title: Sun Yat-Sen University Cancer Center Human microRNA array

status: Public on Nov 29 2013

city: Guangzhou

first: Zhenhua

last: Chen

address: NO.58,ZhongShan 2nd Road

department: Urology

country: China

institute: The First Affiliated Hospital,Sun Yat-sen University

organism: Homo sapiens

technology: spotted oligonucleotide

distribution: non-commercial

manufacture_protocol:
1.Oligos are arrayed in Greiner 384-well flat-bottom plates. Each well contains 600 pmol of 70-mer oligo.
2. Resuspend oligos in water to 20 uM and rearray 5 µL into 384-well, Genetix polystyrene V-bottom plates (cat# X6004).
3. Allow Genetix plates to dry through passive water evaporation in a protected environment (e.g., chemical hood).
4. Before printing, add 5 µL of 1X Printing Buffer to each well. This can be done the night before a print run is started.
5. Seal plates with Corning seals.
6. Incubate at 37°C for 30 minutes to aid resuspension of DNA.
7. Shake plates near maximum rotational speed on flat-bed shaker for 1 minute.
8. Centrifuge plates at 2000 rpm for 3 minutes.
9. Remove seals and cover with plate lids. Place in appropriate location of plate cassette. This should be done with first plates just before print run is started to minimize evaporation time before printing. For second and third cassettes, wait until 30
10. Make sure plates rest behind both holding clips in the cassettes. Push plates back into the cassettes as far as they will go, putting them in the proper position for the server arm.
11. After the print run is completed, allow plates to dry through passive evaporation in a protected environment.
12. For each subsequent preparation of these plates for a print run, add water to the wells instead of sodium phosphate buffer. The amount of water should be decreased by 0.25 µL per print run, as this is the amount drawn up by the pin capillary during ea


title: Illumina Genome Analyzer (Thermus thermophilus HB27)

status: Public on Nov 26 2013

last: GEO

country: USA

organism: Thermus thermophilus HB27

technology: high-throughput sequencing

distribution: virtual


title: 10K immunosignaturing peptide microarray version 2

status: Public on Dec 14 2013

city: Phoenix

first: Phillip

last: Stafford

state: AZ

address: 1001 S. McAllister

department: Center for Innovations in Medicine

institute: Biodesign Institute

organism: synthetic construct

technology: spotted peptide or protein

description: Non-contact Piezo printing (by Applied Microarrays, Tempe, AZ) onto Schott Nexterion A+ aminosilane slides using maleimide conjugation to the free sulfur on the cysteine of the NH3-terminus of peptides

distribution: custom-commercial

manufacturer: Arizona State University (available at www.peptidearraycore.com)

manufacture_protocol: Standard bead-based synthesis of peptides followed by HPLC purification and MALDI QC by Sigma Genosys, St, Louis, MO.  Printing by AMI, Inc., Tempe, AZ.


title: Micro-CRIBI microRNA Platform (mirVana Probe Set V1, Ambion)

status: Public on Jul 14 2014

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

organism: Mus musculus

manufacturer: Microcribi - Microarray Service (CRIBI - University of Padova)

manufacture_protocol: The mirVana oligo set (Ambion, Austin, TX; Catalog number 1564V1) consists of a collection of about 400 amine-modified DNA oligonucleotides. The probes are 42-46 nucleotides (nt) long, of which an 18-24 nt segment targets a specific known human, mouse, or rat miRNA, and the remaining sequence serves as spacer. Negative control probes were designed using sequences from Escherichia coli; positive control probes (spikes) are sequences from Mytilus galloprovincialis. Each oligonucleotide is spotted by our robotic station Biorobotics Microgrid II in four replicates on a Nexterion Slide E glass slide (Cat No 1066643) provided by SCHOTT. Nexterion Slide E is designed to covalently immobilize amine-modified DNA for microarrays. The deposition is qualitatively assessed by a scan of the spotted slide at 10 micron resolution, using a GSI Lumonics scanner and a protocol that allows the detection of spotted features through the salts derived from the dried solution in which oligonucleotides are dissolved. Microarray slides that meet the quality standards, are washed as recommended by the supplier and the glass slides are stored, ready for use, in the dark under deep vacuum.


title: CINVESTAV - Dengue 0.6k diagnostic chip

status: Public on Nov 30 2015

city: México

first: Maria

middle: L

last: Muñoz

address: Av. Instituto Politécnico Nacional 2508

department: Genetics and Molecular Biology

country: Mexico

institute: CIVESTAV-IPN

organism:
dengue virus type 1
dengue virus type 2
dengue virus type 3
dengue virus type 4

technology: spotted DNA/cDNA

last: Munoz

first: Alvaro

last: Diaz-Badillo

first: Gerardo

last: Perez-Ramirez

manufacture_protocol:
RNA extraction
Total RNA from cell culture supernatant of viruses from the different serotypes obtained from infected cells and from mosquitoes collected and frozen in the field was obtained using Trizol LS (GIBCO BRL, Gaithersburg, Md.) according to the manufacturer’s recommendations. Total RNA from acute-phase plasma collected from patients in the epidemiologic surveillance program by the Secretaria de Salud Oaxaca, Mexico during 2000- 2001 and 2004-2006 was also obtained by using the Viral Nucleic Acid Extraction Kit from Real Genomics (Real Biotech Corporation). The RNA suspended in 50 μl of H2O treated with diethylpyrocarbonate (DEPC, SIGMA-ALDRICH) was used as a template to obtain different DNA products by Reverse Transcription with the Polymerase Chain Reaction (RT-PCR).
Multiplex dengue RT-PCR (reverse transcription-polymerase chain reaction)
A multiplex one step RT-PCR (SuperScriptTM One-Step RT-PCR with Platinum Taq, invitrogen) was performed to determine the serotype in each sample. Briefly, five primers targeting the NS3 gene were included in the assay, resulting in products of different sizes (DENV-1, 169 pb; DENV-2, 362 pb; DENV-3, 272 pb; DENV-4, 472 pb). Then, 5 µl of extracted RNA was used as template in 25 µl reaction volume. Essentially, the protocol of Seah et al. [12] was followed to confirm the DENV serotype. The thermocycler was set to: 10 cycles at 95 ˚C for 30 sec, annealing at 50 ˚C for 1 minute, and then a 72 ˚C temperature for 1 min with a ramp time of 1 min and 25 cycles at 95˚C for 30 sec, 50˚ C for 30 sec, and 72˚C for 30 sec with a ramp time of 30 sec. Finally, 7 min extension at 72˚ C was added. Reaction mixtures were stored at 4˚ C until further processing.
The specific primers for DENV-1, DENV-2, DENV-3, and DENV-4 were synthesized with 5´ C6 amino linker by The Midland Certified reagent Company Inc. (Midland, TX, USA) as follow: 5´-(Texas Red) AGTTTCTTTTCCTAAACACCTCG-3´; DENV-1;
5´-(_6 FAM) CCGGTGTGCTCRGCYCTGAT-3´, DENV-2;
5´-(_CY5) TTAGAGTYCTTAAGCGTCTCTTG-3´, DENV-3;
5´-(_Yakima Yelow) CCTGGTTGATGACAAAAGTCTTG-3´, DENV-4. Synthesis was validated using each pair of oligonucleotides by RT-PCR and found to yield PCR products of the expected size.
DNA microarray fabrication
DNA (RT-PCR product) capture probe was immobilized according to the procedure described by Zammatteo, et al. [32]. Briefly, phosphorylated capture probes were denature for 10 min at 92°C and diluted to a concentration of 1.6 mM CHAPS, 1% CAPS, 50% DMSO buffer pH 6.5. The DNA was UV-cross link at 250 mJ and finally incubated at ambient temperature by 16 h as the specifications of the Schott´s protocol. Samples were spotted using the Robot Spotter GeneTAC G3 arraying system (Genomic Solutions, Harvard Bioscience, Inc., Massachusetts, USA). Each solid pin deliver a volume of around 1 nl, designed to create a spot diameter of 300 µm. The center-to-center spacing of bright spots was 500µm.
DNA microarray chip was prepare for hybridization by washing extensively with 0.1% SDS, rinsed twice with double deionizer water and heated in double deionizer water for 3 min at 95° C. After blocking with prehybridization buffer (4X SSC, 1 %SDS nd 10 mg/ml BSA) for 45 min at 42° C, DNA microarray chip was washed with double deionizer water for 20 s and dried under filtered air flow.
Hybridization and Detection
The hybridization of specific fluorescent primers for DENV was performed onto the specific immobilized probe DNA microarrays. A volume of 5 µl containing the specific primer for each DENV-1 -4 serotype was used. The microarray substrates and coverslips were sealed in a chamber from BIO-RAD (Bio-Rad Laboratories, Inc., Ca., USA) and incubated at 42o C for 16–18 h at high humidity. The tested concentrations for each specific primer of DENV-1 to -4 were 0.1, 0.2, 0.4, 1.0, 5, 10 and 20 µM. Coverslip and supports were gently removed (4× SSC in a wash bottle) and arrays were washed by immersion into 1× SSC, 0.1% SDS for 10 min (10 slides in 250 ml), 0.1× SSC, 0.1% SDS twice for 10 min and 0.1× SSC twice for 10 min. Finally, blow the slide dry with air by pushing the liquid away from the spots and towards the outer edges. Slides were scanned using Scanner GeneTac LS IV (Genomic Solutions, Molecular Dynamics Generation III) to detect Texas Red, FAM, Yakima yellow and Cy5 fluorescence. For the detection of DENV serotypes we used the excitation lines at 583, 494, 530 and 646 nm wavelength of a laser scanner (Scanner Gene TAC LSIV from Genomic Solutions) by adding pixel intensities of each spot image.
Establishment of threshold intensities
To analyze the results, we needed to determine whether a particular median pixel intensity value was indicative of hybridization. For this purpose, we defined threshold intensities as the value for normalized median pixel intensities above which hybridization was judged to be positive.


title: Illumina HumanCore-12v1 SNP array

status: Public on Apr 06 2014

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

country: France

institute: Ligue Nationale contre le Cancer

technology: oligonucleotide beads

manufacture_protocol: see Illumina web site


title: 2007-02-15_Dros_300bp_60mer

city: Kyoto

first: Yukako

last: Hattori

address: Sakyo-ku

department: Graduate School of Biostudies

country: Japan

institute: Kyoto University

organism: Drosophila melanogaster

technology: in situ oligonucleotide

description: Release 4 genome from the Berkeley Drosophila Genome Project (BDGP).  60-bp probes at approximately 300 bp intervals, preferably no GATC sequences, CG content as close to 50% as possible, non-repetitive. Probe sequences, except for QC probes, are the same as those of GPL9290 (2005-09-13_Dros_300bp_60mer), but their positions on microarrays are different.

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


title: Agilent-049074 Pinus massoniana 8* 60K Array

status: Public on Nov 30 2013

city: Guiyang

first: Fuhua

last: Fan

address: Xiahui Street, Huaxi

institute: Guizhou University

organism: Pinus massoniana

manufacture_protocol: see manufacturer's web site


title: Agilent-031931 TGP_Rat_miRBase16and15 (miRNA_IDs)

status: Public on Nov 27 2013

city: TSUKUBA CITY

first: Keiichi

last: Minami

state: IBARAKI

address: 17-2 WADAI

department: Tsukuba Research Institute

institute: Ono pharmaceutical

organism: Rattus norvegicus

description:
TGP_Rat_miRBase16and15

Arrays of this design have barcodes that begin with 16031931 or 2531931.

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: RT-qPCR array 2 (64 genes)

city: UNSW, SYDNEY

first: Kenneth

middle: K

last: Hsu

state: NSW

address: Rm422, 4E, Wallace Wurth Bld,

department: School of Medical Sciences

country: Australia

institute: University of New South Wales

technology: RT-PCR

description:
The qPCR primers were designed using Primer3 web based software (Nucleic Acids Research 40(15):e115) or from PrimerBank ( Nucl. Acids Res. 2010 38:D792-9).
Each primer pair was tested on RT-qPCR with single distinctive melting curve and then run on agarose gel (2%) with a single bend of right predicted size.
Primer spotting and qPCR setting used  epMotion automated pipetting systems (Eppendorf International)


title: RT-qPCR array 1 (64 genes)


title: [PhyloChip] Affymetrix G2 PhyloChip (Nov2013v)

city: San Francisco

first: Shoko

last: Iwai

state: CA

address: 513 Parnassus Ave.

department: Medicine

institute: University of California San Francisco

organism:
Bacteria
Archaea

description: new classification of the GPL15537 probes/annotations

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


title: [MoGene-1_1-st] Affymetrix Mouse Gene 1.1 ST Array [transcript (gene) version] [CDF: MoGene11stv1_Mm_ENTREZG_13.0]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: Brainarray: MoGene11stv1_Mm_ENTREZG.cdf

manufacture_protocol: See manufacturer's web site


title: Brucella melitensis 10K original GAL (2005)

status: Public on Nov 24 2013

city: College Station

first: Leslie

middle: Garry

last: Adams

state: TX

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

organism: Brucella melitensis

description: The array consists of 48 blocks each containing 17 columns and 13 rows

first: Garry

manufacture_protocol: Construction of cDNA microarrays. A set of unique 70-base oligonucleotides representing 3,227 ORFs of B. melitensis strain 16M and unique / divergent genes from B. abortus and B. suis were designed at the Pathogen Expression Core and purchased from Sigma-Genosys (The Woodland, TX). Oligonucleotides were suspended in 3X SSC (Ambion) at the final concentration of 40 ÿM before robotic arraying in triplicate onto ultraGAPS coated glass slides (Corning) using a Spotarray 72 microarray printer (Perkin Elmer, Downer’s Grove, ILL). Printed slides were steamed and UV cross-linked and stored in a desiccators until use.


title: CRUK Manchester Institute/Wafergen human cancer cell lines RT-PCR array

city: Manchester

first: Ged

last: Brady

address: Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Rd

department: Clinical and Experimental Pharmacology

country: United Kingdom

institute: Caner Research UK Manchester Institute

description:
PCR assay
Assays added to Wafergen SmartChip MyDesign

manufacture_protocol: see manufacturer's website


title: NimbleGen Glycine Max Array [100526_Brach_MoGene_exp]

status: Public on Nov 21 2013

city: Dallas

first: Paul

middle: J

last: Rushton

state: Texas

address: 17360 Coit Road

institute: Texas A&M AgriLife Research & Extension Center

organism: Glycine max

description:
DESIGN_ID: 12029

native array description file: 100526_Brach_MoGene_exp.ndf
native array description file: 100526_Brach_MoGene_exp.ncd

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


title: Exiqon miRCURY LNA ready-to-spot probe set  v.11.0 (miRBase v16.0)

city: Leicester

first: Dalbir

middle: Kaur

last: Dhiraj

state: Leicestershire

address: Lancaster Road

department: MRC Toxicology Unit

institute: Medical Research Council

organism:
Mus musculus
Rattus norvegicus

manufacturer: MRC Toxicology Unit, Systems Toxicology Group

manufacture_protocol: miRCURY LNA probes (Exiqon, 208210-A v.11), generated from miRBase v16.0, were supplied dried down at 300 pmol concentration in Genetix 384 well plates. The full printing set consists of 6 plates. Prior to printing probes were resuspended in 3 x SSC, 1.5 M Betaine, 30% ethylene glycol to a final concentration of 20 µM. Plates were loaded onto an ArrayJet Ultra-Marathon II microarrayer; and the slides used were Genetix aldehyde plus. Printing was performed using an inkjet-style technology to deposit an equal quantity of probe on each slide, with 5 repeats down the slide. The layout of the print was 3 blocks, each one consisting of 32 columns and 32 rows. A marker plate was also included top and bottom to make aligning the features easier.


title: Agilent-028412 CGH chicken array focus on unknown chromosomes

status: Public on Nov 22 2013

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

organism: Gallus gallus

description:
including chr 1, 2, 3, 16, z, w
Arrays of this design have barcodes that begin with 16028412 or 2528412.
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: Wnt Signaling phospho antibody array

city: London

first: Daniel

middle: Peter Sayer

last: Osborn

address: Human Genetics Research Centre

institute: St George's University of London

technology: antibody


title: AB SOLiD 4 System (Macaca fascicularis)

last: GEO

organism: Macaca fascicularis


title: Illumina HiSeq 2000 (Limonium bicolor)

status: Public on Nov 20 2013

organism: Limonium bicolor


title: UHNMAC Yeast 6.4 K array (Y6.4K) version 7 [Probe-level version]

city: Paterna

first: Jordi

last: Tronchoni

address: Avda. Agustín Escardino, 7

country: Spain

institute: CSIC

organism: Saccharomyces cerevisiae

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

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

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


title: Illumina Genome Analyzer IIx (Mycobacterium tuberculosis H37Rv)

organism: Mycobacterium tuberculosis H37Rv


title: 35K Human Genome Array

city: Zhengzhou

first: Fang

last: Wang

address: 1st of Jianshe Road

institute: The first affiliated hospital of zhengzhou university

organism: Homo sapiens

manufacture_protocol: as described in CapitalBio Corporation Manual


title: Agilent-044804 Custom Mouse Coding and LncRNA array 028005 (Feature Number version)

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

description:
SurePrint G3 Mouse GE 8x60K Microarray customized by Vikram
The Agilent eArray platform was used to customize the SurePrint G3 Mouse GE 8x60K microarray to add 3 custom-designed probes (60nt length) each against several categories of genes, namely pseudogene, genes with small RNA overlap, low stringency lncRNAs and high stringency lncRNAs.
Arrays of this design have barcodes that begin with 16044804 or 2544804.

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.

distribution: commercial


title: CombiMatrix Mouse array

status: Public on Nov 19 2013

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

institute: University of Parma


title: CombiMatrix Human array


title: Custom-designed TaqMan Low Density Arrays (TLDA) 7900 HT Micro Fluidic Cards

city: Seville

first: Purificacion

last: Estevez-Garcia

state: Seville

address: Manuel Siurot avenue

department: Molecular Oncology

institute: Institute of Biomedicine

description: PCR assay


title: ProtoArray Custom Service

city: East Lansing

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

department: Biochemistry and Molecular Biology

institute: Michigan State University

manufacture_protocol: All probing conditions and procedure was followed as described in invitrogen website. (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf


title: Agilent-034490 Bdellovibrio bacteriovorus HD100 Array [Feature Number version]

city: Ulsan

first: Robert

middle: J.

last: Mitchell

address: 50 UNIST-gil

department: School of Life Sciences

country: South Korea

institute: Ulsan National Institute of Science and Technology (UNIST)

organism: Bdellovibrio bacteriovorus HD100

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


title: 100319_HG19_Immunity_JD_CGH Array

city: Tallahassee

first: Jonathan

middle: Hancock

last: Dennis

state: FL

address: 319 Stadium Dr.

department: Biological Science

institute: The Florida State University

description:
designname=100319_HG19_Immunity_JD_CGH  designid=11672
We used a custom-designed high-resolution DNA microarray that covers 2 kb flanking the TSS 472 immunity- and inflammation-related genes.  Only unique probes were printed on the microarray, and repeats were masked around the TSS.  Both forward and reverse DNA strands were printed on the microarray.  The 60-mer oligonucleotide probes were tiled with an average 47-bp overlap.  We used NimbleGen’s 12-plex and HD2 design for our microarrays.  Each locus on the microarray contains approximately 180 probes of a median spacing of 12.5 bps.  Samples were labeled (nucleosomally protected DNA Cy3 and genomic DNA Cy5) and hybridized to the custom tiling microarray (Roche) according to manufacturer’s instructions.

manufacture_protocol: Details on the manufacture protocol can be found on http://www.nimblegen.com/technology/index.html


title: Helicos HeliScope (Schizosaccharomyces pombe)

organism: Schizosaccharomyces pombe


title: Exiqon miRCURY LNA microRNA microarray v.11.0

city: Kasugai

first: Yasuo

last: Ouchi

state: Aichi

address: 1200 Matsumoto-cho

department: Department of Biomedical Sciences

institute: Chubu University

organism: Danio rerio

description: The grid file of the miRCURY LNA microRNA microarray v.11.0 is based on miRbase version 16.0(Zebrafish).


title: RT2 ProfilerTM PCR array related to allergy and asthma (PAMM-067A)

city: Tokushima

first: Naozumi

last: Ishimaru

address: 3-18-15 Kuramoto

department: Department of Oral Molecular Pathology

institute: Institute of Health Biosciences The University of Health Biosciences

organism: Mus musculus

description:
PCR assay
SABiosciences RT² Profiler panel of PCR assays.


title: Illumina MiSeq (Human poliovirus 1)

organism: Poliovirus 1


title: Agilent-031554 Thellungiella salsuginea 4x44

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

country: Germany

institute: MPI of Molecular Plant Physiology

organism: Eutrema salsugineum

description:
Thelungiella 4x44 Hincha

Arrays of this design have barcodes that begin with 16031554 or 2531554.

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-028384 SurePrint G3 Mouse Promoter Microarray 2x400K

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
SurePrint G3 Mouse Promoter Microarray 2x400K

Arrays of this design have barcodes that begin with 16028384 or 2528384.

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: Illumina MiSeq (Hepatitis C virus subtype 1a)

organism: hepatitis C virus genotype 1a


title: Illumina Genome Analyzer IIx (Human poliovirus 1)


title: Agilent-025450 Mm_bwtie_as

status: Public on Nov 16 2013

city: Baltimore

first: Kathleen

middle: Helen

last: Burns

address: 720 Rutland Ave Ross 524

department: Pathology

institute: Johns Hopkins University School of Medicine

description:
Mouse repeat probes designed for antisense strand

Arrays of this design have barcodes that begin with 16025450 or 2525450.

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-025451 Mm_bwtie_ss

description:
Mouse repeat probes for sense strand

Arrays of this design have barcodes that begin with 16025451 or 2525451.

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-025411 Hs_bwtie_imno_ss

description:
Hs repeat array, immuno controls, sense strand

Arrays of this design have barcodes that begin with 16025411 or 2525411.

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: Lawrence Livermore Microbial Detection Array version 2e

status: Public on Nov 15 2013

city: Livermore

first: Kevin

last: McLoughlin

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

organism: synthetic construct

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


title: Agilent-022273 MM_repeat

description:
Mouse repeat class probes

Arrays of this design have barcodes that begin with 16022273 or 2522273.

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: Illumina Genome Analyzer IIx (Volvox carteri)

status: Public on Nov 13 2013

organism: Volvox carteri


title: Agilent Candida glabrata 12K

city: Tulln

first: Christoph

last: Schueller

address: Konrad Lorenz Strasse 24

department: Department of Applied Genetics and Cell Biology

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna (BOKU)

organism: Nakaseomyces glabratus CBS 138


title: NimbleGen Homo sapiens HG18 60mer array [probe-level version]

city: Chicago

first: Sergey

last: Malchenko

state: IL

address: 2300 Children's Plaza

institute: Northwestern University's Feinberg School of Medicine

description: Expression design for human (hg18; NCBI Build 36). 8 60mer probes per gene. 47633 exemplar genes

first: Vasily

last: Galat

manufacture_protocol: See manufacturer's website at http://www.nimblegen.com/. 2006-08-03_HG18_60mer


title: Human Common Cytokines RT² Profiler™ PCR Array

city: Brescia

first: Pascal

last: Seeger

address: Viale Europa 11

department: Department of Molecular and Translational Medicine

institute: University of Brescia

description: PCR assay panel for analysis of common cytokines


title: Illumina Genome Analyzer IIx (Neurospora crassa)

status: Public on Nov 12 2013

last: GEO

organism: Neurospora crassa


title: Illumina HiSeq 2000 (Ericerus pela)

status: Public on Nov 08 2013

organism: Ericerus pela


title: NimbleGen C. elegans 120K

status: Public on Nov 14 2013

city: Nanjing

first: Di

last: Chen

state: Jiangsu

address: 12 Xuefu Rd, Pukou

department: Model Animal Research Center

institute: Nanjing University

organism: Caenorhabditis elegans


title: Illumina Genome Analyzer IIx (Saccharomyces cerevisiae W303)

status: Public on Nov 07 2013

organism: Saccharomyces cerevisiae W303


title: Illumina Genome Analyzer II (Ricinus communis)

organism: Ricinus communis


title: Illumina Genome Analyzer IIx (Schizosaccharomyces japonicus)

organism: Schizosaccharomyces japonicus


title: Illumina Genome Analyzer IIx (Schizosaccharomyces octosporus)

organism: Schizosaccharomyces octosporus


title: Serhan Lab Human Inflammation PCR panel

city: Boston

first: Yongsheng

last: Li

state: MA

address: 77 Ave Louis Pasteur, HIM836

department: Anethesiology

institute: Brigham and Women's Hospital

organism: Homo sapiens

description: PCR assay

manufacture_protocol:
Primers were designed with Primer3 software and SYBR Green I were used for specific detection.
Primers were synthesized by Applied Biosystems or Integrated Device Technology


title: Illumina Genome Analyzer II (Manihot esculenta)

organism: Manihot esculenta


title: Agilent-024502 Dicentrarchus labrax oligonucleotide-microarray (LOQ) (Probe Name version)

city: Barcelona

first: Noelia

middle: T

last: Díaz Blanco

state: Barcelona

address: Passeig Marítim de la Barceloneta 37-49

department: Marine Renewable Resources

institute: Institute of Marine Sciences (ICM-CSIC)

organism: Dicentrarchus labrax

description: Oligonucleotide probes were used to construct a high-density seabass microarray based on the Agilent 4 × 44 K design format (http://www.agilent.com/), which covers 13,199 unique transcripts of Dicentrarchus labrax. Oligonucleotides, 60-mer plus a “linker”, are synthesized directly on glass slides using the Agilent’s SurePrint Tecnology; oligo design was carried out by Agilent. This microarray includes 6275 annotated transcripts, each with x3 specific probes, and 4516 ESTs with 1 probe/target sequence.


title: NimbleGen D. melanogaster Gene Expression 12x135K Array [090828_Dmel_exp]

status: Public on Nov 06 2013

city: Columbia

first: Elizabeth

middle: G

last: King

state: MO

address: 105 Tucker Hall

department: Biological Sciences

institute: University of Missouri

organism: Drosophila melanogaster

description: This array is based on GPL15352. We have used CG ids (which tend to be more stable than FBgn ids) so anyone can identify the relevant genes.

manufacture_protocol: NimbleGen


title: Agilent-044504 lincRNA_hs_SBC 028279

status: Public on Nov 05 2013

city: shanghai

first: qian

last: jin

address: libing road

institute: MSP

description:
Arrays of this design have barcodes that begin with 16044504 or 2544504.

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: NimbleGen Human 385K custom array (Probe ID version) [2007-05-01_SwitchGear_hg17_tiling]

city: Aurora

first: Louise

last: Glover

state: CO

institute: University Colorado Anschutz Medical Campus

description: UCSC human genome build hg17

manufacture_protocol: Standard NimbleGen protocol.


title: Candida albicans 181K tiling ChIP array (assembly Ca20) (Agilent Feature Number version)

city: San Francisco

first: Jose

middle: Christian

last: Perez

department: Microbiology and Immunology

institute: University of California, San Francisco

organism: Candida albicans

manufacture_protocol: See manufacturer's website.


title: Illumina GoldenGate custom 96 SNP microarray

city: Seoul

first: Hee-Jun

last: Kim

address: Heukseok-Ro, Dongjak-gu

institute: Chung-Ang University Hospital

manufacture_protocol: See manufacturer's website


title: Agilent custom array zfin ID: 041401

status: Public on Nov 04 2013

city: Madrid

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

institute: INIA

organism: Danio rerio

description: One glass slide formatted with eight high-definition 15K arrays. Custom Array zfin ID. 041401 GE 8 arrays/slide 11.59K

first: Paloma

last: Encinas

manufacture_protocol: Agilent 60-mer HD SurePrint technology (see manufacturer's web site at http://www.agilent.com/). Custom Gene Expression Microarray, 8x15K.


title: Candida albicans 181K tiling ChIP array (assembly Ca20) (Probe version)

state: CA


title: AB SOLiD 4 System (Escherichia coli K-12)

organism: Escherichia coli K-12


title: Madhani lab C. neoformans var. grubii H99 expression array

first: Hiten

last: Madhani

department: Biochemistry and Biophysics

organism: Cryptococcus neoformans H99

description: This platform is an updated version of GPL4522.  Oligos have been filtered based on scores from BLASTing the Broad Institute annotation of the Cryptococcus neoformans var. grubii transcriptome.

manufacture_protocol: Oligonucleotides were synthesized and applied to poly-L-lysine glass slides by contact printing


title: Madhani lab C. neoformans var. grubii H99 whole genome array

first: Brian

last: Tuch

first: Paul

middle: D

last: Hartley

manufacture_protocol: Oligonucleotides were synthesized and applied using inkjet technology developed by Agilent


title: [DMET_Plus] Affymetrix human DMET Plus array

city: Osaka-Sayama

first: Yoshihiko

last: Fujita

address: 377-2 Ohno-Higashi

institute: Kinki university School of Medicine

description:
NCBI human genome build 37.
dbSNP version 132.

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


title: St. George's Hospital, Clostridium difficile 7.5K array [full version]

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

organism: Clostridioides difficile 630

manufacturer: Bacterial Microarray Group, St. George's Hospital, London, UK

manufacture_protocol:
http://bugs.sgul.ac.uk/A-BUGS-20
Array design name: BuG@S C.difficile 9792 CDv1_0_0


title: NimbleGen Second Generation Apple 26K Array

city: University Park

first: Timothy

last: McNellis

address: 318 Buckhout Lab

department: Plant Pathology and Environmental Microbiology

institute: The Pennsylvania State University

organism: Malus domestica

description: This set includes 60-mer oligonucleotides that are a subset of those in our previous platform, GPL3715.  This second-generation array was a 12-plex array containing 135,000 probes perplex, representing 26,017 transcripts.  This second-generation array represents the transcripts with the best-performing probe sets from the first-generation array and includes the transcripts that showed differential expression between any two scion/rootstock combinations.  Transcripts that had high variability among their probes were left off of the second-generation array. The five best performing probes of the original six probes per transcript were used in the second-generation array to increase the number of different transcripts that could be queried by the second-generation .DNA microarray

manufacture_protocol: NimbleGen proprietary software used to identify 4 or 5 perfectly matched 60-mer oligonucleotides for each apple gene.


title: CIM10Kv3

city: Tempe

first: Joseph

middle: Barten

last: Legutki

state: Arizona

address: 1001 S. McAllister Ave

department: Center for Innovations in Medicine

institute: The Biodesign Institute at Arizona State University

organism: synthetic construct

description: Non-contact Piezo printing (by Applied Microarrays, Tempe, AZ) onto Schott Nexterion A+ aminosilane slides using maleimide conjugation to the free sulfur on the cysteine of the NH3-terminus of peptides

manufacturer: The Biodesign Institiue's Center for Innovations in Medicine

manufacture_protocol: Piezo spotted, commericially synthesized peptides


title: Illumina MiSeq (Staphylococcus epidermidis)

last: GEO

organism: Staphylococcus epidermidis


title: Illumina Genome Analyzer IIx (Drosophila pseudoobscura)

organism: Drosophila pseudoobscura


title: NanoString nCounter Mouse Gene Expression Custom Chip_MG400

status: Public on Nov 01 2013

first: Oleg

last: Butovsky

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

institute: Brigham and Women's Hospital, Harvard Medical School

organism: Mus musculus

technology: other

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


title: [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [HuGene20stv1_Hs_ENTREZG_16.0.0]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: Brainarray: HuGene20stv1_Hs_ENTREZG_16.0.0

manufacture_protocol: See manufacturer's web site


title: NimbleGen Mouse MM9 Deluxe Promoter Array (100718_MM9_Promoter_MeDIP_HX1)

status: Public on Nov 02 2013

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

description:
genome build mm9
100718_MM9_Promoter_MeDIP_HX1.ndf
100718_MM9_Promoter_MeDIP_HX1.pos

manufacture_protocol: standard NimbleGen protocol


title: Agilent-024017 Bsu_Nicholson_8x15K [gene-level version]

city: Merritt Island

first: Samantha

last: Waters

state: Florida

address: Space Life Sciences Lab 505 Odyssey Way

department: Microbiology and Cell Science

institute: University of Florida

organism: Bacillus subtilis subsp. subtilis str. 168

description:
Gene expression array with probes designed for protein coding sequences.

Arrays of this design have barcodes that begin with 16024017 or 2524017.

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: NanoString nCounter Mouse miRNA expression chip (mirBase 15)

description: Nanostring mouse miRNA kit


status: Public on Nov 03 2013

city: Kami

first: Kojiro

last: Ishii

state: Kochi

address: 185 Miyanokuchi, Tosayamada

institute: Kochi University of Technology

organism: Schizosaccharomyces pombe

description:
The LSI Schizosaccharomyces pombe genome tiling array 4x44K_v1.0 consists of 60-mer oligonucleotide probes with an average spacing of approximately every 230 bp across the whole genome, including the repetitive portion and mating-type region.
This array is designed for Agilent 4x44K slide set.
Orientation:
Features are 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.

first: Yuki

last: Ogiyama

first: Koji

last: Nagao

first: Kohta

last: Takahashi

manufacture_protocol: see manufacturer's web site


title: Agilent Pimephales promelas 15K

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

organism: Pimephales promelas

manufacture_protocol: see manufacturer's website


title: [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [HuGene20stv1_Hs_ENTREZG_17.0.0]

organism: Homo sapiens

description: Brainarray: HuGene20stv1_Hs_ENTREZG_17.0.0


title: Agilent-021217 Shewanella oneidensis MR-1 Chip 2.0 (Feature Number version)

city: San Diego

first: Lars

last: Plate

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

organism: Shewanella oneidensis MR-1

description:
Shewanella oneidensis MR-1 ORF array
Arrays of this design have barcodes that begin with 16021217 or 2521217.
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: LC Sciences Pig miRNA Array (miRPig_18_NFAU_120402)

city: XI'AN

first: Li

last: Dengyun

address: Xinong Raod 22

institute: NWSUAF

organism: Sus scrofa

description:
Part No. MRA-1013C
LCS_miRPig_18
Based on Sanger miRBase Release 18

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


title: CombiMatrix 90K Solanum torvum array

city: Fiorenzuola D'Arda

first: Paolo

last: Bagnaresi

address: Via S. Protaso 302

department: Genomics

institute: CRA-GPG

organism: Solanum torvum

description: SRA experiment: SRX268284; SRA run: SRR830592; TSA: GAIC00000000

manufacturer: University of Verona -Department of Biotecnology- 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: LC Sciences Pig miRNA Array (miRPig_17_NAFU_110505)

description:
Part No. MRA-1013C
LCS_miRPig_17
Based on Sanger miRBase Release 17

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: NimbleGen Danio rerio 12x135K Arrays [090818_Zv7_EXPR]

status: Public on Mar 24 2011

city: Corvallis

first: Robert

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

description:
NimbleGen design build Zv7 of Zebrafish, with 38,489 target genes. Each probe is replicated 3 times.  The design includes random GC and other control probes.  This platform has 12 arrays per slide.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.

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


title: Candida albicans 181K tiling ChIP array (assembly Ca20)

status: Public on Jun 09 2011

city: Merced

first: Clarissa

middle: Jane

last: Nobile

address: 5200 North Lake Rd

department: Molecular and Cell Biology

institute: University of California - Merced

organism: Candida albicans

relation:
Alternative to: GPL17891
Alternative to: GPL17892

manufacture_protocol: see  manufacturer's website


title: Custom TaqMan Low Density Arrays format 24

city: Parma

first: Silvia

last: Rossi

state: Parma

address: Viale Usberti, 11/A

department: Genetics, Microbiology, Anthropology ed Evolution

institute: COMT - Centre for Molecular and Translational Oncology, University of Parma

description:
PCR assay
The assays were chosen among the TaqMan Gene Expression Assay library: http://www.appliedbiosystems.com/absite/us/en/home.html


title: Agilent-036574 FHM_8x60K_V2

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

description:
Fathead minnows array with annotated targets. Arrays of this design have barcodes that begin with 25365741.
Arrays of this design have barcodes that begin with 16036574 or 2536574.
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.

first: Arun

last: Rawat

first: Markus

last: Hecker

first: Steve

last: Wiseman

first: Nancy

last: Denslow

first: Ed

last: Perkins


title: [Gilmorea520187F] Affymetrix Custom Array - Gilmore SLARE E. faecalis

status: Public on Nov 05 2012

first: GEO

last: admin

organism: Enterococcus faecalis

description:
Comment[ArrayExpressAccession] A-AFFY-84
affymetrix_netaffx tigr_cmr
Term Source File http://www.affymetrix.com/analysis/ http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl


title: Bacillus subtilis WGD14 platform [BS_ID_Col_Row]

city: Houston

first: Jue

middle: D.

last: Wang

state: TX

address: 1 Baylor Plaza, Rm T932

department: Molecular and Human Genetics

institute: Baylor College of Medicine

organism: Bacillus subtilis

manufacture_protocol: Please read Britton et al. Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis.  J Bacteriol. 2002 Sep;184(17):4881-90


title: Agilent-032260 Bemisia tabaci Oligo Microarray 15K G2545A (Probe Name version)

city: Beijing

first: Nina

last: Yang

state: Beijing

address: 12 Zhongguancun Nandajie, Haidian District

institute: Chinese Academy of Agricultural Sciences

organism: Bemisia tabaci

description:
Agilent whitefly Oligo Microarrays (G2545A)

The array contains~15,000 probes representing 6,226 genes

The file 'database_454_unigene+all_other_anno_unigene.fa.txt' list all the target IDs corresponding transcripts sequence.

The ID column represents the Agilent Probe Names.


title: Illumina HiSeq 2000 (Trypanosoma brucei brucei)

status: Public on Apr 29 2013

last: GEO

organism: Trypanosoma brucei brucei


title: NimbleGen Zebrafish 12x135K Array [090818_Zv7_EXPR]

status: Public on May 28 2013

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Danio rerio

description:
NimbleGen design build Zv7 of Zebrafish, with 38,489 target genes. Each probe is replicated 3 times.  The design includes random GC and other control probes.  This platform has 12 arrays per slide.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.

relation:
Alternative to: GPL17947
Alternative to: GPL13318


title: NimbleGen Human Whole-Genome Tiling Array Set (3of10) [0701_HG18_TILE_03_HX1]

status: Public on Jul 14 2011

description:
Whole human genome tiling array
Array 3 of 10
Designnames:
0701_HG18_TILE_07, 0701_HG18_TILE_08, 0701_HG18_TILE_09
Build: HG18

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


title: NimbleGen Human 385K custom array [2007-05-01_SwitchGear_hg17_tiling]

status: Public on Oct 01 2009

first: Danette

last: Hartzell

address: 2800 Woods Hollow Road

institute: Promega

description: UCSC human genome build hg17

manufacture_protocol: Standard NimbleGen protocol.


title: Agilent-036574 FHM_8x60K_V2 [Probe name version]


title: GeoChip 4.0

status: Public on Jul 13 2013

first: Gao

last: Ying

address: Qinghua East Street

institute: Tsinghua University

organism: Bacteria

description: Soil microbes


title: Nimblegen Custom Mouse Endoderm Array (Zaret)

status: Public on Jun 01 2011

city: Philadelphia

first: Kenneth

middle: S.

last: Zaret

state: PA

address: 9-132, SCTR, 3400 Civic Center Boulevard

department: Cell and Developmental Biology

institute: University of Pennsylvania School of Medicine

description: Annotation in this record based on NCBI mouse build 34. Additionally, contains 210 genomic loci relevant to endoderm, liver, pancreas, gut, development, transcription, signaling, cancer.

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


title: JCVI PFGRC Mycobacterium tuberculosis 16K v5 array designed primarily based on strain H37Rv

status: Public on Jul 01 2010

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Mycobacterium tuberculosis

description: This set includes 4735 oligonucleotides, has 16416 spots distributed in 48 blocks.

manufacture_protocol: 5QMT, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Ocimum Biosolutions Human 40k OciChip

status: Public on Oct 08 2009

city: Hyderabad

first: Ocimum

last: Biosolutions

email: govind.a@ocimumbio.com, sandhya.p@ocimumbio.com, hazira.b@ocimumbio.com, anwaruddin.m@ocimumbio.com

state: Andhra Pradesh

address: Banjara Hills Road No., 1 VI Floor Reliance Classic

department: Bioinformatics

country: India

institute: Ocimum Biosolutions

first: Govind

middle: A

last: Roa

first: Rashmi

last: Sharma

first: Sandhya

middle: P

last: Kiran

first: Karthik

last: Srinivasan

first: Aruna

last: Gandhaveeti

first: Deepak

last: Manohar

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


title: ASU_random-sequence peptide microarray

status: Public on Nov 23 2011

city: Phoenix

first: Phillip

last: Stafford

state: AZ

address: 1001 S. McAllister

institute: Biodesign Institute

organism: synthetic construct

description: random-sequence peptide microarray

manufacture_protocol: Peptides were designed using a random sequence generator, all amino acids were used except cysteine, which was reserved for attachment to the slide at the Carboxy-terminus.  Peptides were synthesized at Sigma Genosys and were checked by mass spec for purity.  Peptides were diluted to 1ug/ul in 1xPBS pH 8 and spotted onto Schott Aminosilane Nexterion A+ slides using a NanoPrint 60 from Arrayit.  Slides are stored under Argon until use.  10286 peptides per array are printed.


title: JCVI PFGRC Mycobacterium tuberculosis 22K v4 array designed primarily based on strain H37Rv

status: Public on Oct 10 2007

description: This set includes 4742 oligonucleotides, has 22176 spots distributed in 48 blocks.

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


title: INRA-CNRS-UEVE Arabidopsis thaliana 73K [120228_Athal_CATMA62_AA_exp]

status: Public on Jul 05 2013

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

organism: Arabidopsis thaliana

description:
The CATMAv6-HD12 array contains 73228 oligos in forward and reverse strands tagging TAIRv8 gene prediction (31227 oligos including 476 Chloro/mito probes) and some specific EUGENE genes (1289). In addition, we including oligos corresponding to repeat_element (5352), miRNA (658) and 36 human controls oligos.
This is triplex slide of the '100701_Athal_CATMA6_SB_exp' design [GPL15719]

designname=120228_Athal_CATMA62_AA_exp
designid=566601


title: Illumina HiSeq 2000 (Solanum lycopersicum)

status: Public on Nov 30 2012

organism: Solanum lycopersicum