title: UMN Mouse 11K V 11_22_04 BMAP

status: Public on Nov 23 2006

city: Minneapolis

first: Ajay

last: Yekkirala

state: MN

address: 308 Harvard St 8-120

country: USA

institute: University of Minnesota

organism: Mus musculus

technology: spotted DNA/cDNA

distribution: non-commercial

manufacturer: Bio-Medical Genomics Center, University of Minnesota.

manufacture_protocol:
Basic protocol for generation of mouse microarrays
i) Obtain cDNA library
(1) thousands of bacterial stocks in 96-well plates
(2) each bacterial stock contains a standard eukaryotic expression
plasmid that contains a unique stretch of mouse cDNA inserted in
the multiple cloning site
ii) Replicate the library
iii) PCR amplify each cDNA clone in 96 well reactions
iv) Check PCR reactions on an agarose gel
v) Purify PCR reactions with a Millipore filter
vi) Elute purified DNA with 3XSSC (spotting buffer)
vii) Spot DNA onto glass slides using a DNA spotting robot


title: CapitalBio Rat 27k long oligo array

status: Public on Nov 25 2006

city: Beijing

first: Guangxin

last: Xiang

address: Tsinghua University

country: China

institute: Medical Systems Biology Research Center

organism: Rattus norvegicus

technology: spotted oligonucleotide

description: This set includes 27k oligonucleotides, mostly 70-mers, designed based upon the Ensembl Rat Database Version v19.3b.2 and Rat Genome Project.

distribution: custom-commercial

first: Liang

last: Zhang

manufacture_protocol: as described in CapitalBio Labs manual


title: SHGK

status: Public on Nov 10 2006

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism: Homo sapiens

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: GenoToul/Biopuces operon_yeast22x22

status: Public on Nov 03 2006

city: Toulouse

first: Serguei

last: Sokol

address: 135 av de Rangueil

department: Lab. Biotech. and Bioprocess

country: France

institute: INSA

organism: Saccharomyces cerevisiae

description: Dendrislides are prepared according to Trevisiol et al. 2003, New J. Chem. 27, 1713-1719

first: Klaudia

last: Kuranda

first: Veronique

last: Le Berre

first: Grazyna

last: Palamarczyk

first: Jean-Marie

last: Francois

manufacture_protocol:
Oligos sold by Operon 70-mer NH2 modified,
put in phosphate buffer 0.3 M, pH 9 at 20 µM
spotted on dendrislide (Le Berre et al. Nucleic Acids Research, 2003, Vol. 31, No. 16 e88).
Robot is ChipWriterPro (Biorad) with 4x8 pins
each pin has spotted a block of 22x22 spots.
Each well is spotted in duplicate.


title: FHCRC Arabidopsis Tiling Array

status: Public on Nov 26 2006

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

organism: Arabidopsis thaliana

technology: in situ oligonucleotide

description: Arabidopsis tiling array using NimbleGen platform (DesignID=2482). TIGR release 5.0, 1/22/2004 (ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/). Entire genome, isothermal probes averaging 50 base pairs at 300 base pair intervals.

first: Steven

first: Robert

last: Tran


title: oyster MPSS

city: Hayward

first: Christian

middle: D

last: Haudenschild

address: 25861 Industrial Blvd

institute: Solexa, Inc.

organism: Magallana gigas

technology: MPSS

description:
Sequencing from the 3' most DpnII site from mRNA using Solexa's MPSS technology.
MPSS allows a comprehensive survey of all expressed transcripts in a cell or tissue, without apriori knowledge.

distribution: virtual

first: Dennis

last: Hedgecock

first: Jing-Zhong

last: Lin

first: Shannon

last: DeCola

first: Eli

last: Meyer

first: Donal

middle: T

last: Manahan

first: Ben

last: Bowen


title: Agilent-013847 Drosophila ChIP-on-Chip Set 44K, Array 10 (G4475A)

status: Public on Nov 08 2006

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Drosophila melanogaster

description:
ChIP array

Arrays of this design have barcodes that begin with 16013847 or 2513847.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

distribution: commercial

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


title: C. elegans small RNA sequences

status: Public on Nov 17 2006

first: Andrew

last: Fire

address: 300 Pasteur Drive RML235 M5324

department: Pathology and Genetics

institute: Stanford University

organism: Caenorhabditis elegans

technology: other

description: Small RNA sequences from wild type animals fed on sel-1 dsRNA producing bacteria.

manufacture_protocol:
grind
make small RNA
linkers on both ends
RT
PCR
sequence


title: TAGC Human 1075 Clones

status: Public on Nov 18 2006

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

institute: Institut Paoli-Calmettes

first: Elisabeth

last: Devilard

first: Aurelia

last: Giacconia

first: Francois

last: Bertucci

first: Cathy

last: Nguyen

first: Beatrice

last: Loriod

manufacture_protocol: We used DNA microarrays to compare the mRNA expression profiles of ~1.000 selected genes between primary, HS, and HR tumors in the LuCaP 23.1 xenograft model of prostate carcinoma. RNA extracts were pooled according to the three distinct stages of tumor progression in the LuCaP 23.1 model (4 samples / tumor stage). DNA microarray hybridizations were done as previously described (14, 15) on home-made nylon DNA microarrays (TAGC, Marseille-Luminy, France), which contained spotted PCR products from 945 human cDNA clones. Most genes were selected for a proven or putative implication in cancer and/or in immune reactions (the list is available on the web site: http:/tagc.univ-mrs.fr/pub/Cancer/).


title: Human Ultimate ORF spotted protein array

status: Public on Nov 30 2006

city: cambridge

first: Nazila

last: Salamat-Miller

state: MA

address: 700 main street

institute: Shire

technology: spotted peptide or protein

description: Modified glass

first: Jianwen

last: Fang

first: Christopher

last: Seidel

first: Yassen

last: Assenov

first: Mario

last: Albrecht

first: CRussell

last: Middaugh

manufacture_protocol: The human arrays employed contain 4,985 doubly spotted proteins on a proprietary polymer coating.  These proteins were derived from the human Ultimate™ ORF (open reading frame) Clone Collection (for more information see http://orf.invitrogen.com) and expressed in insect cells using a baculovirus expression system as N-terminal GST-fusion proteins


title: Agilent-013842 Drosophila ChIP-on-Chip Set 44K, Array 6 (G4475A)

description:
ChIP array

Arrays of this design have barcodes that begin with 16013842 or 2513842.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Agilent-013841 Drosophila ChIP-on-Chip Set 44K, Array 5 (G4475A)

description:
ChIP array

Arrays of this design have barcodes that begin with 16013841 or 2513841.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Zebra finch brain cDNA microarray (v1)

status: Public on Nov 09 2006

city: New York

first: XiaoChing

last: Li

state: NY

address: 1230 York Avenue

institute: Rockefeller University

organism: Taeniopygia guttata

manufacture_protocol: Based on the redundancy analysis, highly redundant clones were removed, and in the re-assembled printing set, each gene transcript was represented one or two times.  The cDNA inserts were PCR amplified.  The PCR products were purified, checked by gel electrophoresis and quantified by UV absorption.  The DNA samples were dissolved in 35% DMSO and printed in duplicate onto glass slides (UltraGAPS, Corning) using the MicroGrid (BioRobotics).  Slides were then cross-linked by UV radiation at 360J.


title: NimbleGen Mouse 388K NCBI34

status: Public on Nov 21 2006

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

manufacture_protocol: Maskless array synthesis was used to construct isothermal arrays.  Probes were selected with a minimum probe spacing of 4.5 kb and the resulting array had a median probe spacing of 5.2 kb.  Probes were synthesized using an isothermal format (Tm =  76°C) and varied in length from 45 to 75 bp.


title: Agilent-013844 Drosophila ChIP-on-Chip Set 44K, Array 8 (G4475A)

description:
ChIP array

Arrays of this design have barcodes that begin with 16013844 or 2513844.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Valencia yeast v5

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: Nylon macroarray (7 x 11 cm) with 6019 single spotted yeast ORF probes. Probes are PCR fragments comprising the whole ORF (5568 cases) or a 1000 bp-fragment from the ORF 3' end (451 cases).

manufacturer: Seccion de Chips de DNA-SCSIE (University of Valencia)

middle: E

last: Garcia-Martinez

manufacture_protocol: See Alberola et al. (2004), International Microbiology 7:199-206


title: NML Salmonella Typhimurium LT2 array

city: Winnipeg

first: George

middle: Ryan

last: Golding

state: Manitoba

address: 1015 Arlington St

department: Nosocomials

country: Canada

institute: NML

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

first: Adam

last: Olson

first: Louis

last: Bryden

first: Claude

last: Oulette

manufacture_protocol: Qiagen Operon


title: Lieb Lab at UNC-CH_Yeast Whole-genome Array (PCR-based)_for Buck MJ et al.

city: Chapel Hill

first: Jason

middle: D.

last: Lieb

state: NC

department: Biology

institute: Univeristy of North Carolina at Chapel Hill

description: Whole-genome microarrays with PCR-amplified products represent ORFs, intergenic regions, and other noncoding regions (rDNA, tRNA, transposons, transposon long terminal repeats, telomeres, centromeres, and introns). Generally, each ORF was represented from start codon to stop codon. The intergenic regions consisted of the DNA between annotated ORFs divided such that PCR products were not longer than 1.5 kb, with a few exceptions. The noncoding regions conform to boundaries as annotated by the Saccharomyces Genome Database (SGD) as of the year 2000. Mitochondrial segments did not necessarily conform to annotated functional boundaries. This platform covers several print runs, in which print plates were arranged in different orders.

first: Michael

middle: J

last: Buck

manufacture_protocol: see Iyer et al. 2001, Nature 409: 533-538


title: NimbleGen Saccharomyces cerevisiae oligonucleotide photolithographic maskless array

status: Public on Nov 28 2006

city: Madison

middle: G

last: Benton

state: WI

address: 1415 Engineering Drive

department: Chemical and Biological Engineering

institute: University of Wisconsin-Madison

manufacture_protocol: photolithographic maskless oligonucleotide arrays as described at Nimblegen


title: Custom Anopheles gambiae AG_GAMBER array

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

organism: Anopheles gambiae

description: AGILENT IN SITU AG_GAMBER

manufacture_protocol: AGILENT IN SITU


title: Agilent-013845 Drosophila ChIP-on-Chip Set 44K, Array 9 (G4475A)

last: Agilent Technologies

description:
ChIP array

Arrays of this design have barcodes that begin with 16013845 or 2513845.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Galbraith Laboratory Operon Long Oligonucleotide Microarray version 3.0 (ATv305.02.Z)

city: Tucson

first: David

middle: William

last: Galbraith

state: AZ

address: 303 Forbes Building

department: Plant Sciences and Bio5 Institute

institute: University of Arizona

manufacturer: The Galbraith Laboratory, University of Arizona

middle: W

manufacture_protocol: GeneMachines Omnigrid 300


title: Vilimas (Agilent Mouse Microarray G4121A)

status: Public on Nov 29 2006

city: Collegeville

first: Tomas

last: Vilimas

state: PA

address: 1250 S. Collegeville Rd.

department: Oncology Discovery Technology Group

institute: GlaxoSmithKline

description:
This is a custom representation of Agilent's Mouse Microarray G4121A
This platform is formatted specifically for this user's normalized data and should not be referenced by other users.


title: Agilent-013843 Drosophila ChIP-on-Chip Set 44K, Array 7 (G4475A)

description:
ChIP array

Arrays of this design have barcodes that begin with 16013843 or 2513843.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Pea aphid cDNA array, INRA Rennes, 3360 spots, v1

city: Le Rheu

first: Denis

last: TAGU

department: UMR 1099 BiO3P

institute: INRA Rennes

organism: Acyrthosiphon pisum

description: Corning UltraGAPS II slides (Corning, NY, USA). Spotted by a Microgrid II spotter (Biorobotics, Cambridge, UK)

manufacturer: OUEST-Genopole transcriptomic platform, Rennes, France

first: Beatriz

last: SABATER-MUNOZ

first: Nathalie

last: PRUNIER

first: Gaël

last: LE TRIONNAIRE

manufacture_protocol: cDNAs were amplified from bacterial lysates and PCR products were resuspended into 20 µl of 1.5 M betaine, 3x SSC buffer.


title: NimbleGen_C.novyi-NT

status: Public on Nov 20 2006

first: Xin

last: Huang

address: 1650 Orleans Street, CRB I, Room 520

department: Oncology

institute: Johns Hopkins University

organism: Clostridium novyi NT

manufacture_protocol:
NimbleGen selects 5 optimal probes for each of the 2325 predicted coding sequences of Clostridium novyi-NT using a proprietary probe screening system developed exclusively for the MAS platform. Probe sets are selected which uniquely represent the genomic target or gene transcripts of interest, and which are predicted to have excellent hybridization characteristics. Our predictive software is based on a combination of NimbleGen's innovative Tm-balanced probe selection coupled with heuristic and AI predictive methods derived from a growing volume of experimental data.
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.


title: Agilent-013848 Drosophila ChIP-on-Chip Set 44K, Array 11 (G4475A)

description:
ChIP array

Arrays of this design have barcodes that begin with 16013848 or 2513848.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: SRC Mouse Compugen Printed Long Oligonucleotide 22K set version 6

status: Public on Nov 14 2006

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute for Molecular Bioscience, Uni of Qld

manufacture_protocol: Please see the SRC microarray facility website http://microarray.imb.uq.edu.au/


title: Capitalbio Human 22K oligo array v1.0

city: Beijing

first: Chen

middle: Ai

last: Liang

address: Haidian District

department: Medical  School

institute: Tsinghua University

description:
This set includes 22k oligonucleotides, mostly 70-mers; design based upon representative sequences in the human UniGene database.
Catalog# 400010

last: Ailiang

first: Zhang

manufacture_protocol: The 22 K oligonucleotide microarrays were constructed in CapitalBio Corp. (Beijing, China) using the Human Genome Oligo Set Version 1.0 (Operon, Huntsville, AL), which consist of 21,329 5'-amino-modified 70-mer probes. In addition to internal controls provided by the Oligo Set vendor, eight intergenic sequences from the yeast used as external controls were synthesized. All nucleotides were dissolved in DNA Spotting Solution (CapitalBio Corp.) at 20 M and printed on amino silaned glass slide using a SmartArrayTM microarrayer (CapitalBio Corp.). After printing, the slides were baked for 1 h at 80oC and stored dry at room temperature untill use. Prior to hybridization, the slides were rehydrated over 65oC water for 10 seconds and UV cross-linked at 250 mJ/cm2 energy. The unimmobilized oligonucleotides were washed off with 0.5% SDS for 10 min at 42oC and SDS was removed by dipping the slides in anhydrous ethanol for 30 seconds. The slides were spin-dried at 1000 rpm for 1 min. An aliquot of 5 µg total RNA was used to produce fluorescent dye-labeled cDNA with Eberwine’s linear RNA amplification method and subsequent enzymatic reaction according to a previous published protocol (Guo et al., 2005). The labeled DNA was purified with PCR Clean-up NucleoSpin kits (Macherey-Nagel), resuspended in Elution buffer, and quantified by UV spectrophotometry. Labeled control and test samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed into 80 µL hybridization solution (3×SSC, 0.2% SDS, 25% formamide and 5×Denhart’s). DNA in hybridization solution was denatured at 95oC for 3 min prior loading on a microarray. Hybridization was performed under LifterSlipTM (Erie Company), which allows for even dispersal of hybridization solutions between the microarray and coverslip. The hybridization chamber was placed on a 3D-Tilting Agitator (CapitalBio Corp.) to facilitate the microfluidic circulation under the coverslip. The array was hybridized at 42oC overnight and washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42℃ for 5 min, and 0.2% SSC for 5 min at room temperature). After hybridization, microarrays were scanned with a confocal LuxScanTM scanner (CapitalBio Corp.), and the data of obtained images were extracted with SpotData Software (CapitalBio Corp.). The raw data was normalized using a space and intensity-dependant LOWESS program (Yang et al., 2002). The data from faint spots was removed, in which the intensity was lower than the average intensity plus 2 standard deviations of the negative controls on the array. For each test and control sample, two hybridizations were performed by using a dye-swap strategy.


title: BIOTEC P. falciparum 6912

city: Pathumthani

first: Philip

middle: James

last: Shaw

state: Pathumthani

address: 113 Phahonyothin Road

department: National Center for Genetic Engineering and Biotechnology

country: Thailand

institute: National Science and Technology Development Agency

organism: Plasmodium falciparum

first: Napawan

last: Ponmee

first: Nitsara

last: Karoonuthaisiri

first: Sumalee

last: Kamchonwongpaisan

first: Yongyuth

last: Yuthavong

manufacture_protocol: Arrays printed using UltraGAPS slides (Corning) using manufacturers' standard protocol and 70-mer oligonucleotides (30 micromolar solutions in 3xSSC). The oligonucleotides were derived from the P. falciparum optimized set (Operon, version 1.1.1) representing the entire genome and the human control set (Operon, version 4.0)


title: Agilent-013840 Drosophila ChIP-on-Chip Set 44K, Array 4 (G4475A)

institute: Agilent Technologies

description:
ChIP array

Arrays of this design have barcodes that begin with 16013840 or 2513840.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

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


title: Agilent-013839 Drosophila ChIP-on-Chip Set 44K, Array 3 (G4475A)

description:
ChIP array

Arrays of this design have barcodes that begin with 16013839 or 2513839.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Agilent-013838 Drosophila ChIP-on-Chip Set 44K, Array 2 (G4475A)

description:
ChIP array

Arrays of this design have barcodes that begin with 16013838 or 2513838.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Agilent-013837 Drosophila ChIP-on-Chip Set 44K, Array 1 (G4475A)

description:
ChIP array

Arrays of this design have barcodes that begin with 16013837 or 2513837.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Sanger/Nimblegen Human array painting array_Case 1

status: Public on Nov 01 2006

city: Hinxton

first: Nigel

middle: Paul

last: Carter

state: Cambirdge

address: Wellcome Trust Genome Campus

department: Molecular Cytogenetics

country: United Kingdom

institute: Wellcome Trust Sanger Institute

manufacture_protocol:
Breakpoint spanning oligonucleotide arrays were designed essentially as described previously (Selzer et al., 2005).   Briefly, the regions of interest were repeat-masked.  The array design  contained both 50-mer fixed length probes and isothermal probes that ranged in length from 45 bp to 77 bp. Probes were generated from both strands, and replicated on the array 3 times. The arrays were constructed by maskless array synthesis technology (NimbleGen Systems Inc.), with up to 385,000 oligonucleotides being synthesized by photolithography.

Selzer, R. R. et al. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44, 305-19 (2005).


title: UFZ/Cell Toxicology_Danio rerio_14k

city: Leipzig

first: Doris

last: Voelker

address: Permoser Str. 15

department: Cell Toxicology

country: Germany

institute: UFZ Centre for Environmental Research Leipzig-Halle

organism: Danio rerio

manufacturer: MWG Biotech AG, Ebersbach, Germany/ Leiden Genome Technology Centre, Leiden, The Netherlands

first: Christoph

last: Vess

first: Georg

last: Otto

first: Robert

last: Geisler

first: Kristin

last: Schirmer

first: Stefan

last: Scholz

manufacture_protocol: The MWG zebrafish 14k array oligo set (MWG Biotech AG, Ebersbach, Germany) consists of 14067 zebrafish specific genes based on the NCBI Genbank release 128.0. Every gene is represented by one oligonucleotide. 173 Arabidopsis genes serve as negative controls. Spotting of the oligo set on poly-L-lysine-cotted glass slides was performed by the Leiden Genome Technology Centre (University of Leiden, NL, for details see Meijer et al., 2005).


title: UNC-CH Lieb lab Saccharomyces cerevisiae yOIH_R array

first: Jason

last: Lieb

address: 203 Fordham Hall CB# 3280

institute: UNC-Chapel Hill

description: This array contains entire yeast genome and Chr III at resolution of 200bp

manufacture_protocol: as described in Iyer et al


title: salivary gland secretion

status: Public on Nov 05 2006

city: Rochester

first: Alaka

last: Srivastava

address: 601 Elmwood Avenue

department: Oral Biology

institute: University of Rochester Medical Center

organism:
Homo sapiens
Mus musculus

manufacturer: University of Rochester Medical Center, Rochester, NY

first: James

last: Melvin

manufacture_protocol: Probes for target genes were designed to include key water and ion transport proteins, as well as many secretion-associated signaling molecules and representative secretory proteins.  Human and mouse cDNAs representing 188 genes were obtained from either Open Biosystems (Huntsville, AL) or the “Mouse 15K cDNA Clone Set” (National Institute of Aging).  PCR primers were designed to amplify 200-1200 bp products from the 3’ ends of highly homologous regions of the human and mouse genes.  PCR products of the expected length were purified sequence verified, and dried.  Products were resuspended at 200 ng/µl in Pronto printing buffer (Corning Inc., Corning, NY) and printed onto UltraGap Gamma Amino Propyl Silane slides (Corning, NY) using a BioRad VersaArray arrayer and 8 SMP3B stealth pins (TeleChem International Inc., Sunnyvale, CA).  Each cDNA was printed (~125 μm diameter) in duplicate at adjacent sites with spot to spot separation of 375 μm.


title: Sanger/Nimblegen Human array painting array_Cases 2-4

manufacture_protocol:
Breakpoint spanning oligonucleotide arrays were designed essentially as described previously (Selzer et al., 2005). Briefly, the regions of interest were repeat-masked. The array design contained both 50-mer fixed length probes and isothermal probes that ranged in length from 45 bp to 77 bp. Probes were generated from both strands, and replicated on the array 3 times. The arrays were constructed by maskless array synthesis technology (NimbleGen Systems Inc.), with up to 385,000 oligonucleotides being synthesized by photolithography.

Selzer, R. R. et al. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44, 305-19 (2005).


title: TIGR Staphylococcus aureus version2 array

city: Heidelberg

first: Benjamin

middle: Peter

last: Howden

state: Victoria

address: Studley Rd

department: Infectious Diseases

institute: Austin Health

organism: Staphylococcus aureus

description: Microarrays were constructed by The Institue for Genomic Research, Rockville, MD. They are amplicon based arrays containing all ORF's from Staphylococcus aureus COL (genbank ID CP000046), and selected ORF's from Staphylococcus aureus MW2 (genbank ID BA000033), N315 (Genbank ID BA000018) and Mu50 (Genbank ID BA000017). All genes are spotted in triplicate, including control spots (40 amplicons and 500 70-mers from A. thaliana).

middle: P

first: John

middle: K

last: Davies


title: Xylella USP microarray v2 (Koide et al. 2004 J.Bact.)

status: Public on Dec 20 2005

city: Ribeirao Preto

first: Ricardo

last: Vêncio

state: SP

address: Av. Bandeirantes, 3900

department: Computing and Mathematics Department

country: Brazil

institute: Universidade de São Paulo

organism: Xylella fastidiosa

manufacturer: Instituto de Química da Universidade de São Paulo (IQ-USP)

first: Tie

last: Koide

first: Paulo

middle: A

last: Zaini

manufacture_protocol:
A 4608-spot DNA microarray was printed containing unique internal fragments of 2692 CDS representing 94.5% of all of the 2848 CDS annotated by Simpson et al. (2000, Nature) (http://aeg.lbi.ic.unicamp.br/xf).

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 for the complete CDS list, automatically testing many parameter settings and also guaranteeing that primers hybridized only to a single genome location. A full list of primers, PCR product sizes, and their nucleotide sequences are available at the project site (http://verjo19.iq.usp.br/xylella/microarray/).

Oligonucleotides were synthesized by MWG and Operon Technologies. Genomic or cosmid DNA, obtained in the X. fastidiosa genome sequencing project, 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 µM, in a total volume of 100 µl. A 5min denaturing step at 95°C was applied, followed by 40 cycles of 95°C for 45s, 50°C for 30s, 72°C for 1min and a final step at 72°C for 10min. 4 µl 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/µl final concentration).

Generation III DNA spotter (Amersham Biosciences) was used to array the samples onto coated type-7 glass slides (Amersham Biosciences). This spotter arrays two technical replicas of each sample, one in each longitudinal half of the slides. However, this platform describes only one side of the replicated sides.

After deposition, the spotted DNA samples were crosslinked to the coated slides by applying 50 mJ of UV light and the slides were stored desiccated at ~10% relative humidity at room temperature until use.


title: SAM3.0

status: Public on Apr 01 2006

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

organism: Zea mays

manufacturer: Schnable Laboratory at Iowa State University(ISU)

middle: S

manufacture_protocol: The ISU microarray facility has generated a maize gene chip that contains 16,000 spotted cDNA inserts. After removing empty spots, unspecified spots, etc., 14,401 informative spots will be returned.


title: GSF/IEG mouse array

status: Public on May 01 2006

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

organism: Mus musculus

first: Marion

last: Horsch

first: Johannes

last: Beckers

manufacture_protocol: PCR amplification of cDNA clones, purification of PCR product using 96-well filter plates, 3x SSC as spotting buffer. spotting robot: Microgrid II


title: MWG E. coli K12 V2 Array

city: San Francisco

first: Tara

last: Sigdel

state: CA

address: 513 parnassus

department: Surgery

institute: University of California San Francisco

organism: Escherichia coli

last: Easton

first: Michael

last: Crowder

manufacture_protocol:
MWG E. coli K12 V2 Array
The MWG E. coli Array contains 4,288 gene specific
oligonucleotide probes representing the complete E. coli (K12) genome. Specifications:
Total number of genes: 4,288 ORFs of E. coli strain K12
covered by 4239 oligos
Information sources: NCBI/Genbank
NC00913, U00096.1
Strand analyzed: Sense strand
Number of slides: 1
Length of probes: 50 mer
Number of oligonucleotides per gene:1
Total number of spots: 4,608
Replicated spots: 47
Production control oligos (ara): 48
Spot area: 1.8 x 1.8 cm