title: 454 GS (Chlamydophila pneumoniae CWL029)

status: Public on Oct 28 2010

last: GEO

country: USA

organism: Chlamydia pneumoniae CWL029

technology: high-throughput sequencing

distribution: virtual


title: Biocenter Innsbruck EBV SHORT, 6152 v1.0

status: Public on Oct 30 2010

city: Innsbruck

first: Roland

last: Hutzinger

address: Fritz-Pregl-Str. 3

country: Austria

institute: Biocenter Innsbruck

organism:
Homo sapiens
Human herpesvirus 4 strain B95-8

technology: in situ oligonucleotide

description: In total, approximately 4.300 probes of 30 nt in size or shorter, dependent on the cDNA sequence length, recognizing sense and antisense transcripts, as well as intra-array replicates were synthesized in situ on the microchip and analyzed with febit Geniom One technology (Supplementary Table 3) (Baum et al., 2003; Vorwerk et al., 2008). Sequence candidates longer than 30 nt were covered with multiple, overlapping probes.

distribution: non-commercial

manufacture_protocol: A custom microchip for the detection of all novel identified ncRNA candidates was generated by the company febit biomed gmbh (Heidelberg, Germany). In addition, probes for the detection of selected cellular ncRNA genes, including rRNA (5S, 5.8S), snRNAs, miscellaneous RNAs (7SL RNA, 7SK RNA, RNase MRP RNA, RNase P RNA, vault RNAs and Y RNAs), known human and EBV miRNAs (from miRBase; release 11.0; (Griffiths-Jones et al., 2006) as well as human snoRNAs (115 box C/D snoRNAs, 82 H/ACA snoRNAs, 25 scaRNAs; from snoRNA-LBME-database, version 3; (Lestrade & Weber, 2006) were included. DNA oligonucleotide probesets were designed using febit´s Geniom Client software.


title: Illumina Genome Analyzer (Metarhizium anisopliae)

status: Public on Oct 26 2010

organism: Metarhizium anisopliae


title: SMD Print_1447 Homo sapiens

status: Public on Oct 25 2010

city: Stanford

first: Hongjuan

last: Zhao

state: CA

address: 300 Pasteur Dr

department: Urology

institute: Stanford

organism: Homo sapiens

technology: spotted DNA/cDNA

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine

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


title: 454 GS (Danio rerio)

status: Public on Oct 22 2010

organism: Danio rerio


title: SMD Print_1524 Homo sapiens


title: Drosophila melanogaster Aubergine ChIP

city: Worcester

first: Hervé

last: Seitz

state: MA

address: 364 Plantation Street

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

organism: Drosophila melanogaster

technology: other

description: Chromatin immunoprecipitation was performed with an antibody against histone H3 methylated on K9, from fly ovaries from heterozygous (aubQC/CyO) or trans-heterozygous (aubQC/HN2) aubergine mutants. Immunoprecipitated DNA was fragmented and polished, then analyzed by deep-sequencing on a Solexa apparatus, according to the manufacturer's protocol.

first: Vasily

middle: V

last: Vagin


title: Illumina Genome Analyzer (Capsicum annuum; Meloidogyne incognita)

organism:
Capsicum annuum
Meloidogyne incognita


title: 454 GS (Caenorhabditis elegans; Escherichia coli)

organism:
Escherichia coli
Caenorhabditis elegans


title: Agilent Human 1 cDNA Microarray (G4100A) [layout A]

status: Public on Jan 02 2004

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
12,814 unique clones, 97% map to named human genes
Sourced from Incyte's UniGene 1 and Human Drug Target DNA clone sets
Barcode location:Bottom
Scan Side:Front

This platform should be used for the following prints:

000437_D_20030121_FSPortraitBcodeDown
000437_D_20010620_FSPortraitBcodeDown

Please reference this platform if you used an array with the same layout, even if the print lot is different than specified above. The GEO staff will update the description of this platform to include additional print lots as encountered.

Print-specific information should be accounted for in the sample hybridization tables (eg. NULL value insertions for spots to be ignored).

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: Nimblegen S. pombe 10K

status: Public on Oct 31 2010

city: Tsukuba

first: Tomoyasu

last: Sugiyama

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

organism: Schizosaccharomyces pombe

technology: spotted oligonucleotide

description: Nimblegen #5543959 Euk Expr 4x72K Catlog (090408 Spom exp X4) 4977 genes 2 replicates

distribution: custom-commercial

manufacture_protocol: see Nimblegen web site


title: Synechocystis sp. strain PCC 6803 12K full genome array version 4

city: Dunedin

first: Tina

last: Summerfield

address: 464 Great King Street

department: Botany

country: New Zealand

institute: University of Otago

organism: Synechocystis sp. PCC 6803

manufacturer: Robert Burnap Oklahoma State University, Lou Sherman Purdue University

manufacture_protocol: Construction and Preparation of Synechocystis Spotted Microarrays: 3168 genes or putative ORFs of Synechocystis sp. PCC6803 were PCR amplified in two stages. Primary amplification was achieved using gene-specific up-stream and down-stream primers modified with adaptamer sequences and genomic DNA template. Secondary amplification was achieved using adaptamer primers and individual primary PCR product templates. The quality of the PCR products was determined by agarose gel electrophoresis. The PCR products were purified using Millipore Multi-screen plates and resuspended in Micro Spotting buffer (TeleChem; Sunnyvale, CA) to a concentration of 500ng/ul. Each probe was then printed (spotted) in triplicate onto TeleChem SuperAmine substrates at room temperature and 50% relative humidity using a GeneMachines Omnigrid 100 (Genomic Solutions; Ann Arbor, MI) robot fitted with 4x4 TeleChem SMP4 pins. After printing, each slide was rehydrated by holding the slide with the array side down over a container of steaming water for 1 s and snap-dried on a warm hot plate. Printed slides were baked at 80°C for 1 h and then subjected to a UV-cross-linking at a dose of 1500 mJ cm2. Slides with immobilized probes were then stored in slide holders and placed in a desiccator at room temperature.


title: Affymetrix Toxoplasma gondii GeneChip Individual Expression Probes (Tgondiia520372)

status: Public on May 02 2011

city: St Louis

first: Michael

middle: Sean

last: Behnke

state: MO

address: 660 S. Euclid Ave

department: Molecular Microbiology

institute: Washington University School of Medicine

organism: Toxoplasma gondii

description: Please see http://ancillary.toxodb.org/docs/Array-Tutorial.html for a complete description of the array design as well as for library files.

first: Amit

last: Bahl

first: David

middle: S

last: Roos

last: Kulp

manufacture_protocol: Affymetrix photolithographic array - 169 format.


title: UPenn_canine_retinal_EST_4.5k array

city: Philadelphia

first: Sem

last: Genini

state: PA

address: 3900 Delancey Street

department: Clinical Studies

institute: University of Pennsylvania

organism: Canis lupus familiaris

description:
GPL9743 represents two different print sets, v1 and v2.  While the order of the clones are not exactly the same in v1 and v2, the clones themselves are identical.
The Platform data table reflects a condensed representation of the print sets' replicate features.
The v1 and v2 full array layout (.gal) files, representing all of the individual features, are linked below as supplementary files.

manufacturer: W.M. Keck Center for comparative and Functional Genomics, University of Illinois at Urbana-Champaign

first: Barbara

last: Zangerl

first: Gregory

middle: M

last: Acland

first: William

middle: A

last: Beltran

first: Gustavo

middle: D

last: Aguirre

manufacture_protocol: EST clones were obtained from a normalized canine retinal library cloned into pGEM 11ZF(+) vector (Promega). Inserts were amplified using T7_20 and Sp6_20 primers, purified and printed on Telechem Superamine slides. For further details see Zangerl et al., IOVS 2006 and Paez et al., Mol Vis, 2006.


title: Illumina Genome Analyzer (Meloidogyne incognita)

status: Public on Oct 20 2010

last: GEO

organism: Meloidogyne incognita


title: NimbleGen Homo sapiens 385K CGH array

status: Public on Oct 27 2010

city: Montreal

first: Johnny

middle: Yvan

last: Deladoëy

state: QC

address: 3175 Côte Sainte-Catherine

department: Pediatrics; U of Montreal

country: Canada

institute: Research Center CHU Sainte-Justine

manufacture_protocol: see manufacturer's website


title: Illumina Genome Analyzer II (Polysphondylium pallidum)

organism: Heterostelium pallidum


title: Agilent-024656 ATCC17978_ec

city: Adelaide

first: Bart

last: Eijkelkamp

state: SA

address: North Tce

country: Australia

institute: University of Adelaide

organism: Acinetobacter baumannii

manufacture_protocol: see Agilent


title: Brucella 16M whole genome microarray

city: Beijing

first: Zeliang

last: Chen

address: NO. 20,Dongdajie

country: China

organism: Brucella melitensis bv. 1 str. 16M

manufacturer: Beijing Institute of Disease Control and Prevention, P. R.China.

manufacture_protocol:
1.Primers specifc for each of the ORFs of 16M genome sequence are designed by Arraydesigner 3.0. Primers are synthesized in 96-well plates.
2. Products of each of the ORFs were amplified in 96-well plate.
3. PCR products are purified in 96-well plates.
4. PCR products are disolved in 50% DMSO, gyrB, glk and 16s rRNA are included in each of the blocks as positive contrl, and 50% DMSO as negative control. These products are transferred into 384-well plates.
5. Products are printed in duplicate on VAL S25 glass slides (ECL); Each slide is composed of 32 sub-arrays in 18 columns and 12 rows.
6. After the print run is completed, allow plates to dry through passive evaporation in a protected environment.


title: Affymetrix GeneChip Mouse Genome 430 2.0 Array [CDF: Mouse4302_Mm_REFSEQ]

status: Public on Apr 12 2011

city: Piscataway

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

organism: Mus musculus

description: This identical to GPL1261 but a custom CDF environment was used to extract data.  The .cdf and mapping files, as well as an R package are provided as supplementary files.

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


title: [CustOva1a520455F] Affymetrix  Homo sapiens  0.6K Custom GeneChip

status: Public on Jun 14 2011

city: boston

first: panagiotis

last: konstantinopoulos

address: 330 brookline av

department: hem/onc

institute: bidmc

description: This array contains standard Affymetrix probe sets from U133A

manufacture_protocol: see the manufacturer's website


title: ECB human 19K oligoarrays

status: Public on Oct 21 2010

city: Rotterdam

first: Rute

last: Marques

address: Dr Molewaterplein 50

country: Netherlands

institute: Erasmus MC

manufacturer: Erasmus Center for Biomics, Erasmus Medical Center, Rotterdam, The Netherlands

manufacture_protocol: The microarrays used in this study were produced by the Erasmus Center for Biomics. Compugen human oligonucleotide library containing 18861 60-mer oligonucleotides was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). Oligonucleotides were spotted on aminosilane slides using a Virtek Chipwriter Professional arrayer (Virtek Vision International, Waterloo, Canada). Control spots included landmarks, spotting buffer, alien oligonucleotides (SpotReport Alien Oligo Array, La Jolla, Stratagene), poly d[A]40-60, salmon sperm DNA, and human COT-1 DNA. Oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions


title: Mouse Interferon α, β RT² Profiler PCR Array (PAMM 016)

city: Doylestown

first: Saifur

last: Rahman

address: 3805 Old Easton Rd

department: Microbiology and Immunology

institute: Drexel University

technology: RT-PCR

description: Housekeeping genes (GAPDH and b-Actin) were marked on spots H04 and H05. To check for mouse genomic contamination (H06). Reverse transcription controls (H07-H09). Positive PCR controls (H10-H12).


title: Illumina Genome Analyzer (Metarhizium acridum)

organism: Metarhizium acridum


title: Illumina Genome Analyzer (Aedes aegypti)

organism: Aedes aegypti


title: Mouse Dendritic and Antigen Presenting Cell RT² Profiler PCR Array (PAMM 406)


title: University of Padova_Dicentrarchus labrax_4x44K array_v1.0

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

organism: Dicentrarchus labrax

description: GE 4x44k oligo microarray that covers 19,035 unique transcripts of the European sea bass (Dicentrarchus labrax). Oligonucleotides, 60-mer plus a “linker”, are synthesized directly on glass slide using the Agilent’s SurePrint Tecnology ; oligo design was carried out by eArray and two non overlapping probes  were designed for each ESTs cluster. Both independent probes designed for the same transcript are named with an univocal ID and distinguished by suffix _1 or _2. Sequence and description of each gene (cluster) are available in the DLPD database (http://enne.cribi.unipd.it:5556/biomart/martview),  where cluster ID corresponds to probe ID  on the array.

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


title: [GLYCOv2a520086F] Custom Affymetrix Glyco v2 GeneChip

status: Public on Oct 23 2010

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

organism:
Homo sapiens
Mus musculus

description:
The Glyco v2 array was designed in 2003 and consists of probesets targeting genes coding for glycosyl transferases, carbohydrate binding proteins, glycan degradation enzymes, nucleotide sugar transporters, mucins, adhesion molecules, chemokines, cytokines, growth factors and their receptors, interleukins and their receptors and proteoglycans. In addition, a set of "housekeeping" and control genes are included on the array. The array contains probe set for both mouse and human gene sequences and can be use to analyze RNA from both species.

Most of the human and mouse probe sets on the Glyco v2 array were taken directly from the v1 array (based on commercial U133A,B human array) with some  probesets designed by Affymetrix from accessions for genes not well represented by the U133A,B. Additional carbohydrate related genes were added to the v2 array relative to the v1 array. In most cases, probesets consist of 11 probe pairs designed using the Perfect Match/Mismatch approach developed by Affymetrix.

Immediately prior to our deadline for submittal of the v2 array design, Affymetrix introduced format changes to their custom array product line that substantially increased the available space on the v2 array. To address we represented most probe sets in triplicate or duplicate on the array. For example, the probe set for thrombomodulin (THBD) appears as:  203887 _Copy1_at,  203887 _Copy2_at,  203887 _Copy3_at where each copy represents an identical and independent set of probe pairs targeting the thrombomodulin transcript.


title: [GLYCOv3_Mm] Affymetrix Glyco v3 GeneChip

description:
The Glyco v3 array was designed in 2005 and consists of probesets targeting genes coding for glycosyl transferases, carbohydrate binding proteins, glycan degradation enzymes, nucleotide sugar transporters, mucins, adhesion molecules, chemokines, cytokines, growth factors and their receptors, interleukins and their receptors and proteoglycans. In addition, a set of "housekeeping" and control genes are included on the array. The array contains probe set for both mouse and human gene sequences and can be use to analyze RNA from both species.

This custom chip is to tile pre-selected probes from the Affymetrix HGU133 set, the MOE430 sets, the v1 custom array, and the v2 custom array.  We kept the original 11 probepairs from these pre-selected probes, while adding 10 more newly designed probepairs for a total of 21 probepairs per probeset within the 3' terminal 600 bases of each targeted transcript. Standard Affy controls (houskeeping and normalization genes) remain at 11 probepairs per probe set.

This array also includes 8505 "GC bin" probes for use in background correction. GC content ranges from 3/25 to 25/25. These probes can be used as an alternative to the PM/MM-based background correction methods.

There are separate library files for human and mouse probesets. The human library file includes all probesets on the array except mouse probes and vis versa for the mouse library file.  The human CDF file is named: "GLYCOv3_Hs" and the mouse CDF file is named: "GLYCOv3_Mm".


title: NCode Multi-Species miRBase Microarray V2

status: Public on Oct 17 2010

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

institute: Health Canada

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


title: [GLYCOv3_Hs] Custom Affymetrix Glyco v3 GeneChip

organism: Homo sapiens


title: Agilent-012750 Human Genome CGH Microarray 44A (Probe name version)

status: Public on Oct 19 2010

last: Agilent Technologies

description:
Human Genome CGH Microarray 44A is a high-resolution, high performance 60-mer oligonucleotide-based microarray that contains over 40,000 probes sourced from the NCBI genome (Build 34).  The probes, empirically validated in multiple model systems, span coding and noncoding sequences of the human genome with an average spatial resolution of 35kb.  Coupled with Agilents optimized assay protocols and CGH Analytics software, this microarray enables genome-wide survey and molecular profiling of genomic aberrations (i.e. copy number changes) on a single chip.

*** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL2873.

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


title: NimbleGen Zmays 120K CGH array [091006_NS_Zmays_CGH_exp]

status: Public on Oct 15 2010

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

organism: Zea mays

description: product # OID24389

first: Ruth

last: Swanson-Wagner

first: Sunita

last: Kumari

first: Peter

last: Tiffin

first: Joshua

middle: C

last: Stein

first: Doreen

last: Ware

first: Nathan

last: Springer

manufacture_protocol: Roche NimbleGen manufactures custom, high-density DNA arrays based on its proprietary Maskless Array Synthesizer (MAS) technology. The MAS system is a bench top, solid-state, high-density DNA array fabrication instrument comprised of a maskless light projector, a reaction chamber, a personal computer, and a DNA synthesizer. Roche NimbleGen builds its arrays using photo-mediated synthesis chemistry with its MAS system.    At the heart of the system is a Digital Micromirror Device (DMD), similar to Texas Instruments' Digital Light Processor (DLP), employing a solid-state array of miniature aluminum mirrors to pattern 786,000 to 4.2 million individual pixels of light. The DMD creates virtual masks that replace the physical chromium masks used in traditional arrays.    These virtual masks reflect the desired pattern of UV light with individually addressable aluminum mirrors controlled by the computer. The DMD controls the pattern of UV light projected on the microscope slide in the reaction chamber, which is coupled to the DNA synthesizer. The UV light selectively cleaves a UV-labile protecting group at the precise location where the next nucleotide will be coupled. The patterns are coordinated with the DNA synthesis chemistry in a parallel, combinatorial manner such that 385,000 to 2.1 million unique probe features are synthesized in a single array.


title: Illumina Genome Analyzer (Tachyglossus aculeatus)

status: Public on Oct 14 2010

last: GEO

organism: Tachyglossus aculeatus


title: EMBL/CodeLink Mouse 0.4K miCHIP v11

city: Heidelberg

first: Mirco

last: Castoldi

address: Im Neuenheimer Feld 156

department: Department of Pediatric Oncology, Hematology and Immunology

country: Germany

institute: University of Heidelberg

description:
miChip v11.0 annotation was done for mouse (miRBase v11.0).

miChip array are spotted on CodeLink slides (GE Life Science, cat. no. 30001100). CodeLink glass slides are coated with N-hydroxysuccinimide.

NOTE: Probe sequences used in this array are proprietary, belonging to Exiqon.

manufacturer: Array was spotted by the Genomics Core Facility, EMBL, Germany. LNA-modified capture probes were manufactured by Exiqon, Denmark.

manufacture_protocol:
LNA-modified oligonucleotide (Exiqon) capture probes are designed to have a close to uniform Tm of 72 Celsius against their complementary targets. This is achieved by adjustment of LNA content and length of capture probes (miRCURY Array probes, Exiqon, http://www.exiqon.com). A C6-amino linker is added to the 5'-end of all capture probes. The desiccated capture probe set is available in a 384-well plate format. Capture probes are printed onto N-hydroxysuccinimide glass surfaces (Codelink, GE Healthcare Life Science) using the Lucidea Array Spotter (GE Healthcare Life Science).

Additional material required for array preparation: post-coupling blocking solution [50 mM ethanolamine, 0.1 M Tris (pH 9)], post-coupling washing solution (4 XSSC, 0.1% SDS), a water bath (50C) and a tabletop centrifuge (Eppendorf, 5810R) fitted with rotor (A4-62) adaptors for microplate carriers or for 50 ml tubes.

miRCURY Array probes (Exiqon) are diluted to a final concentration of 20 uM in 3X printing buffer [(150 mM sodium phosphate (pH 8.5)] prior to spotting. Probe set are spotted on CodeLink (GE Healthcare Life Science), where slides are printed using the Lucidea array spotter (GE Healthcare Life Science) with 65% humidity and a temperature of 21C.

Each spot measures about 120 um in diameter with a center-to-center spacing between spots of 300 um. To obtain a reliable read-out, each capture probe is printed in quadruplicate using a re-dip after four slides. Spotted glass slides are subjected to post processing as recommended by the manufacturer. In brief, CodeLink slides are designed to covalently immobilize amine-modified oligonucleotides for microarrays. However, the reactive groups are moisture sensitive and slides must be stored desiccated, hence the coupling of C6-amino linker oligonucleotides to the surface takes place in a humid environment following printing. Consequently, following printing, arrays are collected and introduced into bottom-sealed racks (e.g. microscope slide racks) that are placed in boxes containing a saturated solution of sodium chloride.

(Note: To prepare a saturated solution of sodium chloride, add as much solid NaCl to water as needed to form a 1 cm deep slurry in the bottom of the box). Boxes are sealed with saran wrap or airtight lids, and stored overnight at room temperature. The next day, printed arrays are transferred into glass racks and residual reactive groups on the CodeLink surface are inactivated by incubation with post-coupling blocking solution (pre-warmed to 50C) for 30 min in the water bath (50C). Then the slides are rinsed twice with deionized water and a third time with post-coupling washing solution (pre-warmed to 50C) for 30 min on the shaker. Slides are then briefly rinsed with deionized water. Subsequently, the racks are placed into microplate carriers, and centrifuged for 2 min at 1500 rpm.

Ready-to-hybridize slides can be stored for up to 6 months at room temperature in a dessicator.


title: Illumina Genome Analyzer (Ornithorhynchus anatinus)

organism: Ornithorhynchus anatinus


title: Microarrays Inc. Human Genomic 49K MI Ready Array [HEEBO]

city: New Haven

first: Vanja

last: Duric

state: CT

address: 34 Park Street

institute: Yale University

manufacture_protocol:
MI Ready Array – Human utilizes the whole genome probes developed by the Human Exonic Evidence Based Oligonucleotide (HEEBO) collaboration.  This optimized collection of 70mer probes was largely derived from constitutively expressed exons, and allows for the interrogation of nearly 25,000 human genes.  The exon-centric probe design can be used to differentiate alternatively expressed exons.  The HEEBO design also supports comparative genome hybridization (CGH) analysis. These arrays also contain an extensive assortment of controls that may facilitate accurate evaluation of expression results
Production: MI precisely prints these 48,958 probes onto a single 1” x 3” standard-sized slide within HEPA filtered, environmentally controlled clean-rooms.  Our manufacturing processes utilize MI proprietary technologies and intellectual property licensed through Oxford Gene Technology.


title: Bovine Oligo array 25K

city: Quebec

first: Isabelle

last: Gilbert

state: Quebec

address: Pavillon INAF

department: Sciences Animales

institute: Universite Laval

organism: Bos taurus

manufacturer: Texas A&M University and University of Missouri

manufacture_protocol:
1.The Bovine oligo array has a total of 25, 200 oligonucleotides including unknown sequence, positive and negative control
2.16,846 oligo sequences correspond to protein-encoding transcripts taken from the Bovine Oligo Microarray Consortium database (BOMC, http://www.bovineoligo.org).
3. The oligos are 70-mer in length
4. The array is printed in singlet using an Arrayjet Supermarathon instrument onto Corning GAPS II slides.
5. The DNA is cross linked to each slide and blocked using a BSA block
6. Each batch of slides is QC checked for the deposition of the oligonucleotides and a with test hybridisations using amplified RNA probes.


title: SBC Rat cDNA Microarray

city: Shanghai

first: xk

last: teng

state: Shanghai

address: 151 LiBing R.d

department: technical support

institute: ShanghaiBio

organism: Rattus norvegicus

manufacture_protocol: The cDNA fragments of selected genes were amplified by PCR and the final concentration is ranged from 200 ng/µl to 250 ng/µl. The cDNA fragments were spotted on poly-lysine coated slides by using OmniGrid 100 spotter and cross linked in 400 mJ UV. Keep temperature(room temperature: around 20℃) and the humidity(50%-55%).


title: Agilent 020807 Shanghai Institutes for Biological Sciences Bombyx mori 15K array

status: Public on Oct 12 2010

first: Shuai

last: Zhan

address: 300 Fenglin Road

organism: Bombyx mori

description: 14623 silkworm candidate genes according to SilkDB were arranged on the Agilent 8*15K two-color chips.

first: Yongping

last: Huang

manufacture_protocol: see Agilent official protocal


title: S. cerevisiae Chr 3, 6, and other regions on both DNA strands at 10-bp resolution

city: Bethesda

first: Carl

last: Wu

state: MD

address: 37 Convent Dr, 6068

department: LBMB

institute: NIH/NCI

organism: Saccharomyces cerevisiae

description: Genome build: S. cerevisiae, USCS sacCer1, SGD, October 2003

first: Ed

last: Luk

manufacture_protocol: Custom array, CGH


title: Agilent-023080 Drosophila Exon Array 105K (Feature Number version)

status: Public on Oct 11 2010

city: Helsinki

first: Heli

last: Pessa

address: Haartmaninkatu 8

department: Faculty of Medicine; Research Programme in Translational Immunology

country: Finland

institute: University of Helsinki

organism: Drosophila melanogaster

description:
Arrays of this design have barcodes that begin with 16023080 or 2523080.
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).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.
Agilent-023080 DM_exonarray (custom array)
Platform based on file 023080_D_GEO_20090225.txt
*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL10915.


title: J.Kim Yeast Operon (2005,2006,2007)

city: Philadelphia

first: Daniel

middle: Francis

last: Simola

address: 1041 BRB II/III

department: Cell and Developmental Biology

institute: University of Pennsylvania

description:
This 'platform' represents the following three prints of the Operon Saccharomyces cerevisiae (yeast) AROS V1.1. All three gal files and additional annotations are present in the supplementary files (links below).
30 August 2005: 15538 spots
11 July 2006: 15552 spots
26 March 2007: 15552 spots

manufacturer: Operon Biotechnologies merged with Eurofins MWG Operon

manufacture_protocol: Corning UltraGAPS glass slides spotted using the Operon AROS for Saccharomyces cerevisiae, V1.1 target library


title: Lawrence Livermore Microbial Detection Array version 2

city: Livermore

first: Kevin

last: McLoughlin

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

organism: synthetic construct

description: Array design is described in Gardner S, Jaing CJ, McLoughlin KS, Slezak TR, 'A Microbial Detection Array (MDA) for Viral and Bacterial Detection', submitted to BMC Genomics, 2010.

manufacture_protocol: see manufacturer's web site www.nimblegen.com


title: Lawrence Livermore Microbial Detection Array version 1

description: Array design is described in Gardner S, Jaing CJ, McLoughlin KS, Slezak TR, 'A Microbial Detection Array (MDA) for Viral and Bacterial Detection', submitted to BMC Genomics, 2010. Sample Viral_mix_5 was analyzed using NDF file 943009.ndf; all others with 2007-08-13_943009_viral_LL.ndf, for array with identical probe designs but different layout.


title: Laval University-Arborea project 3.4K Populus trichocarpa x P. deltoides hybrid (clone H11-11)

city: Québec

first: John

middle: J

last: MacKay

state: Québec

address: 1030 avenue de la medecine

department: Wood and forestery Departement

institute: Laval University - ARBOREA

organism: Populus trichocarpa x Populus deltoides

description:
The cDNAs were printed on Corning UltraGaps slides with the Chipwriter Pro microarray printer (Bio-Rad Laboratories, Hercules, CA, USA). SMP3 Microspot quill pins (TeleChem International, Sunnyvale, CA, USA) in a 48-pin tool were used to deposit ~7 nL (~0.2 ng cDNA) per spot onto the slide.
Populus trichocarpa x Populus deltoides hybrid (clone H11-11)

manufacture_protocol: EST sequence production and analysis  Five cDNA libraries were constructed from primary or secondary stem tissues, or from leaf tissues of young trees (80 to 120 cm tall) grown under greenhouse conditions (Table 1). Four of the libraries (GQ009 to GQ012) used healthy plants of Populus trichocarpa x P. deltoides hybrid (clone H11-11) subjected to conditions that altered plant N-status, and one library (GQ014) was made from leaves of naturally occurring Populus deltoides x P. balsamifera (jackii) inoculated with the rust-causing fungal pathogen Melampsora medusae Thüm. (1878). A complete description of the tissues and methods used for these libraries, together with other Populus libraries developed by the Arborea project (Université Laval), has been made available at www.arborea.ulaval.ca. For each library, cDNA was prepared from 500 ng poly A+ selected RNA, directionally ligated into the pBluescript II SK (+) vector (Stratagene, La Jolla, CA, USA), and transformed by electroporation into Escherichia coli DH10B cells (Invitrogen, Carlsbad, CA, USA) for propagation. The high-throughput sequencing procedures, which included colony selection, plasmid isolation, sequencing reactions and capillary analysis, were conducted as previously described by Pavy et al. (2005). Sequencing of 7,680 random cDNA inserts was performed from the 5’ end by using purified plasmid as templates. The sequencing results are summarised in Supplementary Table 1.       The sequence data from the 7680 cDNAs were trimmed to remove vector and low-quality portions of the reads. In total, 5851 quality reads with at least 100 contiguous nucleotides were obtained that had Phred20 quality scores. Cluster analysis was carried out as described by Pavy et al. (2005) and produced 4628 unique sequences, comprising 956 contigs (alignment of sequences from two or more cDNAs) and 3052 singleton ESTs.         Functional annotations of the resulting unique consensus sequences (from contigs and singletons) were performed by sequence similarity searches using BLAST and HMM against several databases (nr, pfam, PopGI) as well as gene ontology assignment and classification into multigene families. The similarity searches were updated in March 2009.     Selection of cDNA clones, amplicon production and microarray printing  We selected 3444 unique cDNA clones to use in microarray production, based on the following criteria and procedures. First, we counter-selected against redundant sequences by forming clusters of sequences sharing greater than 95% identity over 100 bp and selecting a single cDNA per cluster to create a target, as described in Pavy et al. (2008). Second, we selected cDNAs to restrict the insert length to between 400 bp and 2000 bp for efficient PCR amplification and to ensure relative uniformity of amplicon concentrations (Pavy et al., 2008). Finally, to avoid including putative Melampsora cDNAs from library GQ014, we removed the sequences unique to that specific library and which did not match sequences from the first (unassembled) release of reads from the poplar genome sequence.       The cDNA clones selected for inclusion on the microarray were robotically rearrayed from daughter glycerol stock and PCR amplified as described in Pavy et al. (2008). All of the rearrayed clones were sequenced from the 5’ end to enable validation of the identity of each cDNA spotted on the microarray (Table 1). A sequence was obtained for 3120 (90%) of the original clones. Among the quality sequences (Phred 20 over 100 nt), 95% gave an exact match with the original sequence of the cDNA clone.        Plasmid inserts were PCR-amplified in a GeneAmp PCR System 9700 (Applied Biosystems, Foster City, CA, USA) by using 2.5 µL of lysed culture, 0.2 µM M13 reverse, 0.2 µM -21M13 forward, 15 mM MgCl2, 100 mM Tris-HCl, 500 mM KCl, 250 µM dNTPs, 9U AmpliTaq, and nuclease-free H2O to bring the final volume to 100 µL. PCR conditions were as follows: 5 min at 94°C denaturation; 31 cycles of 30 sec at 94°C, 30 sec at 50°C, and 2 min at 72°C; and 7 min at 72°C. Three L of each PCR product were run on a 1.2% agarose gel (E-Gel® Pre-cast Agarose Electrophoresis System, Invitrogen) to assess quality and yield was determined at 260 nm with a SpectraMax plus (Molecular Devices, Sunnyvale, CA, USA). Of the 3444 clones, more than 94% of the amplicons consisted of a single product, which had sufficient intensity and the expected size.       PCR products were robotically purified on Multiscreen PCR filter plates (Millipore, Etobicoke, ON, Canada), consolidated into 384-well plates, lyophilised by speed-Vac, and resuspended in 20 µL 50% DMSO. The cDNAs were printed on Corning UltraGaps slides with the Chipwriter Pro microarray printer (Bio-Rad Laboratories, Hercules, CA, USA). SMP3 Microspot quill pins (TeleChem International, Sunnyvale, CA, USA) in a 48-pin tool were used to deposit ~7 nL (~0.2 ng cDNA) per spot onto the slide. The PCR products were randomised prior to spotting to avoid a biased distribution of cDNA from libraries or tissues. The resulting microarrays have a 4 x 6 subgrid layout with 160 spots per subgrid, with each spot having an approximate diameter and pitch of 100 µM and 200 µM, respectively.


title: National Institute of Fruit Tree Science/Fruit Genome Research Team -Pyrus pyrifolia-18,862-ver017286

city: Tsukuba

first: Chikako

last: Nishitani

institute: National Institutes of Fruit Tree Science

organism: Pyrus pyrifolia

manufacture_protocol: Agilent custom array 60mer probes


title: PhotorhabdusTT01-4144 genes

status: Public on Oct 13 2010

city: Montpellier

first: Sophie

last: Gaudriault

address: case courrier 54, Place Eugène Bataillon

country: France

institute: Université Montpellier 2 - Institut National de la Recherche Agronomique

organism: Photorhabdus laumondii subsp. laumondii TTO1

description: spotted PCR amplicons (300-600 bp)

manufacturer: BayerCropScience, 4 rue Pierre Fontaine 91058 Evry

manufacture_protocol:
1. Primers were designed by use of a modified version of Primer 3 software (CAAT-Box) to amplify specific fragments (300 to 600 bp).
2. Primers were synthetized by Operon (25pmol/µl). The mix of the forward and reverse primers were provided in 96 deepwell plates.
3. Primers were transfered in 384 well plates Thermofast Abgenes (Merck) and mixed  with dNTP (25mM),  Titanium DNA polymerase (5U/µL; Clontech) and Photorhabdus luminescens TT01 genomic DNA (30 ng/µL).
4. Probes were amplified in a Genmate robot (hybridization temperature: 62°C, elongation time: 1 min; 35 cycles). Two rounds of PCR were performed in order to have more than 1 µg of PCR product.
5. Quality and quantity of the final matrix were checked by gel electrophoresis of the amplified probes and sequencing of 96 randomly chosen amplified probes.
6. Probes wer purified on Multiscreen PCR filter plates according to the manufacturer protocol (Millipore).
7. The probes concentration were evaluated with picrogreen labelling and spectrophotometer measure (Spectra Fluor S).
8. The plates were lyophilized at low temperature and the probe concentrations were adjusted to 30ng/µl in 50% DMSO.
9. 10 µL of each well was transferrred in a 384 well plate compatible with the spotter Gen III (Amersham).
10. Spotting was performed using the Gen III Amersham spotter (distance between spots : 260 µm, spots diameter :230 µm, atmosphere humidity : 50%). Each probes is spotted twice on a slide (Rep1 and Rep2 in the raw data files)


title: 454 GS 20 (Petromyzon marinus)

status: Public on Oct 08 2010

organism: Petromyzon marinus


title: Agilent-013282 Human Genome CGH Microarray 44B (Probe name version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Human Genome CGH Microarray 44B, high-resolution, high performance 60-mer oligonucleotide, allowing genome-wide survey and molecular profiling of DNA copy number changes on a single chip.  It provides comprehensive genome-wide coverage with emphasis on the most commonly studied genomic regions and cancer-related genes.  It consists of ~43,000 60-mer oligonucleotide probes, empirically validated in multiple model systems, spanning coding and noncoding sequences with average spatial resolution of 35kb.  It replaces 44A (G4410A), includes all biological probes from 44A, mapped to the latest NCBI build, 35), plus an additional ~ 2,500 probes to expand coverage in the human genome.  Agilent has taken extra measures to design the microarray that truly represents the coverage and performance needed for this application.  Agilent has developed and optimized assay protocols that enable researchers to use nanogram levels of total genomic DNA without genome complexity reduction.

*** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL2879.


title: FDA/CBER-human-16K-OMAD v1.0 & OMAD v1.1

status: Public on Oct 16 2010

first: Falko

last: Schmeisser

address: 8800 Rockville Pike, building 29A, room 3C-05

department: DVP

institute: FDA/CBER

manufacture_protocol: All seven sub-series used the same platform. In-house human oligo arrays were printed on glass slides coated with poly-L-lysine. The arrays contained a total of 16 659 seventy-mer oligonucleotides chosen from 750 bases of the 3' end of each open reading frame (ORF) (Operon - Human Genome Oligo Set V1.1 and V1.0, OMAD Release: 01/14/2003, Qiagen). Printing was performed using the Omnigrid Arrayer (GenomicSolutions). For detailed reference and quality control see Yang et al., 2006. Analysis of the Quality of Contact Pin Fabricated Oligonucleotide Microarrays. Molecular Biotechnology 34: 303-315.


title: Agilent-025188 Custom Agilent Myzus Persicae Array

status: Public on Oct 07 2010

city: Harpenden

first: Chris

last: Bass

state: Hertfordshire

address: West Common

department: Biological Chemistry

country: United Kingdom

institute: Rothamsted Research

organism: Myzus persicae

description: All sequences on which the array probes are designed are publically available at http://www.aphidbase.com/aphidbase/downloads under Myzus454(fasta) and MyzusSanger(fasta).

manufacture_protocol: The custom microarray used in this study was designed using the Agilent eArray platform (Agilent Technologies) by the Georg Jander Lab and is based on a previously described array containing probes for >10, 000 M. persicae unigenes produced by Sanger sequencing (Ramsey, Wilson et al. 2007) augmented with an additional 30,517 probe set designed on EST unigene sequences identified in a 454 sequencing project (Ramsey, Rider et al. 2010). The final slide layout consists of four arrays of 45,220 60-mer probes and these are produced by Agilent by in situ oligonucleotide synthesis. References: Ramsey, J. S., D. S. Rider, et al. (2010). "Comparative analysis of detoxification enzymes in Acyrthosiphon pisum and Myzus persicae." Insect Molecular Biology 19: 155-164. Ramsey, J. S., A. C. C. Wilson, et al. (2007). "Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design." BMC Genomics 8.


title: TCI University of Hannover Oryza sativa 864 oligo array

status: Public on Oct 04 2010

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

institute: Universität Hannover

organism: Oryza sativa

description: The microarray presents 262 oligonucleotides (50mers) spottet in triplicate encoding for selected genes involved in suberin and lignin synthesis in Oryza sativa. Synthetic 50mer oligonucleotides (Ocimum Biosolutions, Ijsselstein, Netherlands) were spotted in triplicates on aldehyde modified glass slides (VSS25, CEL Associates, Inc., Pearland, TX, USA) using an Affymetrix 417 arrayer.

first: Alexander

last: Fleck

first: Philipp

last: Rüdinger

manufacture_protocol: Oligonucleotide design and synthesis: 50mer oligonucleotides with a 5’ aminolink were designed and synthesised by Operon (Cologne, Germany). Spotting protocol: To produce microarrays silylated slides were purchased from TeleChemTM International Inc. (Sunnyvale, CA, USA) and the printing of the oligonucleotides was performed by using an AffymetrixTM 417 arrayer. Oligonucleotide solutions were prepared in 96-well-plates containing each 30 µl. The concentration of the printed oligonucleotides was 50 µM in 1x ArrayItTM Microarray Spotting Solution Plus. After spotting, the slides were incubated at 80 °C for 2 h. Slides were blocked in SSC containing 1% BSA (Sigma) for 45 min and rinsed with water for 5 min.


title: Micro-CRIBI Human Oligo Array (Operon V2.0)

city: Chieti

first: Florina

last: Raicu

state: Abruzzo

address: Via Colle dell'Ara

department: Aging Research Center (CESI)

institute: G. d’Annunzio University Foundation Chieti

manufacturer: CRIBI University of Padova microarray facility (http://microcribi.cribi.unipd.it)

manufacture_protocol:
This set consists of 21,329 70mer oligonucleotides (Operon version 2.0) designed on Human Unigene clusters, mainly in the 3 end terminal region. Each oligonucleotide is spotted by our robotic station Biorobotics Microgrid II, in two replicates on a MICROMAX glass slide SuperChip I (Cat No MPS696) provided by PerkinElmer Life Sciences Inc. The deposition is qualitatively assessed by a scan of the spotted slide at 10 micron resolution, using a GSI Lumonics scanner and a protocol that allows the detection of spotted features through the salts derived from the dried solution in which oligonucleotides are dissolved. Microarray slides that meet the quality standards, are washed as recommended by the supplier and the glass slides are stored, ready for use, in the dark under deep vacuum.
Keywords = Oligo
Keywords = probe 70mer
Keywords = MicroCribi
Keywords = probe set 21.329


title: SMD Print_1538 Helicobacter pylori

city: Seattle

first: Nina

middle: Reda

last: Salama

state: WA

address: 1100 Fairview Ave. N

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

organism: Helicobacter pylori

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


title: Winzeler Lab Plasmodium vivax tiling array (PvivaxLib520507)

status: Public on Oct 02 2010

city: La Jolla

first: Neekesh

last: Dharia

state: CA

address: 10550 N Torrey Pines Road

institute: The Scripps Research Institute

organism: Plasmodium vivax

first: Elizabeth

last: Winzeler

manufacture_protocol: Whole genome tiling at 6 bp spacing, see manufacturer's website.


title: University of Alberta Bovine 24K long oligo array

first: Masaaki

last: Taniguchi

state: Ibaraki

address: 2 Ikenodai

department: Division of Animal Breeding and Reproduction Research

institute: Institute of Livestock and Grassland Science National Agriculture Food Research Organization

description:
UniGene ID of sequence used to design oligonucleotide probe, Gene symbol, GenBank accession number and gene description were annotated in the GeneSifter based on the UniGene ID.

The oligonucleotide sequences are provided as a supplementary file.

manufacturer: Oligo design: Bovine Oligo Microarray Consortium; Array preparation: University of Alberta, Agricultural Genomics and Proteomics Unit

manufacture_protocol:
1.Oligos are arrayed in 384-well flat-bottom plates. Each well contains 300 pmol of 70-mer oligo.
2. Resuspend oligos in 15 µL of 150 mM sodium phosphate buffer (pH 8.5).
3. Transfer 0.25 µL from each well to to a new set of plate.
4. Seal plates and centrifuge plates at 2000 rpm for 3 minutes to allow the solution sink to the bottom.
5. Up take 0.5 nL from each well to spot the oligos onto the UltraGap slides (Corning, USA).
6. The 70-mer oligonucleotides were spotted at room temperature and 42% humidity with 100 µm centre-spacing using Q-array system with Telechem 946MP2 pins.
7. The spot diameters were 55 µM with duplicate of 24,000 spots on each slide.
8. After the print run is completed, allow plates to dry through passive evaporation in a protected environment.
9. The slides were cross-linked by UV.
10. The slides were stored at room temperature in dessicators.
11. After printed the slides, the plates were vacuum dried for storage.


title: Nimblegen_Custom_PAH_array_V01

status: Public on Oct 01 2010

city: AUBIERE

first: TERRAT

last: Sebastien

address: 24, avenue des Landais, Campus des Cézeaux

department: Génomique Intégrée des Interactions Microbiennes

institute: UMR CNRS 6023

organism: Sphingomonas paucimobilis

description: The Platform data table reflects a condensed representation of the expression array's replicates (SEQ_ID) features.  The .ndf file is linked below as a supplementary file.

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


title: [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array - custom CDF (ATH1-121501.TAIR8)

city: Blacksburg

first: Andy

last: Pereira

state: VA

address: Washington Street MC0477

department: Virginia Bioinformatics Institute

institute: Virginia Tech

organism: Arabidopsis thaliana

description: The custom CDF was built by uniquely mapping 232,697 probe sequences to 21,389 Arabidopsis (TAIR8) gene-based probe sets in the following manner: (i) probes that have perfect sequence identity with a single target gene were selected, (ii) probes mapping to reverse complements of genes were annotated separately as antisense probes (not used in the above counts), and finally, (iii) probes were grouped into probe sets, each corresponding to a single gene, and probe sets having at least 3 unique sequences were retained (>99% probe sets have >=5 probes). Note that these stringent criteria used to construct the CDF make it possible to reliably measure expression values of members of multigene families (free from cross-hybridization between paralogs showing high sequence similarity).

relation: Alternative to: GPL198 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site.


title: Agilent-023080 Drosophila Exon Array 105K (Probe Name version)

first: Heli

last: Pessa

description:
Agilent-023080 DM_exon array (custom array)

*** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL10921.

manufacture_protocol: Drosophila melanogaster exon sequences were retrieved from Ensembl database (build BDGP5.4). In addition, exon-exon junction probes were designed for genes containing U12-type introns. 60-mer probes were designed with Agilent eArray design tool using the default parameters. A total of 56,163 probes were utilized for producing Agilent 105K arrays. For details, see manufacturer's web site at http://www.agilent.com/


title: Arabidopsis thaliana 34K NARC serie 8

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

description: Norwegian Arabidopsis Research Center (NARC)

manufacturer: Norwegian Microarray Consortium, Trondheim

first: Atle

last: Bones

first: Torfinn

last: Sparstad

first: Hallgeir

last: Bergum

manufacture_protocol:
1. Oligos used in the production of the microarrays are from the Qiagen-Operon Arabidopsis Genome Array Ready Oligo Set (AROS) Version 3.0, while the custom made oligos were produced by Operon (Alameda, CA, USA) or MWG (Ebersberg, Germany). Information about the AROS probes is available at: http://omad.operon.com/arabidopsis/
2. Oligos are arrayed in Genetix X6004 384 well plates with V-shaped bottom. Each well contain 600 pmol 70 mer oligo
3. Oligos were resuspended in 16 µl Milli-Q-filtered DNase free water and 8 µl from each well were transfered to new set of Genetix X6004 384 well plates using a Tecan Genesis RSP 200 liquid handling workstation.
4. 8 µl DMSO were added to each well giving a final oligo consentration of ~20 µM and 50% DMSO.
5. The plates were sealed with ABgene Adhesive PCR Foil seals and centrifuged at 1000 rpm in a Sorvall RT6000B centrifuge. The plates were stored at -20C.
6. The plates were thawed and placed on a rotary shaker for 12 hour before printing of oligos.
7. The oligos were printed on amino silane coated UltraGaps slides (Corning, NY, USA) using a BioRobotics MicroGrid II robot (Genomic Solutions, MI, USA).
8. After printing the micorarray slides were exposed for UV light in a Stratalinker 2400 UV crosslinker (Stratagene), at 800 milijoules/cm2.
9. Microarray slides were stored under low humidity conditions and not exposed to light.


title: 454 GS (Caenorhabditis elegans)

last: GEO

organism: Caenorhabditis elegans


title: MIT/Sinskey-R. eutropha-10100-1 custom array [reutropha520723F]

status: Public on Aug 27 2010

city: Cambridge

first: Christopher

middle: John

last: Brigham

state: MA

address: 31 Ames Street

department: Biology

institute: Massachusetts Institute of Technology

organism: Cupriavidus necator


title: ARK-Genomics bovine 25k array v2

status: Public on Jul 27 2010

city: Roslin

first: Michael

middle: Bryan

last: Watson

state: Midlothian, EH25 9PS

address: Roslin Biocentre

department: ARK-Genomics

institute: The Roslin Institute

organism: Bos taurus

first: Richard

last: Talbot

manufacture_protocol: Oligos were resuspended in Corning Pronto Epoxide spotting solution to give a final concentration of 20uM. DNA was printed on Corning Epoxide slides using a Genomic Solutions MicroGrid II arrayer and the MicroSpot 10K pins, according to manufacturer's instructions. All printing was carried out in conditions of constant humidity (52% RH) and temperature (20C) in a room supplied with HEPA filtered air. Prior to printing the pins were cleaned by ultra-sonication in water and if necessary 50mM potassium hydroxide. A test print of all pins was carried out by printing Cy3 streptavidin conjugate dye in printing buffer onto epoxide slides and printing 100 features per pin. When all pins were printing consistent size spots for more than 80 features they were accepted as ready to print. The MicroGrid II was then programmed for the array print run, with a grid layout file prepared to allow duplicate printing at random within a patch. At the end of the print run the slides were removed following the program instructions in preparation for post processing. Slides dessicated overnight and then transferred to a humid chamber (45% humidity, 42C) for 8 hours. The slides were then washed in 0.2% SDS (room temperature) for 2 minutes with agitation before being rinsed in three water washes (30seconds, 30 seconds, 1 minute) with agitation. After these steps the slides were then incubated in water at 50C for 20 minutes before spin drying. The slides were then stored in a desiccator in the dark ready for use.


title: University of Alberta Escherichia coli 19K v1.0

status: Public on Jul 13 2010

city: Ann Arbor

first: Dongjuan

last: Dai

state: MI

address: 109 Observatory St

department: Environmental Health Sciences

institute: University of Michigan

organism: Escherichia coli

description: Escherichia coli K12, O157:H7 (EDL933, Sakai)

manufacturer: University of Alberta, Department of Biological Sciences, Microarray and Proteomics Facillity

manufacture_protocol:
1. It contains 5,978 70mer oligos and a control set of 12 positive and 12 negative controls.
2. A total of 19086 spots are printed at 200 um spacing in a 4 by 4 block of sub-arrays in triplicate in each slide.
3. Oligos are dissolved to a final concentration of 18.75 uM in 150 mM NaPO4 buffer (pH 8.7) prior to printing.
4. Slides are Corning Epoxide slides.
5. Oligos represing 4,289 ORF's in Escherichia coli K12, 5,029 ORF's in O157:H7 (EDL933), and 4,836 ORF's in O157:H7 (Sakai).
6. All probes are designed within ORFs from both clones and predicted ORF's.
7. All probes are Tm nomalized to 75 (+/- 5) degree C and have a 5' amino linker.


title: MEEBO Mus musculus Oligo 70mer Array V36547

status: Public on Aug 24 2010

city: San Francisco

first: Sajeev

last: Batra

institute: UCSF

organism: Mus musculus

manufacturer: UCSF Center for Advanced Technology (CAT)

first: Ash

last: Alizadeh

first: Max

last: Diehn

first: Chris

last: Seidel

first: Lik

last: Mui

first: Mike

last: Hagen

first: Catherine

last: Foo

first: Jess

last: Leber

first: David

last: Erle

first: Jean

last: Yang

first: Andrea

last: Barczak

first: Derisi

last: Joesph

first: Jing

last: Zhu

first: Pat

last: Brown

first: Kate

last: Rubins

first: Stephen

last: Popper

first: Joesph

last: Marquis

last: Fero

first: John

last: Coller

first: Peng

last: Zhang

first: Niki

last: Chin

first: Elena

last: Seraia

last: Pollack

first: Young

last: Kim

first: Terri

last: Gaasterland

first: Ben

last: Snyder

first: Alexey

last: Novoradovsky

first: Mihaela

last: Zavolan

manufacture_protocol: Oligos are arrayed in Genetix x7020 384-well plates.  Each well contains 200pmol of 70-mer oligo.  During the first round of resuspension, oligos were resuspended in 3XSSC to a final concentration of 30 micromolar.  After each print, oligos are dried in a vacuum centrifuge.  During subsequent prints, oligos are resuspended in water to a final concentration of 30 micromolar taking into consideration the amount of oligo printed in the previous printrun.  Oligos are printed using 48 Parallel Synthesis silicon 50 micrometer printing tips on a DeRisi-style custom built microarrayer.  A sector width of 28 and a spacing of 155 microns is employed.


title: NimbleGen_Zymomonas mobilis ZM4_4x72K array

city: Beppu

first: Takeshi

last: Hayashi

address: Kitaishigaki 82

department: Faculty of Food and Nutrition

institute: Beppu university

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

description: NimbleGen design name 2008-07-30_RDKK095_Zmob_60mer_expr.  1,998 genes from Zymomonas mobilis ZM4 with eighteen 60-mer probe pairs (PM/MM) per gene.  Each probe is replicated 2 times.


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene10stv1_Mm_ENSG]

city: Bar Harbor

first: Ricardo

middle: Alejandro

last: Verdugo

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

relation: Alternative to: GPL6246 (Alternative CDF [official])

manufacture_protocol: This is identical to GPL6246 but a custom cdf environment was used to extract data.  The  custom CDF file is based on Ensembl (NCBI 37, Ensembl 49) genes (from http://brainarray.mbni.med.umich.edu, V 11.0.1). The custom cdf is linked below as a supplementary file.


title: Agilent-029784 ETEC_CGH

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

description: ETEC CGH Microarray. Oligos designed for conserved regions. Arrays of this design have barcodes that begin with 16029784 or 2529784.. 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).. To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions..

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


title: Francisella tularensis full genome qRT-PCR

last: Braisted

address: 9704 Medical Center Dr

institute: J Craig Venter Institute

organism: Francisella tularensis

first: Marcus

last: Jones

first: Qiang

last: Sun

first: Tatiana

last: Dracheva


title: Agilent-029850 T_vaginalis_array

status: Public on Oct 05 2010

organism: Trichomonas vaginalis

description: T. vaginalis array designed using the T. vaginalis overkill array data. Oligos expressed in different conditions and have intensity above the 95th percentile of the negative control arabidopsis oligos were chosen. For the annotated transcripts, all the oligos designed 1 oligo/transcript is included in this array.. Arrays of this design have barcodes that begin with 16029850 or 2529850.. 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).. To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions..


title: SMD Print_1482 Helicobacter pylori

first: Nina

last: Salama


title: EOHSI-BRTC_Mosquito_11,361_v1

status: Public on Jul 05 2010

city: Irvine

first: Osvaldo

last: Marinotti

address: University of California, Irvine

department: Molecular Biology & Biochemistry

institute: University of California, Irvine

organism: Aedes aegypti

description: Design ID: 016929


title: HAC Human 2.3K

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

organism: Homo sapiens

first: Dirce

last: Carraro

first: Helena

last: Brentani

first: Alex

last: Fiorine

first: Joana

last: Palha

manufacture_protocol:
Glass arrays with 2,352 elements were prepared with the aid of the Flexis Robot (Genomic Solutions, UK). Bacteria were grown in LB medium containing ampicillin (250mg/ml). Inserts were amplified by PCR using M13 reverse and forward primers and products were submitted to 1% agarose gel for quality control. cDNA clones with single amplicons were filtrated in Sephadex G50 (GE Healthcare, UK), printed onto Corning glass slides (Corning, USA) and fixed by UV crosslink (Eisen & Brown, 1999; Brentani et al., 2005). There were 1364 unique genes in the array. Those genes were defined trough literature search for genes related to
neurodevelopmental pathways.


title: Agilent-021219 New15K60mer-EfetidaArray

city: Vicksburg

first: Natalie

last: Barker

state: MS

address: 3909 Halls Ferry Rd.

institute: Engineer Research and Development Center

organism: Eisenia fetida


title: Eichler-NimbleGen Human 2.1 HD2 CGH chip

status: Public on Feb 18 2010

first: Jeffrey

last: Kidd

address: 1705 NE Pacific St

department: Department of Genome Sciences

institute: University of Washington

first: Can

last: Alkan

first: Evan

middle: E

last: Eichler

manufacture_protocol: 2.1 Million genome wide CGH chip based on UCSC hg18


title: NimbleGen Human HG18 RefSeq Promoter 385K tiling array

city: Chiyodaku

first: Yujiro

last: Tanaka

state: Tokyo

address: 2-3-10 Kandasurugadai

department: School of Biomedical Science

institute: Tokyo Medical and Dental University

description:
Source: UCSC
Build: HG18, NCBI 36
Probe Length: 50-75mer
Median Probe Spacing: 100bp
Design Name: Human ChIP 385K RefSeq Prom Arr Ser

Native NimbleGen files (ndf, ngd, pos) linked below as supplementary files.

manufacture_protocol: see manufacturer's web site


title: University of Sao Paulo-FCFRP/Molecular Biology Lab Aspergillus niger 4 X 44K v. 1.0

status: Public on Oct 20 2010

city: Ribeirao Preto

first: Wagner

middle: Rodrigo

last: de Souza

state: Sao Paulo

address: Av do Cafe

department: Pharmaceutical Sciences

institute: University of Sao Paulo

organism: Aspergillus niger

manufacture_protocol: in situ oligonucleotide were synthesized directly on the glass microarray surface according to SurePrint Technology (Agilent Technologies), as described in manufacturer's protocol. Basically, in situ oligonucleotides were synthesized base by base on a solid glass surface, one layer at a time, based on standard phosphoramadite chemistry.


title: FZ_IBT1_Cglutamicum_10K_ver2

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

organism: Corynebacterium glutamicum ATCC 13032

description: C. glutamicum ATCC 13032, based on the genome sequence entry NC_006959

manufacture_protocol: spotted with 70-mer oligonucleotides obtained from Operon (Cologne, Germany)


title: NimbleGen_2007-06-15_WiCell_HG18_p14

status: Public on Dec 07 2009

city: Madison

first: Melodee

last: Patterson

state: WI

address: 510 Charmany Dr Ste 58 & 59

institute: WiCell

first: Karen

last: Montgomery

first: Chuhu

last: Yang

manufacture_protocol: Standard NimbleGen maskless array synthesis for standard 60-mer hg18 gene expression array


title: Human Tumor Necrosis Factor (TNF) Ligand and Receptor PCR Array cat. #PAHS-063

status: Public on Jul 29 2009

city: Tainan

first: Chang-yi

last: Lin

address: No.1, University Road

department: institute of basic medical science

country: Taiwan

institute: National Cheng Kung University

description: The Human Tumor Necrosis Factor (TNF) Ligand and Receptor Signaling Pathways RT² Profiler™ PCR Array profiles the expression of 84 genes whose expression is controlled by or involved in the TNF ligand and TNF receptor signaling pathways. Members of the TNF Superfamily and TNF Receptor Superfamily are represented on this array. Genes involved in the TNFR1 and TNFR2 Signaling Pathways are also included. Using real-time PCR, you can easily and reliably analyze expression of a focused panel of genes related to the TNF signaling with this array.

manufacture_protocol: see website


title: Genotypic Human Promoter 244K Microarray

status: Public on Jul 28 2009

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description:
Covers -5.5kb upstream to +2.5kb downstream of ~15000 known transcripts start site and Known ENCODE regions. Substitute for Agilent catalog human ENCODE array.
Design ID: 019469

first: Raja

last: Mugasimangalam

first: Rohit

last: Shukla

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


title: Illumina Genome Analyzer II (Arabidopsis lyrata)

last: GEO

country: USA

organism: Arabidopsis lyrata


title: Illumina HumanWG-6 v3.0 expression beadchip [Entrez ID - condensed version]

city: milan

first: Federico

last: Colombo

address: via F. Sforza 35

institute: fondazione IRCCS Ca' Granda

technology: oligonucleotide beads

description: This platform represents Entrez ID condensed version of Illumina HumanWG-6 v3.0 expression beadchip GPL6884.

manufacture_protocol: see manufacturer's website


title: Human lincRNA 364k Tiling Array V1

status: Public on Jul 09 2009

city: Cambridge

first: Mitchell

last: Guttman

address: 7 Cambridge Center

institute: Broad Institute

description:
Platform annotation based on genome build hg18, NCBI Build 36.1.
50mer oligos.
The .ncd, .ndf and .pos files are linked below as supplementary files.

first: Ahmad

last: Khalil

first: Eric

middle: S

last: Lander

first: John

middle: L

last: Rinn

manufacture_protocol: see manufacturer's web site www.nimblegen.com


title: Human lincRNA 391k Tiling Array V2

description:
Human lincRNA array, same as GPL8791 but included ~1000 protein coding genes as controls.
Platform annotation based on genome build hg18, NCBI Build 36.1.
50mer oligos.
The .ncd, .ndf and .pos files are linked below as supplementary files.


title: NimbleGen Mus musculus MM9 Expression Array (12x135k)_ALL PROBES

city: Montpellier

first: Laurent

last: Journot

address: 141 rue de la Cardonille

institute: MGX - Montpellier GenomiX

description:
This is a whole mus musculus genome array in 12-plex format provided by nimblegen.
Here we consider all the probes of the array separately (132489 ID). Alternative Platform GPL10192 represents only the ID for the GenBank Accession Number (44170 ID).

Design name: 090901_MM9_EXP_HX12.
Format: 12x135K
Source: NCBI
Build: MM9
Probe Length: 60mer
Genes: 44,170
Probes/ Target: 3
Replicates: 1
NimbleGen description file(s) linked below:
GPL10994_090901_MM9_EXP.ndf
GPL10994_090901_MM9_EXP_ALL_PROBES.ngd

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


title: Nimblegen 2.1M HD2 Human Economy tiling array of hg18 at 205bp resolution set 03 of 4

status: Public on Mar 01 2009

city: Dallas

first: Gary

middle: Chung

last: Hon

state: TX

address: 5323 Harry Hines Blvd.

department: OB/GYN

institute: UT Southwestern

description: The 4 genome scan arrays were based on NCBI36 build of the human genome (hg18) and contained a total of 4 * 2.1 million 50 to 75-mer oligonucleotides, positioned at about every 205 basepairs (bp) throughout the human genome. There are a total of 3 arrays. This is set 03.

first: Nathaniel

last: Heintzman

first: David

last: Hawkins

first: Pouya

last: Kheradpour

first: Alexander

last: Stark

first: Rhona

middle: K

last: Stuart

first: Lindsey

middle: F

last: Harp

first: Zhen

last: Ye

first: Leonard

last: Lee

first: Keith

middle: A

last: Ching

first: Christina

middle: W

first: Jessica

last: Antosiewicz

first: Hui

last: Liu

first: Xinmin

last: Zhang

first: Roland

last: Green

first: Ron

last: Stewart

first: James

last: Thomson

first: Gregory

last: Crawford

first: Manolis

last: Kellis

first: Bing

last: Ren

manufacture_protocol: Whole human genome tiling arrays


title: Nimblegen 2.1M HD2 Human Economy tiling array of hg18 at 205bp resolution set 04 of 4

first: Gary

last: Hon

description: The 4 genome scan arrays were based on NCBI36 build of the human genome (hg18) and contained a total of 4 * 2.1 million 50 to 75-mer oligonucleotides, positioned at about every 205 basepairs (bp) throughout the human genome. There are a total of 3 arrays. This is set 04.

first: Nathaniel

middle: D

last: Heintzman

middle: C

first: David

last: Hawkins

first: Pouya


title: Nimblegen 2.1M HD2 Human Economy tiling array of hg18 at 205bp resolution set 01 of 4

description: The 4 genome scan arrays were based on NCBI36 build of the human genome (hg18) and contained a total of 4 * 2.1 million 50 to 75-mer oligonucleotides, positioned at about every 205 basepairs (bp) throughout the human genome. There are a total of 3 arrays. This is set 01.

last: Kheradpour

first: Alexander

last: Stark

first: Rhona

last: Stuart

first: Lindsey

first: Zhen


title: Nimblegen human 60-mer gene expression array, set 1 of 1

description: The arrays were based on NCBI36 build of the human genome (hg18) and contained a total of 390k oligonucleotides representing genes throughout the human genome. There is a total of 1 array.

last: Harp

last: Ye

first: Leonard

last: Lee

first: Keith

first: Christina

first: Jessica

manufacture_protocol: Whole human genome expression array


title: Nimblegen 2.1M HD2 Human Economy tiling array of hg18 at 205bp resolution set 02 of 4

description: The 4 genome scan arrays were based on NCBI36 build of the human genome (hg18) and contained a total of 4 * 2.1 million 50 to 75-mer oligonucleotides, positioned at about every 205 basepairs (bp) throughout the human genome. There are a total of 3 arrays. This is set 02.

last: Ching

last: Antosiewicz

first: Hui

last: Liu

first: Xinmin

first: Roland

first: Ron


title: MEEBO Mus musculus Oligo 70mer Array V37315

city: San Francisco

first: Sajeev

last: Batra

institute: UCSF

first: Ash

last: Alizadeh

first: Max

last: Diehn

first: Chris

last: Seidel

first: Lik

last: Mui

first: Mike

last: Hagen

first: Catherine

last: Foo

first: Jess

last: Leber

last: Erle

first: Jean

last: Yang

first: Andrea

last: Barczak

first: Derisi

last: Joesph

first: Jing

last: Zhu

first: Pat

last: Brown

first: Kate

last: Rubins

first: Stephen

last: Popper

first: Joesph

last: Marquis

last: Fero

first: John

last: Coller

first: Peng

last: Zhang

first: Niki

last: Chin

first: Elena

last: Seraia

last: Pollack

first: Young

last: Kim

first: Terri

last: Gaasterland

first: Ben

last: Snyder

first: Alexey

last: Novoradovsky

first: Mihaela

last: Zavolan


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 38 of 38

first: Gary

last: Hon

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 38.

first: Nathaniel

last: Heintzman

first: David

last: Hawkins

first: Pouya

last: Kheradpour

first: Alexander

last: Stark

first: Rhona

last: Stuart

first: Lindsey

last: Harp

first: Zhen

last: Ye

first: Leonard

last: Lee

first: Keith

last: Ching

first: Christina

first: Jessica

last: Antosiewicz

first: Hui

last: Liu

first: Xinmin

first: Roland

last: Green

first: Ron

last: Stewart

first: James

last: Thomson

first: Gregory

last: Crawford

first: Manolis

last: Kellis

first: Bing

last: Ren

manufacture_protocol: Whole human genome tiling arrays and the design principle of this array has been described previously (Kim et al., 2005b).


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 37 of 38

first: Gary

last: Hon

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 37.

first: Nathaniel

last: Heintzman

first: David

first: Pouya

last: Zhang


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 36 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 36.

last: Hawkins

last: Kheradpour

first: Alexander

last: Stark

first: Rhona

first: Lindsey

first: Zhen


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 28 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 28.

last: Stuart

last: Harp

last: Ye

first: Leonard

first: Keith

first: Christina

first: Jessica


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 30 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 30.

last: Lee

last: Ching

last: Antosiewicz

first: Hui

first: Xinmin

first: Roland

first: Ron


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 29 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 29.

last: Liu

last: Green

last: Stewart

first: James

first: Gregory

first: Manolis

first: Bing


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 34 of 38

first: Gary

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 34.

first: Nathaniel

first: David

first: Pouya

last: Thomson

last: Crawford

last: Kellis


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 35 of 38

last: Hon

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 35.

last: Heintzman

first: Alexander

first: Rhona

first: Lindsey

first: Zhen

last: Ren


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 31 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 31.

last: Hawkins

last: Kheradpour

first: Leonard

first: Keith

first: Christina

first: Jessica

last: Zhang


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 32 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 32.

last: Stark

last: Stuart

last: Harp

first: Hui

first: Xinmin

first: Roland

first: Ron


title: Affymetrix GrapeGen Vitis vinifera Microarray [CDF: GrapeGena520510F]

city: Mountain Grove

first: Susanne

last: Howard

state: MO

address: 9740 Red Spring Rd

department: William H. Darr School of Agriculture

institute: Missouri State University

organism: Vitis vinifera

manufacture_protocol: Affymetrix Standard 3' design using 25-mers, 11 match/mismatch probepairs per transcript, 11 micron array. GeneChips were designed as described by the manufacturer in their GeneChip Custom Express Array Design Guide (www.affymetrix.com). Poly-A control sequences of dap, lys, phe, and trp from Bacillus subtilis were also included.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 33 of 38

first: Gary

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 33.

last: Ye

last: Lee

last: Ching

last: Antosiewicz

first: James

first: Gregory

first: Manolis

first: Bing


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 19 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 19.

first: Nathaniel

first: David

first: Pouya

first: Alexander

first: Rhona

last: Liu

last: Green

last: Stewart

last: Thomson


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 20 of 38

last: Hon

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 20.

last: Heintzman

first: Lindsey

first: Zhen

first: Leonard

first: Keith

first: Christina

last: Crawford

last: Kellis


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 26 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 26.

last: Hawkins

last: Kheradpour

first: Jessica

first: Hui

first: Xinmin

last: Zhang

first: Roland

first: Ron

last: Ren


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 24 of 38

first: Gary

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 24.

last: Stark

last: Stuart

last: Harp

first: James

first: Gregory

first: Manolis


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 23 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 23.

first: Nathaniel

first: David

first: Pouya

last: Ye

last: Lee

last: Ching

first: Bing


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 21 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 21.

first: Alexander

first: Rhona

first: Lindsey

first: Zhen

last: Antosiewicz

last: Liu

last: Green


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 22 of 38

last: Hon

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 22.

first: Leonard

first: Keith

first: Christina

first: Jessica

last: Stewart

last: Thomson


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 27 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 27.

last: Heintzman

first: Hui

first: Xinmin

first: Roland

first: Ron

last: Crawford

last: Kellis


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 17 of 38

first: Gary

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 17.

last: Hawkins

last: Kheradpour

last: Zhang

first: James

first: Gregory

first: Manolis


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 18 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 18.

first: Nathaniel

first: David

first: Pouya

last: Stark

last: Stuart

first: Bing

last: Ren


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 25 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 25.

first: Alexander

first: Rhona

first: Lindsey

last: Harp

first: Zhen

last: Ye

last: Lee


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 16 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 16.

first: Leonard

first: Keith

last: Ching

first: Christina

first: Jessica

last: Antosiewicz

last: Liu


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 15 of 38

last: Hon

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 15.

first: Hui

first: Xinmin

first: Roland

last: Green

first: Ron

last: Stewart


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 13 of 38

first: Gary

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 13.

last: Heintzman

first: James

last: Thomson

first: Gregory

last: Crawford

first: Manolis


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 11 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 11.

first: Nathaniel

first: David

last: Hawkins

first: Pouya

last: Kheradpour

last: Kellis

first: Bing


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 12 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 12.

first: Alexander

last: Stark

first: Rhona

last: Stuart

first: Lindsey

first: Zhen

last: Zhang


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 14 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 14.

last: Harp

last: Ye

first: Leonard

first: Keith

first: Christina

first: Jessica

last: Ren


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 10 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 10.

last: Lee

last: Ching

last: Antosiewicz

first: Hui

first: Xinmin

first: Roland

first: Ron


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 09 of 38

first: Gary

last: Hon

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 09.

last: Liu

last: Green

first: James

first: Gregory

first: Manolis


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 07 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 07.

first: Nathaniel

last: Heintzman

first: David

first: Pouya

last: Stewart

last: Thomson

first: Bing


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 08 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 08.

last: Hawkins

last: Kheradpour

first: Alexander

first: Rhona

first: Lindsey

first: Zhen

last: Crawford


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 01 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 01.

last: Stark

last: Stuart

first: Leonard

first: Keith

first: Christina

first: Jessica

last: Kellis


title: Condensed array spanning predicted enhancers in HeLa cells. This is set 03 of 3

description: The condensed array was based on the NCBI35 build of the human genome (hg17) and contained a total 2.1 million 50-mer oligonucleotides, positioned at about every 100 basepairs (bp), focusing on places containing a H3K4me1 enhancer chromatin signature in HeLa cells. There are a total of 3 arrays. This is set 03.

last: Harp

last: Ye

first: Hui

first: Xinmin

last: Zhang

first: Roland

first: Ron

manufacture_protocol: Condensed tiling array


title: Condensed array spanning predicted enhancers in HeLa cells. This is set 01 of 3

first: Gary

description: The condensed array was based on the NCBI35 build of the human genome (hg17) and contained a total 2.1 million 50-mer oligonucleotides, positioned at about every 100 basepairs (bp), focusing on places containing a H3K4me1 enhancer chromatin signature in HeLa cells. There are a total of 3 arrays. This is set 01.

last: Lee

last: Ching

first: James

first: Gregory

first: Manolis

last: Ren


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 05 of 38

last: Hon

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 05.

first: Nathaniel

first: David

first: Pouya

last: Antosiewicz

last: Liu

first: Bing


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 03 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 03.

last: Heintzman

first: Alexander

first: Rhona

first: Lindsey

first: Zhen

last: Green

last: Stewart


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 02 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 02.

last: Hawkins

last: Kheradpour

first: Leonard

first: Keith

first: Christina

first: Jessica

last: Thomson


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 06 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 06.

last: Stark

last: Stuart

first: Hui

first: Xinmin

first: Roland

first: Ron

last: Crawford


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution set 04 of 38

first: Gary

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 38 * 390k 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 04.

last: Harp

last: Ye

first: James

first: Gregory

first: Manolis

last: Kellis


title: Nimblegen 2.1M HD2 Human Economy tiling array of hg18 at 205bp resolution set 12 of 12

description: The 12 genome scan arrays were based on NCBI36 build of the human genome (hg18) and contained a total of 12 * 2.1 million 50 to 75-mer oligonucleotides, positioned at about every 205 basepairs (bp) throughout the human genome. There are a total of 12 arrays. This is set 12.

first: Nathaniel

first: David

first: Pouya

last: Lee

last: Ching

last: Zhang

first: Bing


title: Nimblegen 2.1M HD2 Human Economy tiling array of hg18 at 205bp resolution set 06 of 12

last: Hon

description: The 12 genome scan arrays were based on NCBI36 build of the human genome (hg18) and contained a total of 12 * 2.1 million 50 to 75-mer oligonucleotides, positioned at about every 205 basepairs (bp) throughout the human genome. There are a total of 12 arrays. This is set 06.

first: Alexander

first: Rhona

first: Lindsey

first: Zhen

last: Antosiewicz

last: Ren


title: Condensed array spanning predicted enhancers in HeLa cells. This is set 02 of 3

description: The condensed array was based on the NCBI35 build of the human genome (hg17) and contained a total 2.1 million 50-mer oligonucleotides, positioned at about every 100 basepairs (bp), focusing on places containing a H3K4me1 enhancer chromatin signature in HeLa cells. There are a total of 3 arrays. This is set 02.

last: Heintzman

first: Leonard

first: Keith

first: Christina

first: Jessica

last: Liu

last: Green


title: Nimblegen 2.1M HD2 Human Economy tiling array of hg18 at 205bp resolution set 11 of 12

description: The 12 genome scan arrays were based on NCBI36 build of the human genome (hg18) and contained a total of 12 * 2.1 million 50 to 75-mer oligonucleotides, positioned at about every 205 basepairs (bp) throughout the human genome. There are a total of 12 arrays. This is set 11.

last: Hawkins

last: Kheradpour

first: Hui

first: Xinmin

first: Roland

first: Ron

last: Stewart


title: Nimblegen 2.1M HD2 Human Economy tiling array of hg18 at 205bp resolution set 08 of 12

first: Gary

description: The 12 genome scan arrays were based on NCBI36 build of the human genome (hg18) and contained a total of 12 * 2.1 million 50 to 75-mer oligonucleotides, positioned at about every 205 basepairs (bp) throughout the human genome. There are a total of 12 arrays. This is set 08.

last: Stark

last: Stuart

first: James

last: Thomson

first: Gregory

first: Manolis


title: Nimblegen 2.1M HD2 Human Economy tiling array of hg18 at 205bp resolution set 05 of 12

description: The 12 genome scan arrays were based on NCBI36 build of the human genome (hg18) and contained a total of 12 * 2.1 million 50 to 75-mer oligonucleotides, positioned at about every 205 basepairs (bp) throughout the human genome. There are a total of 12 arrays. This is set 05.

first: Nathaniel

first: David

first: Pouya

last: Harp

last: Ye

last: Crawford

first: Bing


title: Nimblegen 2.1M HD2 Human Economy tiling array of hg18 at 205bp resolution set 01 of 12

description: The 12 genome scan arrays were based on NCBI36 build of the human genome (hg18) and contained a total of 12 * 2.1 million 50 to 75-mer oligonucleotides, positioned at about every 205 basepairs (bp) throughout the human genome. There are a total of 12 arrays. This is set 01.

first: Alexander

first: Rhona

first: Lindsey

first: Zhen

last: Lee

last: Ching

last: Kellis


title: Nimblegen 2.1M HD2 Human Economy tiling array of hg18 at 205bp resolution set 07 of 12

last: Hon

description: The 12 genome scan arrays were based on NCBI36 build of the human genome (hg18) and contained a total of 12 * 2.1 million 50 to 75-mer oligonucleotides, positioned at about every 205 basepairs (bp) throughout the human genome. There are a total of 12 arrays. This is set 07.

first: Leonard

first: Keith

first: Christina

first: Jessica

last: Antosiewicz

last: Zhang


title: Nimblegen 2.1M HD2 Human Economy tiling array of hg18 at 205bp resolution set 03 of 12

description: The 12 genome scan arrays were based on NCBI36 build of the human genome (hg18) and contained a total of 12 * 2.1 million 50 to 75-mer oligonucleotides, positioned at about every 205 basepairs (bp) throughout the human genome. There are a total of 12 arrays. This is set 03.

last: Heintzman

first: Hui

last: Liu

first: Xinmin

first: Roland

first: Ron

last: Ren


title: Nimblegen HG18 RefSeq promoter array

status: Public on Jan 12 2009

first: W. Lee

last: Kraus

institute: UT Southwestern Medical Center

manufacture_protocol: 2006-07-18_HG18_RefSeq_promoter	Promoter design based only on normal RefSeq genes (NM_) for human (HG18; NCBI Build 36). Includes 2200 bp upstream of transcriptional start and 500 bp downstream. Isothermal probes using dual tm/cycle restriction:, 50-75 bp, tm 76, 148 cycles, 15-mer frequency of 50. Interval spacing of 100 bp.


title: Nimblegen 2.1M HD2 Human Economy tiling array of hg18 at 205bp resolution set 04 of 12

first: Gary

description: The 12 genome scan arrays were based on NCBI36 build of the human genome (hg18) and contained a total of 12 * 2.1 million 50 to 75-mer oligonucleotides, positioned at about every 205 basepairs (bp) throughout the human genome. There are a total of 12 arrays. This is set 04.

first: Nathaniel

last: Hawkins

last: Kheradpour

last: Green

last: Stewart

first: James

first: Gregory

first: Manolis


title: Nimblegen 2.1M HD2 Human Economy tiling array of hg18 at 205bp resolution set 10 of 12

description: The 12 genome scan arrays were based on NCBI36 build of the human genome (hg18) and contained a total of 12 * 2.1 million 50 to 75-mer oligonucleotides, positioned at about every 205 basepairs (bp) throughout the human genome. There are a total of 12 arrays. This is set 10.

first: David

first: Pouya

first: Alexander

last: Stark

first: Rhona

last: Stuart

last: Harp

last: Thomson

first: Bing