title: [Ye6100SubD] Affymetrix Yeast Genome 6K SubD Array

status: Public on May 14 2002

city: Santa Clara

last: Affymetrix

state: CA

country: USA

institute: Affymetrix, Inc.

organism: Saccharomyces cerevisiae

technology: in situ oligonucleotide

description:
Affymetrix GeneChip Yeast Genome 6K SubD Array Ye6100subD.
Based upon the September 1996 release of the Saccharomyces Genome Database (SGD) and contains probes for the approximately 6100 ORFs identified at that time.

Annotations derived from Affymetrix 'Ye6100subD Probe Set Description' file (31 KB, 3/28/03)

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: [Ye6100SubC] Affymetrix Yeast Genome 6K SubC Array

description:
Affymetrix GeneChip Yeast Genome 6K SubC Array Ye6100subC.
Based upon the September 1996 release of the Saccharomyces Genome Database (SGD) and contains probes for the approximately 6100 ORFs identified at that time.

Annotations derived from Affymetrix 'Ye6100subC Probe Set Description' file (30 KB, 3/28/03)


title: [Ye6100SubB] Affymetrix Yeast Genome 6K SubB Array

description:
Affymetrix GeneChip Yeast Genome 6K SubB Array Ye6100subB.
Based upon the September 1996 release of the Saccharomyces Genome Database (SGD) and contains probes for the approximately 6100 ORFs identified at that time.

Annotations derived from Affymetrix 'Ye6100subB Probe Set Description' file (31 KB, 3/28/03)


title: BGI-RicechipB

status: Public on Apr 22 2009

city: Beijing

first: lihuang

last: Zhu

address: Datun Road, Chaoyang District,100101 Beijing China

department: Plant Gene Research Center

country: China

institute: The Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences (CAS)

organism: Oryza sativa

technology: spotted oligonucleotide

distribution: non-commercial

first: Gang

last: Wei

first: Qiang

last: Gan

first: Haipang

last: Zeng

first: Chen

last: Chen

first: Yulin

last: Han

first: Hongai

last: Xia

first: Yong

last: Tao

manufacture_protocol: 48 contact printer; TeleChem Stealth SMP3 split pins


title: Riken_Human_QPCR

status: Public on Apr 19 2009

city: Yokohama

first: Piero

last: Carninci

department: Center for Life Science Technologies

country: Japan

institute: RIKEN

organism: Homo sapiens

technology: other

manufacture_protocol: QPCR


title: Agilent custom 44K frog array

status: Public on Apr 15 2009

city: San Francisco

first: Esther

middle: T

last: Chan

state: California

address: 1500 Owens Street, Suite 500

institute: Celgene Corporation

organism: Xenopus tropicalis

distribution: custom-commercial

first: Miles

last: Trochesset

manufacture_protocol: Oligos were designed against known and predicted transcripts using the JGI 4.0 version of the frog genome and printed by Agilent via inkjet technology.


title: Pea aphid cDNA array, INRA Rennes, 7344 spots, v2

status: Public on Apr 25 2009

city: Le Rheu

first: Denis

last: TAGU

department: UMR 1099 BiO3P

country: France

institute: INRA Rennes

organism: Acyrthosiphon pisum

technology: spotted DNA/cDNA

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: Gael

last: LE TRIONNAIRE

first: Nathalie

last: PRUNIER-LETERME

first: Geraldine

last: DUCROS

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: Carnegie Xenopus Laevis 44K Microarray (60-mer Oligo)

city: Baltimore

first: Donald

last: Brown

state: MD

address: 3520 San Martin Dr

department: Department of Embryology

institute: Carnegie Institution

organism: Xenopus laevis

description: Carnegie Xenopus laevis 44K Microarray contains 33206 60-mer oligonucleotides representing over 20,000 known and predicted Xenopus laevis genes.

manufacture_protocol: As descripted by Agilent manuals under Platform_web_link


title: RNG-MRC_HU25k_EVRY

status: Public on Apr 08 2005

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

first: Kévin

last: Le Brigand

first: Pascal

last: Barbry


title: BU_Shewanella_100k_v1.0

city: Boston

first: Qasim

middle: K

last: Beg

state: MA

address: 44 Cummington St

department: Biomedical Engineering

institute: Boston University

organism: Shewanella oneidensis MR-1

description: A custom manufactured, high-density oligonucleotide expression array, with 11 micron features, comprising a total of 102,906 probe pairs targeting 10,058 sequences.

first: Michael

middle: E

last: Driscoll

first: Timothy

middle: S

last: Gardner

first: Alex

last: Beliaev

first: Margaret

middle: F

last: Romine

first: Jim

last: Fredrickson

manufacture_protocol: See Affymetrix manufacturing details for GeneChip® CustomExpress® Array Program, 49-5241 format arrays.


title: Lillicrap Lab, Mouse Balb/c 4K array version 1

status: Public on Apr 30 2009

city: Kingston

first: Mohammad

last: Qadura

state: Ontario

address: 88 Stuart St.

department: Pathology

country: Canada

institute: Queen's University

organism: Mus musculus

description: This record represents a condensed array layout.

manufacture_protocol: Microarray was designed by Agilent


title: GenAu MB BCELL v2.0

status: Public on Apr 27 2009

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

country: Austria

institute: Instutute of Molecular Pathology

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

first: Shane

last: McManus

manufacture_protocol: as described in www.nimblegen.com


title: BGI-RicechipA

first: lihuang

last: Zhu

first: Gang

last: Wei

first: Qiang

last: Gan

first: Haipan

last: Zeng

first: Chen

last: Chen

first: Hongai

last: Xia

first: Yuning

last: Han

first: Yong

last: Tao

manufacture_protocol: 48 contact printer; TeleChem Stealth SMP3 split pins;


title: CME-Human-3K6_7

status: Public on Apr 26 2009

city: Leuven

first: Thierry

last: Voet

address: Herestraat 49

department: Department of Human Genetics

country: Belgium

institute: KULeuven

manufacturer: MicroArray Facility, VIB, KULeuven, Herestraat 49, B-3000 Leuven, Belgium

manufacture_protocol: 1. Microgrid (Genomics Solutions, UK).  2. 384 microtiter plates (X7022, Genetix)  3. 16 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 Phosphate buffer, 0.000125% sarcosyl at concentrations ranging between 300 ng/ul and array in 384 microtiter plates.  2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 185 um, row pitch = 185 um; Humidity 55%; 61 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 60 to 120 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. Continue spotting the next morning until all plates are printed.  7. After spotting, 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.     Support: glass   Coating: aminosilane  Description: The array contains BAC and PAC sequences, amplified by DOP - PCR and printed in 2 replicates.


title: CSHL-Human-MOMA2, 368K CpG tiling array

status: Public on Apr 28 2009

city: Cold Spring Harbor

first: Robert

last: Lucito

state: NY

address: 1 Bungtown Road

department: Genome Center

institute: Cold Spring Harbor Laboratory

manufacture_protocol: Our approach to map genome-wide methylation involves tiling all the predicted CpG islands. All annotated CpG islands were obtained from the UCSC genome browser. These islands were predicted using the published Gardiner-Garden and Frommer (1) definition and involves the following criteria: length >= 200bp, %GC >= 50%, observed/expected CpG >= 0.6. There are ~26219 CpG islands in the range of 200bp to 2000bp in the genome. These islands are well covered by Msp I restriction fragmentation. Arrays were manufactured by Nimblegen Systems Inc using the 390K format to the following specifications. The CpG island annotation from human genome build 33 (hg17) was used to design a 50 mer tiling array. The 50 mers were shifted on either side of the island sequence coordinates to evenly distribute the island. The 390K format has 367,658 available features which would not fit all islands with a 50 mer tiling. Therefore we made a cutoff on the islands to be represented based on size, with only CpG islands of size 200b-2000b being assayed. The array represents classical CpG islands and does not include imprint control regions or other non-island promoters known to be methylated. Background hybridization signal could be high with probes of high GC content since by definition these probes will be. Therefore, control probes which are not in a MspI representation were designed to represent background signal, and these probes were used to calculate signal to noise


title: INSA Lactococcus lactis IL1403 (lot de PCR n°2)

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

organism: Lactococcus lactis

description:
nylon membrane positively charged (Roche)
8*12 cm

manufacturer: Eurogentec/Biochips Platform INSA Toulouse France

manufacture_protocol: Amplicons (PCR) were designed and amplified by Eurogentec. A mean length of 535 bp and final concentrations between 40 and 380 µg/l were obtained. PCR were diluted in DMSO 50 % in 384 wells spot plates and spotted (4 deposits/ spot) in duplicate on positively charged nylon membranes (Roche) with a Biogrid spotter (Biorobotics) with a 4*4 pattern.


title: Affymetrix GeneChip Rat Genome 230 2.0 Array [CDF: Brainarray_Rn230_Rn_UG_v10.cdf]

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

country: Germany

institute: University Heidelberg

organism: Rattus norvegicus

description: Custom CDF (Brainarray v10); UniGene build 165

relation: Alternative to: GPL1355 (Alternative CDF [official])


title: Agilent custom 44K chicken array

first: Esther

last: Chan

organism: Gallus gallus

first: Miles

last: Trochesset

manufacture_protocol: Oligos were designed against known and predicted (GENSCAN) transcripts using the WASHUC1 version of the chicken genome and printed by Agilent via inkjet technology.


title: IU Promoter CpG oligo array 44K

status: Public on Apr 17 2009

city: Bloomington

first: Meng

state: IN

address: 1001 E 3rd Street

department: Medical Sciences

institute: Indiana University

manufacture_protocol:
1. customized probes by picking probes with that bracks CpG dinucleotides from Agilent probe database.
2. array chip manufactured by Agilent following standard protocols.


title: Agilent-011868_D_WithSGCtrls_20030627 Rat Oligo Microarray

city: RTP

first: Pierre

middle: Robert

last: Bushel

state: NC

department: Biostatistics and Computational Biology Branch

institute: NIEHS

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


title: Agilent custom 44K tetraodon array

organism: Tetraodon nigroviridis

manufacture_protocol: Oligos were designed against known and predicted transcripts using the Genoscope TETRAODON7 assembly of the tetraodon genome and printed by Agilent via inkjet technology.


title: UCSD-CpgMIP-targeted-bisulfite-sequencing

city: La Jolla

first: Kun

last: Zhang

address: 9500 Gilman Drive, MC0412

department: Bioengineering

institute: University of California at San Diego

description: Illumina Genome Analyzer II

distribution: virtual


title: Bifidobacterium longum NCC2705 Agilent 11K

city: Zurich

first: Valeria

last: Mozzetti

address: Schmelzbergstrasse 7

department: D-AGRL

country: Switzerland

institute: ETH

organism: Bifidobacterium longum NCC2705

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


title: Human ORESTES NoMatch 4.8k v1.0

status: Public on Apr 12 2009

city: Sao Paulo

first: Barbara

middle: Pereira

last: Mello

state: SP

address: R. Prof. Antonio Prudente, 211

department: Centro de Pesquisa

country: Brazil

institute: Hospital A. C. Camargo

description: Glass slide array composed by ORESTES (open reading frame expressed sequence tags) from the HCGP (Human Cancer Genome Project) that did not align to known genes.

first: Alex

last: Fiorini

manufacture_protocol: Bacteria were grown in LB (Luria-Bertani) medium containing ampicillin (250mg/ml). Inserts were amplified by PCR using M13 reverse and forward primers and products were submitted to 1% agarose gel stained in ethidium bromide for quality control. cDNA clones with single amplicons were purified by filtration in Sephadex G50 (GE Healthcare), following the manufacturer’s directions, printed onto Corning glass slides (Corning) and fixed by UV crosslink.


title: RPCI Human 19K

city: Buffalo

first: Amanda

last: Perez

address: Elm and Carlton Streets

institute: Roswell Park Cancer Institute

manufacture_protocol:
Isolation of BAC plasmid DNA: BAC clone plasmid DNAs, used as templates for PCR representations are prepared using a Qiagen BioRobot 3000. Each clone is retrieved from archival copies of the RPCI-11 BAC Resource, maintained at RPCI. The clones are streaked to single colony, grown overnight (16-18 hours) as 1.0ml pre-cultures in 96 deep-well plates at 37 C in a New Brunswick environmental shaker, and then re-inoculated as 2ml prep-cultures in 48 deep-well plates. After incubation, the cultures are RNase treated and prepped in the BioRobot 3000 using R.E.A.L. Prep 96 BioRobot kits (Qiagen). The BAC DNAs are resuspended in TE and serve as templates for restriction digestion and PCR amplification. We have found that Qiagen prepared DNA is of high quality and outperforms phenol:chloroform extraction methods for the highly sensitive restriction digestion and ligation steps.
Ligation of adapters: The adapters are ligated to the digested DNA by first annealing Mse-21 and Mse-12 primers. 1 ul of each digest (1 ng/ul), is added to 0.5 ul of 100 uM Mse-12 (TAACTAGCATGC), 0.5 ul of 100 uM Mse-21 (5’ aminolinker AGTGGGATTCCGCATGCTAGT) in a final volume of 7.5 ul using a thermalcycler (MJ Research). The mixture is incubated at 65 C for 1 min followed by ramping the temperature down to 15 C with a ramp-speed of 1.3 C per minute. When the temperature reaches 15 C, ligation proceeds with 1 ul of 10 mM ATP, 0.5 ul One-Phor-All-Buffer-Plus (10x) and 1 ul T4-DNA ligase (5 U/ul, Invitrogen) added to each tube and incubated at 15 C overnight.
PCR amplification: Two rounds of amplification are required to produce enough product for array generation as described in Cowell, J. K. and N. J. Nowak. 2003. High-resolution analysis of genetic events in cancer cells using bacterial artificial chromosome arrays and comparative genome hybridization. Adv Cancer Res 90:91-125. A single BAC PCR-representation produces enough printing solution for over 4,000 arrays. Preparation of DNA spotting solutions: PCR products (100 ul) are purified for printing by a series of ethanol precipitation steps, followed by resuspension of the pellets in 20 ul of 25% DMSO in H2O (final DNA concentration ~0.8 ug/ul) using a Qfill2 (Genetix). The DNA solutions are rearrayed into Genetix 384-well V-bottom plates using a Hydra 96-PP liquid handling system, and stored at 4 C until printing. We determined that DNA prepared using LM-PCR performed superiorly over other methods, including degenerate oligonucleotide primer PCR, inter Alu PCR and amplification of BAC subclones mixtures. 25% DMSO has several properties that make it an ideal solution for resuspending the amplicons. First, it acts as a denaturant, rendering the printing solution single-stranded for optimal slide binding and subsequent hybridization. Secondly, DMSO does not evaporate, so the printing solution volume is not affected by exposure to the environment during multiple print runs.
Array printing: Slides are printed using a MicroGrid ll TAS arrayer (Genomic Solutions) using 10K Microspot pins at 48% relative humidity, 22?C. We have a climate controlled, HEPA filtered room to minimize environmental changes that can affect printing. In addition, the arrayer is supplied with HEPA filtered air to further maintain a dust-free environment. We print each BAC clone in triplicate to create an array of on amino-silanated glass slides (Schott Nexterion, Type A+). The printed slides dry overnight, and are UV-crosslinked (350 mJ) in a Stratalinker 2400 (Stratagene). The slides are visually inspected and stored in a dessicated environment and are hybridized without additional treatment. Attempts at post-print processing or inclusion of pre-hybridization steps resulted in background issues that made the images difficult to analyze. We found no indication of DNA loss from the spots at any stage of the procedure when we performed hybridization in formamide buffers at 37°C (via DAPI staining).


title: Systemix Institute Arabodpsis miRNA target high resolution 126K 36mer tiling array

status: Public on Apr 10 2009

city: Los Altos

first: Manoj

last: Samanta

address: 2240 Homestead Court #309

institute: Systemix Institute

organism: Arabidopsis thaliana

description:
Custom array was designed with 15,000 36-mer oligonucleotide probes tiling 200 base upstream and downstream (3 n.t. resolution) of miRNA target sites in
Arabidopsis thaliana. TAIR8 chromosome version was used in the design (chr1 = NC_003070.6, chr2 = NC_003071.4, chr3 = NC_003074.5, chr4 = NC_003075.4, chr5 = NC_003076.5).
The 22 target genes on the arrays were chosen based on the abundance of associated smRNAs that mapped to the loci, the amplitude of the antisense transcription signals in published whole genome tiling microarray experiments and a representative cross section of miRNA families.

first: Qing-Jun

last: Luo

middle: P

first: Fatih

last: Köksa

first: Jaroslav

last: janda

first: David

middle: W

last: Galbraith

first: Casey

middle: R

last: Richardson

first: Fangqian

last: Ou-Yang

first: Christopher

middle: D

last: Rock

manufacture_protocol: Agilent inkjet technology


title: MSU_Cotton_3K_v1.0

status: Public on Apr 16 2009

city: East Lansing

first: Jeffrey

last: Landgraf

state: MI

address: 612 Wilson Rd.

department: RTSF

institute: Michigan State University

organism: Gossypium hirsutum

manufacturer: Michigan State University Research Technology Support Facility

first: Jeff

manufacture_protocol: PCR products were amplified from an EST library using universal vector primers, ethanol precipitated, and resuspended in 3X SSC print buffer. Aliquots were run on gels for quality control. Any wells containing multiple bands or no product were labeled "Fail QC" in the probe list. 16 pin replicate arrays were printed on Corning UltraGAPS slides using a GenMachines Omnigrid spotting robot and Telechem Chipmaker 3 pins.


title: CME-Human-4K3

first: Thierry

last: Voet

manufacture_protocol: MicroGrid Printing Protocol  Equipment:  1. Microgrid (Genomics Solutions, UK).  2. 384 microtiter plates (X7022, Genetix)  3. 48 MicroSpot quill pins - 10K (cat# BR001489, Genomics Solutions, UK)  4. Codelink slides (cat# 30001100, GE Healthcare).  Printing 2 array of 4x4 blocks on 1 microscope slide:  1. Dissolve PCR products in 250mM Phosphate buffer, 0.00025% sarcosyl at concentrations ranging between 300 and 600 ng/ul and array in 384 microtiter plates.  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%; 123 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 60 slides on the slide-deck.  6. Start spotting early in the morning and continue over night. Leave spotter overnight with vaccuum and humidity settings on. Empty the spotter the next morning.  7. After spotting, incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.  8. Block 1%NH4OH, 0.1% SDS, H2O.  9. Slides can be stored for at least 6 months in a dry-cabinet.    Support: glass   Coating: aminosilane  Description: The array contains BAC and PAC sequences, amplified by DOP - PCR and printed in 2 replicates.


title: Roswell Park Cancer Institute Human 19K


title: Systemix Institute Arabodpsis miRNA target high resolution 126K 25mer tiling array

description:
Custom array was designed with 15,000 25-mer oligonucleotide probes tiling 200 base upstream and downstream (3 n.t. resolution) of miRNA target sites in
Arabidopsis thaliana. TAIR8 chromosome version  was used in the design (chr1 = NC_003070.6, chr2 = NC_003071.4, chr3 = NC_003074.5, chr4 = NC_003075.4, chr5 = NC_003076.5).
The 22 target genes on the arrays were chosen based on the  abundance of associated smRNAs that mapped to the loci, the amplitude of the antisense  transcription signals in published whole genome tiling microarray experiments and a  representative cross section of miRNA families.


title: Lin_Arabidopsis_70mer_28k_loo1

city: Urbana

first: Yun

last: Lin

state: IL

address: 183 NSRC, 1101 W. Peabody Dr.

department: Crop Sciences

institute: University of Illinois

first: Shui

last: Wang

manufacture_protocol: Qiagen-Operon Arabidopsis Genome Array Ready Oligo Set (AROS) Version 3.0 were printed on glass slides. Print version: AT v3.2.3.Z


title: NimbleGen Drosophila melanogaster 385K Array

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Drosophila melanogaster

description: Expression design for Drosophila melanogaster (Release 4.3). 12 60mer probes per gene, 2 replicates. 15634 exemplar genes representing a total of 19384 transcripts/variants.

manufacture_protocol: Drosophila melanogaster 385K Array.  (See manufacturers website http://www.nimblegen.com/products/exp/index.html).


title: Johns Hopkins University/Affymetrix GeneChip Genome-Wide Human SNP Array 6.0

status: Public on Apr 11 2009

city: Baltimore

first: George

middle: S.

last: Bova

address: 600 N. Wolfe St

institute: Johns Hopkins University

description:
This platform is based on a Segmented Copy Number derived from .CEL files of GPL6801 (Affymetrix GeneChip Genome-Wide Human SNP Array 6.0) using Partek Genomic Suite 6.4 Segmentation Algorithm

Annotations correspond to hg18 (NCBI 36.1)

manufacture_protocol: see manufacturer's web site


title: Rosetta/Merck HumFLL 44k 1.0 A1 microarray

status: Public on Apr 09 2009

city: Seattle

first: Amit

middle: V

last: Kulkarni

state: WA

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description: Oligonucleotide array on glass.

first: John

last: Castle

manufacture_protocol: HumFLL 44k 1.0 A1 microarray Merck, See manufacturer's website


title: Rosetta/Merck HumFLL 44k 1.0 A3 microarray

description: Oligonucleotide array on glass.

manufacturer: Rosetta Inpharmatics / Merck Pharmaceuticals

manufacture_protocol: HumFLL 44k 1.0 A3 microarray Merck, See manufacturer's website


title: Rosetta/Merck HumFLL 44k 1.0 A2 microarray

description: Oligonucleotide array on glass.

manufacture_protocol: HumFLL 44k 1.0 A2 microarray Merck, See manufacturer's website


title: Rosetta/Merck HumanSplicingV3_6_of_6 microarray

description: Oligonucleotide array on glass.

manufacture_protocol: HumanSplicingV3_6_of_6 microarray Merck, See manufacturer's website


title: Rosetta/Merck HumanSplicingV3_3_of_6 microarray

description: Oligonucleotide array on glass.

manufacture_protocol: HumanSplicingV3_3_of_6 microarray Merck, See manufacturer's website


title: Rosetta/Merck HumanSplicingV3_5_of_6 microarray

description: Oligonucleotide array on glass.

manufacture_protocol: HumanSplicingV3_5_of_6 microarray Merck, See manufacturer's website


title: Rosetta/Merck HumanSplicingV3_2_of_6 microarray

description: Oligonucleotide array on glass.

manufacture_protocol: HumanSplicingV3_2_of_6 microarray Merck, See manufacturer's website


title: Rosetta/Merck HumanSplicingV3_1_of_6 microarray

description: Oligonucleotide array on glass.

manufacture_protocol: HumanSplicingV3_1_of_6 microarray Merck, See manufacturer's website


title: Rosetta/Merck HumanSplicingV3_4_of_6 microarray

description: Oligonucleotide array on glass.

manufacture_protocol: HumanSplicingV3_4_of_6 microarray Merck, See manufacturer's website


title: MCD_Mouse_22K_2

status: Public on Apr 02 2009

city: Tsukuba

first: Nathan

last: Mise

state: Ibaraki

address: Koyadai, 3-1-1

department: BioResource

institute: RIKEN

first: Kuniya

last: Abe

first: Rieko

last: Ikeda

manufacture_protocol: in situ oligo, positive strnd, 60-mer


title: Affymetrix GeneChip Human Genome U133A 2.0 Array [CDF: Brainarray Version 10, Hs133Av2_Hs_ENSG]

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

description:
This is identical to GPL571 but a custom CDF environment was used to extract data (CDF: Brainarray Version 10, Hs133Av2_Hs_ENSG).
The custom CDF is linked below as a supplementary file.
See Dai et al., NAR 2005 33(20), PMID: 16284200.

relation: Alternative to: GPL571 (Alternative CDF [official])

manufacture_protocol: Affymetrix standard protocol


title: Human Stress & Toxicity PathwayFinder PCR Array PAHS-003A

status: Public on Apr 08 2009

first: Michael

middle: J

last: Plewa

address: 1101 W Peabody Dr

institute: University of Illinois at Urbana-Champaign

technology: RT-PCR

description: From manufacturer SA biosciences (former superarray) website: The Human Stress and Toxicity PathwayFinder™ RT²Profiler™ PCR Array profiles the expression of 84 genes whose expression level is indicative of stress and toxicity. The array includes genes that are directly up-regulated by oxidative or metabolic stress and by heat shock. The array also includes genes representative of pathways activated by prolonged stress, which range from cell death by apoptosis or necrosis to growth arrest and senescence to proliferation and carcinogenesis. This kit is also designed to include only those genes that have been reported in the literature to respond to a toxic compound at the transcriptional level. Using real-time PCR, you can easily and reliably analyze expression of a focused panel of genes related to Stress & Toxicity Pathway with this array.

first: Mark

last: Muellner

first: Matthew

last: Hudson

first: Matias

last: Attene-Ramos

first: Elizabeth

last: Wagner


title: UHN Homo Sapiens HCGI 15K

status: Public on Apr 04 2009

city: COPENHAGEN

first: Silvio

last: Zaina

address: Blegdamsvej 9

department: Clinical Biochemistry

country: Denmark

institute: Rigshospitalet

description: HCGI 15k is a Single-spotted array containing 14,923 CpG-island clones containing the UHN's HCGI8.1K set and a new 6.8K set generated by sequence-specific primers targeting potential CpG-island clones that are not currently in any of the UHN collection.  HCGI 8.1k CpG-island clones are consolidated from the UHN's HCGI12K set and an independent 8.5K set obtained from Tim Huang at the Ohio State University (Columbus, OH).  So HCGI15k array has some clones of HCGI12 and also other additional clones.

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: M. tuberculosis (PFGRC)_version 3

status: Public on Apr 07 2009

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

organism: Mycobacterium tuberculosis

description:
http://pfgrc.jcvi.org/index.php/microarray/array_description/mycobacterium_tuberculosis/version3.html
Microarray Version: 3
Number of Grids: 48
Element Type: 70mer Oligonucleotide
Surface Coating: Epoxy
Oligonucleotides Designed: 4750
Replicate Oligo Printings: 6x
Controls: 500 Arabidopsis thaliana 70mers

The Platform data table is a condensed representation of the array's replicate oligos.
The full array layout file is linked below as a supplementary file.
The oligo sequence info for this array (obtained at: ftp://ftp.jcvi.org/pub/data/PFGRC/microarray_annotation/M_tuberculosis/version3/M_tuberculosis_3_H37Rv.ann) has been linked below as a supplementary file.

manufacturer: Pathogen Functional Genomics Resource Center

first: Smriti

last: Mehra

manufacture_protocol: PFGRC protocol


title: Institut Pasteur of Lille Cichorium intybus 1.5k cDNA array

status: Public on Apr 06 2009

city: Villeneuve d'Ascq

first: Anca

last: Lucau

address: Cité Scientifique

department: Biology

institute: University Lille 1

organism: Cichorium intybus

description:
Ci2kcDNA
The Platform data table is a condensed representation of the array.
The full array layout is linked below as a supplementary file.

first: Laurent

last: Laborde

first: Sylvain

last: Legrand

first: David

last: Hot

first: Ludovic

last: Huot

first: Yves

last: Lemoine

first: Simon

last: Hawkins

first: Jean-Louis

last: Hilbert

first: Marie-Christine

last: Quillet

first: Theo

last: Hendriks

first: Anne-Sophie

last: Blervacq

manufacture_protocol:
Chicory annotated ESTs (Legrand et al, 2007), representing 1,098 unique genes, were used to produce microarrays. ESTs are integrated to the Compositae Genome Project library (http://compgenomics.ucdavis.edu/compositae_index.php).
Six microliters of bacterial culture stored with glycerol were put into 100 µl TTE buffer (1% triton ×100, 20 mM Tris-HCl, 2 mM EDTA, pH 8.0) in 96 well plates. Plates were incubated 10 min at 95°C and spinned at 1,200 g for 5 min. The cDNA inserts were amplified using aminated adaptator-specific forward primer NP1 and reverse primer NP2 (both from Clontech) flanking the cDNA insert. For each clone, 3 independent reactions were carried out in a volume of 100 µl containing 1× ThermoPol Detergent Free Reaction Buffer (Biolabs), 2 mM MgCl2, 0.25 mM of each dNTP, 0.25 µM of each primer, 2.5 U of Taq DNA Polymerase (Biolabs) and 7 µl of DNA template in TTE buffer. The PCR reaction was performed for 3 min at 94°C, 35 cycles at 94°C for 30 s, 60°C for 30 s, and 70°C for 90 s, and 70°C for an additional 10 min. The 3 PCR products were mixed and purified using the Multiscreen-PCR Kit (Millipore), analyzed by gel electrophoresis, and quantified by OD measurement at 260 nm. The DNA was dried in a Speed Vac (Savant Instruments), and resuspended in spotting solution (0.1 M MES, 20% DMSO) to obtain a final concentration of 0.5 µg/µl. Preparation and hybridization of cDNA microarrays were performed according to Hot et al. (2003) with several modifications. PCR fragments were spotted three times onto 25×75 mm Codelink Activated Slides (Amersham) using the Affymetrix 417 Arrayer. Spotted slides were treated with blocking solution (50 mM Trizmahydrocloride, 50 mM Tris(hydroxymethyl)aminomethane, 0.3% ethanolamine, pH 9), containing 0.1% SDS at 50°C for 30 min. Slides were washed twice in distilled water for 2 min at room temperature, once in SSC 4× 0.1% SDS for 60 min at 50°C, once in distilled water for 1 min at room temperature, once in distilled water for 2 min at 95°C, and finally twice in distilled water for 2 min at room temperature, before being dried by centrifugation for 5 min at 180 g.


title: MCD Mouse 22k ver. 1

first: Nathan

last: Mise

first: Kuniya

last: Abe

first: Rieko

last: Ikeda

manufacture_protocol: in situ oligo, positive strand, 60-mer


title: PNL mixed species lignin-degrading enzymes microarray

status: Public on Apr 01 2009

city: Richland

first: Katrina

middle: M

last: Waters

address: 902 Battelle Blvd; MSIN J4-18

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

organism:
Cryphonectria parasitica
Neurospora crassa
Phlebia radiata
Pleurotus ostreatus
Pleurotus eryngii
Trametes versicolor
Schizophyllum commune
Agaricus bisporus
Lentinula edodes
Fusarium oxysporum
Trametes cinnabarina
Heterobasidion annosum
synthetic construct
Botrytis cinerea
Gelatoporia subvermispora
Coriolopsis gallica
Dichomitus squalens
Trametes coccinea
Fusarium proliferatum
Phanerodontia chrysosporium

manufacturer: in-house, Pacific Northwest National Laboratory

manufacture_protocol: Probes were printed at 100 µM (in 100 mM Na2HPO4, 200 mM NaCl, 0.01% SDS print buffer) concentrations on epoxysilane-coated glass slides by a Microgrid II printing system (PerkinElmer Life And Analytical Sciences, Inc., Waltham, MA).  Control spots were present as buffer, beacon, biotin, polyA and polyT oligonucleotides.  The buffer spots were spots of blank print buffer (defined below) intended to ensure probe spots were well-spaced.  The beacon spot was a spot of Cy3 dye (always fluorescent), used to identify the orientation of the slide.  The biotin spot was included to check that biotin reporting was not hindered by the conditions used during hybridization or washing.  PolyA and polyT probes were included as positive and negative controls for the polyA-modified eukaryotic genes that are then reverse-transcribed to generate polyT tagged cDNA.


title: VU University Orchesella cincta array 7K

city: Amsterdam

first: Dick

last: Roelofs

state: Noord-Holland

address: De Boelelaan 1085

department: Animal Ecology

country: Netherlands

institute: VU University

organism: Orchesella cincta

description: hydrophilic polymer containing N-hydroxysuccinimide (NHS) ester reactive groups

first: Thierry

last: Janssens

first: Martijn

last: Timmermans

first: Ben

last: Nota

first: Janine

last: Marien

first: Bauke

last: Ylstra

first: Zoltan

last: Bochdanovits

first: Nico

last: Van Straalen

manufacture_protocol:
We amplified cDNAs from our previously obtained cadmium exposed SSH library together with clones derived from a cDNA library of cadmium-exposed gut tissues with amine-linked primers. Amine-tagged cDNAs were spotted onto Codelink Activated slides (GE Healthcare). Each cDNA was printed twice on one array and two arrays were printed on one slide, so that each cDNA was four times technically replicated on a slide. Pins of the printer resampled the cDNAs before printing the replicate array, so each slide contains two separately printed arrays.
Printing procedure:
The amine-labeled PCR products (0.1–1 kb)were diluted at a concentration of 0.1–0.5 mg/ml DNA in printing buffer (50 mM sodium phosphate, pH 8.5).
Printing occured in an environment with relative humidity < 50% to
retain binding activity.
DNA was printed onto the Codelink activated slides to produce microarrays on a Biorobotics MicroGrid arrayer
Printed slides were placed into a slide storage box in the saturated NaCl chamber.
chamber was sealed and incubated overnight at room temperature
residual reactive groups were blocked using pre-warmed blocking solution
(0.1 M Tris/0.1 % SDS, 50 mM ethanolamine, pH 9.0)at 50 °C for 30 min.
slides were rinsed twice with deionized water.
slides were washed with 4X SSC / 0.1% SDS (pre-warmed to 50 °C)
for 30 min on the shaker. At least 10 ml per slide was used.
Slides were placed into boiling water
for 2 minutes to denature double stranded DNA
slides were rinsed twice with deionized water.


title: CEA Equine / Murine Oligonucleotide Expression Microarray

city: Evry

first: Olivier

last: ALIBERT

address: 2 rue Gaston Crémieux

department: IRCM

institute: CEA

organism: Equus caballus

first: Peggy

last: Maltere

first: Amélie

last: Robert

first: Simon

last: Tendil

first: Nicolas

last: Jeansoule

first: Eric

last: Barrey

manufacture_protocol:
The equine microarray includes 384 probes and controls of gene transcripts involve din muscle contraction, enegy metabolism and inflammation. The method to design and manufacture the equine microarray was derived from Le Brigand K et all, An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. Nucleic Acids Res. 2006 Jul 19;34(12).
These 384 equine oligonucleotides (50nt) were printed in phosphate buffer with MicroGridII (BioRobotics). They were added to the following mouse  oligonucleotide microarray (25K).
The mouse oligonucleotide microarray contains 25344 features (probes and controls): 24109 oligonucleotides from mouse RNG/MRC collection (Le Brigand K et all, An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. Nucleic Acids Res. 20 06 Jul 19;34(12)). Oligos printed in phosphate buffer with MicroGridII (BioRobotics).


title: Duke MicroRNA microarray

city: Durham

first: Jen-Tsan

last: Chi

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

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

first: Holly

last: Dressman

manufacture_protocol:
1.Oligos are arrayed in Greiner 384-well flat-bottom plates. Each well contains 600 pmol of 70-mer oligo.
2. Resuspend oligos in water to 20 uM and rearray 5 µL into 384-well, Genetix polystyrene V-bottom plates (cat# X6004).
3. Allow Genetix plates to dry through passive water evaporation in a protected environment (e.g., chemical hood).
4. Before printing, add 5 µL of 1X Printing Buffer to each well. This can be done the night before a print run is started.
5. Seal plates with Corning seals.
6. Incubate at 37°C for 30 minutes to aid resuspension of DNA.
7. Shake plates near maximum rotational speed on flat-bed shaker for 1 minute.
8. Centrifuge plates at 2000 rpm for 3 minutes.
9. Remove seals and cover with plate lids. Place in appropriate location of plate cassette. This should be done with first plates just before print run is started to minimize evaporation time before printing. For second and third cassettes, wait until 30
10. Make sure plates rest behind both holding clips in the cassettes. Push plates back into the cassettes as far as they will go, putting them in the proper position for the server arm.
11. After the print run is completed, allow plates to dry through passive evaporation in a protected environment.
12. For each subsequent preparation of these plates for a print run, add water to the wells instead of sodium phosphate buffer. The amount of water should be decreased by 0.25 µL per print run, as this is the amount drawn up by the pin capillary during ea


title: Yeast two-species array for S.cerevisiae and S.paradoxus (2 X 105K)

city: Rehovot

first: Itay

last: Tirosh

address: herzl

department: Molecular genetics

country: Israel

institute: Weizmann Institute of Science

organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus

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


title: University of Helsinki 9.6K Populus euphratica stress cDNA array

city: Umeå

first: Nathaniel

last: Street

address: Umeå University

department: Plant Physiology

country: Sweden

institute: Umeå Plant Science Centre

organism: Populus euphratica

description:
Plant material for EST library construction:
The Ein Avdat valley is located in the Negev desert in Israel at 450 m above sea level and a latitude of 30° 49' 30" N, and a longitude of 34° 46' 0" E. The average rainfall is 100 to 200 mm per year with most of the rain falling during winter time. Adult heart shaped leaves were collected from trees in areas A, B, and C for the cDNA library during the summer seasons of 2000 to 2001. Material was also harvested from young in vitro plantlets of a clone (clone B2) derived from a single tree from area B. Samples for microarray analysis were taken from areas A, B, and C and from the Ein Avdat parking lot (area P, 1 km from the valley) on 27 November 2003, and for ion, isotope and metabolite profiling on 27 November 2003 and 13 October 2004. The parking lot trees were irrigated with non saline tap water for 24 hours once a week.
For normalized control libraries, leaves, shoots and roots were harvested from 8 month old P. euphratica seedlings. Seeds were obtained from the Forest Administration Division, Xinjiang Corps of Production and Construction, Urumqi, PR China. The seeds were sown on sand that had a high content of clay (6%) and germinated at 12 hours light with 250 μmol m-2 s-1 photosynthetically active radiation, 25°C, and a relative air humidity of 60% in a climate chamber (Weiss, Giessen, Germany). The seedlings were potted into soil (Fruhstorfer Erde N, Archut, Germany), transferred to a greenhouse with natural light and watered daily with Long Ashton macronutrient solution [52].
For stress treatments, leaves and roots were harvested from P. euphratica subjected to the following treatments: elevated CO2 (plants submitted to an atmosphere of 700 ppm for 60 days); different irradiance levels (plants under three different irradiance regimes corresponding to 48%, 18% and 8% external irradiance) for 60 days; drought stress (plants submitted to a 21 day cycle of drought with 5% to 3% volumetric soil humidity) before harvesting; flooding stress (plants submitted during 21 days to a complete submergence of the root system); ozone (plants submitted to 200 nl l-1 of O3 for 7 and 20 h); cold and freezing (leaves harvested from plants acclimated at 5 days of +2°C and from plants exposed to two and seven days of -2°C following the acclimation period); salt stress (leaves and xylogenic cambium harvested from plants exposed to 150 mM NaCl for 0.5 h, 1 h, 1.5 h, 2 h, 5 h, 10 h, 24 h and 48 h and roots harvested after 40 minutes, 1.5 h, 8 h and 20 h); cadmium stress (plants were stressed with 50 μM CdCl2 and roots harvested after 12, 24 and 48 h).
Above text copied from
Brosche et al. (2005) Genome Biology 6:R101
doi:10.1186/gb-2005-6-12-r101
PMID: 16356264

first: Mikael

last: Brosché

first: Jaakko

last: Kangasjärvi

manufacture_protocol: 5 μL of purified fragments were transferred to a 384 printing plate together with 5 μL of 6 × SSC solution. The ESTs were printed onto poly-lysine coated slides with a Genemachines OmniGrid 100 (Genomic Solutions, Ann Arbor, MI, USA) using 16 SMP3 pins (TeleChem International, Sunnyvale, CA, USA). Printing conditions were 48% to 50% humidity and 21°C.


title: TAU/KBA_mouse_206_v4.0

city: Tel Aviv

first: Karen

middle: B

last: Avraham

address: Levanon St.

department: Human Molecular Genetics and Biochemistry

institute: Tel Aviv University

organism:
Homo sapiens
Mus musculus

first: Noam

last: Shomron

first: Eran

last: Hornstein

first: Sumeet

last: Gupta

manufacture_protocol: According to Ambion's recommendations for mirVana miRNA Probe Set version 1


title: Microarray of P. syringae pv phaseolicola NPS3121

status: Public on Sep 01 2008

city: Irapuato

first: Jose Luis

last: Hernandez-Flores

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León

department: Ingeniería Genética

country: Mexico

institute: Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional

organism: Pseudomonas savastanoi pv. phaseolicola

description: All samples were printed in triplicate in a contiguous arrangement of 12 grids of 24 rows x 24 columns. The microarray was printed twice in the same slide. The printed conditions were: 20oC of temperature and 60% of humidity.

first: Alejandro

last: Hernández-Morales

first: Susana

last: De la Torre-Zavala

first: Enrique

last: Ibarra-Laclette

first: Ariel

last: Alvarez-Morales

manufacture_protocol: A 4X genomic library of P. syringae pv phaseolicola NPS3121 was constructed. 30% of the genomic library were randomly chosen and partially sequenced using a forward M13-primer in a single sequencing reaction. 2880 sequences with an average size of 531 pb were obtained. Using MUMmer system each sequence was aligned and annotated against the complete genome of P. syringae pv. phaseolicola 1448A (Joardar, 2005), this strategy allowed us to select 1911 clones that provided a 1X coverage of the genome, eliminate redundancy and to have information regarding the identity of each clone. The select clones were independently amplified by PCR using a M13 forward and reverse primers (5´-CCCAGTCACGACGTTGTAAAACGAC and 5´-AGCGGATAACAATTTCACACAGGAA, respectively). The PCR products were purified and transferred to 384 well source plates. The obtained DNA samples were adjusted at 120 ng/µl in 3X SSC and spotted onto amino Propyl Silane slides (Corning Inc., Corning, NY, U.S.A.) using the Virtek Chiprender Professional Arrayer. The array contained 1911 inserts with average size of 2.4 Kbp that cover at least 85% of the P. syringae pv phaseolicola NPS3121 genome. In the microarray were printed various positive and negative controls Lucidea Universal ScoreCard (Amersham) to monitor target labeling and hybridization efficiency, as well as many genes (argK, phtA, phtD, desI, phtL, phtMN, amtA) derived from our previous and ongoing research in phaseolotoxin synthesis. Additionally were printed PCR products for genes involved in the synthesis of type III secretion system (hrpRS, hrpTU, hrpOP, hrpJ, virPphA, avrPphC, avrPphD, avrPphE), quorum sensing (ahlI, ahlR, algD), global regulators (rpoD, gacA, rpoN, gacS, rsmA).


title: TIGR Aspergillus nidulans array condensed (no spot replicas)

status: Public on Feb 02 2008

city: Vienna

first: Harald

last: Berger

address: Muthgasse 18

institute: University of Natural Resources and Applied Life Sciences, Vienna

organism: Aspergillus nidulans

description:
This set includes 11481 oligonucleotides (ss oligo 70 mer), has 23962 spots (2x oligo replicates).
Two versions are available, version 1 is already available at GEO: Platform GPL5397. Version 2 of the .GAL file is attached as raw data file.

manufacturer: TIGR PFGRC (The Pathogen Functional Genomics Resource Center)

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


title: TAU/KBA_mouse_206_v2.0


title: PCR Array Mouse Angiogenesis(PA-012)

city: Beijing

first: Huan

last: Meng

address: Mailbox 918, Yuquan Road 19

institute: Lab of Bioeffects of Nanosized Materials, Institute of High Energy Physics

organism: Mus musculus

description: We synthesize a novel nanoparticle with functional surface coating, which inhibits tumor growth without detectable cytotoxicities by suppress angiogenesis in the tumor mass. Quantitative counting RTPCR-array analysis was used to evalute the pro-angiogenic factor(s) on mRNA level.

first: Gengmei

last: Xing

first: Yuliang

last: Zhao

first: Chengcheng

last: Zhang

first: Zhen

last: Chen

first: Ning

first: Hui

last: Yuan

first: Feng

first: Chunying

first: Hao

last: Lei

first: Xuxia

last: Wang

first: Xinjie

last: Liang


title: NIAID Mmca -- Mouse 38K

status: Public on May 02 2008

city: Bethesda

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

manufacturer: NIAID Microarray Research Facility (NIH/NIAID)

first: Guojian

last: Jiang

manufacture_protocol:
Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions ( http://www.genomicsolutions.com ) that is fitted with a printhead and 48 SMP2 print tips from Telechem ( http://www.arrayit.com ).
The mouse genome microarray (Mmca) probe set is based on 70mer oligonucleotides from Operon's (AROS) Mouse Genome Oligo Set Version 4.0 ( http://omad.operon.com/download/index.php ).
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. Spot densities are 155 microns (center-to-center).
The microarrays are printed on Epoxy Slides from Corning (Catalog # 40042) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: LUH Illumina human-6 v2.0 expression beadchip

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

institute: Lund University

organism: Homo sapiens

technology: oligonucleotide beads

description: Researchers can generate whole genome expression profiles for multiple samples on a single BeadChip. Researchers can profile six or eight samples perBeadChip, with more than 48,000 transcript probes per sample using the Human-6 v2 beadchip.

manufacture_protocol: see manufacturer's website


title: UCMerced_Mfav_v3

city: Thuwal

first: Christian

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

organism: Orbicella faveolata

first: Jodi

middle: A

last: Schwarz

first: Julia

last: Schnetzer

first: Shinichi

last: Sunagawa

first: Michael

middle: K

last: DeSalvo

first: Mary-Alice

last: Coffroth

first: Alina

last: Szmant

first: Monica

last: Medina

manufacture_protocol: Microarrays consist of PCR-amplified cDNAs from M. faveolata. 1,314 PCR-amplified cDNAs were spotted in duplicate on poly-lysine-coated slides yielding a microarray with 2,628 total features. cDNAs were chosen from EST libraries described in (Schwarz et al., 2008).  To annotate the cDNAs, we performed a BLASTx analysis (E-value cut-off 1e-5) against the GenBank non-redundant DNA and protein database (nr).


title: LC_MRA-1001_miRHuman_10.0_070802

city: Houston

first: Christoph

last: Eicken

address: 2575 W. Bellfort

country: USA

institute: LC Sciences, LLC

description: Human miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 10.0

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


title: LC_MRA-1001_miRHuman_10.1_071219

description: Human miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 10.1


title: [Bacillus_anthraci530025] Affymetrix Bacillus anthracis Array

status: Public on Jul 12 2007

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Bacillus anthracis

manufacture_protocol: see manufacturer's web site


title: [Mu6500subA] Affymetrix Murine Genome 6500A Array

status: Public on Feb 09 2005

description:
high density oligonucleotide array
Keywords = oligonucleotide


title: [Ecoli_antisense] Affymetrix E. coli 1286 Antisense Array

status: Public on Mar 07 2007

organism: Escherichia coli K-12

description:
The GeneChip E. coli 1286 Antisense Array (manufactured circa 2001) can be used for examining expression of E. coli genes. The array contains probe sets to detect the antisense strand of open reading frames.
Keywords = high density oligonucleotide array


title: LC_MRA-1001_miRHuman_11.0_080411

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


title: Wistar Institute Ursus americanus 9.6 k BA01

status: Public on Mar 10 2009

city: FAIRBANKS

first: Anna

last: Goropashnaya

state: AK

address: 311 Irving I Building

department: Institute of Arctic Biology

institute: University of Alaska Fairbanks

organism: Ursus americanus

description: All our EST's for the array are submitted to The Gene Index Project http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gireport.pl?gudb=bear

manufacture_protocol: cDNA spot array on nylon membrane http://www.wistar.org/research_facilities/facilities/genomics/review.html


title: MHP Human Chromosome 7 tiling-path CGH array

status: Public on Oct 30 2008

city: Cambridge

first: David

middle: T W

last: Jones

address: Box 231, Level 3 Lab Block, Addenbrooke's Hospital

department: Pathology

country: United Kingdom

institute: University of Cambridge

description: The chromosome 7 tile path array clone set has been assembled by the Mapping Core, Map Finishing and Microarray Facility groups of the Wellcome Trust Sanger Institute, Hinxton, UK. Additional clones were also kindly supplied by the Wellcome Trust Sanger Institute. The 5Mb clone set has been selected from the 1Mb clone set assembled in the Wellcome Trust Sanger Institute. The array has 16 subarrays (4 rows by 4 columns), each subarray consisted of 18 rows by 19 columns.

manufacturer: Department of Pathology, University of Cambridge

first: Koichi

last: Ichimura

first: Danita

last: Pearson

last: Carter

first: Anthony

last: Brown

first: V

last: Collins

manufacture_protocol:
Spotted DNA array
1.BAC/PAC clones were grown in 2xTY medium in a deep-well titre plate at 37°C overnight with chloramphenicol 25µg/ml (BAC) or kanamycin 20µg/ml (PAC).
2. DNA was extracted from BAC or PAC clone using modified alkali-lysis method (microprepping).
3. Approximately 5ng of BAC/PAC DNA was PCR-amplified using three DOP-primers (Fiegler H, Genes Chromosomes Cancer 36:361-374, 2003).
4. Two microlitre of the DOP-PCR products was further amplified using 5'-Aminolink universal primer (Fiegler H, Genes Chromosomes Cancer 36:361-374, 2003).
5. Three volumes of the Amino-PCR products were mixed with one volume of 4xSpotting buffer (1M Sodium phosphate buffer, pH8.5, 0.001% Sarkosyl) to make a spotting mix.
6. The spotting mix was filtered through Corning 96 well white polystyrene filter plate with modified styrene insert (0.2µm PVDF) by centrifugation.
7. The filtered spotting mix was transferred to a 384-well plate.
8. The spotting mix was printed printed in duplicate onto a CodeLink slide (GE Healthcare) using a MicroGrid II robot (Genomic Solutions, Huntingdon, UK) in 4x4 subarrays.
9. The printed slides were incubated at room temperature for 24-72 hours in a humidified chamber.
10. The slides were treated with 1% ammonium hydroxide at room temperature for 5 min, then with 0.1% SDS at room temperature for 5min.
11. The slides were heat-denatured in a boiling water for 2 min, cooled, rinsed with water and dried.


title: NSWCAG 16K

status: Public on Apr 23 2009

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

organism:
Hordeum vulgare
Triticum aestivum

manufacture_protocol: The cDNA clones were grown overnight in 250 ml TYPGN medium [20 g tryptone, 19 g yeast extract, 10 ml 80% (v/v) glycerol, 5 g Na2HPO4, 10 g KNO3 per litre] supplemented with 100 lg/ml ampicillin, in 96-well microtiter plates. These plates were replicated in 150 µl of fresh medium and grown overnight. The replicate plate was stored at 80 oC after the addition of 100 µl 80% (v/v) glycerol. Plasmid preparations were made from cultures following standard alkaline lysis procedures, and the inserts were amplified by PCR using the M13/pUC forward and reverse sequencing primers (New England Biolabs, Beverly, Mass.). For quantitative and qualitative evaluation of the amplification procedure, 1 µl of the PCR reaction was run on a 2% (w/v) agarose gel in Tris-borate buffer, pH 8, and the image recorded. The remainder of the PCR products were ethanol-precipitated, resuspended in 6 µl 50% (w/v) dimethyl sulfoxide and transferred from the 96-well plates to 384-well microtiter plates for printing. The PCR products were printed onto CMTGAPS-coated microscope slides (Corning, USA) using an Omnigrid Microarrayer (Genemachines, San Carlos, Calif.) with ChipMaker2 quill pins (TeleChem, Sunnyvale, Calif.). Prior to hybridisation the slides were baked at 80 oC for 2 h.