title: Illumina Genome Analyzer II (Nannochloropsis oceanica)

status: Public on Mar 30 2012

last: GEO

country: USA

organism: Nannochloropsis oceanica

technology: high-throughput sequencing

distribution: virtual


title: Febit Homo Sapiens, miRBase v14

status: Public on Apr 09 2012

city: Vancouver

first: Victoria

last: Svinti

address: 2350 Health Sciences Mall

country: Canada

institute: University of British Columbia

organism: Homo sapiens

technology: in situ oligonucleotide

distribution: commercial

first: Emma-Kate

last: Loveday

first: Sandra

last: Diederich

first: John

middle: M

last: Pasick

first: Francois

last: Jean

manufacture_protocol:
MicroRNAs (miRNAs) are endogenous, non-coding RNAs that play a fundamental role in gene regulation and have critical functions across various biological processes. Pairing to mRNAs of protein-coding genes, They direct posttranscriptional repression by altering the stability or translational efficiency of their target mRNAs.
Recent studies indicate that miRNAs are involved in the development of human malignancies, suggesting that they represent a promising new class of cancer biomarkers. Identifying miRNAs involved in specific cancers could provide useful diagnostic information, allow disease classification and reveal potential treatment targets.
MPEA: On-Chip Labeling for Highest Sensitivity
Enzymatic labeling assay requires minimal sample amount
In addition to the standard hybridization of pre-labeled RNA, the microfluidic Geniom Biochip enables a highly sensitive enzymatic labeling protocol.
MPEA benefits
* Higher sensitivity and specificity
* miRNA hybridization without preceding treatment like enrichment, PCR -based amplification or labeling eliminates potential bias
* High discriminatory power
* Minimal amount of sample RNA needed (more than or equal 20 ng total RNA)
* Easy to use protocol for Geniom RT Analyzer
The unique Microfluidic Primer Extension Assay (MPEA) uses unlabeled miRNAs for hybridization. In a second step, Klenow fragment of DNA polymerase I is added directly into the channels of the microfluidic chip, where the specific elongation of the bound miRNAs takes place.
The method combines the specificity of a hybridization assay with the discriminatory power of an enzymatic extension and reduces the required sample amount to a minimum.
Details provided at www.febit.com


title: Synechococcus WH 7803 custom tiling array

status: Public on Mar 31 2012

city: Freiburg

first: Gregor

middle: Josef

last: Gierga

department: Institut of Biology III -Genetics

country: Germany

institute: University of Freiburg

organism: Synechococcus sp. WH 7803

distribution: custom-commercial

manufacturer: formerly CombiMatrix now CustomArray Inc.

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


title: NimbleGen_GenAu MB BCELL v2.5

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

country: Austria

institute: Instutute of Molecular Pathology

organism: Mus musculus

description:
Custom array.
genomic regions of potential pax5 target genes from mm6, including IGH and surrounding genes
isothermal tiling oligos at 100bp

first: Shane

last: McManus

first: Anja

last: Ebert

first: Maria

last: Novatchkova

manufacture_protocol: as described in www.nimblegen.com


title: ILLING Xerophyta 1709 v1.0.

city: Rondebosch

first: Nicola

last: Illing

state: Western Cape

address: Chemistry Rd

department: Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

organism: Xerophyta humilis

technology: spotted DNA/cDNA

distribution: non-commercial

manufacturer: CAPAR Microarray Lab, Department of Molecular and Cell Biology, University of Cape Town, Western Cape, South Africa

manufacture_protocol:
(1) The inserts of 3105 X. humilis clones (1450 clones from LD cDNA library;  1453 clones from RD cDNA library; 107 clones from LR cDNA library; and 95 clones from RR cDNA library) were PCR amplified in Corning Thermowell 96-well plates (Corning Incorporated, NY, USA).  For each cDNA clone, 1 µl of 25% glycerol stock culture was added to 100 µl of a PCR mixture containing 0.3 µM T3 primer, 0.3 µM T7 primer, 200 µM dNTPs, 2.5 mM MgCl2, 1X PCR reaction buffer and 0.1 µl (5U/µl) Super-therm polymerase (Southern Cross Biotech, South Africa). PCR was performed as follows: at 94°C for 1 min; for 10 cycles at 94°C for 20 sec, 56°C for 20 sec, 72°C for 2 min; for 30 cycles at 94°C for 20 sec, 51°C for 20 sec, 72°C for 2 min; and at 72°C for 7 min.
(2) PCR reactions were transferred to Millipore 96-well Multiscreen PCR plates (Millipore, MA, USA) fit on vacuum apparatus, then allowed to pass through the filters for 10 minutes.  Filters were then washed by passing 100 µl H2O for 10 minutes twice.  PCR products were resuspended in 50 µl 50% DMSO with vigorous agitation for 60 minutes. Twenty microlitres of which were pipette-transferred into 384-well plates (Amersham, Germany) for slide printing.
(3) The purified cDNAs, together with Lucidea controls (Amersham Biosciences, Germany) were printed onto Corning GAPS II coated slides (Corning Incorporated, NY, USA) by MicroGrid II Arrayer (BioRobotics, Cambridge, UK) with 16 10 µm split pins in a 4x8 configuration following manufacturer's instructions. The printed slides were UV-crosslinked (900 mJ cm2), and baked at 80°C for 2 hours. Each printed block was designed to contain random unbiased mixture of cDNAs originated from LD, RD, LR and RR library clones.


title: Mycobacterium tuberculosis 4.6k array_TB-Oligos

status: Public on Aug 11 2007

city: Stanford

first: SMD

last: Staff

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism: Mycobacterium tuberculosis

technology: spotted oligonucleotide

manufacturer: Tina, Boussard. Stanford University, School of Medicine, Department of Genetics. Stanford, CA 94305 United States. Phone: 650-736-0077. Email:  boussard@genome.stanford.edu

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


title: Gallus gallus 1x385K gene expression array_GFC105_Ggul

city: Tsukuba

first: Yuko

last: Uchida

country: Japan

institute: National Institute of Animal Health

organism: Gallus gallus

description:
A 1:2 density and 60-mer expression design was used for the custom design. 38,723 genes from Gallus gallus were targeted and each gene have 9 independent probes.  There is no replication so that there are totally 348,102 probes on the array.  NimbleGen's design name is 2006-02-10_GFC105_Ggul_60mer.  The .ndf and .ngd files are linked below as supplementary files.

native array description file :2006-02-10_GFC105_Ggul_60mer.ndf
native array description file :2006-02-10_GFC105_Ggul_60mer.ngd
DESIGN_ID : 3053

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


title: Progenika P putida KT2440 oligo array (probe-level)

status: Public on Jul 08 2012

city: Harpenden

first: Andrew

middle: L

last: Neal

state: Herts

address: West Common

country: United Kingdom

institute: Rothamsted Research

organism: Pseudomonas putida KT2440

manufacture_protocol: The P. putida KT2440 DNA microarray developed contains 5539 oligonucleotides (50-mer) spotted in duplicate onto aminosylane treated 25x75 mm microscope slides, covalently linked to the slide with UV light and heat. The spots, 180 um in diameter, are separated from each other by 265 um and arranged in 48 subarrays (16 columns and 15 rows each). The spotted area is 17x54 mm. The oligonucleotides, designed by BioAlma (www.bioalma.com), are specific for each ORF in the array. These include the 5350 ORFs annotated in the P. putida KT2440 genome (obtained from www.ncbi.nlm.nih.gov, Refseq NC_002947; GenBank accession number AE015451.1), the 140 ORFs defined for the TOL plasmid pWW0 (obtained from www.ncbi.nlm.nih.gov, Refseq NC_003350; GenBank accession number AJ344068.1), and other genes of diverse origins such as commonly used reporter genes (lacZ, gfp) or antibiotic resistance markers. Two oligonucleotides, coding for the rpoD and rpoN genes, respectively, were spotted at 20 different positions of the slide to serve as homogeneity controls. Negative controls (spotting buffer, 50% [vol/vol] dimethylsulfoxide) were spotted in duplicate at 203 positions evenly distributed throughout the printed area. The array was printed by Progenika Biopharma (www.progenika.com).


title: Transcriptional responses of mouse BMM and TEPM to lipopolysaccharide (LPS)

status: Public on Mar 29 2012

city: Brisbane

first: Kate

last: Schroder

state: QLD

address: University of Queensland, St Lucia

country: Australia

institute: Institute for Molecular Bioscience

description: 60-mer spotted oligonucleotide probes.

first: Katharine

last: Irvine

first: Matthew

middle: J

last: Sweet

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


title: NimbleGen Honeybee 2.1M array

status: Public on Sep 15 2012

city: Baltimore

first: Brian

middle: R

last: Herb

state: MD

address: 855 North Wolfe Street

department: Center for Epigenetics

institute: JHU

organism: Apis mellifera

description: Annotation based on Baylor College of Medicine Human Genome Sequencing Center honeybee genome assembly Oct 2006 (Amel_4.0)

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


title: Systemic Analysis of Araboidopsis Promoters (SAP, Benhamed et al. 2008) [Membrane A]

city: Gatersleben

first: Astrid

last: Junker

address: Corrensstrasse 3

department: Molecular Genetics

institute: Leibniz Institute for Plant Genetics and Crop Plant Research

organism: Arabidopsis thaliana

manufacturer: Weisshaar lab (Bielefeld University, Chair of Genome Research); Altschmied lab (IPK Gatersleben)

manufacture_protocol: For large scale identification of precipitated and amplified chromatin fragments, a macroarray was spotted using 11,904 PCR products comprising upstream regions of Arabidopsis genes which were obtained from the European SAP-project (Systemic analysis of Arabidopsis promoters, (Benhamed et al., 2008). Amplicons were purified by reverse osmosis using MinElute plates (Qiagen, Hilden, Germany) and resuspended in 20µl TE buffer and analyzed on 1% agarose gels before spotting. Approximately 75% of the amplicons appeared as single bands. Amplicons were mixed 1:1 (v/v) with 1M NaOH, 5M NaCl and spotted in duplicate onto positively charged Biodyne B nylon membranes (Pall, Dreieich, Germany) at a density of 140 spots/cm2 using a Microgrid III robot (BioRobotics, Cambrigde, England). After spotting, membranes were washed with 0,5M NaOH, 1,5M NaCl for 5min, neutralized in 1,5M NaCl, 0,5M Tris-HCl, pH 7,4 for 5min, cross-linked in a UV-Stratlinker 2400 (Stratagene, Cedar Creek, United States) at 120mJ and baked for 30min at 80°C in a thermal oven. Amplicons were distributed on two membranes (membrane A and B).


title: Agilent-027973 Aspergillus fumigatus Af293 8x15k Expression Array

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

organism: Aspergillus fumigatus Af293

description:
Aspergillus fumigatus Af293 fumigatus 8x15k designed by Genotypic Technology Pvt. Ltd. (AMADID: 027973)
Contact: earray@genotypic.co.in

first: Mugasimangalam

middle: C

last: Raja

first: AjayKumar

last: KM


title: Atlas Mouse 1.2 Array II (Cat. #7857-1)

status: Public on Oct 01 2002

city: Palo Alto

last: BD Biosciences Clontech

address: 1020 East Meadow Circle

institute: BD Biosciences Clontech

description: Nylon, broad-coverage murine cDNA array.  The cDNA fragments (200-600 bp) are PCR-amplified using gene-specific primers, and are selected so that they lack repetitive elements and have minimal homology with other genes on the array.

manufacture_protocol: see manufacturer's web site


title: NimbleGen E. coli K12 Mg1655 385K array

city: Taipei

first: Chi

last: Yang

address: No.155, Sec.2, Linong Street

department: Institute of BioMedical Informatics

country: Taiwan

institute: National Yang-Ming University

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

description:
This is a commercial 385K high density tiling array from NimbleGen for E. coli K12 MG1655 (Cat. No. 05542901001). The design contains 50-mer probe with 24 bp median probe spacing and the control probes are also included.
native array description file: 2006-07-18_Ecoli_K12_ChIP.ndf
native array description file: 2006-07-18_Ecoli_K12_ChIP.pos


title: Agilent-020666 EHEC_EDL933_O157_H7_Antisense

city: Parkville

last: Wakefield

state: VIC

address: 1G Royal Parade

department: Bioinformatics

institute: Walter and Eliza Hall Institute

organism: Escherichia coli

description:
EHEC EDL933 O157:H7 from plasmid NC_007414 chromosome NC_002655
Arrays of this design have barcodes that begin with 16020666 or 2520666.
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: Agilent-015618 Lactobacillus plantarum WCFS1 244k tiling array forward strand

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: TB-1

status: Public on Aug 26 2005

last: Stanford Microarray Database

manufacturer: John,,Matese; Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Room 135, Princeton, NJ, United States; (609) 258-8309; jcmatese@genomics.princeton.edu


title: Illumina Sentrix Array Matrix (SAM) - GoldenGate Methylation Cancer Panel I

city: Philadelphia

first: Nahid

last: Turan

state: PA

address: 3307 North Broad Street, AHB

department: Fels Institute

institute: Temple University School of Medicine

technology: oligonucleotide beads

description:
High-Throughput DNA Methylation Profiling with Illumina GoldenGate® Technology
Experimentally validated Oligo pool for Methylation  Assay (OMA) for 1,505 CpG sites selected  in promoter regions and/or first exon of over  800 genes. Sufficient for the analysis of 96  samples.


title: miRRat_17

status: Public on Mar 25 2012

city: Shanghai

first: Jing

last: Li

address: South Chongqing Road

country: China

institute: Institue of Health Sciences

organism: Rattus norvegicus

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: Agilent-029126 order_cottus_expression_array_1 [FeatureNumber version]

status: Public on Mar 27 2012

city: Ploen

first: Till

last: Czypionka

address: August-Thienemann-Strasse 2

department: Evolutionary Genetics

institute: MPI for Evolutionary Biology

organism: Cottus

description:
Expression array with sense probes for transcripts with blasthit and with detected polyA strand.

Arrays of this design have barcodes that begin with 16029126 or 2529126.

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: Transcriptional responses of human monocyte-derived macrophages (HMDM) to lipopolysaccharide (LPS)

description: 60-mer spotted oligonucleotide probes.


title: Agilent-015640 Lactobacillus plantarum WCFS1 244k tiling array reverse strand


title: Systemic Analysis of Araboidopsis Promoters (SAP, Benhamed et al. 2008) [Membrane B]


title: Agilent-029126 order_cottus_expression_array_1 [ProbeName version]


title: Operon Rat V3.0 OpArray

status: Public on Mar 23 2012

city: Seoul

first: Seong

last: Je kyung

country: South Korea

institute: Seoul National University


title: FZ_IBG-1_Gluconobacter oxydans 621H_10K_V1

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

organism: Gluconobacter oxydans 621H

description: G.oxydans 621H, based on the genome sequence entry NC_006677

manufacturer: Operon (Cologne, Germany) and Microarrays Inc. (Huntsville, USA)

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


title: Illumina HiSeq 2000 (Monodelphis domestica)

last: GEO

organism: Monodelphis domestica


title: GlassLab-Ncrassa-10k-V1

status: Public on Mar 26 2012

city: Tianjin Airport Economic Area

first: Chaoguang

last: Tian

state: Tianjin

address: Xiqi Dao 32

institute: Tianjin Institute of Industrial Biotechnology, CAS

organism: Neurospora crassa

manufacture_protocol:
Designed 70mer oligonucleotide immobilized probes using ArrayOligoSelector
the _10_000 open reading frames (ORFs) derived mainly from the N.crassa databases at the Broad Institute were used.
Oligomers were re-suspended in 3xSSC to a final concentration of 40 uM and spotted onto poly(L)-lysine-coated microscopic slides


title: Ehime University Human Custom 2K array

city: Toon-shi

first: Hidetaka

last: Ohnuki

state: Ehime

address: Shitsukawa

department: Department of Biochemistry and Molecular Genetics

institute: Ehime University

organism: Homo sapiens

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 2000 (Alternaria brassicicola)

organism: Alternaria brassicicola


title: PLBIO-DX - WH/GEX

city: Mumbai

first: Muralidhara

last: Padigaru

state: Maharashtra

address: 1, Nirlon Compex, Off Western Express Highway

department: Translational Research

institute: Piramal Lifesciences India Limited

manufacturer: Biomarker Discovery, Translational Research, Piramal Healthcare India Limited

manufacture_protocol: A microarray chip with 37,632 transcripts representing the whole human genome were purchased from Operon Biotechnologies (Operon, USA). Every gene was confirmed for function and sequence with the latest RefSeq genome build and represented as a unique 70-mer oligonucleotides sequence. A 40μM concentration of the oligos was achieved by dissolving the oligos with 50% DMSO solution. The MTP plates were vortexed at 150 rpm for 2 hours and spun down at 1200 rpm in a swing out rotor centrifuge. Every gene/oligo was printed with a robotic arrayer – OG100 (Genomic Solutions, Ann Arbor, USA) on aminosilane coated glass slide (ArrayIT, USA). The relative humidity and the temperature were maintained at 45% RH and 23°C. The printing is achieved by contact disposition of 20nL of the oligo suspension onto the glass slide with stealth microarray pins (SMP3) having an uptake capacity of 250nL. Post printing, the slides were air dried for 6 hours in the printing environment and then cross-linked at 650 mL/sec2 with an UV cross-linker. The slides were then packed and stored under vacuum in the dark at room temperature.


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

status: Public on Mar 21 2012

organism: Oryza sativa Japonica Group


title: Calanus physiology microarray

city: Groton

first: Ebru

last: Unal

state: CT

address: 1080 Shennecossett Road

department: Department of Marine Sciences

institute: University of Connecticut

organism: Calanus finmarchicus

manufacturer: Printed in Mount Desert Island Biological Laboratory, Salisbury Cove, Maine

first: David

middle: W

last: Towle

first: Petra

middle: H

last: Lenz

first: Patrick

last: Hassett

first: Andrew

middle: E

last: Christie

first: Ann

last: Bucklin

manufacture_protocol: A normalized cDNA library for C. finmarchicus was previously created by David Towle (Mount Desert Island Biological Laboratory, Maine) and analyzed for ~10,000 ESTs from the library clones. The software program “Partigene” (http://xyala.cap.ed.ac.uk/bioinformatics/PartiGene/) was used to cluster the sequences into contigs, which were subsequently annotated by obtaining the ten best hits for each contig using the Tera-Blast P algorithm on a local Decypher processor (http://decypher.mdibl.org). Functional analysis was done to sort the ESTs by putative physiological function and to identify transcripts that encode proteins involved in the generation/regulation of population dynamics. A total of 995 ESTs that matched genes of known function were selected for inclusion in a custom “Calanus physiology microarray” printed with unique 50 base-pair oligonucleotide probes. Microarray slides were printed by using an arraying robot equipped with pin heads (OmniGrid Accent Arrayer) that prints the probes for EST contigs onto the Corning UltraGAPS slides by using Pronto Universal Spotting Solution (Corning). Each oligonucleotide probe was printed in duplicate. After printing, the slides were dried overnight in a vacuum desiccator and cross-linked in a UV Stratalinker (Stratagene) at a setting of 6000 x 100 μJ.


title: The Oligo GEArray® Mouse Diabetes Microarray OMM-023

status: Public on Mar 18 2012

first: Wen-Jun

last: Shen

address: 3801 Miranda Avenue

department: Medicine

institute: Stanford University

organism: Mus musculus

description:
Catalog Number: OMM-0230-200807
The Oligo GEArray® Mouse Diabetes Microarray profiles the expression of 84 genes related to the onset, development, and progression of diabetes.  They include genes that contribute to obesity, insulin resistance, the early onset of diabetes, and complications from diabetes mellitus. These genes are grouped into six functional categories: receptors, transporters and channels; nuclear receptors; metabolic enzymes; secreted factors; signal transduction proteins; and transcription factors.  Many of the genes included have a tissue-specific or tissue-biased expression pattern which can also be affected by different pathophysiological states.  This array can be used to study models of obesity and diabetes, to screen for therapeutics and their targets, and to profile the effect of various epidemiological and environmental factors on gene expression in various tissues or cell lines.  Through a simple side-by-side hybridization experiment you can determine differential gene expression between your samples with this array.


title: Illumina Genome Analyzer (Giardia intestinalis)

status: Public on Mar 14 2012

organism: Giardia duodenalis


title: China CDC Shigella flexneri 4224

city: Beijing

first: Hua

last: Fu

address: 6#, Rongjing East Street

institute: Institute of pathogen biology

organism: Shigella flexneri

manufacturer: Institute of Pathogen Biology, Chinese Academy of Medical Sciences

manufacture_protocol: The S. flexneri whole genome microarrays were designed by using our sequenced strain and were constructed in accordance with previous reports[5,11]. Generally, Sf301 ORFs were amplified with ORF-specific primer pairs. Amplified products, which mostly ranged between 300 and 700 bases in length, were purified by using MultiScreen-PCR plates (Millipore). Concentrations of PCR products were measured by Spectra MAX 190. Then, the PCR products were readjusted to 100 ng/μl of concentration with deionized water and double diluted into spotting solution containing 60% DMSO. The PCR products were spotted onto gamma amino propylsilan-coated GAPII slides (Corning) by using Omni-Grid™ microarrayer (GeneMachines).


title: AB SOLiD System 3.0 (Bacillus anthracis)

organism: Bacillus anthracis


title: KTH RAT 27k Oligo Microarray platform

status: Public on Mar 10 2012

city: Las Palmas de Gran Canaria

first: Leandro

last: Fernandez-Perez

state: Las Palmas

address: Dr. Pasteur s/n-Campus of San Cristobal

department: Clinical Sciences

country: Spain

institute: University of Las Palmas de Gran Canaria


title: NuGO array (human) NuGO_Hs1a520180 [CDF: Hs_ENTREZG_14]

status: Public on Mar 22 2012

city: Dublin

first: Melissa

last: Morine

address: Belfield

country: Ireland

institute: University College Dublin

relation: Alternative to: GPL7020 (Alternative CDF [official])

manufacture_protocol: This array is identical to GPL7020 but a custom, remapped CDF environment is used to extract data. This is version 14 of the remapped CDF. The CDF for various platforms can be found at the Web link below.


title: Illumina HiSeq 2000 (Setaria italica)

status: Public on Mar 09 2012

organism: Setaria italica


title: Agilent-020736 miRNA-v3.1-7species-8x15K array

city: San Francisco

first: Andrea

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

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

description:
miRNA microarray probe design, v3.1 (2/19 2008)
miRNAs (1776 targets) were taken from the Sanger miRNA database, version 11.
Total targets (excluding mismatches):
1776(miR)+14(siRNA)+24(snRNA)+30(spike-in)+30(mRNA) = 1874
Full-length; 5prime G; Hsa,Mmu,Dre,Gga,Rno,Dme,Cel
Arrays of this design have barcodes that begin with 16020736 or 2520736.
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: miRCURY LNA microRNA Array, v.11.0 - hsa, mmu & rno [probe-level]

city: Hellerup

first: Marianne

middle: Bengtson

last: Løvendorf

address: Niels Andersens Vej 65

department: Dermato-Allergology

country: Denmark

institute: Gentofte Hospital

organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

description:
ProductNumber = 208200-A,208201-A,208202-A

Array covering Sanger miRBase 15.0 and Exiqon miRPlus mature miRNAs.

The platform information provided is from the time of the design.

Names, accession numbers and sequences are listed for mature miRNAs in miRBase 15.0. Some probes may target multiple miRNAs, in which case multiple miRNA names, accession numbers and sequences are listed separated by '/'

manufacture_protocol: See manufacturers website (www.exiqon.com),


title: NuGO array (human) NuGO_Hs1a520180

status: Public on Jul 08 2008

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description:
This array has been designed by NuGO and manufactured by Affymetrix.
NuGO is a European Union-funded Network of Excellence, the full title of which is 'The European Nutrigenomics Organisation: linking genomics, nutrition and health research'. This array contains aproximately 24.000 probesets, relevant to nutrigenomics studies.
More info:
http://www.nugo.org
http://blog.bigcat.unimaas.nl/~martijn/NuGO/index.html

first: Martijn

last: van Iersel

middle: D

last: Koks

first: Ruan

last: Elliott

first: Philippe

last: Rocca-Serra

relation: Alternative to: GPL7144 (Alternative CDF)

relation: Alternative to: GPL15362 (CDF: Hs_ENTREZG_14)


title: Illumina Genome Analyzer II (Burkholderia glumae)

status: Public on Mar 13 2012

last: GEO

organism: Burkholderia glumae


title: Helicos HeliScope (Vibrio cholerae O1 str. C6706)

status: Public on Mar 08 2012

organism: Vibrio cholerae O1 str. C6706


title: Illumina Genome Analyzer II (Myceliophthora thermophila)

organism: Thermothelomyces thermophilus


title: LC Sciences G. gallus miRChicken_17 (condensed version)

city: Roslin

first: Michael

middle: Bryan

last: Watson

state: Midlothian, EH25 9PS

address: Roslin Biocentre

department: ARK-Genomics

institute: The Roslin Institute

organism: Gallus gallus

manufacture_protocol: In situ synthesis of oligonucleotides (http://www.lcsciences.com/technology/)


title: MI Rat 39K oligo array

status: Public on Mar 07 2012

city: Miami

first: Salil

last: Sharma

state: Florida

address: 1600 NW 10th Ave

department: Molecular and Cellular Pharmacology

institute: University of Miami

organism: Rattus norvegicus

description: Oligonucleotide Long-mer oligonucleotide spotted array.

manufacture_protocol: Capillary Pin Deposition


title: SBRI_110930_Msme_MC2155_TR_til_exp_HX12

city: Seattle

first: Tige

last: Rustad

state: WA

address: 307 Westlake Avenue N, Suite 500

department: Pathobiology

institute: Seattle Biomedical Research Institute

organism: Mycolicibacterium smegmatis MC2 155

manufacture_protocol: See manufacturer website


title: Agilent-015058 O. sativa (Rice) Oligo Microarray 4x44K (Probe Name version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Oryza sativa

description:
This array will enable researchers to simultaneously characterize thousands of rice genes associated with biological functions, growth processes, and biotic and abiotic stress response. Probes on this array are designed to selections from the extensive ric

Arrays of this design have barcodes that begin with 16015058 or 2515058.

*** 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 GPL15304.

relation: Alternative to: GPL15304 (Feature Number version)


title: Illumina Genome Analyzer IIx (Equus asinus)

organism: Equus asinus


title: Illumina Genome Analyzer IIx (Equus asinus x caballus)

organism: Equus asinus x Equus caballus


title: Illumina Genome Analyzer IIx (Equus caballus x asinus)

organism: Equus caballus x Equus asinus


title: Illumina Genome Analyzer IIx (Physcomitrella patens)

status: Public on Mar 05 2012

organism: Physcomitrium patens


title: Nimblegen Homo sapiens HG18 Expression Array (12x135k) [gene-level]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Homo sapiens

description: This is a whole human genome array in 12-plex format provided by Roche Nimblegen. See manufacturer's website at http://www.nimblegen.com/.

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


title: NCSU Payne_Aspergillus Flavus_22683_AFLAVUSa520391F [probe-level]

city: Raleigh

first: Ignazio

last: Carbone

state: NC

address: 851 Main Campus Drive, Suite 233

department: Plant Pathology

institute: North Carolina State University - Center for Integrated Fungal Research

organism:
Zea mays
Aspergillus flavus
Aspergillus oryzae

manufacture_protocol: Standard Affymetrix protocols were followed and can be found at http://www.affymetrix.com/support/technical/manual/technical_manual.afx


title: Ceriporiopsis subvermispora RP-B expression Roche NimbleGen microarrays

first: Dan

last: Cullen

address: One Gifford Pinchot Dr

institute: UW/FPL

organism: Gelatoporia subvermispora

manufacture_protocol: proprietary maskless array in situ oligonucleotide synthesis. See http://www.nimblegen.com/


title: Invitrogen ProtoArray v5.0 (full array layout)

status: Public on Mar 16 2012

city: Stanford

first: Hogune

last: Im

state: CA

address: 300 Pasteur Dr. Alway M308

department: Genetics

institute: Stanford

technology: spotted peptide or protein

manufacture_protocol: see manufacturer's website


title: Combimatrix Thiomicrospira crunogena array

status: Public on Mar 04 2012

city: Tampa

first: Kathleen

last: Scott

state: FL

address: 4202 E Fowler Ave

institute: University of South Florida

organism: Hydrogenovibrio crunogenus

description: Oligonucleotide arrays were fabricated with probes designed to represent all genes within the T. crunogena genome, with two or three probes per gene, and a probe length of 35 nucleotides (Combimatrix, Mukilteo, WA).

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


title: Schistosoma japonicum gender-associated differentially expressed gene array

city: Shanghai

first: Yanxun

last: Xia

address: 3 Lane 345,Shilong Road

institute: Shanghai Institute of Domestic Animal Parasitology,Chinese Academy of Agricultural Sciences

organism: Schistosoma japonicum

first: JiaoJiao

last: Lin

first: Chunxiu

last: Yuan

first: Guoqing

last: Li

manufacture_protocol: The PCR products of cDNA were amplified by use of the polymerase chain reaction (PCR) and then purified with isopropanol precipitation. All PCR products were examined by agarose gel electrophoresis to ensure the quality and the identity of the amplified clones as expected. Then the amplified PCR products were dissolved in a buffer containing 3X SSC solution. The solution with amplified PCR products were spotted onto silylated slides(Biostar, Shanghai, China) with a Omnigrid Arrayer(Gene Machine,CA) fitted with 16 Major Precision split pins.


title: University Health Services (Toronto) Yeast ORF, Version 6.4k

status: Public on Mar 02 2012

city: Boston

first: Pamela

last: Silver

state: MA

address: 200 Longwood Avenue WAB 536

department: Systems Biology

institute: Harvard Medical School

organism: Saccharomyces cerevisiae

manufacture_protocol: Full length cDNAs from roughly 6000 S. cerevisiae ORFs are printed in duplicate on each array, along with controls


title: Illumina Genome Analyzer IIx (Brassica rapa)

organism: Brassica rapa


title: Agilent-037680 S. cerevisiae simr_msm_antisense_44k

status: Public on Mar 03 2012

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

description: reverse complement of original agilent yeast 1x44k design 012713.

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


title: Agilent-037746 S. cerevisiae simr_msm_sense_44k

description: Probes taken from agilent-designed 1x44k yeast tiling array 012713 (G4486A), GEO platform (GPL3737), which was no longer commercially available.


title: LC Sciences G. gallus miRChicken_17


title: Roche Nimblegen G.zeae 135K microarray

status: Public on Mar 01 2012

city: Seoul

first: Won

middle: Kyong

last: Cho

address: 5103-ho, 200-dong, Daehak-dong, Kwanak-gu

department: Department of Agricultural Biotechnology and Center for Fungal Pathogenesis

institute: Seoul National University

organism: Fusarium graminearum


title: Phalanx Human OneArray [Annotation HOA5 release 1.0]

status: Public on Mar 15 2012

city: rochester

first: keyi

last: liu

address: 1425 portland ave

institute: Rochester General Research Institute

description:
Annotation is based on two databases:
- NCBI RefSeq release 41
- Ensembl release 58 cDNA sequences and homo_sapiens_core_58_37c annotations

Probes are classified into three groups based on the number of genes can be hit in the databases. The number of probes for each group is as follows.

Group 1 - one gene hit         27110
Group 4 - multi-gene hits       1174
Group 5 - no hit                 903
-----
Total HOA5 probes:             29187

relation: Alternative to: GPL6254 (Alternative annotation [official])

manufacture_protocol: See http://www.phalanxbiotech.com/ for updated protocols


title: Weiss SABiosciences Custom RT-PCR profiler array CAPR 100083, 96, v1.0

city: Manhattan

first: Mark

last: Weiss

state: KS

address: Coles Hall, Room 115

department: Anatomy and Physiology

institute: Kansas State University

technology: RT-PCR

description:
rat ESC RT-PCR custom array, see information on layout of array below, see PCR efficiency data provided by manufacturer, below.
SABiosciences RT² Profiler panel of PCR assays.


title: Washington University/Genome Sequencing Center C. elegans 23K [oligoID version]

city: Cambridge

first: Marko

last: Jovanovic

address: 7 Cambridge Center

department: Core Group (Regev group) member

institute: Broad Institute of MIT and Harvard

organism: Caenorhabditis elegans

manufacturer: Genome Sequencing Center, Washington University in St. Louis


title: Affymetrix Glycine max A1GMa520113

city: Saint Louis

first: Jim

last: Morrell

state: Missouri

address: 800 North Lindbergh Blvd

department: Biotechnology

institute: Monsanto Co.

organism: Glycine max

description: Affymetrix chip designed from EST sequences by Monsanto and Affymetrix. PM only

manufacture_protocol: See manufacturer's web site


title: Clostridium thermocellum ATCC 27405

city: Hanover

first: Lee

last: Lynd

state: NH

address: 8000 Cummings Hall

department: Thayer School of Engineering

institute: Dartmouth College

organism: Acetivibrio thermocellus ATCC 27405


title: Illumina Genome Analyzer IIx (Equus caballus)

last: GEO

organism: Equus caballus


title: NimbleGen rhesus macaque promoter

city: Los Angeles

first: Jinkai

last: Wang

address: 650 Charles E. Young Drive South, CHS 33-228

institute: University of California, Los Angeles

organism: Macaca mulatta

description:
Annotation in this record based on UCSC rheMac2
The tilling array of orthologous regions of the NimbleGen human hg18 refseq promoter array (GPL9448)

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


title: 454 GS FLX Titanium (Pseudomonas aeruginosa)

organism: Pseudomonas aeruginosa


title: Agilent-027437 Pare Neurospora crassa (PROBE_ID)

city: New York

first: Adam

last: Paré

state: NY

address: 1275 York Avenue

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

organism: Neurospora crassa

description:
Arrays of this design have barcodes that begin with 16027437 or 2527437.

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-023723 UCSF Multi-species custom 8x15K miRNA array

city: San Francisco

first: Andrea

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

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

description:
miRNA microarray probe design, v3.4 (4/17/2009).
miRNA probes were designed using Sanger miRBase, version 13 (from ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/).
Custom array contains multiple replicates for each miRNA probe for 7 species: human, mouse, rat, chicken, zebrafish, C.elegans and Drospohila).
Total unique probe sequences:
2270(miR)+14(siRNA)+24(snRNA)+16(snoRNA)+3(tRNA)+30(spike-in)+30(mRNA)+192 = 2579


title: Phytophthora ramorum 4x72K v1.0

city: Davis

first: Takao

last: Kasuga

address: 382 Huchison Hall

institute: USDA-ARS

organism: Phytophthora ramorum

description:
The IDs used correspond to the first 5 or 6 digits of the gene model # in the following link: http://vmd.vbi.vt.edu/download/data/prTranscript2.0Annot, which includes 15,743 gene models predicted by JGI and additional 419 models predicted by VBI.
A few IDs of gene models have suffix M or RC as 97363M and 97571RC which corresponds to modified and reverse complement sequences of the original gene models, respectively.

manufacture_protocol: Roche NimbleGen’s proprietary Maskless Array Synthesis technology was to synthesize long oligo, high-density DNA microarrays.  Approximately four 60mer oligo probes were designed for each target on the array. Targets include 15,751 Phytophthora ramorum genome according to Gene models Phytophthora ramorum v1.0   (http://genome.jgi-psf.org/ramorum1/ramorum1.home.html).


title: Affymetrix Human Genome U133 Plus 2.0 Array [Brainarray Version 15.0.0, HGU133Plus2_Hs_ENTREZG]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Homo sapiens

description: This array is identical to GPL570 but the data were analyzed with a custom CDF Brainarray Version 15, hgu133plus2hsentrezg.

manufacture_protocol: see the Affymetrix website (www.affymetrix.com).


title: WSU_Salmonella Enteritidis_11977_v1

city: Pullman

first: Devendra

last: Shah

address: 100 Dairy Rd

department: Veterinary Microbiology and Pathology

institute: Washington State University

organism: Salmonella enterica subsp. enterica serovar Enteritidis

first: Carol

last: Casavant

first: Quincy

last: Hawley

first: Tarek

last: Addwebi

first: Douglas

last: Call

first: Jean

last: Guard

manufacture_protocol:
Proprietary Light Directed Oligonucleotide Synthesis
We do not spot presynthesized oligonucleotides. We directly synthesize them on a microscope slide. Our synthesis is using the robust phosphoramidite chemistry refined since the 1970's for commercial oligonucleotide synthesis. In standard oligonucleotide synthesis, the terminal acid-labile protective group of a growing oligomer is removed by a treatment with a strong acid.
The only modification we have introduced in our process is the usage of a photo-generated acid. At a given synthesis cycle, each spot that needs to be deprotected is exposed to light in the presence of a photogenerated acid precursor, leading to local acid production and cleavage of the terminal protective group. Only the deprotected spots will be able to react with a new monomer. By so doing, we can synthesize tens of thousands oligonucleotides in parallel on the same microarray substrate.
The advantage of using the phosphoramidite chemistry is that we can synthesize oligonucleotides at a reduced cost compared to other chemistries while maintaining our stepwise yield well above 99%.
To expose the oligonucleotide spots to light during the deprotection step of the synthesis cycle, we do not use any physical mask but instead we use a digital micromirror device (DMD) made of several hundred of thousands individually addressable mirrors. At each deprotection step, a computer simply generates an image to be projected on the microarray surface. Using this digital photolithography approach, we can synthesize any custom microarray with no upfront design cost or minimal order size.
High Quality Glass Substrates
We synthesize our microarrays on high quality microscope slides. For uniform synthesis and hybridization and enhanced scanner image quality, we use only low-background glass slides polished to atomic flatness (±20 angstroms). Their precise physical dimension (25 ± 0.2 mm x 76 ± 0.3 mm x 0.940 mm ± 0.025 mm) is compatible with all major brands of slide microarray scanners.


title: Agilent-026441 Gallus gallus (Chicken) Oligo Microarray v2 (Probe Name version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Gallus gallus

description:
G. gallus (Chicken) Oligo Microarray v2

*** 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 GPL13790.


title: Stillman Lab Porcelain Crab Array 3

city: Tiburon

first: Jonathon

last: Stillman

address: 3152 Paradise Drive

department: Romberg Tiburon Center

institute: San Francisco State University

organism: Petrolisthes cinctipes

manufacture_protocol: Purified PCR products representing a unigene set from 62K cloned cDNAs were spotted on erie poly-L-lysine slides using parallel synthesis silicon pins with 100µm tips.  Arrayer is a Joe DiRisi custom built machine.


title: Rice_135k_tiling_V2 array

city: Yongin

first: Su-Hyun

last: Park

address: 38-2 Nam-dong

institute: Myongji University

organism: Oryza sativa

description:
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID; 27,488 Rice Gene Name : IRGSP, RAP2 database (http://rapdb.lab.nig.ac.jp)) features.  The .ndf file is linked below as supplementary files.
native array description file: Rice_135k_tiling_V2.ndf


title: Agilent Salmon Immunity and Quality 44k custom array_SIQ3

status: Public on Jul 21 2010

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

organism:
Oncorhynchus mykiss
Salmo salar

description:
SIQ3 (Salmon Immunity and Quality) is the third version of oligonucleotide platform for Atlantic salmon containing probes to protein encoding transcripts from Unigene, Genbank (complete cds) and Gene Index - DFCI with addition of EST from own leukocyte library. Rainbow trout sequences correspond to genes that have not been identified in salmon.

Versions SIQ3 and SIQ2 (GPL10679) contain the same array features, but different layouts.


title: Agilent-019315 Sarcophaga crassipalpis custom cDNA array

status: Public on May 20 2010

city: Gainesville

first: Greg

last: Ragland

department: Entomology and Nematology

country: USA

institute: University of Florida

organism: Sarcophaga crassipalpis

description:
Probesets: UF_Scr_NF_100001 to UF_Scr_NF_100103: four forward probes for each NCBI record of Sarcophaga crassipalpis genes
Probesets: UF_Scr_NM_100104 to UF_Scr_NM_100206: four reverse (minus strand) probes for each NCBI Sarcophaga crassipalpis record
Probesets: UF_Scr_AF_100207 to UF_Scr_AF_123337: two forward probes for each annotated S. crassipalpis EST
Probesets: UF_Scr_AM_123338 to UF_Scr_AM_134993: one reverese (minus strand) probe for each annotated S. crassipalpis EST
Probesets: UF_Scr_UN_134994 from UF_Scr_UN_145629: one forward probe for each unannotated S. crassipalpis EST

manufacture_protocol: 60-mer oligo probes designed from S. crassipalpis EST contigs and singletons using Agilent eArray v2.0 and synthesized in situ by an ink-jet printing (Agilent) method on glass slides.


title: Agilent-019838 Yeast Oligo Microarray 8×15K G2509F (Probe Name version)

status: Public on Jun 29 2011

city: Boston

first: Xu

last: Zhou

address: 300 Longwood Ave

department: Pediatrics

institute: Boston Children's Hospital

organism: Saccharomyces cerevisiae

description: The ID column represents the Agilent Probe Names.


title: OMRF Human Oligonucleotide Microarray

status: Public on Dec 04 2008

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

description: gamma amino propyl silane coated slides (Corning UltraGAPS)

first: M

middle: B

first: R

last: Cadwell

manufacture_protocol: Qiagen Operon Human Genome Oligo Set version 2 70-mer oligonucleotide library was resuspended in 3x SSC as a printing buffer and spotted on Corning UltraGAPS slides using a GeneMachines OmniGrid 100 arrayer with a 32 pin configuration.


title: Agilent Salmon Immunity and Quality 44k custom array_SIQ4

organism: Salmo salar

description: SIQ4 (Salmon Immunity and Quality) is fourth version of oligonucleotide platform for Atlantic salmon containing probes to protein encoding transcripts from Unigene, Genbank (complete cds) and Gene Index - DFCI with addition of EST from own leukocyte library. Rainbow trout sequences correspond to genes that have not been identified in salmon.


title: Agilent-019159 Rat miRNA Microarray (miRBase release 12.0 miRNA ID version)

status: Public on Sep 14 2010

organism: Rattus norvegicus

description: Rat miRNA Microarray 1.0


title: Affymetrix Drosophila Genome Tiling Array 1.0F (Dm35b_MF_v02)

status: Public on Oct 18 2007

first: Dale

last: Dorsett

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

organism: Drosophila melanogaster

description:
35bp Resolution Oligonucleotide Tiling Array.
Annotation in this record is based on the April 2004 release of the Drosophila melangaster genome sequence (Berkeley Drosophila Genome Project).
Probe mappings and array coordinates (7G scanner) are available in the supplementary .tpmap file linked to this submission.

manufacture_protocol: See manufacturer's website.


title: Agilent-016320 rainbow trout 37K oligo array [Feature number version]

status: Public on Oct 24 2007

city: Morgantown

first: Mohamed

last: Salem

state: WV

address: Division of Animal and Nutritional Sciences, West Virginia University

institute: West Virginia University

organism: Oncorhynchus mykiss

description: Custom Microarrays

first: Caird

last: Rexroad

first: Jianbo

last: Yao

manufacture_protocol: A total of 37,394 unique rainbow trout transcript-specific oligonucleotide probes were used to construct a high-density rainbow trout microarrays. The probes, 60-mer long,  were designed  based on sequences from Rainbow Trout Gene Index TCs (Release 6.0, June 19, 2006, http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/tc_ann.pl?gudb=r_trout). Probes were checked for possible non-specific mRNA cross-hybridization problems by comparing all individual probes with all rainbow trout transcriptome sequences. A probe design file was created to print the probes randomly on an Agilent 4 X 44 design format that contains 1417 Agilent control spots for quality control. The microarrays were synthesized in situ using the non-contact inkjet technology.


title: Virtual Platform for Peptidome Submissions

status: Public on Oct 16 2008

last: GEO

organism: Mus musculus

technology: other

description:
ESI-QUAD-TOF
ESI-ION-TRAP
ESI-FTICR-CID
ESI-FTICR-ECD
MALDI-QUAD-TOF
MALDI-TOF-TOF
MALDI-TOF-PSD
ESI-4SECTOR
ESI-QUAD
FTMS-ECD
ETD-TRAP
MALDI-QUAD-TOF
MALDI-QIT-TOF
ETD+W
TRAP-FTMS

manufacture_protocol: not applicable


title: NimbleGen Zilberman Arabidopsis HD2 array [080709_AT8_DZ_ChIP_HX1]

city: Berkeley

first: Toshiro

last: Nishimura

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

organism: Arabidopsis thaliana

description:
TAIR 8
designname: 080709_AT8_DZ_ChIP_HX1
designid: 7848

manufacture_protocol: see manufacturer's website


title: [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [Alternative CDF: BrainArray version 14: MoEx10stv1_Mm_ENTREZG]

status: Public on Aug 31 2011

city: Seattle

first: Daniel

middle: Edward

last: Zak

address: 307 Westlake Ave N, Suite 5

institute: Seattle Biomedical Research Institute

relation: Alternative to: GPL6096 (Alternative CDF[official])

manufacture_protocol: This is identical to GPL6096 but a custom cdf environment was used to extract data. The cdf can be found at the link below.


title: Progenika P putida KT2440 oligo array

status: Public on Jan 17 2011

city: Hannover

first: Sarah

address: Carl-Neuberg-Str. 1

department: Clinic for Paediatric Pneumology and Neonatology

institute: Medical School Hannover

organism: Pseudomonas putida KT2440

description: The P. putida KT2440 DNA microarray developed contains 5539 oligonucleotides (50-mer) spotted in duplicate onto aminosylane treated 25x75 mm microscope slides, covalently linked to the slide with UV light and heat. The spots, 180 um in diameter, are separated from each other by 265 um and arranged in 48 subarrays (16 columns and 15 rows each). The spotted area is 17x54 mm. The oligonucleotides, designed by BioAlma (www.bioalma.com), are specific for each ORF in the array. These include the 5350 ORFs annotated in the P. putida KT2440 genome (obtained from www.ncbi.nlm.nih.gov, Refseq NC_002947; GenBank accession number AE015451.1), the 140 ORFs defined for the TOL plasmid pWW0 (obtained from www.ncbi.nlm.nih.gov, Refseq NC_003350; GenBank accession number AJ344068.1), and other genes of diverse origins such as commonly used reporter genes (lacZ, gfp) or antibiotic resistance markers. Two oligonucleotides, coding for the rpoD and rpoN genes, respectively, were spotted at 20 different positions of the slide to serve as homogeneity controls. Negative controls (spotting buffer, 50% [vol/vol] dimethylsulfoxide) were spotted in duplicate at 203 positions evenly distributed throughout the printed area. The array was printed by Progenika Biopharma (www.progenika.com).

manufacture_protocol: see manufacturer's web site


title: Agilent-019584 Clostridium perfringens 15K

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

organism: Clostridium perfringens

description: The DNA microarray contains two probes for all protein-coding sequences in the three genome-sequenced C. perfringens strains (type A strains 13, ATCC13124, and SM101).

manufacture_protocol: Agilent 60mers. 8x15K.


title: Agilent-016320 rainbow trout 37K oligo array [Probe name version]

status: Public on Feb 21 2012

department: Division of Animal and Nutritional Sciences

description: Custom Microarrays


title: NimbleGen Mouse CGH Whole-Genome Tiling Array [080411_MM9_CGH_HX1]

status: Public on Dec 30 2010

city: Madison

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
NimbleGen description files linked below:
080411_MM9_CGH_HX1.ndf
080411_MM9_CGH_HX1.pos

manufacture_protocol: See www.nimblegen.com


title: Roche NimbleGen | A. thaliana Gene Expression 385K Arrays

status: Public on Feb 14 2012

city: Saskatoon

first: Ed

last: Tsang

address: 110 Gymnasium Place

department: Plant Bioinformatics Institute

country: Canada

institute: National Research Council of Canada

first: Zhangjun

last: Fei

first: Edward

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


title: Bifidobacterium bifidum PRL2010 array

status: Public on Jan 05 2012

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

country: Italy

institute: University of Parma

organism: Bifidobacterium bifidum PRL2010

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

manufacture_protocol: Probes are directly synthesized on a 90k 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: Agilent MQD Lab Human 60K probes v1.0 - custom oligo array of 2Kb resolutoin covering 7q region

status: Public on Apr 01 2011

city: Cambridge

first: Alan

last: Watkins

address: Addenbrooke's Hospital

institute: University of Cambridge

organism: Homo sapiens

description:
Agilent-026031
NCBI human genome Build 36 (UCSC hg18).
Custom made oligonucleotide array covering the 7q region with 60K probes at 2000bp resolution.

manufacture_protocol: Agilent SurePrint G3 platform


title: Agilent-014695 Mouse Genome CGH Microarray 244A (G4415A)(Probe Name version)

status: Public on Dec 31 2011

last: Agilent Technologies

institute: Agilent Technologies

description:
This microarray is Agilent’s premium product for mouse DNA copy-number profiling. Over 235,000 60-mer oligonucleotide probes, specifically optimized for copy-number measurement, span coding and non-coding genomic sequences with median spacing of 6.2 kb and 15.2 kb respectively. This microarray is designed for use with Agilent’s optimized assay protocols, enabling researchers to use nanogram levels of total genomic DNA without complexity reduction.

Arrays of this design have barcodes that begin with 16014695 or 2514695.

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.

*** 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 GPL4092

relation: Alternative to: GPL4092 (Feature Number version)

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


title: Illumina HiSeq 1000 (Drosophila melanogaster)

status: Public on Mar 08 2012