title: UGI Human 14112 V2.0

status: Public on Sep 25 2008

city: Shanghai

first: Mei

last: Jiang

address: Handan Road

department: Institute of Genetics

country: China

institute: Fudan University

organism: Homo sapiens

technology: spotted DNA/cDNA

distribution: non-commercial

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 14061 sequences including full-length and partial cDNAs representing novel, known, and control genes provided by United Gene Holdings Group Co., Ltd. Genes represented in the arrays were identified with high similarity to the sequences in Unigene database of NCBI by performing Blast (http://www.ncbi.nlm.nih.gov/).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.


title: USITB Escherichia coli W3110 9.2k array v 1.0

status: Public on Sep 23 2008

city: Stuttgart

first: Karin

last: Lemuth

address: Allmandring 31

country: Germany

institute: Universität Stuttgart

organism: Escherichia coli str. K-12 substr. W3110

technology: spotted oligonucleotide

description: epoxy coated

manufacturer: University of Stuttgart, Institute of Technical Biochemistry, Allmandring 31, 70569 Stuttgart

first: Rolf

middle: D

last: Schmid

manufacture_protocol:
Whole genome E. coli K12 DNA-microarrays were printed using the Microgrid II robot of Biorobotics (now Genomic Solutions, Huntingdon, United Kingdom) by spotting oligonucleotides (50mer, dissolved in buffer A; E. coli K-12 V2 Oligo set from MWG, Ebersberg, Germany) representing all E. coli K-12 ORFs on epoxy-coated glass slides (MWG) as duplicates. Oligonucleotides were delivered in 12 384 polypropylene microtiter plates with F-bottom (Greiner, Frickenhausen, Germany). For details on probe design please see the manufacturer’s protocol (http://ecom2.mwgdna.com/services/array/download.tcl). Tungsten microarray split pins (PT 3000 – Point Technologies, Inc., Colorado, USA) were used for spotting. 27 slides were manufactured per printing process. 3 slides were discarded as so called “pre-spot slides”, 24 slides were used for microarray experiments.
Printing was performed using the following conditions (Software: TAS Application Suite V. 2.6.0.2):
•	Tool: 4x4 configuration
•	Group (Tool Type): 2. Micro Spot (384 Well)
•	Source Action: dwell/remove one lid at a time
•	60 spots / source visit, 10 of them were pre spots
•	soft touch distance: 1.5 mm
•	humidity control: minimal: 58%; target humidity: 63%
•	washing conditions: 3 x at the beginning, 5 x at the end, bath 1 two seconds, bath 2 three seconds (2 mm wiggle); washing solution: ddH2O.
•	all replikates were printed on the first slide first.
After printing, microarrays were incubated in a hybridization oven (Whatman Biometra) at 42°C over night together with a ddH2O filled petri dish covered with looped aluminium foil. Afterwards, microarrays were washed stirring constantly with 0.2 % SDS solution (2 min), two times in ddH2O (1 min) at room temperature and afterwards incubated in the hybridization oven (Whatman Biometra) for 20 min in ddH2O at 50°C. Microarrays were nitrogen dried and stored in a dark and dry place until hybridization.
Quality control: staining with SYBR SafeTM DNA Gel Stain (MolecularProbes) by incubation of the printed area with 750 µL of the solution and incubation for 3 min at room temperature. Arrays were washed four times with 0.5 x TBE-Puffer (5 x stock solution: Tris-Borat 0.45 M; EDTA 0.01 M) and scanned afterwards.
For data analysis, a “gal file” was produced using the software TAS application suite version 2.6.0.2 from Genomic Solutions.


title: UGI Human 14112 V1.0

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 14061 sequences including full-length and partial cDNAs representing novel, known, and control genes provided by United Gene Holdings Group Co., Ltd. Genes represented in the arrays were identified with high similarity to the sequences in Unigene database of NCBI by performing Blast (http://www.ncbi.nlm.nih.gov/).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 cancerous samples and normal samples were labeled with Cy5-dUTP. The common reference samples, a pool of RNA from mixed human embryo tissues,were labeled with Cy3-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: SAGE:26:NlaIII:Cicer arietinum

status: Public on Sep 17 2008

last: GEO

country: USA

organism: Cicer arietinum

technology: SAGE NlaIII

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

distribution: virtual


title: LC Sciences_miRNA_Human_v9(1).1

status: Public on Sep 26 2008

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

country: Spain

institute: University of Navarra/ Clínica Universidad de Navarra

technology: in situ oligonucleotide

description: This platform contain probes for the human 470 miRNA described in miRBase v9.1

distribution: custom-commercial

first: Izidore

middle: S

last: Lossos

manufacture_protocol: Microarrays designed for genome-wide microRNA expression profiling and built on the flexible and powerful µParaflo® microfluidic on-chip synthesis platform. The current probe content comes from version 9.1 of the miRBase sequence database. This version has been updated (see GPL6668)


title: LC Sciences_miRNA_Human_v10(1).0

description: This microarray contains probes for the 711 human miRNAs in miRBase release 10.0.

manufacture_protocol: Microarrays designed for genome-wide microRNA expression profiling and built on the flexible and powerful µParaflo® microfluidic on-chip synthesis platform. The current probe content comes from version 10.0 of the miRBase sequence database. This version has been updated (see GPL6668)


title: EcoArray Fathead Minnow 8 x 15K Microarray v1.0

status: Public on Sep 27 2008

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

organism: Pimephales promelas

description: This microarray contains 60-mer probes for 15,208 fathead minnow sequences.  Because there are eight arrays per slide, this is the most economical array.  This microarray is 100% ANNOTATED.  Genes included on this array matched the Nonredundant database with an evalue <E-05, or the Nucleotide database with evalue <E-06.  All duplicate accession numbers were removed.  The genes are part of a wide variety of biological pathways and processes including: reproduction, cell communication, metabolism, homeostasis, and others.  This array is perfect for those researchers who do not want to worry about “no hits.”

middle: J

first: Patrick

middle: M

last: Larkin

manufacture_protocol: EcoArray selected Agilent Technologies as the manufacturer of our microarrays for environmental toxicology.  Agilent Technologies is a leading supplier of genomics and proteomics products.  Using their SurePrint inkjet deposition of in situ synthesized 60-mer oligonucleotides, all microarrays are manufactured on superior quality 1” x 3” (24.2 mm x 76.2 mm) treated glass slides for overall excellent performance.  See their website for details: http://www.agilent.com.


title: Compugen/Sigma-Genosys_Drerio_16399

status: Public on Sep 20 2008

city: Berkeley

first: Aaron

last: Garnett

state: CA

address: 555 LSA

institute: UC Berkeley

organism: Danio rerio

manufacture_protocol: The commercial Zebrafish oligo library from Compugen/Sigma-Genosys consists of 16,399 oligos (65nt) representing 16,288 unique gene clusters. The oligos are modified with a 5' amino C6 linker. The library includes 172 zebrafish beta-actin oligos distributed over the entire library as internal controls (approximately 4 per 384-well plate). Amersham Code Link activiated glass silides were prepared using a hydrophillic polymer containing N-hydroxysuccinimide ester groups covalentely attached to the silane base coat by the vendor. The oligos were resuspended in 50mM phosphate buffer, pH 8.0, at 20mM concentration. The individual oligo probes were printed on Code Link activated slides under 45% humidity by Gene Machine Omni Grid 100 Microarrayer in 4 X 12 pin configuration and 20 x 20 spot configuration of each subarray. The spot diameter was 100um and distance from center to center was 200um. The printed Zebrafish microarrays were further immobilized via convalent coupling methods at 70% humidity overnight. Samples were hybridzed after additional 100mM Taurine/Bicine blocking and 4X SSC/0.1% SDS washing steps.


title: Oligoarray Muenster-Hematology, Version 2

status: Public on Sep 16 2008

city: Muenster

first: Carsten

last: Müller-Tidow

address: Domagkstrasse 3

institute: University Hopital Muenster

description:
- Total of 33696 spots
- Each of the 11000 genes is covered by ~3 different oligos (differing in their distance from the transcriptional start site (TSS), i.e., between ~1000 upstream and ~+500 downstream of the TSS)

manufacturer: CeBiTec, Department for Genetics, University of Bielefeld, Germany

manufacture_protocol: Oligonucleotides (25 µM) in 1.5 M betaine, 3xSSC (1xSSC is 0.15 M sodium chloride, 0.015 M sodium citrate) were printed onto Nexterion Slide E (Schott AG, Mainz, Germany) using the MicroGrid II 610 spotter (BioRobotics, Cambridge, UK) equipped with 48 SMP3 stealth pins (TeleChem International, Sunnyvale, CA, USA) delivering ~600 pl per spot. The spotting procedure was performed at 22°C, rel. humidity 40%. DNA was cross-linked to the surface by incubation of the arrays for 2h at 85 °C. (Oligonucleotides were purchased from Operon Biotechnologies GmbH, Nattermannallee 1, 50829 Koeln, Germany)


title: TIGR PFGRC Aspergillus nidulans version 2 array designated primarily based on strain FGSC A4

city: Sendai

first: Daisuke

last: Hagiwara

state: Miyagi

address: 6-6-10 Aoba Aramaki

department: New Industry Creation Hatchery Center

country: Japan

institute: Tohoku university

organism: Aspergillus nidulans

description: This set includes 11481 oligonucleotides (ss oligo 70 mer), has 23962 spots (2x oligo replicates) distributed in 48 blocks.

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

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


status: Public on Sep 30 2008

city: Zuerich

first: Stefan

last: Baenziger

address: Raemisstrasse 100

department: Department of internal Medicine

country: Switzerland

institute: University Hospital Zurich

organism: Mus musculus

manufacture_protocol:
Mouse Toll-Like Receptor Signaling Pathway PCR Array: PAMM-018
The Mouse Toll-Like Receptor Signaling Pathway Microarray RT² Profiler™ PCR Array Array profiles the expression of 84 genes related to TLR-mediated signal transduction. This array includes members of the TLR signaling family as well as key mediators of the TLR signaling pathway including adaptors and proteins that interact with toll-like receptors. Effectors of TLR signaling are represented. Members of the NFKB, JNK/p38, NF/IL6, and IRF signaling pathways downstream of TLR signaling are also included on this array. Using real-time PCR, you can easily and reliably analyze expression of a focused panel of genes related to TLR-mediated signal transduction with this array.


title: CapitalBio human/mouse/rat non-coding RNA microarray

status: Public on Sep 21 2008

city: Guangzhou

first: Jian-Rong

last: Yang

address: No. 74, Zhongshan 2nd Road

institute: Sun Yat-sen University

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

distribution: commercial

first: JianQing

last: Zhao

manufacture_protocol:
Mature miRNA sequences were downloaded from the miRNA Registry (http://microrna.sanger.ac.uk; miRBase Release 7.0, accessed June. 2005). We collected 347 human/mouse/rat mature miRNA sequences in the microarray. All miRNA probe sequences were designed to be complementary to the full-length mature miRNA. 122 predicted miRNA sequences (i.e., Nature PREDICTED_MIR* array features in the Description column) from a published reference (Xie et al., Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature. 2005 Mar 17;434(7031):338-45) were also included. The miRNAs described as "Cell_predict*" probes were designed after the predicted human miRNAs from this paper: Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RHA, Cuppen E: Phylogenetic shadowing and computational identification of human microrna genes. Cell 2005, 120:21-24. Sequences of human tRNA and rRNA shorter than 200nt were downloaded from Rfam. And as for the 281 snoRNA and other non snRNA shorter than 200nt, they were downloaded from snoRNA-LBME-db (http://www-snorna.biotoul.fr/index.php) and NONCODE (http://noncode.bioinfo.org.cn/) respectively. After removing the redundancy sequences, we designed 2115 probes complementary to these non-coding RNAs.
In addition, we designed 8 short oligos (i.e., Y2, Y3, Zip*) possessing no homology with all existed RNA sequence and produced their corresponding synthetic miRNAs by in vitro transcription using Ambion's miRNA Probe Construction kit (Cat#. 1550). We spike various amounts of synthetic miRNAs into the interrogated RNA samples.
To facilitate probe immobilization on aldehyde modified glass slides, the probe sequence were concatenated up to 40 nt and modified with 5'-amino-modifier C6. Oligonucleotide probes were synthesized at MWG Biotech. Company and dissolved in EasyArray(TM) spotting solution (CapitalBio Corp.) at 40 uM concentration. Each probe was printed in triplicate using a SmartArrayTM microarrayer (CapitalBio Corp.); the data table below corresponds to the condensed representation of the array.


title: PHAC_Booth_Lab_miRNA_microarray_v.2006

city: Winnipeg

first: Reuben

last: Saba

state: Manitoba

address: 1015 Arligton Street

department: Medical Microbiology

country: Canada

institute: University of Manitoba: Public Health agency of Canada

manufacturer: Public Health Agency of Canada microarray core facility

manufacture_protocol: A microarray containing oligonucleotide probes complimentary to published miRNAs was constructed. These probes consisted of all the non-redundant miRNA sequences from the miRNA registry (Release 8.2). The arrays were spotted in-house on Corning® epoxide coated slides; Probes were spotted in duplicate and additionally two full arrays were printed per slide. The probes were in sense orientation relative to the mature miRNAs and thus complimentary to either the cDNA or aRNA that would be derived from the mature miRNAs. The probes also had a 15 nucleotide long poly(T) tract at the 5'end for steric distancing from the array surface. Each probe was printed in duplicate and the signal intensities for averaged.


title: University of Minnesota multi-species miRNA 480

city: Minneapolis

first: Xiaoxiao

last: Zhang

address: 312 Church St. SE

institute: University of Minnesota

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

manufacturer: Biomedical Genomics Center Microarray Facility at the University of Minnesota

manufacture_protocol: A miRNA probe set was purchased from Invitrogen, which was designed based on the Sanger miRBase Sequence Database, Release 9.0.  The set contains approximately 1,140 oligonucleotides of 34 to 44 nt long as probes.  They are complementary to C. elegans, Drosophila, zebrafish, mouse, rat, and human miRNAs, and also include a number of internal and negative control probes.  The oligonucleotides were dissolved in 3 x SSC and quadruply printed on Corning® GAPSTM II coated slides  using a BioRobotics Microgrid II spotter


title: VIB Bacillus thuringiensis 1K VIB_Bt_1K_2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

organism: Bacillus thuringiensis

description:
The array design contains 784 features printed in a layout of 4 meta rows and 4 meta columns; consisting out of 7 rows and 7 columns per block. The array measures the expression of 180 unique sequences, spotted with four replicates. A set of 64 spots remained empty.
The platform data table reflects a condensed representation of the array. The complete array layout file representing the replicated features as well is linked as a supplementary file.

first: Géraldine

last: Van der Auwera

first: Paul

last: Van Hummelen

manufacture_protocol:
Equipment:
1. Microgrid II (Genomic Solutions, Huntingdon, United Kingdom).
2. 384 microtiter plates (Genetix)
3. 16 MicroSpot quill pins - 10K (cat# BR001489, Genomics Solutions, UK)
4. Codelink slides (cat#: 30001100, GE Healthcare).
Printing 2 arrays of 4x4 blocks on 1 microscope slide:
1.  All oligos were obtained from Sigma Genosys, all at a concentration of 50µM.  Oligos were diluted with a 250mM Na-Phosphate buffer plus 0.000250% sarcosyl to a final concentration of 25 µM.  Re-array the oligos in 384 microtiter plates.
2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 190 um, row pitch = 190 um; Humidity 55-60%; 101 spots per source visit.
3. Make sure room temperature is between 20-24 degrees Celsius.
4. Place microtiter plates in the plate hotel with A1 in front left corner.
5. Place 25 slides on the slide-deck.
6. After spotting, incubate the slides in humid chamber with saturated NaCl for min 24 hours.
7.  Slides were treated with 1% NH4OH solution on a shaker for 5 min, followed by 0.1% SDS for 5 min. The slides were rinsed in MQ-water, placed in 95°C water bath for 2 min, and
then at -20°C for 1 min. The slides were rinsed again twice in MQ-water and finally dried by centrifugation (1min at 1000rpm). These slides were kept in the incubator at 24°C.


title: ABI 1700 Genome Expression Human Microarray

city: Busan

first: Young

middle: Hyun

last: Yoo

address: 3-1 Dongdaesin-Dong

department: Dept Anatomy and Cell Biology

country: South Korea

institute: Dong-A Univ Coll Med

description:
The Applied Biosystems Gene expression Array system:
Each probe constructed based on Celera Genomics data and public RefSeqs data

manufacture_protocol: see manufacturer's web site


title: University of Minnesota nematode, fruit fly, zebrafish, mouse, rat, and human miRNA array 1K version 1

manufacture_protocol: A miRNA probe set was purchased from Invitrogen, which was designed based on the Sanger miRBase Sequence Database, Release 9.0.  The set contains approximately 1,140 oligonucleotides of 34 to 44 nt long as probes.  They are complementary to C. elegans, Drosophila, zebrafish, mouse, rat, and human miRNAs, and also include a number of internal and negative control probes.  The oligonucleotides were dissolved in 3 x SSC and quadruply printed on Corning® GAPSTM II coated slides  using a BioRobotics Microgrid II spotter. Full platform provided as supplementary file.


title: EcoArray Fathead minnow 44K v1.0

description:
Our fathead minnow(FHM) microarray was constructed by first compiling all known gene sequences for fathead minnows: 250,000 ESTs published by the JGI plus our own proprietary sequences obtained from suppression subtractive hybridizations and normalized library construction. We then assembled these genes to discern ~47,000 non-overlapping unique sequences (contigs and singlets). Homology searches (Blast) were performed on these sequences in order to provide annotation (gene name) and ontology (gene function) information where present. A total of 21,495 contigs were assembled. Probes were designed using Agilent’s web-based E-Array program.
The content of our FHM microarray is located on our web site and contains 21,495 contigs (probes spotted in duplicate) of which:
• 17,588 are annotated and represented by one sense or antisense probe.
• 1,331 are annotated and represented by one reverse complement for the probe.
• 2,576 are poorly annotated (e-value >0.0001) and represented by one probe.

first: Nancy

last: Denslow

manufacture_protocol: EcoArray selected Agilent Technologies as the manufacturer of our microarrays for environmental toxicology. Agilent uses SurePrint inkjet deposition of in situ synthesized 60-mer oligonucleotides and superior quality 1” x 3” (24.2 mm x 76.2 mm) treated glass slides for overall excellent performance of their microarrays. This process minimizes variability across each production lot (batch to batch) and provides the highest consistency in slide-to-slide comparisons. These glass slide microarrays are designed for either a one- or two-color (cyanine-3 and cyanine-5) labeling reaction, the most reliable and sensitive methods for detecting differentially expressed genes. Agilent’s Feature Extraction software, when used with a high-resolution (5μm) scanner, provides QA metrics for each individual microarray, ensuring quality results.  Each slide contains four individual 44K arrays.


title: Nimblegen 385K pig array CGH

status: Public on Sep 15 2008

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

organism: Sus scrofa

description:
The probes on the array covered part of the chromosomes 4, 7, 14 and 17 for the Sus Scrofa preliminary assembly version 3, August 2007. The sequence data were produced by the Sus Scrofa Sequencing Group at the Sanger Institute.
Detailed information about probe design is available in the Nimblegen technical note (see Web Link).

first: Joao

last: Fadista

first: Lars-Erik

last: Holm

first: Bo

last: Thomsen

first: Christian

last: Bendixen

manufacture_protocol: Maskless array synthesis was used to construct isothermal arrays. Probes were selected with a minimum probe spacing of 285 bp and the resulting array had a median probe spacing of 409 bp. Probes were synthesized using an isothermal format (Tm = 76°C) and varied in length from 50 to 75 bp.


title: SKLMVGE_TR_FC_V1.0

city: Beijing

first: Qi

last: Jin

state: Beijing

address: BDA Rong Jing east street No.6, 3rd floor

department: National Institute for Viral Disease Control and Prevention

institute: Chinese Center for Disease Control and Prevention

organism: Trichophyton rubrum

description: In this chip there were two fields named A and B, they described the upper and lower part (location) of the chip. Each field contains 10,000 spots. The spots in field A are same with those in field B.

manufacturer: State Key Laboratory For Molecular Virology and Genetics Engineering Beijing,China

manufacture_protocol:
Materials are transferred from microtiter plate wells to the slide surface by an automated print head
The cDNA libraries were constructed following the protocols of the SUPERSCRIPTTM Plasmid System with GATEWAYTM Technology for cDNA Synthesis and Cloning (Invitrogen).  The cDNA plasmids were isolated by the Millipore method using MADV filter plates.  Sequencing was performed with a generic T7 primer located 5' upstream of the inserted segments, following the protocol for the PRISM Big Dye terminator kit on an ABI 3700 automated sequencer(Applied Biosystems, Foster City, CA).
EST processing pipeline and annotation
Phred quality assessment and computational analysis were carried out as described previously [4].
cDNA microarrays
PCR fragments used for printing the microarray chip were amplified from the ESTs library in 96-well plates using vector-PCR amplification with T7 and SP6 universal primers.  PCR products were analyzed on gels to confirm the success of the reactions and were subsequently purified using MultiScreen-PCR plates (Millipore Corporation, Bedford, USA).  Purified PCR products were resuspened in 12 ¦Ìl of spotting solution containing 50% DMSO to produce the microarrays.  A set of microarrays containing a total of 10,000 spots (including 8,997 clones in the form of PCR products, and 1,003 controls in each block, including blank, negative, and positive controls) were spotted in duplicated onto coated glass slides (Corning, NY) with a Cartesian arrayer.


title: cDNA microarray chips (Human 19K version 8), Latner Thoracic Surgery Lab, University Health Network Microarray Centre

city: Toronto

first: Masaki

last: Anraku

state: Ontario

address: 101 College Street, TMDT 2-816

department: Surgery

institute: Toronto General Research Institute

first: Shaf

last: Keshavjee

first: David

last: Kelvin

first: Thomas

middle: K

last: Waddell

first: Mingyao

last: Liu

first: Mark

last: Cameron

first: Tamara

last: Arenovich

first: Marc

last: de Perrot

first: Andrew

middle: F

last: Pierre

first: Masaaki

last: Sato

first: Marcelo

last: Cypel

manufacture_protocol: Human ss-H19K8, Arrayer used - SDD26, Slide type - Corning ultraGAP


title: Lactobacillus reuteri F275 11K 60-mer array, Version 1

city: Amsterdam

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

country: Netherlands

institute: Vrije Universiteit Amsterdam

organism: Limosilactobacillus reuteri subsp. reuteri F275

description: This array contains 60-mer probes that are designed for L. plantarum strain F275. The sequence of this organism is present in public databases, Acc. Nr. CP000705 (NC_009513).

first: Filipe

last: Santos

first: Jeroen

last: Hugenholtz

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


title: Porcine oligonucleotide microarray version 4 (POM4)

city: Copenhagen

first: Kerstin

last: Skovgaard

address: Bülowsvej 27

department: Immunology and Parasitology

institute: National Veterinary Institute

manufacturer: National Veterinary Institute, DTU, Denmark

first: Shila

last: Mortensen

first: Peter

last: M. H. Heegaard

manufacture_protocol:
1. This microarray is holding 384 different 60-70mer oligonucleotide probes representing more than 200 different immune related porcine genes and 8 synthetic array control oligonucleotide probes (ArrayControl)
2. The porcine target sequences used for oligo design were obtained from public databases (NCBI, National Center for Biotechnology Information, GenBank (http://www.ncbi.nlm.nih.gov/) and the Gene Index Project (http://compbio.dfci.harvard.edu/tgi/tgipage.html)
3. Probes were designed using Oligowiz (http://www.cbs.dtu.dk/services/OligoWiz2/)
4. Probes were synthesized at DNA Technology A/S (Århus, Denmark)
5. Probes were diluted to 50uM in 50% DMSO while array controls were diluted to 30uM in 50% DMSO
6. Probes were spottet on Corning UltraGAPS Coated Slides using a VersArray Chip Writer Pro, software version 2.1.1., equipped with 8 SMP3 pins (TeleChem International, Inc)
7. Oligonucleotides were spottet in tripilcate in 8 sub-arrays each holding 10 x 15 spots, these 8 sub-arrays were repeated 3 times vertically on the slide.
8. After printing , slides were dried, UV cross-linked and stored in a vacuum desiccator at room temperature until use.
9. Prior to hybridization the slides were pre-hybridized according to manufactures protecol


title: Histone TAG Array 06A

status: Public on Sep 19 2008

city: Baltimore

first: Daniel

last: Yuan

state: MD

address: 733 N. Broadway, Suite 351

department: Molecular Biology and Genetics

institute: Johns Hopkins Univ School of Medicine

organism: Saccharomyces cerevisiae

description:
Microarray repurposed for profiling a comprehensive barcoded library of synthetic histone mutations expressed in yeast.
Each entry is represented by five replicates each of UpTag and DnTag sequences in a microarray originally designed for use in profiling the Yeast Knockout strain collection (Pubmed ID 15994458).
Keywords = histone, synthetic, yeast, tag, barcode

first: Edel

last: Hyland

first: Jef

last: Boeke

manufacture_protocol: in situ synthesis by an inkjet technology


title: Illumina small RNA sequencing

status: Public on Sep 10 2008

city: San Francisco

first: James

middle: Graham

last: Ruby

address: 1700 4th Street QB3 s404

department: Biochemistry

institute: UCSF

technology: other

description: Sequencing was carried out using the 1G Illumina Genome Analyser (Solexa)


title: WIS_Exiqon_miRCURY™ LNA Array (v.8.1)

city: Rehovot

first: reut

last: shalgi

address: Weizmann Institute of Science

country: Israel

institute: Weizmann Institute of Science

description: LNA miRNA microarray

manufacture_protocol: Exiqon_miRCURY™ LNA Array (v.8.1)


title: Populus trichocarpa microarray

city: Gainesville

first: Matias

last: Kirst

institute: University of Florida

organism: Populus trichocarpa

manufacture_protocol: In situ synthesised microarray using "maskless" technology.


title: Zea mays 22K Agilent array, Ver2 - designed by Walbot Lab

city: Stanford

first: John

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

organism: Zea mays

manufacture_protocol: 22,500 60-mer oligo probes were designed from the August, 2003 EST assembly at ZmDB and synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry on glass slides.


title: 454 small RNA sequencing

description: Sequencing was carried out using 454 GS


title: Princeton Biocomplexity Project, BC007 and BC008

status: Public on Sep 12 2008

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Guyot Hall

department: Geosciences

institute: Princeton University

organism:
Phaeodactylum tricornutum
Dunaliella tertiolecta
Chlamydomonas reinhardtii
Pseudochlorella pringsheimii
Asterionellopsis glacialis
Cylindrocystis sp. UTEX 1925
uncultured eukaryote
uncultured Chlorophyta
Haptophyta environmental samples

manufacture_protocol: 70-mer oligonucleotides, spotted using DiRisi type arrayer


title: Small RNA SBS signatures indentified from maize using Illumina's SBS technnology

city: Davis

first: Blake

middle: C.

last: Meyers

address: 451 Health Sciences Dr.

department: UC Davis Genome Center

institute: University of California - Davis

middle: C


title: PHAC_Booth_Lab_miRNA_microarray_v.2005

first: Reuben

last: Saba

manufacture_protocol: A microarray containing oligonucleotide probes complimentary to 557 miRNAs was constructed. These probes consisted of all the non-redundant miRNA sequences from the miRNA registry (Release 5.0). The arrays were spotted in-house on Corning® epoxide coated slides; Probes were spotted in duplicate and additionally two full arrays were printed per slide. The probes were in sense orientation relative to the mature miRNAs and thus complimentary to either the cDNA or aRNA that would be derived from the mature miRNAs. The probes also had a 15 nucleotide long poly(T) tract at the 5'end for steric distancing from the array surface. Each probe was printed in duplicate and the signal intensities for averaged.


title: Nimblegen_HD2_Arabidopsis

city: Los Angeles

first: Steve

middle: E

last: Jacobsen

address: 621 Charles E. Young Dr. South

department: Molecular Cell and Developmental Biology

institute: University of California, Los Angeles

organism: Arabidopsis thaliana

description: The probes were based on TIGR5 Arabidopsis genome, release date 01212004.

manufacture_protocol: please see manufacturer's web site


title: Wheat 8K cDNA microarray version 2 (WA.v2)

city: Albany

first: Debbie

last: Laudencia-Chingcuanco

address: 800 Buchanan Street

department: Western Regional Research Center

institute: USDA-ARS

organism: Triticum aestivum

manufacturer: USDA-ARS, Western Regional Research Center, Genomics and Gene Discovery Research Unit

manufacture_protocol: Laudencia-Chingcuanco et. al. (2007) Plant Molecular Biology 63:651-668


title: UF Nimblegen Populus trichocarpa Array

status: Public on Sep 06 2008

description: Populus trichocarpa 'Nisqually-1'

manufacture_protocol: The 60-mer oligonucleotide probes were designed based on v.1.1 of the P. trichocarpa genome sequence and NimbleGen standard procedures. Briefly, 24-mers tiling each possible 60-mer oligonucleotide were analyzed for sequence similarity to other regions of the genome. Each perfect match of a 24-mer to a segment of the genome was given a score of 1. Because 37 24-mers are required to fully tile a 60-mer, the best possible uniqueness score for a 60-mer probe is 37. In addition, a weighted similarity score that favors probe uniqueness at the core 12 nucleotides was used. A minimum of three unique positions in the core 12 nucleotides were required for the probe to be considered.  Resulting oligonucleotides were subsequently subjected to additional filtering steps that considered self-complementarities, GC/AT content, and homopolymer runs.


title: SWEGENE_BAC_33K_Full

status: Public on Sep 09 2008

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

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

organism: Homo sapiens

description: The 33k tiling BAC Array set contains 33,370 large-insert clones with complete genome coverage. The clone set consists of the 32k BAC clone library (GEO accession GPL4723) with additional clones located in the telomeric regions (Knight SJ et al., Am J Hum Genet 2000) and clones covering microdeletion syndromes (Vissers LE et al., Am J Hum Genet 2003).

first: A

last: Borg

manufacture_protocol: Arrays were produced using amplified genomic DNA targets from BAC clones. Target amplification was performed using degenerate oligonucleotide primed PCR and products were purified by size-exclusion filtration and verified by agarose gel electrophoresis. After purification, products were dried down, recovered in 50% DMSO to a concentration of 500-1000 ng/µl, and printed on amino-silane-coated glass slides (UltraGAPS from Corning) using a MicroGrid2 robot (BioRobotics) equipped with MicroSpot2500 pins (BioRobotics).


title: UWAPG Yeast 6K v1.0

status: Public on Sep 05 2008

city: Madison

first: David

last: Berry

state: WI

address: 3456 Genetics Biotech. Building

department: Laboratory of Genetics

institute: University of Wisconsin: Madison

manufacturer: University of Wisconsin Genome Expression Center

manufacture_protocol: Spotted DNA arrays were made in house using an OmniGrid spotting microarrayer to deposit 70mer oligos representing each yeast open reading frame (Qiagen Yeast Oligos V1.1.1) onto custom made poly-lysine coated glass microscope slides.


title: VIB Bacillus thuringiensis 1K VIB_Bt_1K_1

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

institute: VIB

description:
The array design contains 672 features printed in a layout of 4 meta rows and 4 meta columns; consisting out of 7 rows and 6 columns per block. The array measures the expression of 150 unique sequences, spotted with four replicates. A set of 72 spots remained empty.
The platform data table reflects a condensed representation of the array. The complete array layout file representing the replicated features as well is linked as a supplementary file.

first: Géraldine

last: Van der Auwera

first: Paul

last: Van Hummelen

manufacture_protocol:
Equipment:
1. Microgrid II (Genomic Solutions, Huntingdon, United Kingdom).
2. 384 microtiter plates (Genetix)
3. 16 MicroSpot quill pins - 10K (cat# BR001489, Genomics Solutions, UK)
4. Codelink slides (cat#: 30001100, GE Healthcare).
Printing 2 arrays of 4x4 blocks on 1 microscope slide:
1.  All oligos were obtained from Sigma Genosys and dissolved in H2O to a concentration of 100µM. Subsequently, oligos were diluted with a 156.25mM Na-Phosphate buffer plus 0.00015625% sarcosyl to a final concentration of 20 µM.  Re-array the oligos in 384 microtiter plates.
2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 190 um, row pitch = 190 um; Humidity 55-60%; 123 spots per source visit.
3. Make sure room temperature is between 20-24 degrees Celsius.
4. Place microtiter plates in the plate hotel with A1 in front left corner.
5. Place 25 slides on the slide-deck.
6. After spotting, incubate the slides in humid chamber with saturated NaCl for min 24 hours.
7.  Slides were treated with 1% NH4OH solution on a shaker for 5 min, followed by 0.1% SDS for 5 min. The slides were rinsed in MQ-water, placed in 95°C water bath for 2 min, and then at -20°C for 1 min. The slides were rinsed again twice in MQ-water and finally dried by centrifugation (1min at 1000rpm). These slides were kept in the incubator at 24°C.


title: Cornell-CGEP Tomato 9K v2

city: Rishon Le-Zion

first: Igor

middle: Michael

last: Kolotilin

address: Dereh Ha-Macabim

department: Plant sciences

institute: Volcani inst.

organism: Solanum lycopersicum

manufacture_protocol: Twelve-thousand-eight-hundred-sixty EST clones representing ~8,500 independent tomato loci were inoculated into 384-well plates containing LB+Amp and incubated for 24-48 hrs at 37 oC. Resultant cultures were used to inoculate duplicate PCR reactions, which contained 10 mM Tris-Cl (pH 9.2), 25 mM KCl, 3.5 mM MgCl2, 0.5 mM dATP, 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dUTP, 0.04 uL Taq polymerase, 200 nM T3 primer, and 200 nM T7 primer. PCR reactions were incubated at 95 oC for 2 min, followed by 39 amplification cycles (94 oC for 20 sec, then 52 oC for 20 sec, then 72 oC for 1.5 min), and then incubated at 72 oC for 10 min. Products from duplicate 15 uL PCR reactions were combined and purified using a Genesis RSP 200 Liquid Handler (TECAN Inc., NC) and 384-well filter plates (# S384PCR10; Millipore Inc., MA). Purified products were dehydrated under vacuum, re-suspended in 12 uL of spotting buffer (3X SSC, 1.5 M betaine), and printed onto glass slides coated with g-amino-propyl-silane (25.3 X 75.5 mm, UltraGAPS; Corning Inc., NY) using a MicroGrid Pro arrayer (BioRobotics Inc., MA) with 32 MicroSpot2500 printing pins. Temperature and humidity inside the arrayer were maintained at 18-21 oC and 35-45% RH, respectively. Dwell time, spots per visit, pin wash time, and pin dry time were set at 1 second, 27 spots, 7 seconds, and 10 seconds, respectively. cDNA was fixed to the slides by treatment with 300 mJoules of UV irradiation followed by a two-hour incubation at 85oC. Array fabrication was completed with a 2 minute wash in 0.2% SDS, three rinses in Milli-Q® water, and a final rinse in 90% EtOH. EtOH was removed immediately via centrifugation (2 min at 500 rpm) and resulting microarrays were stored in a dust-free plexiglass chamber (~21oC, 0% RH).


title: UWAPG Yeast 6K v1.1


title: MRC Homo sapiens 5.97K

status: Public on Sep 01 2008

city: Leicester

first: Timothy

middle: William

last: Gant

address: Hodgkin Building, University of Leicester

department: Systems Toxicology

country: United Kingdom

institute: Medical Research Council Toxicology Unit

manufacturer: Systems Toxicology Group. Medical Research Council

middle: W

first: Katie

last: Ridd

manufacture_protocol: Spotted cDNA array utilising IMAGE EST clones on poly-L-lysine. Spotted using a spotter of the Stanford design. Labelling is indirect two color using Alexa dyes. Full details and downloads available at www.systems-toxicology.com


title: OSU-CCC (Ohio State University microRNA microarray v4)

status: Public on Sep 25 2008

city: Bethesda

first: Giang Huong

last: Nguyen

address: 37 Convent Drive

department: CCR

institute: NCI

organism:
Homo sapiens
Mus musculus

description:
OSU-CCC hsa-miRNA-chip version 4
miRNA oligo sequences may be found in the .gal file linked below as a supplementary file.

manufacturer: Microarray Shared Resource, Comprehensive Cancer Center, The Ohio State University (OSU-CCC)

manufacture_protocol: Manufacured using GE Healthcare's CodeLink (TM) 3-D Gel Matrix Technology. CodeLink(tm) Activated Slides are designed to covalently immoblize amine-modified DNA for microarrays. The slides are coated with a 3-D surface chemistry comprised of a long-chain, hydrophilic polymer containing amine-reactive groups. This polymer is covalently crosslinked to itself and to the surface of the slide. The crosslinked polymer, combined with end-point attachment, orients the immobilized DNA, and holds it away from the surface of the slide. The 1x printing buffer consists of 50 mM sodium phosphate at pH 8.5. Codelink slides are manufactured by SurModics and were formally sold as 3D-Link(tm) Activated Slides.   Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions (http://www.genomicsolutions.com ) that is fitted with a printhead and 16 SMP3 print tips from Telechem (http://www.arrayit.com). The microRNA microarray probe set is based on 40mer oligonucleotides from Sigma-Genosys.   Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normalized 25 micromolar concentration. The miRNA microarray spot densities are 200 microns (center-to-center). The microarrays are printed on Codelink Activated Slide (PN300011)) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: TMHRI Streptococcus agalactiae 2K array version1

city: Warsaw

first: Izabela

last: Sitkiewicz

address: Chełmska 30/34

department: Epidemiology and Clinical Microbiology

country: Poland

institute: National Medicines Institute

organism: Streptococcus agalactiae

first: Laurent

last: Mereghetti

first: Nicole

last: Green

first: James

last: Musser

manufacture_protocol: Standard Affymetrix procedures


title: cGRASP Salmon 16k cDNA array

city: Québec

first: Nicolas

last: Derome

state: QC

address: Av de la médecine

department: Biologie

institute: Université LAVAL

organism: Salmo salar

manufacturer: cGRASP (consortium for Genomic Research on All Salmon Project)

first: Bérénice

last: Bougas

first: Sean

last: Rogers

first: Andrew

last: Whiteley

first: Aurélie

last: Labbe

first: Jérôme

last: Laroche

first: Louis

last: Bernatchez

manufacture_protocol: see Methods section of related Citation (PMID: 16164747).


title: Udall global cotton16 EST assembly array

status: Public on Sep 11 2008

city: Athens

first: Alan

middle: R

last: Gingle

state: GA

address: 111 Riverbend Rd.

department: Center for Applied Genetics Technologies

institute: University of Georgia

organism: Gossypium

description: We have designed and implemented a novel NimbleGen microarray platform capable of measuring global gene expression in Gossypium species. This custom designed microarray features ~60mer generic probes those were created by first assembling EST contigs from G.arboreum, G.raimondii, and G. hirsutum libraries and has the ability to measure total gene expression.

first: Bhupendra

last: Chaudhary

first: Ran

last: Hovav

first: Ryan

last: Rapp

first: Neetu

last: Verma

first: Joshua

middle: A

last: Udall

first: Jonathan

last: Wendel

manufacture_protocol: Oligonucleotide arrays were synthesized by NimbleGen Systems, Inc by maskless array synthesis using a digital micromirror array-mediated,parallel synthesis process incorporating 5'-photoprotected phosphoramidites. Synthesized arrays were deprotected by incubation in ethanolamine:ethanol (1:1) at room temperature for two hours, washed extensively in distilled water, and stored desiccated until used. This custom design has 42,460 cotton genes and includes ~290,000 expression probes.


title: Sterolgene V0 mouse

status: Public on Nov 26 2007

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

organism: Mus musculus

manufacturer: Center for Functional Genomics & Bio-Chips, Faculty of Medicine, Univ. of Ljubljana, Slovenia; Lek Pharmaceuticals d.d., Ljubljana, Slovenia; Genome Scale Biology, Biozentrum, Univ. of Basel, Basel, Switzerland; GODMAP, CGM, CNRS, Gif-sur-Yvette, France

first: Tadeja

last: Rezen

first: Klementina

last: Fon Tacer

first: Drago

last: Kuzman

first: Adrian

last: Roth

first: Denis

last: Pompon

first: Lawrence

middle: P

last: Aggerbeck

first: Urs

last: Meyer

first: Damjana

last: Rozman

manufacture_protocol: Will be provided later.


title: Agilent Human miRNA Microarray, pre-commercial version 6.0

status: Public on Jul 21 2008

city: Santa Clara

first: Robert

last: Ach

address: 5301 Stevens Creek Boulevard

department: Agilent Laboratories

institute: Agilent Technologies

description:
Agilent design ID 015508. miRNA probes were designed using Sanger miRBase, release 9.1.
Platform data table represents all of the replicate probes per miRNA.

*** The ID column represents Agilent Feature Extraction feature numbers.  A different version of this platform with ascending integers (i.e., 1 to 470) in the ID column, arbitrarily assigned to the unique miRNAs, is assigned accession number GPL7341.

first: Hui

last: Wang

first: Bo

last: Curry

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


title: Shirahige S.cerevisiae Tiling1.0R Array

status: Public on May 12 2006

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

first: Yuki

last: katou

first: Takehiko

last: Itoh

manufacture_protocol: Affymetrix tiling array for cerevisiae whole genome, 2micron plasmid, and mitochondrial DNA. 5bp resolution chip. Covers Crick strand.


title: Affymetrix Custom Array - enterocha520147F

status: Public on Apr 08 2008

city: Norman

first: Tyrrell

last: Conway

state: OK

address: 101 David L. Boren Blvd.

department: Advanced Center for Genome Technology

institute: University of Oklahoma

organism:
Bacillus anthracis
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Escherichia coli O157:H7 str. EDL933
Escherichia coli CFT073
Enterococcus faecalis V583
Bacteroides thetaiotaomicron VPI-5482
Escherichia coli O157:H7 str. Sakai
Escherichia coli str. K-12 substr. MG1655

description: This array is designed for use with the 7 listed genomes.  Associated with each Series is a supplementary filter file that was used for data analysis.  The filter file contains only the probeset ID's for the associated Samples.

manufacture_protocol: Array with 511706 features, in 1 zones, with 24826 biosequences representing 254179 reporters and 24826 composite sequences, with surface type unknown


title: CGC Legionella whole-genome microarray v1.0

city: New York

first: Sergey

last: Kalachikov

state: NY

address: NWC Bld, 550 West 120th Street Rm 1002

department: Chemical Engineering

institute: Columbia University

first: Pavel

last: Morozov

first: Irina

last: Morozova

last: Pampou

first: Howard

last: Shuman

first: James

last: Russo

first: Jingyue

last: Ju

manufacture_protocol:
70-mer oligonucleotides specific for each of the unique genes in the Legionella pneumophila subsp. pneumophila str. Philadelphia 1
genome (2976 total of the unique probes) were dissolved in 50% DMSO at 30 micromolar concentration and spotted in duplcate on Corning UltraGAPS microarray coated slides (Corning) using SpotArray 72 Microarray printing system (Perkin Elmer). After the manufacturing the arrays were stored dessicated in vacuum at ambient temperature until further use. Piror to use, the oligonucleotides were UV-crosslinked to the slide surface.


title: Whitehead/Bartel Schizosaccharomyces pombe 454 sequencing ago1 associated small RNAs

city: Stanford

first: Noah

last: Spies

address: 300 Pasteur Dr

department: Pathology

institute: Stanford University

organism: Schizosaccharomyces pombe

description: 454 sequencing


title: University Health Network Yeast 6.4Kv3.48 microarray slide

status: Public on Sep 03 2008

city: Bloemfontein

first: Hugh

last: Patterton

state: Free State

address: 1 Mandela Avenue

department: Biotechnology

country: South Africa

institute: University of the Free State

manufacturer: Microarray Center, University Health Network

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


title: AtTile1R to Arabidopsis Tiling 1.0R

status: Public on Apr 21 2005

city: La Jolla

first: Joseph

middle: R.

last: Ecker

address: 10010 N. Torrey Pines Road

department: Genomic Analysis Laboratory

institute: The Salk Institute

description: Affymetrix Whole Genome Tiling Array Chip designed by the Salk Institute and Affymetrix.

first: Huaming

last: Chen

first: Junshi

last: Yazaki

manufacture_protocol: see manufacturer's web site


title: AtTile1F to Arabidopsis Tiling 1.0F


title: UCBerkeley Dehalococcoides v1.0

city: Berkeley

first: Kimberlee

last: West

address: 207 O'Brien Hall

department: Civil and Environmental Engineering

institute: University of California, Berkeley

organism: Dehalococcoides mccartyi 195

first: David

last: Johnson

first: Ping

last: Hu

first: Todd

middle: Z

last: DeSantis

first: Eoin

middle: L

last: Brodie

first: Patrick

last: Lee

first: Helene

last: Feil

first: Gary

last: Andersen

first: Stephen

middle: H

last: Zinder

first: Lisa

last: Alvarez-Cohen

manufacture_protocol: Manufacturer's protocol used: Affymetrix Prokaryotic Sample and Array Processing protocol; 100 Format (Midi)


title: S_pombea520106F

status: Public on Jun 29 2004

first: Katsuhiko

last: Shirahige

description: Affymetrix High-density genome tiling array for S.pombe chromosome 2 and 3 (Left arm). 11X25bp oligo-nucleotide were set for every 250bp in average.

first: Yuki

last: Katou

first: Takehiko

last: Itoh

first: Jun-ichi

last: Nakayama


title: UWAPG Yeast 6K v1.0

city: Madison

first: Audrey

middle: P.

last: Gasch

address: 425-g Henry Mall

institute: University of Wisconsin Madison

manufacturer: Gasch Lab, University of Wisconsin-Madison

first: Adriana

last: Alejandro-Osorio

first: Dana

middle: J

last: Huebert

first: Dominic

middle: T

last: Porcaro

first: Megan

middle: S

last: Sonntag

first: Jessica

last: Will

manufacture_protocol: Qiagen 70mer oligos representing the S. cerevisiae genome (one 70mer per gene) were spotted in house on a Gene Machines spotting microarrayer onto poly-lysine coated glasss slides, also made in house.  A full description of microarray printing, slide preparation, and post-processing protocols can be found in Gasch A.P. (2002), Methods in Enzymology 350:393-414


title: Operon Mouse 36k v4.0

first: Daniel

last: Haag

state: Santa Clara

address: 265 Campus Drive

department: ISCBRM

institute: Stanford School of Medicine

description: The array format contains of 36480 spots in 48 subarrays each of which is build of 28 columns, 27 whole rows and 4 spots within a 28th row. This number includes empty buffer spots, sporadic replicates of single oligos and control sequences. Each subarray is printed by one spotting pin. The distance between spot centers is about 155µm. Spot diameter is approximately 100µm.

manufacturer: German Cancer Research Center, Department of Molecular Genetics

manufacture_protocol: Lyophilized 70mer oligonucleotides in 384well plates obtained from Operon are dissolved in 3x SSC, 1,5 M Betaine at a concentration of 20µM (35852 probes from Mouse Genome Oligo Set Version 4.0). Oligos are spotted on epoxysilane coated glass slides using 48 Micro Spotting Pins (946MP3, ArrayIt) in a Versarray Chipwriter Pro System (BioRad). Spotted Chips are baked for 60 minutes at 70°C and stored airtight under dry condition at 4°C. Before hybridization processing slides containing spotted arrays are blocked with 0,3% ethanolamine, 0,1% SDS in 0,1M Tris (pH 9,0).


title: Stress response in yeasts (C. glabrata)

city: Paris

first: Gaëlle

last: Lelandais

address: 2, place Jussieu

country: France

institute: INSERM

organism: Nakaseomyces glabratus

first: Frédéric

last: Devaux

manufacture_protocol:
Manufacture protocols are available at :
http://www.pasteur.fr/recherche/genopole/PF2/index_en.html


title: Stress response in yeasts (S. cerevisiae)

organism: Saccharomyces cerevisiae

manufacture_protocol:
Manufacture protocols are available at :
http://www.transcriptome.ens.fr/


title: Borrelia burgdorferi 70-mer oligoarray

city: Dallas

first: zhiming

last: ouyang

state: TX

address: 6000 Harry Hines Blvd

department: Department of Microbiology

institute: UT Southwestern Medical Center

organism: Borreliella burgdorferi B31

first: Michael

middle: V

last: Norgard

first: Zhiming

last: Ouyang

manufacture_protocol: Oligonucleotides representing all annotated ORFs and pseudogenes of B. burgdorferi B31MI in the TIGR or NCBI genome databases were synthesized by QIAGEN-Operon (Alameda, CA) according to a proprietary algorithm that optimizes the melting temperature (Tm) for all oligonucleotides within 5°C of each other. The target Tm was 70°C, and only five oligonucleotides (BB0150, BB0609, BBH39, BBK001, and BBQ83) failed to have a minimum Tm of 65°C. All oligonucleotides are 70 nucleotides in length and are at least 40 nucleotides from the 3' end of the ORF sequence (except for a number of short ORFs, where these criteria could not be met). In addition, 19 random-sequence 70-mers were synthesized as negative controls.


title: Sterolgene v1 mouse

status: Public on Aug 21 2008

first: Peter

last: Juvan

first: Tadeja

last: Rezen

first: Damjana

last: Rozman

first: Klementina

last: Fon Tacer

first: Drago

last: Kuzman

first: Uros

last: Urleb

first: Adrian

last: Roth

first: Urs

last: Meyer

first: Herve

last: Delacroix

first: Nicolas

last: Agier

first: Lawrence

last: Aggerbeck

first: Denis

last: Pompon

first: Sandrine

last: Imbeaud

manufacture_protocol:
Spotter : Microgrid
Number of pins used : 2
Probes : cDNA
Slides : Aminosillane (GapsII - Corning)
Number of probes : 120
Number of probes replicates : each probe has been spotted 6 times on each slide
Normalization controls: Lucidea spike in (Amersham)
Number of blocks : 4
Block size : 17 x 17 spots
Pitch between spots : 230 µm
Spot size : between 110 and 130 µm
Printed : 80 slides + 2 for quality control
Process length : 19H05
Humidity : 37.6% in the room, 40% in the spotter
Temperature : 20.1 °C


title: BWH_Comstock_Bacteroides fragilis_4.3k array

status: Public on May 01 2008

city: Boston

last: Coyne

state: MA

address: 181 Longwood Avenue

department: Medicine

institute: Brigham & Women's Hospital

organism: Bacteroides fragilis NCTC 9343

description:
NimbleGen design name 2005-08-12_B_fragilis_24mer, NimbleGen design ID 2451.  A 1:2 expression design for 4,302 genes from Bacteroides fragilis NCTC 9343 and associated plasmid pBF9343 with fourteen 24-mer probe pairs (PM/MM) per gene.  Each probe is replicated 3 times.  The design includes random GC and other control probes.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.

first: Laurie

last: Comstock

first: Maria

last: Chatzidaki-Livanis

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology.  See http://www.nimblegen.com/


title: Alternative Mouse Exon 1.0 ST Array [CDF: MmEx10stv1_Mm_REFSEQ_8]

status: Public on Jun 06 2008

city: Stockholm

first: Rickard

last: Sandberg

address: Berzelius vag 35

department: Department of Cell and Molecular Biology

institute: Karolinska Institutet

description: Custom CDF linked to this submission as a supplementary file

manufacture_protocol: See manufacturer's web site


title: ORFs of Cryptococcus neoformans var. grubii (serotype A, H99)

status: Public on Jan 09 2007

city: San Francisco

first: Cheryl

last: Chun

state: CA

institute: UC San Francisco

organism: Cryptococcus neoformans

first: Hiten

middle: D

last: Madhani

first: Oliver

last: Liu

first: Eric

last: Chow

first: Sean

last: O'Brien

manufacture_protocol: Gene models for serotype A strain H99 were developed using BLAST in combination with the gene models previously predicted by TIGR and Stanford centers for serotype D strains JEC21 and B-3501.  Based on these gene models, 70-mer oligos were designed using the program ArrayOligoSelector (Bozdech etal, DeRisi Lab, UCSF).  The oligonucletodies were printed on polylysine-coated glass microscope slides using a custom robot and silicon tips at UC San Francisco's Center for Advanced Technology.


title: Affymetrix S. pombe Tiling 1.0FR Array

status: Public on Jun 13 2006

first: Katsuhiko

last: Shirahige

description: The S. pombe tiling Array consists of 6 million probe pairs tiled through the complete Schizosaccharomyces pombe genome. Probes are tiled for both strands of the genome at an average of 20 base pair resolution, as measured from the central position of adjacent 25-mer oligos, creating an overlap of approximately 5 base pairs on adjacent probes. The information of oligo probes on the arrays (sequence and location on the chip) is available from Affymetrix.

first: Yuki

last: Katou

first: Takehiko

last: Itoh

manufacture_protocol: 20bp resolution tiling array for S.pombe. Including repetitive sequences such as centeromere and mat.


title: Shirahige S.cerevisiae Tiling1.0F Array

last: katou

manufacture_protocol: Affymetrix tiling array for cerevisiae whole chromosome, 2micronDNA, and mitochondrial DNA. 5bp resolution chip. Cover Watson strand.


title: Affymetrix GeneChip Human Genome U133A 2.0 Array [CDF: MBNI Version 9 (UniGene 199)]

status: Public on Aug 06 2008

city: Mannheim

first: Xiaolei

last: Yu

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: This is identical to GPL571 but a custom CDF environment was used to extract data. See Dai et al., NAR 2005 33(20), PMID: 16284200.

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

manufacture_protocol: Affymetrix standard protocol


title: ChromosomeVI tiling array (rikDACF)

manufacture_protocol: Affymetrix tiling array for cerevisiae chromosome VI. Also contains several ARS regions from other chromosomes.


title: SC3456a520015F

description: Affymetrix High-density Oligo-nucleotide Tiling Array for Saccharomyces cerevisiae chromosome III, IV, V and VI. In average, 11X25bp oligos are set for every 300bp.


title: rikDacFC6

status: Public on Aug 27 2003

description:
Highdensity Yeast Chromosome VI tiling oligo-nucleotide array which can analyze chromosome VI at 300bp resolution. Produced by Affymetrix. Can be purchased directly from Affymetrix. Product name rikDACF. P/N 510636.
Keywords = chromosome VI tiling array

first: Masashige

last: Bando

first: Hideki

last: Noguchi

first: Yutaka

last: Kanoh

first: Hirokazu

last: Tanaka

first: Toshihiko

last: Ashikari

first: Katsunori

last: Sugimoto


title: Steroltalk v2 mouse

status: Public on Aug 23 2008

first: Peter

last: Juvan

institute: Faculty of Medicine, University of Ljubljana

first: Tadeja

last: Rezen

first: Damjana

last: Rozman

first: Klementina

last: Fon Tacer

first: Drago

last: Kuzman

first: Uros

last: Urleb

first: Adrian

last: Roth

first: Urs

last: Meyer

first: Herve

last: Delacroix

first: Nicolas

last: Agier

first: Lawrence

last: Aggerbeck

first: Denis

last: Pompon

first: Sandrine

last: Imbeaud

manufacture_protocol:
Spotter: Biorobotics Microgrid II
Number of pins: 2
Probes: cDNA
Slides: Corning Gaps II
Number of probes (for each array): 285 mouse + 5 human in 3 replicas, 570 control
Number of blocs: 6 per array, 2 arrays per slide
Block size: 16x15 spots (height x width)
Pitch between spots: 260 µm
Spot size: between 110 and 170 µm
Printed: 50 slides (100 chips) + 1 control slide
Process length: ~19H
Humidity: 40% in the room
Temperature: 20 °C +/- 0.5
Buffer conditions: formamide 50%, Chaps 1%


title: EcoArray 1 x 22K Fathead Minnow Microarray (v1 and v2)

status: Public on Sep 20 2008

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

country: USA

institute: Applied Food Technologies

organism: Pimephales promelas

description: This second generation array has approximately 22,000 fully-annotated genes; 90% of these genes have been matched (e-score < E-04) to named genes in the published databases. The genes are part of a wide variety of biological pathways and processes including: reproduction, cell communication, metabolism, homeostasis, and others.  The full list of genes is on our website: www.ecoarray.com.  These arrays are low-density (10 um scanner) and are no longer produced by Agilent.  They have been replaced by our higher density FHM 4 x 44K and the 8 x 15K arrays.

first: Patrick

middle: M

last: Larkin

manufacture_protocol: See manufacturer's web site at http://www.agilent.com/. These genes are spotted onto microarrays created for EcoArray by Agilent Technologies, a leading supplier of genomics and proteomics products.  Agilent uses their SurePrint inkjet deposition of in situ synthesized 60-mer oligonucleotides, to manufacture these chips on superior quality 1” x 3” (24.2 mm x 76.2 mm) treated glass slides for overall excellent performance.  This process minimizes variability across each production lot (batch to batch) and provides the highest consistency in slide-to-slide comparisons.  These glass slide microarrays are designed for either a one- or two-color (cyanine-3 and cyanine-5) labeling reaction, the most reliable and sensitive method for detecting differentially expressed genes.  Each individual microarray produces QA metrics to ensure quality.