title: UHN_yeast_6.4kv4

status: Public on Sep 11 2007

city: Rehovot

first: Ofer

last: Sarig

address: Weizmann Institute of Science

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

organism: Saccharomyces cerevisiae

technology: spotted DNA/cDNA

distribution: commercial

manufacture_protocol:
Refer to the manufacturer website:
www.microarray.ca


title: Farnham human whole genome Hg17Tiling Set07

status: Public on Sep 29 2007

city: Davis

first: Kimberly

middle: Rose

last: Blahnik

state: CA

address: GBSF 1 Shields Ave

department: Genome and Biomedical Sciences

country: USA

institute: University of California Davis

organism: Homo sapiens

technology: in situ oligonucleotide

description: Probes are 50bp long, separated by 100bp.

distribution: custom-commercial

manufacture_protocol: as described on Nimblegen Systems website


title: Farnham human whole genome Hg17Tiling Set36


title: Farnham human whole genome Hg17Tiling Set21


title: Farnham human whole genome Hg17Tiling Set23

manufacture_protocol: as described on Nimblegen website


title: Farnham human whole genome Hg17Tiling Set32


title: Farnham human whole genome Hg17Tiling set 18


title: Farnham human whole genome Hg17Tiling Set17


title: Farnham human whole genome Hg17Tiling Set27


title: Farnham human whole genome Hg17Tiling Set35


title: Farnham human whole genome Hg17Tiling Set28


title: Farnham human whole genome Hg17Tiling Set33


title: CodeLink UniSet Human I Bioarray

status: Public on Aug 23 2006

city: Pittsburgh

first: Mandal.

middle: K.

last: Singh

state: PA

address: 3460 Fifth Ave

department: Transplant

institute: Childrens Hospital of Pittsburgh

technology: spotted oligonucleotide

description: ~10 000 human genes (unique accession numbers)- one specific, prescreened 30-mer probe per gene,


title: Full_Burkholderia_pseudomallei_Genome

status: Public on Oct 01 2006

city: Singapore

first: Fiona

last: Rodrigues

address: 60 Biopolis Street, #02-01 Genome

department: Cell and Medical Biology

country: Singapore

institute: Genome Institute of Singapore

organism: Burkholderia pseudomallei K96243

description:
spotted DNA
This set includes 8836 PCR probes (30 mers) designed in-house using Primer 3

distribution: non-commercial

first: Patrick

last: Tan

manufacture_protocol: as described in DSO/NCC Labs manual


title: Farnham human whole genome Hg17Tiling Set22


title: CampyChip1.2

status: Public on Mar 03 2004

city: Ottawa

first: John

middle: H

last: Nash

state: Ontario

address: 100 Sussex Drive

department: Institute for Biological Sciences

country: Canada

institute: National Research Council

organism: Campylobacter jejuni

description:
A microarray with 5760 spot features corresponding to almost all ORFs in the Campylobacter jejuni 11168 genome (spots in triplicate).
Blocks per chip:24
Columns per block:15
Rows per block:16

first: Eduardo

middle: N

last: Taboada

first: Catherine

middle: D

last: Carrillo

first: Wendy

middle: A

last: Findlay


title: Farnham human whole genome Hg17Tiling Set05


title: Farnham human whole genome Hg17Tiling Set04

manufacture_protocol: as described on Nimblegen Systems website.


title: Farnham human whole genome Hg17Tiling Set37


title: OU/OMRF Zebrafish 14K oligo array

status: Public on Aug 03 2007

city: Norman

first: Han

last: Wang

state: OK

address: 101 David L. Boren Boulevard

department: Zoology/Stephenson Research and Technology Center

institute: University of Oklahoma

organism: Danio rerio

description: gamma amino propyl silane (Corning UltraGAPS slides)

manufacturer: Oklahoma Medical Research Foundation  Microarray Research Facility

first: Qingchun

last: Zhou

first: Jason

middle: W

last: Kesinger

first: Chad

last: Norris

first: Cammi

last: Vladez

manufacture_protocol: Ocimum/MWG 50-mer oligonucleotide library resuspended in 3XSSC; printed on Cornings UltraGAPS slides with GeneMachines OmniGrid 100 arrayer, 32 pin configuration.


title: Farnham human whole genome Hg17Tiling Set16


title: Farnham human whole genome Hg17Tiling Set29


title: Farnham human whole genome Hg17Tiling Set10


title: Farnham human whole genome hg17Tiling Set03


title: Farnham human whole genome Hg17Tiling Set 11


title: Farnham human whole genome Hg17Tiling Set25


title: Farnham human whole genome Hg17Tiling Set31


title: Farnham human whole genome Hg17Tiling Set24


title: Farnham human whole genome Hg17Tiling Set15


title: Farnham human whole genome Hg17Tiling Set08


title: Farnham human whole genome Hg17Tiling Set06


title: Farnham human whole genome Hg17Tiling Set38


title: Farnham human whole genome Hg17Tiling Set20


title: Farnham human whole genome Hg17Tiling Set13


title: Farnham human whole genome Hg17Tiling Set30


title: Farnham human whole genome Hg17Tiling Set19


title: Farnham human whole genome Hg17Tiling Set09


title: Farnham human whole genome Hg17Tiling Set14


title: Farnham human whole genome Hg17Tiling Set12


title: Farnham human whole genome Hg17Tiling Set01


title: Farnham human whole genome Hg17Tiling Set02


title: SHDO

status: Public on Sep 26 2007

city: Paris

first: Corneliu

last: Henegar

state: Ile de France

address: 15 Rue de l'Ecole de Medecine

country: France

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

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: Host and Pathogen Microarray

status: Public on Sep 27 2007

city: London

first: Paul

last: Kellam

state: London

address: 46 Cleveland Street

department: Infection

country: United Kingdom

institute: UCL

organism:
Homo sapiens
Human gammaherpesvirus 8

first: Cheryl

last: Li

first: Edward

last: Tsao

first: Ken

last: Choi

manufacture_protocol: The purified DNA probes in spotting buffer were deposited onto aminopropyl silane-coated Nexterion Slide A (Schott, UK) using the Qarray2 arrayer (Genetix, UK) with a 12-pin print head of Genetix aQu 75um split pins (Genetix, UK).  Spotted arrays were air-dried for 12+ hours, followed by heating at 80 °C in dry oven for 3 h to immobilise the DNA.  Unbound surfaces on the arrays were inactivated by immersing in 60 ml blocking solution: 5× SSC, 0.5% (w/v) bovine serum albumin (BSA, Sigma, UK), 0.5% (w/v) non-fat powdered milk (Tesco, UK) at 50 °C for 45 min, followed by washing 2 times in deionised water.  Then the arrays were incubated in deionised water at 95 °C for 2 min to denature the DNA.  Denatured arrays were washed and blocked again (with fresh solution) at 50 °C for 30 min.  Finally the arrays were washed 2 times in deionised water, immersed in isopropanol (Sigma, UK) for 30 seconds and immediately dried by spinning at 200 g, 2 min.  Processed arrays were stored in a dry environment for use within 24 hours.


title: mod

city: Stanford

first: Ling-Chun

last: Chen

address: 318 Campus Drive

department: Molecular Pharmacology

institute: Stanford University

organism: Mus musculus


title: Monsanto Custom Arabidopsis Genome Array

city: Hayward

first: Don

middle: R

last: Maszle

address: 3935 Point Eden Way

institute: Mendel Biotechnology, Inc.

organism: Arabidopsis thaliana

description: The Monsanto Arabidopsis Genome Array is a custom array designed using Affymetrix GeneChip CustomExpress Array Design Guidelines.  Feature size is 18 micron; and there are 9 probe pairs per transcript randomly distributed across the array. The sequences used for probe selections are mostly based on gene models released by TIGR in 2001. Additional gene models from Monsanto EST collections were also used. Probe sets have been mapped to TAIR AGI identifiers whenever possible.  There are 27,385 probe sets on the array, which consists of perfect match and mismatch probe pairs.  Standard Affymetrix controls have been used on the chip along with control made from internal sequences.

manufacture_protocol: see manufacturer's web site


title: SHDL


title: Paro_D.melanogaster_0.9k_v4

status: Public on Sep 25 2007

city: Basel

first: Christian

last: Beisel

address: Mattenstrasse 26

department: Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

organism: Drosophila melanogaster

description: Nexterion E Slides are epoxy coated

first: Andreas

last: Buness

first: Britta

last: Koch

first: Stefan

last: Haas

first: Marc

last: Hild

first: Renato

last: Paro

manufacture_protocol:
Primers were designed using the GenomePRIDE software (Haas et al., 2003) to amplify 545 fragments representing the Drosophila Antennapedia complex, ANT-C, (AE001572) and 339 fragments covering the Drosophila Bithorax complex, BX-C, (U31961(Martin et al., 1995)). The fragments are about 1 kb in size with 20-200 bp overlap between neighbouring fragments. PCRs, and spotting of the fragments were carried out as described (Hild et al., 2003). PCR products were purified with Nucleofast 96 (Macherey-Nagel) and spotted onto Nexterion E slides (Peqlab). Non-Drosophila cDNAs were spotted as spike-in controls. The array contains 8 spotted replicates of each PCR fragment.
Haas, S. A., Hild, M., Wright, A. P., Hain, T., Talibi, D., & Vingron, M. (2003) Nucleic Acids Res 31, 5576-5581.
Martin, C. H., Mayeda, C. A., Davis, C. A., Ericsson, C. L., Knafels, J. D., Mathog, D. R., Celniker, S. E., Lewis, E. B., & Palazzolo, M. J. (1995) Proc Natl Acad Sci U S A 92, 8398-8402.
Hild, M., Beckmann, B., Haas, S. A., Koch, B., Solovyev, V., Busold, C., Fellenberg, K., Boutros, M., Vingron, M., Sauer, F., et al. (2003) Genome Biol 5, R3.


title: SHDR


title: Paro_D.melanogaster_0.9k_v3

description: Nexterion E slides are epoxy coated.

manufacture_protocol:
Primers were designed using the GenomePRIDE software (Haas et al., 2003) to amplify 545 fragments representing the Drosophila Antennapedia complex, ANT-C, (AE001572) and 339 fragments covering the Drosophila Bithorax complex, BX-C, (U31961(Martin et al., 1995)). The fragments are about 1 kb in size with 20-200 bp overlap between neighbouring fragments. PCRs, and spotting of the fragments were carried out as described (Hild et al., 2003). PCR products were purified with Nucleofast 96 (Macherey-Nagel) and spotted onto Nexterion E slides (Peqlab). Non-Drosophila cDNAs were spotted as spike-in controls. The array contains 10 spotted replicates of each experimental PCR fragment.
Haas, S. A., Hild, M., Wright, A. P., Hain, T., Talibi, D., & Vingron, M. (2003) Nucleic Acids Res 31, 5576-5581.
Martin, C. H., Mayeda, C. A., Davis, C. A., Ericsson, C. L., Knafels, J. D., Mathog, D. R., Celniker, S. E., Lewis, E. B., & Palazzolo, M. J. (1995) Proc Natl Acad Sci U S A 92, 8398-8402.
Hild, M., Beckmann, B., Haas, S. A., Koch, B., Solovyev, V., Busold, C., Fellenberg, K., Boutros, M., Vingron, M., Sauer, F., et al. (2003) Genome Biol 5, R3.


title: Farnham human whole genome Hg17Tiling Set34

first: Kimberly

last: Blahnik


title: Ontario Cancer Insititute Single Spot Human 19Kv6

status: Public on Sep 21 2007

city: Brisbane

first: Traute

last: Flatscher-Bader

state: Queensland

address: Queensland Biosciences Precinct, Level 5, CSIRO LI, 306 Carmody Road

department: Faculty of Natural Resources, Agriculture and Veterinary Science

country: Australia

institute: University of Queensland

description:
Ontario Cancer Institute (OCI, Toronto, Canada) human single-spotted 19k (version 6) microarray consisting of 19,008 characterized and unknown human ESTs from Image Consortium each with a unique Genbank ID.
Slide specifications:
Grid Rows: 12
Grid Colums: 4
Rows: 20
Columns:	20
Grid to Grid Distance (um): 4500
Spot to Spot Distance (um): 200

first: Naomi

last: Landis

first: Peter

last: Wilce

manufacture_protocol: The microarrays were printed on UltraGAPS™ slides (Corning Inc.) using high-precision robotics. Printed arrays are processed following Corning's protocol and were ready-to-use.


title: WUSTL Caenorhabditis elegans Whole Genome 23k Oligo Array

city: Boulder

first: liang

last: zhang

state: CO

address: University of Colorado at Boulder, Han lab, Department of MCD Biology, Campus box 0347

institute: university of colorado at boulder

organism: Caenorhabditis elegans

manufacturer: washington university microarray core facility

manufacture_protocol:
General Information
Arrays printed on Corning Epoxy slides
Slides have been post-processed and are ready to hyb.
Common spot diameter – 90-110μ
Spot to spot distance – 200μ
• 22614 features
• 22490 oligo features
• 124 control features
• 12 Rows
• 4 Colums
• 48 Subarrays
Feature Concentration Information
A. thaliana Features printed at 50 uM
Controls (Positive and Negative) printed at 40 uM
Poly(dA)40–60 oligonucleotide printed at 0.01 μg/μL
Salmon sperm DNA printed at 0.1 μg/μL
Human COT-1 DNA® printed at 0.1 μg/μL
Control Feature Information
Control Oligonucleotides
Number Arabidopsis thaliana Gene Identification
Positive Controls (70-mer)
10 Oligonucleotide 1 (Cab) A. thaliana photosystem I chlorophyll a/b-binding
protein
(GenBank® database accession # X56062)
10 Oligonucleotide 2 (RCA) A. thaliana RUBISCO activase
(GenBank database accession #X14212)
10 Oligonucleotide 3 (rbcL) A. thaliana ribulose-1,5-bisphosphate
carboxylase/oxygenase large subunit
(GenBank database accession#U91966)
10 Oligonucleotide 4 (LTP4) A. thaliana lipid transfer protein 4
(GenBank database accession #AF159801)
10 Oligonucleotide 5 (LTP6) A. thaliana lipid transfer protein 6
(GenBank database accession #AF159803)
10 Oligonucleotide 6 (XCP2) A. thaliana papain-type cysteine endopeptidase
(GenBank database accession #AF191028)
10 Oligonucleotide 7 (RCP1) A. thaliana root cap 1
(GenBank database accession #AF168390)
10 Oligonucleotide 8 (NAC1) A. thaliana NAC1
(GenBank database accession #AF198054)
10 Oligonucleotide 9 (TIM) A. thaliana triosphosphate isomerase
(GenBank database accession #AF247559)
10 Oligonucleotide 10 (PRKase) A. thaliana PRKase gene for ribulose-5-phosphate
kinase
(GenBank database accession #X58149)
Negative Controls
10 E. coli – B1444 oligonucleotide
8 E. coli – rRNA oligonucleotide
2 Poly(dA)40–60 oligonucleotide
2 Salmon sperm DNA
1 Human COT-1 DNA®
1 3X SSC/0.75 M Betaine
124 – Total Control Features


title: Farnham human whole genome Hg17Tiling Set26


title: SHFB

first: Corneliu

last: Henegar


title: Ehrlichia chaffeensis strain Arkansas 147K genome tiling array

status: Public on Sep 20 2007

city: Columbus

first: Koshiro

last: Miura

state: OH

address: 1900 Coffey Rd

department: Veterinary Biosciences

institute: The Ohio State University

organism: Ehrlichia chaffeensis

first: Yasuko

last: Rikihisa

manufacture_protocol: DNA microarray was constructed by selecting 29-mer oligonucleotides every 8 bases in the genome sequence of E. chaffeensis Arkansas (GenBank accession no. CP000236) using light-directed oligonucleotide synthesis technology.


title: University Health Network Human 19K array version 8 (19Kv8)

status: Public on Sep 23 2007

description: The University Health Network Gene layout is linked as a Supplementary file at the foot of this record.

manufacture_protocol:
The manufacture protocols for this platform are available from the University Health Network Microarray Centre website at: http://www.microarrays.ca/support/proto.html
Microarray Centre
University Health Network
Toronto Medical Discovery Tower
101 College Street, Rm 9-301
Toronto, Ontario, M5G 1L7


title: SAGE:11:NlaIII:Mus musculus

status: Public on Sep 18 2007

last: GEO

technology: SAGE NlaIII

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

distribution: virtual


title: Verrando Homo sapiens 9K cDNA array

status: Public on Sep 15 2007

city: Zürich

first: Keith

middle: S

last: Hoek

address: private

institute: Currently unaffilliated

description: normalized cDNA library was used to minimize redundancy. All clones on the microarray were sequence-verified and carefully mapped to NCBI's GenBank/UniGene database on 3 April 2000. An update was performed at the end of this work on 12 March 2001 and the list of clones (name, GenBank's accession numbers) was modified accordingly. After amplification, more than 9000 human cDNA clones were deposited on the solid support through optimized key processes. Thirty percent of them were EST as defined by the GenBank release on 12 March 2001. cDNA sizes ranged from 500 to 5000 bp, with an average of 1 kb.

first: Patrick

last: Verrando

first: Christine

last: Valery

first: Jean-Jacques

last: Grob

manufacture_protocol: cDNA clones deposited on solid support.


title: Affymetrix Human Exon 1.0 ST Array (v2 mapping)

status: Public on Sep 24 2007

city: PROVIDENCE

first: Alexander

last: Brodsky

state: RI

address: 593 Eddy St.

department: MCB

institute: Rhode Island Hospital/Brown University

description:
This file maps HuExon 1.0 st exon probesets to RefSeq transcripts where the exon probesets are fully contained within the RefSeq transcripts.

This file contains RefSeqs at the time of the exon chip design. For more up to date RefSeq associations use the NetAffx CSV annotation files.
create_date=Thu Aug 11 22:41:16 PDT 2005
lib-set-name=HuEx-1_0-st
lib-set-version=v2
genome-species=Homo sapiens
genome-version=hg16
genome-version-ncbi=34
genome-version-create_date=2003 July

Exon-level probeset annotations provided in supplementary CSV file linked at foot of this record.

manufacture_protocol: Standard Affymetrix manufacturing procedures.


title: SHCV


title: Quantitative proteomics of anaerobic and aerobic yeast cultures

city: Delft

first: Marco

middle: J.L de

last: Groot

state: Zuid Holland

address: Mekelweg 4

department: Mediamatics

country: Netherlands

institute: Delft University of Technology

technology: MS

description: Proteins identified in quantitative analysis of anaerobic and aerobic yeast cultures

middle: J

last: de Groot

first: Pascale

last: Daran-Lapujade

first: Bas

last: van Breukelen

first: Theo

last: Knijnenburg

first: Erik

last: de Hulster

first: Marcel

last: Reinders

first: Jack

middle: T

last: Pronk

first: Albert

last: Heck

first: Monique

last: Slijper


title: SHGI

first: Corneliu

last: Henegar


title: mouse 22.4k cDNA array

city: Toronto

first: Solmaz

last: Alizadeh-Azami

state: ON

address: 1 King's college circle

department: Pharmacology

institute: University of Toronto

manufacture_protocol:
Single-spotted array containing both the 15K and 7.4K clone sets of mouse ESTs from the National Institute of Aging (NIA).
Detailed information on the construction of the library and sequences can be found at the NIA/NIH Mouse Genomics website.


title: LC-42

city: Palo Alto

last: Dieterich

address: 3801 Miranda Avenue

department: Department of Microbiology & Immunology

institute: VA hospital


title: Set 30 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3

status: Public on Sep 14 2007

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

description: 38 chip array set covering the non-repetitive portion of the human genome (14.5 million features). Resolution 100bp (50bp probe and 50bp gap).

first: Guangjin

last: Pan

first: Shulan

last: Tian

first: Jeff

last: Nie

first: Chuhu

last: Yang

first: Hairong

last: Wei

first: Gudrun

last: Jonsdottir

first: Ron

last: Stewart

first: James

last: Thomson

manufacture_protocol: Maskless array synthesis of tiling arrays. See Nimblegen.com for more information.


title: Set 29 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: CGH-CHORI-32K-Chr. 12 X Y

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: The array contains 4012 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. In total the array design contains 16092 features printed in a layout of 4 meta rows, 4 meta columns, 23 rows per block and 22 columns per block.This grid is printed twice on the glass slides allowing for two microarray arrays per slide.

first: Guy

last: Froyen

first: Paul

last: Van Hummelen

first: Joris

last: Vermeesch

manufacture_protocol:
MicroGrid Printing ProtocolEquipment:
1. Microgrid (Genomics Solutions, UK).
2. 384 microtiter plates (X7022, Genetix)
3. 4x4 MicroSpot quill pins - 10K (cat# BR001489, Genomics Solutions, UK)
4. Codelink slides (cat#: 30001100, GE Healthcare).
Printing 2 arrays of 4x4 blocks on 1 microscope slide:
1. Dissolve PCR products in 125mM Na-Phosphate  (pH 8.45) buffer, 0.000125% sarcosyl at concentrations of 300 ng/ul.

2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 185 um, row pitch = 185 um; Humidity 55%; 60 spots per source visit.
3. Make sure room temperature is between 20-24 degrees Celsius.
4. Place microtiter plates in the plate hotel with A1 in front left corner.
5. Place 30 slides on the slide-deck.
6. Start spotting early in the morning and stop spotting procedure at end of the day and remove pin set. Leave spotter overnight with vacuum and humidity settings on.
7. Incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH.
9. Slides can be stored for at least 6 months in a dry-cabinet.


title: Set 28 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: 10K CombiRat Array

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

institute: The Westmead Institute for Medical Research

organism: Rattus norvegicus

description: Combined MWG and Compugen 10K glass slide spotted rat oligonucleotide-arrays were used. Each microarray slide consisted of 21,888 spots, including 10,752 probes and 192 control spots, printed in duplicate. The combined 5K Compugen and 5K MWG rat oligonucleotide probe sets dated back to 2002. The 5K Compugen (SigmaGenosys) consists of 65-mer oligos compared to 5K MWG has 50-mer oligo set.

manufacturer: The Clive and Vera Ramaciotti Centre for Gene Function Analysis (CVRC), University of New South Wales, Australia

manufacture_protocol: All slides printed at the Ramaciotti Centre were generated on ESI ChipWriter (Bio-Rad). To avoid carryover, pins were treated for 1 cycle with a 5 min ddH2O sonication, 5 s 100% isopropanol wash and dry for 1 min with compressed air between print loads. Printing solution was MWG Spotting Buffer (MWG-Biotech, Ebersberg, Germany). Oligonucleotides were from 5' amine modified 65-mer for Rattus norvegicus (5K Compugen Rat OligoLibraryTM, SigmaGenosys) and similarly 5' amine modified 50-mer for Rattus norvegicus (MWG 5K, SigmaGenosys). The slide type for this batch of printing was Schott Nexterion A (Inbio, Bioinsight Pty Ltd). In addition, LucideaTM Universal ScoreCardTM controls (GE Healthcare Life Sciences) were printed on the array. Both libraries and controls were printed in duplicates. Printing was performed in 65 % (SD ± 2%) humidity at 21 °C. The array printer used a print head with a 12 x 4 arrangement of print-tips and each microarray slide was partitioned into a 12 x 4 grid of tip groups. Each grid consists of 22 x 24 spots that were printed with a single print-tip.


title: WASHU_C.elegans_22.5K_V1

city: St. Louis

first: Elaine

last: Mardis

state: MO

address: 4444 Forest Park Pkwy

department: Genome Sequencing Center

institute: Washington University

manufacturer: Washington University Genome Sequencing Center

manufacture_protocol:
Long oligo probe design:
An oligo selection algorithm program called TOP was modeled after PICK70 (http://se.osxgnu.org/pub/mirrors/sourceforge/arrayoligosel/). The algorithm utilizes FASTA input files in oligo selection. The oligo selection routine was designed to follow these steps: mask out any repetitive sequence elements or any highly similar portions of the input gene sequences using BLAST comparison, ensures all bases conform to A,C,G or T, checks that the defined oligo length conforms to a user defined Tm and G/C content, requires that the oligo conform to a user cutoff for homopolymer bases, assign secondary structure scores to oligos, and finally export oligos to a directory as text files (see supplementary material). The cumulative oligo scores assigned indicates the relative deviation of the oligo from the desired parameter. For genes that do not result in an oligo being selected we manually examine the input sequences and then if desired relax certain algorithmic parameters in order to select an oligo (see supplementary material for program details).
Microarray slide production:
Caenorhabditis elegans probes (oligos) were purchased from Illumina (http://www.illumina.com).  Oligonucleotides were solubilized at 50um in 3X SSC and 0.75 M betaine for printing.  The oligonucleotides were spotted onto epoxy coated glass slides (Corning) using a linear servo arrayer (P. Brown; Stanford University). The printed slides were placed in a 42C oven at 40% humidity for 12-14 hours.  After incubation, the slides were cross-linked using the UV Stratalinker 2400 (Stratagene) at 150 ujoules/cm2.  The slides were processed by submersing and shaking in a 0.2% SDS solution for 2 minutes, followed by three separate room temperature water baths, all at one minute per bath.  The final step was to place the slides in a 50 water bath for 20 minutes and then spin the slides dry.  The processed slides were placed in a light proof slide box and stored in a dessicant cabinet for future hybridization experiments.


title: Set 25 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 26 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 24 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 23 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 22 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 21 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 18 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 27 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 17 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 19 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 10 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 20 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 11 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 14 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 12 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 2 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 15 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 16 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 1 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3

description: 38 chip array set covering the non-repetitive portion of the human genome (14.5 million features).  Resolution 100bp (50bp probe and 50bp gap).

manufacture_protocol: Maskless array synthesis of tiling arrays.  See Nimblegen.com for more information.


title: Set 4 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 3 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 34 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 35 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 36 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 33 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 6 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 38 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 13 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 37 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 5 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


title: Set 32 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3


status: Public on Sep 13 2007

city: Cologne

first: Bernhard

last: Gerstmayer

address: Stockheimer Weg 1

country: Germany

institute: Miltenyi Biotec GmbH

description: The PIQOR Immunology Microarray Mouse Antisense comprises 1076 genes (including six housekeeping genes and six controls).

first: B.

first: K.

last: Hofmann

first: A.

last: Bosio

manufacture_protocol: Defined 200-400 bp fragments of selected cDNAs were generated by RT-PCR, cloned and sequence-verified. Amplified and purified cDNA inserts were spotted in quadruplicate on PIQOR slides using a proprietary piezoelectric spotter. The PIQOR slides were coated in a 2 step process generating a surface which covalently binds DNA molecules.


title: Set 31 of 38 - Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3

first: Victor

last: Ruotti

first: Guangjin

last: Pan

first: Shulan


title: Galbraith Laboratory Operon Long Oligonucleotide Microarray version 3.0 (ATq306.03.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

description: This oligonucleotide array is produced from the Operon Version 3.0 Array-Ready Oligo set (AROS), which comprises 29,110 70-mer oligonucleotides representing 26,173 protein-coding genes, and 28,964 protein-encoding gene transcripts, and 87 microRNA gene precursors. AROS design is based on ATH1 release 5.0 of the TIGR Arabidopsis genome annotation database, and Release 4.0 of the miRNA Registry at the Sanger Institute. Various additional elements are printed as controls. Microarrays can be ordered from the Galbraith laboratory. This platform represents slides ATq3.06.03.001-ATq3.06.03.400 (http://www.ag.arizona.edu/microarray).

manufacturer: The Galbraith Laboratory, University of Arizona


title: Arabidopsis mRNA MPSS signatures

city: Manchester

first: Junfeng

last: Chen

address: Kilburn Building, Oxford Road

department: School of Computer Science

institute: University of Manchester

technology: MPSS

description:
mRNA MPSS signatures capture the 17 bases from near the 3' end of poly(A)+ transcripts.
All MPSS was performed as described by Brenner et al. (Nat Biotechnol. 2000 18:630).

first: Blake

middle: C

last: Meyers

manufacture_protocol: MPSS


title: Illumina Human-6 v2 expression beadchip

status: Public on Sep 12 2007

city: Leiden

first: Ellen

last: Sterrenburg

address: Wassenaarseweg 72

department: Center for Human and Clinical Genetics

institute: Leiden University Medical Center

technology: oligonucleotide beads

manufacture_protocol:
Illumina's Human-6 v2 BeadChips enable genome-wide expression analysis of multiple samples in parallel on a single microarray. The Human-6 v2 Expression BeadChips offer experimental scale for RNA profiling with six or eight samples profiled per BeadChip.
The Human-6 v2 2 Expression BeadChips open doors to high-confidence target discovery, disease classification, and pathway studies. Researchers can profile six or eight samples per BeadChip, more than 48,000 transcript probes per sample using the Human-6. Low per-sample pricing means you can do more for less and generate statistically better results.


title: Salmonella-specific oligonucleotide microarray

city: Bratislava 45

first: Tomas

last: Majtan

address: Dubravska cesta 21

department: Department of Molecular Genomics

country: Slovakia

institute: Institute of Molecular Biology SAS

organism: Salmonella

description:
Salmonella spp. sequences spotted on the array.  Corynebacterium phage BFK20 sequences included as controls.

The data table reflects the condensed representation of the Platform.  The complete array layout file representing the quadruplicate-spotted features is linked as a supplementary file.

manufacture_protocol: Dried HPLC-purified oligonucleotides were resuspended in 1x Micro Spotting Solution Plus (ArrayIt) and spotted in duplicates on the SuperEpoxy slides (ArrayIt). Submitted dataset represent one grid composed of two identical subgrid spotted above each other and two grids are present on the each slide. Each probe is spotted in quadruplicate for one slide. Spotted slides were dried overnight and stored in the dark at the cold place untill use.


title: Illumina_mouse_Sentrix-6 BeadChip_v1

manufacture_protocol:
Illumina has developed two multi-sample BeadChips that enable genome-wide expression analysis of mouse. Mouse-6 Expression BeadChips offer a new level of experimental scale for RNA profiling.
The Mouse-6 opens doors to high-confidence studies using this important model organism. Researchers can profile six samples per Mouse-6 BeadChip and more than 47,000 transcripts per sample (see our Gene List ).  Low per-sample pricing means you can do more for less and generate statistically better results.
www.illumina.com


title: Streptococcus pyogenes M1, M3, M18 GAS 2.3k array (condensed version)

status: Public on Sep 11 2007

city: Atlanta

first: Samantha

middle: Ann

last: Roberts

state: GA

address: 1510 Clifton Road

department: Microbiology

institute: Emory University

organism: Streptococcus pyogenes

description:
oligonucleotide array containing unique ORFs from M1, M3 and M18 Streptococcus pyogenes.

The Platform data table reflects a condensed representation of the oligo probes which were printed in triplicate. The full array layout (GPL5822_full_layout.txt) is linked as a supplementary file at the foot of this record.

manufacturer: Oligonucleotide probes were designed and synthesized by Qiagen Operon (Valencia, CA) and were printed at Microarrays Inc (Nashville, TX; http://microarrays.com).

manufacture_protocol:
Probes were designed utilizing a proprietary algorithm to target unique non-repetitive ORFs (TIGR annotation as of 2 December, 2002) found in the sequenced genomes of serotypes M1 (SF370), M3 (MGAS315) and M18 (MGAS8232) and resulted in 2328 oligonucleotide probes (1932-M1, 165-M3, 231-M18). As the TIGR ORFs have been updated, all probes are referenced using their original Spy designation whenever possible (University of Oklahoma Sequencing Project). Oligonucleotide 70-mer probes were synthesized on a 0.2 μM scale and passed through several stringent parameters before synthesis, including a melting temperature of 76 ± 5°C, ≤ 70% cross hybridization identity to another gene within the same strain, ≤ 20 contiguous bases in common with another gene, probe location within 3' end of ORF (within 40 bp if possible), and hairpin/stem loop structures ≤ 8.
Lyophilized oligonucleotides in 384 well plates were resuspended in sodium phosphate at a final concentration of 40 μM. Approximately 10 picolitres of each oligonucleotide probe was spotted onto slides (UltraGAPS2; Corning) using a 12 pin contact printer. Printed slides were held over steaming water for 5 s followed by drying on a heat block (70°C) for 5 s. Slides were then cross-linked using a Stratalinker (Stratagene) at 65 mJ. To reduce background, slides were post-processed in a blocking solution (0.16 M Succinic Anhydride in 1-methyl-2-pyrrolidinone followed by the addition of 0.2 M Boric Acid pH 8.0 to 0.02 M) with shaking for 15–20 min. Slides were subsequently rinsed in 95°C water for 2 min followed by a 95% ethanol wash and dried using a table top centrifuge with a microtiter plate carrier. Post-processed slides were stored in a slide storage box protected from light at ambient temperature.


title: TJU-DBI Rat array v2.0

city: Philadelphia

first: Egle

last: Juskeviciute

address: 1020 Locust st. JAH 527

department: Pathology

institute: Thomas Jefferson University

manufacture_protocol:
ResGen clones for Rat
Tip Configuration: Standard 48 tip
Columns per Subarray: 20
Rows per Subarray: 19
Column Spacing: 225
Row Spacing: 225


title: Sentrix BeadChip Array HumanHap300 Genotyping BeadChip 317K, TagSNP Phase I, v1.1

city: Brisbane

first: Mitchell

last: Stark

address: 300 Herston Rd Herston

institute: QIMR

first: Nicholas

middle: K

last: Hayward

manufacture_protocol: see manufacturer's website


title: Compugen Danio rerio 16k spotted oligo array

city: Eggenstein Leopoldshafen

first: Ferenc

last: Muller

address: Hermann-von-Helmholtz Platz 1

department: Institut for toxicologie and genetics

institute: Forschungszentrum Karlsruhe

manufacturer: Institut for Toxicology and Genetics Forschungszentrum Karlsruhe

first: Lixin

last: Yang

manufacture_protocol: tealth 3 Micro Spotting Pins called SMP3 (100 um features with 0.25 ul standard uptake) holding up to 48 Micro Spotting Pins on code link slides. See the Microarray Stealth Spotting Pins and Printheads web page at the TeleChem International, Inc. website.


title: Nimblegen Custom HOX array

status: Public on Sep 07 2007

city: Stanford

first: John

middle: Louis

last: Rinn

state: CA

address: 2155 CCSR

department: Dermatology

institute: Stanford University

description: Spotted 50 mer oligos 400,000 features


title: NCSU_Glycine max_5.7K

city: Tallahassee

first: Andre

middle: Southernman Teixeira

last: Irsigler

state: FL

address: Chieftan Way

department: Biology

institute: Florida State University

organism: Glycine max

manufacture_protocol: The cloned cDNA fragments from soybean libraries were amplified with M13 primers, purified using PCR Cleanup Filter Plates (Millipore, Bedford, MA), and eluted in water (according to the manufacturer’s protocol). An aliquot of each amplified fragment reaction was separated through a 1% (w/v) agarose gel and visualized with ethidium bromide to assess size, quality and quantity. The purified PCR products were transferred to 384-well plates, and diluted with an equal volume of DMSO (Sigma). Finally, the PCR products were arrayed onto UltraGAPS slides (Corning, Corning, NY) using a 417TM Arrayer (Affymetrix, Santa Clara, CA), cross-linked by exposure to UV light at 250 mJ and baked at 75°C for 2 h


title: MIT-Chisholm Lab Prochlorococcus and cyanophage microarray - MD4-9313 (MD4-9313a520062)

city: Haifa

first: Debbie

last: Lindell

address: Technion City

department: Department of Biology

institute: Technion - Israel Institute of Technology

organism:
Prochlorococcus marinus subsp. pastoris str. CCMP1986
Prochlorococcus marinus str. MIT 9313
Prochlorococcus phage P-SSM4
Tiamatvirus PSSP7

description: Array format - Midi; Synthesis area - 8.1 mm; Feature size - 18 micron

manufacturer: Custom-made high density antisense Affymetrix array

manufacture_protocol: The MD4-9313 array (MD4-9313a520062) is a custom-made high density antisense Affymetrix array. This array detects labeled cDNA that is antisense to the original RNA. It contains probes for the genomes of two cyanobacterial strains, Prochlorococcus MED4 and Prochlorococcus MIT9313, as well as two dsDNA phages that infect Prochlorococcus MED4 – the podovirus P-SSP7 and the myovirus P-SSM4. For the Prochlorococcus genomes, the array contains probe sets to detect all predicted open reading frames with probe pairs approximately every 80 bases. For short open reading frames (ORF), the length of the gap was reduced to ensure a minimum of 11 probe pairs per ORF where possible. Probes were designed for intergenic regions longer than 35 bases and were spaced every ca 45 bases on both strands. For short intergenic regions the gap between probe pairs was reduced to ensure a minimum of 4 probe pairs where possible. For some short sequences, where insufficient high performance probes were designed using this approach, the best probes possible were designed with no regard for their spacing along the genome feature. For the phage isolates, probe pairs were designed across the genomes for both strands at an approximate interval of 90 bases. Probes are 25 bases long and each probe pair consists of a perfect match probe (identical to the sequence) and a mismatch probe (containing a single base change at the center of the probe).


title: Penn Homo sapiens 0.3K

status: Public on Sep 08 2007

first: zhe

last: zhang

state: PA

address: 401 Johnson Pavilion, 36th and Hamilton Walk

institute: University of Pennsylvania

first: Zhe

last: Zhang

first: William

last: Reenstra

first: Daniel

last: Weiner

first: Jean-Pierre

last: Louboutin

first: James

middle: M

last: Wilson

manufacture_protocol: A small scale cDNA microarray was carried out using NF-κB target gene array kit (Panomics, Inc., Redwood City, CA).  A long sense-strand oligonucleotide for each of the 111 human genes that have been previously shown to be regulated by NF-B signaling pathway was spotted in duplicate on the nitrocellulose membrane. Biotinylated DNA was spotted along the right and bottom sides of the array membrane as control of the array. The arrays were performed according to the manufacturer’s instructions. In brief, HAECs were stimulated for 18 hours with the heat-killed bacteria PAO1 or PAK (multiplicity of infection: 100:1). Cells incubated with medium were used as control. mRNA of HAECs was isolated using biotin-labeled oligo(dT)20 and streptavidin-conjugated magnetic particles (Roche, Germany). 500 ng mRNA of each sample was used to prepare biotin-labeled cDNA probes through incorporation of biotin-dUTP into cDNA via reverse transcription reactions. Each biotin-labeled cDNA probe was hybridized to an array membrane at 42°C overnight in a hybridization incubator (Fisher Scientific, Pittsburgh, PA). The membrane was washed after hybridization and subject to incubations with blocking buffer and subsequent streptavidin-conjugated horseradish peroxidase (HRP). The detection was carried out through chemiluminescence reactions and 1 min exposure to Hyperfilm ECL X-ray films (Amersham, Piscataway, NJ). The dots on the array were quantified through densitometric analysis using GeneTools (Syngene, Frederick, MD) and the value of each dot is determined in the equation D = (raw value – background value)/mean value of biotinylated DNA dots. Ratio (Dbacteria: Dcontrol) was used to determine the effect of bacteria stimulation on the gene regulation.


title: Miltenyi Biotec miRNA microarray (716)

status: Public on Jun 17 2007

city: COLOGNE

first: Frank

last: Huebel

state: NRW

address: Stoeckheimer Weg 1

department: MACS Molecular 9

institute: Miltenyi Biotec GmbH, MACS Molecular Business Unit

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: Each microarray contained a total of 3540 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 771 miRNA sequences and 114 controls with all probes spotted in quadruplicates. The 771 miRNAs sequences covered sequence verified miRNAs of the species human (494) mouse (383) and rat (352) as well as viral miRNAs (64) as described in the present study (http://www.mirz.unibas.ch/smiRNAdb). The 114 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (45 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 38 internal positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 26 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

manufacture_protocol: Microarrays were manufactured by Miltenyi Biotec. Briefly, 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted four times on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides using a customized piezoelectric spotter.


title: SuperArray Oligo GEArray Mouse Inflammatory Cytokines and Receptors Microarray

status: Public on Sep 06 2007

city: Frederick

first: SuperArray

last: Bioscience Corporation

state: MD

address: Suite 101, 7320 Executive Way

institute: Technical Support

description: The Oligo GEArray® Mouse Inflammatory Cytokines and Receptors Microarray profiles the expression of 113 key genes involved in the inflammatory response. This array contains genes involved in mediating immune cascade reactions during inflammation. The chemokines, interleukins, and TNF ligands involved in the inflammatory response are represented as well as their receptors.

manufacture_protocol: see manufacturer's web site at www.superarray.com


title: Human 40K A

city: Bologna

first: rossella

last: solmi

address: Via Belmeloro 8

country: Italy

institute: University of Bologna

manufacture_protocol: see manifacturer website www.ocimumbio.com


title: H19Kv4ab

city: Baltimore

first: Pinaki

last: Panigrahi

address: 22 South Greene Street, Room N5W68

department: Pediatrics

institute: University of Maryland

description: One glass microarray has: 8 Metagrid rowws, 4 Metagrid collumns, 25 rows and 24 collumns.  Each gene/EST is printed in duplicate.  The 19,008 charactherized and unknown human ESTs are placed on two glass arrays (a and b).

manufacture_protocol: Microarrays are printed on UltraGAPS (TM) slides (Corning Inc.) using high precision robotics.  Printed arrays are processed following Corning's protocol and are ready-to-use.  Single-spotted array containing 19,008 charactherized and unknown human ESTs.  The clone set has ben sequence-verified at the Microarray Centre after printing, the slide are subjected to processing and performance testing based on true labelling, hybridization and scanning procedures.


title: ISU-Maize-Oligo1.1

status: Public on Jun 04 2007

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

organism: Zea mays

manufacturer: Schnable Laboratory at Iowa State University(ISU)

manufacture_protocol: 70-mer oligonucleotides were synthesized by Integrated DNA Technologies (Coralville, IA), resuspended at 50 uM in 3X SSC and spotted on Corning (Lowell, MA, USA) UltraGaps slides. Together, the sense and corresponding antisense oligos are termed S/A pairs and were spotted in adjacent positions on the oligoarray. Each S/A pair was spotted in duplicate on the array, flipping the physical location of each member of the S/A pair. In total, 7,419 unique S/A pairs were printed in duplicate on the microarray representing 4,765 non-redundant pairs of both strand-specific transcripts since some genes have more than one oligo pairs.


title: SWEGENE human strand-specific cDNA array (cSense)

status: Public on Sep 01 2007

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

organism: Homo sapiens

description: Arrays contain strand specific cDNA probes. Probes are deposited as dsDNA and linked to the surface by NH2-modified ends. The deposited dsDNA is subsequently digested in situ in a strand-specific manner.

manufacture_protocol:
Probe templates were amplified three times using different combinations of 5’-amino modified M13 universal sequencing primers. One reaction set used 5’-amino C-6 link modified M13 forward paired with non-modified reverse primer. A second reaction used 5’-amino C-6 link modified M13 reverse primer paired with unmodified forward primer. A third reaction used 5’-amino C-6 link modified primers in both orientations.
After amplification, all PCR products were precipitated with ethanol and resuspended in phosphate buffer at approximately 100ng/µl for further deposition on arrays.
Amino-modified PCR products were spotted onto CodeLink activated slides (Amersham) using a MicroGrid II array robot (BioRobotics).
After printing, slides were coupled in a saturated NaCl chamber overnight at room temperature, blocked in 50mM ethanolamine, 0,1 MTris (pH 9) at 50degC 30 min followed by washes in distilled water and 4xSSC/0.1% SDS at 50degC.
The deposited dsDNA was subsequently digested in situ in a strand-specific manner with T7 exonucelase 6. Slides were overlaid with 45ul exonuclease reaction mixture (1U/µl T7 exonuclease 6 in 1x reaction buffer, New England Biolabs), covered with a coverslip and left to incubate for 30 minutes at 25degC in a CMT Corning hybridization chamber. Following in situ digestion, probes were denatured by immersing the arrays in boiling water for two minutes.


title: CGEP TOM1 Tomato 13.4k cDNA microarray

status: Public on Sep 05 2007

city: Nashville

first: Suping

last: Zhou

state: TN

address: 3500 John A Merritt Blvd

department: IAGER

institute: Tennessee State University

organism: Solanum lycopersicum

manufacturer: Center for Gene Expression Profiling (CGEP), Boyce Thompson Institute for Plant Research

manufacture_protocol: The array contains approximately 12,000 unique elements. In an effort to make these arrays useful for a wide range of gene expression research these unigenes have been selected at random from a number different cDNA libraries made from a range of tissue including leaf, root, fruit, and flowers. As well as the random unigenes the arrays will contain both positive and negative control spots. The gene fragments are printed in 32 sub-grids, in a 21 by 20 spot arrangement per sub-grid. Complete meta-grid size is 13,440 spots per array.


title: Galbraith Lab Arabidopsis 29K v3.0

city: Blacksburg

first: Andy

last: Pereira

state: VA

address: Washington Street MC0477

department: Virginia Bioinformatics Institute

institute: Virginia Tech

first: R

last: Elumalai

first: F

last: Gong

last: Formosa

first: M

last: Gchachu

first: H

last: Ozkan

first: T

last: Watson

first: L

last: Cheam

manufacture_protocol:
The long oligonucleotide 70-mer Operon array spotted in David Galbraith's Laboratory, comprising 29,000 genes of Arabidopsis were used.
The Arabidopsis thaliana AROS V3.0 contains 29,110 longmer probes and represents 26,173 protein-coding genes, 28,964 protein-coding gene transcripts, and 87 microRNA genes from Arabidopsis thaliana.
Pseudogenes are excluded from this oligo design which is based on the ATH1 release 5.0 of the TIGR Arabidopsis genome annotation database and release 4.0 of the miRNA Registry at the Sanger Institute and allows detection of alternative splicing variants using common, partial common, or individual transcript oligos.
All probes are Tm normalized to 78ºC (±5ºC) and have a 5' amino linker.
The oligonucelotide probes were spotted onto slides at the Galbraith lab following the protocol described.
15 mL of 3XSSC were added to each well of the 300 pM oligonucleotide set to make a 20 microM oligonucleotide solution.
These were transferred onto an orbital shaker for 1 h at RT at 100 rpm and used for printing.
The Arabidopsis oligonucleotide microarrays are printed on aminosilane-coated "Superamine" slides (Telechem) or "Powermatrix" slides (Full Moon Biosystems), using Telechem Type SMP3 printing pins.
The printing conditions used are: Single array element printed per oligonucleotide, 48 pins in the print head, 31% relative humidity, redipping after every 50 slides.
The print head Z- velocity is set to a maximum of 10 mm/sec.
The slides are then baked for 2h at 80oC, and stored dry and in darkness at RT prior to use.


title: CampyChip3

status: Public on Jul 29 2005

city: Ottawa

first: John

middle: H

last: Nash

state: Ontario

address: 100 Sussex Drive

department: Institute for Biological Sciences

institute: National Research Council

organism: Campylobacter jejuni

description:
Campylobacter jejuni microarray with 4608 spot features corresponding to 1600 of the 1634 ORFs of strain NCTC 11168, 181 ORFs from strain RM1221, 48 ORFs from the pVir plasmid of strain 81-176, and 32 ORFs from other strains. All genes are spotted in duplicate and sheared total genomic DNA from strain NCTC 11168 was used as a control.
Blocks per chip:24
Columns per block:12
Rows per block:16

first: Eduardo

middle: N

last: Taboada

first: Catherine

middle: D

last: Carrillo

first: Wendy

last: Findlay

manufacture_protocol: PCR amplicons spotted onto microarray slides.


title: JCVI PFGRC Haemophilus influenzae 32K vt1 array designed primarily based on strain HK12 [FULL_FEATURE_LAYOUT]

status: Public on May 25 2007

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Haemophilus influenzae

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

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


title: AtMap1.0

city: Kitashirakawa, Sakyoku

first: Ikuko

last: Hara-Nishimura

state: Kyoto

address: Oiwakecho

department: Depertment of Botany

country: Japan

institute: Kyoto University

description:
The AtMap1 array was designed on 4 x 44k format custom oligonucleotide microarray with the eArray system ver. 4.5 (Agilent Technologies, Palo Alto, CA). Data probes were selected from high-density tiling probes designed by Agilent. A control grid (IS-45220-4-V1_4x44K_LA_At_V20060828) for tiling array was used as control probes.
The ID column represents the Agilent Feature Extraction feature number.
Supplementary file is ExternalFullGEML2 file.

first: Atsushi

last: Nagano

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


title: KLMBR Bacteriophage 40k V1.0

status: Public on Aug 26 2006

city: xiamen

first: xiaobo

last: zhang

address: No. 178 Daxue Rd.,

country: China

institute: Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration,China

organism: Geobacillus virus E2

manufacture_protocol: Dang T.L., Motoshige Y., Ikuo H., Takashi A. (2005) Transcription Program of Red Sea Bream Iridovirus as Revealed by DNA Microarrays. J. Virol. 79: 15151-15164