title: Illumina Genome Analyzer II (Herpesvirus saimiri (strain 11))

status: Public on Jul 30 2011

last: GEO

country: USA

organism: Herpesvirus saimiri (strain 11)

technology: high-throughput sequencing

distribution: virtual


title: Ocimum Biosolutions Human 40k OciChip A

status: Public on Jul 31 2011

city: Kolkata

first: Nitai

middle: Pada

last: Bhattacharyya

state: West Bengal

address: 1/AF Bidhannagar

department: Crystallography and Molecular Biology division

country: India

institute: Saha Institute of Nuclear Physics

organism: Homo sapiens

technology: spotted oligonucleotide

distribution: commercial

manufacture_protocol: Array Design Protocol: Human 40K OciChip consisting of 20,160 spots was printed on Corning® epoxy-coated glass slides using Omnigrid (Gene Machines). Chip has been printed using 4x12 SMP4 pins on 75.5x 25.5x1.3mm microarray glass slides. The origin offset values were 0 for X direction and 0 for Y direction. The dot to dot distance is 220 um; distance between subarrays is 150um and no of dots per array is 20x21=420. Oligos were printed using spotting buffer A from Ocimum Biosolution at 50% humidity and temperature at 22°C. The time taken by the robotic gridder to print 20160 spots was 25 hrs. Each probe was checked for its performance by standard QC process followed at Ocimum Biosolutions. Printed slides were stored in a light-tight box in a bench-top dessicator, with desiccant and were kept at 4 deg C until they were used for hybridization.


title: Ocimum Biosolutions Human 40k OciChip B


title: Illumina Genome Analyzer (Silene latifolia)

status: Public on Jul 26 2011

organism: Silene latifolia


title: 454 GS (Cimex lectularius)

status: Public on Jul 28 2011

organism: Cimex lectularius


title: Illumina HiSeq 2000 (Crassostrea gigas)

organism: Magallana gigas


title: Illumina Genome Analyzer II (Arachis hypogaea)

status: Public on Jul 29 2011

organism: Arachis hypogaea


title: Affymetrix Chinese Hamster Ovary (CHO)-specific custom array

city: Dublin

first: Colin

last: Clarke

address: Collin's Av.

department: NICB

country: Ireland

institute: Dublin City University

organism: Cricetulus griseus

technology: in situ oligonucleotide

description: WyeHamster2a oligonucleotide microarray

distribution: custom-commercial

manufacture_protocol: see manufacturer's web site


title: PFGRC Porphyromonas gingivalis 1.9K version 1

city: New York

first: Emil

last: Kozarov

state: NY

institute: Columbia University

organism: Porphyromonas gingivalis

description: see the JCVI's Porphyromonas gingivalis version 1 web page

distribution: non-commercial

first: Svetlana

last: Dolgilevich


title: Scerevisiae_tlg Array [StanFormated.bpmap]

city: London

first: Adam

last: Giess

address: Hammersmith Hospital, Du Cane Road

country: United Kingdom

institute: MRC Clinical Sciences Centre

organism: Saccharomyces cerevisiae

description: The platform contains 25 nucleotide probes spaced every 8 bp covering one strand of the whole /Saccharomyces cerevisiae/ genome sequence and a second set of probes offset 4 bp from the first set to cover the other strand.  Lee et al. (2007) Nature Genetics 39: 1235-1244.


title: Illumina Genome Analyzer II (Phaseolus vulgaris)

organism: Phaseolus vulgaris


title: Illumina Genome Analyzer (Silene vulgaris)

organism: Silene vulgaris


title: [Celegans] Affymetrix C. elegans Genome Array [CDF: Celegans_Ce_REFSEQ version 13.0.0]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Caenorhabditis elegans

description: This is identical to GPL200 but a custom CDF environment was used to extract data [Brainarray Version 13.0.0, Celegans_Ce_REFSEQ].

relation: Alternative to: GPL200 (Alternative CDF [official])


title: UW Nimblegen Rattus norvegicus custom array design 532663

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

organism: Rattus norvegicus

manufacture_protocol: see Nimblegen's site


title: Illumina Genome Analyzer IIx (Larix kaempferi)

status: Public on Jul 27 2011

organism: Larix kaempferi


title: [Celegans] Affymetrix C. elegans Genome Array [CDF: Celegans_Ce_REFSEQ version 14.0.0]

description: This is identical to GPL200 but a custom CDF environment was used to extract data [Brainarray Version 14.0.0, Celegans_Ce_REFSEQ].


title: Swine Protein-Annotated Oligonucleotide Microarray, 20K

city: Wuhan

first: Tao

middle: Wen

last: Li

state: Hubei

address: No.1, Shizi_shan street, Hongshan district

department: Division of Animal Infectious Disease

country: China

institute: Huazhong agricultural university, State Key Laboratory of Agricultural Microbiology

organism: Sus scrofa

manufacturer: Illumina (Oligo synthesis); University of Arizona (Array printing)

manufacture_protocol: Printing protocols available at: http://ag.arizona.edu/microarray/protocol1A.doc Information on oligonucleotide design available at: http://www.pigoligoarray.org/


title: Illumina Genome Analyzer IIx (Gossypium hirsutum)

organism: Gossypium hirsutum


title: Swegene Mouse 36k oligo array (Operon libraries Version 4.0)

city: Malmö

first: Harry

last: Björkbacka

address: CRC 91:12, UMAS entrance 72

department: Dept. of Clinical Sciences, Malmö

country: Sweden

institute: Lund University

organism: Mus musculus

description: Mouse array-ready oligonucleotide libraries Version 4.0 from Operon (Operon Biotechnologies, Germany)

manufacture_protocol: Microarrays were produced at the Swegene DNA Microarray Resource Center, Department of Oncology, Lund University, Sweden (http://swegene.onk.lu.se). Mouse array-ready oligonucleotide libraries Version 4.0, comprising 35 852 unique probes, were obtained from Operon (Operon Biotechnologies, Germany). Probes were printed on aminosilane coated glass slides (UltraGAPS, Corning) using a MicroGrid2 robot (BioRobotics, Cambridgeshire, UK) equipped with MicroSpot 10K pins (BioRobotics).


title: CombiMatrix TomatoArray 2.0

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

organism: Solanum lycopersicum

description:
Spots size: 25 microns
Total number of spots: 94,928
Tomato Gene Index Version 12 (LeGI v.12).

manufacturer: University of Verona - Biotechnology Department - Functional Genomics Centre

first: Paola

last: Tononi

first: Noel

last: Dago

first: Massimo

last: Delledonne

manufacture_protocol: Probes are directly synthesized on a 12k CombiMatrix array by an in situ oligo synthesis system developed by CombiMatrix Corporation (Mukilteo, USA) using the CombiMatrix CustomArray synthesizer. The standard synthesis protocol provided by CombiMatrix was used.


title: AB SOLiD System 3.0 (Schmidtea mediterranea)

organism: Schmidtea mediterranea


title: Illumina Genome Analyzer II (Schmidtea mediterranea)


title: NimbleGen human CGH 4x72K Whole Genome Array [80101_HG18_WG_CGH_v2_X4]

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Homo sapiens

description:
design ID : 6916
native array description file : 080101_HG18_WG_CGH_v2_X4.ndf
native array description file : 080101_HG18_WG_CGH_v2_X4.pos

first: Cristina

last: Robledo

first: Jesus

middle: M

last: Hernandez

first: Juan

middle: L

last: Garcia

manufacture_protocol: NimbleGen human CGH 4x72K Whole Genome v2.0 array (Roche NimbleGen, Inc). Placenta DNA was used as the reference. The CGH array protocol from NimbleGen Systems was followed. Briefly, 500 ng of tumour and reference DNA were labelled with Cy3 and Cy5, respectively. Labelled material was co-hybridized to microarrays consisting of 71341 oligonucleotide probes spaced at approximately 40000 bp intervals throughout the human genome, washed and scanned at 10 µm resolution using the GenePix 4000B dual scanner (Axon Instruments, Burlingame, CA). Raw data were extracted using NimbleScan software v2.5 (Roche NimbleGen, Inc), which enables automated grid alignment, extraction and generation of data files.


title: Agilent Human Genome CGH Microarray 44 k

city: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: CIC

manufacture_protocol: The microarray contains 44255 in situ synthesized 60-mer probes spaced at 43000 bp intervals throughout the human genome and includes 3877 controls. The probes are, according to the manufacturer’s description, enriched in cancer-relevant genes, representing both coding and non-coding sequences on the chromosomes. Experiments using Agilent arrays were performed using human placenta genomic DNA as reference and following Agilent’s recommended standard protocol. The arrays were scanned using the Agilent scanner, and data were extracted, filtered and normalized using the Feature Extraction program (Agilent Technologies). The Agilent CGH Analytics Software 3.4 trial (Agilent Technologies) was used to export the CGH array data.


title: NimbleGen_CGH-array_HG18_CHR7

description:
native array description file : 2006-09-22_HG18_CHR7_FT.ndf
native array description file : 2006-09-22_HG18_CHR7_FT.pos
design ID : 4706

manufacture_protocol: These arrays were designed at higher resolution with fine-tiling analysis of chromosome 7 (chromosome7:117711–158805222 bp). This array was constructed by maskless array synthesis technology (Roche NimbleGen, Inc.), with up to 385110 oligonucleotides, with a median probe spacing of 365 bp, and synthesized by photolithography on an array by previously described methods. Arrays were scanned at 5 µm resolution using the NimbleGen MS 200 Microarray scanner (Roche NimbleGen, Inc) data were extracted from the scanned images using NimbleScan software v2.5 (Roche NimbleGen, Inc).


title: BAC CGH-array 1Mb

technology: spotted DNA/cDNA

first: Eva

manufacture_protocol: Slides containing 3063 BACs were produced in “Centro de Investigación del Cáncer” (Salamanca, Spain). The particular BAC and P-1 derived artificial chromosome set used to produce this array is distributed to academic institutions by the Welcome Trust Sanger Institute (Cambridge, United Kingdom) and contains targets spaced at 1 Mb density over full genome, a set of subtelomeric sequences for each chromosome arm, and a few hundred probes selected for their involvement in oncogenesis. The clone content is available in the “Cytoview” windows of the Sanger Institute mapping database site, Ensembl (http://www.ensembl.org/). According to this database, clones were ordered along the chromosomes. These clones were isolated from their bacterial cultures with the relevant antibiotics and the DNA was extracted with standard protocol Welcome Trust Sanger Institute (Cambridge, UK). 10 ng of DNA (BAC/PAC) was used as a template for three DOP-PC. These products were ethanol precipitated and dissolved in distilled water. A minimum of three replicates per clone were printed by Microgrid II (Biorobotics) on each slide (Ultragaps Coated Slides, Corning) using the aqueous dimethylsulfoxide buffer as spotting solution. Briefly, for labelling reactions, 1 μg of nonamplified genomic DNA, test and reference were digested separately with DpnII restriction enzyme (New England Biolabs, Beverly, MA). For microarray hybridization, the digested DNAs were separately labelled using random primers (Bioprimer labelling kit, Invitrogen) and cyanine dye-3-dCTP and cyanine dye-5-dCTP fluorescent dye to paired hybridisation samples (Amersham Biosciences). The incorporated of the label nucleotide was quantified using the Nanodrop spectrophotometer. Labelled test and reference DNAs were mixed equitably, co-precipitated in presence of Cot-1 human DNA (Roche, Indianapolis, IN) with ethanol, washed, and resuspended in hybridization solution (50% Formamide, 10% Dextran sulfate, 2X standard saline citrate, 10 mM Tris pH 7.6, 2.7% sodium dodecyl sulfate and 10 μg/ μl of yeast tRNA). DNA mixtures were hybridized to the arrays in the GENETA according to the manufacturer’s recommended protocol. Images and signal intensities were acquired using GenePix4000B (Axon Instruments, Burlingame, CA) dual laser scanner in combination with GenePixPro4.0 (Axon Instruments) imaging software.


title: Lactobacillus plantarum WCFS1 15K 60-mer array, Version 3.1, our ID LPAG3.1_8

status: Public on Sep 30 2011

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

organism: Lactiplantibacillus plantarum

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


title: Affymetrix Aspergillus oryzae custom array

city: Tsukuba

first: Yasunobu

last: Terabayashi

country: Japan

institute: Tsukuba University

organism: Aspergillus oryzae RIB40


title: DOME_Dsv.halophilus_5040_v1

city: Vienna

first: Doris

last: Steger

state: Vienna

address: Althanstrasse 14

department: Department of Microbial Ecology

country: Austria

institute: University of Vienna

organism: Pseudodesulfovibrio halophilus

manufacturer: University of Vienna, Department of Microbial Ecology

manufacture_protocol: A published 16S rRNA-targeted oligonucleotide probe, DVHO831 (S-*-Dv.h.o-0831-a-A-18, 5’-GAA CCC AAC GGC CCG ACA-3’), synthesized by MWG Biotech (Ebersberg, Germany), was used for microarray spotting. The 5’ end of the oligonucleotide was tailed with 12 dTTPs (T-spacer) and the terminal dTTP was aminated to enable covalent coupling of the oligonucleotide to aldehyde group-coated VSS-25 glass slides (CEL Associates). The probe concentration was adjusted to 50 pmol/µl in 50% dimethyl sulfoxide. Microarrays were printed with a single split pin (MicroSpot 2500, Zinsser Analytic GmbH) using a BioRobotics MicroGrid spotter (Genomics Solutions) at 20°C and greater than 50% humidity. Square arrays of identical spots (approximate diameter 150 µm) were produced (70x72 spots). Spotted microarrays were incubated overnight at room temperature in a wet chamber and processed with sodium borohydride, as described previously.


title: Arabidopsis thaliana AtSNPtile 1

city: Münster

first: Fei

last: He

address: Hüfferstr. 1

department: Münster University

country: Germany

institute: Institute for Evolution and Biodiversity

organism: Arabidopsis thaliana

description: This array contains both SNP probes and tiling probes. SNP probes interrogate ~250K SNPs obtained from resequencing of 20 diverse Arabidopsis thaliana strains (Clark et al. 2007). Each SNP is interrogated by the middle base of four 25mer probes, representing 2 alleles on 2 strands. Tiling probes interrogate ~1.5M unique sequences tiled along the Arabidopsis thaliana genome with ~35 bp resolution. The reference genome for the array design is Columbia-0. The array is based on The Arabidopsis Information Resource (TAIR) genome release TAIR9.

manufacture_protocol: see web site


title: UW Nimblegen Rattus norvegicus custom array design 4845

status: Public on Jul 23 2011

manufacture_protocol: Nimblegen


title: Illumina Genome Analyzer II (Saccharomyces cerevisiae S288c)

status: Public on Jul 25 2011

last: GEO

organism: Saccharomyces cerevisiae S288C


title: Mouse Testis 2 array

city: Noda

first: Masakazu

last: Umezawa

state: Chiba

address: 2641 Yamazaki

department: Department of Hygienic Chemistry, Faculty of Pharmaceutical Sciences

institute: Tokyo University of Science

manufacture_protocol: cDNAs were amplified from plasmid using universal forward/reverse primers, purified, dissolved in spotting solution and spotted onto amino-modified glass slides using pin-type arrayer (THK-Riken arrayer) and cross-linked by UV radiation.


title: miRXplore TM Microarray (928)

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec GmbH

description: The miRXplore TM Microarray is composed of 6432 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 1511 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 1511 miRNA sequences covered sequence verified miRNAs of the species human (898) mouse (703) and rat (448) as well as viral miRNAs (147) as deposited in the miRBase sequence database version 14.0. The 97 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (43 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 36 positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 13 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences. Microarrays were manufactured by Miltenyi Biotec. Briefly, 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides in quadruplicates using a customized piezoelectric spotter.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

manufacture_protocol: Defined 200-400 bp fragments of selected cDNAs were generated by RT-PCR, cloned and sequence-verified. Amplified and purified cDNA inserts were spotted in quadruplicate on PIQOR slides using a proprietary piezoelectric spotter. The PIQOR slides were coated in a 2 step process generating a surface which covalently binds DNA molecules.


title: miRXplore TM Microarray (930)


title: FGP Nuphar 11K v1.0

status: Public on Jul 20 2011

city: Gainesville

first: Andre

last: Chanderbali

state: FL

address: Museum Road

institute: Univrsity of Florida

organism: Nuphar advena


title: Cambridge/CodeLink UniSet Human 20K I Bioarray

city: Cambridge

first: Muna

last: Affara

address: Tennis Court Road

department: Pathology

institute: University of Cambridge

description: CodeLink UniSet Human Bioarray content was based on the public UniGene and RefSeq databases, and sequences for design were derived from Incyte LifeSeq™ Gold and Foundation databases. Well-annotated mRNA or coding sequences were chosen to ensure usefulness for a large range of applications in basic research, biotechnology, and drug development. Each sequence was carefully screened to ensure high quality, specific probe design, and to reduce redundancy of gene targets. Every probe was functionally validated against multiple tissues to ensure best representation of the gene so that the results will be biologically relevant. Every bioarray is also functionally validated during production to further ensure quality performance.

manufacture_protocol: See manufacturer's website


title: Illumina Genome Analyzer (Heterocephalus glaber)

status: Public on Jul 18 2011

organism: Heterocephalus glaber


title: 454 GS FLX (Oryza sativa Japonica Group)

status: Public on Jul 15 2011

organism: Oryza sativa Japonica Group


title: UHNMAC Yeast 6.4 K array (Y6.4K) version 7

city: Paterna

first: Amparo

last: Gamero

state: Valencia

address: Avda. Agustín Escardino 7

department: Food Biotechnology

institute: IATA-CSIC

organism: Saccharomyces cerevisiae

description:
spotted DNA/cDNA (double-spotted array containing 6240 yeast ESTs derived from PCR amplification of synthetic EST clones, plus 320 control spots of Arabidopsis totalling 6.4K).
Grid rows: 12; grid columns: 4; rows: 17; columns: 16, grid to grid distance: 4500 um; spot to spot distance: 200 um; spot size: 100 um.

manufacturer: Microarray Centre - University Health Network - Toronto - Canada

manufacture_protocol:
1. Acquisition of bacterial clone set — our Yeast 6.4k clone set is derived from Research Genetics Genepairs. Detailed information about the ORFs and sequences can be found at http://www.yeastgenome.org/
2. Clone set is PCR amplified and DNA purified in working 96 well plates.
3. The purified DNA is then transferred to 384 well source plates with DNA concentration ranging from 0.10ug/ul to 0.25ug/ul.  These are used for spotting.
4. Microarrays are printed on UltraGAPS ™  slides (Corning Inc.) using hihg-precision robotics (up to 48 pins or print heads). Printed arrays are processed following Corning's protocol and are ready-to-use.
Up to 120 slides are printed in each batch and batches that result in greater than 95% printing fidelity are selected for post printing quality control tests
(measuring spot morphology, quality of background and signal intensity in a real hybridization using yeast total RNA, vector probe labeling method and terminal transferase tailing method).


title: Nimblegen Salmonella Typhimurium LT2 TI99287 60mer

first: Daniel

last: Shippy

address: 1675 Observatory Dr

institute: University of Wisconsin-Madison

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

description: Catalog design for Salmonella typhimurium LT2 (Taxonomy Id: 99287) covering NC_003197, NC_003277. Probes selected for 4527/4527 sequences. Median number of probes/sequence is 17 with an average of 17.00. Each probe will be replicated 5 times on the chip. Probes are randomly distributed over the surface of the array. Unused features have been filled with randomly generated probes of comparable GC content.

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


title: Illumina Genome Analyzer II (Proteus mirabilis)

organism: Proteus mirabilis


title: Illumina Genome Analyzer IIx (Anas platyrhynchos)

organism: Anas platyrhynchos


title: Illumina Genome Analyzer II (Dasypus novemcinctus)

organism: Dasypus novemcinctus


title: IMPPC Homo sapiens 6.8K

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

manufacture_protocol: see manufacturers web page (http://www.febit.com/)


title: HPA Pan_Pathogen Microarray 9248- V5.1

city: Salisbury

first: Karen

middle: Elizabeth

last: Kempsell

state: Wiltshire

address: Porton Down

department: Science Group

institute: UK Health Security Agency

organism: synthetic construct

description: 2312 Oligonucleotide features spotted in quadruplicate;  1648 respiratory viral probes from (http://derisilab14.ucsf.edu/data/virochip/), 539 HPA 'in house' designed pathogen probes, 2 random oligomer positive controls,   one each Human actin and GAPDH Clinical positive controls, 40 Cy3 dye only positive controls, 81 DMSO buffer only negative controls,

manufacturer: Diagnostic Technologies Group, Health Protection Agency Porton, UK

manufacture_protocol: 50 and 70 mer DNA oligonucleotides, printed 'in house' on  epoxy-coated Nexterion E slides (Schott UK Ltd., http://www.schott.com /uk/) using a BioRobotics Microgrid II gridder


title: Axon/Agilent-015061:C. elegans Oligo Microarray 4x44K

city: Ithaca

first: Gizem

last: Rizki

address: 526 Campus Road, 341 Biotech

institute: Cornell University

organism: Caenorhabditis elegans

description: Agilent-015061:C. elegans Oligo Microarray 4x44K, but viewed in the AXON orientation (DNAFront_BCBottom), the arrays have the following dimensions: 1 block, 266 columns, 107 rows.


title: University of Groningen Lactococcus lactis MG1363 amplicon/oligo 2 X 2.5K

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

organism: Lactococcus cremoris subsp. cremoris MG1363

manufacture_protocol: General Microgrid II spotting protocol on superamine slides


title: Illumina Genome Analyzer IIx (Coturnix japonica)

organism: Coturnix japonica


title: Operon Human 37.6K V4.0.1 Oparray

organism: Homo sapiens

manufacture_protocol: see manufacturers web site (http://www.eurofinsdna.com/)


title: XEBLIB96 Oligo Set

city: Aurora

first: Charles

last: Sagerstrom

state: CO

address: 12801 East 17th Avenue

department: Pediatrics

institute: University of Colorado Medical School

organism: Danio rerio

manufacturer: Oligo set designed by Compugen/Sigma-Genosys. Arrays used in this study were spotted by Kimmel Cancer Center core facility at Thomas Jefferson University.


title: Cryptococcus neoformans 243K tiling chip

city: San Francisco

first: Cheryl

last: Chun

state: CA

institute: UC San Francisco

organism: Cryptococcus neoformans

middle: D

first: Jessica

middle: C

last: Brown

first: Hiten

last: Madhani

manufacture_protocol: standard Agilent protocol


title: JCVI PFGRC Mycobacterium smegmatis 22K v3 array designed primarily based on strain MC2 155 [ORF-centered version]

city: St Louis

first: Christina

middle: Leigh

last: Stallings

state: Mo

address: 660 South Euclid Avenue, Box 8230

department: Molecular Microbiology

institute: Washington University School of Medicine

organism: Mycolicibacterium smegmatis

description: This is an ORF-centered version of the GEO Platform GPL5862

manufacture_protocol:
4QMS, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000
Slides were cross-linked in a Stratalinker (Stratagene), using the “auto-link” function at 3000ujoulesx100. Prior to hybridization, slides were pre-hybridized for 2 hours at room temperature in 0.2% SDS then rinsed in filtered water (10 sec) then in 70%.EtOH (5sec). Slides were dried by centrifugation at 1000rpm for 3 min.


title: NimbleGen Human Whole-Genome Tiling Array Set (8of10) [0701_HG18_TILE_08_HX1]

status: Public on Jul 14 2011

city: Madison

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
Whole human genome tiling array
Array 8 of 10
Designnames:
0701_HG18_TILE_22, 0701_HG18_TILE_23, 0701_HG18_TILE_24
Build: HG18

manufacture_protocol: see manufacturer's website http://www.nimblegen.com/


title: NimbleGen Human Whole-Genome Tiling Array Set (9of10) [0701_HG18_TILE_09_HX1]

description:
Whole human genome tiling array
Array 9 of 10
Designnames:
0701_HG18_TILE_25, 0701_HG18_TILE_26, 0701_HG18_TILE_27
Build: HG18


title: NimbleGen Human Whole-Genome Tiling Array Set (10of10) [0701_HG18_TILE_10_HX1]

description:
Whole human genome tiling array
Array 10 of 10
Designnames:
0701_HG18_TILE_28, 0701_HG18_TILE_29, 0701_HG18_TILE_30
Build: HG18


title: Eawag Chlamydomonas reinhardtii 44K v1.0 (16K unique probes)

city: Dübendorf

first: Beat

middle: B

last: Fischer

address: Ueberlandstr. 133

department: Department of Environmental Toxicology

country: Switzerland

institute: Eawag

organism: Chlamydomonas reinhardtii

manufacture_protocol: see manufacturer's website


title: SABiosciences Mouse Wnt Signaling Pathway RT² Profiler™ PCR Array (PAMM-043A)

city: Kurashiki

first: Tsutomu

last: Nohno

address: 577 Matsushima

department: Molecular and Developmental Biology

institute: Kawasaki Medical School

organism: Mus musculus

technology: RT-PCR


title: NimbleGen Human Whole-Genome Tiling Array Set (6of10) [0701_HG18_TILE_06_HX1]

description:
Whole human genome tiling array
Array 6 of 10
Designnames:
0701_HG18_TILE_16, 0701_HG18_TILE_17, 0701_HG18_TILE_18
Build: HG18


title: NimbleGen-Pesudomonas fluorescens Pf0-1-positive match expression array-v1.0 [2007-07-17_GO_P_fluor_expr]

city: Hanover

first: Peter

last: Newell

state: NH

address: 1 North College Street

department: Microbiology and Immunology

institute: Dartmouth Medical School

organism: Pseudomonas fluorescens Pf0-1

description:
NimbleGen design name: 2007-07-17_GO_P_fluor_expr, NimbleGen design ID: 6074.
A perfect match expression design for 5733 annotated open reading frames from Pseudomonas fluorescens, Pf0-1 (Refseq: NC_007492) with twenty 60-mer postive match (PM) probes per gene. Each probe is replicated 3 times.  The design includes random GC and other control probes.


title: NimbleGen Human Whole-Genome Tiling Array Set (7of10) [0701_HG18_TILE_07_HX1]

description:
Whole human genome tiling array
Array 7 of 10
Designnames:
0701_HG18_TILE_19, 0701_HG18_TILE_20, 0701_HG18_TILE_21
Build: HG18


title: NimbleGen Human Whole-Genome Tiling Array Set (4of10) [0701_HG18_TILE_04_HX1]

description:
Whole human genome tiling array
Array 4 of 10
Designnames:
0701_HG18_TILE_10, 0701_HG18_TILE_11, 0701_HG18_TILE_12
Build: HG18


title: NimbleGen Human Whole-Genome Tiling Array Set (2of10) [0701_HG18_TILE_02_HX1]

description:
Whole human genome tiling array
Array 2 of 10
Designnames:
0701_HG18_TILE_04, 0701_HG18_TILE_05, 0701_HG18_TILE_06
Build: HG18


title: NimbleGen Human Whole-Genome Tiling Array Set (5of10) [0701_HG18_TILE_05_HX1]

description:
Whole human genome tiling array
Array 5 of 10
Designnames:
0701_HG18_TILE_13, 0701_HG18_TILE_14, 0701_HG18_TILE_15
Build: HG18


title: Illumina Genome Analyzer IIx (Frankia sp. CcI3)

last: GEO

organism: Frankia casuarinae


title: NimbleGen Human Whole-Genome Tiling Array Set (1of10) [0701_HG18_TILE_01_HX1]

description:
Whole human genome tiling array
Array 1 of 10
Designnames:
0701_HG18_TILE_01, 0701_HG18_TILE_02, 0701_HG18_TILE_03
Build: HG18


title: Illumina Genome Analyzer II (Plasmodium yoelii)

status: Public on Jul 12 2011

organism: Plasmodium yoelii


title: Illumina Genome Analyzer IIx (Pachycladon fastigiatum)

organism: Pachycladon fastigiatum


title: Illumina Genome Analyzer IIx (Pachycladon enysii)

organism: Pachycladon enysii


title: Illumina Genome Analyzer (Campylobacter jejuni)

organism: Campylobacter jejuni


title: Illumina Genome Analyzer (Neospora caninum)

organism: Neospora caninum


title: Illumina Genome Analyzer II (Citrobacter rodentium)

organism: Citrobacter rodentium


title: Illumina Genome Analyzer (Solanum tuberosum)

organism: Solanum tuberosum


title: Illumina Genome Analyzer II (Neospora caninum)


title: Illumina Genome Analyzer II (Toxoplasma gondii)

organism: Toxoplasma gondii


title: Illumina Genome Analyzer II (Aspergillus fumigatus)

organism: Aspergillus fumigatus


title: Illumina Genome Analyzer II (Cleome gynandra)

organism: Gynandropsis gynandra


title: Illumina Genome Analyzer II (Trypanosoma vivax)

organism: Trypanosoma vivax


title: Illumina Genome Analyzer II (Schistosoma mansoni)

organism: Schistosoma mansoni


title: Illumina Genome Analyzer II (Solanum tuberosum)


title: MRA-1041_miRHumanViruses_13.0_090309 (miRNA ID version)

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
Gallid alphaherpesvirus 2
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Gallid alphaherpesvirus 3
Human gammaherpesvirus 8
Macacine gammaherpesvirus 4
Merkel cell polyomavirus
Macaca mulatta rhadinovirus
Betapolyomavirus hominis
Betapolyomavirus macacae

description: Human and Virus miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 13.0.

first: C

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


title: MRA-1004_miRZebrafish_12.0_080901

organism: Danio rerio

description: Zebrafish miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 12

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


title: Illumina Genome Analyzer II (Ovis aries)

organism: Ovis aries


title: MRA-1001_miRHuman_15

organism: Homo sapiens

description: Human miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 15


title: Salmonella enterica 17K STv7S_MMCC

city: Boston

first: Richelle

middle: C.

last: Charles

state: MA

address: 55 Fruit Street, Gray 504

department: Infectious Diseases

institute: Massachussetts General Hospital

organism: Salmonella enterica

manufacture_protocol: Custom made Salmonella array, amplified ORFs


title: 2006-07-17_MM8Tiling_Set24 Set 24 of 38

status: Public on Jul 09 2011

city: MARSEILLE CEDEX 09

first: Christelle

last: Cayrou

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

organism: Mus musculus

manufacture_protocol: Mouse whole genome tiling arrays


title: SMD Print_1679 Russell_Lab_Spotted_Oligos_2

first: David

last: Russell

state: NY

address: C5 171 Veterinary Medical Center

department: College of Veterinary Medicine

organism: Mycobacterium tuberculosis

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: Cavalli_Dmel_1_tiling

organism: Drosophila melanogaster

manufacture_protocol: Drosophila whole genome tiling arrays


title: LMGFM E. faecalis V583 oligo 3.6K v.2

organism: Enterococcus faecalis V583

first: Margrete

last: Solheim

manufacture_protocol:
Oligos representing 3219 chromosomal E. faecalis V583 ORFs + 10 MMH594 PAI ORFs spotted in 24 subarrays. Stratagene SpotReport ALien Oligo report system included for validation.
- spotted_ss_oligo_features


title: NimbleGen Mouse ChIP-chip 385K Promoter Array 1 of 2 (385k, Build MM8)

status: Public on Jul 08 2011

description: The 385K - Two Array Set contains all annotated splice variants and alternative transcription start sites.

manufacture_protocol: See NimbleGen website (http://www.nimblegen.com/products/chip/promoter/mouse/index.html)


title: Agilent-020166 Ca21_GE_plus_tiling_2.0 [ORF-centered version]

city: Merced

first: Clarissa

middle: Jane

last: Nobile

address: 5200 North Lake Rd

department: Molecular and Cell Biology

institute: University of California - Merced

organism: Candida albicans

description:
This is an expression array built off of the C. albicans genome assembly 21 orf list, with the alpha locus and additional tiling probes spanning the WOR1, WOR2, WOR3, CZF1 and EFG1 loci. This is the same as AMADID 020128 with the exception of the additional tiling probes for mapping transcription start sites.

Arrays of this design have barcodes that begin with 16020166 or 2520166.

This is an ORF-centered version. The full array layout is provided in the supplementary file linked below.

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


title: NimbleGen Rice CGH 3x720K Whole-Genome Tiling Arrays [100816_CB_Osat_NCBI_CGH]

status: Public on Jul 11 2011

city: Hangzhou

first: Ping

last: Yu

state: Zhejiang Province

address: 359 Tiyuchang Road

department: Rice Germplasm Evaluation

institute: China National Rice Research Institute

organism: Oryza sativa

description:
Annotation in this record based on NCBI Oryza sativa Japonica Group.
715,851 oligonucleotide probes with a median probe spacing of 500 bp.

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


title: Illumina Genome Analyzer II (Capra hircus)

status: Public on Jul 02 2011

organism: Capra hircus


title: Agilent-021158 Mouse CNV Microarray (Probe Name version)

city: Brisbane

first: Traute

last: Flatscher-Bader

state: Queensland

address: The University of Queensland, Upland Road, QBI Building (79)

department: The Queensland Brain Institute

country: Australia

institute: The University of Queensland

description: Platform is based on mouse genome build NCBI37/mm9.

manufacture_protocol: See manufacturer website (www.agilent.com).


title: Paralichthys olivaceus oligo microarray 8x15K v1.1 (Agilent custom)

status: Public on Jul 07 2011

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

institute: Tokyo University of Marine Science and Technology

organism: Paralichthys olivaceus

description: This 8x15 K oligo DNA array was custom designed against Japanese flounder (Paralichthys olivaceus) mRNA sequence (data obtained on 5, Oct. 09' from DDBJ) and assembled EST sequences (data obtained on 27, Aug. 09' from DDBJ).

first: Yoshiaki

last: Suzuki

first: Takashi

last: Aoki

first: Ikuo

last: Hirono

manufacture_protocol: Agilent (http://www.agilent.com) proprietary. http://www.chem.agilent.com/Library/technicaloverviews/Public/5988-8171en.pdf ("Agilent SurePrint Technology Content centered microarray design enabling speed and flexibility")


title: Illumina Genome Analyzer II (Porphyromonas gingivalis W83)

status: Public on Jul 06 2011

organism: Porphyromonas gingivalis W83


title: 3D-Gene Human Oligo chip 25k V2.1

city: Kamakura

first: Satoshi

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: Ultra-sensitive DNA chip for human genome wide gene expression analysis

manufacture_protocol: See manufacture's site


title: Keck Glycine max 18kA cDNA Prints101-108

city: New York

first: Ying

last: Li

address: 12 Waverly Place

department: Biology

institute: New York University

organism: Glycine max

manufacturer: Vodkin laboratory, University of Illinois and W.M. Keck Center, University of Illinois

manufacture_protocol: amplified cDNAs printed with Genemachines Omnigrid


title: Keck Glycine max 18kB cDNA array_prints 201-206


title: Rosetta Genomics human miRNA array v34 (condensed)

status: Public on Jul 01 2011

city: Rehovot

first: Einat

last: Sitbon

address: 10 Plaut St

country: Israel

institute: Rosetta Genomics

description:
ROSG hsa 720 v.34
Compared to v33, the v34 design strengthened the probes for 4 miRs galfile v.34 by adding AG at their end. The strengthened probes are: hsa-miR-21, hsa-miR-374a, hsa-miR-365, hsa-miR-369-3p.
The array probes were planned according to mirBase 9. The naming of the probes was updated to match miRbase 15.
The Platform data table reflects a condensed representation of the array's triplicate features.

manufacture_protocol: Custom microRNA microarrays were spotted on Slide E coated microarray slides (Schott Nexterion, Mainz, Germany) ~650 DNA oligonucleotide probes representing microRNAs (Sanger database version 9 and additional microRNAs predicted and validated by Rosetta Genomics).Probes spotted in triplicate using the BioRobotics MicroGrid II microarrater (Genomic Solutions, Ann Arbor,MI) according to the manufacturer’s directions. Fifty-four negative control probes were designed using the sense sequences of different microRNAs. Two types of positive control were included in the experimental design: (i) synthetic small RNAs were spiked into each RNA sample before labeling to verify labeling efficiency; and (ii) probes for abundant small RNAs were spotted on the miRdicator™ array to validate RNA quality.


title: NimbleGen Mouse ChIP-chip 385K Promoter Array 2 of 2 (385k, Build MM8)

first: Inc

last: Nimblegen Systems

state: WI


title: ICAT_UMBPB Pyrus communis 3.5K cDNA microarray

city: Lisbon

first: Vanessa

middle: Tolentino

last: Pereira

address: Ed. ICAT, Campus da FCUL, Campo Grande

country: Portugal

institute: FCUL/ICAT/BioFIG

organism: Pyrus communis

manufacturer: Plant Systems Biology Lab/Unit of Molecular Biology and Plant Biotechnology, ICAT, FCUL, Lisbon, Portugal

manufacture_protocol:
1. Amplified  cDNA inserts were purified with MultiScreen96-PCR plates (Millipore), transferred to printing plates (Microtiter V plates, Sigma), dried through passive water evaporation in a protected environment and resuspended in 10 µl of Pronto! Universal Spotting Solution (Corning, Life Sciences, USA) to a final concentration of 150 to 200 ng/µl.
2. cDNAs were spotted in duplicate onto glass UltraGAPS™ Coated Slides (Corning, Life Sciences, USA) using VersArray ChipWriter Compact System ® (Bio-Rad Lab., Hercules, CA, USA). Humidity: 50%-55%. Temperature: 22°C. Pins: 12 printing pins (Telechem International, Sunnyvale, CA, USA). Pin configuration: 2 x 6. Number of repeats: spots are repeated once on the same subgrid in the same order. Printing plates: 36 x 2 (96 wells). Printing scheme: 12 subgrids, each subgrid with 24 columns and 24 rows. Distance between spots: 300μm. This is a condensed version of the physical array, 7K. The full array linked as a supplementary file.
3. After printing, microarrays were processed with heat and UV crosslinking following manufacturer's instructions (Corning, Life Sciences, USA).


title: [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array [CDF: Brainarray TAIRG, Version 12.1.0]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

country: USA

institute: NCBI/NLM/NIH

organism: Arabidopsis thaliana

description:
This is identical to GPL198 but a custom CDF environment was used to extract data [Brainarray TAIRG, Version 12.1.0].

CDF and other files can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12.1.0/tairg.asp

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

manufacture_protocol: see manufacturer's web site


title: Agilent-025553 Spym49N131_01 Custom Array GE 8x15K (Feature Number version)

status: Public on Jul 05 2011

city: Rostock

first: Nikolai

last: Siemens

state: MV

address: Schillingallee 70

department: IMIKRO

institute: University of Rostock

organism: Streptococcus pyogenes NZ131

description:
Custom Array GE 8x15K; Agilent [025553_D_GEO_20090929.txt]

Arrays of this design have barcodes that begin with 16025553 or 2525553.

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: Agilent-025553 Spym49N131_01 Custom Array GE 8x15K (Probe Name version)

description: Custom Array GE 8x15K; Agilent [025553_D_GEO_20090929.txt]


title: NimbleGen custom human 385K ChIP-chip array (DP_FAIRE_HG18)

city: Hinxton

first: Dirk

middle: Stefan

last: Paul

address: Wellcome Trust Genome Campus

department: Human Genetics

institute: Wellcome Trust Sanger Institute

description:
Annotation in this record is based on NCBI human build 36 (hg18)
We profiled chromatin structure at 62 non-redundant genetic loci representing all known associations (as of November 2009, CEU population) with 11 cardiovascular traits: coronary artery disease (CAD), (early-onset) myocardial infarction (MI), mean platelet volume (MPV), platelet counts (PLT), platelet signaling (PLS), white blood cell counts (WBC), red blood cell counts (RBC), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), systolic blood pressure (SBP), diastolic blood pressure (DBP), hypertension (HYP). We considered only genetic loci that reached genome-wide significance with the threshold of P<5x10-8 in a genome-wide association (GWA) study conducted with individuals of European ancestry. In addition, we selected genetic loci based on biological evidence, where there was suggestive evidence of association. For each locus, we included the entire recombination interval of the index SNP. If a recombination interval exceeded 500 kb, we included the closest target gene ±10 kb. In order to assess patterns of cell type specificity, we included eight lineage-specific reference genes (±2 kb) for each of megakaryocytes, erythroblasts and monocytes on the array.


title: CyanoChip Ver.1.6 (Takara bio.)

city: Kawasaki

last: Osanai

address: 1-1-1, Higashimita, Tamaku

department: School of Agriculture

institute: Meiji University

organism: Synechocystis sp. PCC 6803

description: CyanoChip is commercially produced by Takara Bio. Inc.


title: Agilent-020166 Candida albicans 8 x 15k Custom Expression Array v2

city: San Francisco

first: Changbin

last: Chen

state: California

address: HSE450, 513 Parnassus Avenue

department: Department of Microbiology & Immunology

institute: University of California, San Francisco

description:
A unique iron homeostasis regulatory circuit with reciprocal roles in Candida albicans commensalism and pathogenesis.
Suzanne Noble lab --- Candida albicans - 8 x 15k Agilent ID020166  Expression Array v2
Genome version: Assembly 19; 24-Aug-2009; http://www.candidagenome.org/download/sequence/
60-mer oligonucleotides.

first: Kalyan

last: Pande

first: Sarah

last: French

first: Brian

last: Tuch

first: Suzanne

last: Noble

manufacture_protocol: Arrays were custom designed Agilent 8*15k Microarrays [AMADID #020166] containing a minimum of 2 independent probes for each ORF.  Probes were 60bp, designed with the Agilent Probe design tool set to Best Distribution.  For ORFs whose 2 probes had a history of divergent results in previous designed, 3 additional probes were added [for a total of 5 per ORF].  See manufacturer's website for more details.


title: ENS SGDB Trichoderma virens Tv10_Tiling93_1

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

institute: École normale supérieure

organism: Trichoderma virens

description:
Trichoderma virens Tiling array. One probe has been design every 93 base every other strand.
The probe design has been done according to T. virens v1.0 genome assembly from the DOE JGI available here: http://genome.jgi-psf.org/Trive1/Trive1.home.html
The probe ID is a code to find genome localisation of each probe: Scaffold_Start_Strand.
The first number merge to Tv suffix indicates the scaffold number
The second number is the start position of the probe
The third number is the strand FWD or REV

last: Le Crom

first: Laurent

last: Jourdren

manufacture_protocol: In situ oligonucleotide synthesis of 60mer custom oligos. See manufacturer's web site at http://www.agilent.com/.


title: Illumina DASL microarray (Cancer Panel TM v1)

first: Victor

middle: Piana

last: Andrade

address: 408E 69th Street z427E

department: Breast Surgery

institute: Memorial Sloan-Kettering Cancer Center

organism: Homo sapiens

technology: oligonucleotide beads

description:
Cancer Panel GS0006426
Array type: Illumina DASL Sentrix Array Matrix (SAM)


title: MRA-1041_miRHumanViruses_13.0_090309

city: Houston

first: Christoph

last: Eicken

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
Gallid alphaherpesvirus 2
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Gallid alphaherpesvirus 3
Human gammaherpesvirus 8
Macacine gammaherpesvirus 4
Merkel cell polyomavirus
Macaca mulatta rhadinovirus
Betapolyomavirus hominis
Betapolyomavirus macacae

description: Human and Virus miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 13.0

first: C

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


title: ENS SGDB Trichoderma reesei Tr20_Tiling93_1

organism: Trichoderma reesei

description:
Trichoderma reesei Tiling array. One probe has been design every 93 base every other strand.
The probe design has been done according to T. reesei v2.0 genome assembly from the DOE JGI available here: http://genome.jgi-psf.org/Trire2/Trire2.home.html
The probe ID is a code to find genome localisation of each probe: Scaffold_Start_Strand.
The first number merge to Tr suffix indicates the scaffold number
The second number is the start position of the probe
The third number is the strand FWD or REV


title: MPB Murine 32K Oligo printrun 4.1

city: Winnipeg

first: Rhiannon

middle: LCH

last: Huzarewich

state: MB

address: 1015 Arlington St.

department: Molecular PathoBiology

country: Canada

institute: Public Health Agency of Canada

organism: Mus musculus

manufacture_protocol: Arrays were made using the mouse genome oligo set from Qiagen’s Array-Ready Oligo SetTM (AROS) version 3.0. Each set contained 31,769 arrayable 70mers representing 24,878 genes and 32,829 gene transcripts. The array design is based on the Ensembl (http://www.ensembl.org/) Mouse 14.30 Database and Mouse Genome Sequencing Project and contains alternative splicing variants using common, partial common, or individual transcript oligos. The set is provided in 84, 384-well plates containing 31,769 70mers each containing a 5’ C6 amino linker. Each well in the plate contained 600 pmol of the specified 70mer (including control elements) lyophilized and were resuspended in ArrayIt buffer (1x, Telechem) for a final concentration of 40 µM. After resuspension, the plates were resealed and shaken on an orbital shaker at 60 rpm overnight at room temp. The 70mers were spotted onto CMT-GAPS-coated glass slides (Corning, NY, Cat. 2549) using the Stealth micro-spotting pins (Telechem).


title: ENS SGDB Trichoderma atroviride Ta10_Tiling93_1

organism: Trichoderma atroviride

description:
Trichoderma atroviride Tiling array. One probe has been design every 93 base every other strand.
The probe design has been done according to T. atroviride v1.0 genome assembly from the DOE JGI available here: http://genome.jgi-psf.org/Triat1/Triat1.home.html
The probe ID is a code to find genome localisation of each probe: Scaffold_Start_Strand.
The first number merge to Ta suffix indicates the scaffold number
The second number is the start position of the probe
The third number is the strand FWD or REV


title: MPB Murine 16K BMAP-MSV printrun 9.1

manufacture_protocol: Arrays were prepared in house from two individual libraries, the Brain Molecular Anatomy Project (BMAP) library and the Mouse Sequence Verified (MSV) Unigene library. There were a total of ~17,000 individual spots on the array including control elements. Inserts from the two libraries was amplified by PCR, and the amplicons were subsequently purified using Millipore multiwell purification plates. The lyophilized PCR products were resuspended in 1x Microspotting Solution Plus (Telechem) to a final concentration of 0.25-0.75 µg/µl. The DNA amplicons were spotted onto CMT-GAPS-coated glass slides (Corning, NY, Cat. 2549) using the Stealth micro-spotting pins (Telechem).


title: 454 GS 20 (Symplocarpus renifolius)

last: GEO

organism: Symplocarpus renifolius


title: Illumina Genome Analyzer IIx (Pongo pygmaeus)

organism: Pongo pygmaeus


title: Illumina Genome Analyzer IIx (Gorilla gorilla)

organism: Gorilla gorilla


title: Illumina Genome Analyzer IIx (Pan paniscus)

organism: Pan paniscus


title: MPB Murine 16K BMAP-MSV printrun 7.1


title: Illumina Genome Analyzer IIx (Pan troglodytes)

organism: Pan troglodytes


title: Illumina Genome Analyzer (Macropus eugenii)

organism: Notamacropus eugenii


title: Rosetta Genomics human miRNA array v33 (condensed)

first: Einat

last: Sitbon

description:
ROSG hsa 720 v.33
The array probes were planned according to mirBase 9. The naming of the probes was updated to match miRbase 15.
The Platform data table reflects a condensed representation of the array's triplicate features.

manufacture_protocol: Custom microRNA microarrays were spotted on Slide E coated microarray slides (Schott  Nexterion, Mainz, Germany) ~650 DNA oligonucleotide probes representing microRNAs (Sanger database version 9 and additional microRNAs predicted and validated by Rosetta Genomics).Probes spotted in triplicate using the BioRobotics MicroGrid II  microarrater (Genomic Solutions, Ann Arbor,MI) according to the manufacturer’s directions. Fifty-four negative control probes were designed using the sense sequences of different microRNAs. Two types of positive control were included in the experimental design: (i) synthetic small RNAs were spiked into each RNA sample before labeling to verify labeling efficiency; and (ii) probes for abundant small RNAs were spotted on the miRdicator™ array to validate RNA quality.


title: Illumina Genome Analyzer IIx (Monodelphis domestica)

organism: Monodelphis domestica


title: AB SOLiD System 3.0 (Carica papaya)

organism: Carica papaya


title: Illumina Genome Analyzer IIx (Ornithorhynchus anatinus)

organism: Ornithorhynchus anatinus


title: Illumina Genome Analyzer II (Oryza sativa Japonica Group)

organism: Oryza sativa Japonica Group


title: NimbleGen_Ferroglobus placidus strain DSM 10642_v1.0

status: Public on Jan 05 2011

city: Amherst

first: Dawn

middle: E

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

department: Microbiology

institute: University of Massachusetts Amherst

organism: Ferroglobus placidus DSM 10642

description: 4-plex expression for Ferroglobus placidus strain DSM 10642; from http://genome.ornl.gov/microbiol/fpla, 15jan09 gene models; 2613 starting genes; 9 probes per target, 45-60mer probes, 2613 exemplars for 2613 genes, 3 copies of each probe on the array

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


title: Agilent-029066 Propionibacterium acnes KPA171202

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

organism: Cutibacterium acnes KPA171202

manufacture_protocol: sure print systhesis


title: SALSIFY, Agilent-026881 S. Typhimurim

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

description:
Probes for ORFs from S. Typhimurim str. SL1344, LT2, 14028S. Design was aimed to have one probe for ORFs shorter than 200 bp and 2 probes for longer ones.
Probes starting with 'm_' match multiple paralogous ORFs; probes starting with 'x_' are extras, i.e. a 3rd probe for long ORFs; probes starting with 'p_' are problem cases where no proper probe could be designed (normally due to short length of ORF).

first: Jay

last: Hinton

first: Karsten

last: Hokamp

first: Jörg

last: Vogel

manufacture_protocol: SurePrint


title: NimbleGen Drosophila melanogaster Gene expression array [DM4_3_60mer_expr]

status: Public on Jun 28 2011

city: Madison

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Drosophila melanogaster

description:
Expression design for Drosophila melanogaster (Release 4.3).
DESIGN_ID: 5046
DESIGN_NAME: DM4_3_60mer_expr
SLIDE_LAYOUT_NAME: NimbleChip_X4

manufacture_protocol: See manufacturer's website at http://www.nimblegen.com/


title: [rhofispaa520260F] Custom Vibrio parahaemolyticus GeneChip Array (Affymetrix)

status: Public on Nov 05 2010

city: Iowa City

first: Linda

last: McCarter

state: Iowa

address: 3-401 BSB  51 Newton Rd

institute: University of Iowa

organism: Vibrio parahaemolyticus RIMD 2210633

first: Ryan

middle: J

last: Kustusch

first: Cindy

last: Gode-Potratz

first: Patrick

last: Breheny

first: David

middle: S

last: Weiss

manufacture_protocol: Custom GeneChips (11 uM feature size) representing >99% of the annotated open reading frames in the V. parahaemolyticus RIMD 2210633 genome, as well as 40 intergenic regions greater than 500 bp, were constructed by Affymetrix Inc. (Santa Clara, CA). 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: UW_NimbleGen_Rat_321K_Array design 081105

status: Public on Oct 15 2010

first: John

last: Svaren

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

organism: Rattus norvegicus

first: Nolan

last: Gokey


title: Agilent-032741 Neisseria_CGH

status: Public on Apr 06 2011

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Neisseria meningitidis

description: Arrays of this design have barcodes that begin with 16032741 or 2532741.. 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: Chen Lab Cotton 25k oligo array

status: Public on Dec 01 2008

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

organism: Gossypium hirsutum

description: Used in the study 'Transcriptional and functional analyses of fiber genes in cotton.'

manufacturer: The University of Texas at Austin, Dr. Jeff Chen's lab

first: Jinsuk

last: Lee

first: Jeff

first: Josh

last: Udall

first: Jonathan

last: Wendel

first: Foo

last: Cheung

first: Chris

last: Town

manufacture_protocol: The first set of 1,536 oligonucleotide probes was designed from a pilot set of cotton microarray in the previous work (Lee et al., 2006). The second set of 12,006 oligonucleotide was designed from an exemplar sequence set which was chosen from a clustere set of unigenes by single-linkage clustering with BLASTN using Picky v1.0 (Chou et al., 2004; Udall et al., 2006; Udall et al., 2007). The 12,006 oligonucleotide probes include genes encoding a large number of transcription factors, and several thousand genes that had homology to Arabidopsis genes (Udall et al., 2007). The third set of 9,629 oligonucleotides probes was designed from CGI8 (http://compbio.dfci. harvard.edu/tgi) that contained 55,673 unique sequences using Picky v2.0. This GH_TMO ESTs showed the accumulation of genes encoding putative transcription factors such as MYB and WRKY and genes encoding predicted proteins involved in auxin, brassinosteroid (BR), gibberellic acid (GA), abscisic acid (ABA) and ethylene signaling pathways (Yang et al., 2006). The probes that target the same genes as in the first two probe sets were excluded in the third set. This large set of cotton oligonucleotide microarray may include about 46–60% of the total genic diversity and most of the probes had a single target (Udall et al., 2007).


title: NimbleGen Schistosoma mansoni 385K v1

status: Public on May 29 2010

city: Sao Carlos

first: Ricardo

last: DeMarco

state: Sao Paulo

address: Av trabalhador Sao Carlense 400

country: Brazil

institute: Universidade de Sao Paulo

organism: Schistosoma mansoni

description: The annotations provided are the results from mapping to version f of the S. mansoni genome assembly at GeneDB.org. As the annotations are continually evolving, if re-mapped to the current version, newer annotations may be available.


title: NimbleGen Mouse 385kb array [2006-07-26_MM8_WG_CGH]

status: Public on Jan 21 2011

city: Amsterdam

first: Rinske

last: Drost

address: Plesmanlaan 121

institute: The Netherlands Cancer Institute

organism: Mus musculus

description:
CGH design for whole mouse genome (mm8; NCBI Build 36).
native array description file: 2006-07-26_MM8_WG_CGH.ndf
native array description file:  2006-07-26_MM8_WG_CGH.pos

manufacture_protocol: Probes selected from mm8_tiling database using 5250 bp interval and 500 bp window. Isothermal probes with min length of 50 bp and max length of 75 bp and target Tm of 76C. Cycle restricted to 148 synthesis cycles. Interval spacing: 5756 bp (mean); 5782 bp (median). N random probes added. chrY_random added since the majority of sequence for chrY is found there.


title: Rattus norvegicus 0.2K Percutaneous Collagen Induction (PCI)

status: Public on May 31 2008

city: Hanover

first: Cornelia

last: Repenning

address: Callinstrasse 3

department: Institut fuer Technische Chemie

institute: Leibniz University of Hanover

first: Frank

last: Stahl

manufacture_protocol: Oligonucleotide design and synthesis: 70mer 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: NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Array (Build MM9) [080603_MM9_WG_CGH_HX3]

status: Public on Sep 29 2010

city: Los Angeles

first: Markus

last: Müschen

state: CA

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

description:
Format: 3x720K
Source: UCSC
Build: NCBI37, MM9
Probe Length: 50-75mer
Median Probe Spacing: 3537

NimbleGen description files linked below:
080603_MM9_WG_CGH_HX3.ndf
080603_MM9_WG_CGH_HX3.pos

manufacture_protocol: See www.nimblegen.com


title: JCVI PFGRC Mycobacterium smegmatis 25K v4 array designed primarily based on strain MC2 155

status: Public on Dec 13 2007

organism: Mycolicibacterium smegmatis

description: This set includes 7148 oligonucleotides, has 25392 spots distributed in 48 blocks.

manufacture_protocol: 4QMS, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: GAP_TIGR_I

status: Public on Jan 05 2006

city: Lynchburg

first: Michael

last: Price

state: VA

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

organism: Aspergillus flavus

description:
The microarrays used in this study were printed at The Institute for Genome Research (TIGR) with amplicons (approx. 530bp) generated from genomic DNA using primers selected from EST sequences.  A total of 5002 genes, including 31 known aflatoxin and sugar utilization cluster genes, were arrayed in three duplications (or more) for a total of 17,991 spots.
Keywords = aflatoxin
Keywords = Aspergillus parasiticus

first: Jiujiang

last: Yu

first: William

last: Nierman

first: Stanley

last: Kim

first: Bethan

last: Pritchard

first: Deepak

last: Bhatnagar

first: Thomas

last: Cleveland

first: Gary

middle: A

last: Payne


title: Custom CGH array tiling selected regions on MM6 [2007-04-16_MM6_GK_CGH]

status: Public on Dec 31 2010

city: Lausanne

first: Charlotte

middle: N.

last: Henrichsen

address: Quartier Sorge

department: Center for Integrative Genomics

institute: University of Lausanne

description:
tiling of various regions on mm6, tiled every 10bp, selecting win50, int300 , max 5, mean 350bp, median 351
native array description file: 2007-04-16_MM6_GK_CGH.ndf
native array description file: 2007-04-16_MM6_GK_CGH.pos

manufacture_protocol: NimbleGen