title: Phanerochaete chrysosporium RP-78 microarrays

status: Public on Mar 30 2009

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

country: USA

institute: UW/FPL

organism: Phanerochaete chrysosporium RP-78

technology: in situ oligonucleotide

description: The .ndf file is linked below as a supplementary file.

distribution: custom-commercial

manufacture_protocol: Proprietary maskless array in situ oligonucleotide synthesis. See http://www.nimblegen.com/


title: Arabidopsis 26K spotted oligo microarray

status: Public on Mar 11 2009

city: Columbia

first: Robert

middle: Thomas

last: Gaeta

state: MO

address: 117 Tucker Hall, Department of Biological Sciences, University of Missouri

department: Biological Sciences

institute: University of Missouri

organism: Arabidopsis thaliana

technology: spotted oligonucleotide

distribution: non-commercial

middle: T

first: Yoo

last: Suk-Young

first: Joseph

middle: C

last: Pires

first: Rebecca

middle: W

last: Doerge

last: Chen

first: Osborn

last: Thomas

manufacture_protocol: Arabidopsis 70-mer oligo nucleotides were spotted onto Super Amine microarray slides (ArrayIt, Sunnyvale, CA) using the OmniGrid Accent microarrayer (GeneMachines, San Carlos, CA) according to protocols described in detail by Wang et al., 2005.


title: Lactobacillus acidophilus NCFM whole genome 7K oligoarray [4 reps]

status: Public on Mar 24 2009

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

state: NC

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

organism: Lactobacillus acidophilus NCFM

description: A total of 1,823 oligos (97.8% of the total number of genes in the chromosome) were spotted on glass slides.  Each oligo (representing each gene) was spotted 4 times in a random pattern.  To assess the reliability of the platform, we conducted a microarray hybridization experiment labeling cDNA from the same RNA sample with Cy3 and Cy5.  Hybridization data revealed a linear correlation (R value) in the relative expression level of  0.98 of 11,520 spots

manufacturer: T. R. Klaenhammer laboratory and Genomics Sciences Laboratory at NC State University

first: Maria

middle: A

last: Azcarate-Peril

middle: R

manufacture_protocol: OligoArray 2.1 (Rouillard et al., 2003) was selected based on literature, availability (free software for academic use), and user-friendly accessibility for oligonucleotide design.  The oligonucleotide length range was set to 60-70 nt, the melting temperature (Tm) range to 80-96°C and the GC content range to 25-50% according to the GC content of the NCFM genome (34.71%). The thresholds to reject oligonucleotides that can form stable secondary structures and to start to consider putative cross-hybridizations were both set to 65°C. Oligonucleotides containing either AAAAA, TTTTT, GGGGG, CCCCC or longer homopolymers were rejected.  A total of 1,823 oligos (97.8% of the total number of genes in the chromosome) meeting the above criteria were obtained. No primers could be obtained for 41 genes mainly due to the presence of prohibited sequences (homopolymers). Twenty-four of the oligonucleotides obtained were unspecific.  Oligonucleotides were purchased from Integrated DNA Technologies (Coralville, IA).


title: Schistosoma japonicum 3.1K

status: Public on Mar 10 2009

city: shanghai

first: yuan

last: chunxiu

country: China

institute: shanghai research institute of domestic animal parasitolgy

organism: Schistosoma japonicum

technology: spotted DNA/cDNA

description: Spotted Schistosoma japonicum differentially expressed gene array on glass.this set includes 3118 gene clone ,2 tubulin control and 16 blank. These gene clone are from subtracted cDNA library. The PCR products of cDNA were amplified by use of the polymerase chain reaction (PCR) and then purified with isopropanol precipitation. All PCR products were examined by agarose gel electrophoresis to ensure the quality and the identity of the amplified clones as expected. Then the amplified PCR products were dissolved in a buffer containing 3X SSC solution. The solution with amplified PCR products were spotted onto silylated slides(Biostar, Shanghai, China) with a Omnigrid Arrayer(Gene Machine,CA) fitted with 16 Major Precision split pins.Glass slides with spotted cDNA was then hydrated for 2 hours in 70% humidity, dried for 0.5 hour at room temperature, UV cross-linked (65mj/cm). They were further processed at room temperature by soaking in 0.2% sodium dodecyl sulfate (SDS) for 10 min, distilled H2O for 10 min, and 0.2% sodium borohydride (NaBH4) for 10 min. The slides were dried again and ready for use.

first: Chunxiu

last: Yuan

first: Xingang

last: Feng

first: Jiaojiao

last: Lin


title: Miltenyi Biotec/UT Southwestern Mouse 1K v1.0

city: Dallas

first: Steve

last: Kernie

state: TX

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

organism: Mus musculus


title: IntelliGene® HS Human Expression CHIP (Array A&B)

status: Public on Mar 21 2009

city: Osaka

first: Hiroki

last: Shima

address: 3-7-41 Nakatsu YAMAMOTO  Bild. 4F. Kitaku

country: Japan

institute: SHIMA Institution for Quantum Medicine

organism: Homo sapiens

distribution: commercial

manufacture_protocol:
1.About 300 bp of cDNA are amplified for each gene, purified, and resuspended to 0.1 ug/ul dH2O. The 5'-end of primer used with amplification is labeled with amino residue.
2. Add equal volume of the spotting buffer to the cDNA solution.
3. Spot to TaKaRa-Hubble Slide Glass.
4. After the print run is completed, process the fixation protocol of the glass.


title: KKI/Pevsnerlab Human 550K SNP

city: Baltimore

first: Jonathan

last: Pevsner

state: MD

address: 707 N. Broadway

department: Neurology

institute: Kennedy Krieger Institute

technology: oligonucleotide beads

description: Illumina’s HumanHap550 Genotyping BeadChip enables whole-genome genotyping of over 555,000 tag SNP markers derived from the International HapMap Project (www.hapmap.org). The HumanHap550 Genotyping BeadChip contains > 555,000 SNP loci with high-density tag SNP content that provides comprehensive genomic coverage across multiple populations. In addition, there are 4,300 SNPs in recently reported copy number polymorphism regions of the genome, 7,800 nsSNPs, 1,800 tag SNPs in the Major Histocompatibility Complex (MHC), 177 mitochondrial SNPs, and 11 Y-chromosome SNPs. (Source: http://www.illumina.com/pages.ilmn?ID=154)

manufacture_protocol: see manufacturer's website


title: Rice 2K cDNA microarray

city: Wuhan

first: Yuanyuan

last: Wang

department: College of Life Sciences

institute: Wuhan University

organism: Oryza sativa

manufacturer: Key Laboratory of Ministry of Education for Plant Development Biology, College of Life Sciences, Wuhan University and TaKaRa (Dalian) Co., Ltd.

first: Xiaolan

first: Hongyu

first: Guangcun

last: He

manufacture_protocol: Subtractive cDNA library has been constructed from the BPH-infested B5 and MH63 plants using SSH technique (Yuan et al., 2005; Wang et al., 2005). To reduce the bias caused by SSH technology, equal numbers of clones were randomly selected from the each of the SSH cDNA libraries and a total of 1920 clones were used in the cDNA microarray analysis. The cDNA microarrays were custom-made and analyzed at TaKaRa (Dalian) Co., Ltd. To determine the detection sensitivity limit, the PCR-amplified fragment from lambda-A and Puc19 were used as external controls, and the PCR-amplified fragments from the mouse (Mus musculus) ß-actin gene and Human TFR gene were used as negative controls. Inserts of cDNA clones were PCR-amplified with T7 and M13R primers. The purified PCR products were dissolved in H2O at a concentration of 1.0 mg/ml and arrayed in paired dots from 384-well microtiter plates on poly-l-Lys-coated micro glass slides using a microarray stamping machine (Affymetrix 417 Arrayer, Affymetrix, Inc. Co, Santaclara, CA, USA). Such slides were post-processed according to the manufacturer’s protocols at TaKaRa Co., Ltd.


title: Streptococcus pyogenes Type M1 and M18 microarray

status: Public on Mar 16 2009

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

organism: Streptococcus pyogenes

description: The oligonucleotides were spotted onto poly-L-lysine microarray slides by a robotic microarrayer (Omni GRAD 100 microarrayer) using 12 pin spotter at the Center of Applied Genomics (CAGE) of the Public Health Research Institute, Newark, NJ. Arrays were distributed in 16 blocks each with 12 columns and 12 rows.

manufacturer: Pancholi Laboratory, Public Health Research Institute

first: Hong

last: Jin

manufacture_protocol: Sense strand oligonucleotides with mainly 55-mer, representing the 1,769 open reading frames (ORFs) in the genome of S. pyogenes Type M1, strain SF370 and 175 ORFs (those absent in SF370 strain) of Type M18 (Strain MGAS8232) were designed and produced by Illumina (http://www.illumina.com).  They were obtained as 1.35 nmoles quantity at 50 uM concentration in 27 ul of water in shallow well plates.


title: Lactobacillus acidophilus NCFM whole genome 11K oligoarray [6 reps]

description: A total of 1,823 oligos (97.8% of the total number of genes in the chromosome) were spotted on glass slides. Each oligo (representing each gene) was spotted 6 times in a random pattern.

manufacture_protocol: OligoArray 2.1 (Rouillard et al., 2003) was selected based on literature, availability (free software for academic use), and user-friendly accessibility for oligonucleotide design. The oligonucleotide length range was set to 60-70 nt, the melting temperature (Tm) range to 80-96°C and the GC content range to 25-50% according to the GC content of the NCFM genome (34.71%). The thresholds to reject oligonucleotides that can form stable secondary structures and to start to consider putative cross-hybridizations were both set to 65°C. Oligonucleotides containing either AAAAA, TTTTT, GGGGG, CCCCC or longer homopolymers were rejected. A total of 1,823 oligos (97.8% of the total number of genes in the chromosome) meeting the above criteria were obtained. No primers could be obtained for 41 genes mainly due to the presence of prohibited sequences (homopolymers). Twenty-four of the oligonucleotides obtained were unspecific. Oligonucleotides were purchased from Integrated DNA Technologies (Coralville, IA).


title: BOTL3 Bos taurus 1.4K 7_18_03

status: Public on Mar 31 2009

city: College Station

first: Kathryn

middle: M

last: MacKinnon

address: 2881 F&B Road

institute: USDA-ARS-SPARC

organism: Bos taurus

description:
Bovine Total Leukocyte cDNA microarray
Third Generation Microarray
Keywords = microarray, cDNA, bovine
Also see Platform GPL363

manufacture_protocol:
SEE: http://nbfgc.msu.edu

Michigan State University
Department Animal Science
Lab Center for Animal Functional Genomics
B215 Anthony Hall
East Lansing, MI 48824


title: NBFGC Bos taurus 22.8K cDNA microarray

description: National Bovine Functional Genomics Consortium cDNA microarray.


title: OSU-CCC microRNA microarray v3 4x8 130D

first: Terry

last: Camerlengo

address: Biological Research Tower 12 ave

department: Biomedical Informatics

manufacturer: Microarray Shared Resource, Comprehensive Cancer Center, The Ohio State University (OSU-CCC)

middle: L

first: Jeff

last: Palatini

first: Timothy

last: Wise

manufacture_protocol: Manufacured using GE Healthcare's CodeLink (TM) 3-D Gel Matrix Technology. CodeLink(tm) Activated Slides are designed to covalently immoblize amine-modified DNA for microarrays. The slides are coated with a 3-D surface chemistry comprised of a long-chain, hydrophilic polymer containing amine-reactive groups. This polymer is covalently crosslinked to itself and to the surface of the slide. The crosslinked polymer, combined with end-point attachment, orients the immobilized DNA, and holds it away from the surface of the slide. The 1x printing buffer consists of 50 mM sodium phosphate at pH 8.5. Codelink slides are manufactured by SurModics and were formally sold as 3D-Link(tm) Activated Slides.   Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions (http://www.genomicsolutions.com ) that is fitted with a printhead and 16 SMP3 print tips from Telechem (http://www.arrayit.com). The microRNA microarray probe set is based on 40mer oligonucleotides from Sigma-Genosys.   Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normalized 25 micromolar concentration. The miRNA microarray spot densities are 200 microns (center-to-center). The microarrays are printed on Codelink Activated Slide (PN300011)) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: Toxoplasma gondii ChIP-chip genome-wide tiling array

status: Public on Mar 19 2009

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

country: France

institute: CNRS

organism: Toxoplasma gondii ME49

description:
Tiling microarray encompassing 65 Mb of Toxoplasma gondii (strain ME49) genome (chromosomes Ia, Ib, II, III, IV, V, VIIa, VIIb, VIII, IX, X, XI and XII). RefSeq genome accession: NZ_ABPA00000000.1.
50mer probes selected at 82 bp interval spacing
From : TOXODB release 4.0
Genomic sequence available at: http://toxodb.org/common/downloads/release-4.0/
Native NimbleGen files (ndf, pos) are linked below as supplementary files.

first: Philippe

last: Ortet

first: Olivier

last: Bastien

first: Mohamed

last: Hakimi

manufacture_protocol:
NimbleGen manufactures custom, high-density DNA arrays based on its proprietary Maskless Array Synthesizer (MAS) technology. The MAS system is a bench top, solid-state, high-density DNA array fabrication instrument comprised of a maskless light projector, a reaction chamber, a personal computer, and a DNA synthesizer. NimbleGen builds its arrays using photo-mediated synthesis chemistry with its MAS system.
At the heart of the system is a Digital Micromirror Device (DMD), similar to Texas Instruments' Digital Light Processor (DLP), employing a solid-state array of miniature aluminum mirrors to pattern up to 786,000 individual pixels of light. The DMD creates "virtual masks" that replace the physical chromium masks used in traditional arrays.
These "virtual masks" reflect the desired pattern of UV light with individually addressable aluminum mirrors controlled by the computer. The DMD controls the pattern of UV light projected on the microscope slide in the reaction chamber, which is coupled to the DNA synthesizer. The UV light selectively cleaves a UV-labile protecting group at the precise location where the next nucleotide will be coupled. The patterns are coordinated with the DNA synthesis chemistry in a parallel, combinatorial manner such that up to 786,000 unique probe features are synthesized in a single array.


title: SMD Print_1320

status: Public on Mar 13 2009

city: Stanford

first: Hugh

middle: O

last: McDevitt

state: CA

department: Departments of Microbiology and Immunology and Medicine

institute: Stanford University School of Medicine

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: AFFYMETRIX Human Chromosomes 21 & 22 v2.0

city: Santa Clara

first: Thomas

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

manufacture_protocol: Affymetrix standard array manufacture protocol. Please refer to http://www.affymetrix.com/technology/manufacturing/index.affx for details.


title: Pathwork Diagnostics Pathchip

status: Public on Mar 28 2009

city: Sunnyvale

first: Ljubomir

last: Buturovic

address: 1196 Borregas Avenue

department: Application Development

institute: Pathwork Diagnostics

description:
An FDA-cleared GeneChip platform for the Tissue Of Origin (TOO)
cancer diagnostic test. Based on Affymetrix U133A array.
Keywords = high density oligonucleotide array

manufacturer: Affymetrix, for Pathwork Diagnostics, Inc.

manufacture_protocol: see manufacturer's web site for U133A


title: Escherichia coli O157:H7 EDL933 Spotted PCR Array

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

organism: Escherichia coli O157:H7 str. EDL933

description: Corning UltraGAPS substrates (catalog #40016)

manufacturer: Chris Minion Laboratory at Iowa State University

first: Melissa

last: Madsen

manufacture_protocol: The Escherichia coli O157:H7 EDL933 microarray consists of PCR products (100-500 bp) spotted to Corning UltraGAPS™ substrates. Each probe was printed in duplicate, in non-adjacent spots to reduce non-uniform substrate errors in replicated probes. The array consisted of 48 subarrays, with a 15-column x 15-row configuration.


title: Vanderbuilt University miRNA Bioarray

status: Public on Mar 22 2009

city: Nashville

first: Christine

middle: H.

last: Chung

state: TN

address: 777 PRB

department: Internal Medicine

institute: Vanderbilt University

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description:
Manufactured using GE Healthcare’s CodeLink (TM) 3-D Gel Matrix Technology
Surface type: non-adsorptive
Attachment: covalent
The mirVana miRNA Bioarrays are an Ambion product that is manufactured by GE Healthcare and incorporates the CodeLink™ 3-D Gel Matrix slide surface. This aqueous environment elevates the probes away from the surface of the slide, allowing for maximum interaction between the probes and targets.

manufacture_protocol:
CodeLink(tm) Activated Slides are designed to covalently immobilize amine-modified DNA for microarrays. They are easy to use and are compatible with most available arraying and scanning instruments. CodeLink Activated Slides are coated with a novel 3-D surface chemistry comprised of a long-chain, hydrophilic polymer containing amine-reactive groups. This polymer is covalently crosslinked to itself and to the surface of the slide. The crosslinked polymer, combined with end-point attachment, orients the immobilized DNA, and holds it away from the surface of the slide.
Technical specifications:
Slide dimensions: 25 × 75 × 1 mm
1× Printing buffer: 50 mM sodium phosphate at pH 8.5
Codelink slides are manufacured by SurModics and were formally sold as 3D-Link(tm) Activated Slides.


title: Print_1468

city: South San Francisco

first: Adam

middle: S

last: Adler

address: 1 DNA Way

institute: Genentech


title: NCode Caenorhabditis elegans miRNA Microarray Kit V2

city: Stockholm

first: Suvi

middle: Tuulia

last: Asikainen

state: Huddinge

address: Karolinska University Hospital

department: CLINTEC

country: Sweden

institute: Karolinska Institutet

organism: Caenorhabditis elegans

manufacture_protocol: Corning Epoxide-Coated Glass Slides. Printed with optimized probe sequences targeting all of the known mature miRNAs in the miRBase Sequence Database, Release 9.0 for C.elegans. More information in website at www.invitrogen.com/ncode.


title: Ambion_mirVana Bioarray V2

city: Singapore

first: Yu

last: Wang

address: 11 Hospital Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore


title: CodeLink Expression UniSet Mouse 1

city: Pittsburgh

first: John

middle: Michael

last: Krill-Burger

state: PA

address: Rm. WG21.3 Shadyside Hospital

institute: University of Pittsburgh Medical Center

description:
Mouse Uniset 1 including positive and negative bacterial controls provided by the manufacturer: External RNA controls for monitoring performance of CodeLink Whole Genome Bioarrays
http://www.appliedmicroarrays.com/Reference_Materials.html

first: William

last: LaFramboise

first: Robert

last: Wiseman

first: Kelly

last: Bombach

first: David

middle: P

last: Ankrapp

manufacture_protocol:
http://www.appliedmicroarrays.com/CodeLink.html
iExpress assay reagent kit protocol
1-assay Bioarray Processing protocol


title: Payne Aspergillus flavus 13,548 v1.0

status: Public on Mar 25 2009

city: Raleigh

first: Carrie

middle: A.

last: Smith

address: 2510 Gardner Hall

department: Department of Plant Pathology

institute: NC State University

organism: Aspergillus flavus

manufacture_protocol: Standard Affymetrix protocols were followed and can be found at http://www.affymetrix.com/support/technical/manual/technical_manual.afx


title: Citrus 19K cDNA

first: Qing

last: Liu

address: Shizishan street NO.1

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

organism: Citrus sinensis

first: Andan

last: Zhu

first: Lijun

last: Cai

first: Wenjing

last: Zhou

first: Keqin

last: Yu

first: Xiuxin

last: Deng

manufacture_protocol: The amplified cDNA PCR products were precipitated with the addition of 100 μl of anhydrous ethanol and resuspended in 15 μl of 50% dimethyl sulphoxide (DMSO) at a final concentration of 0.1-0.5 μg/μl and then spotted onto amino silaned glass slides (CapitalBio.Corp, Beijing, China) with a SmartArrayerTM microarrayer (CapitalBio Corp.). Each clone was printed in triplicate. After printing the slides were baked for 1 h at 80 °C and stored dry at room temperature


title: Affymetrix Lactobacillus casei antisense CDS array

status: Public on Mar 17 2009

city: Madison

first: Hui

address: 1605 Linden Dr

institute: University of Wisconsin

organism:
Lacticaseibacillus casei
Lactobacillus helveticus

description: Platform includes 2,661 (97%) chromosomal and 17 (85%) plasmid CDSs predicted to occur in Lb. casei ATCC 334, as well as all predicted CDSs in the draft Lb. helveticus CNRZ 32 genome.  CDSs that were not included in the microarray design were all transposase-encoding genes.

manufacture_protocol: E. coli Antisense Array Protocol


title: OVCA-454-smallRNAs

status: Public on Mar 12 2009

city: Seattle

first: Muneesh

last: Tewari

state: WA

address: 1100 Fairview Ave, N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

technology: other

description: Instrument model: 454 GS 20

distribution: virtual


title: Cornell Human promoter 37K

status: Public on Mar 14 2009

city: new york

first: weimin

last: ci

state: NY

address: 1300 York ave

department: medicine

institute: weill cornell college of medicine

first: Weimin

last: Ci

manufacture_protocol:
software=NimbleScan	version=2.4.27
designname=2006-10-26_HG17_min_promoter
date=Tue Dec 11


title: GE Healthcare/Amersham Biosciences CodeLink™ Mouse Whole Genome Bioarray


title: Agilent 8x15k synthetic construct custom array experiment 4

status: Public on Mar 01 2009

city: Mol

first: Jef

last: Hooyberghs

address: Boeretang 200

country: Belgium

institute: VITO nv

organism: synthetic construct


title: NimbleGen/UWash Human 385K Design 1

status: Public on Mar 06 2009

first: Tomas

last: Marques-Bonet

address: 1705 NE Pacific St,

department: Genome Sciences

institute: University of Washington

description: This design was targeted to the "union" human regions (B35) that have at least one segmental duplication in any primate species analyzed (human, chimp, orang and macaque).

first: Jeffrey

last: Kidd

first: Mario

last: Ventura

first: Tina

last: Graves

first: Ze

last: Cheng

first: LaDeanna

last: Hillier

first: Zhaoshi

last: Jiang

first: Carl

last: Baker

first: Ray

last: Malfavon-Borja

first: Lucinda

last: Fulton

first: Can

last: Alkan

first: Gozde

last: Aksay

first: Santhosh

last: Girirajan

first: Priscillia

last: Siswara

first: Lin

last: Chen

last: Cardone

first: Arcadi

last: Navarro

first: Elaine

last: Mardis

first: Richard

middle: K

last: Wilson

first: Evan

middle: E

last: Eichler

manufacture_protocol: Manufactured by NimbleGen according to manufacturer's protocol.


title: Bovine oviduct and endometrium (BOE) 1.7K cDNA array version 1.2

city: Lindau

first: Stefan

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

manufacturer: Laboratory for Functional Genome Analysis (LAFUGA) - Genomics Unit, Gene Center of the LMU Munich, Munich, Germany

manufacture_protocol: Fifteen microliters of PCR reactions of amplified cDNA clones were transferred to 384 well microtiter plates (AbGene, Epsom, Surrey, UK) containing 15 µl of 2 x spotting buffer (40 mmol/l Tris-HCl pH 8, 2 M NaCl, 2 mmol/l EDTA, and bromphenol blue). PCR products were spotted onto amphoterous nylon membranes (Nytran plus, Schleicher & Schuell, Dassel, Germany) within an area of 2 x 5 cm. For spotting an Omnigrid Accent microarrayer (GeneMachines, San Carlos, CA) was used with solid pins (0.015 inches in diameter, SSP015; Telechem International; Sunnyvale, CA). Spotting was performed 6 times for each PCR product on the same position for sufficient and equal application. Twenty-eight arrays were produced simultaneously. The spotted DNA was denatured with 0.5 N NaOH for 20 min at room temperature. DNA was immobilized by baking for 30 min at 80 °C and UV crosslinking (120 mJ/cm2).


title: Agilent 8x15k synthetic construct custom array experiment 1

first: Jef

last: Hooyberghs


title: IMBA Ago-1 and TRIM32-bound small RNAs from E14.5 mouse brain (454 GS FLX system)

status: Public on Mar 09 2009

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

technology: MPSS

manufacturer: Institute of molecular Biology of the Austrian Academy of Sciences (IMBA)

first: J

last: Schwamborn

first: E

last: Knoblich

manufacture_protocol: small RNA deep sequencing


title: IFR ShEcoli 7.6k v1.0

status: Public on Mar 04 2009

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

country: United Kingdom

institute: Institute of Food Research

organism:
Escherichia coli
Shigella flexneri

first: Arthur

last: Thompson

first: Jay

last: Hinton

manufacture_protocol:
PCR product microarray of ORF's from Escherichia coli K12 MG1655 (U00096), Escherichia coli O157 EDL933 (AE005174), Shigella flexneri 2a str. 301 (AE005674). In addition, virulence-related genes from various pathogenic E. coli were amplified and added. For the description of PCR amplification and printing procedures see:
Lucchini et al. (2005) Infect. Immun. 73(1):88-102


title: UHN Murine 15K Spotted cDNA array

city: Hyderabad

first: Jyotsna

last: Dhawan

state: Andhra pradesh

address: Uppal road

department: Cell Biology

country: India

institute: Centre for cellular and Molecular Biology

manufacture_protocol: pre spotted


title: Streptococcus mutans 10.7K oligonucleotide array version 1

city: Halifax

first: Yung-Hua

last: Li

state: NS

address: 5981 University Ave. Rm5215

department: Applied Oral Sciences

country: Canada

institute: Dalhousie University

organism: Streptococcus mutans UA159

manufacturer: The Pathogen Functional Genomic Resource Center (PFGRC)

manufacture_protocol: Glass slides with aminosiane coating, 4X replicate oligo printing


title: FGSC-N. crassa-10918-NC_10/04/05 UCB_11k oligo array

city: Hanover

first: Chen-Hui

state: NH

address: 702 Remsen

department: Genetics

institute: Dartmouth College

organism: Neurospora crassa

manufacturer: N. Louise Glass's lab in Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.

manufacture_protocol: To construct a gene-specific microarray of N. crassa genome, we designed 70-mer oligonucleotide immobilized probes using ArrayOligoSelector, and the approximately 10,000 open reading frames (ORFs) derived mainly from the N. crassa databases at the Broad Institute and MIPS. ArrayOligoSelector selects a unique segment to identify each ORF considering the predicted sequences of all genes. The program avoids selecting internal self-annealing structures and internal repeat sequences, and preferentially chooses oligonucleotides within a narrow range of GC content, which are biased towards the 3' terminal region of each gene. Oligomers were synthesized (Illumina, San Diego, CA) for all ORFs. Analysis of oligomer placement in predicted genes indicated the desired strong 3' bias. Oligomers were re-suspended in 3x SSC to a final concentration of 20µM, and spotted. Eight 40mM ArrayControl Sense Oligo spots, which were complementary to the eight ArrayControl RNA spikes (Ambion, Austin, TX, USA), were also included.  Amplified DNA may be precipitated in 96-well format with isopropanol, washed with 70% EtOH, and resuspended in a salt spotting solution such as 3X SSC. DNA is commonly spotted on polylysine-coated glass slides or γ-aminopolysilane (GAPS)–coated glass slides (Corning, Corning, NY), using a microarraying robot. GAPS slides are more expensive but have a better shelf life and tend to be less variable in quality than poly-lysine coated slides.   10,918 oligomers are on the chip. 10,526 oligos are based on MIPS or Broad Institute predicted ORFs. 8 oligos are Abmion ArrayControl Sense Oligo Spots (#1781). The remaining 384 oligos (ChIP_Chip) were mainly designed in the intergenic regions. 40uM oligos in 3x SSC were printed onto Corning UltraGAPS slides. Slides are not post-processed. Rehydration is optional. Oligos need to be cross-linked with 600mJ UV. Slides should be stable for a year at room temperature in desiccator.  Slides may display unacceptable levels of green background and the way we know to remove is using the Pronto!™ Background Reduction Kit (Item #40029) from Corning. It is not 100% effective so we recommend prescanning after prehybridization and identifying spots that are 3x standard deviation above background for possible elimination. For fast, easy, successful fist microarrays, we recommend to use Corning/Promega kit: 40076 Pronto Plus Indirect System and RPN5661 Amersham Post-labeling Reactive Dye Pack, which are expensive but always give brilliant results.


title: Streptococcus pneumoniae 3K version 6

city: Memphis

first: Jason

last: Rosch

address: 262 Danny Thomas Place

department: Infectious Disease

institute: St Jude Children's Hospital

organism: Streptococcus pneumoniae TIGR4

first: Michael

last: Wang

manufacture_protocol: spotted oligos of pneumococcus TIGR4 genome version 6.


title: NimbleGen/UWash Human 385K Design 2

first: Tomas

last: Marques-Bonet

first: Jeffrey

last: Kidd

first: Mario

last: Ventura

first: Tina

last: Graves

first: Ze

last: Cheng

first: LaDeanna

last: Hillier

first: Zhaoshi

last: Jiang

first: Carl

last: Baker

first: Ray

last: Malfavon-Borja

first: Lucinda

last: Fulton

first: Can

last: Alkan

first: Gozde

last: Aksay

first: Santhosh

last: Girirajan

first: Priscillia

last: Siswara

first: Lin

last: Chen

last: Cardone

first: Arcadi


title: NimbleGen 2006-05-26_CE_WS158_ChIP design_ID 3801

city: Berkeley

first: Barbara

middle: J.

last: Meyer

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

manufacture_protocol: Iso-thermal (Tm=76) tiling design for regions from C. elegans (wormbase release 158).  Interval at 50 bases. No repeat masking, so removed probes with 15mer frequency  greater than 50.


title: GE Healthcare/Amersham Biosciences CodeLink™ Rat Whole Genome Bioarray

first: John

last: Krill-Burger

organism: Rattus norvegicus

first: William

last: LaFramboise

manufacture_protocol: CodeLink rat whole genome microarrys protocol


title: GenAu MB BCELL v1.0

status: Public on Aug 23 2007

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohr-Gasse 7

country: Austria

institute: Research Institute of Molecular Pathology

organism: Mus musculus

description:
genomic regions of potential pax5 target genes from mm6,
isothermal tiling oligos at 100bp

first: Shane

last: McManus

first: Maria

last: Novatchkova

manufacture_protocol: as described in www.nimblegen.com


title: C_elegans_Aprint_YMD

status: Public on Dec 31 2003

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

institute: Yale University School of Medicine

description: A print at Yale University, made 7/01


title: Agilent_Dm_4.3_112_tiling_d

status: Public on Mar 05 2009

city: Durham

first: David

last: MacAlpine

state: NC

address: Box 3813 DUMC

department: Pharmacology and Cancer Biology

institute: Duke University Medical Center

organism: Drosophila melanogaster

manufacture_protocol: Agilent Technologies


title: Agilent_Dm_4.3_112_tiling_c

description: ChIP resolution tiling array for modENCODE. Average probe spacing of 112 bp for Drosophila genome (5.1). 3 of a 4 array set.


title: C_elegans_GHIstanfordprint_YMD2.gal.txt

status: Public on Dec 24 2003

description: Gene list for C. elegans arrays produced at Stanford and used by Reinke lab at Yale


title: SAGE:15:NlaIII:Mus musculus

last: GEO

technology: SAGE NlaIII

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


title: Oxford Gene Technology/Agilent 60-mer oligonucleotide 22K feature array

city: Madrid

first: Ramon

last: Diaz-Uriarte

state: Madrid

address: Melchor Fernandez Almagro 3

department: Structural Biology and Biocomputing Programme

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: microarray services: Oxford Gene Technology

manufacture_protocol: Oligonucleotide Array-based CGH for genomic DNA analysis. Protocol Version 2.0 (August 2005). Agilent Technologies


title: Luminex Mus musculus 0.2K microRNA

city: Boston

first: Sek Won

last: Kong

state: MA

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: Capture oligonucleotides were crosslinked to uniquely coloured Luminex xMap beads, which serve as discriminator of probe identity. This platform includes 261 unique probes, designed based on the microRNA registry Rfam 7.

first: SekWon

first: Jun

last: Lu

manufacture_protocol: other


title: Human 27.7K oligo probe set v 3.0

city: Silver Spring

first: Rasha

last: Hammamieh

state: MD

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

organism: Homo sapiens

manufacture_protocol: The oligonucleotide targets were deposited in 3X saline sodium citrate (SSC) at an average concentration of 165 μg/ml on CMT-GAPS II aminopropyl silane-coated slides (Corning, Corning, NY) using a VersArray microarryer (Bio-Rad, Inc). Arrays were post processed by UV-cross linking at 1200 µJoules/cm2  100 using UV Stratalinker 2400 (Stratagene Inc., La Jolla, CA). Then slides were baked for 4 hours at 800C, and the positively charged amine groups on the slide surface were treated with succinic anhydride/N-methyl-2-pyrrolidinone.


title: UHN Human CpG 12K Array (HCGI12K)

status: Public on Jul 03 2005

city: Basel

first: Michael

last: Weber

address: Maulbeerstrasse 66

department: Epigenetics

institute: Friedrich Miescher Institute

description:
This array contains single-spotted clones representing 12,192 CpG-island clones from the Sanger Institute.
The CpG Library was originally prepared by Sally Cross in the laboratory of Adrian Bird at The Wellcome Trust Centre for Cell Biology (University of Edinburgh). For information on the preparation of the original library, please see Cross, S.H., et.al., Purification of CpG islands using a methylated DNA binding column. Nature Genetics (1994) 6:236- 244.
Individual clones were sequenced by the UHN Microarray Centre.

manufacture_protocol: Microarrays are printed on GAPS II or UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol. For detailed information see  http://www.microarrays.ca/


title: Agilent 8x15k synthetic construct custom array experiment 3

first: Jef

last: Hooyberghs

address: Boeretang 200

institute: VITO nv


title: Agilent 8x15k synthetic construct custom array experiment 2


title: NimbleGen 071121_Celegans180_ChIP03_design_ID_6737

manufacture_protocol: HX1 design for catalog for C elegans 180/  40bp interval


title: NimbleGen 080319_C_elegans_ChIP_03_design_ID-7348

manufacture_protocol: Tiling of C elegans at 50bp spacing for ChIP chip.  Uses the stringency template.


title: Mouse Genome 430 2.0 Array [Mouse4302_Mm_ENSG (v11.0.1) CDF]

status: Public on Dec 01 2008

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

description: Probes that were estimated to have a mismatch in their sequence between Mus musculus and Mus spretus were removed from the CDF environment. The details of the procedure are described in the paper. For some probesets, all probes were masked, and they are therefore not represented in the CDF file.

relation: Alternative to: GPL1261 (Alternative CDF [official])

manufacture_protocol: This is identical to GPL1261 but a custom cdf environment was used to extract data. We used custom chip definition files (CDF) based on Ensembl gene annotation from build 46 rather than Affymetrix annotation (Dai et al., PMID: 16284200).


title: Hollings Marine Laboratory Crassostrea cDNA Array

status: Public on Jul 13 2006

city: Charleston

first: MarineGenomics

last: Project

state: SC

address: 331 Fort Johnson Rd

organism:
Crassostrea virginica
Magallana gigas

manufacturer: Hollings Marine Laboratory, Genomics Core

first: Matthew

last: Jenny

first: Paul

last: Gross

first: Pauline

last: Cupit

first: Gregory

last: Warr

first: Robert

last: Chapman

manufacture_protocol: contact spotting of cDNA clones using a Q-ArrayMax (Genetix) machine, baked for 2 h at 80C, and stored under vacuum until used