title: CIT-CGH Homo sapiens BAC [HG19]

status: Public on Sep 29 2015

city: paris

first: François

last: Radvanyi

state: -- Please Select --

address: 12 rue Lhomond

department: UMR144 CNRS

country: France

institute: Institut Curie

organism: Homo sapiens

technology: spotted DNA/cDNA

distribution: custom-commercial

manufacture_protocol:
This platform the features of the CIT-CGH Homo sapiens 3K BAC clones:
The IntegraChipTM microarray was designed by the CIT-CGH consortium (Olivier Delattre Laboratory, Curie Institute, Paris; Charles Theillet Laboratory, CRLC Val d'Aurelle, Montpellier; Stanislas du Manoir Laboratory, IGBMC, Strasbourg) and the company IntegraGenTM (http://www.integragen.com). Bacterial artificial chromosome (BAC) clones were chosen to obtain a systematic coverage of the genome, and detailed coverage of regions containing genes previously implicated in carcinogenesis. The median gap between two successive clones is 850 kb. Four replicate spots were deposited on the slides. For each sample, 500-600 ng of sonicated DNA was labelled by Random-Priming (Bioprime Labelling kit, Invitrogen, Carlsberg, CA, USA) according to the suppliers\x{2019} instructions, but for 18h. For tumour DNA, final concentrations of nucleotides were 0.02 mM of dCTP-Cy5 (Amersham Biosciences), 0.1 mM of dATP, dGTP, dTTP and 0.025 mM dCTP. For control DNA, 0.04 dCTP-Cy3 (Amersham Biosciences), 0.2 mM of dATP, dGTP, dTTP and 0.05 mM dCTP. Labelled DNAs were purified using MicroSpin-G50 columns (Amersham Biosciences). COT Human DNA (70 \x{03bc}g, Roche Diagnostics) and Salmon Testes DNA (30 \x{03bc}g, Sigma Chemical Co.) were added to the mixed tumour and reference DNAs. They were subsequently concentrated using a microcon YM-30 (Millipore) and resuspended to obtain 200 \x{03bc}l of hybridization solution (final concentration: 50% formamide, 0.8 x SCC, 10% W/V dextran sulfate, 2% SDS, pH=7). Finally, the probes were pre-annealed for 3 hours at 37°C. Every step was carried out in the HS 4800 hybridization station (Tecan). Slide pre-treatment included rinsing with 2 x SSC, 0.1% SDS at 30 °C for 30s, 2 x SSC at 30 °C for 30s and drying. After probe injection, hybridization was performed for 68h at 37°C under low agitation. Four post-hybridization washes were carried out: 50% formamide, 2 x SSC, 0.1% SDS at 45 °C for 37 s, 4 times; 2 x SSC, 0.1% SDS at 45 °C for 37 sec, 4 times; 4 x SSC, 0.1 Tween 20 at 45 °C for 37 sec, 4 times; slides were finally nitrogen dried and scanned using a ScanArray 4000 (Packard Bioscience). Images were quantified using UCSF Spot 2.1cc (Jain et al., 2002).


title: Agilent-017131 DasSarma Laboratory Halobacterium sp. NRC-1 array (Feature Number version)

status: Public on Mar 31 2015

city: Baltimore

first: Priya

last: DasSarma

state: MD

address: 701 East Pratt Street, Suite 236

department: Microbiology

country: USA

institute: UMB

organism: Halobacterium salinarum NRC-1

technology: in situ oligonucleotide

first: Shiladitya

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


title: Illumina HiSeq 2500 (Campylobacter lari)

last: GEO

organism: Campylobacter lari

technology: high-throughput sequencing

distribution: virtual


title: Illumina MiSeq (Homo sapiens; Mus musculus)

organism:
Homo sapiens
Mus musculus


title: Oxford Gene Technology 4x44K S. Typhimurium SL1344 60-mer oligonucleotide array

city: Norwich

first: Arthur

last: Thompson

address: Colney Lane

country: United Kingdom

institute: Institute of Food Research

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

description: Design ID 019399

manufacture_protocol: The oligonucleotide array is made up of 4 X 44K 60 mer oligonucleotides printed onto glass slides


title: Illumina HiSeq 2500 (Campylobacter coli)

organism: Campylobacter coli


title: Illumina HiSeq 2000 (Citrus trifoliata)

organism: Citrus trifoliata


title: NimbleGen Nicotiana tabacum custom expression array [090605_Ntab_MT_EXP]

city: Dallas

first: Roel

last: Rabara

state: Texas

address: 17360 Coit Road

institute: Texas A&M AgriLife Research

organism: Nicotiana tabacum

description: Tobacco (Nicotiana tabacum) cv. Burley 21

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


title: Agilent-038119 IMB Flyr5.41_AgiV2

status: Public on Mar 30 2015

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Drosophila melanogaster

description:
Arrays of this design have barcodes that begin with 16038119 or 2538119.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

distribution: commercial

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


title: nCounter Human Inflammation panel V1

city: Seattle

first: NanoString

last: Technologies

address: 530 Fairview Ave N  |  Suite 2000

institute: NanoString Technologies

technology: other

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


title: Agilent-020164 Yeast genomic 44K tiling Microarray [Cairns-RSC-ISWI-44K]

city: Salt Lake City

first: Timothy

middle: J

last: Parnell

state: UT

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute

organism: Saccharomyces cerevisiae

description:
The column 'Chr_coordinate' represents the original coordinates based on the SGD (Saccharomyces Genome Database) genome release version 55 to which the array was originally designed. These coordinates are also listed in the raw Agilent text data files.
The RANGE_START, RANGE_End columns represent the coordinates based on the recent and stable genome version 64 (equivalent to UCSC SacCer3) and the coordinates used in GSE65591 study.

manufacture_protocol: The HybMap microarray was custom designed to represent genes with a range of RSC and ISW1 occupancies, and included 448 coding genes, 93 tRNA genes, and 52 non-coding genes. Gene regions were extended by either 300 bp (coding and non-coding) or 150 bp (tRNA). Probes were selected from a pool of tiled 60mers and adjusted for length to match melting temperatures as necessary. Both strands for each probe were included in the design. Probes have a mean spacing of ~ 50 bp. As a control, 502 probes with sequences from zebra fish were included as non-hybridizing control probes; sequences were confirmed not to have significant homology to yeast sequences.


title: Roche NimbleGen Heliconius melpomene malleti custom-designed 12x135K [120910_Hmel_CPD_expr]

city: Bogota

first: Carolina

last: Pardo-Diaz

address: Carrera 24 # 63C-69

department: Programa de Biología

country: Colombia

institute: Universidad del Rosario

organism: Heliconius melpomene malleti

description:
The microarray design included two components. The first involved the tiling of 400,000 bp of each of three genomic regions, corresponding to the colour pattern loci HmAc, HmBD and HmYb/Sb/N. The second corresponded to a whole-genome gene expression array. The HmAc locus was tiled with 6,560 probes staggered every 10bp on average, the tiling of the HmBD locus involved 10,716 probes distanced every 10bp on average and the HmYb locus tiling comprised 9,979 probes at 10bp distanced on average. The whole-genome gene expression array, on the other hand, was composed of a total of 107,898 probes targeting (i) each annotated gene in the H. melpomene genome version 1.1 and (ii) each transcript not included in the genome annotation but predicted as such by RNA-seq evidence.
Each probe was 60 bp.

Design name: 120910_Hmel_CPD_expr
Design ID = 574331
Native array description file: 120910_Hmel_CPD_expr.ndf
Native array description file: 120910_Hmel_CPD_expr.ngd

manufacture_protocol: See manufacturer's website.


title: nCounter Human Inflammation panel V2


title: Illumina Genome Analyzer IIx (Phaseolus vulgaris)

organism: Phaseolus vulgaris


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [alternative CDF: Brainarray MoGene10stv1_Mm_REFSEQ version 18]

organism: Mus musculus

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

June 03, 2009: annotation table updated with netaffx build 28
June 07, 2012: annotation table updated with netaffx build 32

manufacture_protocol: See manufacturer's web site


title: Agilent-046065 Mouse_miRNA_V19.0_Microarray [Probe Name version]

description: Mouse miRBase version 19.0


title: Illumina HiSeq 2000 (Capsella grandiflora x Capsella rubella)

status: Public on Mar 27 2015

organism: Capsella grandiflora x Capsella rubella


title: University of Alberta Arabidopsis thaliana 26K 70-mer oligonucleotide DNA microarray

city: Saskatoon

first: Dwayne

last: Hegedus

address: 107 Science Place

country: Canada

institute: Agriculture Canada

organism: Arabidopsis thaliana

technology: spotted oligonucleotide

description: Oligos were from the Arabidopsis Genome Microarray Oligo Set v1.0 purchased from Qiagen-Operon Technologies.

distribution: non-commercial

manufacturer: University of Alberta, Microarray Facility

manufacture_protocol: Slides were printed on SuperAmine slides from Telechem using a 32-pin gridding robot. The slide outline is comprised of 8 metarows and 4 metacolumns, and each subarray is comprised of 29 columns and 29 rows.


title: Illumina HiScanSQ (Caenorhabditis elegans)

status: Public on Mar 28 2015

organism: Caenorhabditis elegans


title: NanoString nCounter human PanCancer Pathways Panel

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


title: Illumina HiSeq 2000 (Capsella rubella)

organism: Capsella rubella


title: GeoChip 5.0

city: Beijing

first: Yunfeng

last: Yang

address: No.1 Qinghuayuan, Haidian District

department: School of Environment

country: China

institute: Tsinghua University

organism:
Bacteria
Archaea
Eukaryota
Viruses


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene10stv1_Mm_ENSG v.18.0.0]

status: Public on Mar 26 2015

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

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 CDF is available here: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/ensg.asp


title: Illumina MiSeq (Cyanidioschyzon merolae strain 10D)

organism: Cyanidioschyzon merolae strain 10D


title: MI Ready Array Mouse 49K (MEEBO)

city: Madrid

first: Jesus

last: Garcia Lopez

address: C/Ramiro de Maeztu 9

department: Cellular and Molecular Biology

country: Spain

institute: Cib (CSIC)

manufacture_protocol: see manufacturer's web site


title: NimbleGen Human Whole Genome CGH array [090527_HG18_WG_CGH_v3.1_HX12]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Homo sapiens

description: Build: Hg18, NCBI 36

manufacture_protocol: see manufacturer's website for details


title: [sySYNG003a] Custom designed rice whole-genome Affymetrix GeneChip array

status: Public on Mar 25 2015

city: Guelph

first: JOSE

middle: A

last: CASARETTO

state: ON

address: 50 Stone Road E

department: MCB

institute: University of Guelph

organism: Oryza sativa Japonica Group


title: AB SOLiD 4 System (Paenibacillus riograndensis SBR5)

organism: Paenibacillus riograndensis SBR5


title: Illumina HiSeq 2500 (Haemaphysalis flava)

status: Public on Mar 24 2015

organism: Haemaphysalis flava


title: Illumina MiSeq (Drosophila melanogaster; Drosophila sechellia)

organism:
Drosophila melanogaster
Drosophila sechellia


title: NimbleGen Human Whole Genome CGH array [090210_HG18_WG_CGH_v3.1_HX12]

description: Build: Hg18, NCBI 36


title: Illumina HiScanSQ (Saccharomyces cerevisiae)


title: Agilent-033207 Viro5AGRS-60k (Probe Name version)

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

organism: Viruses

description: This platform includes more than 60000 oligonucleotides for the detection and discovery of both known and novel viruses.  The sequences of ~36,000 of the viral probes on this platform have been previously published in the GEO database as MegaViro  (GPL1834), Viro3 (GPL3429), and Viro4 (GPL6862). For comparison purposes, both 70mer and 60mer representations of these viral oligos are present. Some viral probes corresponding to phages and other less critical targets have been removed. More than 20,000 additional probes have been added for (1) better subtyping of respiratory and diarrheal viral as well as nonviral pathogens, and (2) enhanced detection of specific viral families.   Control oligonucleotides are also included in the design. Abbreviations: BSRI = Blood Systems Research Institute, San Francisco, CA; CMO = Callicebus (titi monkey).


title: Illumina NextSeq 500 (Drosophila melanogaster x Drosophila sechellia)


title: Illumina MiSeq (Drosophila melanogaster x Drosophila sechellia)


title: NanoString nCounter GX Cancer Reference Kit with custom made ITESM  (14 genes associated with prostate cancer)

city: Monterrey

first: Roberto

last: Portillo Lara

state: Nuevo León

address: Ave. Eugenio Garza Sada 2501 Sur Col. Tecnológico

department: División de Biotecnología y Alimentos

country: Mexico

institute: Tecnológico de monterrey

description: nCounter Human Cancer Reference GX Kit with 14 prostate cancer associated genes


title: Agilent-026418 Viro5AGL-60k

description:
This platform includes more than 60000 oligonucleotides for the detection and discovery of both known and novel viruses.  The sequences of 36,432 of the viral
probes on this platform have been previously published in the GEO database as MegaViro  (GPL1834), Viro3 (GPL3429), and Viro4 (GPL6862), collectively now designated V3 / V4 viral probe sets
For comparison purposes, both 70mer and 60mer representations of these viral oligos are present.
Some viral probes corresponding to phages and other less critical targets have been removed.
More than 20,000 additional probes have been added for (1) better subtyping of respiratory and diarrheal viral as well as nonviral pathogens,
(2) enhanced detection of specific viral families, and (3) subtyping of HIV/SIV strains.   Control oligonucleotides are also included in the design.


title: Illumina MiSeq (Entamoeba invadens)

organism: Entamoeba invadens


title: Vibrio vulnificus MO6-24_30K

city: Seoul

first: Juri

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Environmental Medical Biology

country: South Korea

institute: Yonsei University

organism: Vibrio vulnificus MO6-24/O

manufacture_protocol: ss-DNA is synthesized in situ on glass substrates functionalized with amines. The synthesis process is proprietary but uses digital micromirror mediated photolithography to generate sufficient acid locally to remove acid labile protecting groups on 5'-terminal phosphoramidite monomers where the next phosphoramidite base will be coupled. The arrays can be used to hybridize cRNA or cDNA.


title: Agilent-038215 Clostridium beijerinckii 15K array

city: Ulsan

first: Siseon

last: Lee

address: UNIST-gil 50

institute: Ulsan National Institute of Science and Technology

organism: Clostridium beijerinckii

description:
Arrays of this design have barcodes that begin with 16038215 or 2538215.

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 (Drosophila sechellia)

last: GEO

organism: Drosophila sechellia


title: Illumina MiSeq (Entamoeba histolytica)

organism: Entamoeba histolytica


title: Illumina HiSeq 2500 (Haemophilus ducreyi 35000HP)

organism: [Haemophilus] ducreyi 35000HP


title: Illumina HiSeq 1500 (Drosophila melanogaster)

organism: Drosophila melanogaster


title: Illumina HiSeq 2000 (Phaeomoniella chlamydospora)

organism: Phaeomoniella chlamydospora


title: Illumina HiSeq 2000 (Conopomorpha sinensis)

organism: Conopomorpha sinensis


title: PacBio RS II (Caenorhabditis elegans)

status: Public on Mar 20 2015

organism: Caenorhabditis elegans


title: Agilent-049514,  Anidulans_whole_metZ_R_tiles_v3

status: Public on Mar 22 2015

city: Warszawa

first: Marek

last: Skoneczny

email: kicia@ibb.waw.pl, mrksknc@gmail.com

address: Pawińskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

organism: Aspergillus nidulans


title: Exiqon miRCURY LNATM microRNA Array, v.11.0 [miRBase 12.0]

status: Public on Mar 23 2015

city: Singapore

first: Lee Lee

last: Wong

address: 14 Medical Drive, 08-01

department: Medicine

country: Singapore

institute: National University of Singapore

organism: Homo sapiens

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


title: Agilent-047069 CATMAv7

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

organism: Arabidopsis thaliana

description:
sens agilent gene: triplicate and  no_gene: single
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: Sandrine

last: BALZERGUE

first: Véronique

last: BRUNAUD

first: Etienne

last: DELANNOY

first: Marie-Laure

last: MARTIN-MAGNIETTE

first: Ludivine

last: TACONNAT


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [Gene-level, 10K]

status: Public on Mar 21 2015

city: Essen

first: Sven

last: Lindner

address: Hufelandstraße 55

institute: University Hospital Essen

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

June 03, 2009: annotation table updated with netaffx build 28
June 06, 2012: annotation table updated with netaffx build 32

manufacture_protocol:
see manufacturer's web site

Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts
All probe sets represented on the GeneChip Human Genome U133 Set are identically replicated on the GeneChip Human Genome U133 Plus 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz Golden-Path human genome database (April 2001 release).
In addition, there are 9,921 new probe sets representing approximately 6,500 new genes. These gene sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from the UniGene database (Build 159, January 25, 2003) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the NCBI human genome assembly (Build 31).


title: Human genome-wide mRNA microarray

city: Hangzhou City, Zhejiang Province

first: Liangjing

last: Zhou

address: no. 3,QingChun east road,Jianggan District, Hangzhou City, Zhejiang Province

department: Department of General Surgery

institute: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China


title: Lawrence Livermore Microbial Detection Array version 2g (MDAv2g.ndf)

status: Public on Mar 19 2015

city: Livermore

first: Kevin

last: McLoughlin

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

organism: synthetic construct

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


title: Illumina HiSeq 2000 (Mycobacterium tuberculosis HN878)

status: Public on Mar 18 2015

organism: Mycobacterium tuberculosis HN878


title: Custom Taqman qPCR: RotorGene 6000; Corbett Research (Sydney, Australia)

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

technology: RT-PCR

description:
Custom made-to-order or pre-designed TaqMan assays were used with protocol recommended by the producer (Life Technologies Corp., Carlsbad, CA, USA)
qPCR was performed in RotorGene 6000 produced by Corbett Research (Sydney, Australia)

manufacturer: Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic


title: Illumina HiSeq 2500 (Bacillus subtilis)

organism: Bacillus subtilis


title: Illumina HiSeq 2500 (Musca domestica)

organism: Musca domestica


title: Illumina HumanHT-12 V3.0 expression beadchip [ILMN_gene symbol]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

technology: oligonucleotide beads

description: The HumanHT-12 V3.0 Expression BeadChip features up-to-date content derived from the National Center for Biotechnology Information Reference Sequence (NCBI RefSeq) database (Build 36.2, Release 22).

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2000 (Cordyceps militaris)

status: Public on Mar 16 2015

organism: Cordyceps militaris


title: Illumina HiSeq 2500 (Phaeodactylum tricornutum)

status: Public on Mar 17 2015

organism: Phaeodactylum tricornutum


title: Agilent-021463 ScBarcode v1.1 08-09-12

first: Adrianna

last: Skoneczna

address: Pawinskiego 5A

department: Laboratory of Mutagenesis and DNA Repair

institute: Institute of Biochemistry and Biophysics

organism: Saccharomyces cerevisiae


title: FDA / CBER Human 16K (Well ID version)

status: Public on Mar 14 2015

city: Belgrade

first: Vladan

middle: Predrag

last: Cokic

address: Dr Subotica 4

country: Serbia

institute: Institute for Medical Research

description: Well ID is a unique identifier which refers back to the original inventory plate from the microarray printing center.

manufacturer: Operon's Human Genome Array-Ready Oligo Set (Operon Inc. Valencia, CA)

manufacture_protocol:
The arrays were produced in house by spotting oligonucleotides on poly-L-lysine coated glass slides by Gene Machines robotics (Omnigrid, San Carlos, CA).
High quality oligonucleotide glass array containing a total of 16,659 seventy-mer oligonucleotides chosen from 750 bases of the 3' end of each ORF


title: NimbleGen Atlantic Cod Oligonucleotide 135k Array Version 1 [100610_GM_FY_EXP] (gene-level)

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

organism: Gadus morhua

description:
NimbleGen design name: 100610_GM_FY_EXP
NimbleGen design ID: 531893
Native array description file: 100610_GM_FY_EXP.ndf
Native array description file: 100610_GM_FY_EXP.ngd
44k cDNAs were used (26k assembled EST contigs and 18 singletons from the cod genome sequencing consortium; see The genome sequence of Atlantic cod reveals a unique immune system Starr et al., 2011; Nature 477:207 [PMID 21832995]). Three 60mer probes were prepared for each cDNA sequence, 125826 cod probes in total.  The array contains 137604 features, including  11779 Nimblegen control probes.
The supplementary file 'cDNA_seqs.txt' contains all cDNA sequences used in the design of the probes.

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


title: MBPL human 30k P8

city: Hsinchu

first: Chaang Ray

last: Chen

address: 101, Section 2, Kuang-Fu Road

department: Biomedical Engineering and Environmental Sciences

country: Taiwan

institute: National Tsing Hua University

description: spotted DNA/cDNA

manufacture_protocol: Arrayer obtained from Dr. Patrick O. Brown MGuide II and ArrayMarker program version 2.3.2 (Dr. Joseph DeRisi, University of California, San Francisco) with 48 spotting pins (TeleChem).We control printing condition in temperature 25~26°C and Humidity about 49~51%, and printing on January 2009. cDNA clones were purchased from Incyte Genomics and 7334 sequence-verified clones were amplified by PCR.We purified these 7334 clones by isopropanol precipitation and used 3× saline-sodium citrate (SSC) as spotting solution. cDNA spotted on GAPS II coated slides (Corning Incorporated) coating of pure gamma amino propylsilane.


title: Operon Human Genome Array-Ready Oligo Set V.4.0

manufacturer: Eurofins MWG Operon (Huntsville, AL, USA)

manufacture_protocol:
The human version 4.0 is constructed based on the Ensembl human database build (NCBI-35c), with a full coverage on NCBI human Refseq dataset.
High quality oligonucleotide glass array contains 35,035 oligonucleotide probes, representing approximately 25,100 unique genes and 39,600 transcripts excluding control oligos.


title: Illumina Miseq (Schizosaccharomyces pombe)

status: Public on Mar 13 2015

last: GEO

organism: Schizosaccharomyces pombe


title: Corynebacterium glutamicum array [CG_050317]

city: Bielefeld

first: Hironori

last: Taniguchi

department: Biology

institute: Bielefeld University

organism: Corynebacterium glutamicum ATCC 13032

manufacture_protocol: Described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532


title: Illumina MiSeq (Mycobacterium bovis BCG str. Pasteur 1173P2)

organism: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2


title: Illumina HiSeq 2000 (Strongylocentrotus purpuratus)

organism: Strongylocentrotus purpuratus


title: Agilent-038658 F. graminearum_8x15k

city: Yokohama

first: Alagu

last: Manickavelu

state: Kanagawa

address: Maioka 641-12

country: Japan

institute: Yokohama City University

organism: Fusarium graminearum

description:
Arrays of this design have barcodes that begin with 16038658 or 2538658.

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: USDA-ARS PSMRU Campylobacter jejuni version 10

city: Albany

first: Craig

middle: T

last: Parker

address: 800 Buchanan St

department: PSM

institute: USDA ARS

organism: Campylobacter jejuni

description: non-commercial array

manufacturer: Produce Safety and Microbiology, USDA-ARS, Albany CA

manufacture_protocol: PCR product array of ORF's from Campylobacter jejuni strains NCTC 11168, 81-176, RM1048, RM1050, RM3193 (260.94), RM1045, RM1555, 43446. PCR products resuspended in resuspended to an average concentration of 0.1-0.2 µg µl-1 in 20 µl of 50% dimethyl sulfoxide (DMSO) containing 0.3× Saline-Sodium Citrate (SSC). Spotted on Corning barcoded UltraGAPS slides using a GeneMachine Accent printer with ChipMaker pins.


title: AB 5500xl Genetic Analyzer (Macaca fascicularis)

organism: Macaca fascicularis


title: Illumina HiSeq 2000 (Pseudoalteromonas sp. A2)

status: Public on Mar 11 2015

organism: Pseudoalteromonas sp. A2


title: Candida albicans MI-CA-8.2k

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

institute: University of Sheffield

organism: Candida albicans

manufacture_protocol: 70-mer oligonucleotide set from Qiagen was printed on glass slides.


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [CDF: Brainarray Version 16.1.0, HsEx10stv2_Hs_REFSEQ]

city: Vienna

first: Andreas

last: Wernitznig

address: Dr.-Boehringer-Gasse 5-11

department: Oncology - Pharmacology

country: Austria

institute: Boehringer Ingelheim

organism: Homo sapiens

description: Probe set data extracted from custom CDF [Brainarray Version 16.1.0, HsEx10stv2_Hs_REFSEQ]

relation: Alternative to: GPL5175 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site.


title: Arizona Gallus gallus 20.7K Oligo Array v1.0

city: Saint Paul

first: Sunantha

last: Kosonsiriluk

state: Minnesota

address: 495 AnSci/VetMed 1988 Fitch Ave

department: Animal Science

country: USA

institute: University of Minnesota

organism: Gallus gallus

manufacturer: Genomics Research Laboratory, Steele Children's Research Center, University of Arizona

manufacture_protocol:
The chicken oligos were designed by Carre et al. (2007) using gene predictions from Ensembl, TIGR, full-length cDNAs from the BBSRC UMIST ChickEST database, and chicken bursal EST sequences from Jean-Marie Buerstedde's DT40 database. Sequences from these resources were aligned and 70mer oligos designed against regions common to more than one aligned sequence. Oligos were then designed using OligoArray2.0.
The chicken oligo set [Gallus gallus (chicken) Roslin/ARK CoRe Array V1.0] was manufactured by Operon Technologies, Inc.. The chicken oligo set (Catalog # 851102) contains 20,460 long oligo probes (300 pmol) arrayed in 54 384-well plates. Four wells in each of the 54 384-well plates contained the Operon Production Tracking Oligo opHsV04NC000001, which is a randomly-generated oligo sequence with a length of 30 bases.
The 20.7K chicken oligo array contains 20,676 features that include 20,460 70mer oligos and 216 control spots of the Operon Production Tracking Oligo opHsV04NC000001.


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Broad GenePattern]

status: Public on Mar 12 2015

city: Stanford

first: Christopher

last: Dove

address: Room 3005, 265 Campus Drive, 3rd Floor

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

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: Agilent-046633 [ORF version]

status: Public on Mar 10 2015

city: Tsukuba

first: Takeshi

last: Izawa

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

organism: Oryza sativa

description:
The probe target is followin. 44k(build 3), eArray Best, eArray 2nd, Masked Best(IRGSP 1.0), Koshihikari eArray, Koshihikari 44k, PPNT protein cording, PPNT non protein cording, Cufflinks(IRGSP 1.0).
Arrays of this design have barcodes that begin with 16046633 or 2546633.
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.

relation: Alternative to: GPL19684 (Feature Number version)


title: Agilent-038578 Teleaulax Gene Expression 4 X 44K array (Probe name version)

city: Kongju

first: Jong Won

last: Han

state: Chungnam

address: Sinkwandong

institute: Kongju National University

organism: Teleaulax amphioxeia

description:
Agilent’s Agilent E-array (Teleaulax) (44K)
15,654 genes designed from Teleaulax amphioxeia ESTs


title: Illumina HiSeq 2000 (Cercis gigantea)

organism: Cercis gigantea (nom. inval.)


title: Illumina Genome Analyzer (Cercis gigantea)


title: 454 GS FLX (Danio rerio)

status: Public on Mar 09 2015

organism: Danio rerio


title: HIV-1 v1; PfPv500 version1.

city: Irvine

first: Johannes

middle: S.

last: Gach

address: 843 Health Sciences Rd

institute: University of California Irvine

organism: Human immunodeficiency virus 1

technology: spotted peptide or protein

manufacturer: University of California Irvine, Protein Microarray Laboratory

manufacture_protocol: The arrays used in this study came from a commercially available source,  Purified HIV-1 envelope proteins and peptides were spotted onto nitrocellulose-coated slides. Multiple spots consisting of reactions lacking proteins are present on each array and used for data normalization. The array is called PfPv500 version1.


title: Illumina HiSeq 2000 (Rhizoctonia solani AG-3 Rhs1AP)

organism: Rhizoctonia solani AG-3 Rhs1AP


title: Illumina Genome Analyzer IIx (Kluyveromyces marxianus)

status: Public on Mar 06 2015

organism: Kluyveromyces marxianus


title: LC-MS/MS on Orbitrap Q Exactive

city: Boston

first: Catherine

last: Wu

state: MA

address: 450 Brookline Ave.

institute: Dana Farber Cancer Institute

organism: Mus musculus

technology: MS

manufacture_protocol: see website


title: Agilent-050087 Wigglesworthia_v1

city: Montpellier

first: Anne

last: Geiger

address: Laboratoire de Recherches et de Coordination sur les Trypanosomoses TA,A-17 / G Campus international de Baillarguet

country: France

institute: UMR 177 IRD-CIRAD

organism: Wigglesworthia glossinidia endosymbiont of Glossina morsitans


title: Illumina HiSeq 2000 (Bacillus amyloliquefaciens subsp. plantarum str. FZB42)

organism: Bacillus velezensis FZB42


title: Illumina HiSeq 2000 (Yersinia enterocolitica)

status: Public on Mar 04 2015

organism: Yersinia enterocolitica


title: Murine 16K long oligo array

status: Public on Mar 05 2015

city: San Francisoc

first: Mehdi

last: Nosrati

state: California

address: 475 Brannan, Suite 220

department: Research Institute

institute: California Pacific Medical Center

manufacture_protocol: PCR amplified DNA/cDNA spotted onto Poly-L-Lysine coated slides (using a custom-made microarrayer develop by Joe DeRisi ); UV-cross-inked and blocked with succinate anhydride/boric acid/1-M-2-Pyrrolidinone; washed with water and ethanol; dried by centrifugation @ 100 xg


title: Institut Curie_RPPAplatform_RATHER_ILC

status: Public on Mar 07 2015

city: Paris

first: Leanne

last: de Koning

address: 26 rue d'Ulm

department: Department of translational research

institute: Institut Curie

description: Reverse Phase Protein Arrays (RPPA)

manufacture_protocol: Samples were printed onto nitrocellulose covered slides (Sartorius, Grace Biolabs or Maine Manufacturing) using a dedicated arrayer (2470 Arrayer, Aushon Biosystems)


title: Agilent-060228 Human LncRNA v5 4X180K [Probe Name Version]

city: shanghai

first: qian

last: jin

address: libing road

institute: MSP

description:
SBC_hg19_lncrna_V1

Arrays of this design have barcodes that begin with 16060228 or 2560228.

Orientation:

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).


title: NCSU_P.furiosus_COM1_hybrid_array

city: Raleigh

first: Aaron

last: Hawkins

state: NC

address: 840 Main Campus Dr

department: Chemical Engineering

institute: North Carolina State University

organism: Pyrococcus furiosus COM1

manufacture_protocol: A DNA microarray was designed and constructed based on at least 2032 protein-coding sequences in the P. furiosus COM1 genome obtained from the Department on Energy?s Joint Genomes Institute (http://genome.ornl.gov/microbial/msed) plus over 100 protein-encoding sequences from other thermophilic microorganisms. OligoArray 2.1 (Rouillard, 2003) was used to generate at least one 60-mer oligonucleotide probe sequence for each open reading frame. The probes were synthesized (Integrated DNA Technologies, IA), re-suspended in 50% DMSO, and printed onto Ultragap microarray slides (Corning, NY) using a QArrayMini arrayer (Genetix, UK). Each probe was spotted five times onto each array to fortify statistical analysis.


title: Agilent-046633 Oryza sativa 180K array os_180k_130118 (Feature Number version)

status: Public on Mar 31 2015

description:
The probe target is following 44k(build 3), eArray Best, eArray 2nd, Masked Best(IRGSP 1.0), Koshihikari eArray, Koshihikari 44k, PPNT protein cording, PPNT non protein cording, Cufflinks(IRGSP 1.0).

Arrays of this design have barcodes that begin with 16046633 or 2546633.

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 (Fasciola hepatica)

status: Public on Mar 03 2015

last: GEO

organism: Fasciola hepatica


title: Agilent-046808 Mm CGH TL-Focus 2013 BLYTH [Feature Number Version]

city: Inage-ku

first: Benjamin

middle: John

last: Blyth

state: Chiba

address: 4-9-1 Anagawa

department: Centre for Radiation Protection

institute: National Institute of Radiological Sciences

description:
Genomic tiling plus high density coverage of key TL loci.

Arrays of this design have barcodes that begin with 16046808 or 2546808.

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.

relation: Alternative to: GPL19767 (Probe Name Version)


title: Illumina HiSeq 2000 (Human herpesvirus 1 strain KOS; Mus musculus)

organism:
Mus musculus
Human alphaherpesvirus 1 strain KOS


title: Agilent Brassica juncea 44K

city: Varanasi

first: Sudhakar

last: Srivastava

address: Lanka

department: INSTT. OF ENV.  AND SUST. DEV.

country: India

institute: Banaras Hindu University

organism: Brassica juncea

description: A set of 53939 sequences, which include EST and nucleotide sequences of Brassica sp., were downloaded from GenBank. These sequences were subjected to clustering and analyzed using  CAP3/tgicl program and other in-house tools. A set of 26881 non-redundant sequences was created, which was used for probe design. This set included 1720 Brassica juncea, 15259 Brassica   napus and 5075 Brassica rapa sequences; and 6456 from other species. Probes were designed for the non-redundant sequences using Agilent eArray tool. Best probe composition algorithm with   the option to design multiple probes for each sequence was the main criteria used for the probe design. Agilent’s 4x44 array was selected to print the oligos. A set of positive and negative controls   were also added on to the microarray chip. A set of replicate probes were also added for calculating the intra-array reproducibility. The quantity and purity of the RNA was determined by absorbance   at 260 nm and 260/280 absorbance ratio respectively.  Each of the total RNA preparations was individually assessed for RNA quality based on the 28S/18S ratio and RIN measured on an   Agilent 2100 Bioanalyzer system using the RNA 6000 Nano LabChip Kit .With the use of Agilent’s 1-Color Quick Amp Labeling Kit, 500 ng of high quality total RNA was denatured in the presence of   a T7 promoter primer and a 1-Color RNA Spike-In Kit. Reverse transcriptase was used to reverse-transcribe the mRNA. cDNA was used as a template for in vitro transcription where a T7 RNA polymerase   simultaneously amplified target material and incorporated cyanine 3-labeled CTP.  Labeled cRNA was purified using spin columns from the Qiagen RNeasy Mini Kit and the quantity   and quality of the cRNA was determined by Nanodrop ND-1000 UV-VIS spectrophotometer.    With the use of Agilent’s Gene Expression Hybridization Kit, 1.65 µg of cyanine 3-labeled linearly amplified cRNA was added to a hybridization cocktail and then fragmented. The hybridization   cocktail was then dispensed into the wells of gasket slides on top of which a Brassica 4x44K Gene Expression Microarray was placed. This microarray “sandwich” was then sealed in a hybridization chamber.   The microarrays were hybridized at 65°C rotating at 10 RPMs for 17 hours. Slides were washed in Agilent’s Gene Expression Wash Buffers according to manufacturer specifications.   The microarrays were scanned on the Agilent Microarray Scanner. Scanner data extraction and analysis was performed using Agilent Technologies Feature Extraction software version 10.7.3.1.Microarray data   quality was evaluated by reviewing ten standard QC metrics generated by the Feature Extraction Software [Consult the Agilent Technologies Feature Extraction Software version 10.7.3.1 reference guide   for a full explanation of the QC metrics]. To determine if there was a large hybridization, staining, or wash artifacts, a visual examination of each array was   performed by loading the array image into Feature Extraction Software. Microarrays were determined to be free of any large artifacts (≥ 10% of total surface area) that could have affected the   quality of the data.

manufacture_protocol: see manufacturer's website


title: HumanOmniZhongHua-8 v1.1 Beadchip

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Homo sapiens

manufacture_protocol: See manufacturer's website


title: 3D-Gene Rat Oligo chip 20k_1.0.0

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

organism: Rattus norvegicus

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 2000 (Methanosarcina acetivorans)

organism: Methanosarcina acetivorans


title: nCounter PanCancer Immune Profiling Panel

city: Seattle

first: NanoString

last: Technologies

address: 530 Fairview Ave N  |  Suite 2000

institute: NanoString Technologies

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


title: Illumina HiSeq 2500 (gamma proteobacterium HTCC2207)

organism: gamma proteobacterium HTCC2207


title: Illumina HiSeq 2500 (Ruegeria pomeroyi DSS-3)

organism: Ruegeria pomeroyi DSS-3


title: Illumina HiSeq 2500 (Candidatus Pelagibacter ubique HTCC1062)

organism: Candidatus Pelagibacter ubique HTCC1062


title: Illumina HiSeq 2500 (Polaribacter sp. MED152)

organism: Polaribacter sp. MED152


title: Celegans_Ce_ENTREZG version 19.0.0, Alternative to GPL200

city: Philadelphia

first: Zhe

last: Zhang

state: PA

address: Translational Research Lab

institute: University of Pennsylvania

organism: Caenorhabditis elegans

manufacture_protocol: see manufacturer's web site


title: Illumina HiSeq 2500 (Nothobranchius furzeri)

organism: Nothobranchius furzeri


title: LC Sciences MRA human miRBase v17

status: Public on Mar 01 2015

city: Madrid

first: Lidia

middle: Ángeles

last: Daimiel-Ruiz

state: Madrid

address: Ctra. Cantoblanco, Km 8

department: Nutritional Genomics of Cardiovascular Disease and Obesity

institute: Institute IMDEA Food


title: [HG-U219] Affymetrix Human Genome U219 Array (ENSG Brainarray CDF Version 18.0.0)

status: Public on Mar 02 2015

description: CDF downloaded from: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp#v18


title: Life Technologies Custom Taqman Low Density Arrays

city: Toledo

first: Daniel

last: Garcia-Ovejero

state: Toledo

address: Finca La Peraleda s/n

department: Neurología Experimental

institute: Hospital Nacional de Parapléjicos (SESCAM)

description: Custom Taqman Low Density Arrays


title: Pseudomonas aeruginosa 080529_PA01_TO_EXP

city: Worcester

first: Donald

last: Moir

state: Massachusetts

address: 1 Innovation Dr.

department: Anti-infectives

institute: Microbiotix, Inc.

organism: Pseudomonas aeruginosa PAO1

description:
NimbleGen design name 080529_PA01_TO_EXP, NimbleGen design ID 7679.  Expression design based on AE004091 downloaded 5/29/2008 - Pseudomonas aeruginosa PA01 - 14probes per target; 5553 with probes; N=77656 probes; Probes put on array a total of 5 times
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features by "Block".  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: Illumina MouseWG-6 v2.0 expression beadchip [MouseWG-6_V2_0_R1_11278593_A version]

first: Danika

middle: Mei Po

last: Khong

address: 51 Blossom Street

department: Massachusetts General Hospital

institute: Harvard Medical School

organism: Mus musculus

description:
The MouseWG-6 v2.0 Expression BeadChip offer the most up-to-date content for whole-genome expression profiling in the mouse. Featuring content derived from the National Center for Biotechnology Information Reference Sequence (NCBI RefSeq) database (Build 36, Release 22).

MouseWG-6_V2_0_R1_11278593_A


title: GeoChip 4.0

status: Public on Dec 10 2014

city: Nanjing

first: zhang

middle: kao

last: ping

address: 71 East Beijing Road

institute: Chinese Academy of Sciences

organism: Bacteria


title: KU_Wheat_Genome_135K array

status: Public on Feb 24 2015

city: Urbana

first: Tong Geon

last: Lee

state: IL

address: 1101 W Peabody

institute: University of Illinois

organism: Triticum aestivum

description: MATA135K. 52,589 probes. 60-mer probe pairs. The probes were designed with a Tm value ranging between 75 to 85°C. Random GC probes for monitoring the hybridization efficiency and four corner fiducial controls were included to assist with overlaying the grid on the image.

manufacture_protocol: High-density DNA array. See manufacturer's website at http://www.nimblegen.com/.


title: Agilent-029001 qchip Hemo custom array v1

status: Public on Dec 04 2014

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

institute: Hospital Clínic

description:
versio 1.3 del xip de CLL

Arrays of this design have barcodes that begin with 16029001 or 2529001.

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: StepOnePlus Real-Time PCR system

city: Tokyo

first: Tomoko

last: Nozoye

address: 1-1-1 yayoi bunkyo-ku

institute: The University of Tokyo

organism: Zea mays

description: PCR assay

manufacturer: Applied Biosystems, Foster City, CA, USA


title: Functional gene array GeoChip 4.2

status: Public on Dec 31 2014

city: Beijing

first: Yu

last: Xia

state: Beijing

address: Tsinghua University, Haidian District

department: Environmental school

institute: Tsinghua Univeristy

organism:
Bacteria
Archaea
Eukaryota
Viruses

description:
Custom microarray.
50-nt oligonucleotide probes.


title: Agilent G2534A oligonucleotide-microarray (AMADID:026869) (Feature Number version)

status: Public on Nov 30 2014

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

institute: Institut Pasteur

organism: Candida albicans

manufacture_protocol: Agilent G2534A oligonucleotide-microarray (AMADID:026869) containing 15744 Candida albicans probes, corresponding to 6105 genes.


title: Illumina HiSeq 2000 (Trichoderma reesei)

status: Public on Dec 24 2013

last: GEO

organism: Trichoderma reesei


title: Agilent-037880/INRA Sus scrofa 60K v1 (enriched with immune system muscle and adipose tissue genes) [Feature numbers]

status: Public on Mar 25 2014

city: Saint-Gilles

first: Isabelle

last: Luron

state: Rennes

address: Domaine de la Prise

department: Human Nutrition Division

institute: National Institute for Agronomical Research (INRA)

organism: Sus scrofa

description:
Arrays of this design have barcodes that begin with 16037880 or 2537880
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: A

last: Vincent

first: M

last: Jegou

first: F

last: Moreews

first: I

last: Louveau

last: Damon

first: C

last: Rogel-Gaillard

first: L

last: Liaubet

last: Le Huerou-Luron

manufacture_protocol: see manufacturer's web site at http://www.genomics.agilent.com/GenericB.aspx?PageType=Custom&SubPageType=Custom&PageID=2011


title: NimbleGen Atlantic Cod Oligonucleotide 135k Array Version 1 [100610_GM_FY_EXP]

status: Public on Jan 22 2013

city: Bergen

first: Fekadu

last: Yadetie

address: Thormøhlensgt. 53A/B

department: Biology

institute: University of Bergen

organism: Gadus morhua

description:
NimbleGen design name: 100610_GM_FY_EXP
NimbleGen design ID: 531893
Native array description file: 100610_GM_FY_EXP.ndf
Native array description file: 100610_GM_FY_EXP.ngd
44k cDNAs were used (26k assembled EST contigs and 18 singletons from the cod genome sequencing consortium; see The genome sequence of Atlantic cod reveals a unique immune system Starr et al., 2011; Nature 477:207 [PMID 21832995]). Three 60mer probes were prepared for each cDNA sequence, 125826 cod probes in total.  The array contains 137604 features, including  11779 Nimblegen control probes.
The supplementary file 'GPL15700_cDNA_seqs.txt' contains all cDNA sequences used in the design of the probes.


title: [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [probe set (exon) version]

status: Public on Sep 30 2014

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Homo sapiens

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

#%chip_type=HuGene-2_0-st-v1
#%lib_set_name=HuGene-2_0-st
#%lib_set_version=v1
#%genome-species=Homo sapiens
#%genome-version=hg19
#%genome-version-ucsc=hg19
#%genome-version-ncbi=GRCh37
#%genome-version-create_date=2009-02-00
#%genome-lifted-method=liftOver
#%genome-lifted_from-species=Homo sapiens
#%genome-lifted_from-version-ucsc=hg19
#%genome-lifted_from-version-ncbi=GRCh37
#%netaffx-annotation-date=2013-08-30
#%netaffx-annotation-netaffx-build=34


title: Agilent-024283 Viro5AG-60k (Probe Name version)

status: Public on Sep 01 2012

city: San Francisco

first: Charles

last: Chiu

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

organism: Viruses

description: This platform includes more than 60,000 oligonucleotides for the detection and discovery of both known and novel viruses. The sequences of 36,432 viral probes from this platform have been previously published in the GEO database as MegaViro  (GPL1834), Viro3 (GPL3429), and Viro4 (GPL6862), collectively now designated as V3/V4 viral probe sets. For comparison purposes, both 70mer and 60mer representations of these viral oligos are present. Some viral probes corresponding to phages and other less critical targets have been removed. More than 20,000 additional probes have been added for (1) better subtyping of respiratory and diarrheal viral as well as nonviral pathogens, (2) enhanced detection of specific viral families, and (3) subtyping of HIV/SIV strains. Control oligonucleotides are also included in the design.


title: Genotypic Technology Pvt. Ltd. designed Custom Whole Genome Candida albicans 8x15k GE Microarray (AMADID-026377)

status: Public on Apr 22 2011

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

first: Raja

middle: C

last: Mugasimangalam


title: Agilent-020938 S. salar (Salmon) Oligo Microarray (Feature Number version)

status: Public on Jul 25 2008

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Salmo salar

description:
S. salar (Salmon) Oligo Microarray

Arrays of this design have barcodes that begin with 16020938 or 2520938.

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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7303.


title: TIGR PFGRC Aspergillus nidulans v1 array based on strain FGSC A4 (condensed - does not contain replicate spots)

status: Public on May 01 2008

city: Norwich

first: Andrew

last: Breakspear

address: Norwich Research Park

country: United Kingdom

institute: John Innes Centre

organism: Aspergillus nidulans

description: This set includes 11481 oligonucleotides distributed in 48 blocks

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


title: Agilent-024283 Viro5AG-60k

status: Public on Nov 01 2010

description: This platform includes more than 60,000 oligonucleotides for the detection and discovery of both known and novel viruses.  The sequences of ~36,000 of the viral


title: Agilent-020908 Oryctolagus cuniculus (Rabbit) Oligo Microarray (Probe Name version)

status: Public on Mar 16 2011

organism: Oryctolagus cuniculus


title: [dsmM_ANIGERa_anColl] DSM Aspergillus niger CBS513.88 14k v1

status: Public on Apr 24 2008

city: Delft

first: Wilbert

last: Heijne

address: PO Box 1

department: DFS/R&D/Genetics

country: Netherlands

institute: DSM Food Specialties

organism: Aspergillus niger CBS 513.88

first: Noël

middle: M

last: van Peij

first: Hein

last: Stam

first: Herman

last: Pel

middle: H

manufacture_protocol: Based on the genome sequence of A. niger CBS513.88, a proprietary GeneChip®, dsmM_ANIGERa_coll511030F, was designed for DSM according to the GeneChip® CustomExpress™ program by Affymetrix (Affymetrix, Inc., Santa Clara, CA). The chips of the 49 format contain 11μm features. There are 12 pairs of 25-oligonucleotides in each probe set representing each of approximately 14259 annotated ORFs and genetic elements of A. niger. The probe sequences were designed based on maximally the 600 bp region in the (predicted) coding sequence stretching from the 3’-end. Typical Affymetrix control probe sets were included (B. subtilis, E. coli, Bacteriophage P1 and A. thaliana spike controls). For several constitutive A. niger genes, separate 3’-end, middle and 5’-end probe sets were designed that allow monitoring of the efficiency of the in vitro transcription reaction. Genes of one gene family can be represented by a unique and a shared probe set. In total 14554 probesets are measured through the dsmM_ANIGERa_coll511030F GeneChip®.


title: Agilent-023795 Human DNA Methylation Microarray 244k

status: Public on Sep 02 2010

description:
Human DNA Methylation Microarray 244k

Arrays of this design have barcodes that begin with 16023795 or 2523795.

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.