title: Agilent-018632 kluyveri_V1

status: Public on Jan 31 2013

city: Paris

first: AGIER

last: nicolas

address: 15 rue de l'école de médecine

department: microorganism genomic

country: France

institute: CNRS-UPMC

organism: Lachancea kluyveri

technology: in situ oligonucleotide

description:
Arrays of this design have barcodes that begin with 16018632 or 2518632.
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: custom-commercial

first: Nicolas

last: Agier

first: Orso

last: Romano

first: Fabrice

last: Touzain

first: Marco

last: Cosentino

first: Gilles

last: Fischer

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


title: TaqMan® Human MicroRNA Array v3.0 A/B

status: Public on May 14 2012

city: Shanghai

last: Shen

address: 145 Shan Dong Middle Road

department: Department of Rheumatology

country: China

institute: Renji Hospital, JiaoTong University School of Medicine

organism: Homo sapiens

technology: RT-PCR

description: PCR assay

distribution: virtual

manufacture_protocol: see manufacturer's website


title: TaqMan® Rodent MicroRNA Array v3.0 A/B

organism: Mus musculus

description: PCR assay


title: Nimblegen Salmonella Typhimurium LT2 4.5K [081014_Styp_LT2_EXP]

status: Public on Apr 30 2012

city: Seoul

first: Yong Keun

last: Park

address: Anam-dong 5Ga, Seoungbuk-Gu

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

description:
Catalog number : A8811-00-01
Design Name : 081014 Styp LT2 EXP X4
Format : 4 X 72K (Arrays Per Slide: 4, Probes Per Array: 72,000, Array Size: 7.8mm x 5.7mm, Feature Size: 16¥ìm x 16¥ìm, Slide Size: 1" x 3" (25 x 75mm))
Accession Numbers : NC_003277, NC_003197
Target Genes : 4,504
Probes per target : 7
Replicates : 2

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


title: Streptococcus pneumoniae whole genome expression array

status: Public on Apr 27 2012

first: Heekuk

address: Heukseok-dong

department: Department of Medical Microbiology

institute: Chung-Ang University College of Medicine

organism: Streptococcus pneumoniae R6

description:
Catalog Number: A6701-00-01, Design Name: 071112, Spne R6 EXP X4, Description: Streptococcus pneumoniae R6, Accession Numbers: NC_003098, Genes: 2037, Probes/Transcript: 17, Probes: 4 x 72,000, Replicates: 2
Nimblegen Expression Streptococcus pneumoniae R6 4X72K, Probe Length: 60mer, Number of Probes per, Target:2-7, Number of Replicate probe Sets per Array: 1-3, Feature Size: 16x16um, Array Size: 7.8x5.7mm, Slide size: 1x3 in.(25x76mm)

manufacture_protocol: NimbleGen Systems Inc.


title: Compugen Rat 5K - 65nt

status: Public on Aug 23 2004

city: Leiden

first: Henk

last: Buermans

state: ZH

address: Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

organism: Rattus norvegicus

technology: spotted oligonucleotide

description: Compugen 5K rat oligonucleotide library, 5' C6-amino modifier printed on CodeLink Activated Slides

distribution: non-commercial

middle: P

first: Bauke

last: Ylstra

first: Warner

middle: S

last: Simonides


title: Agilent-019553 Gallus gallus (chicken) Genome CGH Microarray 244K (Probe Name version)

city: Palo Alto

last: Agilent Technologies

state: CA

country: USA

institute: Agilent Technologies

organism: Gallus gallus

description: *** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL11041.

distribution: commercial


title: Illumina Genome Analyzer IIx (Thermotoga maritima MSB8)

status: Public on Apr 20 2012

last: GEO

organism: Thermotoga maritima MSB8

technology: high-throughput sequencing


title: Illumina Genome Analyzer IIx (Pseudochlorella pringsheimii)

organism: Pseudochlorella pringsheimii


title: CodeLink Human Whole Genome Bioarray

status: Public on Apr 28 2012

city: Shimotsuke

first: PIYANUCH

last: SRIPAYAP

state: Tochigi

address: 3311-1 Yakushiji

department: Medicine, Division of Hematology

country: Japan

institute: Jichi Medical University


title: Applied Biosystems/University of Birmingham Human RT-PCR array

status: Public on Apr 24 2012

city: University of Birmingham

first: Rowan

middle: Samuel

last: Hardy

state: West Midlands

address: 2nd floor IBR

department: Clinical and Experimental Medicine

country: United Kingdom

institute: University oif Birmingham

description:
PCR assay.
96-well custom gene expression array.
Catalog number of plate: 4391524

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


title: Illumina Genome Analyzer IIx (Camponotus floridanus)

status: Public on Apr 23 2012

organism: Camponotus floridanus


title: NimbleGen Human Gene Expression 12x135K Array [2007-09-12_HG18_opt_expr, 070925_HG18_expr]

status: Public on Apr 26 2012

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
Designname: 2007-09-12_HG18_opt_expr_HX12 [equivalent to 070925_HG18_expr_HX12]
Designid: 6364
Build: HG18
FEAT_TYPE: transcript
Probe Length: 60mer
Target Genes: 45,033
Probes per Target: 3


title: BiostarH-140s

city: guangzhou

first: yang

middle: ze

last: min

address: Panyu university cener

department: Pi-Wei Institute

institute: Guangzhou University of Chinese Medicine

technology: spotted DNA/cDNA

manufacture_protocol: see manufacturer's web site


title: Agilent-035154 HFM87_33500_exp_v2

city: Beijing

first: Jing

last: Han

address: NO.1 West Beichen Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

organism: Haloferax mediterranei

description:
Arrays of this design have barcodes that begin with 16035154 or 2535154.

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: Affymetrix Saccharomyces cerevisiae GeneChip_DNA_Tag3 array

city: Segrate, Milano

first: Clelia

last: Peano

address: Via Fratelli Cervi 93

department: Institute of Biomedical Technologies

country: Italy

institute: National Research Council

organism: Saccharomyces cerevisiae

manufacture_protocol: See manufacturer's web site.


title: NimbleGen Synechocystis sp. PCC 6803 Gene Expression Array [101018_TI1148_60mer_exp]

status: Public on Apr 19 2012

organism: Synechocystis sp. PCC 6803

description:
Design Name: TI1148 60mer
Genes:3567
Probes:13
Replicates:4
Accession Numbers: NC_000911, NC_004967, NC_005229, NC_005230, NC_005231, NC_005232


title: Illumina HiSeq 2000 (Capra hircus)

organism: Capra hircus


title: Operon Oligonucleotide Set Innate Immunity and Aspergillosis 7MM

status: Public on Apr 17 2012

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

country: Germany

institute: University of Wuerzburg

description: Nexterion® Slide E

manufacturer: University of Wuerzburg microarray facility

first: Juergen

last: Loeffler

first: Oliver

middle: C

last: Morton

middle: E

first: Helga

last: Sennefelder

first: Ruth

last: Bauer

first: Jasmin

last: Kungl

manufacture_protocol:
1. Oligos are arrayed in 96 well plates. Each well contains 500 pmol of 55–70 nucleotides (nt) long oligos and consist of an 18–24 nt segment that targets  specific known human cytokine, chemokine and innate immunity genes
2. Add  3 x SSC + 1,5 M Betaine (in Rnase-free water) to 10 uM
3. Seal plates and wrap them in saran wrap
4. Let it resuspend in a humid chamber on a shaker (60 rpm) over night
5. Centrifuge plates at 2000 rpm for 3 minutes.
6. Rearray 10 µL into 384-well, V-bottom plates
7. Centrifuge plates at 2000 rpm for 3 minutes.
8. 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 15 minutes before next cassette is needed to begin centrifugation.
9. After the print run is completed, allow plates to dry through passive evaporation in a protected environment.
10. Spots are printed in quadruplicates, assiciated data contain median values of quadruplicates
11. For each subsequent preparation of these plates for a print run, add water to the wells instead of print 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 each dip.


title: DUKE Mouse 1.8K miRNA-AI

status: Public on Apr 13 2012

city: Los Angeles

first: ting

last: Xie

address: 127 San Vicente Blvd

department: Pulmonary

institute: Cedars-Sinai Medical Center

description: The array probes were purchased from Ambion and Invitrogen, and actual probe sequences are not known.

manufacturer: Duke Microarray Facility, Ambion and Invitrogen


title: Agilent-032577 Custom Caulobacter crescentus NA1000 15k array

status: Public on Apr 25 2012

city: Cambridge

first: Emily

middle: J

last: Capra

state: MA

address: 31 Ames Street, 68-570

department: Biology

institute: Massachusetts Institute of Technology

organism: Caulobacter vibrioides NA1000

description:
Arrays of this design have barcodes that begin with 16032577 or 2532577.

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 (Papio hamadryas)

organism: Papio hamadryas


title: Exiqon miRCURY LNA microRNA array v.10.0 Extended Version

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

description: Array represents miRBase version 10.0 with additional features.

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


title: Agilent-021656 Sphingomonas wittichii RW1 [ORF Name version]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Rhizorhabdus wittichii RW1

description:
Sphingomonas wittichii RW1

Arrays of this design have barcodes that begin with 16021656 or 2521656.


title: Agilent-031368 Trichoderma reesei custom microarray [Probe Name version]

status: Public on Apr 14 2012

city: Rockville

first: Panos

last: Pan

address: 9430 Key West Avenue

institute: Arraystar Inc.

organism: Trichoderma reesei QM6a


title: Agilent-031368 Trichoderma reesei custom microarray [Feature Number version]


title: NimbleGen Drosophila melanogaster 135K (080813_Dmel_exp), probe-level version

organism: Drosophila melanogaster

description:
Native array description files:
080813_Dmel_exp.ndf
080813_Dmel_exp.ngd
080813_Dmel_exp_HX12.ncd

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


title: Agilent-023642 SurePrint G3 Human High-Resolution Discovery Microarray 1x1M (Probe Name version)

last: Agilent Technologies

organism: Homo sapiens

description:
SurePrint G3 Human High-Resolution Discovery Microarray, 1x1M

Arrays of this design have barcodes that begin with 16023642 or 2523642.

Data table annotations based on build hg18:NCBI36:Mar2006.

The ID column represents the Agilent Probe Name.


title: Agilent-024835 CDv2_0_1 [ProbeName version]

city: Coleraine

first: Nigel

middle: G

last: Ternan

state: Co. Londonderry

address: Cromore Road

department: School of Biomedical Sciences

institute: University of Ulster

organism: Clostridioides difficile 630

description:
BuG@S CDv2.0.1 - CD630_genome

Arrays of this design have barcodes that begin with 16024835 or 2524835.

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 Bacillus cereus ATCC 14579 Gene Expression Array [2006-07-27_TI226900_60mer]

status: Public on Apr 12 2012

last: Nimblegen Systems

organism: Bacillus cereus ATCC 14579

description:
Design Name: TI226900 60mer
Format: 385K
Accession Numbers: NC_004721, NC_004722
Target Genes: 5,255
Probes per Target: 18
Replicates: 4


title: [HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [probe set (exon) version]

status: Public on Apr 16 2012

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

description: Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html


title: Illumina HiSeq 2000 (Oxytricha trifallax)

status: Public on Apr 18 2012

last: GEO

organism: Oxytricha trifallax


title: VTT_KB_Aspergillus nidulans v4.0_135K array

city: Espoo

first: Kirsi

last: Bromann

address: Tietotie 2

department: TK402, Cell Factory

country: Finland

institute: VTT Technical Research Centre of Finland

organism: Aspergillus nidulans FGSC A4

description: Nimblegen design name 100608_Anid_KB_exp, Nimblegen design ID 531573. Expression + Tiling design for Aspergillus nidulans FGSC A4 using customer-provided transcript set. Expression portion -- selected 6 probes per transcript for 10546 out of 10597 transcripts (51 not found, 18 less than 6 probes per transcript, 114 duplicate probes/exemplars).  2 replicates of 63,130 probes for a final expression total of 126,260 probes. Tiling portion -- Used customer provided list of 36 long transcripts.  Selected 5651 tiling 50-75mers and tiled at a 66bp interval (int=56/win=10/mm=1). 2 replicates on final array for 11302 tiling probes.  Created .pos and probe_locations.gff to go with tiling portion.  Annotation for these regions can be found in the .ngd file


title: LC Sciences Gallus gallus miRChicken_15

city: Guangzhou

first: Hongmei

last: Li

address: Guangzhou tianhe wushan street

institute: south china agricultural university

organism: Gallus gallus

description:
Part No.: MRA-1005
Name: Chicken miRNA Array
Version No.: miRChicken_15

No. of Unique Chicken Probes: 542; No. of Repeats: 6

Based on Sanger miRBase Release 15.

manufacture_protocol: Arrays are made based on µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://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: University of Wisconsin Arabidobpsis Millichip 1K

first: Jamison

last: Wolfer

address: 425 Henry Mall

department: Biotechnology Center

institute: University of Wisconsin

organism: Arabidopsis thaliana

manufacture_protocol: Maskless array synthesizer


title: Illumina HiSeq 1000 (Pan troglodytes)

status: Public on Apr 11 2012

organism: Pan troglodytes


title: Illumina HiSeq 2000 (Cunninghamia lanceolata)

status: Public on Apr 10 2012

organism: Cunninghamia lanceolata


title: Illumina HiSeq 2000 (Xenopus (Silurana) tropicalis)

organism: Xenopus tropicalis


title: Agendia_human_DiscoverPrint_v1

city: Amsterdam

first: Paul

last: Roepman

address: Science Park 406

institute: Agendia

manufacture_protocol: Microarrays were prepared by Agilent technologies using their Agilent SurePrint Technology. Breifly, 60-mer oligonucleotides are synthesized base-by-base in repetitive print layers on a solid glass substrate, using standard phosphoramidite chemistry.


title: Agilent-020839 Teleopsis dalmanni 579_FLS_slide_II (Feature Number version)

status: Public on Apr 09 2012

city: College Park

first: Gerald

last: Wilkinson

address: Bldg 144, 4094 Campus Dr

institute: University of Maryland

organism: Teleopsis dalmanni

description:
Arrays of this design have barcodes that begin with 16020839 or 2520839.

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: 3D-Gene Human miRNA V17_1.0.0

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

manufacture_protocol: See manufacture's web site


title: Illumina Genome Analyzer IIx (Meleagris gallopavo)

organism: Meleagris gallopavo


title: Agilent-028233 Danio rerio Leiden custom 180k array

city: Leiden

first: Michiel

last: van der Vaart

address: Einsteinweg 55

department: IBL

institute: University of Leiden

organism: Danio rerio

manufacture_protocol: Agilent Ink Jet manufactured


title: Agilent-023363 Human 180K UMCG_april09 (Probe Name version)

status: Public on Apr 05 2012

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

description:
NCBI Build 36 (hg18).

Arrays of this design have barcodes that begin with 16023363 or 2523363.

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


title: 090316-Mouse DNA Methylation 2.1M Deluxe Promoter Array

status: Public on Apr 07 2012

first: Aik

middle: T

last: Ooi

address: 650 Charles E Young Dr S, Factor 9-240

department: Pediatrics

institute: UCLA

organism: Mus musculus

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


title: NimbleGen Streptococcus sanguinis SK36 080319_BK_mixed_bact_expr [DesignID: 7345]

status: Public on Apr 04 2012

city: Rostock

first: Sylvio

last: Redanz

state: Mecklenburg Vorpommern

address: Schillingallee 70

department: Institute of microbiology, virology and hygiene

institute: hospital university rostock

organism: Streptococcus sanguinis SK36

description:
385K-format:3 replicates of up to 13 probes per gene, 60 mer oligonucleotides, 3510 randomized sequence probes

The array includes probes for Porphyromonas gingivalis W83, Fusobacterium nucleatum DSMZ 25586, Streptococcus sanguinis SK36, Actinobacillus actinomycetemcomitans HK1651, and Streptococcus mutans UA159. The probes for all of these organisms are represented in the supplemental files '080319_BK_mixed_bact_expr.ndf' and '080319_BK_mixed_bact_expr.ngd'. However, the Platform table includes probes only for Streptococcus sanguinis SK36.

DesignID: 7345

native array description file: 080319_BK_mixed_bact_expr.ndf
native array description file: 080319_BK_mixed_bact_expr.ngd


title: NimbleGen Human 100309_AS_human_100426_pz array [gene-level version]

city: Beijing

first: Song

last: Wang

email: wscookie@163.com, chenjl@im.ac.cn

address: West Beichen Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences


title: Agilent-017368 Human 8x15k v2.0 (Probe Name version)

city: chicago

first: chunjiang

last: he

state: il

address: 900 east 57th st

institute: university of chicago

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


title: Agilent-014817 Drosophila Whole Genome ChIP-on-Chip Set 244K, Microarray 2 of 2 (G4495A) (Probe Name version)

status: Public on Apr 03 2012

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Drosophila Whole Genome ChIP-on-Chip Set 244K, Microarray 2 of 2

Arrays of this design have barcodes that begin with 16014817 or 2514817.


title: SMD Print_652 MSU-4_01-02

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

manufacturer: Pam Green's lab, Michigan State University

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


title: SMD Print_598 MSU3_09-01


title: SMD Print_593 MSU3_07-01


title: SMD Print_403 MSU2_12-00


title: Agilent-014816 Drosophila Whole Genome ChIP-on-Chip Set 244K, Microarray 1 of 2 (G4495A) (Probe Name version)

description:
Drosophila Whole Genome ChIP-on-Chip Set 244K, Microarray 1 of 2

Arrays of this design have barcodes that begin with 16014816 or 2514816.


title: Mouse 4K miRNA LC_MRA-1002_miRMouse_14 [miRNA_ID version]

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

description:
miRNA ID version of GPL9341
Mouse miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 14

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


title: NimbleGen_Custom_Chloroethene_array_V02

city: AUBIERE

first: Peyret

last: Pierre

address: 24, avenue des landais

institute: CNRS - Blaise Pascal University

organism:
Shewanella
Pseudomonas
Methylosinus
Nitrosomonas
Mycobacterium
Geobacter
Thauera
Desulfitobacterium
Dehalobacter
Sulfurospirillum
Dehalococcoides

description:
Format: 12x135K

Each probe on the microarray was synthesized in eight replicates, and a total of 5,707 random probes was used to determine the background noise.

Chlorinated solvents metabolic capacities (Environmental).

The Platform data table reflects a condensed representation of the expression array's replicate features.  The .ndf file is linked below as a supplementary file.

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


title: Agilent-029031 Sorghum bicolor 44K TLL_JSY_V1.1 022520

status: Public on Apr 08 2012

city: Singapore

first: Shu-Ye

last: Jiang

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory, National University of Singapore

organism: Sorghum bicolor

description:
Arrays of this design have barcodes that begin with 16029031 or 2529031.

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: Illumina Genome Analyzer IIx (Oryza sativa)

last: GEO

organism: Oryza sativa


title: [Agilent-019442] Agilent/INRA FH Sus scrofa 15K muscle array [Probe Name version]

city: saint-gilles

first: marie

last: damon

address: domaine de la prise

institute: INRA

organism: Sus scrofa

description:
A custom repertoire of 15,000 60-mer DNA probes targeting transcripts expressed in growing pig skeletal muscle.
This repertoire was print on a multiplex microarray format : 8-plex microarray (eight individual 15K microarrays printed on a single slide)

first: Marie

last: Damon

first: Frederic

last: Hérault

first: Pierre

last: Cherel


title: Human_HG18_Deluxe_Promoter_HX1_HD2.2 tiling array

status: Public on Apr 01 2012

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

organism: Homo sapiens

description:
Oligo coordinates based on genome build HG18.
The array tiles RefSeq genes from -7000 to +3000 relative to the TSS, with 100bp probe spacing.

first: Miao

last: Sun

first: Gary

middle: D

last: Isaacs

first: Nasun

last: Hah

first: Nina

last: Heldring

first: Elizabeth

middle: A

last: Fogarty

first: William

middle: L

manufacture_protocol: See NimbleGen website.


title: An oligonucleotide microarray for mouse imprinted genes profiling

city: Paris

first: Jean-Philippe

last: Jais

address: 149 rue de Sevres

institute: Université Paris Descartes - Hopital Necker-Enfants Malades

organism:
Mus musculus
Rattus norvegicus

first: Alexandre

last: Vigé

first: Catherine

last: Gallou-Kabani

first: Marie-Sylvie

last: Gross

first: Alban

last: Fabre

first: Claudine

last: Junien

manufacture_protocol: Specific 50-mer oligonucleotides synthesized by Operon were resuspended in 150 mM phosphate buffer pH 8.3 at a concentration of 20 micromoles. For each gene, two different oligonucleotide probes, one corresponding to the 3’ non-coding region and one corresponding to the coding region were designed. The resulting application targeted microarray contained 992 gene-specific oligonucleotide probes generated from 63 imprinted genes and 15 genes encoding proteins involved in epigenetic marking (BORIS, brother of regulatory imprinting sequence, 5 DNMT, DNA methyltransferases and 9 HDAC, histone deacetylases), as well as 256 genes encoding proteins involved in neurotransmission and 157 genes encoding proteins involved in energy homeostasis. These sequences correspond to mouse imprinted genes listed at http://www.geneimprint.com or reported in published papers. Probes were spotted on NHS-PEG (N-hydroxysuccinimide-polyethyleneglycol-vinylsulfone) activated glass slides (Genescore) (Pintchovski et al., 1979). Each probe was spotted in duplicate (at least) on each slide. The various oligonucleotide solutions were applied on the slides by contact printing, using a Biorobotics Microgrid II apparatus (Genomic Solutions, Ann Arbor, MI) with one BioRobotics MicroSpot 2500 pin. The oligonucleotide spots were 80–100 micrometers in diameter, and the center-to-center distance between adjacent spots was 220 micrometers. Each slide contained one array in a conformation of four rows and two columns. During spotting, relative humidity was maintained at 50%. After spotting, the arrays were left in the humidity chamber for a short period and were then stored in a desiccation chamber at 20 ° C until use.


title: RIMB/Wutz laboratory Mus musculus 385K Tiling array [2007-01-30_chrXs_2.aw]

status: Public on Apr 02 2012

first: Celine

last: Morey

address: 35 rue Hélène Brion

department: University Paris 7

institute: UMR7216-Epigenetics and stem cell

description: DESIGN_ID: 5181; DESIGN_NAME: [2007-01-30_chrXs_2.aw]. 162,5 Mb of the mouse X chromosome and 14,6 Mb of the mouse chromosome 17 tiled at 250 bp spacing excluding repeat masked regions. Native NimbleGen file (ndf, pos) are linked below as supplementary files

manufacture_protocol: NimbleGen Systems Inc.


title: Homo sapiens 389K Hg18 RefSeq promoter

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


title: Agilent-024425 Thunnus thynnus 2009 (Feature Number version)

city: Pacific Grove

first: Nishad

last: Jayasundara

address: 120 Oceanview Blvd

institute: Stanford University

organism: Thunnus thynnus

description:
Arrays of this design have barcodes that begin with 16024425 or 2524425.

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: GenoToul/ Biopuces platform - Saccharomyces cerevisiae [2009]

city: MONTPELLIER

first: Sylvie

last: Dequin

address: 2 PLACE PIERRE VIALA

organism: Saccharomyces cerevisiae

manufacture_protocol: See company website: http://biopuce.insa-toulouse.fr


title: Custom NimbleGen 12x135 Maize (4a.53) expression array

city: Saint Paul

first: Nathan

middle: M

last: Springer

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

organism: Zea mays

description: 3-4 long oligonucleotides were synthesized for each of the 32,540 genes in the FGS annotation of maize (4a.53)

manufacture_protocol:
Standard NimbleGen synthesis
A subset of the probes were selected for normalization and analysis.  Two filters were applied to identify the subset of probes.  First, only genes that exhibited signal above background levels were retained.  Second, only probes that do not show substantially lower CGH signal in at least 2 genotypes were retained.  The list of probes that were used for generating the normalized data are provided in the file titles 091006_NS_Zmays_CGH_exp_subset.txt and contain the same columns as the .ndf file. The linked platform table represents only the subset of probes that were included in the final analysis (see supplementary files for complete listings).


title: SABiosciences Human Cell Development & Differentiation miRNA PCR ArrayHuman panel

city: kumamoto

first: Noritoshi

last: Honda

state: kumamoto

address: 1-1-1 Honjo

department: Department of Dermatology and Plastic Surgery

institute: Kumamoto University

description: PCR assay

manufacture_protocol: see manufacturer's website


title: NimbleGen Mixed bacteria 080319_BK_mixed_bact_expr (technical proves averaged)

status: Public on Dec 09 2011

first: Sylvio

last: Redanz

organism:
Fusobacterium nucleatum
Streptococcus mutans UA159
Porphyromonas gingivalis W83
Aggregatibacter actinomycetemcomitans HK1651
Streptococcus sanguinis SK36

description:
385K-format: 3 replicates of up to 13 probes per gene, 60-mer oligonucleotides, 3510 randomized sequence probes.

The array includes probes for Porphyromonas gingivalis W83, Fusobacterium nucleatum DSMZ 25586, Streptococcus sanguinis SK36, Actinobacillus actinomycetemcomitans HK1651, and Streptococcus mutans UA159.
A condensed version of this platform is assigned  accession number GPL10873.
Alternative version of this Platform including probes only for Streptococcus sanguinis SK36 is  assigned accession number GPL15399.

relation: Alternative to: GPL15399 (S. sanguinis SK36 probes only)


title: NimbleGen Drosophila melanogaster gene expression 12X135K array

status: Public on Mar 30 2012

city: Atlanta

first: Edward

last: Ramos

state: GA

address: 1510 Clifton Rd NE

institute: Emory University

organism: Drosophila melanogaster

description:
NimbleGen design catalog # 05543762001.

The Platform data table is a gene-level representation of the expression array's features.

The .ndf and .ngd files are linked below as supplementary files.
Native array description file: 100718_Dmel_exp.ndf
Native array description file: 100718_Dmel_exp.ngd


title: Agilent-020839 Teleopsis dalmanni 579_FLS_slide_II (condensed version)

city: College Park

first: Gerald

last: Wilkinson

address: Bldg 144, 4094 Campus Dr

institute: University of Maryland

description:
Probes were based on EST sequences obtained from eye-imaginal disc tissue. A total of 3424 annotated genes along with 274 contigs with either large open reading frames (>500 bp) or relatively high representation in the EST database (>4 cDNA clones).  In a previous study, we created 10 probes for each gene and used them to conduct comparative genomic hybridization for several Teleopsis species, including T. dalmanni and T. quinqueguttata.  For this study, we chose the five probes for each gene that had the highest CGH intensities for both species, suggesting that they had the least sequence divergence, and replicated each two times at random locations on the array.

AMADID 020839
44K Oligoarray MFexpression slide

manufacture_protocol: Custom designed using eArray, chemical synthesis.


title: Agilent-021656 Sphingomonas wittichii RW1 [Feature Name version]

status: Public on Jan 19 2011

city: Dübendorf

first: David

middle: R

last: Johnson

address: Uberlandstrasse 133

department: Environmental Microbiology

country: Switzerland

institute: Eawag

organism: Rhizorhabdus wittichii RW1

description:
Sphingomonas wittichii RW1

Arrays of this design have barcodes that begin with 16021656 or 2521656.

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 Drosophila melanogaster 135K (080813_Dmel_exp)

status: Public on May 26 2011

city: Iowa City

first: Alejandro

last: Pezzulo

state: IA

address: 169 Newton Rd 6334 PBDB

department: Internal Medicine

institute: University of Iowa

description:
Native array description files:
080813_Dmel_exp.ndf
080813_Dmel_exp.ngd
080813_Dmel_exp_HX12.ncd

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


title: NIDDK-Drosophila-Illumina-DNASeq-S2 cells

status: Public on Dec 31 2009

city: Bethesda

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

technology: other

description:
High throughput sequencing
Instrument model: Illumina Genome Analyzer


title: Agilent-023363 Human 180K UMCG_april09 (Feature Number version)

status: Public on Jun 22 2010

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

institute: Vrije Universiteit Medical Center

description:
NCBI Build 36 (hg18).
Arrays of this design have barcodes that begin with 16023363 or 2523363.
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: NIDDK-Drosophila-Illumina-RNASeq-S2 cells


title: Agilent-011447 Yeast Oligo Microarray G4140A (Probe Name version)

status: Public on Oct 08 2008

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Replaced by 013384, G4140B.  This oligonucleotide microarray will enable researchers to simultaneously characterize expression of many thousands of yeast genes and identify gene activity during important biological processes, such as yeast growth, adaptation, response to drug candidates and reproduction.

*** 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 GPL884.


title: Agilent-011472 Mouse Development Oligo Microarray G4120A (Probe Name version)

description:
The content on this microarray was derived from the National Institute on Aging/National Institute of Health cDNA mouse clone set that includes genes from sequences of stem cells and very early-stage embryo cDNA libraries.

*** 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 GPL922.


title: GenoToul/ Biopuces platform - Saccharomyces cerevisiae [2010]


title: Agilent-015068 Chicken Gene Expression Microarray 4x44k (Probe Name version)

status: Public on Jul 05 2011

organism: Gallus gallus

description: *** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL8764


title: Agilent-015061 C. elegans Oligo Microarray 4x44K G2519F (Probe Name version)

status: Public on Feb 20 2009

organism: Caenorhabditis elegans

description:
This microarray provides genome-wide coverage of C. elegans with over 21,000 predicted genes from WormBase, a public C. elegans genome database.

The ID column represents the Agilent probe names.


title: miRCURY LNA microRNA Array, 5th generation [Human miRBase 17]

status: Public on Nov 22 2011

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

institute: Lund University, Sweden

organism:
Homo sapiens
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: This platform is identical to GPL9908, but with updated microRNA names to miRBase 17.

manufacture_protocol: See manufacturers website


title: Agilent-013162 Whole Rat Genome Microarray G4131A (Probe Name version)

organism: Rattus norvegicus

description:
With a focus on well known rat genes and homologues to human and  mouse genes with useful annotation, Agilent's Whole Rat Genome Oligo Microarray provides researchers with a new tool for modeling human biology in the rat model organism. For researchers, this means they now have access to a microarray made up of relevant content that has been empirically validated by Agilent.

*** 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 GPL2877.


title: Agilent-011868 Rat Oligo Microarray G4130A (Probe Name version)

description:
This microarray contains representative sequences derived from rat RefSeq, high-quality public rat mRNA accessions, homologs to human and mouse RefSeq, EST clusters determined by a leading biopharmaceutical company and the Incyte Zooseq database as well as toxicology markers determined by the National Institute of Environmental Health Sciences (NIEHS) and others. Many of the toxicology markers used in the design of this microarray were released to the public domain for the first time and will be used on this unique microarray product.

*** 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 GPL890.


title: Agilent-012106 Rice Oligo Microarray G4138A (Probe Name version)

organism: Oryza sativa Japonica Group

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 rice (japonica) cDNA library of Japans National Institute of Agrobiological Sciences.

*** 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 GPL892.


title: Agilent-011839 Arabidopsis 2 Oligo Microarray G4136A (Probe Name version)

organism: Arabidopsis thaliana

description:
Replaced by 013324, G4136B.  The content on this microarray is derived from the ATH1 v. 3 database of The Institute for Genomic Research (TIGR) and represents 21,500 genes. This microarray will be useful for scientists studying gene activity associated with various plant organ functions, stages of growth, and biotic and abiotic stresses.

*** 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 GPL888.


title: [HT_HG-U133B] Affymetrix HT Human Genome U133B Array

status: Public on Sep 15 2009

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The GeneChip® HT Human Genome U133 Array Plate Set enables researchers to perform large-scale studies by analyzing whole-genome expression for up to 96 samples at a time. The set comprises a U133A and U133B plate, measuring expression levels for more than 33,000 well-characterized genes and UniGene clusters.

manufacture_protocol: see manufacturer's web site


title: Agilent-015354 Bovine Oligo Microarray (4x44K) (Probe Name version)

status: Public on Nov 23 2009

organism: Bos taurus

description:
Design ID: 015354
Agilent has developed a genome-wide bovine microarray to enable scientists to study gene expression profiling at the global level. Agilent's Bovine Oligo – 4X44K microarray covers 21,475 unique genes and transcripts of Bos Taurus, two probes for each gene are produced. Oligonucleotides, 60-mers, are synthesized directly on glass slide using the Agilent’s SurePrint Technology.

*** 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 GPL7053.

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


title: Mouse 4K miRNA LC_MRA-1002_miRMouse_14

status: Public on Nov 13 2009

city: Houston

first: Christoph

last: Eicken

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism: Mus musculus

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


title: Agilent-011521 Human 1A Microarray G4110A (Probe Name version)

description:
Agilent's Human 1A Oligo Microarray (V2) includes over 17K 60-mer oligonucleotide probes, sourced from the Incyte Foundation Database and are designed to span conserved exons across the transcripts of the targeted full length genes. Coupled with Agilent's probe selection and validation processes, this design method gives the customer maximum confidence in data quality and prevents redundancy in gene coverage.

*** 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 GPL885.


title: Exiqon Mus musculus miRNA 0.5K (exiqon_miRCURY_mmu_v7.1)

status: Public on Feb 23 2008

city: Philadelphia

first: Joshua

last: Friedman

state: PA

address: ARC 1007B, 3615 Civic Center Blvd.

institute: University of Pennsylvania School of Medicine

manufacture_protocol: The LNA capture probes are intelligently designed and Tm-normalized ensuring all miRNA targets hybridize to the array with equal affinity under high stringency hybridization conditions.


title: Nimblegen Dyak expression custom array/2005-06-03_D_yakuba_50mer

status: Public on Nov 08 2007

organism: Drosophila yakuba

description: Nimblegen custom design array for Drosophila species expression: An average of 10 array element probes per predicted genes was selected without-bias vis-a-vis position within the gene model. Sources of gene predictions include EIS (Annotations from Eisen lab v.1.0, Feb. 2005), GID (ab-initio GeneID predictions on draft assembly), and GBK (EST sequence from GeneBank). Probes have been remapped to final genome assemblies (Comparative Assembly Freeze 1 CAF1, http://rana.lbl.gov/drosophila/caf1.html) and  genome annotation (GLEANR set, http://rana.lbl.gov/~venky/AAA/freeze_20061030/protein_coding_gene/GLEANR/annotation). Arrays are described in detail on http://intramural.niddk.nih.gov/research/multifly/multifly.htm.

last: Sturgill

first: Yu

last: Zhang

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


title: Nimblegen Dvir expression custom array/2005-06-03_D_virilis_50mer

organism: Drosophila virilis


title: Nimblegen Dsim expression custom array/2005-06-03_D_simulans_50mer

organism: Drosophila simulans


title: Nimblegen Dmoj expression custom array/2005-06-03_D_mojavensis_50mer

organism: Drosophila mojavensis


title: Nimblegen Dana expression custom array/2005-06-03_D_ananassae_50mer

organism: Drosophila ananassae


title: Nimblegen Dpse expression custom array/2005-06-03_D_pseudoobscura_50mer

organism: Drosophila pseudoobscura


title: NimbleGen Human 3x720k Whole Genome CGH [100718_HG18_WG_CGH_v3.1_HX3]

status: Public on Dec 06 2011

city: Madison

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Homo sapiens

description:
Build: Hg18, NCBI 36
60mer probes.

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


title: Nimblegen Drosophila melanogaster expression array/2005-10-17_Dmel4_60mer_exp

organism: Drosophila melanogaster


title: Toxoplasma gondii Chromosome 1b 1230000-1880000 tiling array

status: Public on May 22 2007

city: Tampa

first: Kami

last: Kim

state: FL

address: 3720 Spectrum Blvd, Suite 304

department: Internal Medicine Medicine

institute: University of South Florida

organism: Toxoplasma gondii

description: Tiling microarray encompassing .65Mb (nts 1230000-1880000) of Chromosome 1b, accession number AM055943.1.

first: Mathieu

last: Gissot

first: Krystina

last: Kelly

first: James

middle: W

last: Ajioka

first: John

last: Greally

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


title: Agilent-013223 D. rerio (Zebrafish) Oligo Microarray G2518A Option 001 (Probe Name version)

status: Public on Sep 03 2008

state: CA

organism: Danio rerio

description:
Agilent has developed a genome-wide zebrafish microarray to enable scientists to study gene expression profiling at the global level and enhance our understanding of zebrafish biology and gene functions related to mammalian models.

*** 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 GPL2878.

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


title: Agilent-011978 Mouse Microarray G4121A (Probe Name version)

status: Public on Feb 06 2008

description:
Mouse is the most widely used mammalian model in biological research and target identification. This microarray will enable researchers to simultaneously characterize expression activities of many thousands of mouse genes associated with various biological functions and processes. Content for this empirically validated microarray includes a comprehensive set of toxicology markers determined through collaboration with leaders in toxicogenomics including NIEHS, Toxicogenomics Research Consortium, and Paradigm Genetics

*** 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 GPL891.


title: Agilent-015064 D. rerio (Zebrafish) Oligo Microarray 4x44K G2519F (Probe Name version)

description:
Design ID: 015064

Agilent has developed a genome-wide zebrafish microarray to enable scientists to study gene expression profiling at the global level and enhance our understanding of zebrafish biology and gene functions related to mammalian models.

*** 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 GPL6563.


title: Agilent-013326 Mouse Oligo Microarray (V2) G4121B (Probe Name version)

description:
Consisting of highly-sensitive 60-mer oligonucleotide probes that target human genes present in Incyte LifeSeq Foundation partial sequence database, the Agilent Human 1B Oligo Microarray Kit queries more rare human transcripts where full-length information is not available. The microarray is fully annotated to allow customers to access public or Incyte LifeSeq databases for additional bioinformatics data about the genes.

*** 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 GPL2881.


title: Agilent-015059 Arabidopsis 3 Oligo Microarray 4x44K G2519F (Probe Name version)

description:
The content on this microarray is derived from the ATH1 v.5 database of The Institute for Genomic Research (TIGR) and from the Arabidopsis MPSS database at the University of Delaware.  Nearly 40,000 features represents 28,500 genes from TIGR and more than 10,000 unannotated transcripts from University of Delaware. This microarray will be useful for scientists studying gene activity associated with various plant organ functions, stages of growth, and biotic and abiotic stresses.

*** 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 GPL6177.


title: Agilent-015072 Yeast Oligo Microarray 4x44K G2519F (Probe Name version)

status: Public on Sep 25 2009

organism: Saccharomyces cerevisiae

description:
This oligonucleotide microarray will enable researchers to simultaneously characterize expression of many thousands of yeast genes and identify gene activity during important biological processes, such as yeast growth, adaptation, response to drug candidates and reproduction.

Arrays of this design have barcodes that begin with 16015072 or 2515072.

The ID column represents 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 GPL7542.


title: SAGE:10:NlaIII:Homo sapiens

status: Public on Sep 28 2000

last: GEO

technology: SAGE NlaIII


title: Agilent-018972 D. melanogaster (FruitFly) Oligo Microarray 4x44K G2519F (Probe Name version)

description:
Agilent has developed a genome-wide fruit fly microarray to enable scientists to study gene expression profiling at the global level and enhance our understanding of fruit fly biology and gene functions.

*** 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 GPL6385.


title: Agilent-012097 Human 1A Microarray (V2) G4110B (Probe Name version)

description:
Agilent's Human 1A Oligo Microarray (V2) includes over 20K 60-mer oligonucleotide probes, sourced from the Incyte Foundation Database, RefSeq, and GenBank, and are designed to span conserved exons across the transcripts of the targeted full length genes. Coupled with Agilent's probe selection and validation processes, this design method gives the customer maximum confidence in data quality and prevents redundancy in gene coverage.

*** 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 GPL887.


title: Agilent-019161 D. rerio (Zebrafish) Oligo Microarray (V2) G2519F (Probe Name version)

description:
Agilent has developed a genome-wide zebrafish microarray to enable scientists to study gene expression profiling at the global level and enhance our understanding of zebrafish biology and gene functions related to mammalian models.

*** 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 GPL6457.