title: NimbleGen Zea Mays 2.1M array

status: Public on Nov 19 2009

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

country: USA

institute: Iowa State University

organism: Zea mays

technology: in situ oligonucleotide

description:
Probe sequences were aligned to Maize pseudomolecules from the Arizona Genome Institure (AGI) released on March, 20th, 2009 to determine their positions in the genome (positions are reflected in the Platform data table).
Due to the fact that our array was designed using B73 genomic sequence and the high rate of polymorphism between B73 and Mo17, the CGH data violated the assumption for the regularly used Q-spline normalization to make two channels of hybridization intensities comparable. We used a subset of 840,289 probes that were known to have identical sequence in B73 and Mo17 (based on B73 BAC sequences and Mo17 WGS data) as a control set to obtain a best-fitting cubic spline function (Workman et al., 2002), assuming that most of these probes should have the same hybridization intensities after normalization. The spline function was then globally applied for all probes to normalize the two channels.  After within-chip normalization, linear model analyses using LIMMA (Smyth 2004; Smyth 2005) were conducted for the data from all microarrays. The linear model for each probe included effects for dyes and genotypes (B73, Mo17, RIL M0022, and RIL M0023), and p-values were calculated to test for a signal difference between Mo17 and B73 genotypes as part of each linear model analysis.
NimbleGen .ndf array description file linked below as supplementary file.

distribution: custom-commercial

manufacture_protocol: A high-density (2.1 million feature) oligonucleotide microarray was designed by Roche NimbleGen to perform comparative genomic hybridization (CGH) of maize B73 and Mo17 inbred lines.  A set of 14,423 maize BACs (downloaded March 2008) was used to design isothermal probes, varying in length from 45 bp to 85 bp and with a target Tm of 76C at a fixed interval of 50 bp.  Probe sequences were repeat-masked by calculating the average 14-mer frequency for each probe, based on a frequency table generated from the complete set of BAC sequences available as of that date, and removing probes with an average 14-mer frequency higher than 400. Probe uniqueness was determined by comparing each probe to the B73 reference genome, using SSAHA (http://www.sanger.ac.uk/Software/analysis/SSAHA/) with a step-size of 1, nmer-size of 12 and a minimum match length of 33 bp. Up to five insertions/deletions were allowed in each match. Probes with <=15 close matches in the genome were included in the array design. Median final probe spacing was 450 bp.  It should be noted that this set of probes was designed to facilitate sequence capture (Albert et al., 2007); if NimbleGen's CGH probe design criteria had been utilized it is likely that the choice of probes would have been slightly different. See manufacturer's website for more details.


title: Affymetrix GeneChip Rat Genome 230 2.0 Array (CDF: rat2302rnentrezgcdf_11.0.1)

status: Public on Nov 24 2009

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

organism: Rattus norvegicus

description: Custom CDF (Brainarray Entrez Gene v11.0.1); UniGene build 165

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: Agilent-021376 shrimp_oligo_v1

status: Public on Nov 25 2009

city: Charleston

first: Marine

last: Genomics

state: SC

address: 331 Ft. Johnson Road

institute: Medical University South Carolina

organism: Penaeus vannamei

description:
Pacific Whiteleg Shrimp oligo array, Litopenaeus vannamei, contigs and singlets
Arrays of this design have barcodes that begin with 16021376 or 2521376.
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: Bacillus cereus Bc10987 - 1st design (1X22K)

city: Wageningen

first: Maarten

last: Mols

address: Bomenweg 2

department: ATV

country: Netherlands

institute: Wageningen University

organism: Bacillus cereus ATCC 10987

first: Roy

last: Moezelaar

first: Tjakko

last: Abee

first: Menno

last: van der Voort

manufacture_protocol:
Agilent manufacture protocol.
Agilent uses its inkjet technology to print oligos onto glass slides.


title: Genopal Human 216 Autoimmunity Array v.1

status: Public on Nov 30 2009

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

organism: Homo sapiens

technology: spotted oligonucleotide

first: Tatsunobu

last: Fukushima

first: Takahiro

last: Tougan

first: Tomonori

last: Ishii

first: Shigeto

last: Kobayashi

first: Takashi

last: Akita

first: Hiroshi

last: Nojima

manufacture_protocol:
Custom-made fibrous oligonucleotide DNA microarray GenopalTM (Mitsubishi Rayon) with a total of 216 genes which were selected from autoimmune disease related genes.

All oligonucleotide capture probes (65 mer in length), including those for negative controls, were designed to have approximately the same annealing temperature (Tm) 　throughout a microarray. In addition, they were designed also to hybridize to the target antisense RNA specifically with a domain within 1 kb from 3’-end.

The oligonucleotide DNA microarray, GenopalTM (Mitsubishi Rayon), was made in the following manner. Plastic hollow fibers, in which oligonucleotide capture probes were chemically bonded to hydrophilic gel, were bundled in an orderly arrangement, hardened with resin to form a block (12 rows × 19 columns) and then sliced into thin chips. Finally, three thin chips were set into a holder together.


title: Illumina Genome Analyzer (Oryza sativa Indica Group)

last: GEO

organism: Oryza sativa Indica Group

technology: high-throughput sequencing

distribution: virtual


title: Affymetrix Rat Expression 230A Array [CDF: RAE230A_Rn_ENTREZG]

description:
Custom CDF (Brainarray v11.0.1); Entrez Gene.
Affymetrix RAE230A with Alternative Entrez Gene ID Mappings (v11.0.1).

relation: Alternative to: GPL341 (Alternative CDF[official])

manufacture_protocol: GPL341 using Entrez Gene custom CDF available from: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/entrezg.asp


title: Vitis vinifera miRNA Combimatrix array

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: Vitis vinifera

description:
Spots size: 25 microns
Total number of spots: 12544
Number of spots replicates per oligo: 3

distribution: non-commercial

manufacturer: University of Verona - Scientific and Technological Department - Plant Functional Genomics Centre

first: Erica

last: Mica

first: Viviana

last: Piccolo

first: Massimo

last: Delledonne

first: Mario

last: Pezzotti

first: Cesare

last: Casati

first: Cristian

last: Del Fabbro

first: Giorgio

last: Valle

last: Policriti

first: Michele

last: Morgante

first: Graziano

last: Pesole

first: Enrico

middle: M

last: Pè

first: David

middle: S

last: Horner

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. Standard synthesis protocol provided by Combimatrix was used.


title: Zhejiang university human 449 oligonucleotide array

city: Hangzhou

first: youying

last: mao

address: Yuhangtang Road,NO.388

country: China

institute: Zhejiang University

description:
Preparation of microarray: 449 immune related genes were included. Specific 70mer oligonucleotides of each gene was searched in the human_V4.0.1_genelist_s+ (Qiagen-Operon).Another 10 housekeeping genes were also included. Oligos (1OD) were dissolved in 100 ul ddH2O and printed on Immobilon-Ny+ Transfer T Membranes (Millipore, Bedford, MA, USA) using GeneTAC M G3 arrayer (Genomic Solutions, Ann Arbor, MI, USA). Each oligo was duplicated triple in each array to verify the reproducibility of experiments.
Preparation of labeled cDNA probe: The RNA samples were labeled with 33P-dCTP during the first-strand reverse transcription reactions. The labeling reaction contained 20mmol/L each of dATP, dTTP and dGTP, 10mmol/L dCTP and 3ul of alpha-33P-dCTP (10mCi/ml, Amersham Biosciences, Buckinghamshire, UK), 10ul of First-Strand Buffer, 0.5mmol/L DTT and 400 unit SuperScriptTM II RNase H- Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA), 0.3 ug oligo(dT)16 primer, 0.1 ug random hexamer primer and total RNA at the optimal concentration in a reaction volume of 50 ul. The reaction proceeded at 42C for 2 hours and products were purified using a G-50 column (Amersham Pharmacia Biotech, Piscataway, NJ, USA).

manufacturer: Bioinformatics and Gene Network Research Group, Zhejiang university


title: AB SOLiD System (Rattus norvegicus)

status: Public on Nov 17 2009


title: University of Chicago - HumanMouse tRNA array - 768 - v1.0

status: Public on Nov 26 2009

city: Chicago

first: Tao

last: Pan

state: IL

address: 929 East 57th street

department: Biochemistry & Molecular Biology

institute: University of Chicago

organism:
Homo sapiens
Mus musculus

manufacture_protocol: Oligonucleotides are resuspended in 3xSSC, 0.01%SDS to a final concentration of 50uM.  Each oligonucleotide is spotted on the Genetix K2615 slides and immobilized by UV crosslinking.


title: NCode 0.24K multi-species miRNA microarray dual color version 2

city: Roskilde

first: Thomas

last: Werge

address: Boserupvej 2

department: Institute of biological Psychiatry

country: Denmark

institute: Psychiatric Center, Sct. Hans Hospital

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

manufacture_protocol:
The microarray is contact-printed using microquill pins on Corning® Epoxide-Coated Glass Slides. The array specifications are: Total subarrays per slide: 3, Subarray layout: 8 blocks (4 rows × 2 columns), Block layout: 192 spots (12 rows × 16 columns), Block dimensions: 4 mm × 3 mm
Average spot diameter: 120 μm, Spot center-to-center spacing: 265 μm. The array is printed with NCode™ miRNA probes, which are unmodified oligonucleotides  (34–44 bases long) containing all known mature miRNAs in the miRBase Sequence Database, Release 9.0, for human, mouse, rat, D. melanogaster, C. elegans, and Zebrafish. Species-specific probes were designed using a proprietary algorithm that generates miRNA sequences with enhanced hybridization properties. The probes provide comparable sensitivity to wild-type sequences, while offering maximum specificity for discerning between closely related miRNAs and normalized melting temperatures for uniform hybridization. Probes have been validated for their ability to distinguish between wild-type and mismatched miRNA sequences with ≥1 base mismatch.


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array [CDF: HGU133Plus2_Hs_ENTREZG v11.0.1]

first: Paul

last: Boutros

manufacture_protocol: GPL570 based on custom CDF from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/entrezg.asp


title: Affymetrix GeneChip Rat Genome 230 2.0 Array (CDF: Rat2302_Rn_ENTREZG.cdf version 12.0.0)

status: Public on Nov 23 2009

description: Custom CDF (Brainarray Entrez Gene v12.0.0)

relation: Alternative to: GPL1355 (Alternative CDF [official])


title: UCSD-Moores Cancer Center in-house tyrosine kinase DNA chip

status: Public on Nov 21 2009

city: La Jolla

first: Yong

last: Jiang

state: CA

address: 3855 Health Science Dr.

department: Medicine

institute: UCSD-Moores Cancer Center

manufacture_protocol: Design two specific 60mer oligos for each of the 90 human tyrosine kinase genes and 1 to 3 oligos for each of  the tyrosine kinase ligands, the oligos were synthesized by IDT, and printed on codelink activated slides at microarray core facility(UCSD biogem) following manufacturer's instruction.


title: LMU Drosophila ananassae 1.2K

city: Planegg-Martinsried

first: Sonja

last: Grath

address: Grosshaderner Str. 2

department: Department Biology II

country: Germany

institute: LMU

organism: Drosophila ananassae

technology: spotted DNA/cDNA

first: John

middle: F

last: Baines

last: Parsch

manufacture_protocol: PCR products were purified using genPURE PCR 96 well filter plates (Genetix) and spotted on UltraGAPS slides (Corning) using a GeneMachines OmniGrid Accent microarrayer and standard protocols provided by the manufacturers


title: IPMC/CNRS-Agilent_Ehrlichia ruminantium strains Gardel and Welgevonden_8x15k

status: Public on Nov 20 2009

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

organism: Ehrlichia ruminantium

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


title: Miltenyi PIQOR(TM) Human antisense Ubiquitin-PS Microarray

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec GmbH

description:
The PIQOR (TM) Ubiquitin-PS Microarray is composed of 1278 human specific cDNAs. These cDNAs include for each array six house-keeping genes as positive controls. In addition four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer, respectively. All features are spotted in quadruplicate. The Platform data table reflects a condensed representation of the quadruplicate features.
This Platform represents two different physical arrays (batch714 and batch747) which are identical in terms of spotted cDNA content but differ in the position of some cDNAs.

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: IPMC/CNRS-Agilent_Ehrlichia ruminantium strains Gardel and Welgevonden_4x44k


title: Illumina Genome Analyzer (Burkholderia cenocepacia)

last: GEO

organism: Burkholderia cenocepacia


title: Agilent-020846 Synechococcus elongatus PCC 7942 Oligo Microarray

city: Cambridge

first: Vikram

last: Vijayan

state: MA

address: 52 Oxford Street, Room 440

institute: Harvard University

organism: Synechococcus elongatus PCC 7942 = FACHB-805

description:
Agilent 8x15k
Agilent Array ID 020846
The Platform data table reflects a condensed representation of the array's replicate features.

manufacture_protocol: see manufacturer's website


title: University of Chicago - HumanMouseDroCele tRNA array - 3200 - v1.0

organism:
Caenorhabditis elegans
Drosophila melanogaster
Homo sapiens
Mus musculus

manufacture_protocol: Oligonucleotides are resuspended in 50% DMSO to a final concentration of 40uM.  Each oligonucleotide is spotted on the Sigma SilanePrep slides and immobilized by crosslinking.


title: Trichoderma spp. HDO microarray

city: Villamayor

first: M Belen

last: Suárez

state: Salamanca

address: Rio Duero

department: CIALE

country: Spain

institute: Universidad de Salamanca

organism: Trichoderma harzianum

first: Alberto

last: de Luis

first: Ilanit

last: Samolsky

first: Enrique

last: Monte

first: Belen

last: Suarez

manufacture_protocol: maskless, digital micromirror technology (www.nimblegen.com)


title: Operon Rat V3.0 OpArray

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud


title: Mycobacterium smegmatis MC2 155 241K Whole Genome Tilling Array

status: Public on Nov 15 2009

first: Blair

last: Gordon

address: 1 King's College Circle

department: Molecular Genetics

institute: University of Toronto

organism: Mycolicibacterium smegmatis MC2 155

manufacture_protocol: The tiling oligonucleotide microarray is composed of 241K 60 mer oligonucleotides (20 bp spacing) from NCBI sequence data for M.tb H37Rv. Oligonucleotide probes are printed base-by-base from digital sequence files.


title: PICME Poplar 28K series 4

status: Public on Nov 18 2009

city: Southampton

first: Gail

last: Taylor

address: Bassett Crescent East

country: United Kingdom

institute: University of Southampton

organism:
Populus trichocarpa x Populus deltoides
Populus euphratica
Populus tremula x Populus alba

description:
Support: Corning GAPS II; Coating: Gamma Amino Propyl Silane
Number of spots: 2727648
Number of pins/blocks: 48
Spottdistance in µm: 180
Recurrances spots/slide: 1
Number of spots vertical: 24
Number of spots horinzontal: 24
Vertical offset of first block in µm: 1200
Horizontal offset of first block in µm: 3150
Lot number 13705000B

manufacturer: Austrian Research Centers GmbH - ARC, PICME

first: F

last: Martin

first: J

last: Leple

last: Kangasjarvi

first: S

last: Fluch

manufacture_protocol:
Spottingbuffer: 3xSSC+ 1,5MBetain
Spottingplate setting: Biozym 10µl
Arrayer Hardware: GeneMachines Omnigrid II
Arrayer Software: OmniGrid Gridder 2.2.13
Humidity: 40%
Dipping time in sec: 1


title: Plant and Food Arabidopsis thaliana AROS version 1.0

city: Palmerston North

first: Claudia

last: Voelckel

address: Riddet Road

department: Allan Wilson Centre for Molecular Ecology and Evolution

country: New Zealand

institute: Massey University

organism: Arabidopsis thaliana

manufacture_protocol: The array was produced by spotting the Arabidopsis thaliana AROS™ V1.0 genome set (Operon Biotechnologies, operon.com) onto epoxide coated glass slides (Corning 40044). Each of the 26,282 70mer oligonucleotides was spotted once. Oligos were resuspended in 150 mM NaPO4 Ph8.5 buffer, 0.0001% SDS and spotted using a BioRobotics MicroGridII using SMT-S75 silicon pins (Parallel Synthesis) at 23 C and 66% RH. In total, there were 26,880 probes on the array including controls (e.g. actin) which were arranged in a grid of 4x12 blocks with 576 spots per block (27,648 spots altogether).


title: RUGMCB Pichia angusta 8x15K v1

city: Haren

first: Tim

last: van Zutphen

state: Groningen

address: Kerklaan 30

department: Molecular Cell Biology

institute: University of Groningen

organism: Ogataea polymorpha NCYC 495 leu1.1

manufacture_protocol:
probes designed using  the Agilent eArray designs tools
Agilent’s in situ SurePrint inkjet oligonucleotide synthesis


title: Hebrew University of Jerusalem miRNA spotted array

city: Jerusalem

first: Hermona

last: Soreq

address: Safra Campus, Givat Ram

department: Department of Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

first: Ari

last: Meerson

manufacture_protocol: The mirVana oligo set (Ambion, Austin, TX; Catalog number 1564V1) was used to construct an in-house array with >200 spotted probes complementary to known human and mouse miRs. The mirVana probeset was dissolved in 3XSSC to a final concentration of 20 mM, and each oligo printed on Ultragaps slides (Corning, Corning, NY) 6 or more times, using the MicroGrid spotter (Genomic Solutions, Holliston, MA).


title: Febit Geniom Saccharomyces cerevisiae in situ oligo array

status: Public on Nov 13 2009

city: Barcelona

first: Benjamin

last: Pina

address: Jordi Girona, 18

institute: IDAEA-CSIC

organism: Saccharomyces cerevisiae

description: Geniom One, all-in-one instrument for sample loading, hybridization, washing, staining, and detection of biochips.

manufacture_protocol: The oligonucleotide array was processed in a Febit Geniom One  (febit GmbH, Mannheim, Germany) at Oryzon Genomics (Barcelona, Spain) facilities according to manufacturer. Automated, light-activated in situ synthesis of the array from a convenient database of oligomeric sequences. Five oligonucleotides per gene. Oligo sequences are listed in the supplementary file 'GPL8589_Oligo_Sequences.txt'.


title: Plants 4K miRNA LC_MRA-1038_miRPlants_14

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism:
Chlamydomonas reinhardtii
Physcomitrium patens
Pinus taeda
Gossypium hirsutum
Populus trichocarpa
Arabidopsis thaliana
Brassica napus
Brassica rapa
Brassica oleracea
Malus domestica
Glycine max
Medicago truncatula
Phaseolus vulgaris
Solanum lycopersicum
Oryza sativa
Saccharum officinarum
Sorghum bicolor
Triticum aestivum
Zea mays
Brachypodium distachyon
Vitis vinifera
Populus euphratica
Selaginella moellendorffii
Aquilegia coerulea

description: Plant miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 14

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://microrna.sanger.ac.uk/sequences/) 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: Toxoplasma gondii 4K miRNA LC_miRToxoplasma-gondii_MVI_090604

organism: Toxoplasma gondii

description: Custom miRNA microarray targeting the mature miRNAs of Toxoplasma gondii

first: Quan

last: Liu

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  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: NimbleGen Human 080814_HG18_Deluxe_Promoter_HX1 tiling array

status: Public on Nov 12 2009

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

organism: Homo sapiens

description:
Oligo coordinates based on genome build HG18.
The array tiles RefSeq genes from -7000 to +3000 relative to the TSS, with 100bp probe spacing.
Native NimbleGen files (ndf, pos) linked below as supplementary files.

manufacture_protocol: see the NimbleGen website


title: Nimblegen Homo sapiens 400K custom HOX cluster array 2

city: Boston

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

description: Spotted 50 mer oligos 400,000 features

first: Caroline

middle: J

last: Woo

first: Robert

middle: E

last: Kingston


title: Mycobacterium tuberculosis H37Rv 241K Whole Genome Tilling Array

city: Toronto

last: Gordon

organism: Mycobacterium tuberculosis H37Rv


title: JCVI PFGRC Porphyromonas gingivalis

city: Richmond

first: Janina

middle: P

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

organism: Porphyromonas gingivalis

manufacture_protocol: refer to manufacturer


title: CodeLink UniSet Homo sapiens 19.2K

first: David

middle: A

last: Sullivan

address: 20 Staniford Street

institute: Schepens Eye Research Institute

first: Tomo

last: Suzuki

first: Stephen

last: Richards

first: Shaohui

first: Roderick

middle: V

last: Jensen


title: Agilent-014839 Human Whole Genome ChIP-on-Chip Set 244K - 22 of 25 (Probe Name version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description: *** 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 GPL9634.

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


title: Agilent-014838 Human Whole Genome ChIP-on-Chip Set 244K - 21 of 25 (Probe Name version)

description: *** 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 GPL9633.


title: Agilent-014841 Human Whole Genome ChIP-on-Chip Set 244K - 24 of 25 (Probe Name version)

description: *** 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 GPL9636.


title: Cow 4K miRNA LC_MRA-1011_miRCow_14

organism: Bos taurus

description: Cow miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 14


title: Rat 4K miRNA LC_MRA-1003_miRRat_14

organism: Rattus norvegicus

description: Rat miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 14


title: Agilent-014833 Human Whole Genome ChIP-on-Chip Set 244K - 16 of 25 (Probe Name version)

description: *** 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 GPL9628.


title: Agilent-014830 Human Whole Genome ChIP-on-Chip Set 244K - 13 of 25 (Probe Name version)

description: *** 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 GPL9625.


title: Agilent-014828 Human Whole Genome ChIP-on-Chip Set 244K - 11 of 25 (Probe Name version)

description: *** 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 GPL9623.


title: Bacillus cereus Bc14579 - 2nd design (2x11K)

city: Wageningen

first: Maarten

last: Mols

address: Bomenweg 2

institute: Wageningen University

organism: Bacillus cereus ATCC 14579

first: Roy

last: Moezelaar

first: Tjakko

last: Abee

first: Menno

last: van der Voort

manufacture_protocol:
Agilent manufacture protocol.
Agilent uses its inkjet technology to print oligos onto glass slides.


title: Agilent-014826 Human Whole Genome ChIP-on-Chip Set 244K - 9 of 25 (Probe Name version)

description: *** 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 GPL9621.


title: Agilent-014823 Human Whole Genome ChIP-on-Chip Set 244K - 6 of 25 (Probe Name version)

description: *** 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 GPL9618.


title: CodeLink UniSet Homo sapiens 18.5k

description: GE Healthcare/Amersham Biosciences CodeLink™UniSet


title: Agilent-014822 Human Whole Genome ChIP-on-Chip Set 244K - 5 of 25 (Probe Name version)

description: *** 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 GPL9617.


title: Agilent-014821 Human Whole Genome ChIP-on-Chip Set 244K - 4 of 25 (Probe Name version)

description: *** 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 GPL9616.


title: Agilent-014843 Human Whole Genome ChIP-on-Chip Set 244K - 25 of 25 (Probe Name version)

description: *** 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 GPL9637.


title: Agilent-014840 Human Whole Genome ChIP-on-Chip Set 244K - 23 of 25 (Probe Name version)

description: *** 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 GPL9635.


title: Agilent-015343 Mouse Whole Genome ChIP-on-Chip Set 244K - 24 of 25 (Probe Name version)

organism: Mus musculus

description: *** 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 GPL9583.


title: Agilent-015339 Mouse Whole Genome ChIP-on-Chip Set 244K - 21 of 25 (Probe Name version)

description: *** 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 GPL9580.


title: Agilent-015337 Mouse Whole Genome ChIP-on-Chip Set 244K - 20 of 25 (Probe Name version)

description: *** 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 GPL9579.


title: Agilent-014836 Human Whole Genome ChIP-on-Chip Set 244K - 19 of 25 (Probe Name version)

description: *** 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 GPL9631.


title: Agilent-014835 Human Whole Genome ChIP-on-Chip Set 244K - 18 of 25 (Probe Name version)

description: *** 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 GPL9630.


title: Agilent-015336 Mouse Whole Genome ChIP-on-Chip Set 244K - 19 of 25 (Probe Name version)

description: *** 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 GPL9578.


title: Agilent-014837 Human Whole Genome ChIP-on-Chip Set 244K - 20 of 25 (Probe Name version)

description: *** 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 GPL9632.


title: Agilent-014834 Human Whole Genome ChIP-on-Chip Set 244K - 17 of 25 (Probe Name version)

description: *** 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 GPL9629.


title: Agilent-014829 Human Whole Genome ChIP-on-Chip Set 244K - 12 of 25 (Probe Name version)

description: *** 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 GPL9624.


title: Agilent-015334 Mouse Whole Genome ChIP-on-Chip Set 244K - 17 of 25 (Probe Name version)

description: *** 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 GPL9576.


title: Agilent-015329 Mouse Whole Genome ChIP-on-Chip Set 244K - 13 of 25 (Probe Name version)

description: *** 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 GPL9572.


title: Agilent-015333 Mouse Whole Genome ChIP-on-Chip Set 244K - 16 of 25 (Probe Name version)

description: *** 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 GPL9575.


title: Agilent-015335 Mouse Whole Genome ChIP-on-Chip Set 244K - 18 of 25 (Probe Name version)

description: *** 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 GPL9577.


title: Agilent-015328 Mouse Whole Genome ChIP-on-Chip Set 244K - 12 of 25 (Probe Name version)

description: *** 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 GPL9571.


title: Agilent-014832 Human Whole Genome ChIP-on-Chip Set 244K - 15 of 25 (Probe Name version)

description: *** 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 GPL9627.


title: Agilent-014827 Human Whole Genome ChIP-on-Chip Set 244K - 10 of 25 (Probe Name version)

description: *** 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 GPL9622.


title: Agilent-014831 Human Whole Genome ChIP-on-Chip Set 244K - 14 of 25 (Probe Name version)

description: *** 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 GPL9626.


title: Agilent-015320 Mouse Whole Genome ChIP-on-Chip Set 244K - 7 of 25 (Probe Name version)

description: *** 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 GPL9566.


title: Agilent-014824 Human Whole Genome ChIP-on-Chip Set 244K - 7 of 25 (Probe Name version)

description: *** 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 GPL9619.


title: Agilent-015323 Mouse Whole Genome ChIP-on-Chip Set 244K - 9 of 25 (Probe Name version)

description: *** 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 GPL9568.


title: Agilent-014820 Human Whole Genome ChIP-on-Chip Set 244K - 3 of 25 (Probe Name version)

description: *** 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 GPL9615.


title: Agilent-014825 Human Whole Genome ChIP-on-Chip Set 244K - 8 of 25 (Probe Name version)

description: *** 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 GPL9620.


title: Illumina Genome Analyzer II (Saccharomyces cerevisiae x Saccharomyces paradoxus)

last: GEO


title: Agilent-015344 Mouse Whole Genome ChIP-on-Chip Set 244K - 25 of 25 (Probe Name version)

description: *** 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 GPL9584.


title: SMD Print_940 Homo sapiens

city: Stanford

first: Andrew

last: Beck

address: Stanford

institute: Stanford University

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: Agilent-015341 Mouse Whole Genome ChIP-on-Chip Set 244K - 23 of 25 (Probe Name version)

description: *** 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 GPL9582.


title: SMD Print_1243 Homo sapiens


title: Agilent-014819 Human Whole Genome ChIP-on-Chip Set 244K - 2 of 25 (Probe Name version)

description: *** 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 GPL9614.


title: Agilent-014818 Human Whole Genome ChIP-on-Chip Set 244K - 1 of 25 (Probe Name version)

description: *** 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 GPL9612.


title: Agilent-015321 Mouse Whole Genome ChIP-on-Chip Set 244K - 8 of 25 (Probe Name version)

description: *** 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 GPL9567.


title: SMD Print_1553 Homo sapiens


title: 454 GS 20 (Nicotiana attenuata)

status: Public on Nov 11 2009

organism: Nicotiana attenuata


title: SMD Print_1080 Homo sapiens


title: Agilent-015340 Mouse Whole Genome ChIP-on-Chip Set 244K - 22 of 25 (Probe Name version)

description: *** 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 GPL9581.


title: Agilent Actinobacillus pleuropneumoniae 44K aCGH custom-array

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

institute: Huazhong Agricultural University

organism: Actinobacillus pleuropneumoniae

manufacture_protocol: Sure Print technology (Proprietary, Agilent)


title: Agilent-015330 Mouse Whole Genome ChIP-on-Chip Set 244K - 14 of 25 (Probe Name version)

description: *** 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 GPL9573.


title: Agilent-015332 Mouse Whole Genome ChIP-on-Chip Set 244K - 15 of 25 (Probe Name version)

description: *** 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 GPL9574.


title: Neisseria Version1.0.4

city: Gent

first: Gino

last: Baart

state: East Flanders

address: Technologiepark 927

department: Plant Systems Biology

country: Belgium

institute: Ghent University

organism: Neisseria meningitidis

manufacture_protocol:
Oligos were manufactured by Operon, according to standard protocols, and distributed in 384-wells plates
Oligos were spotted commercially by ServiceXS, Leiden , the Netherlands, according to standard protocols


title: Agilent-015325 Mouse Whole Genome ChIP-on-Chip Set 244K - 10 of 25 (Probe Name version)

description: *** 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 GPL9569.


title: Agilent-015327 Mouse Whole Genome ChIP-on-Chip Set 244K - 11 of 25 (Probe Name version)

description: *** 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 GPL9570.


title: SMD Print_1529 Homo sapiens

status: Public on Nov 10 2009

first: Patrick

middle: O

last: Brown

address: Beckman Center b439

department: Department of biochemistry

institute: Stanford university school of medicine


title: SMD Print_1539 Homo sapiens


title: Agilent-015319 Mouse Whole Genome ChIP-on-Chip Set 244K - 6 of 25 (Probe Name version)

description: *** 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 GPL9565.


title: Bdellovibrio bacteriovorus 194k oligo array version 1

city: Nottingham

first: Carey

last: Lambert

state: Notts

address: Queen's Medical Centre

department: Genetics

institute: Nottingham University

organism: Bdellovibrio bacteriovorus HD100

manufacture_protocol: http://www.nimblegen.com/technology/manufacture.html Catalog design for Bdellovibrio bacteriovorus (Taxonomy Id: 264462) covering NC_005363. Probes selected for 3587/3587 sequences. Median number of probes/sequence is 20 with an average of 20. Each probe will be replicated 2 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.


title: Agilent-015317 Mouse Whole Genome ChIP-on-Chip Set 244K - 5 of 25 (Probe Name version)

description: *** 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 GPL9564.


title: NimbleGen Mouse MM8 Deluxe Promoter Array

status: Public on Nov 09 2009

city: Lund

first: Joanne

last: Attema

address: Tornavagen 10

department: Immunology

country: Sweden

institute: Lund University

manufacture_protocol: standard NimbleGen protocol


title: Songbird Neurogenomics Initiative 20K Array

city: Urbana

first: Kirstin

last: Replogle

address: 1206 W Gregory Drive

institute: University of Illinois

organism: Taeniopygia guttata

manufacturer: University of Illinois, Functional Genomics Lab

last: Clayton

first: Mark

last: Band

first: George

last: Gong

first: Alvaro

middle: G

last: Hernandez

first: Ryan

last: Kim

first: Lei

last: Liu

first: Jyothi

last: Thimmapuram

manufacture_protocol:
cDNAs are arrayed in Genetix 384 well plates and stored frozen. Plates are thawed and spun down.
Plates are placed in storage hotel of an Omnigrid 100 (Genomic Solutions)
Slides are printed in batches of 100 using 1.5M Betaine + 3 x SSC
Following printing slides are baked at 80C for 2 hours
Slides are washed in 0.2% SDS followed by three water washes and an ethanol wash
Slides are dried by spinning in a centriguge at 1000 RPM for 3 minutes
Slides are stored in orange Corning boxes 25 per box
Storage boxes are purged with argon and sealed under vacuum


title: Illumina Genome Analyzer II (Mus musculus musculus)

status: Public on Nov 05 2009

organism: Mus musculus musculus


title: Agilent-015312 Mouse Whole Genome ChIP-on-Chip Set 244K - 3 of 25 (Probe Name version)

last: Agilent Technologies

description: *** 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 GPL9562.


title: Illumina Genome Analyzer II (Mus musculus domesticus)

organism: Mus musculus domesticus


title: Agilent_MIE Plasmodium berghei 4X44k Microarray

status: Public on Nov 06 2009

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

institute: mie university

organism: Plasmodium berghei

manufacture_protocol: see manufacturer's website


title: Agilent-015311 Mouse Whole Genome ChIP-on-Chip Set 244K - 2 of 25 (Probe Name version)

description: *** 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 GPL9561.


title: Illumina Genome Analyzer II (Saccharomyces cerevisiae; Saccharomyces paradoxus)

last: GEO

organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus


title: Agilent-015313 Mouse Whole Genome ChIP-on-Chip Set 244K - 4 of 25 (Probe Name version)

description: *** 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 GPL9563.


title: SMD Print_674 Homo sapiens

last: Beck


title: SMD Print_1185 Homo sapiens


title: Agilent-015310 Mouse Whole Genome ChIP-on-Chip Set 244K - 1 of 25 (Probe Name version)

description: *** 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 GPL9560.


title: SMD Print_1568


title: AB SOLiD System 2.0 (Drosophila melanogaster)

status: Public on Nov 03 2009

organism: Drosophila melanogaster


title: Illumina Genome Analyzer II (Mucor circinelloides)

organism: Mucor circinelloides


title: Print_1385

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


title: Illumina Genome Analyzer (Saccharomyces paradoxus)

organism: Saccharomyces paradoxus


title: NimbleGen Human 400K/250bp oligo array

status: Public on Nov 04 2009

city: The Bronx

first: Eric

last: Bouhassira

address: 1300 Morris Park avenue

institute: Albert Einstein College of Medicine

organism: Homo sapiens

description:
Genome build information hg18
400,000 oligo array representing about 3% of genome, oligo spaced every 250bp

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


title: 454 GS FLX (Hepatitis C virus)

organism: Hepacivirus hominis


title: JCVI PFGRC Chlamydia pneumoniae 10K v1 array designed primarily based on strain J138

city: Rockville

first: PFGRC

last: JCVI

state: MD

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Chlamydia pneumoniae

description: This set includes 2059 oligonucleotides, has 10752 spots distributed in 96 blocks.

manufacture_protocol: QCP, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 2976062, pen id 179, pen cycles -1, operator ROBIN, humidity control On, humidity set point65


title: JCVI PFGRC Chlamydia pneumoniae 10K v1 array designed primarily based on strain AR39


title: AB SOLiD System (Homo sapiens)


title: SMD Print_1524

last: Brown


title: NimbleGen Human 400K/100bp oligo array

description:
Genome build information hg18
400,000 oligo array representing about 1% of genome, each oligo spotted at least in quadruplicate, oligo spaced every 100bp


title: Illumina Genome Analyzer II (Mus spretus)

organism: Mus spretus


title: Illumina Genome Analyzer II (Mus musculus castaneus)

organism: Mus musculus castaneus


title: JCVI PFGRC Streptococcus agalactiae 10K v1 array designed primarily based on strain A909

organism: Streptococcus agalactiae

description: This set includes 2771 oligonucleotides, has 10800 spots distributed in 72 blocks.

manufacture_protocol: QSB, with arrayer LUCIDEA, mode Normal, replicates 3, repeats 1, slide_dips 38, machine cycles 996190, pen id 10185, pen cycles -1, operator Sonal/Ben, humidity control On, humidity set point65


title: NimbleGen E. coli K12 8.5K

city: Dublin

first: Daniel

last: Stoebel

address: Moyne Institute, Trinity College

department: Department of Microbiology

country: Ireland

institute: Trinity College, Dublin

organism: Escherichia coli str. K-12 substr. MG1655

manufacture_protocol: See www.nimblegen.com


title: 454 GS 20 (Mus musculus)

organism: Mus musculus


title: JCVI PFGRC Chlamydia pneumoniae 10K v1 array designed primarily based on strain D/UW-3/CX


title: FSU NimbleGen Mouse 385K Whole Genome Tiling

status: Public on Nov 02 2009

city: Tallahassee

first: Ichiro

last: Hiratani

state: FL

address: 319 Stadium Dr

department: Biological Science

institute: Florida State University

description:
Build: MM8, NCBI 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: NimbleGen


title: Silkworm 23K oligo array version 2.0

city: Beibei

first: Jiubo

last: Liang

state: Chongqing

address: Tiansheng Road No. 2

department: Molecular Biology

institute: Institute of Sericulture and System Biology

organism: Bombyx mori

manufacture_protocol: The 23 K oligonucleotide microarrays consist of 23,134 5'-amino-modified 70-mer probes. In addition to internal controls, eight intergenic sequences from yeast used as external controls were synthesized. The oligonucleotide probes were printed on aminosilane glass slides using a SmartArray microarrayer (CapitalBio Corp.). Microarrays were constructed at CapitalBio Corp. (Beijing, China).


title: MCGI4.6Kv1_CPG_Mouse_Array_UMCG

city: Groningen

first: vincent

last: bloks

department: Pediatrics

institute: UMCG

description: Mouse CpG-island 4.6K Array

manufacture_protocol: Microarrays are printed on GAPS II or UltraGAPS slides ( Corning Inc.) using high-precision robotics. Printed arrays processed following Conrnings protocol . For detailed information see http://www.microarrays.ca/


title: JCVI PFGRC Chlamydia pneumoniae 10K v1 array designed primarily based on strain CWL029


title: JCVI PFGRC Streptococcus agalactiae 10K v2 array designed primarily based on strain NEM316

manufacture_protocol: 2QSB, with arrayer LUCIDEA, mode Normal, replicates 3, repeats 1, slide_dips 38, machine cycles 996190, pen id 10185, pen cycles -1, operator Sonal/Ben, humidity control On, humidity set point65


title: Proprietary Affymetrix NHP GeneChip® Array for Cynomolgus genome derived from Biogen Idec

status: Public on Nov 01 2009

city: Louisville

first: Thomas

middle: B

last: Knudsen

state: KY

address: 501 S Preston St

department: Birth Defects Center

institute: University of Louisville

organism: Macaca fascicularis

description: Biogen Idec’s (NASDAQ: BIIB) proprietary Affymetrix NHP GeneChip® Array platform. This microarray chip contains a comprehensive representation of the Cynomolgus genome derived from Biogen Idec’s proprietary sequencing efforts, from which Gene Logic (www.genelogic.com/) subsequently obtained the exclusive rights to provide as a service (personal communication, Jun Mano, Gene Logic).

first: Makoto

last: Ema

first: Ryota

last: Ise

first: Hirohito

last: Kato

first: Satoru

last: Oneda

first: Akihiko

last: Hirose

first: Mutsuko

last: Hirata-Koizumi

first: Toshio

last: Ihara

first: Amar

last: Singh

manufacture_protocol: see service provider web site www.genelogic.com


title: JCVI PFGRC Streptococcus agalactiae 10K v2 array designed primarily based on strain A909


title: JCVI PFGRC Streptococcus agalactiae 10K v2 array designed primarily based on strain 2603V/R


title: JCVI PFGRC Streptococcus agalactiae 10K v1 array designed primarily based on strain 2603V/R


title: JCVI PFGRC Streptococcus agalactiae 10K v1 array designed primarily based on strain NEM316


title: NimbleGen Human 2.1M array

city: Baltimore

first: Akiko

last: Doi

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

description: Annotation based on UCSC human genome assembly March 2006 (HG18)


title: Texas State University/Ron Walter Oryzias latipes 8k array (version 1)

status: Public on Oct 23 2009

city: San Marcos

first: Ziping

last: Zhang

address: 601 University Drive/Cent. 419

department: Chemistry & Biochemistry

institute: Texas State University

organism: Oryzias latipes

manufacturer: Ron Walter's Laboratory of Texas State university

first: Ron

last: Walter

manufacture_protocol: Medaka expressed sequence tags (ESTs) were downloaded from NCBI GenBank (http://www.ncbi.nlm.nih.gov/). 60-mer oligonucleotides were designed for unigenes using commercial software, ArrayDesigner v3 (Telechem, Sunnyvale, CA, USA) and synthesized by IDT™ (Integrated DNA Technologies, Coralville, IA, USA). The oligonucleotides were diluted in 3×SSC (20×SSC: 3 M NaCl, 0.3 M sodium citrate pH 7.0) and spotted on aminosilane coated Superchip glass slides (Cat no. C18-5131-M20, Erie Scientific, Portsmouth, NH, USA) using a microarraying robot Virtek Chip Writer Pro (Virtek Vision, Waterloo, Ontario, Canada) with 16 Telechem Stealth pins (Cat no.: 946MP3, Telechem). These pins were designed with uptake channels and flat tips, and thus could effectively avoid "donut" spots. The slides were printed in the Genomic Analysis and Technology Core of the University of Arizona (Dr. Ryan Sprissler).


title: Illumina Genome Analyzer (Aspergillus oryzae)

last: GEO

organism: Aspergillus oryzae


title: Plasmodium falciparum 385K tiling array

status: Public on Sep 02 2009

city: Nijmegen

first: Richard

last: Bartfai

address: Geert Grooteplein 26-28

institute: Nijmegen Center of Molecular Life Sciences

organism: Plasmodium falciparum

description:
ChIP on chip:
Chromatin immunoprecipitations were carried out using formaldehyde crosslinked chromatin isolated from synchronized trophozoites (3D7/PfHP1-HA). After formaldehyde crosslinking and saponin lysis, nuclei were separated using a 0.25M sucrose buffer cushion and sheared by sonication in a Bioruptor UCD-200 (Diagenode) for 15min at 30sec intervals (size range 100-500bp). 400-500ng DNA-containing chromatin was incubated with 1ug antibody (anti-HA, ab9110); in presence of 10ul A/G sepharose beads (Santa Cruz Biotechnology) overnight at 4°C. After extensive washes immunoprecipitated chromatin was eluted with 1% SDS and 0.1M NaHCO3 and de-crosslinked at 65°C for 4hrs. DNA was purified using PCR purification columns (Qiagen). For genome-wide analysis 24 individual ChIP reactions were combined using formaldehyde-crosslinked material. Immunoprecipitated DNA was amplified by a modified T7 linear amplification method (A. Salcedo-Amaya et al, PNAS, 2009). Briefly, DNA fragments were dephosphorylated using calf intestinal alkaline phosphatase (NEB) and subsequently G-tailed with terminal transferase (NEB). T7 promoter was incorporated using Klenow polymerase (NEB) and T7C9B primer. RNA was synthesized by T7 polymerase (Ambion T7 megascript kit) and subsequently reverse transcribed using N6 primers. Amplified dsDNA was labeled with Cy3- (ChIP) or Cy5- (input) coupled random heptamers and hybridized to a tiling array at Roche NimbleGen.

first: Christian

last: Flueck

first: Jennifer

last: Volz

first: Igor

last: Niederwieser

first: Adriana

last: Salcedo-Amaya

first: Blaise

middle: T

last: Alako

first: Florian

last: Ehlgen

first: Stuart

last: Ralph

first: Alan

last: Cowman

first: Zbynek

last: Bozdech

first: Hendrik

last: Stunnenberg

first: Till

last: Voss

manufacture_protocol:
DESIGN_ID	DESIGN_NAME	DESCRIPTION
1992	2005-05-10_Plasmodium_3D7_WG_CGH	Plasmodium genome (3D7) tiled at 45 bp spacing. Probes selected at 4 bp primary interval with a 4 bp secondary interval. 10 probes selected at each primary interval and then uniqueness, frequency and basic rule scoring determined. Instead of normal Tm tiling, probes were allowed to grow as long as possible given the 148 synthesis cycle cutoff. Rank selection done for each primary interval 'cluster'. The 478402 probes selected by the rank selection were then filtered further: rules >= -300; frequency <= 25; tm: 60-80. This left 385585 probes for the design. Also added 2883 random tm70 probes with the following parameters: tm 70; 148 cycles; min length: 45; max length: 85; gc: 23%.


title: Queen conch (Strombus gigas) oligonucleotide microarray v1

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

organism: Aliger gigas

first: Robert

last: Griffitt

first: Li

last: Liu

first: Kevin

last: Kroll

last: Glazer

first: David

last: Barber

first: Nancy

middle: D

last: Denslow

manufacture_protocol:
- A normalized cDNA library was constructed and sequenced using the 454/Roche Life Sciences GS-FLX high-throughput sequencer.
- Agilent's eArray service was used to construct a custom 8x15k oligonucleotide microarray.


title: JCVI PFGRC Bacillus anthracis 25K vt3b array designed primarily based on strain Ames

status: Public on Aug 29 2009

first: PFGRC

last: JCVI

organism: Bacillus anthracis

description: This set includes 20262 oligonucleotides, has 25392 spots distributed in 48 blocks.

manufacture_protocol: T3BQBC, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: VMarray Homo sapiens 3.1K cancer apoptosis

city: Ljubljana

first: Vid

last: Mlakar

address: Korytkova 2

department: Department for molecular genetics

country: Slovenia

institute: Faculty of Medicine

manufacturer: Insitute of pathology, Department of molecular genetics

manufacture_protocol: We used Human Cancer Subset V3.0 and Human Apoptosis Subset V2.0 (Operon) oligos. Nexterion slide E (Schott Nexterion) slides were used as support. We used MG1000 (Microgid) spoter to deposit oligos as recomended by slide provider (Schott Nexterion)


title: JCVI PFGRC Bacillus anthracis 25K vt3b array designed primarily based on strain Sterne

country: USA


title: JCVI PFGRC Bacillus anthracis 23K vt3a array designed primarily based on strain Ames

description: This set includes 22332 oligonucleotides, has 23232 spots distributed in 48 blocks.

manufacture_protocol: T3AQBC, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Bacillus anthracis 32K vt1 array designed primarily based on strain Sterne

status: Public on Sep 18 2009

description: This set includes 29994 oligonucleotides, has 32448 spots distributed in 48 blocks.

manufacture_protocol: T1QBC, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: EMBL/CodeLink Mouse 0.4K miCHIP V8.0

status: Public on Oct 06 2009

city: Heidelberg

first: Mirco

last: Castoldi

address: Im Neuenheimer Feld 156

department: Department of Pediatric Oncology, Hematology and Immunology

institute: University of Heidelberg

description:
miChip v8.0 annotation was done for mouse; however miCHIP v8.0 (mouse) contains capture probe matching several human microRNAs that were not validated in mouse (miRBase v8.0).

miChip array are spotted on CodeLink, 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 were spotted by the Genomics Core Facility, EMBL, Germany. LNA-modified capture probes were manufactured by Exiqon, Denmark

first: Vladimir

last: Benes

first: Sabine

last: Schimidt

first: Martine

middle: U

last: Muckenthaler

first: Matthias

middle: W

last: Hentze

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 (50 C) 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 21 C.
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. 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 50 C) for 30 min in the water bath (50 C). Then the slides are rinsed twice with deionized water and a third time with post-coupling washing solution (pre-warmed to 50 C) 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 month at room temperature in a dessicator.


title: JCVI PFGRC Bacillus anthracis 32K vt1 array designed primarily based on strain A2012


title: JCVI PFGRC Bacillus anthracis 32K vt1 array designed primarily based on strain Ames


title: Mouse Custom Oligoarray Targeting Complementary Strand of Known Genes (all)

status: Public on May 01 2009

city: Tsukuba

first: Koji

last: Numata

address: 3-1-1 Koyadai

institute: RIKEN

first: Yuko

last: Osada

first: Yuki

last: Okada

first: Rintaro

last: Saito

first: Noriko

last: Hiraiwa

first: Hajime

last: Nakaoka

first: Naoyuki

last: Yamamoto

first: Kazufumi

last: Watanabe

first: Kazue

last: Okubo

first: Akio

last: Kanai

first: Kuniya

last: Abe

first: Hidenori

last: Kiyosawa

manufacture_protocol: See manufacturer's web site


title: JCVI PFGRC Bacillus anthracis 25K vt3b array designed primarily based on strain A2012

first: PFGRC

last: JCVI


title: IPMC/Agilent Human miRTA - MiRNA Tiling Microarray

status: Public on Apr 02 2009

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: The Homo Sapiens miRNA Tiling microarray miRTA contains probes tiling regions surrounding microRNA and microRNA clusters

first: Karine

last: Robbe

first: Bruno

last: Cardinaud

first: Pascal

last: Barbry

first: Bernard

last: Mari

last: LeBrigand

manufacture_protocol: Customed Array (eArray) 4*44K


title: JCVI PFGRC Bacillus anthracis 23K vt3a array designed primarily based on strain Sterne


title: JCVI PFGRC Staphylococcus aureus array v2

status: Public on Oct 31 2007

city: Normal

first: Arunachalam Muthaiyan

email: amuthai@gmail.com, bjwilkin@ilstu.edu

state: IL

address: Julian Hall

department: Biological Sciences

institute: Illinois State University

organism: Staphylococcus aureus

description:
This set includes 2709 elements on array, has 9747 spots distributed in 72 grids.
This is a condensed template of triplicated features of PFGRC/TIGR Staphylococcus aureus version 2 array.
For full template information please refer to:   http://pfgrc.jcvi.org/descriptionPages.shtml
http://pfgrc.tigr.org/slide_html/annotation_index/S_aureus_index_2.shtml
The GAL Annotation File (GPL6059.gal) is linked as a Supplementary file at the foot of the record.

first: JCVI

last: PFGRC

manufacture_protocol:
Array Type : ss_cdna (amplicons),Surface Coating: Aminosilane,Printing Buffer(s): DMSO,Arraying Machine(s): Lucidea,Oligo Replicates : 3x
Oligos Designed : 2709 ,Controls: 40 A. thaliana (amplicons) and 500 A.thaliana (70-mers).


title: LC_MRA-1001_miRHuman_9.2_070528 (miRNA ID version)

status: Public on Jul 27 2009

city: Houston

first: Christoph

last: Eicken

address: 2575 W. Bellfort

institute: LC Sciences, LLC

description: Human miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 9.2

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://microrna.sanger.ac.uk/sequences/) 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: JCVI PFGRC Bacillus anthracis 23K vt3a array designed primarily based on strain A2012


title: LC_MRA-1001_miRHuman_9.2_070528

status: Public on Jul 25 2009


title: IOLR_Lithognathus mormyrus_4608_v1.0

status: Public on Dec 26 2007

city: Haifa

first: Moshe

last: Tom

department: Marine Biology and Biotechnology

organism: Lithognathus mormyrus

description: The array is printed on a 2.5 x 7.5 cm glass (GAPS II slides, Corning) on an area less than 6 x 2 cm. The grid system includes 4 x 12 sub-arrays, each containing 14 rows and 14 columns, a total of 9408 spots.

manufacturer: Moshe Tom's laboratory - Israel Oceanographic and Limnological Research, Haifa, Israel.

first: Meirav

last: Auslander

first: Vered

last: Chalifa-Caspi

manufacture_protocol: Exposure to pollutants was performed after a one month acclimation period, by injecting 5 xenobiotic mixtures dissolved in a suitable vehicle, totaling 10 compounds, into 5 groups of fish at the first and third day of the experiment. The utilized compounds were: Benzo(a)pyrene, 1,1 dichloro-2.2-bis [p-chlorophenyl] ethylene (pp’-DDE), Aroclor 1254 (polychlorinated biphenyl mixture, perfluoro octanoic acid, tributyl tin chloride, Lindane, methyl mercury chloride, 4-nonylphenol, beta-estradiol and cadmium chloride. Non-injected fish served as reference group. Fish were sacrificed by decapitation at the third and the seventh day after the second injection. Livers were snap frozen in liquid nitrogen and kept at -80oC, aimed at latter RNA purification. The cDNA assemblage was constructed in two stages: (1) SMART (Switching Mechanism At 5' end of the RNA Transcript), aimed at amplification of reverse transcribed cDNAs using a universal primer, linked to both ends of the template cDNA during the reverse transcription stage (Clontech, manufacturer instructions). (2) SSH (Subtractive-Suppression Hybridization method; Diatchenko et al. 1999; PCR-select, Clontech), aimed at T-A cloning of a roughly equally represented cDNAs from the target organs into an expression plasmid (pGEM-Teasy, Promega). biased towards genes differentially expressed in the target tissues in comparison to the reference one. The cloned cDNAs were transfected into E. coli, and 4608 bacterial colonies were isolated, amplified and frozen at -700C. All the 4608 clones were amplified by standard PCR (5’ at 950C; 32 cycles of 0.5’ at 950C, 0.5’ at 680C and 1.5’ at 720C; a final incubation of 4’ at 720C; GeneAmp 5700, ABI) using the PCR-select universal primers located at both ends of each cloned DNA fragment (see Diatchenko et al. 1999; PCR-select, Clontech). PCR products were precipitated from the PCR solution by one volume of isopropanol at room temperature. The dry DNA was dissolved in printing buffer at final concentration of 50% DMSO and 0.3 x SSC and was printed on a glass slide (GAPS II slides, Corning; MGII robot-printer, BioRobotics) in adjacent duplicates. The amplification efficiency was tested by running the PCR products on a 1% agarose gel concurrent with a DNA mass ladder.  Most of the clones were successfully sequenced and assembled by the CAP3 software (Huang and Madan, 1999), to identify unique sequences. All unique sequences were annotated by BLASTN, BLASTX and GO.    References  Diatchenko, L., Lukyanov, S., Lau, Y.F.C. and Siebert, P.D. (1999) Suppression subtractive hybridization: A versatile method for identifying differentially expressed genes. In: cDNA Preparation and Characterization, Meth Enzymol 303: 349-380. San Diego: Academic Press Inc.  Huang, X. and Madan, A. (1999) CAP3: A DNA sequence assembly program. Gen Res 9: 868-877.


title: Rosetta/Merck Mouse RSTA Custom Affymetrix 1.0 microarray

status: Public on Apr 30 2008

city: Seattle

first: Amit

last: Kulkarni

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description:
Standard Affymetrix platform
Contains 25-mer probes grouped together to form probesets.

first: John

last: Castle

manufacture_protocol: see Affymetrix website


title: Duke Cryptococcus neoformans serotype D (JEC21) 8K

status: Public on Jun 27 2009

city: Seoul

first: Yong-Sun

last: Bahn

address: 134 Shinchon-dong Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

organism: Cryptococcus deneoformans JEC21

first: Young-Joon

last: Ko

first: YeongMan

last: Yu

first: Gyu-Bum

last: Kim

first: Gir-Won

last: Lee

first: PilJae

last: Maeng

first: Sang-Soo

first: Anna

last: Floyd

first: Joseph

last: Heitman

manufacture_protocol: 70-mer oligonucleotides.