 90 degrees clockwise (P1 top-left, A1 top-right)
Printhead Dip Dynamics:	top to bottom, right to left
Sector Spotting Dynamics:	left to right, top to bottom
Number of Slides:	254
Plates used in this print, in order.
PLATEID	PLATENAME	PLATE_VISITS	IS_FLIPPED
100700	SBSC_SONIC_1
100508	HYBRIDSB_9
100504	HYBRIDSB_5
100526	HYBRIDSC_14
100522	HYBRIDSC_10
100502	HYBRIDSB_3
100512	HYBRIDSB_13
100525	HYBRIDSC_13
100506	HYBRIDSB_7
100521	HYBRIDSC_9
100511	HYBRIDSB_12
100501	HYBRIDSB_2
100704	SBSC_SUPP_1
100527	HYBRIDSC_15
100510	HYBRIDSB_11
100505	HYBRIDSB_6
100514	HYBRIDSC_2
100528	HYBRIDSC_16
100503	HYBRIDSB_4
100507	HYBRIDSB_8
100509	HYBRIDSB_10
100513	HYBRIDSC_1
100500	HYBRIDSB_1
100529	HYBRIDSC_17
100517	HYBRIDSC_5
100524	HYBRIDSC_12
100519	HYBRIDSC_7
100515	HYBRIDSC_3
100523	HYBRIDSC_11
100520	HYBRIDSC_8
100518	HYBRIDSC_6
100516	HYBRIDSC_4
100700	SBSC_SONIC_1


title: C. elegans 385K ChIP03

city: Toronto

first: DCC

last: modENCODE

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

organism: Caenorhabditis elegans

description: C. elegans whole genome tiling array (3 array set) at 86bp resolution, 385K features per array, 1.15M total features.

manufacture_protocol: see manufacturer's website


title: C. elegans 385K ChIP02


title: sm6koligo

city: Hamilton

first: HONG

last: GUO

address: 1280Main St. West

department: BIOLOGY

institute: MCMASTER UNIVERSITY

organism: Sinorhizobium meliloti 1021

description: Array with 20160 features, in 48 zones, with 6229 biosequences representing 6230 reporters and 0 composite sequences, with surface type epoxy. (Submitter's description 1): Sm6kOligo microarrays represent all currently predicted protein-coding genes of the soil bacterium Sinorhizobium meliloti 1021

manufacturer: Center for Biotechnology (CeBiTec), Bielefeld university,Germany

manufacture_protocol: for more information visit: http://www.cebitec.uni-bielefeld.de/transcriptomics/transcriptomics-facility/sm6koligo.html


title: AGENAE_CattleGeneric2_9216

city: Castanet-Tolosan Cedex

first: Gwenola

last: Tosser-Klopp

address: Chemin de Borde-Rouge  BP 52627

country: France

institute: INRA

organism: Bos taurus

description: 9216 bovine cDNA from several libraries were spotted onto a nylon membrane (2.5 X 7.5 cm).  The information concerning library name, library Unigene name (http://www.ncbi.nlm.nih.gov/UniGene/lbrowse2.cgi?TAXID=9913), and publication is pated below, for the different libraries.  Libraries bcaa (Lib.2819), bcab (Lib.2820), bcac (Lib.2821), bcad (Lib.2822) are described in  Smith et al. Genome Res.114:626-630 (2001).  Library  bcao (Lib. 5505) is described in Sonstegard,T., et al., Mamm Genome 13 (7): 373-379 (2002).  Library bcai (Lib. 15979) is described in Degrelle et al., Developmental Biology 288 (2005) 448-460).  Library  bcas (Lib. 15656) is unpublished Library bcaz (Lib. 17188) has been submitted for publication.

manufacturer: CRB GADIE, Jouy-en-Josas, France(crb-gadie@jouy.inra.fr), Plateforme Genomique-Genopole Toulouse Midi Pyrenees(http://genomique.genotoul.fr/) and UMR444 Laboratoire de Genetique Cellulaire, INRA, Castanet-Tolosan, France(gwenola.tosser@toulouse.inra.fr)

manufacture_protocol: as described in Institute Labs manual


title: Indian Institute of Science, Salmonella Typhimurium 15K array version 1

city: Bangalore

first: Dipshikha

last: Chakravortty

state: Karnataka

address: C.V.Raman AVENUE

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

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

first: DrDipshikha

first: DrSandeepa

last: M E

manufacture_protocol: Refer Manufacturers Protocol


title: JVCI Mycobacterium smegmatis microarray version 4

city: New York

first: Christina

middle: Leigh

last: Stallings

state: NY

department: Immunology

institute: Sloan Kettering Institute

organism: Mycolicibacterium smegmatis

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


title: Affymetrix RML Custom Pathogenic chip 2

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

organism:
Borrelia hermsii
Francisella tularensis
Coxiella burnetii
Rickettsia prowazekii
Burkholderia mallei
Brucella suis

description: custom pathogenic Affymetrix chip 2 manufactured for RML

manufacture_protocol: standard Affymetrix protocol


title: Zebra mussel byssus cDNA microarray

status: Public on Apr 19 2008

city: Chicago

first: Wei

last: Xu

address: 303 E Chicago Ave, Tarry 4-714

department: Surgery

institute: Northwestern University, Feinberg School of Medicine

organism: Dreissena polymorpha

manufacturer: Aquatic Animal Health Laboratory, Department of Pathobiology & Diagnostic Investigation, College of Veterinary Medicine, Michigan State University

first: Mohamed

last: Faisal

manufacture_protocol:
716 E.coli clones were selected from thirty-four 96-well plates and re-arranged into eight new 96-well plates. The overnight cultures from the eight 96-well plates were used to prepare the PCR templates. 10 μl of each bacterial culture was taken to mix with 90 μl sterile double distilled water. Then the mixture was incubated at 100 ℃ for 10 minutes followed by 15 minutes 1200g centrifuge. The supernatant was used as PCR templates. M13 forward (5’- GTT TTC CCA GTC ACG ACG TTG -3’) and reverse (5’- TGA GCG GAT AAC AAT TTC ACA CAG -3’) primers were applied with GoTaq Green Mastermix (Promega, Madison, WI) to yield 100 μl PCR product for each EST. PCR products purification was done by MinElute 96 UF PCR Purification Kit (Qiagen, Valencia, CA). All the purified PCR products were dissolved with 20 μl 50% dimethyl sulfoxide (DMSO). 1 μl of each purified amplicon was loaded on 1.2% agarose TAE gel to detect the presence of the products. All the purified amplicons were transferred to two 384 well plates by Tecan Genosys 150 liguid handling robot (Tecan US, Research Triangle Park, NC) before the microarray spotting.
The cDNA microarray spotting was performed by GeneTAC G3 arraying robot (Genomic Solutions, Ann Arbor, MI) which is equipped with a 48-pin head. The cDNA microarray designed for the 716 genes contains 48 sub-arrays (4 ×12). In each sub array, 64 spots were distributed as an 8 × 8 matrix. The 716 amplicons were spotted in triplicates, which are randomly located in each sub-array. Zebra mussel β-actin was used as positive control spotted in every subarray while the spotting solutions were used as negative controls in each subarray. Meanwhile, twelve spots in each sub-array are left blank for background control and negative control as well.


title: Applied Biosystems TaqMan microRNA Assays

status: Public on Sep 30 2008

city: Rome

first: Enrico

last: De Smaele

state: Rome

address: viale Regina Elena 324

department: Experimental Medicine

institute: Sapienza University of Rome

organism: Homo sapiens

technology: RT-PCR

distribution: virtual


title: C. elegans 385K ChIP01


title: Wheat custom oligonucleotide array for stripe rust study

city: Raleigh

first: Tristan

last: Coram

address: 4118 Williams Hall, NC State University

institute: USDA-ARS, NC State University

organism: Triticum aestivum

manufacturer: Call Lab, Washington State University, Veterinary Microbiology and Path, Bustad 415 Pullman, WA 99164-7040

first: Lisa

last: Orfe

first: Doug

last: Call

first: Xueling

last: Huang

first: Xianming

last: Chen

manufacture_protocol:
Probes were selected for construction of the custom microarray based on their identification as being differentially expressed in previous studies of both Yr5-mediated all-stage resistance and Yr39 high-temperature adult-plant resistance to stripe rust in wheat. These previous studies both used the commercial Affymetrix Wheat GeneChip (Affymetrix, Santa Clara, CA) and identified a total of 343 probes as differentially expressed that could be used in the present study. The unigenes for each of the 343 differentially expressed probes were identified and DNA sequences extracted using HarvEST (Affymetrix Wheat1 Chip version 1.52). Custom 60-mer oligonucleotide probes were designed to each sequence using the publicly available eArray software (Agilent Technologies, Santa Clara, CA). Oligonucleotide probes for six positive housekeeping controls were also designed (Elongation factor 1-alpha, Sucrose synthase, Ubiquitin, CYP86, Actin and GAPDH), as well as antisense-orientated probes for these six to represent negative controls. A biotin-labeled oligonucleotide was included as a hybridization control, and blank-buffer spots were used as background control. In total, there were 385 features on the microarray
The 60-mer oligonucelotide probes were re-suspended at a final concentration of 60 µM in 1X ArrayIt® Micro Spotting solution (TeleChem International, Sunnyvale, CA). All features were arrayed onto 4-well (11-mm) epoxy-coated masked slides (Tekdon, Myakka City, FL) such that each feature was printed twice within each of the four wells of each slide. Slides were printed using a piezo electric dispensing Scienion sciFlexarrayer S3 (BioDot, Irvine, CA). Slides were pre-hybridized in filter-sterilized and pre-warmed (42 ºC) 1% bovine serum albumin (BSA), 15X SSC for 10 min with agitation (80 rpm) at room temperature in a Coplin jar, followed by dip rinsing 20 times in sterile water (repeated 5 times in fresh water) and spinning dry in a slide mini-centrifuge for 15 seconds.


title: Pleiss Lab Agilent Saccharomyces cerevisiae 019521

status: Public on Feb 05 2009

city: Ithaca

first: Jeffrey

last: Pleiss

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

description: 8x15K custom array

manufacture_protocol: 8x15K custom array


title: UCMerced_Apal_v3

status: Public on Mar 31 2009

city: Thuwal

first: Christian

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

organism: Acropora palmata

middle: R

first: Jodi

last: Schwarz

first: Julia

last: Schnetzer

first: Shinichi

last: Sunagawa

first: Michael

middle: K

last: DeSalvo

first: Alina

middle: M

last: Szmant

first: Mary-Alice

last: Coffroth

first: Monica

last: Medina

manufacture_protocol: Microarrays consist of PCR-amplified cDNAs from A. palmata. 2,055 PCR-amplified cDNAs were spotted in duplicate on poly-lysine-coated slides yielding a microarray with 4,110 total features. cDNAs were chosen from EST libraries described in (Schwarz et al., 2008). To annotate the cDNAs, we performed a BLASTx analysis (E-value cut-off 1e-5) against the GenBank non-redundant DNA and protein database (nr).


title: UMSMED custom Ictalurus punctatus 9.2k microarray (v2008)

status: Public on Sep 20 2008

city: Silver Spring

first: Sai

last: Majji

address: 503 Robert Grant Avenue

institute: Naval Medical Research Center

organism: Ictalurus punctatus

first: Venkata

last: Thodima

first: Ana

last: Arnizaut

first: Youping

last: Deng

first: Warren

last: May

first: Donald

last: Sittman

first: Larry

last: Hanson

first: Marvin

last: Cuchens

first: Eva

last: Bengten

first: Gregory

last: Chinchar

manufacture_protocol:
1. Array robot type:  MI's robot is a custom design and is not commercially available
2. Printing Type: Contact printing
3. Deposition Methodology:  MI uses ceramic capillary printing pins.
4. Buffer type: 150mM NaPO4, pH 8.0,
5. DNA concentration: 40umolar
6. Substrate type: Corning UltraGAP


title: CDC C. botulinum ATCC 3502 CGH 385k array version 1

status: Public on Jan 24 2008

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

organism: Clostridium botulinum A str. ATCC 3502

first: Carolina

last: Luquez

first: Loretta

last: McCroskey

first: Lavin

last: Joseph

first: Mark

last: Jacobson

first: Eric

last: Johnson

first: Susan

middle: E

last: Maslanka

first: Joanne

last: Andreadis

manufacture_protocol: Oligonucleotide arrays were synthesized by NimbleGen Systems, Inc by maskless array synthesis.  A custom comparative genomic hybridization design was used based on the C. botulinum ATCC 3502 genome sequence (GenBank accession number: AM412317). The NimbleGen design file (.ndf) linked as supplementary file.