title: NY1

status: Public on Feb 03 2006

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

organism: Saccharomyces cerevisiae

technology: spotted DNA/cDNA

distribution: non-commercial

manufacturer: Janos,,Demeter; Dept. Genetics, CCSR 2255, Stanford, CA, USA, 94305; 726-0075; jdemeter@genome.stanford.edu

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


title: Origin of replication for Pyrococcus abyssi by ChIP-chip

status: Public on Jan 30 2007

city: Gif-sur-Yvette

first: LAWRENCE

last: AGGERBECK

address: Avenue de la Terrasse

department: Centre de Génétique Moléculaire

country: France

institute: Centre National de la Recherche Scientifique

organism: Pyrococcus abyssi

description: Chromatin immunopreciptation coupled with hybridization on a whole genome microarray (ChIP-chip) of P. abyssi.

manufacturer: Gif/Orsay DNA Microarray Platform (GODMAP)

first: Lawrence

last: Aggerbeck

first: Herve

last: Delacroix

first: Marie-Helene

last: Mucchielli

first: Nicolas

last: Agier

first: Annie

last: Glatigny

first: Patrice

last: Durosay

first: Laetitia

last: Marisa

first: Fujihiko

last: Matsunaga

first: Patrick

last: Forterre

manufacture_protocol:
Microarray preparation.
The P. abyssi genome was divided into 353 regions, each of which is 5 kb in length. Each of the 353 DNA regions has a specific ID number. For example, the microarray region 25 corresponds to the genome coordinates 120 000 to 125 000. For the microarrays, each of the 353 regions was amplified with the BD Advantage 2 PCR kit (BD biosciences clontech). The purified PCR products were quantitated and distributed into 384-well source plates at final concentrations of 100 ng/µl in final volumes of 8 µl of water. PCR products were dried using centrifugation under vacuum and then resuspended in 8 µl of 1% CHAPS and 50% formamide (28).
The DNAs were arrayed onto activated GAPSII slides (Corning) using a GeneTAC G3 robot (Genomic Solutions) operating under a controlled environment (20°C and 35% humidity) using thirty-two 150 µ diameter pins. Each fragment was spotted 6 times (3 spots in two different blocks originating from two different pins). P. abyssi plasmid pGT5 and negative controls (lambda DNA, pBluescript, pESP1, 1kb ladder) were also added after linearization by appropriate restriction enzymes. After spotting, the slides were dried overnight, protected from light, at room temperature. The DNA was then UV-crosslinked to the slide using 250 mJ/cm2 (Hoeffer UVC500; Amersham Biosciences). For quality control, one slide from every print batch was stained with SYBR Green II (Invitrogen) diluted 1:10 000. The slides were pre-processed by washing for 5 min each with 1) 2X SSC/0.1% SDS, 2) 0.2X SSC and 3) water and then dried using centrifugation under vacuum. Identical pre-processing was used for slides destined for hybridization.


title: Chicken Immune System-Specific Microarray

status: Public on Jan 25 2007

city: Guelph

first: Shayan

last: Sharif

state: Ontario

address: Ontario Veterinary College

department: Department of Pathobiology

country: Canada

institute: University of Guelph

organism: Gallus gallus

first: Aimie

middle: J

last: Sarson

first: Leah

middle: R

last: Read

first: Hamid

last: Haghighi

first: Melissa

middle: D

last: Lambourne

first: Jennifer

middle: T

last: Brisbin

first: Huaijun

last: Zhou

manufacture_protocol: Each array contained 134 features replicated three times. Each replicate contains 8 columns with 17 rows.


title: UCSFRB Mus musculus miRNA DGCR8knockoutES

status: Public on Jan 31 2007

city: San Francisco

first: Robert

last: Blelloch

address: RMB1018, 35 Medical Center Way

department: Urology

institute: UCSF

organism: Mus musculus

technology: spotted oligonucleotide

first: Yangming

last: Wang

manufacture_protocol: for details, see the Whitehead Institute Center for Microarray Technology website


title: Whitehead Mouse 13K Promoter Array

city: Seatttle

first: Yi

last: Cao

state: WA

address: 1100 Fairview Ave. N

department: Human Biology

institute: Fred Hutchinson CRC

description: To prepare the DNA content of the arrays, the program Primer3 was used to design primers using the sequences described above. PCRs were performed on these primer sets using standard conditions, except for the presence of 1 M betaine in all PCR reactions. Betaine was empirically observed to increase the success rate of the amplification reactions. Of the 13,000 pcr pairs, 70% gave a strong band of the appropriate size, as verified on 2% agarose gels. We have noted, however, that PCR products undetectable by agarose EtBr gel analysis can give valid positive signals when concentrated and printed on the DNA arrays. PCR quality evaluations were performed on the BRIDNA suite of programs from the Biotechnology Research Institute of the National Research Council of Canada. PCR products were recovered from the reaction mixture by ammonium acetate/isopropanol precipitation and resuspended into 3x SSC with 1.5 M betaine to minimize evaporation and improve spot quality. The resuspended DNA was transfered to 384 well plates and printed on GAPS-coated slides (Corning) using a robot from Cartesian Technologies. The quality of the arrays was determined on a batch-wise basis by hybridization with sequence-neutral oligonucleotides covalently linked to Cy3 or Cy5, followed by calculation of usable percentage of spots, combined with direct visual inspection of the quality of the chip. Because the genome was only approximately 70% complete in the April 2001 alignment used to generate the primer sets for this array, the Hu13K array was remapped against the August 2003 final release of the completed human genome post-production.

manufacturer: Center for Microarray Technology Whitehead Institute


title: Zebrafish Oligonucleotide Array (Compugen)

status: Public on Jan 01 2007

city: Chicago

first: Victoria

middle: Emma

last: Prince

state: IL

department: Organismal Biology & Anatomy

institute: University of Chicago

organism: Danio rerio

description: The Compugen set of zebrafish oligonucleotides was designed by Compugen based on ESTs, mostly from the Washington University Zebrafish Genome Assemblies.  Compugen no longer sell or support this product.  Sequences are not for commercial use, copyright reserved to Compugen 2002.

first: Monica

last: Rohrschneider

middle: E

manufacture_protocol: For each gene one 65-mer oligonucleotide probe was designed from the 3' region of the sequence.  Each probe was selected from a sequence segment that is common to a maximum number of splice-variants predicted for each gene.


title: CGEN:Mm010706

status: Public on Jan 05 2006

last: Stanford Microarray Database

manufacturer: Gavin,,Sherlock; School of Medicine, Department of Genetics, Stanford, CA, United States, 94305; 650-498-6012; sherlock@genome.stanford.edu


title: SpliceExpress Human Spliceome 2

status: Public on Jan 17 2007

city: Berkeley

first: Jonathan

middle: L

last: Bingham

address: 733 Allston Way

institute: Jivan Biologics, Inc

organism: Homo sapiens

technology: in situ oligonucleotide

distribution: custom-commercial

first: Subha

last: Srinivasan

first: Adam

middle: C

last: Siepel

manufacture_protocol: NimbleGen standard in situ synthesis using digital light projection.


title: UGI Human 12800 V1.0

status: Public on Jan 24 2007

city: Shanghai

first: xuping

last: fu

country: China

institute: Institute of Genetics, Fudan University

manufacture_protocol: The construction of the microarrays used in this study was carried out following Brown’s method (available at http://cmgm.stanford.edu/pbrown/protocols/index.html).We fabricated a “genome-wide” cDNA microarray consisting of 12800 sequences including full-length and partial cDNAs representing novel, known, and control genes provided by United Gene Holdings Group Co., Ltd. Furthermore, 12262 clones were obtained from large-scale full-length cloning efforts carried out by the company. 10046 clones were identified with high similarity to the sequences in Unigene database of NCBI by performing Blast (http://www.ncbi.nlm.nih.gov/), while others were novel genes, each of which was given an unique code. The cDNA inserts were amplified by polymerase chain reaction (PCR) with universal primers to plasmid vector sequences and then purified. All the PCR products were examined by agarose gel electrophoresis to ensure the quality and identity of the amplified clones as expected. Then the amplified PCR products were dissolved in a buffer containing 3ХSSC solution. The solution with amplified PCR products were spotted onto silylated slides(CEL Associates, Houston, TX) using a Cartesian PixSys 7500 motion control robot (Cartesian Technologies, Irvine, CA) fitted with ChipMaker Micro-Spotting Technology (TeleChem International, Sunnyvale, CA). Glass slides with spotted cDNA were then hydrated for 2 hr in 70% humidity, dried for 0.5 hr at room temperature, and UV cross-linked (65mj/cm). They were further processed at room temperature by soaking in 0.2% sodium dodecyl sulfate (SDS) for 10 min, distilled H2O for 10 min, and 0.2% sodium borohydride (NaBH4) for 10 min. The slides were dried again and ready for use. The fluorescent cDNA probes were prepared through reverse transcription of the isolated mRNAs and then purified according to the methods of Schena et al.. The noncancerous samples were labeled with Cy3-dUTP. The cancerous samples were labeled with Cy5-dUTP. The two color probes were then mixed, precipitated with ethanol, and dissolved in 20μl of hybridization solution [5ХSSC (0.75 M NaCl and 0.075 M sodium citrate), 0.4% SDS, 50% formamide, and 5ХDenhardt’s Solution (0.1% Ficoll, 0.1% polyvinylpyrrolidone, and 0.1% BSA)]. Resultant cDNA was purified and hybridized to the microarray provided by United Gene Holdings Group Co., Ltd. Microarrays were pre-hybridized with hybridization solution containing 0.5 mg/ml denatured salmon sperm DNA at 42℃ for 6 hr. Fluorescent probe mixtures were denatured at 95℃ for 5 min, and the denatured probe mixtures were applied onto the pre-hybridized chip. And then put a cover glass on it. Chips were hybridized at 42℃ for 15–17 hr. The hybridized chips were then washed at 60℃ for 10 min each in solutions of 2ХSSC and 0.2% SDS, 0.1ХSSC and 0.2% SDS, and 0.1ХSSC, and then dried at room temperature.Every slide was scanned by ScanArray 4000B scanner (General Scanning, Watertown, MA). The fluorescent images of Cy5 and Cy3 were scanned separately and saved for further image analysis. The acquired images were analyzed with GenePix Pro 3.0 software (Axon Instruments, Inc., Union City, CA).


title: NimbleGen Saccharomyces cerevisiae_ChIP whole-genome tiling array

status: Public on Jan 22 2007

city: Waltham

first: Dan

last: Tardiff

state: MA

address: 415 South Street

department: Biology

institute: Brandeis University

description: NimbleGen catalog #C4214-00-01; whole genome 50mer tiling at 32 bp spacing.

distribution: commercial

middle: F

first: S

middle: A

last: Lacadie

first: M

last: Rosbash


title: SHCF

manufacturer: Stanford Functional Genomics Facility,  Stanford School of Medicine


title: Homo sapiens Hu2304 Array

status: Public on Jan 18 2007

city: Delhi

first: Anu

last: Sharma

email: anukaush@gmail.com, ramuigib@gmail.com

state: Delhi

address: Mall Road, Near Jubilee Hall

department: Functional Genomics Unit,

country: India

description:
Number of super grid in x-direction: 2
Number of super grid in y-direction: 1
Total number of super grid on slide: 2
Number of samples per grid in x-direction: 24
Number of samples per grid in y-direction: 12
Number of spots per grid in x-direction: 24
Number of spots per grid in y-direction: 24
The distance between two spots in micron: 170
Positive control: beta-actin
Negative control: 50% DMSO

manufacturer: Functional Genomics Unit, Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India

first: Samir

middle: K

last: Brahmachari

first: Srinivasan

last: Ramachandran

manufacture_protocol:
Around 32,000 cDNA clones were procured from M/s Genotypic technologies, Bangalore, India in the form of dried PCR products in 384 well plates. These clones were primarily obtained from Research Genetics in the form of plasmids and the inserts were amplified using degenerate primers designed against the cloning sites of 7 different plasmids used for cloning. The dried PCR products were reconstituted by re-suspending in 26 ul 1X TE buffer (10mM Tris-HCl, 1mM EDTA, pH 8.0). Reconstituted PCR products were aliquoted in two 384 plates by transferring 8 ul to each replica plate using Biomek 2000 (Beckmann) robot. These products were further amplified for printing microarrays by using forward primer F1: 5'GGGTAACGCCAGGGTTTTCCCAGTCAC3' and Reverse primer R1: 5’ ACAATTTCACACAGGAAACAGCTATGACCATG 3'. The clones to be amplified for printing were robotically transferred to 96 well plate and PCR reaction was set up in these plates.

50 ul PCR reaction was set up using 1 ul of reconstituted template, 0.4 pmol of each primer, 1X PCR buffer with 1.5 mM MgCl2, 200uM dNTP mix and 1.5 units Taq polymerase. The PCR conditions used were initial denaturation at 95 °C for 3min, cycling conditions 95°C for 30 secs, 62°C for 30 secs, 72°C for 3 min, for 35 cycles and a final extension step at 72 °C for 7 min. The PCR products were checked for successful amplification by gel electrophoresis on 1% agarose TAE gel.

PEG 8000 (Poly ethylene glycol) was used to precipitate the amplified PCR products. Equal volumes of PEG-Sodium Acetate solution  was added to the amplified products in 96-well plate, mixed and kept in ice for at least 1 hour. It was centrifuged at 12,000 g for 15 minutes and the supernatant (containing PEG) was removed completely from each well. The pellet was washed at least twice with chilled 1ml 70% ethanol for effective removal of PEG. The pellet was air dried and dissolved in 0.1X TE. The purified products were analysed by electrophoresis on 1% agarose TAE gel.

Microarrays were robotically printed using purified PCR products on aminosilane glass slides using Quackenbush protocol (Hegde et al (2000). Chip writer Pro (previously known as SDDC-2 spotter, ESI, Inc.) with SMP3 stealth pins (Telechem Inc.) was used to print all the microarray slides.

The purified probes were resuspended in 50% DMSO for printing on aminosilane coated microscopic glass slides (procured from SIGMA) according to this protocol (Hegde et al, 2000). Printing of probes was carried out in a controlled environment with humidity maintained around 40%-45% and temperature of 25 °C. After completion of printing, the slides were kept inside the closed chamber of the microarray robot for at least 24 hours to allow complete drying of the spots. The spots were cross-linked to the slides by exposing slides to 200 mJ total energy of UV irradiation in a UV cross-linker (Stratagene, CA). The slides were then stored at room temperature in closed slide boxes till further use.

The slides were incubated with pre-hybridization buffer (5X SSC, 0.1% SDS and 1% BSA) at 42 °C for 45 minutes for blocking the slides. The slides were washed in sterile water, rinsed in Isopropanol, air-dried and immediately used for hybridization.


title: Hu/Mu ProtIn oligonucleotide microarray

city: Detroit

first: Kami

last: Moin

state: MI

address: 540 E. Canfield

department: Pharmacology

institute: Wayne State University

organism:
Homo sapiens
Mus musculus

description: Dual species array for profiling protease and protease inhibitor gene expression in tumors and their microenvironment.

manufacture_protocol: See manufacturer's web site


title: MRC Homo sapiens 6K

city: Leicester

first: Jerry

last: Styles

state: Leicestershire

address: Robert Kilpatrick Building, Univ. Leicester

department: Cancer Studies and Molecular Medicine

country: United Kingdom

institute: University of Leicester

first: Ayman

last: Ewies

first: Farook

last: Al-Azzawi

first: Mona

last: El-Shafie

first: Jin

last: Li

first: Adrian

last: Stanley

first: Bryan

last: Williams

first: John

last: Thompson

first: Ian

middle: N

last: White

manufacture_protocol:
5010 EST clones were obtained from Research Genetics (Human known gene set). The actual clones were obtained from the IMAGE collections held at the MRC Human Genome Mapping Project. These clones were sequence verified prior to arraying. All of the plasmid inserts were amplified by use of a universal primer set and a standard PCR mix (ABGene) employed. The products were all electrophoresed on an agarose gel and the gel images stored for future reference.
All PCR products that failed an initial amplification or produced multiple bands were re-amplified using plasmid specific primers. The size of the insert sequence was determined from the agarose gel by comparison with ladder using MultiAnalyst software (BioRad). After PCR the reaction products were precipitated and prepared for array using the methods described by Eisen and DeRisi (DeRisi et al., 1997; Eisen et al., 1999).
Arrays were printed on poly-L-lysine coated slides and UV crosslinked and blocked prior to use (DeRisi et al., 1997; Eisen et al., 1999). The arrays were printedusing an arrayer built essentially according to the Stanford designs and can be seen at the MRC toxicology website.  The centre to centre distance of the features was 210 um and each feature was 90-100 um in diameter


title: pombe 44K_v2

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

organism: Schizosaccharomyces pombe

description:
Agilent 60mer oligo arrays tiling entire S. pombe genome across 3 chromsomes at 300bp interval alternately from the plus and minus strand.
Choromosome locations in data table are based on assembled contigs at ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Chromosome_contigs/OLD/Sep_15_2004/

first: Tomoyasu

last: Sugiyama

first: Hugh

middle: P

last: Cam

first: Rie

first: Ken-ichi

last: Noma

first: Martin

last: Zofall

first: Ryuji

last: Kobayashi

middle: I

manufacture_protocol: Custom 60mer oligonucleotide microarrays based upon Agilent’s non-contact in situ synthesis process.


title: Schneider MF lab mini microarray of mouse skeletal muscle (all spots)

city: Baltimore

first: Xiaodong

last: Mu

address: 108 N. Greene street

department: Biochemistry and Molecular Biology

institute: University of Maryland School of Medicine

last: Schneider

first: Lisa

last: Brown

manufacture_protocol: 60mer pligonucleotides were spotted to glass slides with a Cartesian Microarray Printer, with 6 replicates for each gene. Slides were coated with Poly-L-Lysine before printing and post-processed to further immobilize DNA after printing.


title: ASGRCLI_MWG_Yeast_Oligo_Array

status: Public on Jan 26 2007

city: Taipei

first: Huang-Mo

last: Sung

address: 128 Sec.2 Academia Rd.

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica, Taiwan

description:
6250 gene specific oligonucleotide probes represent the complete Saccharomyces cerevisiae genome on one single slide
Each probe was spotted twice on one single slide.

first: Wen-Hsiung

first: Daryi

last: Wang

first: Dalun

last: Tseng

first: Chih-Jen

last: Huang

manufacture_protocol: see manufacturer's web site


title: Threespine Stickleback RAD marker microarray

city: Eugene

first: Eric

last: Johnson

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular biology

institute: University of Oregon

organism: Gasterosteus aculeatus

description: Awaiting submitter update of Platform features with trackable sequence identifier information.

manufacturer: Michael R Miller - Johnson Lab - University of Oregon

first: Michael

last: Miller

first: Joseph

last: Dunhan

first: Angel

last: Amores

first: William

last: Cresko

manufacture_protocol:
printing robot: DeResi homebuilt;
probe source: non-purified PCR products ;
printing buffer: 3X SSC, 1.5M betaine;
Slide surface: Corning GAPSII


title: Mouse_Tlr4_pathway_Splice_Array

status: Public on Jan 15 2007

city: St Lucia

first: Sean

middle: M

last: Grimmond

state: QLD

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute of Molecular Bioscience, Uni of QLD

first: Christine

last: Wells

first: Alistair

last: Forrest

last: Chalk

first: Darrin

last: Taylor

first: Mark

last: Crowe

manufacture_protocol: Commerical in situ synthesized oligonucleotide array.


title: Grossman Lab WGS1-6

status: Public on Jan 10 2007

city: Cambridge

first: Adam

last: Breier

address: 77 Massachusetts Ave Bldg. 68-540D

institute: Massachsetts Institute of Technology

organism: Bacillus subtilis subsp. subtilis str. 168

first: Alan

last: Grossman

manufacture_protocol: PCR products were prepared using a combination of the Sigma-Genosys Bacillus subtilis ORFmer PCR primer pairs and additional primers designed by the Grossman and Losick labs on a case-by-case basis.  Products were spotted on aminosilane coated glass slides (Corning) using a Genetix Q-Array Mini printer.


title: Homo sapiens Hu800 Array

first: Anu

last: Sharma

institute: Institute of Genomics and Integrative Biology

description:
Number of super grid in x-direction: 1
Number of super grid in y-direction: 1
Total number of super grid on slide: 1
Number of samples per grid in x-direction: 20
Number of samples per grid in y-direction: 10
Number of spots per grid in x-direction: 20
Number of spots per grid in y-direction: 20
The distance between two spots in micron: 200
Positive Control: beta-actin
Negative Control: 50% DMSO (spotting buffer)

first: Samir

last: Brahmachari

first: Srinivasan

last: Ramachandran

manufacture_protocol:
Around 32,000 cDNA clones were procured from M/s Genotypic technologies, Bangalore, India in the form of dried PCR products in 384 well plates. These clones were primarily obtained from Research Genetics in the form of plasmids and the inserts were amplified using degenerate primers designed against the cloning sites of 7 different plasmids used for cloning. The dried PCR products were reconstituted by re-suspending in 26 ul 1X TE buffer (10mM Tris-HCl, 1mM EDTA, pH 8.0). Reconstituted PCR products were aliquoted in two 384 plates by transferring 8 ul to each replica plate using Biomek 2000 (Beckmann) robot. These products were further amplified for printing microarrays by using forward primer F1: 5'GGGTAACGCCAGGGTTTTCCCAGTCAC3' and Reverse primer R1: 5’ ACAATTTCACACAGGAAACAGCTATGACCATG 3'. The clones to be amplified for printing were robotically transferred to 96 well plate and PCR reaction was set up in these plates.

50 ul PCR reaction was set up using 1 ul of reconstituted template, 0.4 pmol of each primer, 1X PCR buffer with 1.5 mM MgCl2, 200uM dNTP mix and 1.5 units Taq polymerase. The PCR conditions used were initial denaturation at 95 °C for 3min, cycling conditions 95°C for 30 secs, 62°C for 30 secs, 72°C for 3 min, for 35 cycles and a final extension step at 72 °C for 7 min. The PCR products were checked for successful amplification by gel electrophoresis on 1% agarose TAE gel.

PEG 8000 (Poly ethylene glycol) was used to precipitate the amplified PCR products. Equal volumes of PEG-Sodium Acetate solution  was added to the amplified products in 96-well plate, mixed and kept in ice for at least 1 hour. It was centrifuged at 12,000 g for 15 minutes and the supernatant (containing PEG) was removed completely from each well. The pellet was washed at least twice with chilled 1ml 70% ethanol for effective removal of PEG. The pellet was air dried and dissolved in 0.1X TE. The purified products were analysed by electrophoresis on 1% agarose TAE gel.

Microarrays were robotically printed using purified PCR products on aminosilane glass slides using Quackenbush protocol (Hegde et al (2000). Chip writer Pro (previously known as SDDC-2 spotter, ESI, Inc.) with SMP3 stealth pins (Telechem Inc.) was used to print all the microarray slides.

The purified probes were resuspended in 50% DMSO for printing on aminosilane coated microscopic glass slides (procured from SIGMA) according to this protocol (Hegde et al, 2000). Printing of probes was carried out in a controlled environment with humidity maintained around 40%-45% and temperature of 25 °C. After completion of printing, the slides were kept inside the closed chamber of the microarray robot for at least 24 hours to allow complete drying of the spots. The spots were cross-linked to the slides by exposing slides to 200 mJ total energy of UV irradiation in a UV cross-linker (Stratagene, CA). The slides were then stored at room temperature in closed slide boxes till further use.

The slides were incubated with pre-hybridization buffer (5X SSC, 0.1% SDS and 1% BSA) at 42 0C for 45 minutes for blocking the slides. The slides were washed in sterile water, rinsed in Isopropanol, air-dried and immediately used for hybridization.


title: Rat Uniset 10K

status: Public on May 01 2005

city: Mountain View

last: Fielden

address: 325 East Middlefield Road

institute: Iconix Biosciences

organism: Rattus norvegicus

description:
Amersham Biosciences CodeLink UniSet Rat I Bioarray
This set is limited to 8,565 functionally validated probes


title: MMK

status: Public on Mar 04 2006

city: Stanford

first: Roger

last: Wagner

address: 300 Pasteur Drive

department: Falk Cardiovascular Research Center

institute: Stanford University School of Medicine

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


title: SA-DEV-VS1

city: Heraklion

first: Elena

middle: Athina

last: Sarropoulou

department: Marine Biology and Genetics

country: Greece

institute: HCMR

organism: Sparus aurata

description:
For the microarray production a cDNA library of mixed embryos/larvae of gilthead sea bream, Sparus aurata (Sarropoulou et al., in press) was used. A total of 10,176 clones were arrayed into 384 square well plates. In order to amplify the inserts culture PCR was performed as followed. The total volume of one PCR reaction was 50 µl, containing 43.5 µl reaction mix (2 µl 10x PCR Puffer, 0.04 µl 100 mM of each dATP, dCTP, dGTP and dTTP, 12.12 µl dH20), 1.5 µl of T7 and 1.5 µl of T3 primer (20 µM), 1 µl Taq polymerase (5U/µl) and 2.5 µl of culture. The PCR program utilized consisted of 1 step of 94ºC for 1 min 20 s, followed by 35 cycles of 94ºC for 1 min, 50ºC for 1 min, 72ºC for 1 min 30 s; the program terminated with a final step of 72ºC for 5min. Each reaction was performed twice; PCR products were combined, separated by agarose gel (2%) electrophoresis and visualized by transillumination in the presence of ethidium bromide (EtBr) in order to check insert size. Purification of PCR products was perfomed via the GFX-96TM Polymerase Chain Reaction (PCR) Purification Kit (Amersham Pharmacia) according to the manufacturer’s instructions. The purified products were then dried down by applying vacuum, re-eluted in 3x SSC and 1.5 M betaine to a volume of 10 ml and transferred to 384 well plates.
The spotting was performed with the OmniGrid 300 robotic system configured with 48 pins. Each glass slide contains 10,176 PCR amplified inserts in duplicate. The spotted glass slides were baked at 80ºC for 2 h in order to cross-link the DNA onto the glass slide. The slides were then incubated in blocking buffer at 50°C for 30 min, washed twice with Millipore water at room temperature for 2 min and dried by spinning in an Eppendorf 5810R centrifuge for 7 min at 800 rpm.

first: Georgios

last: Kotoulas

first: Deborah

last: Power

first: Robert

last: Geisler


title: Matzkin-Markow_Dmojavensis_V1.0

city: Huntsville

first: Luciano

middle: Matias

last: Matzkin

state: Alabama

address: 301 Sparkman Drive

department: Biological Sciences

institute: University of Alabama in Huntsville

organism: Drosophila mojavensis

first: Thomas

last: Watts

first: Benjamin

middle: G

last: Bitler

first: Carlos

last: Machado

first: Therese

last: Markow

manufacture_protocol: Full protocols can be found in Matzkin et. al. (in press) "Functional Genomics of Cactus Host Shifts in Drosophila mojavensis". Molecular Ecology. Additional protocol information can be found at the Genomic Analysis and Technology Core (University of Arizona) website.


title: Millgate Poppy Array #2

city: Acton

first: Anthony

last: Millgate

state: ACT

address: PO Box 1600

institute: CSIRO

organism: Papaver somniferum

description:
Millgate Poppy Array #2
Keywords = Opium Poppy


title: Snyder - Nimblegen S.bayanus WGT 50-60; 50-60

city: Urrbrae

middle: R

last: Borneman

state: South Australia

address: Paratoo Rd

institute: The Australian Wine Research Institute

organism: Saccharomyces bayanus

description: Whole genome tiling array designed for S. bayanus. 50mer oligos tiled every 60 bp on the Watson Strand, 50mer oligos tiled every 60bp on the Crick strand with a 30bp offset.

first: Zhengdong

last: Zhang

first: Joel

last: Rozowsky

first: Michael

last: Seringhaus

first: Mark

last: Gerstein

last: Snyder

manufacture_protocol: maskless-photolithography. Maximum of 396,000 spots per array.


title: Schneider MF lab mini microarray of mouse skeletal muscle (condensed)

first: Xiaodong

last: Mu

first: Martin

last: Schneider

first: Lisa

middle: D

last: Brown


title: SpliceExpress Mouse Spliceome

city: Berkeley

first: Jonathan

last: Bingham

institute: Jivan Biologics, Inc

first: Subha

last: Srinivasan

first: Adam

last: Siepel


title: NimbleGen_DesignID3427_UNC_LiebLab tiling array

status: Public on Jan 19 2007

city: Chapel Hill

first: Jason

last: Lieb

state: NC

address: 408 Fordham Hall, CB# 3280

institute: University of North Carolina at Chapel Hill

organism: Caenorhabditis elegans

first: Sevinc

last: Ercan

first: Paul

last: Giresi

first: Christina

last: Whittle

first: Xinmin

first: Roland

last: Green

manufacture_protocol: see NimbleGen website


title: IPMC - microRNA v4

status: Public on Jan 06 2007

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

last: Le Brigand

first: Pascal

last: Barbry

first: Bernard

last: Mari

manufacture_protocol: Spotted microarray


title: Snyder - Nimblegen S.mikatae WGT 50-60; 50-60

first: Anthony

last: Borneman

organism: Saccharomyces mikatae

description: Whole genome tiling array designed for S. mikatae. 50mer oligos tiled every 60 bp on the Watson Strand, 50mer oligos tiled every 60bp on the Crick strand with a 30bp offset.

first: Zhendong

last: Zhang

first: Joel

last: Rozowsky

first: Michael

last: Seringhaus

last: Gerstein


title: IPMC - microRNA v3


title: UCSF_Gross_Ecoli_v19.txt

city: San Francisco

first: Virgil

middle: Arthur

last: Rhodius

address: Genentech Hall, 600 16th Street

department: Microbiology and Immunology

institute: UCSF

organism: Escherichia coli

description:
A microarray with 5760 spot features.
Tip configuration: Standard 16-tip steel pin
Columns per Sector: 20
Rows per Sector: 18
Column spacing: 210 um
Row spacing: 210 um

first: Eric

last: Guisbert

first: Nidhi

last: Ahuja

first: Emily

last: Witkin

first: Carol

last: Gross

manufacture_protocol: PCR products for 4110 ORFs representing 95.8% of the Escherichia coli K12 MG1655 ORFs were prepared according to Richmond et al (1999; Nucleic Acids Res. 27:3821-35). The products were spotted onto glass slides to make DNA arrays as described in MGUIDE at http://cmgm.stanford.edu/pbrown/mguide/index.html and protocols on http://www.microarrays.org/


title: GUT Homo sapiens 43K Arrays Batch 03

city: Innsbruck

first: Blair

last: Henderson

address: Fritz-Pregl Strasse 3

department: Biocenter

country: Austria

institute: Innsbruck Medical University

manufacturer: Graz University of Technology, Bioinformatics Group

manufacture_protocol:
Microarrays were printed using the Human Oligo 30k Set (A+B+C; MWG-Biotech), on Nexterion epoxysilane coated glass slides (PEQLAB, Erlangen, Germany) using a MicroGrid II spotting robot (BioRobotics, Cambridge, UK).
CAPTURE PROBE
MWG Biotech AG, Ebersberg
Oligonucleotide + 5´-Aminolink 29.952
MWG Human Oligo Set 30K (A+B+C) 78
50 bp 1 / buffer 3x SSC + 1.5 M Betaine 5
SOLID SUPPORT
Supplied by PEQLAB, Erlangen.  Manufactured by SCHOTT Nexterion
Nexterion Glass Slide E, Bar Coded
After spotting, the oligonucleotides were fixed for 60 min at 120 degrees Celsius.


title: DFCI_FISHER_HUMAN_Build35_HG17_388K_v1.0

first: Jun

middle: S

last: Song

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

description: Chromosome coordinates are based on the Build 35 HG17, May 2004 release.

first: Fatih

last: Ozsolak

first: Xiaole

last: Liu

first: David

last: Fisher


title: NADC_Bordetella_bronchiseptica_v1.0

status: Public on Jan 09 2007

city: Ames

first: Tracy

last: Nicholson

state: IA

address: 2300 DAyton Ave

department: Respiratory Diseases of Livestock Research Unit

institute: National Animal Disease Center

organism: Bordetella bronchiseptica RB50

description: Bordetella bronchiseptica 70-mer oligonucleotide array

manufacture_protocol: Using ArrayOligoSelector, one 70-mer  oligonucleotide probe was selected to represent each B. bronchiseptica RB50 ORF. The 70-bp oligonucleotide probes were synthesized (Illumina, San Diego, CA), resuspended in 3XSSC to a final concentration of 60pmol/µL, and spotted onto poly-L-lysine-coated microscope slides, using a BioRobotics Microgrid II microarrayer (Genomic Solutions, Ann Arbor, MI). Each probe was printed three times per slide. Oligonucleotide microarrays were first prehybridized for 1 hour in 5X SSC, 1% BSA and 0.1% SDS at 42oC, followed by washing with H2O and then with isopropanol and dried by centrifugation for 5 minutes at 50xg. Following prehybridization, 45µL hybridization solution (labeled cDNA, 5µg tRNA, 2XSSC, 25% formamide, 0.1% SDS) was applied to oligonucleotide microarrays and incubated in a humidified chamber overnight at 50oC. Arrays were subsequently removed from humidified chambers and quickly submerged and washed in 1XSSC and 0.05% SDS for approximately 2 minutes, followed by two additional washes for 2 minutes each in fresh 0.06XSSC. Slides were then dried by centrifugation for 5 minutes at 50xg, scanned using a GenePix 4000B microarray scanner, and analyzed with GenePix Pro software (Axon Instruments, Union City, CA). Spots were assessed visually to identify those of low quality and arrays were normalized so that the median of ratio across each array was equal to 1.0. Automatically and manually flagged spots, spots with the sum of medians (635/532) signal intensity less than or equal to 100, and spots with signal intensity below threshold (sum of median intensities plus one standard deviation above the mean background) were filtered out prior to analysis. Ratio data from the three biological replicates were compiled and normalized based on the total Cy3% intensity and Cy5% intensity to eliminate slide to slide variation.


title: MPSS 20bp [DpnII: Mus musculus] signature list

city: Boston

first: Winston

middle: Patrick

last: Kuo

address: 188 Longwood Avenue

department: Genetics

institute: Harvard Medical School

technology: MPSS

description:
MPSS signatures detected in Lynx mouse transcriptome analysis experiment.
To generate a complete, annotated mouse signature database, we extracted all the possible signatures (“virtual signatures”) from the mouse genome sequence (NCBI build 33) and the mouse UniGene sequences (UniGene build #145). Each virtual signature is ranked based on its position and orientation in the original sequence. The annotation for that sequence is then assigned to the signature and the resulting signature database is used to annotate the data from the experiments, using our “TopHit” algorithm.
Virtual Signature Class| mRNA Orientation| Poly-Adenelation| Features| Position
------------------------------------------------------------------------------------------
0 Either - Repeat Warning Not applicable Not applicable
1 Forward Strand Poly-A Signal, Poly-A Tail 3' most
2 Forward Strand Poly-A Signal 3' most
3 Forward Strand Poly-A Tail 3' most
4 Forward Strand None 3' most
5 Forward Strand None Not 3' most
6 Forward Strand Internal Poly-A Not 3' most
11 Reverse Strand Poly-A Signal, Poly-A Tail 5' most
12 Reverse Strand Poly-A Signal 5' most
13 Reverse Strand Poly-A Tail 5' most
14 Reverse Strand None 5' most
15 Reverse Strand None Not 5' most
16 Reverse Strand Internal Poly-A Not 3' most
22 Unknown Poly-A Signal Last before signal
23 Unknown Poly-A Tail Last before tail
24 Unknown None Last in sequence
25 Unknown None Not last
26 Unknown Internal Poly-A Not 3' most
1000 Unknown - Derived from Genomic Sequence Not applicable Not applicable

distribution: virtual


title: tomato cDNA array (Ye lab)

city: Ithaca

first: Zhangjun

last: Fei

state: NY

address: Tower Road

institute: Boyce Thompson Institute

organism: Solanum lycopersicum

first: Bo

last: Ouyang

first: Ting

last: Yang

first: hanxia

last: Li

first: Liang

first: Yuyang

first: Junhong

first: Zhibiao

last: Ye

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


title: Rice 10368 cDNA microarray

status: Public on Jan 12 2007

city: Shanghai

first: Li

last: Qun

state: Shanghai

address: 300 Fenglin Road

department: National Key Laboratory of Plant Molecular Genetics

institute: Institute of plant physiology & ecology, SIBS, CAS

organism: Oryza sativa

description: See linked supplementary file for cDNA sequence information.

first: Qun

first: Liangxian

last: Sun

first: Fang

last: Chen

first: Zhongqin

last: Zhang

first: Zuhua

last: He

manufacture_protocol: as described in Biostar Genechip Inc.(Shanghai) manual


title: RNG-MRC_MM25k_EVRY

first: Kevin

last: Lebrigand

organism: Mus musculus

last: Le Brigand

first: Pascal

last: Barbry

manufacture_protocol: Spotted oligonucleotides


title: ScoKao_02-04-29

status: Public on Jan 08 2007

first: Ryan

last: Fong

state: CA

address: 318 Campus Dr. W-300 Clark Center

department: Chemical Engineering

institute: Stanford University

organism: Streptomyces coelicolor


title: ENCODE NimbleGen hg17 tiling array

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

organism: Homo sapiens

description: 391K element tiling array based on NCBI35 build of the human genome (hg17) and contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

first: Nathaniel

last: Heintzman

first: Rhona

last: Stuart

first: Gary

last: Hon

first: Yutao

last: Fu

first: Christina

middle: W

last: Ching

first: David

last: Hawkins

first: Leah

middle: O

last: Barrera

first: Sara

middle: V

last: Calcar

first: Chunxu

last: Qu

first: Keith

first: Wei

last: Wang

first: Zhiping

last: Weng

first: Roland

last: Green

first: Gregory

middle: E

last: Crawford

manufacture_protocol: Tiling array; see NimbleGen website. Contains one 50-mer every 38 nts.


title: Arabidopsis thaliana high-throughput small RNA sequencing

status: Public on Nov 02 2006

city: Cambridge

first: Ramya

last: Rajagopalan

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research, MIT Department of Biology

organism: Arabidopsis thaliana

technology: other

description:
High-throughput sequencing of endogenous small RNAs from Arabidopsis thaliana. This dataset contains sequences of genome-matching small RNAs generated from cDNA libraries of wild-type seedling, rosette, flower and silique tissues, and mapping to the Arabidopsis nuclear, chloroplast and/or mitochondrial genomes.
For isolation protocol please see Axtell, M.J., Jan, C., Rajagopalan, R., and Bartel, D.P. (2006) A two-hit trigger for siRNA biogensis in plants.  Cell 127:565-577.

last: Bartel

manufacture_protocol: See 454 website for details, http://www.454.com/


title: IPMC - microRNA v5LNA

first: Kevin

last: Lebrigand

last: Le Brigand

first: Pascal

last: Barbry

first: Bernard

last: Mari


title: NTU_CGM_MCF Human 672 Metachip

status: Public on May 12 2006

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

institute: National Taiwan University

manufacturer: National Taiwan University Center for Genomic Medicine Microarray Core Facility

first: Hsuan-Yu

last: Chen

first: Chun-Houh

first: Gee-Chen

last: Chang

first: Chih-Yi

first: Ang

last: Yuan

first: Chiou-Ling

last: Cheng

first: Chien-Hsun

first: Harn-Jing

last: Terng

first: Shu-Fang

last: Kao

first: Wei-J

first: Jian-Wei

first: Pan-Chyr

last: Yang

manufacture_protocol:
The whole system included tool pin, adapter, washing slots, sampling slots, sample distribution region, program and automatically changing plate system. Those treated pins were fitted into multiple-pore adapter, which is designed specially to make the pins elastic while spotting samples on membrane. The adapter could be changed for single or multiple pins system according to experimental need. The PCR-amplified cDNA in V-bottomed 96-well microtiter plates were distributed onto a positively charged nylon membrane with spots spaced 150 mm apart by an arraying machine. The arraying machine was a computer controlled XYZ translation system outfitted with Teflon-coated tool pins for sample delivery. It was designed and constructed by Wittech company (Taipei, Taiwan) with position resolution and repeatability better than ± 5 mm. Samples were held at the tip of the pins for delivery by the action of surface tension, and the delivery volume was governed by the diameter of the tips. Every time after DNA was spotted on membranes, by means of movement of translation stage, the solid pin was immersed into washing slots, and washed by 95% ethanol, and deionized water respectively with sonicating.
The nylon membranes carrying 672 PCR-amplified cDNA fragments were prepared by arraying machine built in house. The 672 invasion-associated genes identified in our previous study were re-arrayed in duplicate on a nylon membrane by arraying machine built in house (Chen JJ, Peck K, Hong TM etc. Global analysis of gene expression in invasion by a lung cancer model. Cancer Res 61:5223-5230, 2001).


title: Canvac Human 7kv2 cDNA Array

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description: double spotted Immune specific Array manufacturered for Canvac

first: Jim

last: Woodget

first: Neil

last: Winegarden

first: Robert

last: Clum

first: Mark

last: Cameron

first: David

last: Kelvin

first: Longsi

last: Ran

manufacture_protocol: as described in UHN Microarray Centre Protocols


title: IPMC - microRNA v2

first: Kevin

last: Lebrigand

last: Le Brigand

first: Pascal

last: Barbry

first: Bernard


title: Aplysia Annotated Array AAA

status: Public on Jan 05 2007

city: St Augustine

first: Andrea

middle: B

last: Kohn

state: FL

address: 9505 Ocean Shore Blvd

department: Whitney lab

institute: University of Florida

organism: Aplysia californica

description:
Microarray Probe Design and Aplysia Oligo-array Fabrication. We constructed two custom 44,000 oligonucleotide arrays in collaboration with Agilent TechnologiesTM. The 60-mer oligonucleotide sequences were designed from a set of 56,071 non-redundant Aplysia sequences from the current assembly, based on bioinformatics criteria such as melting temperature and secondary structure.  Based on the content of the arrays we distinguish between an annotated and discovery array. While the annotated array primarily contains probes originating from assembled sequences or full length clones with known identity, the majority of probes on the discovery array are unknown. Briefly, the first 44,000 features array called the Aplysia Annotated Array (AAA) had all annotated sequences consisting of: full length clones from the table 4S (labeled as f), 32 sequences which were truncated sequence from these same clones that were over 1.5 Kb in length (labeled as d); 67 NCBI Aplysia californica specific sequences (labeled as n); and 90 truncated sequences from NCBI (labeled as b). All these sequences have their ‘1st best’ selected probes spotted 3 times, 2nd best probe spotted once, and 3rd best probe spotted once giving (76+67+32+90)*5 = 1325 features which are also spotted on all 2 custom arrays. In addition, AAA represents Aplysia sequences from our EST assembly that have any of the following terms in their blast hit definition: “receptor”, “hormone”, “channel”, “transcription”, “factor”, “RNA”, “Hox”, “Homeobox”, “neuro*”, “synap*”, “calcium”, “cyclic”, “CREB”. These terms are matched as either complete word or part of the word in the transcriptome annotation and account for 6188 sequences. These sequences have their “1st best” probes spotted 3 times, and “2nd best probes” spotted once, occupying 6188*4 = 24,744 features (labeled as m). For all the remaining sequences with nr blastx e-value < 4e-6, their “1st best probes were spotted twice giving 7961 such sequences. They occupy 7961*2 = 15,922 features and are labeled as a. Thus, on AAA we have 1325 + 24,744 + 15,922 = 41,991 features.
All the rest of the Aplysia sequences are regarded as un-annotated sequences and their best probe was spotted once on the 2nd Aplysia array that we named as DAA. There were 72,280 (including both plus and minus directions because direction is unknown) un-annotated Aplysia sequences and if they were contigs, they were spotted on DAA. There were 29,572 un-annotated contigs (labeled as c) leaving 42,708 un-annotated singlets (labeled as s). 11,137 un-annotated singlets were spotted on the 2nd DAA array and the remaining 31,571 un-annotated singlets were spotted on the 3rd array (we did not test this array in the current study). In summary the 2nd DAA array has 1325 + 29,572 + 11,137 = 42,034 features. Finally, each array has 2,000 random Agilent designed sequences that have been used in control tests.

first: Leonid

middle: L

last: Moroz

first: John

last: Edwards

first: Sathyanarayanan

last: Puthanveettil

first: Thomas

middle: J

last: Ha

first: Eric

last: Kandel

manufacture_protocol:
in situ synthesized array
Agilent Proprietary Information


title: MJArray Mus Musculus

status: Public on Feb 18 2004

city: Karlsruhe

first: Michael

middle: J.

last: Pankratz

department: Institute of Genetics

country: Germany

institute: Forschungszentrum Karlsruhe

description:
cDNA microarrays based on the Lion Bioscience (Heidelberg, Germany) clone collection Mouse ArrayTag(r) set A and B.
Each microarray contains 43200 features within two seperate subarrays with each 21600 spots and 20188 spots containing gene probes.
The ID is organized like this:
Letter "A" or "B" to distiguish both subarrays from each other, followed by the # sign an a running index for each subarray (1 to 21600).
probe length: 200 - 600 bp;
printed concentration: 200 - 400 ng/µl;
printing buffer: 150 mM sodium phosphate, pH 8.5, 1.5 M betaine;
substrates: Corning GAPS II;
microarray robot: Genemachines Omingrid 100;
Printhead: Telechem;
Pins: Telechem SMP3;
Keywords = Lion ArrayTag
Keywords = 43k chip
Keywords = Forschungszentrum Karlsruhe

first: Matthias

last: Bauer

first: Anne

middle: C

last: Hamm

first: Melanie

last: Bonaus

first: Joerg

last: Katzenberger


title: Aplysia Discovery (un-annotated) Array DAA


title: SAGE:17:NlaIII:Phanerochaete chrysosporium

status: Public on Jan 04 2007

last: GEO

organism: Phanerodontia chrysosporium

technology: SAGE NlaIII

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


title: Vibrio cholerae Spotted oligonucleotides

status: Public on Jan 03 2007

first: Leyla

last: Slamti

state: MA

address: 136 Harrison Ave

department: Molecular biology and microbiology

institute: Tufts University/HHMI

organism: Vibrio cholerae O1 biovar El Tor str. N16961

manufacturer: Tufts New England Medical Center Expression Array Core

manufacture_protocol: Each microarray consists of about 4000 DNA oligonucleotides spotted onto UltraGAPS coated slides (Corning) using a Biorobotics MicroGrid II. Oligonucleotides were 70mers designed to correspond to unique sequences within V. cholerae open reading frames (Illumina), plus additional control sequences.


title: Affymetrix Research Exon Array

status: Public on Jan 01 2007

city: Menlo Park

first: Tyson

last: Clark

address: 1380 Willow Rd.

institute: Pacific Biosciences

description:
4 Chip set, 49-format, 8um feature pitch.  Approximately 1.4 million probesets designed to detect more than 1 million exons.  Each probeset has up to 4 PM + MM probepairs.
The Research Exon Array annotation is based on the Nov 2002 version of the Human Genome, NCBI Build 33.

first: Anthony

last: Schweitzer

first: Hui

last: Wang

first: Alan

last: Williams

last: Blume

manufacture_protocol: 4 GeneChip Set (A, B, C, D) with 8um feature pitch that is manufactured using standard Affymetrix in-situ synthesis.  Probes are 25-mers that are designed to detect anti-sense target.


title: MPSS 17bp [DpnII: Mus musculus] signature list

first: Winston

last: Kuo

middle: P


title: TakaraBio CyanoCHIP ver1.4-ver1.6

city: Meguro

first: Mitsunori

last: Katayama

state: Tokyo

address: 3-8-1 Komaba

country: Japan

institute: University of Tokyo

organism: Synechocystis sp. PCC 6803

manufacture_protocol: This microarray covered 3,078 of the 3,264 open reading frames of the Synechocystis genome [Kaneko, T. et al.:DNA Res., 3, 109-136 (1996)]. Description of each ID can be obtained from CyanoBase (http://www.kazusa.or.jp/cyano/ index.html) in Kazusa DNA Research Institute.


title: XCC 4.3K cDNA array

city: Beijing

first: Liang

last: Zhang

address: 18 Life Science Parkway,Changping District

institute: CapitalBio Corporation

organism: Xanthomonas campestris pv. campestris

manufacture_protocol: as described in National Engineering Research Center for Beijing Biochip Technology(CapitalBio Corporation) manual


title: IPMC - microRNA v1

status: Public on Dec 13 2005

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

first: Kévin

last: Le Brigand

first: Pascal

last: Barbry

first: Bernard

last: Mari


title: UW Pseudomonas aeruginosa 10K v1.0

city: Seattle

first: David

last: Dargenio

state: WA

department: Microbiology

institute: University of Washington

organism: Pseudomonas aeruginosa

first: Hemantha

last: Kulasekara

first: Robert

middle: K

last: Ernst

first: Theodore

last: Larson Freeman

middle: H

last: Spencer

first: Mitchell

last: Brittnacher

manufacture_protocol: Custom Agilent oligonucleotide (60mer) microarray with unique oligonucleotides representing nonredundant open reading frames in Pseudomonas aeruginosa DNA sequences in the NCBI Entrez database.


title: CEA Saccharomyces cerevisiae 13k Whole Genome Microarray

city: Paris

first: Valerie

last: Borde

address: 26, rue d'Ulm

institute: Institut Curie

organism: Saccharomyces cerevisiae

first: Franck

last: Amiot

first: Xavier

last: Gidrol

manufacture_protocol: Chip contains 13031 features, corresponding to every ORF and intergenic regions of the yeast Saccharomyces cerevisiae.