title: Rhodopseudomonas palustris Affymetrix GeneChip

status: Public on Jun 29 2007

city: Seattle

first: Yasuhiro

last: Oda

state: WA

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

country: USA

institute: University of Washington

organism: Rhodopseudomonas palustris

technology: in situ oligonucleotide

distribution: custom-commercial

first: Caroline

middle: S

last: Harwood

first: Everett

middle: P

last: Greenberg

first: Amy

middle: L

last: Schaefer

manufacture_protocol: A high-density oligonucleotide microarray was custom designed and manufactured by Affymetrix based on the sequences of ORFs and intergenic regions.


title: Sequenced small RNAs from the lycopod Selaginella moellendorffii

status: Public on Jun 30 2007

city: University Park

first: Michael

middle: J

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

organism: Selaginella moellendorffii

technology: other

description: Pyrosequencing of small RNAs from the lycopod Selaginella moellendorffii.

distribution: virtual

first: David

last: Bartel


title: C. acetobutylicum ATCC824 22K ChIP-on-chip array v1

status: Public on Jun 11 2007

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

organism: Clostridium acetobutylicum ATCC 824

description:
C. acetobutylicum ATCC824 ChIP-on-chip array v1 includes over 20K 60-mer oligonucleotide probes, sourced from the official sequenced genome, and are located in the lower 50% or 500 bp (whichever is shorter) of each ORF. This is a proof of principle array and not a definitive design.
The programs Comm_Oligo (Li, He et al. 2005), ROSO (Reymond, Charles et al. 2004), YODA (Nordberg 2005), ArrayOligoSelector (Bozdech, Zhu et al. 2003), OligoWiz 2.0 (Wernersson and Nielsen 2005) and Picky (Chou, Hsia et al. 2004) were used to generate several 60-mers for each Clostridium acetobutylicum ATCC824 chromosome and pSOL1 megaplasmid ORF (Nölling, Breton et al. 2001). Whenever possible the DNA sequences belonging ribosomal RNAs, tRNA and the intergenic regions of the whole genome were used as a negative set (i.e. no match allowed). A maximum identity of 75-85% to any other sequence and other parameters were set to the program defaults. On average, 32 60-mers per ORF where generated.Melting temperatures and DeltaG values for the generated oligomer and its complementary sequence were re-calculated using Hybrid 2.5 (Markham and Zuker 2005) (included in (Rouillard, Zuker et al. 2003)).
For each 60-mer, the best four non-specific matches against the Clostridium acetobutylicum ATCC 824 genome were determined using FASTA (Pearson and Lipman 1988; Pearson 1990). The melting temperatures of the heterodimers formed by a 60-mer and the complementary sequence of each of its non-specific matches were also calculated. The difference between the melting temperature between the 60-mer and each one of the heterodimers was calculated and the minimal value of the differences was recorded. The 60-mers targeting each particular ORF were ranked (in descending order) according to the minimal DeltaT previously recorded.
Control features are automatically included on the array by Agilent and follow their naming convention. The name for our custom 60-mers is composed of the ORF name (CACXXXX or CAPXXXX), the 60-mer number (1,2 or 3), a character (a,b or c) indicating if it is the first (a), second (b) or third (c) occurrence of this specific 60-mer, and a two letter code (Ch, Co or Tr). A Ch 60-mer (shorthand for ChIP-on-chip) is a 60-mer located in the lower 50% or 500 bp (whichever is shorter) of the target ORF and has a rank of four (4) or greater. A Co 60-mer (shorthand for Common) is a 60-mer located in the lower 50% or 500 bp (whichever is shorter) of the target ORF and has a rank of four (3) or smaller.  A Tr 60-mer (shorthand for Transcriptional) is any 60-mer that does not meet the requirements of a Ch or Co 60-mer regarding location and/or rank.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

first: C

last: Paredes

first: R

last: Senger

first: E

middle: T

manufacture_protocol: See manufacturer's web site


title: Whole Human Oligo Microarray_let-7b transfection of WERI

status: Public on Jun 23 2007

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

country: Canada

institute: Best Institute

organism: Homo sapiens

first: Jim

last: Huang

first: Gordon

last: Chua

first: Tim

last: Corson

first: Ben

last: Blencowe

last: Hughes

first: Brendan

last: Frey

first: Quaid

last: Morris

manufacture_protocol: in situ - Agilent


title: LC-44

status: Public on Jun 28 2007

city: Cambridge

first: Kate

last: Rubins

state: MA

address: Nine Cambridge Center

institute: Whitehead Institute for Biomedical Research

technology: spotted DNA/cDNA

distribution: non-commercial

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


title: Rice Chromosome 4 Tilling-Path V2.0

status: Public on Jun 26 2007

city: Shanghai

first: Hao

last: Hu

address: Caobao Road 500,NCGR

country: China

institute: National Center for Gene Research(NCGR)

organism: Oryza sativa

manufacturer: National Center for Gene Research(NCGR); CapitalBio, China

first: Kai

last: Ying

first: Jie

last: Mu

first: Bin

last: Han

manufacture_protocol:
The array represents a minimal tilling-path covering rice chromosome 4. This tilling-path was assembled using 15,141 BAC subclone fragments. All subclone fragments were PCR amplified using universal primers and plasmids containing the genomic DNA fragment as the template. DNA gel electrophoresis was performed for all fragments and poor amplifications were not included here. This tiling array covers 33.8 Mb or 96% of rice Nipponbare chromosome 4.
Keywords = rice
Keywords = chromosome 4
Keywords = tilling array


title: NU C. acetobutylicum ATCC 824 13 K whole genome spotted cDNA array

manufacturer: cDNA's design and synthesis took place at the E.T. Papoutsakis Lab at Northwestern University (Evanston, IL, USA). The arrays were spotted at University of Wisconsin Gene Expression Center (Madison, WI, USA)

first: Keith

middle: V

last: Alsaker

first: Carlos

manufacture_protocol:
The manufacturing protocol is described in:
Design, Optimization and Validation of Genomic DNA Microarrays for Examining the Clostridium acetobutylicum Transcriptome. K. V. Alsaker, C. J. Paredes, and E. T. Papoutsakis. Biotechnology and Bioprocess Engineering, 2005, 10; 432-443.
The manuscript can be retrieved either from the journal website or Prof. Papoutsakis website.


title: MDL human 3k oligo array

status: Public on Jun 15 2007

city: Aarhus N

first: Lars

last: Dyrskjot

address: Brendstrupgaardsvej

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University Hospital, Skejby

technology: spotted oligonucleotide

manufacturer: Molecular Diagnostic Laboratory, Aarhus University Hospital, Skjejby, Denmark

first: Torben

middle: F

last: Orntoft

manufacture_protocol:
Detailed protocol in:
Microarrays for gene expression profiling: Fabrication of Oligonucleotide microarrays, Isolation of RNA, Fluorescent labelling of cRNA, Hybridisation, and Scanning. Kruhøffer M, Magnusson NE, Aaboe M, Dyrskjøt L & Ørntoft TF. Cell Biology 4th edition – a laboratory handbook.


title: Chr. Hansen A/S_Lactococcus lactis subsp. lactis_2208_v1.0

status: Public on Jun 22 2007

city: Cadorago

first: Martin

middle: Bastian

last: Pedersen

state: CO

address: Via Manzoni 29

department: R&D

country: Italy

institute: Sacco Srl

organism: Lactococcus lactis subsp. lactis

middle: B

first: Christel

last: Garrigues

manufacture_protocol: DNA oligos were purchased from Bioneer Corporation at 50nmol synthesis scale with BioRP purification and in lyophilized state (Daedeok-gu, Daejeon, South Korea). Oligos were dissolved at 10uM in 50% DMSO and printed in 4 replicates on UltraGAPS slides (Corning B.V., Schiphol-Rijk, The Netherlands) using a Genpak ARRAY 21 arrayer (Genetix Ltd., Hampshire, United Kingdom) with 16 SMP3 pins, (TeleChem International Inc., Sunnyvale, CA) giving a spot diameter of 100-120mm. Washing was performed between each print cycle for 20s in water followed by 20s in 70% ethanol. The relative humidity was kept at 48 ± 5% by placing a water bath at the appropriate temperature below the air inlet of the arrayer. The oligos were cross-linked to the surface using a Stratalinker 1800 UV Crosslinker set at 70mJ/cm2 (Stratagene). Printed arrays were stored in aluminium pouches with five arrays each and silica gel to remove humidity.


title: AECOM 32K MOUSE OLIGONUCLEOTIDE ARRAY, MO2 printing series

status: Public on Jun 08 2007

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

organism: Mus musculus

manufacturer: Microarray Facility of the Albert Einstein College of Medicine of Yeshiva University

first: Aldo

last: Massimi

manufacture_protocol: The arrays are printed with 31,769 70mer probes Qiagen V3.0 oligo set (http://oligos.qiagen.com/arrays/oligosets_mouse.php ) plus controls. Each slide is composed of 48 blocks, arranged in 4 columns and 12 rows, each block containing 700 spots in staggered pattern in 28 columns and 25 rows. The arrays are printed under rigorous clean-room conditions and quality control is employed all along the way.


title: VUMC MACF human 30K oligo v60

status: Public on Jun 16 2007

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

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

first: Bauke

last: Ylstra

first: Thijs

last: Krugers

first: Alan

last: Mrsic

manufacture_protocol: The Human Release 2.0 oligonucleotide library, containing 60-mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). The oligonucleotides were dissolved at 10 uM concentration in 50 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink slides (Amersham Biosciences), using an OmniGrid 100 microarrayer (Genomic Solutions, Ann Arbor, MI, USA) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). After printing slides were processed and blocked prior to use according to the manufacturer's protocol.


title: Serial Analysis of Ribosomal DNA

city: Tiburon

first: Matthew

last: Ashby

state: CA

address: 3152 Paradise Drive

institute: Taxon Biosciences, Inc.

organism: uncultured bacterium

manufacture_protocol: virtual


title: INSERM Homo sapiens 14K array Liverpool3

city: ROUEN

first: Jean

middle: Philippe

last: SALIER

address: Bvd Gambetta

department: Inserm Unit 519

country: France

institute: Faculty of Medicine and Pharmacy

first: Frédérique

last: Caillot

first: Gaëlle

last: Saint-Auret

first: Carine

last: Bansard

first: Maryvonne

last: Daveau

first: Jean-Philippe

last: Salier

manufacture_protocol: Liverpool2 is a spotted cDNA array for approximately 10,000 nonredundant genes expressed in embryonic, adult, and/or cancerous liver.


title: Van Andel Research Instittue - cDNA Human B chip

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

manufacturer: The arrays were produced by the Laboratory of Microarray Technology at the Van Andel Research Institute

manufacture_protocol: Arrays were produced using purified double stranded PCR products amplified from the Research Genetics IMAGE cloneset. The probes were suspended in 3X SSC buffer. A custom-made (Beta Integrated Concepts and VARI) arrayer was used to spot the probes onto Corning CMT-GapsII amino-silane coated slides.


title: MWG Biotech MEEBO Long oligo array 27K

status: Public on Jun 13 2007

city: Columbia

first: Raja

last: Settivari

state: MO

address: 920 E Campus Drive

department: ASRC

institute: University of Missouri

manufacturer: Division of Animal science, University of Missouri

first: Eric

last: Antoniou

first: Donald

middle: E

last: Spiers

manufacture_protocol: The oligos were obtained commercially from Illumina MEEBO mouse oligo set. Microarrays were prepared by printing 27000 oligos, 70 mers in length, representing mouse genes on GAP II glass slides (MWG Biotech AG, Ebersberg, Germany). Blank spots and 3X SSC were used as negative controls. A robotic microarray printer with 32 printing tips was used to spot the oligos.


title: Finnish Bordetella pertussis Oligoarray v.1

city: Turku

first: Teemu

last: Kallonen

address: Kiinamyllynkatu 13

department: Derpartment of Infectious Disease Surveillance and Control

country: Finland

institute: National Institute for Health and Welfare

organism: Bordetella pertussis

manufacturer: Finnish DNA Microarray Centre, Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland

first: Eriikka

last: Heikkinen

first: Rolf

last: Sara

first: Juhani

last: Soini

first: Qiushui

last: He

manufacture_protocol: Spotted with custom spotter "R-ray"


title: UMC ASRC S140 Bos taurus 19.2K cDNA v1

first: Zhilin

last: Liu

address: 920 East Campus Dr., ASRC S140

institute: University of Missouri-Columbia

organism: Bos taurus

manufacturer: ASRC, S140, University of Missouri-Columbia

first: Allen

middle: H

last: Garverick

first: Robert

last: Youngquist

manufacture_protocol:
The cDNA library used to make the microarrays consists of 17,692 bovine cDNA samples, with 1,536 bovine ovary cDNA (Takasuga et al., 2001) and 16,156 bovine cDNA clones from USDA BOV1-5  libraries (including ovary) (Smith et al., 2001; Sonstegard et al., 2002), representing 15,634 unique genes. The cDNA inserts were amplified in 96-well PCR plates with M13 forward (5’-CCC AGT CAC GAC GTT GTA AAA CG) and reverse (5’-AGC GGA TAA CAA TTT CAC ACA GG) primers (IDT DNA, Coralville, IA). PCR products were visualized in 1% agarose gels using ethidium bromide staining. All products were then purified with 384-well MultiScreen PCR purification plates (Millipore, Billerica, MA). The purified DNA products were dried and stored at -80°C until used.
Before printing, the dried PCR products were re-suspended in 3×SSC for 48 hours. Arrays were printed on poly-L-lysine (Sigma, St. Louis, MO) coated Gold Seal micro slides (Gold Seal Products, Portsmouth, NH) at the MU animal science microarray core. As external controls, the arrays also contained 10 Arabidopsis genes, each of them printed 10 times across the array (Spot report oligo, Stratagene, Cedar Creek, TX). Blank spots and 3× SSC were used as negative controls. A robotic microarray printer with 32 printing tips was used to spot the DNA. The bovine cDNA arrays had a total of 19,200 spots and were organized in 32 blocks arrayed in 8 rows and 4 columns. Each block had 600 spots arranged in 24 rows and 25 columns. Slides were stored in the dark until used.


title: Homo sapiens CCC-HBL5000-Chip 8.7k array

city: Chiba

first: Akira

last: Nakagawara

address: 666-2 Nitona, Chuoh-ku

country: Japan

institute: Chiba Cancer Center Research Institute

description: Spotted long cDNA array on glass. This set includes 5000 cDNAs, whose average size is approximately 2.5kb.

manufacturer: Chiba Cancer Center Research Institute, Chiba, Japan

manufacture_protocol: Approximately 5,000 genes were selected from 12,000 clones randomly picked up from the mixture of oligo-capping cDNA libraries which were generated from hepatoblastomas. Insert DNAs (the average size: approximately 2.5kb) were amplified by polymerase chain reaction (PCR) from these cDNA clones, purified by ethanol precipitation, and spotted onto a glass slide at a high density with an ink-jet printing tool (NGK insulators, Ltd.).


title: SAGE:11:NlaIII:Giardia intestinalis

last: GEO

organism: Giardia duodenalis

technology: SAGE NlaIII

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


title: USP Blastocladiella emersonii 4.6 K Blasto3773 v2

city: São Paulo

first: Raphaela

middle: Castro

last: Georg

state: São Paulo

address: Av. Prof Lineu Prestes, 748

department: Bioquímica

country: Brazil

institute: Universidade de São Paulo

organism: Blastocladiella emersonii

manufacturer: Universidade de Sao Paulo-Instituto de Quimica

middle: C

first: Silvia

middle: M

last: Salem-Izacc

first: Suely

last: Gomes

manufacture_protocol: The array consists of cDNA inserts from representatives ESTs from 3,773 expressed genes that were obtained through Georg and Gomes, 2007 and  Ribichich et al (2005) work. These inserts were PCR amplified with the T7 forward and SP6 reverse primers, and the amplified products were purified with a Millipore Multiscreen Filtration Plate (MAFB NOB), eluted with Tris-HCl 10 mM, pH 8.0 to a final concentration of 100 to 200 ng/μl and spotted onto Star 7 slides (Amersham Biosciences) using a Generation III Microarray SpotterTM (Amersham Biosciences).


title: C. acetobutylicum ATCC824 22K Transcriptional array v1

first: Eleftherios

last: Papoutsakis

first: C

last: Paredes

first: R

middle: S

last: Senger

first: E

manufacture_protocol: See manufacturer's web site


title: LGTC Sigma-Compugen Mouse 22K V1n

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

institute: Leiden University Medical Center

middle: A

manufacture_protocol: Oligonucleotides dissolved in 50% DMSO were deposited with an Omnigrid contact printer on poly-L-lysine coated glass slides


title: SAGE:10:NlaIII:Oryza sativa

status: Public on Jun 07 2007

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


title: DFCI_HUMAN_2005-04-25_HG17_50mer

city: Boston

first: Arjun

middle: Kumar

last: Manrai

address: 44 Binney Street, Mail Stop LW225

department: Department of Biostatistics and Computational Biology

institute: Dana Farber Cancer Institute

first: Jun

last: Song

first: Xiaole


title: GMRCL Human 15K

status: Public on Jun 09 2007

city: Teipei

first: Yun-Shien

last: Lee

address: No.199, Tunghwa Rd.,

country: Taiwan

institute: Chang Gung Memorial Hospital

description: UltraGAPS Coated slides (Corning).

manufacturer: Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital;

first: Tzu-Hao

last: Wang

manufacture_protocol: cDNA microarrays were spotted using PCR products obtained with the Incyte Genomics. Spotters: Qarray Genetix, with split pins (ArrayIt Brand Products, ChipMaker CMP4). Double stranded DNA in Microarray Spotting Solution (Genetix, GSS-50) were binding to the UltraGAPS Coated slides (Corning), by UV-mediated crosslinking.


title: Complementary DNA arrays produced with PCR fragments of 6116 ORFs of Saccharomyces cerevisiae

status: Public on Jun 21 2007

city: Heidelberg

first: Ana

last: Kitanovic

address: Im Neuenheimer Feld 364

country: Germany

institute: Institute for Pharmacy and Molecular Biotechnology

organism: Saccharomyces cerevisiae

manufacturer: Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, D-69120 Heidelberg

first: NICOLE

last: HAUSER

first: MARTIN

last: VINGRON

first: MARCEL

last: SCHEIDELER

first: BERNHARD

last: KREMS

first: KLAUS

last: HELLMUTH

first: KARL-DIETER

last: ENTIAN

first: JÖRG

middle: D

last: HOHEISEL

manufacture_protocol:
Open reading frame PCR-amplification:
A set of 12,232 PCR primers was commercially
obtained (Research Genetics, USA). The DNA
was transferred into microtitre dishes and simultaneously
diluted to a concentration of 4 ìM using
a Biomek-2000 robot (Beckman, USA). The oligomer
sequences were designed to bind close to
either end of the open reading frames (ORFs).
They were about 45 nucleotides in length, of which
two common tag-sequences accounted for 20 and
22 nucleotides at the 5*-end, respectively [forward
primers: d(GGAATTCCAGCTGACCACCATG);
reverse primers: d(GATCCCCGGGAATTGCC
ATG)]. PCR was done in microtitre dishes using
PTC-200 cyclers (MJ Research, USA). For the
amplification of the most 3*-located region of genes,
a second primer set was designed according to the
specifications of the above set but binding about
500 bp upstream of the respective 3* end. The oligonucleotides were obtained from Interactiva
(Germany).
First-round PCR was done on a template of
25 ng genomic DNA in a total volume of 50 ìl
of 10 mM-Tris–HCl, pH 8·8, 50 mM-KCl, 1·5 mMMgCl2,
0·2 mM of each nucleotide triphosphate,
a mixture of 1 unit of Taq-polymerase and 0·25
unit Pfu-polymerase (Stratagene, USA) and both
primers at a concentration of 0·4 ìM each. Initial
denaturation was at 95)C for 3 min, followed by 35
cycles of 1 min at 95)C, 45 s at 50)C and 3·5 min at
72)C; post-treatment at 72)C was for 10 min.
For reactions that failed to yield product under
the above conditions, the Expand= High Fidelity
System (Boehringer Mannheim, Germany) was
used in a second amplification reaction on 25 ng
genomic template DNA under the conditions recommended
by the manufacturer. After 2 min denaturation
at 94)C, there were 10 cycles of 15 s at
94)C, 30 s at 50)C and 4 min at 68)C, followed by
another 26 cycles during which the period at 68)C
was extended by 20 s per cycle. Again, there was a
final incubation at 72)C to fill-in ends.
Array production:
Initially, the PCR-products were transferred to
positively charged filters (Pall Biodyne B; DuPont,
USA) using 96- or 384-pin gadgets mounted to a
BioGrid spotting device (BioRobotics, UK). Flatbottomed
pins of 0·7 mm diameter transferred
about 60 nl of liquid per spotting event, while only
15 nl was spotted with pins of 0·4 mm. PCRproducts
were placed repeatedly onto the same
position in order to accumulate DNA. During
production, filters were kept humid by being
placed onto Whatman 3MM paper soaked in
denaturing solution (1·5 M-NaCl, 0·5 M-NaOH).
For the production of higher-density grids, a
special pin tool (BioRobotics, UK) was used that
produced arrays of densities of up to 750 spots
per square centimetre. More recently, DNA was
placed onto the surface by a device equipped with
an eight-channel array of piezo printing elements
(GeSim, Germany). By this technique, samples
could be sprayed in multiples of 15 picolitres onto
solid support at a grid density of up to 10,000 per
centimetre square.


title: High-throughput pyrosequencing of small RNAs in Chlamydomonas reinhardtii

status: Public on Jun 04 2007

city: Norwich

first: Frank

last: Schwach

state: Norfolk

address: Colney Lane

country: United Kingdom

institute: Sainsbury Laboratory

organism: Chlamydomonas reinhardtii

description: The dataset contains Chlamydomonas reinhardtii endogenous small RNA sequences in the range 16 to 31 nucleotides. High-throughput sequencing was carried out at 454 Life Sciences. Please see www.454.com for details of the technology. Total RNA was extracted from vegetative cells of strain J3(mt-) grown under continuous illumination.

first: Attila

last: Molnar

first: David

middle: J

last: Studholme

first: Eva

last: Thuenemann

last: Baulcombe

manufacture_protocol: see manufacturer website www.454.com


title: Porcine testis cDNA microarray 060717

status: Public on Jun 02 2007

city: Chunan, Miaoli

first: Wen-chuan

address: 52 Ke-dung 2nd Rd.

department: Division of Biotechnology

institute: Animal Technology Institute Taiwan

organism: Sus scrofa

description: GAPS II, Corning

first: B-H

last: Gau

first: I-M

last: Chu

first: M-C

last: Huang

first: K-T

last: Yang

first: S-H

last: Chiou

first: Y-H

last: Fan

first: M-Y

last: Chen

first: J-H

last: Lin

first: C-K

last: Chuang

first: S-Y

first: W-C

manufacture_protocol:
1. Two porcine testes, from mature pigs under heat stress or not, were collected for cDNA libraries construction with SuperScript Cloning System according to the manufacturer’s instructions (Invitrogen).
2. A total of 27 072 cDNA clones were randomly picked from two cDNA librabies for EST sequencing.
3. Plasmids from 12 748 nonredundant cDNA clones were transferred to 96-well microplates.
4. The cDNA were amplified by PCR using T7 primer (5’-TAATA CGACT CACTA TAGGG-3’) and SP6 primer (5’-CATAC GATTT AGGTG ACACT ATAG-3’) in a final volume of 100 μL.
5. Transfer 3 μL of PCR products for gel electrophoresis analysis.
6. PCR products with yield higher than 20 ng/μL were rearranged to new 96-well microplates.
7. PCR products were purified with Montage PCR96 plate (Millipore) under vacuum and resuspended in 100 microliter of Milli-Q water.
8. The amplicons were evaporated under vacuum at mind temperature and resuspended in 20 μL of 50% DMSO.
9. Transfer the probes into 384-well microplates.
10. A total of 9 944 unique Expressed Sequence Tags (ESTs) were selected for cDNA microarray construction.  Twenty control spots (Universal ScoreCard, GE Healthcare, USA) were included in the probes set.
11. All the probes were spotted onto GAPS-II glass slides (Corning) using the OmniGrid Accent microarrayer (Genomic Solutions).
12. The spotted cDNA microarray was cross-linked with UV at 1200 mJ/cm2 and stored in a desiccator.
13. The quality of spotted cDNA microarray was assessed by PARAGON DNA Microarray QC Stain Kit (Invitrogen)


title: Mus Musculus Mm27k_7M Array

status: Public on Jun 20 2007

city: New York

first: Leslie

last: Rogler

state: NY

address: 1300 Morris Park Ave

department: Liver Research Center/ Department of Medicine

institute: Albert Einstein College of Medicine

description: The cDNA  microarrays used in this study were obtained from the Albert Einstein College of Medicine Functional Genomics Facility (http://www.aecom.yu.edu/cancer/new/cores/microarray/default.htm). 27400 sequence verified mouse clones were spotted in each array. The clones are from 3 sources: the 8968 clones in the MGEM1.0 plates from Incyte, the 14208 clones in the MNCI-V1 plates from NCI (see http://lgsun.grc.nia.nih.gov/cDNA/15k.html), and the 4224 clones in the MIMP-V1 plates originally from Research Genetics. The spatial arrangement of the M7 series of this array differs from the previous Mm27K arrays.

first: Dirk

last: Nierhoff

first: Lauretta

last: LeVoci

last: Shafritz


title: IGIB Hs19Kv8

city: Delhi

first: Anjali

last: Verma

state: Delhi

address: Mall road

department: Structural Biology and Genome Informatics Division

country: India

institute: Institute of Genomics and Integrative Biology

manufacturer: The UHN Microarray Centre,Toronto, Canada

manufacture_protocol: Arrays were processed following Corning's protocol.


title: CEA/UWash Yeast Low Density ORF arrays

status: Public on Jun 14 2007

city: Seattle

first: Kenneth

last: Dombek

address: 1959 Pacific St. N.E.

department: Biochemistry

institute: University of Washington

description: This low density platform consists of two slides which together cover the entire yeast transcriptome. Two identical grids of genes were adjacently deposited on each slide.

manufacturer: Center for Expression Arrays, University of Washington, Department of Microbiology, Seattle WA

first: Bumgarner

last: Roger

manufacture_protocol:
1.  Each yeast ORF sequence was amplified from S288C genomic DNA by PCR. The forward primer sequence begins at the start codon and the reverse primer sequence begins at the stop codon of each ORF. The resulting PCR products were full-length ORF DNAs.
2.  PCR products were purified, dried, suspended in 50% DMSO, and deposited on 75- by 25-mm type VII coated glass microscope slides from AP Biotech using a Molecular Dynamics Generation III microarray spotter (Sunnyvale, CA).
3.  After the spotting, the microarrays were air dried, cross-linked at 450 mJ, and stored dessicated under nitrogen until needed.


title: Bauer Center for Genomics Research_Saccharomyces cerevisiae 70mer array, Hartl Lab

status: Public on Jun 01 2007

city: Cambridge

first: Christian

last: Landry

address: 16 Divinity avenue

department: OEB

institute: Harvard University

description: Produced and printed at the Bauer Center for Genomics Research, Harvard University. 70-mer oligonucleotides available through Operon.

manufacturer: Produced and printed at the Bauer Center for Genomics Research, Harvard University. Oligonucleotides available through Operon

middle: R

manufacture_protocol: Refer to Townsend, Cavalieri and Hartl 2003, PMID: 12716989: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=search&term=12716989


title: URGV Arabidopsis thaliana 25K CATMA_v2

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

institute: INRA

organism: Arabidopsis thaliana

description: Corning Ultra-GAPS (TM) slides are spotted with 64 pins (8x8) therefore the spotted area is divided into 3 metablocks, each containning 64 blocks of 144 spots (12x12). The array contains 24576 Gene Specific Tags (GST)

first: Jean-Pierre

last: Renou

first: Ludivine

last: Taconnat

first: Vincent

last: Thareau

first: Pierre

last: Hilson

manufacture_protocol:
A.thaliana genes were predicted with Eugene software (Foissac S. et al., Nucleic Acids Res., 2003) and gene-specific sequence tags were automatically designed (Thareau et al. Bioinformatics, 2003 Nov 22). Two rounds of PCR were performed and PCR products were finally purified and dissolved in 50% DMSO in TE at concentrations ranging between 50-200ng/ul and re-arrayed in 1536 microtiter plates. The pins are washed in 0.1% SDS at 50 °C then three times in bi-distilled water. Spotter settings are 45-55% humidity, and a pitch = 180 um. The room temperature is set between 19 and 21 degrees Celsius and below 40 % humidity. The microtiter plates are placed in the biobank. The four trays are cleaned and 100-120 slides placed on them (30 slides per tray). The spotting lasts 25 hours. The slides are stored in the dark in a dry-cabinet for 3 days and UV-cross-linked at 300 mJ. After crosslinking, the slides are stored in the dark in a dry-cabinet.
24576 Gene Specific Tags (GST)


title: CEA/UWash Yeast High Density ORF array


title: Scoelicolor_UMN_Def_v1.0

city: Minneapolis

first: Karthik

middle: P

last: Jayapal

state: MN

address: 421 Washington Ave SE

institute: University of Minnesota

organism: Streptomyces coelicolor

manufacturer: University of Minnesota - Chemical Engineering and Materials Science - Hu lab

first: Wei

last: Lian

first: Sarika

last: Mehra

manufacture_protocol:
The following text is taken from the authors' previous publication - Mehra et al., "A framework to analyze multiple time series data: a case study with Streptomyces coelicolor", J Ind Microbiol Biotechnol, 2006 Feb;33(2):159-72.
"A whole genome cDNA microarray was constructed for
S. coelicolor. Gene-specific probes with an average
length of 500 bp were designed based on the genomic
sequence database at Sanger Center to represent the
7,825 genes. The primers to amplify these probes were
designed to be 20 bp in length with a melting temperature
around 62 deg C. An iterative primer/probe design
process was adopted. The primers were first Blasted
against the entire genome to check for the specificity to
the corresponding genes. The probe sequences resulting
from these primers were also blasted against the entire
genome to check for possible cross-hybridization with
sequences other than the corresponding gene. Any primer
pair that may give rise to a potentially croshybridizing
probe sequence was redesigned with alternate
coordinates. This probe checking-redesign process
minimized the possibility of cross-hybridization between
a probe and other cDNA species. For some highly
homologous genes, a unique probe was not attainable
and a multigene probe was used. A multigene probe was
designed in such cases. 7,581 genes were successfully
amplified and spotted on the microarray. The microarray
was fabricated on poly-L-lysine slides with duplicate
spots for each probe."


title: URH-TALL_Bovine_Operon V1.1_1

status: Public on Feb 21 2007

city: St Genes-Champanelle

first: Christine

last: Leroux

address: Centre INRA de Theix

department: PHASE

first: Séverine

last: Ollier

first: Lidwine

last: Trouilh

first: Laurence

last: Bernard

first: Muriel

last: Bonnet

first: Yves

last: Chilliard

manufacture_protocol: The Operon Bovine Genome Oligo Set V1.1, which contains 8,329 70-mer oligonucleotides representing 8,329 genes from the Bos taurus genome (http://www.operon.com/arrays/oligosets_Bovine.php), completed with 50 genes chosen for their implication in mammary metabolism, was spotted in duplicate on UltraGAPS Coated Slides (Corning B.V. Life Sciences) at the Biochips platform of the Génopole Toulouse Midi-Pyrénées. Details can be found at http://biopuce.insa-toulouse.fr/protocoles.php#array_prep.


title: The Medicago truncatula Genome Oligo Set Version 1.0 Microarray

status: Public on Mar 08 2007

city: Ithaca

first: Maria

middle: J.

last: Harrison

address: Tower Road, Cornell Campus

institute: Boyce Thompson Institute for Plant Research

organism: Medicago truncatula

manufacturer: The Galbraith lab at the University of Arizona (Tucson, AZ).

first: Jinyuan

last: Liu

first: Ignacio

last: Maldonado-Mendoza

first: Melina

last: Lopez-Meyer

first: Foo

last: Cheung

first: Christopher

last: Town

manufacture_protocol:
The Medicago Genome Oligo Set Version 1.0 (Qiagen Operon, Alameda, CA) includes 70-mer oligonucleotides representing 16,086 M. truncatula tentative consensus sequences (TCs) from The Institute of Genome Research (TIGR) Gene Index Database (www.tigr.org/tdb/tgi/mtgi/) MtGI Release 5.0 as well as both positive and negative controls. Details of this oligo set are available at http://oligos.qiagen.com/arrays/omad.php. The oligos were spotted in 3x SSC onto Superamine (Telechem) glass slides by the Galbraith lab at the University of Arizona (Tucson, AZ). A single array element was printed per oligo. After printing, slides were baked at 80°C for 1 hour and stored at RT.
Keywords = Medicago
Keywords = legume


title: NSF Rice Oligonucleotide Array 45K (23K A)

status: Public on Aug 17 2006

city: Rockville

first: Jia

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

manufacture_protocol: Visit http://www.ricearray.org


title: Arizona Aphid/Buchnera 1

city: Princeton

first: Gregory

middle: K.

last: Davis

state: NJ

address: 106A Guyot Hall, Washington Road

department: Ecology and Evolutionary Biology

institute: Princeton University

organism:
Buchnera aphidicola
Escherichia coli
Acyrthosiphon pisum

description: Dual-genome microarray for the pea aphid, Acyrthosiphon pisum, and its obligate bacterial symbiont, Buchnera aphidicola.

first: Nancy

last: Moran

first: David

middle: L

last: Stern

first: Wayne

last: Hunter

first: Ryan

last: Sprissler

first: Phat

last: Dang

middle: K

first: Alex

last: Wilson

first: Jennifer

last: Brisson

manufacture_protocol: Genes were arranged in duplicate spots on slides, with Buchnera genes grouped into the first and second of 24 subarrays.  In addition to spot duplication, the entire set was printed twice on each slide with the result that each gene was represented by four spots in total.


title: NHGRI_Mouse20k_cDNA_P1_18

city: Bethesda

last: Pan

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

first: Settara

last: Chandrasekharappa

first: Abdel

last: Elkahloun

first: Yidong

last: Chen

first: Youngmi

last: Ji

manufacture_protocol: Spotted cDNA


title: URGV Arabidopsis thaliana 25K CATMA_v2.1

first: Frederique

last: Bitton

description:
Corning Ultra-GAPS (TM) slides are spotted with 64 pins (8x8) therefore the spotted area is divided into 3 metablocks, each containning 64 blocks of 144 spots (12x12).
The arrray contains 24576 Gene Specific Tags (GST) and 615 Chloroplastic and Mitochondrial Tilling array probes.

first: Jean-Pierre

last: Renou

first: Ludivine

last: Taconnat

first: Vincent

last: Thareau

first: Pierre

last: Hilson


title: Human miRNA 2k custom array

status: Public on Apr 20 2007

city: Toronto

first: Tomas

last: Babak

address: 112 College St

department: Banting and Best Department of Medical Research

institute: Best Institute

description: Agilent, custom inkjet. Antisense probes corresponding to mature miRNA sequences, concatenated to 60 nt.

first: Jim

last: Huang

first: Timothy

middle: W

last: Corson

first: Gordon

last: Chua

last: Hughes

first: Benjamin

last: Blencowe

first: Brendan

last: Frey

first: Quaid

last: Morris

manufacture_protocol: Inkjet


title: Affymetrix GeneChip Mouse Genome 430 2.0 Array [CDF: Mm_ENTREZG_8]

status: Public on Mar 19 2007

city: Basel

first: Robert

last: Ivanek

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description:
CDF file was created by Microarray Lab at the Molecular and Behavioral Neuroscience Institute at the University of Michigan.
After probe sequences are BLASTed against the latest UniGene Build and genome sequence, a series of filtering and grouping criteria are applied for different CDF files. For the CDF file based on Entrez Gene:
A probe must hit only one genomic location;
Probes that can be mapped to the same target sequence in the correct direction are grouped together in the same probe set;
Each probe set must contain at least three oligonucleotide probes and probes in a set are ordered according to their location in the corresponding exon;
For detailed description please see the paper.

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

manufacture_protocol: This identical to GPL1261 but a custom cdf environmnet was used to extract data. The cdf can be found at the link below.


title: Affymetrix GeneChip Human Genome U133 Array Set HG-U133A [CDF: Hs133A_Hs_UG_3]

status: Public on Nov 14 2006

city: Ann Arbor

first: Fan

last: Meng

address: 205 Zina Pitcher Place

department: Psychiatry

institute: U of Michigan

description: This identical to GPL96 but a custom CDF environment was used to extract data. We used CDF: Hs133A_Hs_UG_3. The CDF can be found at the Web link below.

first: Jun

middle: Z

last: Li

first: Larisa

last: Tsavaler

first: Simon

last: Evans

first: Prabhakara

middle: V

last: Choudary

first: Hiroaki

last: Tomita

first: Marquis

last: Vawter

first: David

last: Walsh

first: Vida

last: Skokoohi

first: Tisha

last: Chung

first: William

middle: E

last: Bunney

first: Edward

middle: G

last: Jones

first: Huda

last: Akil

first: Stanley

last: Watson

first: Richard

last: Myers

relation: Alternative to: GPL96 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site