title: JYUAO Rainbow trout 8x60K v1.0

status: Public on Dec 21 2015

city: Jyväskylä

first: Eeva-Riikka

last: Vehniäinen

address: Survontie 9, POB 35

country: Finland

institute: University of Jyväskylä

organism: Oncorhynchus mykiss

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol: The array was designed with Agilent eArray using sequences (TCs and ESTs) from RTGI release 8 available from http://compbio.dfci.harvard.edu/cgi-bin/tgi/gimain.pl?gudb=r_trout


title: Agilent-037053 FUB-VibrioParahaemolyticus-8x15K-v1

status: Public on Jan 31 2015

city: Berlin

first: Stephan

last: Huehn

address: Koenigsweg 69

country: Germany

institute: Freie Universität Berlin

organism: Vibrio parahaemolyticus RIMD 2210633

description:
Arrays of this design have barcodes that begin with 16037053 or 2537053.

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: IIllumina Infinium human CytoSNP-850K BeadChip

city: Utrecht

first: Wigard

last: Kloosterman

address: Universiteitsweg 100

country: Netherlands

institute: University Medical Center Utrecht

organism: Homo sapiens

technology: oligonucleotide beads

manufacture_protocol: See manufacturer's website


title: Illumina HiSeq 2500 (Bacteroides thetaiotaomicron)

status: Public on Jan 30 2015

last: GEO

country: USA

organism: Bacteroides thetaiotaomicron

technology: high-throughput sequencing

distribution: virtual


title: Exiqon, miRCURY LNA microRNA array, 7th gen (mmu, miRBase 19)

city: Vedbaek

first: Michael

last: Thorsen

address: Skelstedet 16

country: Denmark

institute: Exiqon

organism:
Mus musculus
Murid betaherpesvirus 1
Murid gammaherpesvirus 4

technology: spotted oligonucleotide

distribution: commercial

manufacturer: Exiqon A/S, Skelstedet 16, 2950 Vedbaek, Denmark

first: Jorg

last: Krummheuer

manufacture_protocol: See Exiqon website


title: Exiqon, miRCURY LNA microRNA array, 7th gen (rno, miRBase 19)

organism: Rattus norvegicus


title: Exiqon, miRCURY LNA microRNA array, 7th gen (hsa, miRBase 19)

organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae


title: BC014

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Washington Road

department: Geosciences

institute: Princeton University

organism: synthetic construct

distribution: non-commercial

manufacture_protocol:
1. The probe oligonucleotides are printed onto Corning Ultragaps or Erie Scientific Epoxy Silane slides using a DeRisi style arrayer (DiRisi et al., 1997) and pins from Parallel Synthesis.
2. The 70-mer oligo probes (Operon Technologies) were adjusted to a concentration of 0.05 mg ml-1 in 50% DMSO and were spotted on CMT-GAPS amino silane-coated glass slides (Corning, Corning, NY).
3. After printing, the slides were baked at 80°C for 3 h and stored in the dark at room temperature under slight vacuum in a dessicator.


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [Version 14]

city: Oslo

first: Sandra

last: Jernström

address: Ullernchausséen 70

department: Genetics

country: Norway

institute: OUS The Norwegian Radium hospital

relation: Alternative to: GPL570 (Alternative CDF [official])

manufacture_protocol: see manufacturer's protocol


title: NimbleGen human hg19 chromosome X tiling array [100331_HG19_HB_ChIP_HX1]

first: Chandr

middle: Sekhar Reddy

last: Chilamakuri

address: Fådveien 15

department: Tumor Biology

institute: The Norwegian Radium Hospital

description:
Custom microarray containing specific tiled regions encompassing 99.2 Mb of the human X chromosome.
Annotation in this record is based on the Human Genome Reference Consortium GRCh37 build (UCSC hg19).
Native array description file: 100331_HG19_HB_ChIP_HX1.ndf
Native array description file: 100331_HG19_HB_ChIP_HX1.pos

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


title: Agilent-043871 9q_others

status: Public on Jan 29 2015

city: Houston

first: James

last: Lupski

address: One Baylor Plaza, 604B

institute: Baylor College of Medicine

description:
Arrays of this design have barcodes that begin with 16043871 or 2543871.

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-041162 Chr6q_10q_14q

description:
Arrays of this design have barcodes that begin with 16041162 or 2541162.

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 mouse mm9 chromosome X tiling array [100331_MM9_HB_ChIP_HX1]

organism: Mus musculus

description:
Custom microarray containing specific tiled regions encompassing 93.84 Mb of the mouse X chromosome.
Annotation in this record is based on NCBI mouse build 37 (MGSCv37; UCSC mm9).
Native array description file: 100331_MM9_HB_ChIP_HX1.ndf
Native array description file: 100331_MM9_HB_ChIP_HX1.pos


title: Illumina HiSeq 2500 (Citrus junos)

organism: Citrus junos


title: Agilent-049577 Chicken gg_v2_60k 026441 [Probe Name Version]

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

institute: Wageningen UR

organism: Gallus gallus

description: Arrays of this design have barcodes that begin with 16049577 or 2549577.


title: Agilent-049577 Chicken gg_v2_60k 026441 [Feature Number Version]

description:
Arrays of this design have barcodes that begin with 16049577 or 2549577.

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: AB 5500xl Genetic Analyzer (Medicago truncatula)

status: Public on Jan 27 2015

organism: Medicago truncatula


title: AB SOLiD System 3.0 (Takifugu rubripes)

status: Public on Jan 28 2015

organism: Takifugu rubripes


title: miRCURY LNA Universal RT microRNA PCR mouse and rat panel I, V1.M

city: Louisville

first: Douglas

last: Darling

state: KY

address: 501 S. Preston St.

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

organism:
Mus musculus
Rattus norvegicus

technology: RT-PCR

description: PCR assay

manufacture_protocol: see manufacturer's website


title: Agilent-042708 Eohaustorius estuarius EE_Microarray_DV (Probe Name version)

status: Public on Jan 26 2015

city: Costa Mesa

first: Alvine

middle: C

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

institute: Southern California Coastal Water Research Project

organism: Eohaustorius estuarius

description: AMPHIPODS

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


title: Illumina HiSeq 2000 (Papilio machaon)

organism: Papilio machaon


title: Agilent-042708 Eohaustorius estuarius EE_Microarray_DV (Feature Number version)

description:
AMPHIPODS

Arrays of this design have barcodes that begin with 16042708 or 2542708.

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 HiSeq 2000 (Papilio xuthus)

organism: Papilio xuthus


title: 090918_Vitus_exp_HX12

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

organism: Vitis vinifera

description:
145868 probes / chamber.Several different probes / gene.

A different version of this platform with the SEQ_ID in the ID column is assigned accession number GPL18213.

first: Massimo

last: Delledonne

first: Sandrine

last: Balzergue


title: 100718_Populus_135K

organism: Populus sp.

description: 146170 probes corresponding to 49475 UniGen


title: Combimatrix B. thuringiensis sv konkukian str. 97-27 4.5k array

city: Cremona

first: Daniela

last: Bassi

state: CR

address: via Milano 24

department: Istituto di Microbiologia

country: Italy

institute: Università Cattolica del Sacro Cuore

organism: [Bacillus thuringiensis] serovar konkukian str. 97-27

description:
Combimatrix Bacillus cereus sensu latu group germination and outgrowth in food model
Complete genome sequence of B. thuringiensis sv konkukian str. 97-27 (NCBI Reference Sequence: NC_005957.1) was chosen for its high homology with B. cereus s.l. UC10070, to design probes corresponding to 5,197 genes spotted in duplicates onto ElectraSenseH 12K microarrays chip.

manufacturer: Università Cattolica del Sacro Cuore, Piacenza and Cremona, Italy

manufacture_protocol: Probes are directly synthesized on a 12k Combimatrix array by an in situ oligo synthesis system developed by Combimatrix Corporation (Mukilteo, USA) using the Combimatrix CustomArray synthesizer. Standard synthesis protocol provided by Combimatrix was used. See manufacturer's website at http://www.combimatrix.com/docs/


title: 121018_Medicago_trun

description: Design:- Sens: Reverse - Triplicate- 1 oligo/target sequence

first: Pascal

last: Gamas

first: Jerome

last: Gouzy


title: LC_MRA-1013-miRPig_20 (miRNA_ID version)

status: Public on Jan 24 2015

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism: Sus scrofa

description:
LC_MRA-1013-miRPig_20
based on miRBase version 20

manufacture_protocol: Pig miRNA microarray with 100% coverage of mature pig miRNAs listed in miRBase version 20. Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes are made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: Illumina HiSeq 2500 (Picea abies)

status: Public on Jan 23 2015

last: GEO

organism: Picea abies


title: Agilent-033934 nONCOchip_2.0_26042011

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

organism: Homo sapiens

description:
nONCOchip_2.0 design containing all custom probes, Agilent lincRNA probes, and Agilent mRNA probes (design id 026652).

Arrays of this design have barcodes that begin with 16033934 or 2533934.

The nONCOchip 2.0, a custom expression microarray, allows to facilitate the analysis of expression changes of disease-associated long non-coding RNAs in parallel with protein-coding genes (human genome version GRCh37/hg19). It comprises 913.413 probes of 60 base pairs each. In overall, 65% of probes correspond to long non-coding RNAs, while the remaining probes correspond to protein-coding mRNAs (20%) and regions antisense to 5’ or 3’ UTRs (11%). The nONCOchip 2.0 contains more than 160,000 probes (18%) for non-coding RNAs that are not available on any other commercial microarray platform. These probes represent RNAs that have been found to be controlled by major cancer-related pathways (controlled by oncogene Stat3, the tumor suppressor protein TP53 or by cyclins) and have been detected by transcriptome-wide expression variation studies utilizing Affymetrix Human Tiling Arrays (PMID 24594072). Further, the nONCOchip 2.0 covers a comprehensive set of known long non-coding RNAs retrieved from public databases as well as genomic regions with conserved secondary structure (identified by RNAz (PMID 15665081) or Evofold (PMID:16628248)).

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: Christian

last: Arnold

first: Katharina

last: Kasack

first: Friedemann

last: Horn

first: Jörg

last: Hackermüller


title: AB 5500xl Genetic Analyzer (Pseudo-nitzschia multiseries; Sulfitobacter sp. SA11)

status: Public on Jan 22 2015

organism:
Pseudo-nitzschia multiseries
Sulfitobacter sp. SA11


title: AB SOLiD 4 System (Pseudo-nitzschia multiseries; Sulfitobacter sp. SA11)


title: Exiqon, miRCURY LNA microRNA Array, 6th generation  - hsa, mmu & rno (hsa, mirbase 17)

city: HAIDARI

first: NIKOLAOS

last: SIAFAKAS

state: ATHENS

address: 1, RIMINI STR.

department: CLINICAL MICROBIOLOGY

country: Greece

institute: ATTIKON UNIVERSITY HOSPITAL

organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

description: gal_208400,208401,208402,208420,208421,208422_lot34010-34010_hsa-and-related-vira_from_mb170,miRPlus.gal

manufacture_protocol: See manufacturers website


title: Exiqon, miRCURY LNA microRNA Array, 7th generation - hsa, mmu & rno (mirbase 19.0)

organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

description: gal_208500,208501,208502,208510_lot35016-35016_hsa-and-related-vira_from_mb190,miRPlus_6gen_probes.gal


title: AB 5500xl Genetic Analyzer (Sulfitobacter sp. SA11)

organism: Sulfitobacter sp. SA11


title: Agilent-015520 Custom wheat 38k array [Probe Name Version]

city: Yokohama

first: Yeonju

last: Jung

state: Kanagawa

address: Maioka-cho 641-12

department: Yokohama City University

country: Japan

institute: Kihara Institute for Biological Research

organism: Triticum aestivum

first: Yasunari

last: Ogihara

first: Keiichi

last: Mochida

first: Kanako

last: Kawaura

manufacture_protocol: see manufacture's web site


title: Macrogen Human BAC clone MacArray Karyo4000

city: Suwon

first: Jaeyoun

last: Cheong

address: 164 Worldcup-ro

country: South Korea

institute: Ajou University School of Medicine

technology: spotted DNA/cDNA

description:
BAC clone Chip
Platform table annotations based on NCBI build 36 (genomic build hg 18)

manufacture_protocol: See manufacturer's protocols


title: Agilent-047931 Listeria monocytogenes 15K array Lmo0503

city: Majadahonda

first: Victoria

last: López-Alonso

address: Crta Majadahonda Pozuelo km 2

department: Computational Biology

country: Spain

institute: Institute of Health Carlos III

organism: Listeria monocytogenes

description:
Microarray L. monocytogenes para serotipo 1/2a food

Arrays of this design have barcodes that begin with 16047931 or 2547931.

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-037962 Campylobacter jejuni subsp. jejuni NCTC 11168 8X15K Microarray (Probe Name version)

city: shanghai

first: qian

last: jin

address: libing road

country: China

institute: MSP

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819


title: Illumina HiSeq 2500 (Raphanus sativus)

status: Public on Jan 21 2015

organism: Raphanus sativus


title: Illumina HiSeq 2000 (Crocus sativus)

status: Public on Jan 20 2015

organism: Crocus sativus


title: Illumina NextSeq 500 (Plasmodium berghei ANKA)

organism: Plasmodium berghei ANKA


title: Illumina HiScanSQ (Bos indicus)

organism: Bos indicus


title: Illumina HiSeq 2000 (Influenza A virus (A/WSN/1933(H1N1)))

organism: Influenza A virus (A/WSN/1933(H1N1))


title: Illumina MiSeq (Typha angustifolia)

status: Public on Jan 19 2015

organism: Typha angustifolia


title: [CanGene-1_0-st] Canine Gene 1.0 ST Array [cangene10st_Cf_ENTREZG v18]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Canis lupus familiaris

description:
This is identical to GPL17403 but a custom CDF environment was used to extract data.
CDF can be downloaded from the Brainarray site:
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/entrezg.asp

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 2500 (Aedes aegypti)

status: Public on Jan 16 2015

organism: Aedes aegypti


title: Fluidigm 48x48 Dynamic Array Chip for Mouse Gene Expression

city: Pittsburgh

first: Guang

last: Li

state: PA

address: 530 45th St. 8116 Rangos Research Center

department: Developmental Biology

institute: University of Pittsburgh

organism: Mus musculus

description:
PCR assay
Microfluidic-based quantifciation of genes expression


title: AB 5500xl Genetic Analyzer (Shewanella oneidensis MR-1)

organism: Shewanella oneidensis MR-1


title: AB SOLiD 4 System (Shewanella oneidensis MR-1)


title: Illumina HiSeq 2000 (Pseudomonas putida)

status: Public on Jan 15 2015

organism: Pseudomonas putida


title: Illumina Genome Analyzer (Oryza sativa Japonica Group)

organism: Oryza sativa Japonica Group


title: Illumina HiSeq 2000 (Deinococcus radiodurans R1)

status: Public on Jan 14 2015

organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539


title: Illumina HiSeq 2000 (Acinetobacter baumannii)

status: Public on Jan 13 2015

organism: Acinetobacter baumannii


title: Illumina HiSeq 2000 (Hypsibius dujardini)

organism: Hypsibius dujardini


title: Illumina HiSeq 2000 (Coturnix japonica)

organism: Coturnix japonica


title: Illumina HiSeq 2000 (Platynereis dumerilii)

organism: Platynereis dumerilii


title: Illumina MiSeq (Bos taurus)

organism: Bos taurus


title: Illumina HiSeq 2000 (Ustilago maydis)

organism: Mycosarcoma maydis


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: mogene10stv1_71_020]

city: Innsbruck

first: Tatsiana

last: Aneichyk

state: - Please choose -

address: Innrain 80/82

department: Molecular Pathophysiology

country: Austria

institute: Medical University Innsbruck

manufacture_protocol: This is identical to GPL6246 but a custom cdf environment was used to extract data. The cdf can be found at the link below.


title: Illumina HiSeq 2000 (Serpula lacrymans)

status: Public on Jan 12 2015

last: GEO

organism: Serpula lacrymans


title: Illumina HiSeq 1500 (Macaca fuscata)

status: Public on Jan 09 2015

organism: Macaca fuscata


title: Illumina HiSeq 2000 (Jaapia argillacea)

organism: Jaapia argillacea


title: Illumina HiSeq 2000 (Hydnomerulius pinastri)

organism: Leucogyrophana pinastri


title: Illumina HiSeq 2000 (Laccaria bicolor)

organism: Laccaria bicolor


title: Illumina HiSeq 2500 (Mus musculus castaneus)

organism: Mus musculus castaneus


title: Illumina HiSeq 2000 (Coniophora puteana)

organism: Coniophora puteana


title: Illumina HiSeq 2000 (Piromyces sp. Finn)

organism: Piromyces finnis


title: Exiqon mouse PCR panel

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

organism: Mus musculus


title: Agilent-019647 Kogan-custom-mouse1 014868 array (Feature Number version)

city: San Francisco

first: Andrea

middle: J

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

description:
Kogan custom mouse array v1
Arrays of this design have barcodes that begin with 16019647 or 2519647.
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 (Piromyces sp. Finn)


title: NimbleGen Mouse 2.2M array [110316_MM9_CHARM_HX1]

status: Public on Jan 06 2015

city: Baltimore

first: Andrew

middle: P

last: Feinberg

state: Maryland

address: 855 N Wolfe St

department: Department of Medicine

institute: Johns Hopkins School of Medicine

description: Annotation based on MM9.

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


title: Illumina HiSeq 2000 (Gossypium barbadense)

organism: Gossypium barbadense


title: Illumina MiSeq (Macaca fascicularis)

organism: Macaca fascicularis


title: QuantiGene 2.0 Multiplex Assay [Custom Mouse Panel]

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

technology: other

description: The QuantiGene Plex 2.0 Assay is a hybridization-based assay using the xMAP® Luminex® magnetic beads and performed on 96-well plates. The assay is based on DIRECT quantification of the RNA targets using xMAP Luminex beads for multiplexing of 3 to 80 RNA targets and branched DNA (bDNA) signal amplification technology. On the first day the sample is lysed to release the RNAs, and incubated overnight with target specific probe sets panel. On the second day the signal amplification tree is build via sequential hybridization of PreAmplifier (PreAmp), Amplifier (Amp) and Label Probe (LP). Each amplification unit gives a 400 x signal amplification and there are six amplification units per target RNA copy leaning to a 2,400 x signal amplification per copy RNA. The signal is detected by adding SAPE substrate and using a Luminex instrument for the read out.

manufacture_protocol: see manufacturer's website (http://www.panomics.com/products/gene-expression/plex-2.0-assay/overview)


title: NimbleGen Human 4.3M array [110913_HG19_CHARM_EB_UX1]

organism: Homo sapiens

description: Annotation based on HG19.


title: Exiqon, 35016_hsa-and-related-vira_from_mb190,miRPlus_6gen_probes (mirbase 19.0)

status: Public on Jan 08 2015

city: Vedbaek

first: Michael

last: Thorsen

address: Skelstedet 16

institute: Exiqon

organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

first: Jorg

last: Krummheuer


title: [S12KCTNOa520614F] Custom Affymetrix Pseudomonas putida S12 Chip

city: Leiden

first: Johannes

middle: H.

last: de Winde

address: Rapenburg 70

institute: Universiteit Leiden

organism: Pseudomonas putida S12

description: Pseudomonas putida S12 080806

manufacture_protocol: see manufacturer's web site


title: Illumina Genome Analyzer IIx (Echinococcus canadensis)

organism: Echinococcus canadensis


title: Illumina HiSeq 2000 (Drosophila melanogaster; Drosophila virilis)

status: Public on Jan 05 2015

organism:
Drosophila melanogaster
Drosophila virilis


title: [hGlue1_0.r3] Custom Affymetrix Human Transcriptome Array

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description: This is a propietary array.


title: Illumina HiSeq 2000 (Selaginella moellendorffii)

organism: Selaginella moellendorffii


title: Illumina HiSeq 2000 (Schmidtea polychroa)

organism: Schmidtea polychroa


title: Agilent Custom Penaeus monodon (Black Tiger Shrimp) 8x60k

status: Public on Jan 02 2015

city: Chennai

first: Shekhar

middle: M

last: S

state: Tamil Nadu

address: 75, Santhome High Road, R.A.Puram

department: Genetics and Biotechnology

country: India

institute: Central Institute of Brackishwater Aquaculture

organism: Penaeus monodon

description: designed by Genotypic Technology Private Limited (AMADID: 041733)


title: Xanthomonas oryzae pv. oryzicola (AMADID-041087) Genotypic Technology Pvt. Ltd. 8x15k Array

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

organism: Xanthomonas oryzae pv. oryzicola


title: Qiagen Mouse Cytokine and Chemokines RT2 profiler PCR array (PAMM-150Z)

status: Public on Jan 01 2015

city: Stanford

first: Hui

last: Zhao

state: California

address: 300 Pasture Drive

department: Pediatrics

institute: Stanford University


title: Medicago truncatula (Mt3.5) NimbleGen 12x135K

city: Dijon

first: Leonardo

last: Casieri

address: 17, rue Sully

institute: INRA

organism: Medicago truncatula

description: NimbleGen design name NimbleChip_HX12, 120621_Mtruncatula_DVT_exp.  A 1:2 expression design for 30,677 genes from Medicago truncatula annotated genome (Mt3.5) with four 60-mer probe pairs (PM/MM) per gene. The design includes random GC and other control probes.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: Agilent-034518 Ruditapes philippinarum 15K v2

city: Stony Brook

first: Bassem

last: Allam

state: NY

address: School of Marine and Atmospheric Sciences

institute: Stony Brook University

organism: Ruditapes philippinarum

description:
Second R.philippinarum oligoarray

Arrays of this design have barcodes that begin with 16034518 or 2534518.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

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


title: Agilent-042949 4×44K Camellia sinensis Microarray

city: Hangzhou

first: Lu

last: Wang

state: Zhejiang

address: 9th, South Meiling Road

institute: Tea Research Institute, Chinese Academy of Agricultural Sciences

organism: Camellia sinensis

description:
Arrays of this design have barcodes that begin with 16042949 or 2542949.
a 44K custom oligo microarray using 454 pyrosequencing data for large scale gene expression analysis in tea plant (Camellia sinensis)
"Gene name" and "definition" was added to the probes which could be aligned to known genes


title: Agilent-016517 17p

status: Public on Nov 01 2014

city: Houston

first: James

last: Lupski

address: One Baylor Plaza, 604B

institute: Baylor College of Medicine

description:
Covering: 1-22100000

Arrays of this design have barcodes that begin with 16016517 or 2516517.

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 Equine 385k custom ChIP array [090728_Eq_SP_ChIP]

city: Bologna

first: Stefania

last: Purgato

address: via Selmi 3

department: Pharmacy and Biotechnology

institute: University of Bologna

organism: Equus caballus

description:
Genome build: Sep. 2007 (Broad/equCab2)
090728_Eq_SP_ChIP.ndf
090728_Eq_SP_ChIP.pos
090728_Eq_SP_ChIP.gff


title: Agilent-052909 CBC_lncRNAmRNA_V3 (Probe Name version)

city: Beijing

first: Qingsheng

last: Yu

address: No 2, East Yinghua Rd, Chaoying District

institute: China-Japan Friendship Institute of Clinical Medical Sciences

description:
Arrays of this design have barcodes that begin with 16052909 or 2552909.
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 probe name.
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: Wanshou

last: Guo

first: Ping

last: Li


title: Roche Nimblegen Fusarium graminearum 135K microarray

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

institute: GreenGene Biotech Inc.

organism: Fusarium graminearum


title: Exiqon miRCURY LNA array 6th gen - hsa, mmu & rno miRBASE version 16.0

city: New York

first: Eva

last: Hernando-Monge

address: 550 1st Ave. Smilow 305

institute: NYU Langone Medical Center

organism: synthetic construct


title: Exiqon miRCURY LNA array version 11.0 miRBASE version 14.0


title: [HT_HG-U133_Plus_PM] Affymetrix HT HG-U133+ PM Array Plate [CDF: HTHGU133PlusPM_Hs_ENTREZG_v15.1.0]

status: Public on Oct 17 2014

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

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
This platform is identical to GPL13158 but a custom cdf environment was used to extract data.

relation: Alternative to: GPL13158 (official platform)


title: Chrysanthemum 135k microarray

organism: Chrysanthemum

description:
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf file is linked below as supplementary files.
120306_Chrysanthemum_GK_expr.ndf
120306_Chrysanthemum_GK_expr_HX12.ncd


title: IRHS_ARyANE_v1 [110411_Mdom_JPR_exp]

status: Public on May 20 2014

city: Beaucouzé

first: Jean-Marc

last: Celton

address: 42 rue Georges Morel

institute: INRA-IRHS

organism: Malus domestica

description:
A dataset of 57,386  quality-filtered predicted unigenes were submitted for probe design and production of the high-density microarray. Two oligoprobes were selected for each sequence, one on the sense strand and one on the anti-sense strand, based on highest hybridization specicifity. The IRHS_ARyANE_v1.0 chip contains a total of 126,022 probes for sense and antisense predicted coding genes and microRNA genes. Annotation is based on the v1.0 apple genome version, MalDomGD1.0.

designname: 110411_Mdom_JPR_exp
designid: 551261

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


title: Illumina HiSeq 2500 (Magnaporthe oryzae)

status: Public on Apr 28 2014

last: GEO

organism: Pyricularia oryzae


title: Agilent-041487 FZ_IBG1_4plex

status: Public on Jan 01 2014

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

organism:
Gluconobacter oxydans
Escherichia coli
Corynebacterium glutamicum
Bacillus subtilis subsp. subtilis str. 168

description:
synthesized oligonucleotides
Based on Corynebacterium glutamicum (NC_006958), Bacillus subtilis str. 168 (NC_000964), Gluconobacter oxydans (NC_006677, NC_006672, NC_006673, NC_006674, NC_006675, NC_006676), Escherichia coli (NC_000913)

manufacturer: Agilent Technologies (Waldbronn, Germany)

manufacture_protocol: see Agilent Technologies


title: NimbleGen Trichoderma reesei Whole Genome array CBS999.97 4x72K  [probe ID verson]

status: Public on Dec 01 2014

city: Taipei

first: Ting-Fang

address: Academia Sinica. 128 Sec. 2, Academia Rd

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

organism: Trichoderma reesei

description: Custom-designed oligonucleotide array by Roche-NimbleGen based on Trichoderma reesei CBS999.97 genome sequence using the 4 x 72000 fromation.  NimbleGen design ID: 568061


title: [CanGene-1_0-st] Canine Gene 1.0 ST Array [transcript (gene) version]

status: Public on Jul 03 2013

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Canis lupus familiaris

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

CanGene-1_0-st-v1.na33.3.canfam2.transcript.csv
#%create_date=Wed May  1 12:11:05 2013 PDT
#%chip_type=CanGene-1_0-st-v1
#%lib_set_name=CanGene-1_0-st
#%lib_set_version=v1
#%genome-species=Canis familiaris
#%genome-version=canfam2
#%genome-version-ucsc=canfam2
#%genome-version-create_date=2005-05-00
#%genome-lifted-method=NONE
#%genome-lifted_from-species=Canis familiaris
#%genome-lifted_from-version-ucsc=canfam2
#%netaffx-annotation-date=2012-09-15
#%netaffx-annotation-netaffx-build=33


title: Illumina HiSeq 2500 (Macaca nemestrina)

status: Public on Jan 04 2015

organism: Macaca nemestrina


title: FhG_IGB_MBT Candida albicans oligo array V1

status: Public on Jul 15 2011

city: Stuttgart

first: Steffen

last: Rupp

address: Nobelstr. 12

department: MBT

institute: Fraunhofer IGB

organism: Candida albicans SC5314

manufacturer: Fraunhofer Institute for Interfacial Engineering and Biotechnology (Department Molecular Biotechnology)

first: Nicole

last: Hauser

first: Karin

last: Lemuth

manufacture_protocol:
1. Oligos (Operon Biotechnologies Custom Array-Ready Longmers, Eurofins MWG Operon, Ebersberg, Germany) are stored at -20°C in Genetix plates (Order. Nr. X6003). Each well contains 600 pmol of 55-70-mer oligos.
2. Allow plates to reach room temperature.
3. Centrifuge oligo plates at 200 g for 2 min.
4. Remove sealing foil and resuspend oligos in 12 µL 3*SSC/1.5 M Betain to 50 µM (working concentration 50 pmol/µL).
5. Centrifuge oligo plates covered with plate lids at 200 g for 2 min.
6. Place in appropriate location of biobank and start print run.
7. Oligos are printed on epoxy coated glass slides (Schott, Jena, Germany) using the Microgrid II robot of Biorobotics (DigiLab Inc., Holliston, USA) by spotting 6,400 oligonucleotides in duplicate including 10 lambda oligonucleotide DNA positive controls. SMP3 pins (Arrayit Corporation, Sunnyvale, CA) are used for spotting.
8. After the print run is completed, allow plates to dry through passive evaporation in a protected environment.
9. For each subsequent preparation of these plates for a print run, add 12 µL water to the wells instead of 3*SSC/1.5 M Betain.
10. After the spotting process, probes were immobilized on glass slides by incubation at room temperature for 30 min at high humidity (> 80 %) and adjacent drying at 80°C for 120 min. DNA-microarrays were stored under argon atmosphere in an exsiccator until used.
11. For data analysis, a gal file was produced using the TAS Application Suite software version 2.7.1.18 from Genomic Solutions.


title: NimbleGen Arabidopsis thaliana 4x72K Array

status: Public on Sep 21 2010

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Arabidopsis thaliana

description:
Gene Expression array
Format: 4x72K
Source: TAIR
Build: 6.0
Probe Length: 60mer
Design Name: ATH6 60mer expr X4
Genes: 30,361
Probes/ Target: 2
Replicates: 1
FEAT_TYPE: transcript

The Platform data table reflects a condensed, gene-level representation of the array.

NimbleGen description files linked below:
ATH6_60mer_expr.ndf
ATH6_60mer_expr.ngd


title: LC_miRMouse_10.0_070802-MA1002 (miRNA ID version)

status: Public on May 24 2011

first: Christoph

last: Eicken

state: TX

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 10.0

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: HOMIM-441-v01.09

status: Public on Sep 17 2011

city: Cambridge

first: Jorge

last: Frias-Lopez

state: MA

address: 245 First street

institute: Forsyth Institute

organism: Bacteria

description: Human Oral Microbe Identification Microarray (HOMIM)

manufacturer: Michigan State University Research Technology Support Facility

manufacture_protocol: 16S rRNA-based oligonucleotide reverse capture probes were custom synthesized with a 5’-(C6)-amine modified base, eight spacer thymidines and 18 to 20-nucleotides of target sequence, and printed on 25 x 76 mm aldehyde-coated glass slides


title: Agilent-037331 Copy_of_C. albicans assembly 21_017942 [ORF name version]

status: Public on Aug 21 2012

city: Lausanne

first: Dominique

last: Sanglard

address: Rue Bugnon 48

country: Switzerland

institute: University of Lausanne and University Hospital Center

organism: Candida albicans

manufacture_protocol: Oligonucleotides were designed the 27th of October 2007 according with the latest Candida albicans annotation from CGD (http://www.candidagenome.org) assembly 21, using eArray from Agilent Technology (Design ID 037331). Each of 6101 open reading frames is represented by two oligonucleotides probes. Mitochondrial genes are indicated by the prefix CaalfMp. The probes were used to generate custom microarrays in a 4x44 K format with a randomized layout.


title: Agilent-019015 HD CGH Microarray (2X105K) Oxford design AMADID#019015 (Feature number version)

status: Public on Apr 18 2010

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

organism: Homo sapiens

first: B

last: Ylstra

first: PP

last: Eijk


title: Agilent-015520 Custom wheat 38k array

status: Public on Dec 19 2009

city: Yokohama

first: Kanako

last: Kawaura

address: Maioka-cho 641-12

institute: Kihara Institute for Biological Research, Yokohama City University

organism: Triticum aestivum

first: Yasunari

last: Ogihara

first: Keiichi

last: Mochida


title: [BacEubMsa520350F] Affymetrix Human gut microbiota community GeneChip

status: Public on Jul 08 2008

city: Ann Arbor

first: Eric

middle: Charles

last: Martens

state: MI

address: 1150 West Medical Center Drive

department: Dept. of Microbiology and Immunology

institute: University of Michigan Medical School

organism:
Bacteroides thetaiotaomicron
Phocaeicola vulgatus
Parabacteroides distasonis
Methanobrevibacter smithii
Lachnospira eligens
Agathobacter rectalis

description: The probeSequence and CDF files are linked below as supplementary files.

first: Michael

last: Mahowald

first: Elizabeth

last: Hansen

first: Jeffrey

last: Gordon

manufacture_protocol: in situ oligonucleotide synthesis using photolithography


title: Illumina HumanCNV370-QuadV3 DNA Analysis BeadChip (HumanCNV370-QuadV3_C)

status: Public on Jun 23 2008

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

description: features more than 380,000 markers, including more than 320,000 uniformly distributed tag SNPs

manufacture_protocol: See manufacturer's website


title: Illumina HiSeq 2500 (synthetic construct)

status: Public on Jan 06 2015

last: GEO


title: Illumina Human1M-Duov3 DNA Analysis BeadChip (Human1M-Duov3_B)

description: over one million markers to interrogate human genetic variation using single nucleotide polymorphisms (SNPs) and copy number variation (CNV) probes


title: Streptococcus pneumoniae, multi strain 7k version7 (full layout)

status: Public on Feb 01 2008

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

organism: Streptococcus pneumoniae

technology: mixed spotted oligonucleotide/cDNA

last: de Jong

manufacture_protocol: ArrayIt superamine slides spotted with a Genpak-array21 spotter.


title: ENS SGDB Saccharomyces cerevisiae 15k_v1.0

status: Public on Oct 29 2007

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

institute: École normale supérieure

organism: Saccharomyces cerevisiae

description:
Yeast expression arrays designed using duplicated probes for each gene.
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: Frederic

last: Devaux

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


title: [Hs_PromPR] Affymetrix Human Promoter 1.0R Array

status: Public on Apr 13 2007

last: Affymetrix

description:
The GeneChip® Human Promoter 1.0R Array is designed for chromatin immunoprecipitation (ChIP) experiments. The Human Promoter Array is a single array comprised of over 4.6 million probes tiled through over 25,500 human promoter regions. Sequences used in the design of the Human Promoter array were selected from NCBI human genome assembly (Build 34). Repetitive elements were removed by RepeatMasker. Promoter regions were selected using sequence information from:

35,685 ENSEMBL genes (version 21_34d, May 14, 2004)
25,172 RefSeq mRNAs (NCBI GenBank®, February 7, 2004)
47,062 complete-CDS mRNA (NCBI GenBank, December 15, 2003)

Probes are tiled at an average resolution of 35 bp, as measured from the central position of adjacent 25-mer oligos, leaving a gap of approximately 10 bp between probes. Each promoter region covers approximately 7.5 kb upstream through 2.45 kb downstream of 5' transcription start sites. For over 1,300 cancer-associated genes, coverage of promoter regions was expanded to include additional genomic content. This more extensive coverage spans from 10 kb upstream through 2.45 kb downstream of transcriptional start sites.

The array interrogates regions proximal to transcription start sites and contains probes for approximately 59 percent of CpG islands annotated by UCSC in NCBI human genome assembly (Build 34). The probes selected for the Human Promoter 1.0R Array are a subset of the probes used in the whole-genome ChIP array set, the GeneChip® Human Tiling 2.0R Array Set (P/N 900772).

BPMAP and other files can be downloaded from the Affymetrix Web site below.


title: [Poplar] Affymetrix Poplar Genome Array

status: Public on Sep 20 2006

organism: Populus sp.

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

In total, the Poplar Genome Array contains more than 61,000 probe sets representing over 56,000 transcripts and gene predictions.

This array was designed based on content from UniGene Build #6 (March 16, 2005) and from GenBank® mRNAs and ESTs for all Populus species up to April 26, 2005. Additional array design content was derived from the predicted gene set v1.1 from the Populus genome project (P. trichocarpa), led by the U.S. Department of Energy and based at the Joint Genome Institute (JGI), Walnut Creek, CA (download date May 4, 2005).


title: Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)

status: Public on Apr 27 2009

description: HumanMethylation27 DNA Analysis BeadChip allows researchers to interrogate 27,578 highly informative CpG sites per sample at single-nucleotide resolution. This 12-sample BeadChip features content derived from the well-annotated NCBI CCDS database (Genome Build 36) and is supplemented with more than 1,000 cancer-related genes described in published literature. Probe content has been enriched to deeply cover more than 150 well-established cancer genes known to show differential methylation patterns. HumanMethylation27 BeadChip content also targets the promoter regions of 110 miRNA genes.