title: Agilent-019738 Custom 8 X 15k Exon Microarray

status: Public on May 31 2013

city: Stanford

first: Craig

middle: Patrick

last: Giacomini

state: CA

address: 269 Campus Drive (CCSR 3245A)

department: Pathology

country: USA

institute: Stanford University

organism: Homo sapiens

technology: in situ oligonucleotide

description:
Agilent-019738 Custom 8 X 15k exon microarray interrogating a set of genes previously known to form oncogenic gene fusions in human cancer.
Sureprint Technology (60mer oligonucleotide)

distribution: custom-commercial

manufacture_protocol: The custom microarray was manufactured by Agilent Technologies using a proprietary non-contact industrial inkjet printing process, in which oligo monomers are deposited uniformly onto specially-prepared glass slides. This in situ synthesis process prints 60-mer length oligonucleotide probes, base-by-base, from digital sequence files. The precise inkjet process enables the delivery of extremely small, accurate volumes (picoliters) of the chemicals to be spotted.  (Source: Agilent website)


title: UCSD, NimbleGen_E_coli_MG1655_371K Tiling_Array_2005 (gene version)

status: Public on Feb 04 2014

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

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

description: NimbleGen design name 2005-04-20_Palsson_Ecoli_ChIP, NimbleGen design ID 1881.  A tiling array design for Escherichia coli K12 MG1655 with 50-mer probe spaced 25bp apart across the genome.  This design also contains control probes.

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


title: UT Southwestern Saccharomyces cerevisiae Spotted ORF 7k Array

status: Public on Aug 26 2006

city: Houston

first: Kevin

middle: A

last: Morano

state: TX

address: 6431 Fannin St, MSB 1.300

department: Microbiology and Molecular Genetics

institute: UT Medical School at Houston

organism: Saccharomyces cerevisiae

technology: spotted DNA/cDNA

distribution: non-commercial

first: Anwu

last: Zhou

manufacture_protocol: PCR products deposited upon glass slide


title: Agilent-037303 Canis familiaris miRNA array (miRNA version)

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

organism: Canis lupus familiaris

description: Arrays of this design have barcodes that begin with 16037303 or 2537303.

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


title: RayBiotech Mouse Cytokine Antibody Array 2

city: Shanghai

first: Qian-qian

last: Yin

state: Shanghai

address: No280, Chongqing South Road

country: China

institute: Shanghai Jiao Tong University School of Medicine

organism: Mus musculus

technology: antibody

manufacture_protocol: see manufacturer's website; http://www.raybiotech.com/antibody-array.html


title: Multiorganism In house printed microRNAExiqon LNA probes microarray v1

city: Roterdam

first: Maikel

last: Wouters

address: Dr. Molewaterplein 50

department: Genetics

country: Netherlands

institute: Erasmus Medical Center

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

technology: spotted oligonucleotide

manufacturer: Center for Biomics, Erasmus MC, CA Rotterdam

manufacture_protocol: The LNA-based capture probeset (Exiqon version 10,) was spotted on Nexterion E slides using a Virtek Chipwriter Pro


title: Homo sapiens in house printed microRNAExiqon LNA probes microarray v2

manufacture_protocol: The LNA-based capture probeset (Exiqon version 7) was spotted on Nexterion E slides using a Virtek Chipwriter Pro


title: Homo sapiens in house printed microRNAExiqon LNA probes microarray v1


title: NimbleGen_C.gla [2009-01-08_RDKK145_Cgla_60mer_expr]

city: Suzuka

first: Hironobu

last: Nakayama

state: Mie

address: 3500-3 Minami-Tamagaki Cho

department: Phamaceutical Science

country: Japan

institute: Suzuka University of Medical Science

organism: Nakaseomyces glabratus

description:
Design ID: 8878; Species: Candida glabrata CBS 138; Data Source:; Database site NCBI; Database name Refseq; Version/Revision; URL; Released date 15-MAY-2008; Type of array: Eukaryotic Expression(4plex); Number of target: 5,217; Length of probes: 60 mer; Number of probes per target: 6 pair; Density: 1 in 2; Replicate: 1; Total number of probes: 62,604; Cutoff value: 1,000; Rocheｿs design ID: RDKK145; Design file name: 2009-01-08_RDKK145_Cgla_60mer_expr_X4; Notice: We set 9,300 random probes to fill empty spots.
native array description file: 2009-01-08_RDKK145_Cgla_60mer_expr.ndf
native array description file: 2009-01-08_RDKK145_Cgla_60mer_expr.ngd


title: Agilent-037303 Canis familiaris miRNA array (Agilent Feature Number version)

description:
Arrays of this design have barcodes that begin with 16037303 or 2537303.

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: Applied Biosystems Human MDR resistance in cancer TaqMan Low Density Array

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

country: Belgium

institute: University of Namur

technology: RT-PCR

description: TaqMan-based qRT-PCR assay

distribution: virtual

manufacture_protocol: see manufacturer's website


title: Rat Oligo chip 20k

status: Public on Oct 18 2013

city: Nagoya

first: Shugo

last: Suzuki

state: Aichi

address: 1 Kawasumi, Mizuho-Cho, Mizuho-Ku

department: Experimental Pathology and Tumor Biology

institute: Nagoya City University Graduate School of Medical Sciences

organism: Rattus norvegicus

description: Description

manufacture_protocol: See manufacturer's web site (http://www.3d-gene.com/)


title: Genopole Canis familiaris 21K cDNA microarray

manufacture_protocol: See manufacturer's website (www.genotoul.fr, genopole-toulouse.prd.fr/index.php?id=57).


title: Human Array MicroRNA Card A v2

status: Public on May 29 2013

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: part number 4398965

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


title: Illumina HiSeq 2000 (Condylura cristata)

last: GEO

organism: Condylura cristata

technology: high-throughput sequencing


title: Illumina Genome Analyzer II (Condylura cristata)


title: Illumina HiSeq 2000 (Yarrowia lipolytica)

status: Public on May 28 2013

organism: Yarrowia lipolytica


title: Illumina Genome Analyzer IIx (Yarrowia lipolytica)


title: AB SOLiD 4 System (Sinorhizobium meliloti 1021)

organism: Sinorhizobium meliloti 1021


title: Agilent-022058 R(D)SVS Yahaya_Ovis aries (Sheep) 15K v1.0 (Feature Number version)

status: Public on May 27 2013

city: Roslin

first: David

last: Collie

address: Easter Bush Veterinary Centre

country: United Kingdom

institute: The Roslin Institute & R(D)SVS

organism: Ovis aries

description:
The custom array was prepared using eArry from Agilent the final design ID was 022058 which was a compilation of design 019921 (original version of the sheep array form Agilent) and probes for the 7 genes listed above.
DesignID: 022058

manufacture_protocol:
www.agilent.com
The array used was a custom manufactured array from Agilent the array was based on the complete set of probes from the sheep array  design ID 019921 with 7 gene added to it, these were (gene name_target sequence) Keratin5_TC8502.f1, Keratin14_TC3860.f1, TubulinB_TC2191.f1, Keratin15_TC6677.f1, Sheep_Foxj1.f1, btFoxJ1_XM582255.f1 and TubulinB_TC453.f1. The probes were designed using the eArray program and added to the standard sheep design to produce a custom Agilent gene expression microarray.


title: Agilent-026176 Alcanivorax borkumensis SK2 (Feature Number version)

city: Frankfurt

first: Daniela

middle: Jasmin

last: Näther

address: Max-von-Laue-Str. 9

department: Molecular Biosciences

country: Germany

institute: Goethe University Frankfurt

organism: Alcanivorax borkumensis SK2

description:
Alcanivorax borkumensis SK2 Gene expression array
Arrays of this design have barcodes that begin with 16026176 or 2526176.
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 HiSeq 2000 (Rhodobacter sphaeroides 2.4.1)

organism: Cereibacter sphaeroides 2.4.1


title: Agilent-040193 Homo sapiens 15K v2

city: Madrid

first: Santiago

last: Rodriguez de Cordoba

state: Madrid

address: Ramiro de Maeztu, 9

department: Medicina Celular y Molecular

country: Spain

institute: Centro de Investigaciones Biologicas

description:
Arrays of this design have barcodes that begin with 16040193 or 2540193.

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.


status: Public on May 25 2013

first: Yiqun

last: Zhang

address: One Baylor plaza

institute: BCM

manufacture_protocol: The M.D. Anderson Cancer Center (MDACC) miRNA Expression Bioarrays are transcriptional profiling products designed to monitor the miRNA and other small non-coding RNA levels of multiple genes. The miRNA Expression Bioarrays utilize nucleic acid hybridization of a 52 biotin-labeled complementary cDNA target with DNA oligonucleotide probes attached to a gel matrix. The biotin-labeled cDNA targets are prepared by a simple reverse transcription into first strand cDNA. Total RNA is primed for reverse transcription by a random Octomer conjugated with two biotins and a 52 poly (A) tail. This procedure results in an equal copy number of biotin cDNA target to the templates of miRNA.


title: AB SOLiD 5500 (Schizosaccharomyces pombe)

organism: Schizosaccharomyces pombe


title: Illumina Genome Analyzer II (Symbiodinium sp. A1)

status: Public on May 24 2013

organism: Symbiodinium sp. A1


title: Illumina HiSeq 2000 (Symbiodinium sp. A1)


title: Agilent-020986 Streptomyces avermitilis MA-4680 microarray

city: Beijing

first: Ying

last: Wen

address: NO.2 Yuanmingyuanxi Road

department: college of biological sciences

institute: China Agricultural University

organism: Streptomyces avermitilis MA-4680 = NBRC 14893


title: miRCURY LNA microRNA Array, 6th generation - miRBase 16.0

city: Nashville

first: Chandravanu

last: Dash

state: TN

address: 1005 Dr. DB Todd Jr Blvd

department: Center for AIDS Health Disparities Research

institute: Meharry Medical College School of Medicine

distribution: commercial

manufacturer: Exiqon 6th generation (Lot #34001.03, miRBase16, Product 208401 Human)

manufacture_protocol: see Exiqon site


title: Illumina HiSeq 2000 (Xenorhabdus nematophila)

organism: Xenorhabdus nematophila


title: Illumina HiSeq 2000 (Avena sativa/Zea mays addition line)

status: Public on May 23 2013

organism: Avena sativa/Zea mays addition line


title: Illumina Genome Analyzer II (Avena sativa/Zea mays addition line)


title: DSL-H20K Human ChIP-on-chip Array

status: Public on May 22 2013

city: Xi'an

first: Wang

last: Simeng

address: Changle Road

department: Xijing Hospital of Digestive Diseases

institute: Fourth Military Medical University

organism: Homo sapiens


title: MAD-ECk12-1-Nimble-E135

city: Amsterdam

first: Nadine

last: Händel

address: Science Park 904

department: Swammerdam Institute for Life Sciences

institute: University of Amsterdam

organism: Escherichia coli

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


title: Human aggressivity cytokine loci tiling for ChIP (Agilent-021772; genome assembly hg18)

city: Montreal

first: Moshe

last: Szyf

state: Quebec

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

department: Pharmacology

country: Canada

institute: McGill University

manufacture_protocol: The oligonucleotide microarray is composed of 44K 45-60mer oligonucleotides from the Agilent's eArray ChIP probe database.


title: Agilent-035430 mouse miRNA array (miRNA_107_Sep09 miRNA ID version)

city: Memphis

first: Yong-Dong

last: Wang

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

organism: Mus musculus

description:
Annotation based on mirBase 17
alternative to GPL15547
Design ID: 035430
Microarray name: Mouse_8x60K-v17

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


title: Valencia yeast 3' 5' (384)

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

organism: Saccharomyces cerevisiae

description: Nylon macroarray (7 x 11 cm) with 768 positions: 754 single spotted of about 300 bp 3' or 5' ORF end region, plus 12 probes for rRNA controls and 2 empty spots.

manufacturer: Seccion de Chips de DNA-SCSIE (University of Valencia)

first: José

middle: E

last: Pérez-Ortín

last: García-Martínez

first: Alfonso

last: Rodrigríguez-Gil

first: Sebastían

last: Chávez

manufacture_protocol: See Rodríguez-Gil et al. (2010), Nucleic Acids Research Vol. 38 No. 14. pp. 4651-4664. PMID 20385590. doi: 10.1093/nar/gkq215.


title: Illumina HiSeq 2000 (Manihot esculenta)

organism: Manihot esculenta


title: Agilent-021886 Lactobacillus delbrueckii subsp. bulgaricus 2038 array (probe version)

status: Public on May 21 2013

first: Zhidong

last: zhu

address: 151# Libing road

institute: shanghai biochip Co.

description:
Arrays of this design have barcodes that begin with 16021886 or 2521886.

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 (Neisseria gonorrhoeae FA19)

status: Public on May 17 2013

last: GEO

organism: Neisseria gonorrhoeae FA19


title: Clostridium thermocellum ATCC 27405 HX12 array (3 x 720k array) [080724_C_thermo_27405_expr]

status: Public on May 16 2013

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

organism: Acetivibrio thermocellus ATCC 27405

description: Custom array


title: University of Padova Anguilla anguilla 8x15K v1.0

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

organism: Anguilla anguilla

description: Target sequences to be included in the European eel microarray were obtained from the assembly of a total of 640,040 sequence reads obtained by 454 sequencing. The array included all annotated sequences with a blast hit to vertebrates and invertebrates but excluding bacteria, virus, plants, fungi and protozoa. For 12,296 contigs, the putative orientation was unambiguous and a single probe was designed. For 1,390 contigs, the putative orientation was ambiguous and two probes were designed. In order to minimize assembler redundancy, 163 contigs differing by less than 3 nucleotide changes were discarded. The final number of probes was 14,913. Probe design was carried out using Agilent eArray Interface which applies proprietary prediction algorithms to design 60-mer oligoprobes. Microarrays were synthesized in situ using the Agilent ink-jet technology with an 8x15K format (8 arrays in a single slide). Each array contained default positive and negative controls.

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


title: Duke/RG_MycMaxMad_v1

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

description:
180K array. 36-bp probes.
In situ oligo synthesized array with proprietary synthetic sequences that target Myc/Max/Mad putative binding sites in a genomic context.
There are three categories of 36-bp sequences: 1) bound probes, 2) unbound probes (or negative controls), and 3) test probes. Bound probes correspond to genomic regions bound in vivo by c-Myc, Max, or Mad2 (ChIP-seq P < 10^(-10) in HeLaS3 or K562 celld (ENCODE)) that contain at least two consecutive 8-mers with universal PBM E-score > 0.4 (Munteanu and Gordan, LNCS 2013). All putative binding sites occurr at the same position within the probes on the array. “Unbound” probes correspond to genomic regions with ChIP-seq P < 10^(-10) and a maximum 8-mer E-score < 0.2. We also designed test probes that contain, within constant flanking regions, all nnCACGTGnn 10-mers and 18 nnnCACGTGnnn 12-mers (where n = A, C, G, or T). Each DNA sequence represented on the array is present in 6 replicate spots.

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


title: NimbleGen S.aureus USA300 FPR3757 12 x 135K array v1.0 [110204_Saureus_FPR3757_JK_exp]

status: Public on May 20 2013

city: Odense M

first: Mette

last: Thorsing

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

organism: Staphylococcus aureus subsp. aureus USA300_FPR3757

description: 12 x 135K expression array covering 2563 genes from Staphylococcus aureus USA300 FPR3757 (Genbank accession NC_007793) and three associated plasmids: pUSA01 (NC_007790.1), pUSA02 (NC_007791.1), and pUSA03 (NC_007792.1). Ten 60-mer probes per target, five replicates per array. Two exemplars, 39 sequences with no probes. Empty features filled with randomly generated probes of comparable G+C content and length. NimbleGen design name 110204_Saureus_FPR3757_JK_exp_HX12, NimbleGen design ID 548181.

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


title: GMRCL Human 7K ver 2

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

manufacturer: Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital

manufacture_protocol: cDNA microarrays were spotted using PCR products obtained with the Incyte Genomics. Spotters: Qarray Genetix, with split pins (ArrayIt Brand Products, ChipMaker CMP4). Double stranded DNA in Microarray Spotting Solution (Genetix, GSS-50) were binding to the UltraGAPS Coated slides (Corning), by UV-mediated crosslinking.


title: [PhyloChip] Affymetrix G3 PhyloChip

city: San Francisco

first: Ivan

last: Vujkovic-Cvijin

state: California

address: 1001 Potrero Ave, Bldg 3

institute: University of California, San Francisco

organism:
Bacteria
Archaea

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


title: Agilent-019029 MycAbs_Design2

status: Public on May 15 2013

city: Paris

first: Alexandre

last: Pawlik

address: 28 rue du Dr. Roux

country: France

institute: Institut Pasteur

organism: Mycobacteroides abscessus

description:
Arrays of this design have barcodes that begin with 16019029 or 2519029.

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: [P-putidaa530009N] Helmholtz Centre for Infection Research Pseudomonas putida 8K array

city: Munich

first: Jacek

last: Puchałka

address: Lindwurmstrasse 2a

department: University Children's Hospital

institute: Munich University Hospital

organism: Pseudomonas putida KT2440

description: The microarrays includes 7,781 probe sets: 5,338 representing 5,350 annotated genes or open reading frames (orfs), and 2,443 targeting intergenic regions.

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. For details see the publication under DOI: 10.1007/s00253-007-0914-z


title: AB SOLiD System 3.0 (Caulobacter vibrioides)

status: Public on May 14 2013

organism: Caulobacter vibrioides


title: Illumina Genome Analyzer (Propionibacterium acnes KPA171202)

status: Public on May 13 2013

organism: Cutibacterium acnes KPA171202


title: Illumina Genome Analyzer II (Pseudomonas syringae)

organism: Pseudomonas syringae


title: Illumina HiSeq 2000 (Pseudomonas syringae)


title: Applied Biosystems TaqMan Array Human microRNA A/B Cards v2.0

city: Columbus

first: Andrea

last: Vecchione

state: OH

address: 460W12th Ave

institute: The Ohio state University

description: PCR assay

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


title: Agilent-018392 Human Oligo Microarray (Feature Number version)

status: Public on May 10 2013

first: Irina

middle: Yurievna

last: Tcherepanova

address: 4233 Technology Drive

department: REsearch and Development

institute: Argos Therapeutics Inc.

description: The ID column represents the Agilent Feature Extraction feature number.


title: NimbleGen Sus scrofa 2.1M CGH array [120529_Sscr_10_2_WG_JH_CGH_HX1]

first: Huimin

last: Kang

state: Beijing

address: Beijing

institute: China Agriculture University

organism: Sus scrofa

description:
Annotation in this record based on NCBI Sscrofa 10.2
2.1M probes in total


title: Illumina HiSeq 2000 (Propionibacterium acnes KPA171202)

status: Public on May 09 2013


title: Illumina HiSeq 2000 (Spodoptera frugiperda)

organism: Spodoptera frugiperda


title: AB SOLiD 4 System (Schizosaccharomyces pombe)

organism: Schizosaccharomyces pombe


title: NCode Human miRNA microarray V3

city: Baltimore

first: Kenneth

middle: W

last: Witwer

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

organism: Homo sapiens

manufacture_protocol: See manufacturer's website


title: [LBL-Phy3b520660] Affymetrix PhyloChip G3 array

city: Fort Pierce

first: muqing

last: zhang

state: Florida

address: 2199 South Rock Road

institute: University of Florida

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


title: Agilent-015720 Mus musculus 15K

city: Taipei

first: Po-Ching

last: Cheng

address: 250 Wuxing St,

department: Department of Parasitology, College of Medicine

institute: Taipei Medical University

organism: Mus musculus

manufacture_protocol: see manufacturer's website


title: Applied Biosystems TaqMan Rodent MicroRNA Array A

city: Orlando

first: Zhenji

last: Gan

state: FL

address: 6400 Sanger Rd

institute: SBMRI

organism:
Mus musculus
Rattus norvegicus

description:
PCR assay
Standard TaqMan Assay

manufacture_protocol: See manufacturer's website.


title: Agilent-026867 Human miRNA Microarray_Hsa_Rel14_V5 (Probe Name version)

city: Seoul

first: Sanghyun

address: 599 Gwanak-ro, Gwanak-gu

department: Department of biology

institute: Seoul National University

description:
Arrays of this design have barcodes that begin with 16026867 or 2526867.

The ID column represents the Agilent Probe name.

Design ID: 026867

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


title: Applied Biosystems TaqMan Rodent MicroRNA Array B

description:
PCR assay
Standard TaqMan Assay


title: Agilent-037367 SALSIFY2 Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 15K

status: Public on May 08 2013

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description:
probe set for SL1344 genes and sRNAs

Arrays of this design have barcodes that begin with 16037367 or 2537367.

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 (Escherichia coli str. K-12 substr. MG1655)

last: GEO


title: Illumina HiSeq 2000 (Thalassiosira pseudonana)

status: Public on May 07 2013

organism: Thalassiosira pseudonana


title: Illumina HiSeq 2000 (Citrus sinensis)

organism: Citrus sinensis


title: 101206_Barley_NS_CGH_HX1

city: Saint Paul

first: María

last: Muñoz-Amatriaín

state: MN

address: 411 Borlaug Hall, 1991Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

organism: Hordeum vulgare subsp. vulgare

description:
Annotation in this record based on whole genome shotgun (WGS) assembly of barley cv. Morex (Assembly1, EMBL-EBI accession no. PRJNA30763).
Probes designed to 200 bp contigs where 10 non-repetitive and unique probes could be design. Contigs at minimum spacing of 500 bp apart.


title: Illumina HiSeq 2000 (Cyanidioschyzon merolae)

organism: Cyanidioschyzon merolae


title: Illumina HiSeq 2000 (Micromonas pusilla)

organism: Micromonas pusilla


title: Illumina HiSeq 2000 (Ostreococcus 'lucimarinus')

organism: Ostreococcus sp. 'lucimarinus'


title: Illumina HiSeq 2000 (Fragilariopsis cylindrus)

organism: Fragilariopsis cylindrus


title: Illumina HiSeq 2000 (Emiliania huxleyi)

organism: Emiliania huxleyi


title: Illumina HiSeq 2000 (Phaeodactylum tricornutum)

organism: Phaeodactylum tricornutum


title: Illumina HiSeq 2000 (Aureococcus anophagefferens)

organism: Aureococcus anophagefferens


title: Illumina HiSeq 2000 (Cryptococcus neoformans var. grubii)

organism: Cryptococcus neoformans


title: NimbleGen Tribolium castaneum Whole-genome Tiling Array Set (2 of 3)

status: Public on May 06 2013

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

organism: Tribolium castaneum

description: This is a Red flour beetle (Tribolium castaneum) whole-genome tiling array set (2 of 3) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen.

first: John

last: Colbourne

first: Jeong-Hyeon

last: Choi


title: Agilent-015028 Mouse Genome CGH Microarray 4x44K (Probe Name version)

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies


title: IBMT Campylobacter jejuni alanine scan [2]

city: Potsdam

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

department: Bioanalytics and Biosensorics

institute: Fraunhofer Institute for Cell Therapy and Immunology

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

technology: spotted peptide or protein

description: Campylobacter jejuni NCTC 11168 cj0669 protein

manufacture_protocol: Pepstar peptide microarrays (JPT)


title: Illumina Genome Analyzer (Trichoderma reesei)

organism: Trichoderma reesei


title: NimbleGen Tribolium castaneum Whole-genome Tiling Array Set (3 of 3)

description: This is a Red flour beetle (Tribolium castaneum) whole-genome tiling array set (3 of 3) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen.


title: NimbleGen Tribolium castaneum Whole-genome Tiling Array Set (1 of 3)

description: This is a Red flour beetle (Tribolium castaneum) whole-genome tiling array set (1 of 3) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen.


title: Illumina HiSeq 2000 (Coffea canephora)

status: Public on May 03 2013

organism: Coffea canephora


title: IBMCP_Tomato_12160_v1.0 (TOM2)

city: Norwich

first: Andreas

last: Magusin

address: Norwich Research Park

department: Crop Genetics

institute: John Innes Centre

organism: Solanum lycopersicum

manufacturer: Genomics Facility at Instituto de Biología Molecular y Celular de Plantas

manufacture_protocol:
The IBMCP_Tomato_12160_v1.0 contains the Array-Ready Oligo Set (AROS) for the tomato genome version 1.0 (Operon Biotechnologies, Inc).
This oligo set contains 12,160 oligos representing 11,862 genes from tomato. Oligos were mostly designed from gene transcript sequences from the Lycopersicon Combined Build#3 unigen database from the Cornell University and a remaining number of oligos were designed from sequences from GenBank.
Oligos were spotted on UltraGAPS coated slides (Corning, Tewksbury MA, USA) using a BioRobotics MicroGrid II arrayer.


title: Agilent 4X44K Aplysia Annotated EST whole-genome array [Probe Name version]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Aplysia californica

description: The array contains 44k 60-mer oligonucleotide probes designed against ESTs derived from Aplysia CNS

manufacture_protocol: Agilent4x44KSurePrint custom oligonucleotide microarray


title: [AraGene-1_1-st] Arabidopsis Gene 1.1 ST Array [CDF: aragene11st_At_TAIRG version 15]

organism: Arabidopsis thaliana

manufacture_protocol: This is identical to GPL17133 but a custom cdf environment was used to extract data. The custom CDF file is based on Ensembl genes (from http://brainarray.mbni.med.umich.edu version 15). The custom cdf is linked below as a supplementary file.


title: Agilent-022085 SIMR Nematostella 44k 11-2008 [Agilent feature number version]

status: Public on May 01 2013

city: Kansas City

first: Chris

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

organism: Nematostella vectensis

description:
The array was designed by Chris Seidel in October of 2008 and comprised a 43,803 60-mer probe set targeting 43,787 sequences consisting of 20,456 JGI predictions and EST clusters, 16,816 StellaBase predictions, and 6,515 UniGene predictions, EST clusters, and mRNAs. Design targets from each source were evaluated for redundancy by BLAST, and probes were picked to represent the broadest representation of genes across sources. For nearly identical design targets from different sources, one probe was chosen to represent both. As such, probes may be named based on a source, but may also represent a sequence from another source. The digits forming the suffix of each probe name reflect the distance between the probe and the 3' end of the target gene model. This probe set was submitted to Agilent for their 4x44k platform under design ID: 022085.

Arrays of this design have barcodes that begin with 16022085 or 2522085.

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: Plasmodium falciparum Rathod09A_10816

city: Seattle

first: Pradipsinh

middle: K

last: Rathod

state: WA

address: Campus Box 351700

department: Chemistry

institute: University of Washington

organism: Plasmodium falciparum

manufacturer: Rathod Lab, University of Washington, USA

first: Rapatbhorn

last: Patrapuvich

manufacture_protocol: Arrays printed using poly-lysine slides and 70-mer oligonucleotides (60 µM solutions in 3xSSC). P. falciparum 70-mer oligo-microarray contained malarial elements representing the entire genome, provided by Manuel Llinas (Hu G, Llinas M, Li J, Preiser PR, Bozdech Z (2007) Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 8: 350) and some in-house elements designed by ArrayOligoSelector. This set has 10,816 spots distributed in 16 array blocks.


title: Illumina HiSeq 2000 (Mus spretus)

organism: Mus spretus


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene10stv1_Mm_ENSG version 15]

state: MD

organism: Mus musculus

relation: Alternative to: GPL6246 (Alternative CDF [official])

manufacture_protocol: This is identical to GPL6246 but a custom cdf environment was used to extract data.  The  custom CDF file is based on Ensembl genes (from http://brainarray.mbni.med.umich.edu version 15). The custom cdf is linked below as a supplementary file.


title: Agilent-029364 ISB Mmp 60K 60mer tiling array

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

institute: Konkuk University

organism: Methanococcus maripaludis S2

description: Whole genome tiling expression array for Methanococcus maripaludis S2

first: Sung-Ho

first: Nitin

middle: S

last: Baliga

manufacture_protocol: 60 bp were tiled every 60 bps. Plus 3 extras per annotated ORF and 9 extras per unannotated transcripts from our previous publication (PMID: 21750103). See manufacturer's web site at http://www.agilent.com/


title: [HG-U133_Plus_2] Affymetrix GeneChip Human Genome U133 Plus 2.0 Array REFSEQ custom CDF (hg19, GRCh37)

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

organism: Homo sapiens

description: This identical to GPL570 but using the altcdenvsf Bioconductor package we created an alternative Chip Description Filewhere only probes univocally mapping RefSeq transcripts (hg19, GRCh37) were retained. For genes with multiple RefSeq transcripts, the longest isoform was considered.

manufacture_protocol: see the Affymetrix website


title: Illumina HiScanSQ (Rattus norvegicus)

organism: Rattus norvegicus


title: Agilent-041078 mouse_60k_MH

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

description:
Arrays of this design have barcodes that begin with 16041078 or 2541078.

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: SYBR green based Human miRNA PCR assay panel

city: Shenyang

first: zining

last: zhang

state: Liaoning

address: No 155, Nanjingbei street, Heping District

department: 1st affiliated hospital

institute: China Medical University

description: This is a SYBR green based qPCR method to achieve higher accuracy and sensitivity of small RNA detection. E. Coli polyA polymerase was employed to add multiple adenines at the end of every RNA molecules in the total RNA pool that lacks of a polyA tail. With retro-transcriptase and oligodT annealing, a universal tag was introduced to the 3’ end of cDNAs. Using this tag, quantitative PCR was performed with microRNA-specific forward primer and reverse universal primer mix.


title: Agilent-020166 Ca21_GE_plus_tiling_2.0 (Probe Name version)

city: San Francisco

first: Aaron

last: Hernday

state: Ca

institute: UC San Francisco

organism: Candida albicans

description:
This is an expression array built off of the C. albicans genome assembly 21 orf list, with the alpha locus and additional tiling probes spanning the WOR1, WOR2, WOR3, CZF1 and EFG1 loci.  This is the same as AMADID 020128 with the exception of the additional tiling probes for mapping transcription start sites.

Arrays of this design have barcodes that begin with 16020166 or 2520166.

*** 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 GPL16243.

relation: Alternative to: GPL16243 (Feature Number version)


title: Agilent-027411 SurePrint G3 Mouse CGH Microarray 4x180K (Probe Name version)

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


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray HGU133Plus2_Hs_UG v.13]

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: This array is identical to GPL570 but the data were analyzed with a custom CDF environment.

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

manufacture_protocol: Refer to Affymetrix manufacture protocol for HG-U133 Plus 2.0 array


title: Candida albicans tiling ChIP array

manufacture_protocol: Agilent


title: TaqMan OpenArray Rodent MicroRNA Panel

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

description: TaqMan OpenArray Rodent MicroRNA Plate Serial Number GOF03

manufacture_protocol: Protocol specified in TaqMan(R) OpenArray(R) MicroRNA Panels User Guide June 2011.


title: [Ce25b_MR] Affymetrix C. elegans Tiling 1.0R Array [custom CDF Ce25b_MR_v02]

status: Public on May 02 2013

city: Nashville

first: William

middle: Clay

last: Spencer

state: TN

address: 465 21st Ave S

department: Cell & Developmental Biology

institute: Vanderbilt University

organism: Caenorhabditis elegans

description:
custom CDF of GPL5634
Tiling array 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 C. elegans Tiling 1.0R Array is designed for identifying novel transcripts or mapping sites of protein/DNA interaction in chromatin immunoprecipitation (ChIP) experiments, or other Caenorhabditis elegans whole-genome experiments. The C. elegans 1.0R Array is a single array comprised of over 3.2 million perfect match/mismatch probe pairs tiled through the complete non-repetitive Caenorhabditis elegans genome. Sequences used in the design of the C. elegans Tiling 1.0R Array were selected from the WormBase web site, www.wormbase.org, release WS140, March 26, 2005.

Probes are tiled at an average resolution of 25 base pair, as measured from the central position of adjacent 25-mer oligos.

BPMAP and other files can be downloaded from the Affymetrix Web site below.
Custom gene-level annotation was provided by a custom chip definition file (CDF) derived from Wormbase version 200 (WS200) (see Spencer, et al. 2011).

manufacture_protocol: see manufacturer's web site


title: [Mouse430A_2] Affymetrix Mouse Genome 430A 2.0 Array [CDF: Brainarray V.10, Mm430A_Mm_ENTREZG_v10]

status: Public on Mar 07 2013

description:
This array is identical to GPL8321 but a custom, remapped CDF environment is used to extract data. This is version 10 of the remapped CDF. The CDF for various platforms can be found at the link below.
For the CDF file based on Entrez Gene:
For detailed description please see the paper and website.

relation: Alternative to: GPL8321 (Alternative CDF[official])


title: [MTbH37Rva520730F] Affymetrix Mycobacterium tuberculosis H37Rv

status: Public on Apr 27 2013

city: Cambridge

first: Brian

last: Weiner

state: MA

address: 7 Cambridge Center

department: GSAP-Microbial Seq & Analysis

institute: Broad Institute of MIT & Harvard

organism: Mycobacterium tuberculosis H37Rv


title: Agilent-027994 DNZ/UoA_Bovine_~415k_v1

city: Auckland

first: Caroline

middle: Gwendolyn

last: Walker

state: Outside the US or Canada

address: 3A symonds st

department: University of Auckland

country: New Zealand

institute: DairyNZ Ltd

organism: Bos taurus

manufacture_protocol: For detailed information see manufacturer's website at http://www.agilent.com/


title: [FinGene-1_0-st] Zebra Finch Gene 1.0 ST Array [transcript (gene) version]

status: Public on Mar 14 2013

city: Santa Clara

last: Affymetrix

country: USA

institute: Affymetrix, Inc.

organism: Taeniopygia guttata

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

#%create_date=Thu Oct 20 14:39:28 PDT 2011
#%chip_type=FinGene-1_0-st-v1
#%lib_set_name=FinGene-1_0-st
#%lib_set_version=v1
#%genome-species=Taeniopygia guttata
#%genome-version=taeGut1
#%genome-version-create_date=2008-07-00
#%annotation-version=design-time

manufacture_protocol: See manufacturer's web site


title: Agilent-019788 Ambystoma mexicanum 44k_v3_20080327 [ProbeName version]

status: Public on Jan 01 2013

city: Dresden

first: Dunja

last: Knapp

address: Fetscherstraße 105

institute: DFG-Center for Regenerative Therapies Dresden

organism: Ambystoma mexicanum

description:
This platform is the Probe Name version of GPL15341.  Please use GPL15341 for Feature Number version.
Arrays of this design have barcodes that begin with 16019788 or 2519788.
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: Herbert

last: Schulz

first: Cynthia

last: Rascon

first: Michael

last: Volkmer

first: Juliane

last: Scholz

first: Eugen

last: Nacu

first: Mu

last: Le

first: Akira

last: Tazaki

first: Sergey

last: Novozhilov

first: Stephanie

last: Protze

first: Tina

last: Jacob

first: Norbert

last: Huebner

first: Bianca

last: Habermann

first: Elly

middle: M

last: Tanaka


title: Utz lab influenza peptide array

status: Public on Jan 12 2013

city: Oberlin

first: Jordan

last: Price

address: 119 Woodland St

institute: Oberlin College

organism:
Influenza B virus
H1N1 subtype
H3N2 subtype

description: Influenza - Orthomyxovidiae, H1N1 (A/Brisbane/59/2007), H3N2 (A/Brisbane/10/2007), and B (B/Brisbane/60/2008)

manufacture_protocol: We printed streptavidin-surface glass slides (Arrayit, Sunnyvale, CA) with biotinylated 19-mer peptides (Sigma Aldrich, St. Louis, MO) diluted to a concentration of 0.5 mg ml-1 in peptide printing buffer [PBS plus 2.5% glycerol (Sigma)] in replicates of three using a VersArray ChipWriter Compact robotic microarrayer and ChipWriter Pro software (BioRad).


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene10stv1_Mm_ENSG version 14]

status: Public on Nov 09 2011

first: GEO

last: admin

manufacture_protocol: This is identical to GPL6246 but a custom cdf environment was used to extract data.  The  custom CDF file is based on Ensembl genes (from http://brainarray.mbni.med.umich.edu version 14). The custom cdf is linked below as a supplementary file.


title: Agilent 4X44K Aplysia Annotated EST whole-genome array

city: New York

last: Kalachikov

state: NY

address: NWC Bld, 550 West 120th Street Rm 1002

department: Chemical Engineering

institute: Columbia University

first: Leonid

middle: L

last: Moroz

first: John

middle: R

last: Edwards

first: Sathyanarayanan

last: Puthanveettil

first: Irina

last: Morozova


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

status: Public on Apr 12 2013

last: Affymetrix

organism: Macaca mulatta

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

Apr 12, 2013: annotation table updated with netaffx build 33


title: Exiqon miRCURY LNA microRNA array v.11.0 [miRBase v13]

status: Public on Dec 20 2012

city: Singapore

first: Prabha

last: Sampath

state: Singapore

address: 8A Biomedical Grove

department: Institute of Medical Biology

country: Singapore

institute: Institute of Medical Biology

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


title: Agilent-029629 b.subt-final-sense-3probes-july29 [Gene-level version]

status: Public on Feb 02 2012

first: Patrick

last: Eichenberger

email: pe19@nyu.edu, arb401@nyu.edu

state: New York

address: 12 Waverly Place

department: Center for Genomics and Systems Biology

institute: New York University

organism: Bacillus subtilis

description:
from random1000 and

Arrays of this design have barcodes that begin with 16029629 or 2529629.

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 GPL15179_029629_D_GEO_20100730.txt supplementary file's 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 Mouse Genome CGH Microarray 44K  (015028)

status: Public on Jul 28 2009

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

description: NCBI Build 36

manufacture_protocol: see manufacturer's website


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

status: Public on Mar 29 2013

organism: Danio rerio

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

Jan 29, 2013: annotation table updated with netaffx build 33


title: Yeast_ALL DNA chip

status: Public on Aug 10 2006

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

institute: Universitat Autonoma de Barcelona

organism: Saccharomyces cerevisiae

manufacturer: DNA microarray facility. Dept. Biochemistry, Universitat Autonoma de Barcelona

first: Joaquin

last: Arino

first: Anna

last: Barcelo

first: Laia

last: Viladevall

manufacture_protocol: Constructed in our laboratory by arraying 6014 different PCR-amplified ORF from S. cerevisiae on UltraGAPS slides (Corning) using a MicroGrid TM II (BioRobotics) machine. Details on the generation of the PRC fragments and chip construction are provided in Alberola et al. Int Microbiol. 2004 7(3):199-206


title: LLNL Thiobacillus denitrificans array (gene-view)

status: Public on Oct 06 2006

city: Livermore

first: Anu

last: Chakicherla

address: 7000 East Avenue, Mail Stop: L-446

institute: Lawrence Livermore National Lab

organism: Thiobacillus denitrificans ATCC 25259

description: The Thiobacillus denitrificans LLNL array is composed of 28,320 60-mer oligonucleotides, representing 2,832 ORFs, spotted onto one glass array. Three replicates of the genome were included per chip and an average of ten different 60-mer probes represented each ORF in the genome. At the time the microarrays were designed, the draft genome was annotated to have 2,832 ORFs; however, the finished genome is annotated to have 2827 ORFs (Beller et al. 2006; J. Bacteriol. 188: 1473-1488).

first: Harry

last: Beller

first: Tracy

last: Letain

middle: Y

first: Staci

last: Kane

first: Tina

middle: C

last: Legler

first: Matthew

last: Coleman


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [HuEx-1_0-st-v2,mainR3,A20071112,EP.cdf]

city: Christchurch

middle: P

last: Pilbrow

address: 2 Riccarton Avenue

department: Medicine

institute: University of Otago Christchurch

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

HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf from Aroma


title: Agilent-015028 Mouse Genome CGH Microarray 4x44K (Feature Number version)

status: Public on Dec 07 2010

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies


title: [Syel6301a520114F] Affymetrix Custom GeneChip Synechococcus 2515 ORFs v1.0

status: Public on Aug 01 2009

city: Tokyo

first: Hideo

last: Iwasaki

address: TWIns 1F 2-2 Wakamatsu-cho, Shinjuku

department: Electrical Engineering & Bioscience

institute: Waseda University

organism:
Synechococcus elongatus PCC 7942 = FACHB-805
Synechococcus elongatus PCC 6301

manufacture_protocol: Affymetrix prokaryotic array protocol (see Affymetrix website)


title: Agilent-013384 Yeast Oligo Microarray (V2) G4140B (Probe Name version)

status: Public on Oct 08 2008

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.  Replaces 011447, G4140A.

*** 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 GPL2883.


title: UCSD, NimbleGen_E_coli_MG1655_371K Tiling_Array_2005

status: Public on Nov 04 2009

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

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

description: NimbleGen design name 2005-04-20_Palsson_Ecoli_ChIP, NimbleGen design ID 1881.  A tiling array design for Escherichia coli K12 MG1655 with 50-mer probe spaced 25bp apart across the genome.  This design also contains control probes.

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 2000 (Schmidtea mediterranea)

status: Public on May 10 2012

last: GEO

organism: Schmidtea mediterranea


title: Escherichia coli O157:H7 virulence and regulatory array

status: Public on Jul 01 2006

city: Lubbock

first: Scot

last: Dowd

state: TX

address: 4321 Marsha Sharp Fwy

department: MBRI

institute: MBRI

organism: Escherichia coli O157:H7 str. EDL933

description: epoxide coated

manufacture_protocol:
Using the transcriptome of E. coli O157:H7 EDL933 an oligonucleotide microarray, made up of 43-45 mers, was designed.  Based upon available funding we were able to choose 610 genes originally, in the current submission 2 additional genes were added for a total of 612 genes [see Additional file 1] (including 10 negative control genes derived from pig EST sequences).  The genes on the O157 array were selected based upon their being associated with virulence or with regulation of virulence genes.  Specifications of oligos were based upon various design characteristics such as temperature of melting, 3’ location, specificity, lack of repeat nucleotides, etc. [32].  Oligos were synthesized and normalized in concentration by Integrated DNA Technologies Inc. (Coralville, IA).  Oligos were resuspended in Epoxide Slide Spotting Solution and printed onto Epoxide Coated Slides (Corning Inc., Corning, NY) using a GeneMachine’s Omnigrid Accent microarray printer (Genomic Solutions Ann Arbor, MI).  Each array consisted of duplicate elements for each gene and each slide contained a duplicate array with spot sizes of 170 µm, separated at a distance of 300 µm.

The full array layout .gal file is available below as a supplementary file.


title: [Porcine] Affymetrix Porcine Genome Array

status: Public on Mar 09 2006

last: Affymetrix

organism: Sus scrofa

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 Porcine Genome Array provides comprehensive coverage of the Sus scrofa transcriptome. The array contains 23,937 probe sets that interrogate approximately 23,256 transcripts from 20,201 S. scrofa genes.

The sequence information for this array was selected from public data sources including UniGene Build 28 (August 2004), GenBank® mRNAs up to August 24, 2004, and GenBank porcine mitochondrial and rRNA sequences. Probe sets consist of up to eleven probe pairs. The array format consists of eleven micron features synthesized on the 100 format.

Keywords = high density oligonucleotide array


title: Agilent-020016 Thaps-BRTC

status: Public on May 16 2013

city: New Brunswick

first: Kim

last: Thamatrakoln

state: New Jersey

address: 71 Dudley Road

institute: Rutgers University

organism: Thalassiosira pseudonana

description:
Arrays of this design have barcodes that begin with 16020016 or 2520016.

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: Aquagenomic Sparus aurata oligonucleotide-microarray (SAQ)

status: Public on Apr 23 2011

city: Chile

first: Sebastian

last: Boltana

state: Bio BIO

address: Edmundo Larenas s/n, Barrio Universitario. Biotechnology Center

department: Oceanografia

country: Chile

institute: Universidad de Concepcion

organism: Sparus aurata

description:
Agilent design ID 024502.

A total of 43,398 oligonucleotide probes were used to construct a high-density seabream microarray based on the Agilent 4 × 44 K design format. 7,285 transcripts with annotated sequences were spotted in triplicate onto the slide (total probes 21,855), as well as 8,377 ESTs without annotation, 183 enriched sequences (GenBank) with 15 replicated probes (total probes 2,745), and finally 1,417 internal control probes of Agilent (N = 43,398). The platform developed used all available public ESTs stored and annotated in the Aquagenomic Consortium seabream library (10K).

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


title: Henikoff_Dmel_r52_ChIP tiling design

status: Public on May 23 2008

city: Seattle

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

organism: Drosophila melanogaster

description: Tiling array using NimbleGen platform (DesignID=6473/6474/6475). FlyBase release 5.2. Complete tiling of Dmel FBr5 pseudo-chromosomes; no filtering; isothermal (target tm=76); mean probe length=53 (range=50 to 75); mean distance between probes=12; every other probe reversed.

first: Steven


title: [HT_Rat230_PM] Affymetrix HT RG-230 PM Array Plate

status: Public on Apr 09 2013

state: CA

institute: Affymetrix, Inc.

organism: Rattus norvegicus

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

April 09, 2013: annotation table updated with netaffx build 33


title: Atlas Human Stress Array (Cat. #7747-1)

status: Public on Oct 01 2002

last: BD Biosciences Clontech

address: 1020 East Meadow Circle

institute: BD Biosciences Clontech

organism: Homo sapiens

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


title: [GenomeWideSNP_5] Affymetrix Genome-Wide Human SNP 5.0 Array

status: Public on Apr 30 2008

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 SNP Array 5.0 is a single microarray featuring all single nucleotide polymorphisms (SNPs) from the original two-chip Mapping 500K Array Set, as well as 420,000 additional non-polymorphic probes that can measure other genetic differences, such as copy number variation.
SNPs on the array are present on 200 to 1,100 base pair (bp) Nsp I or Sty I digested fragments in the human genome, and are amplified using the fifth generation of the Whole-genome Sampling Assay (WGSA).

Platform table covers CDFs:

GenomeWideSNP_5.Full.cdf
GenomeWideSNP_5.Full.r2.cdf
GenomeWideSNP_5.cdf
GenomeWideSNP_5.r2.cdf


title: Agilent-027411 SurePrint G3 Mouse CGH Microarray 4x180K (Feature Number version)

status: Public on May 20 2010

organism: Mus musculus

description:
Arrays of this design have barcodes that begin with 16027411 or 2527411.

Data table annotations based on NCBI Build 37 (UCSC mm9), July 2007.

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 (Drosophila melanogaster)

status: Public on Aug 19 2009

technology: other


title: URGV Arabidopsis thaliana 34.6K CATMA_v5

status: Public on Nov 11 2009

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

organism: Arabidopsis thaliana

description: Corning Ultra-GAPS (TM) slides are spotted with 64 pins (8x8) therefore the spotted area is divide into 3 metablocks, each containing 64 blocks of 196 spots (14x14).

first: Jean-Pierre

middle: J

last: Renou

first: Ludivine

last: Soubigou

first: Sandra

last: Pelletier

first: Sébastien

last: Aubourg

first: Véronique

middle: V

last: Brunaud

first: Vincent

last: Thareau

first: Pierre

last: Hilson

first: Olivier

middle: O

last: Voinnet

manufacture_protocol:
A.thaliana genes were predicted with Eugene software (Foissac S. et al., Nucleic Acids Res., 2003) and gene-specific sequence tags were automatically designed (Thareau et al. Bioinformatics, 2003 Nov 22). Two rounds of PCR were performed and PCR products were finally purified and dissolved in 50% DMSO in TE at concentrations ranging between 50-200ng/ul and re-arrayed in 1536 microtiter plates. The pins are washed in 0.1% SDS at 50 degre Celsius then three times in bi-distilled water. Spotter settings are 45-55% humidity, and a pitch = 180 um. The room temperature is set between 19 and 21 °s Celsius and below 40 % humidity. The microtiter plates are placed in the biobank. The four trays are cleaned and 100-120 slides placed on them (30 slides per tray). The spotting lasts 25 hours. The slides are stored in the dark in a dry-cabinet for 3 days and UV-cross-linked at 300 mJ. After crosslinking, the slides are stored in the dark in a dry-cabinet.This array design contains:
- 32626 Gene Specific Tags (GST)
- 44 Non Protein Coding (NPC)
- 1263 microRNA precursors.


title: Illumina Human610-Quad v1.0 BeadChip

status: Public on Jul 27 2009

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

technology: oligonucleotide beads

manufacture_protocol: See manufacturer's website