title: Pm 5K Random Array II

status: Public on Nov 21 2013

city: University of Melbourne

first: Alex

last: Andrianopoulos

state: Victoria

address: Royal Parade

department: Department of Genetics

country: Australia

institute: University of Melbourne

organism: Talaromyces marneffei

technology: spotted DNA/cDNA

distribution: non-commercial

manufacture_protocol:
1. Two small insert (400-600 bp) DNA libraries of partially digested P. marneffei genomic DNA were generated using Sau3AI or TaqI cloned into the BamHI or ClaI sites of pALX223, respectively.
2. Independent colonies from both libraries were selected for the construction of the microarrays
3. Colonies (5376) were picked using the BioRobotics BioPick machine and individually placed into 384 well plates containing LB broth.
4. Colonies were then grown overnight, DNA prepared from a 2 ml aliquot of each culture and used to PCR amplify the gDNA inserts with M13 forward and reverse primers.
5. The resulting PCR products were purified using Millipore Multiscreen filter plates via a manifold vacuum. The quality and quantity of purified amplified product were ascertained through agarose gel electrophoresis.
6. Amplified DNA inserts were adjusted to 250 ng/ml in 50% DMSO buffer for printing.
7. PCR products from 38 previously characterised P. marneffei sequences were used as controls. Gene IDs for these sequences are PMAA_085540, PMAA_003830, PMAA_006930, PMAA_011430, PMAA_011430, PMAA_014540, PMAA_021220, PMAA_030430, PMAA_030490, PMAA_032950, PMAA_043500, PMAA_054000, PMAA_054000, PMAA_056390, PMAA_056390, PMAA_067280, PMAA_067670, PMAA_067970, PMAA_068110, PMAA_070290, PMAA_071350, PMAA_075300, PMAA_078000, PMAA_078530, PMAA_078530, PMAA_079960, PMAA_080160, PMAA_080470, PMAA_083100, PMAA_084900, PMAA_084960, PMAA_086720, PMAA_093460, PMAA_093460, PMAA_095260, PMAA_099990, PMAA_100040, PMAA_100070.
8. Scorecard Version 2 were also used as controls.
9. The amplified DNA inserts were arrayed in duplicate onto Corning GAPS II aminosilane glass slides using the ESI Virtek Arraying Robot. DNA was spotted using Point Technology split pins.
10. Slides were baked and UV irradiated to crosslink the DNA.


title: Pm 5K Random Array I


title: Agilent-013384 Yeast Oligo Microarray (V2) G4140B (Feature Number version)

status: Public on Sep 24 2005

city: Palo Alto

last: Agilent Technologies

state: CA

country: USA

institute: Agilent Technologies

organism: Saccharomyces cerevisiae

technology: in situ oligonucleotide

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.

Arrays of this design have barcodes that begin with 16013384 or 2513384.

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 GPL7293.

distribution: custom-commercial

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


title: HumanMouseRat miRNA Array [miRBase 10.0]

status: Public on Nov 10 2013

city: Dalian

first: Zhiguang

last: Li

state: Liaoning

address: 9 Lvshun South Road

department: Institute of Cancer Stem Cell

country: China

institute: Dalian Medical University

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

technology: spotted oligonucleotide

description: Array was made by LC Sciences at Houston, Texas based on Sanger miRBase Release 10.0. It included probes for 1094 unique mature miRNAs with 711, 568, and 348 from human, mouse, and rat respectively.  Each probe was repeated 3 x times. Sixty-three control probles with variable repeats were also present on the array.


title: ORB version 1 MicroRNA Microarray (Sanger version 9.0 microRNA database)

status: Public on Sep 30 2013

city: Coral Gables

first: Nanette

middle: Hahr

last: Bishopric

state: FL

address: 10 Edgewater Drive, Apt. 9A

department: Medicine

institute: Nanette Bishopric

manufacture_protocol: proprietary oligonucleotide deposition of Invitrogen Ncode version 2 probe set


title: Applied Biosystems 250 TaqMan microRNA Assay

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

organism: Homo sapiens

technology: RT-PCR

distribution: virtual

manufacture_protocol: see manufacturer's website


title: S. cerevisiae flocculation array

status: Public on Oct 01 2013

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

country: Germany

institute: Universität Hannover

manufacture_protocol: Oligonucleotide design and synthesis: 70mer oligonucleotides with a 5’ aminolink were designed and synthesised by Operon (Cologne, Germany). Spotting protocol: To produce microarrays silylated slides were purchased from TeleChemTM International Inc. (Sunnyvale, CA, USA) and the printing of the oligonucleotides was performed by using an AffymetrixTM 417 arrayer. Oligonucleotide solutions were prepared in 96-well-plates containing each 30 µl. The concentration of the printed oligonucleotides was 50 µM in 1x ArrayItTM Microarray Spotting Solution Plus. After spotting, the slides were incubated at 80 °C for 2 h. Slides were blocked in SSC containing 1% BSA (Sigma) for 45 min and rinsed with water for 5 min.


title: OUHSC Neisseria gonorrhoeae 12K

status: Public on Sep 27 2013

city: Oklahoma City

first: Lydgia

last: Jackson

state: OK

address: 975 NE 10th Street

department: Micorbiology and Immunology

institute: OUHSC

organism: Neisseria gonorrhoeae FA 1090

manufacture_protocol: The present studies were done using a custom 12K microarray designed by CombiMatrix Corporation (Mukilteo, WA).  Probe lengths were 34-35 bp with each ORF having 4-5 probes; representing 1916 genes identified in the NCBI annotation of the N. gonorrhoeae FA1090 genome.  Controls on the array included: no oligo and negative control-bacterial probes, factory probes, and three Arabidopsis thaliana genes as positive controls. Probes also were designed in intergenic regions to include both the sense and antisense strand. Experimental and control probe sets were distributed randomly across the microarray.


title: Methanotrophs microarray_EBL

status: Public on Sep 28 2013

city: Seoul

first: Kyung-eun

last: Moon

address: 52, Ewhayeodae-gil, Seodaemun-gu

country: South Korea

institute: Ewha womans university

organism: Bacteria

manufacture_protocol:
Spotted amplified cDNA array on glass.  Produced with cDNA clones expressed in the methanotrophic bacteria. genomic DNA used to produced the cDNA library,
PCR products were re-arrayed into 384-well plates in 50% DMSO and printed onto glass microscope slides (Digital Genomics, Seoul, Korea) as high-density cDNA microarrays using the MicroGridII TAS arrayer (Genomic Solutions, Ann Arbor, MI)


title: Agilent-026862 SexiArray_v1.0 array (Probe Name version)

city: Burjassot

first: Agata

middle: K

last: Jakubowska

state: Valencia

address: Dr. Moliner 50

department: Genetics

country: Spain

institute: University of Valencia

organism: Spodoptera exigua

description: Microarray features based on Spodoptera exigua transcriptome sequencing project GAOR00000000.


title: Ambion mirVana™ miRNA Probe Set 1564V1

city: Newtown

first: Jennifer

middle: R

last: Gamble

state: NSW

address: Locked Bag No. 6

institute: CENTENARY INSTITUTE


title: 454 GS FLX Titanium (Bupleurum scorzonerifolium)

status: Public on Sep 26 2013

last: GEO

organism: Bupleurum scorzonerifolium

technology: high-throughput sequencing


title: 454 GS FLX Titanium (Bupleurum chinense)

organism: Bupleurum chinense


title: CDC Group I Clostridium botulinum subtyping microarray v. 1

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

organism: Clostridium botulinum

manufacture_protocol: Oligonucleotides (with C6 amino linker) were suspended at 50pmoles/ul in spotting buffer and spotted onto SperEpoxy2 substrate glass slides using 946MP3 Micro Spotting Pins.


title: ITB UniversalArray 49 v2

city: Bologna

first: Simone

last: Rampelli

address: Via Belmeloro 6

country: Italy

institute: University of Bologna

organism: synthetic construct

description:
The Ligase Detection Reaction (LDR) technology of HTF-Microbi.array is based on the discriminative properties of the DNA ligation enzyme. This technique requires the design of a pair of two adjacent oligonucleotides specific for each target sequence: a probe specific for the variation (called "Discriminating Probe", or DS) which carries a 5'-fluorescent label, and a second probe, named "Common Probe" (or CP), starting one base 3'-downstream of the DS that carries a 5'-phosphate group and a unique sequence named cZipCode at its 3'-end. The oligonucleotide probe pairs and a thermostable DNA ligase are used in a LDR reaction with previously PCR-amplified DNA fragments. The LDR products, obtained only in presence of a perfectly matching template by action of the DNA ligase, are addressed to a precise location onto a Universal Array (UA), where a set of artificial sequences, called Zip-codes are arranged. These products carry both the fluorescent label and a unique cZipCode sequence and can be detected by laser scanning and identified according to their location within the array.

Refrence - Candela M, Consolandi C, Severgnini M, Biagi E, Castiglioni B, et al. High taxonomic level fingerprint of the human intestinal microbiota by ligase detection reaction--universal array approach. BMC Microbiol. 2010 Apr 19;10:116. doi: 10.1186/1471-2180-10-116.

manufacture_protocol: Phenylen-diisothiocyanate activated chitosan glass slides were used as surfaces for the preparation of universal arrays, comprising a total of 49 Zip-codes. In particular, glass slides were cleaned by soaking in 1M NaOH for 2 h followed by rinsing with distilled water, immersed in 1N HCl solution overnight a shaker, and then rinsed again in distilled water. Slides were immersed in 96% ethanol for 10 min and then washed three times with distilled water. Slides were immersed in acetone for 10 min, removed, and dried. Then they were treated with 1% (v/v) GOPS (3-glycidoxypropylsilane) in 95% ethanol for 1 h. Excess silane was removed by dipping the slides in 95% ethanol for 1 min. Finally they were dried at 150 °C for 20 min. The polymer solution was prepared by dissolving 10 g of chitosan (400 kDa) in a liter of 50 mM HCl. The solutions were heated at 70 °C, stirred for 1 h, and then filtered. Treated slides were left in a water solution containing 10% PBS and 10% polymer (0.1% w/v) for 1 h on a shaker. The slides were washed five times with distilled water, centrifuged at 800 rpm for 3 min. and dried for 10 min at 45 °C. The slides were then activated by immersion into a 0.2% solution of 1,4-phenylene diisothiocyanate in 90% N,N-dimethylformamide and 10% pyridine. The activation reaction was carried out at room temperature for 2 h. After being washed with methanol and acetone (2 min each), the activated slides were dried and stored, until used, in a dark closed box under vacuum. Solutions of 5‘-amino-modified oligonucleotides with a 5‘-polyA tail, called zip-codes, were transferred into a 384-well microtiter plate in a volume of 30 μL and spotted at a final concentration of 50 μM in 150 mM sodium phosphate buffer (pH 8.5). The spotting was performed using a contact system (MicroGrid II Compact, Biorobotics, UK).


title: Agilent-031068 EmbryoGene Porcine Array Version 1 (EMPV1) [Probe version]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Sus scrofa

description:
EmbryoGENE Porcine Embryo microarray
Custom Microarray GE 4x44K with designID=031068
Specific array desgin from porcine preimplantation development
Arrays of this design have barcodes that begin with 16031068 or 2531068.
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: Stephen

last: Tsoi

first: Chi

last: Zhou


title: NanoString nCounter Human GX Lymphoma Classification Custom CodeSet

status: Public on Sep 25 2013

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

institute: University of Regensburg

technology: other

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


title: NimbleGen - Botrytis cinerea - 4*72K - INRA improved (2009) [091123_INRA_Botrytis_expr]

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

country: France

institute: INRAE

organism: Botrytis cinerea

description: INRA improved (2009) 4plex expression design for Botrytis cinerea, 3 probes per gene (62478 probes covering 20885 gene models + 9559 RANDOM probes), 1 copy on the array.

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 (Crassostrea hongkongensis)

organism: Magallana hongkongensis


title: Utz lab immunodeficiency antigen and serum factor microarray, number 1

status: Public on Sep 24 2013

city: Oberlin

first: Jordan

last: Price

state: OH

address: 119 Woodland St

institute: Oberlin College

organism:
Gallus gallus
Homo sapiens
Bos taurus

technology: spotted peptide or protein

manufacture_protocol: Proteins were printed at 0.2mg/ml (unless otherwise indicated) on nitrocellulose FAST slides (Whatman, Piscataway, NJ) in replicates of six using a BioRad VersArray robot and ChipWriter Pro software (Bio Rad, Hercules, CA).


title: SABiosciences Human PCR assay panel autophagy

city: sendai

first: yosuke

last: shimodaira

address: 1-1, seiryomachi, aoba-ku

country: Japan

institute: tohoku university

description: SABiosciences RT² Profiler panel of PCR assays.


title: AB SOLiD 3 Plus System (Symphysodon aequifasciata)

organism: Symphysodon aequifasciata


title: Illumina HiSeq 2000 (Kineococcus radiotolerans)

status: Public on Sep 23 2013

organism: Kineococcus radiotolerans


title: SABiosciences Human PCR assay panel UPR


title: Illumina MouseWG-6 v1.0 expression beadchip [custom gene-centered version]

city: Montreal

first: Andrea

last: Richter

state: Quebec

address: 3175 chemin Côte-Ste-Catherine

department: Service de Génétique Médicale

country: Canada

institute: CHU Sainte-Justine

organism: Mus musculus

technology: oligonucleotide beads


title: Utz lab immunodeficiency antigen and serum factor microarray, number 2


title: Agilent-033694 MTB_ILD

city: New Delhi

first: Sachin

middle: Kumar

last: Samuchiwal

address: Aruna Asaf Ali Marg,

department: Recombinant Gene Products Group

country: India

institute: International Centre for Genetic Engineering and Biotechnology (ICGEB)

organism: Mycobacterium tuberculosis

description:
Mycobacterium tuberculosis
Arrays of this design have barcodes that begin with 16033694 or 2533694 by iLife discoveries.
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: Ashish

middle: c

last: Trivedi

first: sachin

middle: k

first: Anand

last: Ranganathan


title: Illumina HiSeq 2000 (Methylomicrobium alcaliphilum 20Z)

organism: Methylotuvimicrobium alcaliphilum 20Z


title: Illumina HumanHT-12 V3.0 expression beadchip [gene symbol; HumanHT-12_V3_0_R3_11283641_A]

organism: Homo sapiens

manufacture_protocol: See the manufacturer's website.


title: Lactobacillus rhanmosus ATCC 53103 4x44K Microarrays

status: Public on Sep 19 2013

city: Jeonju

first: Younghoon

last: Kim

address: 567 Baekje-Daero, Deokjin-Gu

department: Department of Animal Science

institute: Chonbuk National University

organism: Lacticaseibacillus rhamnosus GG

manufacture_protocol: see Agilent site


title: Utz lab SLE antigen and serum factor microarray


title: Illumina HiSeq 2500 (Synechococcus elongatus PCC 7942)

organism: Synechococcus elongatus PCC 7942 = FACHB-805


title: Mammalian miRNA Array V3.0 (CapitalBio, Beijing, China)

city: Beijing

first: Subi

last: Wei

state: Beijing

address: Xueyuan Load

department: Medical Systems Biology Research Center

institute: Tsinghua university

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: As described in CapitalBio Corporation Manual


title: Illumina HiSeq 2000 (Glycine soja)

organism: Glycine soja


title: Agilent-036353 S.solea_v2 array (Feature Number version)

status: Public on Sep 20 2013

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

institute: University of Padova

organism: Solea solea

description:
GE 8x15k oligo microarray that covers 12,836 annotated transcripts (Isotigs) of the common sole (Solea solea). Roche 454 sequence reads were produced from a normalized cDNA library constructed using a mixture of RNAs from whole larvae (1-4-6-11-13-18-20-33 days posth hatching) and adult tissues (liver and intestine). All 454 sequences were then assembled into Isotigs, representing putative transcripts, by using Newbler 2.6 software with default settings. All Isotigs are stored in the public database Transcriptome Shotgun Assembly Sequence Database (TSA, http://www.ncbi.nlm.nih.gov/genbank/tsa) under accession number GAAQ00000000 (To be made publicly available after paper publication), transcripts sequences can be retrieved by using IsotigName as search criteria. One probe for annotated sequences with known orientation (10,987) was designed while, whenever possible, two probes with both orientations were designed for Isotigs with unknown/ambiguous orientation (1,849 indicated by Isotig ID plus prefix S_ or AS_ ). A total of 14,674 oligonucleotide probes (60 nt) were in situ synthesized onto the array, using Agilent non-contact ink-jet technology (8 x 15K format, including default positive and negative controls).  Probe ID on the array corresponds to IsotigName.
In situ long-oligonucleotide microarray.

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


title: Illumina Genome Analyzer II (Apis mellifera scutellata)

status: Public on Sep 18 2013

last: GEO

organism: Apis mellifera scutellata


title: Real Time Fast 7900 HT PCR System (Applied Biosystems)

city: Messina

first: Alfredo

last: Conti

state: Sicily

address: via La Farina 15

institute: Alfredo

description: PCR assay


title: Agilent-016989 Synechocystis array [ORF version]

city: Turku

first: Taina

last: Tyystjarvi

address: Pharmacity/Itäinen Pitkäkatu 4 C, 6th floor

department: Biochemistry

country: Finland

institute: University of Turku

organism: Synechocystis sp. PCC 6803

description: The ID column represents the Agilent Systemctic Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL6546

manufacture_protocol:
Agilent’s SurePrint technology
8x15K custom design


title: Illumina HiSeq 2500 (Pseudomonas aeruginosa UCBPP-PA14)

status: Public on Sep 17 2013

organism: Pseudomonas aeruginosa UCBPP-PA14


title: Nanostring nCounter Human miRNA Expression Assay

city: Chapel Hill

first: Afsar

middle: Raza

last: Naqvi

state: North Carolina

address: Brauer Hall 111

department: Periodontics

institute: University of North Carolina chapel Hill

description: +++ Functional tests indicate that this probe has some level of background which may be corrected prior to normalization.

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


title: Agilent-014791 Human CpG Island ChIP-on-Chip Microarray 244K (G4492A) (Probe Name version)_NCBI36/hg18

status: Public on Sep 16 2013

city: Heidelberg

first: Dr Efterpi

last: Kostareli

state: Baden-Wurtenberg

address: Im Neuenheimer Feld 280

institute: DKFZ

description:
Human CpG Island Chip-on-Chip Set 244K
Probe mapping based on genome build NCBI36/hg18.

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


title: Illumina Genome Analyzer IIx (Pseudomonas aeruginosa UCBPP-PA14)


title: Salmonella Typhimurium 8 x 15

city: Hinxton

first: Vanessa

middle: Kuan

last: Wong

state: Cambridgeshire

address: Wellcome Trust Genome Campus

department: Microbial Pathogenesis

country: United Kingdom

institute: Wellcome Trust Sanger Institute

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

manufacture_protocol: Agilent protocol : Agilent Low Input Quick Amp WT Labeling Kit, one-color, Agilent, 5190-2943


title: Salmonella Typhi 8X15K

organism: Salmonella enterica subsp. enterica serovar Typhi


title: Illumina Genome Analyzer II (Oikopleura dioica)

status: Public on Sep 13 2013

organism: Oikopleura dioica


title: OpArray Human Cancer 3.0K

city: Pusan

first: Ho Sung

last: Kang

address: 30, Jangjeon-dong

department: Departmemt of Molecular Biology

institute: Pusan National University

manufacture_protocol: 70mer oligonucleotides, contains 3,096 oligos (genome oligos, positive control oligos, randomized negative control oligos, spiking negative control oligos and alien control oligos). Genome oligos represent 3,034 predicted genes. Spotted on GAPS ll slides (Corning Incorporated) in collaboration with GenoCheck Co.Ltd. to provide the best hybridization kinetics with very low background. Supplied as DNA immobilized ready to use.


title: Agilent-025070 S. cerevisiae 180K tiling 3-6-ARS_CEN_10bp_wc_CGH

last: Ranjan

state: Maryland

address: 37 convent st, room 6114

department: LBMB

institute: NCI

organism: Saccharomyces cerevisiae

description:
Chr3,6,earlyARS,allCEN,10bp res, w&c

Arrays of this design have barcodes that begin with 16025070 or 2525070.

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 II (Drosophila pseudoobscura; Drosophila virilis; Drosophila yakuba)

status: Public on Sep 11 2013

organism:
Drosophila pseudoobscura
Drosophila virilis
Drosophila yakuba


title: Illumina Genome Analyzer II (Drosophila melanogaster; Drosophila pseudoobscura; Drosophila virilis)

organism:
Drosophila melanogaster
Drosophila pseudoobscura
Drosophila virilis


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

city: Chiba city

first: Naohiko

last: Seki

state: Chiba

address: Inohana1-8-1, Chuo-ku

institute: Chiba University

manufacture_protocol: See manufacturers website


title: Illumina Genome Analyzer IIx (Callithrix jacchus)

status: Public on Sep 10 2013

organism: Callithrix jacchus


title: Illumina Genome Analyzer IIx (Loxodonta africana)

organism: Loxodonta africana


title: Princeton uncultured crenarchaeote nirS gene BC014 array

status: Public on Sep 12 2013

city: Princeton

first: Xuefeng

last: Peng

state: NJ

address: Guyot Hall

department: Geosciences

institute: Princeton University

organism: uncultured bacterium

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


title: Illumina HiSeq 2000 (Arabidopsis suecica)

status: Public on Sep 09 2013

organism: Arabidopsis suecica


title: Illumina Genome Analyzer (Arabidopsis thaliana x Arabidopsis arenosa)


title: NimbleGen Burkholderia pseudomallei K96243 385K tiling array [071211_BPK96243_CO_Tiling]

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

organism: Burkholderia pseudomallei K96243

description: NimbleGen design name 071211_BPK96243_CO_Tiling. A 385K tiling expression array fabricated by Roche NimbleGen (Roche NimbleGen, USA) based on the BpK96243 reference genome PRJNA57733_AssemblyASM1154v1 (Holden et al. 2004). The array contains 384,926 50-mer oligonucleotide probes representing both sense and antisense strands, with an overlapping mean distance of 15 bp between adjacent probes. Collectively, 95.1% of the BpK96243  non-repetivitive genome, including genic and intergenic regions, are represented on the array. Control probes without sequence similarity  to BpK96243 were included for background correction and array alignment.


title: NimbleGen Drosophila melanogaster Gene expression array [080306_DMr43_expr; 090901_DMr43_expr]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Drosophila melanogaster

description:
Expression design for Drosophila melanogaster (Release 4.3).
DESIGN_NAME: 080306_DMr43_expr, DESIGN_ID: 7227
DESIGN_NAME: 090901_DMr43_expr, DESIGN_ID: 10557
SLIDE_LAYOUT_NAME: NimbleChip_HX12

distribution: commercial

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


title: Illumina Genome Analyzer IIx (Macaca fascicularis)

organism: Macaca fascicularis


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


title: Illumina HiSeq 2000 (Vernicia fordii)

organism: Vernicia fordii


title: Illumina HiSeq 2000 (Fukomys damarensis)

organism: Fukomys damarensis


title: Agilent-034814 Streptococcus dysgalactiae subsp. Equisimilis 15K J11420

city: Tokyo

first: Shinya

last: Watanabe

address: 1-21-1 Toyama

department: Department of Infectious Diseases

institute: National Center for Global Health and Medicine

organism: Streptococcus dysgalactiae subsp. equisimilis

description:
Arrays of this design have barcodes that begin with 16034798 or 2534798.

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: nCounter Human Reference GX Kit

city: Baltimore

first: Lucio

last: Gama

state: MD - EUA

address: 733 N Broadway St - BRB 831

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins School of Medicine

organism: Homo sapiens

description: nCounter Human Reference GX Kit Gene Expression CodeSet (NanoString Technologies)


title: Illumina MiSeq (Synechocystis sp. PCC 6803)

status: Public on Sep 08 2013

organism: Synechocystis sp. PCC 6803


title: Illumina HiSeq 2000 (Miniopterus schreibersii)

organism: Miniopterus schreibersii


title: Perch 1000 candidate-gene microarray

city: Québec

first: Berenice

last: BOUGAS

state: QC

address: 1030 avenue de la médecine, IBIS, Pavillon Marchand

department: Biology

institute: Laval university

organism: Perca flavescens

manufacturer: Great Lakes Institute for Environmental Research, University of Windsor, ON, Canada

manufacture_protocol: One thousand oligonucleotide probes (58 to 62bp) were designed from a set of transcripts comprising both a yellow perch transcriptome assembled from a previous 454 experiment focusing on metal contaminated and uncontaminated yellow perch (Pierron et al., 2011) and yellow perch transcripts available in online databases. The probes were designed using the command line version of ProDesign (Feng and Tillier, 2007) and synthesized by Sigma®. ProDesign maximizes probe specificity and ensures that each probe cannot be found among the list of interesting genes, as well as among the list of all the unwanted sequences. 6C amine spacers were added to each probe at the 5’ extremity. All probes were resuspended in SSC 3X and stocked in 384-well plates. In total, 219 gene sequences were chosen from the literature according to their role in key biological pathways, such as lipid and energy metabolism, in fish. The other sequences were chosen from the 454 experiment as follows: 40 genes that presented an interesting SNP and 741 genes from the 1297 unique genes that were annotated from either the swissprot or the nr protein database (minimal e-value < 1.0 e-10 using the blastx program from BLAST 2.2.23+, http://blast.ncbi.nlm.nih.gov). Among these 741 genes, 49 genes were manually chosen because of their important role in global metabolism or response to metal exposure, 196 genes were chosen because their expression levels were significantly correlated with hepatic Cd or Cu concentrations (Pierron et al., 2011), and the 496 remaining genes correspond to genes annotated with an e-value lower than 1.0e-30 and that were significantly different among lakes but not directly correlated with metal concentration. We added four positive control spots containing a mix of all probes and four negative spots that only contained SSC 3X and 6C spacers but no DNA probe. The probes were printed on SuperChip®Poly-L-Lysine slides (Thermo Scientific®) with the Spotarray 24 (PerkinElmer Life Sciences). The Stealth 3 Microarray Printing Pins were used to deposit 0.0125 µL (0.011 µg oligonucleotides) per spot onto the slide. The probes were then crosslinked with UV irradiation. The microarray layout consists of a 4-by-4 metagrid with 9×14 spots in the subgrids. Each probe was duplicated side by side and the 1000 probes were deposited in a 4-by-4 metagrid. Finally, the 4-by-4 metagrid is replicated three times on the chip. In total, the 1000 probes are thus replicated six times on each slide, improving the robustness and repeatability of the measurements.


title: LC Sciences Mouse 01_M9.1_070362 miRNA Array

status: Public on Sep 06 2013

city: New haven

first: seyedtaghi

last: takyar

state: CT

address: 300 Cedar street

department: Medicine

institute: Yale School of Medicine

organism: Mus musculus

description: Detects miRNA transcripts listed in Sanger miRBase Release 9.1 (http://www.sanger.ac.uk/Software/Rfam/mirna/). Multiple control probes are included in each chip. The control probes are used for quality controls of chip production, sample labeling and assay conditions. Among the control probes, PUC2PM-20B and PUC2MM-20B are the perfect match and single-based match detection probes, respectively, of a 20-mer RNA positive control sequence that is spiked into the RNA samples before labeling. One may assess assay stringency from the intensity ratio of PUC2PM-20B and PUC2MM-20B, which is normally larger than 30. When the option for custom probes is selected, custom probes are also included.

manufacture_protocol: see manufacturer's website


title: MIT Boissonneault-Housman Ps-n10772 feature cDNA microarray v1

city: Cambridge

first: Katie Rose

last: Boissonneault

state: MA

address: 77 Massachusetts Ave., 76-553

web_link: http://to be added

institute: Massachusetts Institute of Technology

organism: Pseudo-nitzschia multiseries

description:
Pseudo-nitzschia multiseries CL-125 (Ps-n).
A number of the cDNAs printed on the array were sequenced more than once and in both directions (5' and 3'). All the Ps-n ESTs were submitted as separate files to the NCBI EST database. All of the replicate sequences for each cDNA clone have been included in the platform data table, with the corresponding NCBI #, to offer the reader the full dataset for each clone.

manufacturer: Massachusetts Institute of Technology, D.E. Housman Laboratory

manufacture_protocol:
cDNA library: Ps-n strain CL-125 cells from non-axenic cultures were harvested during the late exponential through mid-stationary growth phases, under predominantly toxin-producing conditions. Cultures were split into 250-500 mL aliquots that were centrifuged for 15 min at 1000 g. The loose pellets were pooled, and centrifuged again briefly to remove any residual culture medium. Total RNA was extracted immediately by homogenizing the cells in TRIzol® (Invitrogen Corporation, Carlsbad, CA, USA). Insoluble material was removed by low-speed centrifugation of the samples. RNA was precipitated twice with salt and ethanol, resulting in high-quality total RNA, as indicated by 260/280 O.D. ratios and formaldehyde agarose gel electrophoresis. Poly (A)+ RNA was then isolated from total RNA using a biotin-labeled oligo(dT)20-streptavidin kit (Roche Molecular Biochemicals, Indianapolis, IN, USA) following the manufacturer’s instructions. First-strand cDNA was prepared from 5 µg poly (A)+ RNA using Superscript II (Invitrogen, Grand Island, NY, USA), NC-p7 (an RNA chaperone), and oligo pd(TZ) (an oligo-dT primer with some of the internal thymidine residues replaced with 3-nitropyrrole to minimize mispriming to internal A-rich sequences). Double-stranded cDNA was generated using RNase H, E. coli DNA polymerase I, and E. coli ligase. The ends of the cDNAs were polished with T4 DNA polymerase, and BstXI adaptors were ligated to the cDNA ends. The cDNAs were then fractionated on sucrose gradients, ligated into pMD1 (a pUC-based vector) and transformed, by electroporation, into E. coli DH10B cells [Das et al., 2001]. Following an initial library plating, 19,200 individual colonies were picked and stored at -80ºC in 15% glycerol for further analysis.(cDNA library constructed at McGill University, Pelletier lab (Boissonneault, KR, Harvey, I, Nguyen, N, and Pelletier, J)).
cDNA preparation: 5,265 clones from the Ps-n cDNA library were grown overnight in Luria broth with carbenicillin (50 µg mL-1) at 37ºC on a shaker table. Three vector only and twelve Homo sapiens cDNA control clones (J. Pelletier) were also grown under these conditions.  Ten microliters of bacterial culture were used in 100-µL PCR reactions with primers T7 forward (TAATACGACTCACTATAGGG) and M13 reverse (CAGGAAACAGCTATGAC), which flanked the cloning site of the pMD1 vector. PCR amplification was performed using HiFI Taq polymerase (Invitrogen Corporation). An initial DNA denaturation step at 94ºC for 2 min was followed by 35 amplification cycles (0:30 melting at 94ºC, 0:30 annealing at 55ºC, 1:00 extension at 68ºC). PCR products were purified using MultiScreen size-exclusion filter plates (Millipore, Billerica, MA, USA). The DNA was then resuspended in 100 µL of nuclease-free de-ionized water and transferred to clean plates using a mechanical pipetting station. DNA quality was verified by 1% agarose gel electrophoresis for eight samples per 96-well plate; DNA concentration was determined by PicoGreen fluorescent staining [63]. Fifty µL of each PCR product was dried by vacuum centrifugation and then resuspended in 10 µL of 1.5 M Betain /3X SSC print buffer, yielding an average final concentration of 600 ng µL-1.
Printing Array: Ps-n cDNA probes were printed onto CMT-GAPS slides (Corning, Corning, NY, USA), using a MicroGrid 610 TAS array printer (Biorobotics, Woburn, MA, USA) with quill pins. A total of 5,169 Ps-n cDNAs were printed in duplicate, and 96 were printed in quadruplicate; in addition, 3 vector only cDNAs, 12 H. sapiens control cDNAs, and 10 control cDNAs from SpotReport Alien Array Validation System (Stratagene, La Jolla, CA, USA) were printed in duplicate, resulting in a final chip that included 10,772 features. Spots were printed with a 32 print-tip head, producing a lay-out represented by 8 x 4 grids. Each grid was sub-divided into two sections, representing replicate spots. Individual features were 13 µm in diameter and were separated by 130 µm (from one spot to the next). 0.005 µL of ~600 ng µL-1 DNA (2-3 ng) was transferred to each spot. Final Ps-n arrays displayed a strong signal to noise ratio, with virtually no background. (For visual representation of microarray, see supplementary file: MIT Housman Psn 10772 cDNA v1 Figure). Experimental hybridization results demonstrated a high degree of reproducibility between replicate spots on the Ps-n chip.


title: Agilent-023797 Lymphoma (Agilent Probe ID)

status: Public on Sep 07 2013

city: Rutherford

first: Jane

last: Houldsworth

address: 201 Route 17 North

institute: Cancer Genetics, Inc.

description:
Arrays of this design have barcodes that begin with 16023797 or 2523797.

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: Exiqon LNA RT-PCR Human panels (1 & 2)

first: Maurice

last: Chan

address: 11 Hospital Drive

department: Division of Medical Sciences

institute: National Cancer Centre

description: PCR assay


title: NimbleGen Mouse ChIP-chip 385K RefSeq Promoter Array [2006-07-18_MM8_RefSeq_promoter]

description: Promoter design based only on normal RefSeq genes (NM_) for mouse (MM8; NCBI Build 36). Includes 2000 bp upstream of transcriptional start and 500 bp downstream. Isothermal probes using dual tm/cycle restriction:, 50-75 bp, tm 76, 148 cycles, 15-mer frequency of 100. Interval spacing of 100 bp.

manufacture_protocol: See NimbleGen website (http://www.nimblegen.com/products/chip/promoter/mouse/index.html)


title: Combimatrix Helicobacter pylori Custom 90k Whole Genome Tiling Array

city: Beijing

first: yuanhai

last: you

address: Changbai road 155,Changping district

institute: intitute of communicable disease control and prevention,China CDC

organism:
Helicobacter pylori 26695
Helicobacter pylori J99
Helicobacter pylori HPAG1
Helicobacter pylori Shi470
Helicobacter pylori G27
Helicobacter pylori P12

manufacture_protocol: Probes are directly synthesized on a 90k Combimatrix array by an in situ oligo synthesis system developed by CombiMatrix Corporation (Mukilteo, USA) using the CombiMatrix CustomArray synthesizer. Standard synthesis protocol provided by CombiMatrix was used.


title: Illumina HiSeq 2000 (Jatropha curcas)

last: GEO

organism: Jatropha curcas


title: Agilent-026094 GT Human miRNA Rel14 v1.1

description:
887 miRNA target based on mirBASE Rel14
Arrays of this design have barcodes that begin with 16026094 or 2526094.
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 (Triticum aestivum)

organism: Triticum aestivum


title: NanoString Gene Expression Assay, nCounter Human Cancer Reference kit

city: Columbus

first: Taewan

last: Kim

institute: The Ohio State University

manufacture_protocol: See manufacturer's website.


title: Illumina HiSeq 2000 (Brassica oleracea var. italica)

status: Public on Sep 03 2013

organism: Brassica oleracea var. italica


title: Illumina Genome Analyzer IIx (Human herpesvirus 8)

status: Public on Sep 04 2013

organism: Human gammaherpesvirus 8


title: 3D-Gene Mouse miRNA Oligo chip

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

manufacture_protocol: See manufacture's web site


title: Bacillus subtilis 168 Oligo Array

city: Groningen

first: Arjan

middle: Oedse Geert

last: Oldebesten

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

organism: Bacillus subtilis

manufacture_protocol: oligo spotted on ArrayIt Superamine slides


title: Illumina HiSeq 2000 (Acidovorax avenae subsp. avenae RS-1)

status: Public on Sep 02 2013

organism: Paracidovorax avenae RS-1


title: Agilent-041492 goat_AT 019921 (Probe Name version)

status: Public on Sep 01 2013

city: Nanjing

first: Dong

last: Haibo

state: Jiangsu

department: Nanjing Agricultural University

institute: Nanjing Agricultural University

organism: Ovis aries

description: The ID column represents the Agilent Probe Name.


title: Thermo Fisher Scienctific miRNA expression profiling system

city: Aurora

first: Manoj

last: Pillai

address: Building 500 - 13001 E. 17th Place, Campus Box C290, Room E1354

institute: University of Colorado


title: Illumina HiSeq 2000 (Callithrix jacchus)

organism: Callithrix jacchus


title: Illumina HiSeq 2000 (Human herpesvirus 8)


title: Agilent-029132 At8X60 [Probe Name version]

city: Nueherberg

first: Gitto

middle: Thomas

last: Kuruthukulangarakoola

address: Ingolsteadter Landstrasse 1

department: Biochemical Plant Pathology

institute: Helmholtz Zentrum München

organism: Arabidopsis thaliana

description:
Arrays of this design have barcodes that begin with 16029132 or 2529132.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Probe Name.


title: NimbleGen Arabidopsis thaliana 4x72K Array [ATH6_60mer_expr]

city: Ikoma

first: Diana

middle: Mihaela

last: Buzas

state: Nara

address: 8916-5 Takayama

department: Biological Sciences

institute: NAIST

description:
Gene Expression array
Design Name: ATH6_60mer_expr
Design_ID: 5048

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

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

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


title: NimbleGen Drosophila serrata Custom array [110608_Dser_SC_expr.ndf]

city: Nouzilly

first: Julie

last: Collet

address: Centre INRAE

institute: INRAE

organism: Drosophila serrata

description:
NimbleGen design name: 110608_Dser_SC_expr

Native array description file: 110608_Dser_SC_expr.ndf

NimbleGen design name 110608_Dser_SC_expr.  Five 60-mer probes for 11,631 unique Expressed Sequence Tags (ESTs) from Drosophila serrata.  Each probe is replicated 2 times.  The design includes random and other control probes.

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

The sequences of the ESTs are in the '110608_Dser_SC_expr.ndf' file.

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


title: Agilent-034677 S. Cerevisiae 210K Random Seq Tiling Array v1.0

first: Carl

middle: G

last: de Boer

address: 415 Main St

institute: The Broad Institute

organism: Saccharomyces cerevisiae

description:
Arrays of this design have barcodes that begin with 16034677 or 2534677.

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: Multi-species Autoantigen Microarray

status: Public on Sep 05 2013

city: Dallas

first: yun

last: lian

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacturer: University of Texas Southwestern Medical Center

manufacture_protocol:
Dilute peptides, proteins, protein complexes, or other antigens in PBS-0.1% Tween20 to 0.1 - 0.2 mg/mL.
Transfer diluted antigens transferred to 384-well print plates (15 μL/well).  Antibody or other proteins/peptides prelabeled with Cy-3 and / or Cy-5 (diluted to 0.1 μg/μL) can be added to the print plate to serve as marker spots to orient the arrays post-scanning.
Using a biorobotic arrayer (MicroGrid 610) and quill pins (Genomic Solution) to print antigens on nitrocellulose coated microarray slides (FAST Slide, 16 pad, Whatman Inc). Slides were kept at 75% humidity chamber for 12 hours.
Store arrays at 4°in slide boxes sealed in plastic heat-sealable pouches.  Reactivity is generally best within 1 month of printing, but printed antigens can retain reactivity for months.


title: NimbleGen Streptococcus pyogenes M1 Gene Expression Array [100310_Spyo_exp]

city: Notre Dame

first: Erliang

last: Zeng

state: IN

address: 384 Fitzpatrick Hall

institute: University of Notre Dame

organism: Streptococcus pyogenes

description:
The Roche NimblenGen Streptococcus pyogenes M1 Gene Expression Array contains 135,040 probes representing 1688 genes;
Each gene is queried by 10 probe sequences and each sequence is replicated 8 times on the microarray.

The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.

designname=100310_Spyo_exp
designid=11586

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


title: Illumina MaizeSNP50 BeadChip

city: Freising

first: Eva

last: Bauer

address: Liesel-Beckmann-Str. 2

department: Plant Breeding

institute: Technical University of Munich

organism: Zea mays


title: NIMBLE_MMCCSAL02_380k

city: Heverlee

first: Jos

last: Vanderleyden

address: Kasteelpark Arenberg 20

department: Department of Microbial and Molecular Systems

country: Belgium

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

description:
NC_003197 and NC_003277
This set includes 386350 46~50mer oligonucleotides, mostly 50-mers. The probes were designed based on Salmonella typhimurium LT2 (NC_003197.1) genome, with a moving window of about 12 bases.

manufacture_protocol: design 2007-03-13_Wang_ChIP - ChIP-chip design using customer supplied probes.  Probes truncated at 148 cycles.  Design includes random GC


title: EBT_UA_Daphnia magna_Unique_1.9K_version1

city: Leuven

first: Mieke

last: Jansen

address: Ch. Deberiotstraat 32

institute: KULeuven

organism: Daphnia magna

description:
1918 out of 1924 spots from the cDNA libraries were measured.

This Platform represents two batches of arrays that differ in the control spikes that are spotted. One batch has Lucidea controls, and the other batch has Stratagene controls.

manufacturer: Laboratory for Ecophysiology, Biochemisty and Toxicology, University of Antwerp

manufacture_protocol: Gene expression profiles were determined based on a previously in-house made (UAntwerpen) cDNA microarray of D. magna (Soetaert et al., 2006; Soetaert et al., 2007). This existing cDNA microarray (Vandenbrouck et al., 2009) was extended with three cDNA libraries (i.e. carbaryl, predator and P. ramosa related cDNA libraries; see Orsini et al.). In brief, sequences were assessed for redundancy and consequently the unique sequences per masterset (i.e., either the three existing libraries and the three supplementary libraries) were selected i.e., 1189 unique gene fragments (Vandenbrouck et al., 2009) collected from the three cDNA libraries (life stage, moulting and energy metabolism) were supplemented with 735 unique cDNA fragments identified within the three stressor specific libraries. This last group of sequences was yielded from a collection of 1698 stressor-specific gene fragments (see Orsini et al.). After trimming those 1698 fragments by use of the program CodonCode Aligner (http://www.codoncode.com/aligner/), a group of 1372 fragments remained. Clustering and assembling those ESTs was done with TGICL (Pertea et al., 2003). Default parameters were used for clustering and assembly, which was performed with CAP3 (Huang & Madan, 1999). A total of 1924 gene fragments (1189 + 735) were spotted on amino-coated glass slides (Asper Biotech. Ltd., Estonia) in triplicate (technical spot replication) by using the Qarray Mini (Genetix Ltd., UK). Those two masterset of gene fragments were than analysed for redundant sequences and in the end only 1734 unique sequences were represented, composed of 156 clusters and 1578 singletons (using TIGR Gene Indices Clustering (TGICL), Huang & Madan, 1999; Pertea et al., 2003).


title: PIQOR (TM) Immunology Microarray, human antisense

status: Public on Aug 30 2013

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec GmbH

organism: Homo sapiens

description: The PIQOR (TM) Immunology Microarray is composed of 1076 human specific cDNAs. These cDNAs include for each array six house-keeping genes as positive controls. In addition four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer, respectively. All features are spotted in quadruplicate. The Platform data table reflects a condensed representation of the quadruplicate features.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

manufacture_protocol: Defined 200-400 bp fragments of selected cDNAs were generated by RT-PCR, cloned and sequence-verified. Amplified and purified cDNA inserts were spotted in quadruplicate on PIQOR slides using a proprietary piezoelectric spotter. The PIQOR slides were coated in a 2 step process generating a surface which covalently binds DNA molecules.


title: University of Chicago Weigert Light Chain

city: Chicago

first: Nathan

last: Schoettler

state: IL

address: 924 E 57th Street, R402

institute: University of Chicago

organism:
Homo sapiens
Mus musculus

first: Martin

last: Weigert

first: Dongyao

last: Ni

manufacture_protocol: Microarrays were spotted using a GeneMachines OmniGrid 100 (Genomic Solutions) onto SuperAmine 2 slides (ArrayIt). Each oligonucleotide probe was spotted twelve times per array, and the print layout was such that these twelve replicates were spotted by four different pins. In addition to the human oligonucelotides, the microarrays also had mouse oligonucleotides spotted on the array. After printing, microarrays were dehydrated following the manufacture’s recommendations and stored in the dark at room temperature.


title: [BradiAR1b520742] Custom Affymetrix Brachypodium GeneChip

status: Public on Jul 30 2013

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

organism: Brachypodium

description: The probes present on the Brachypodium Affymetrix Array are mapped to the Bradi V1 Brachypodium genome annotation.

manufacture_protocol: see manufacturer's web site


title: Agilent-043039 Daphnia magna_01_Of_1

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

description:
Arrays of this design have barcodes that begin with 16043039 or 2543039.

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: Bluegnome human 24sure v2.0

status: Public on Feb 01 2013

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 103

department: Research Group of Reproduction and Genetics

institute: Vrije Universiteit Brussel

description: Build 37 of the Human genome

manufacturer: BlueGnome Ltd, Capital Park CPC4, Fulbourn, Cambridge CB21 5XE UK, info@cambridgebluegnome.com


title: Illumina iSelect Human Custom Genotyping BeadChip array (REPAC INSERM network)

status: Public on Aug 27 2013

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

institute: Centre hospitalier de Versailles


title: JCVI PFGRC Porphyromonas gingivalis 2K v2

status: Public on Oct 05 2012

city: Richmond

first: Janina

middle: P

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

organism: Porphyromonas gingivalis

manufacture_protocol: see manufacturer's website


title: Agilent-041492 goat_AT 019921 (Feature Number version)

city: Nanjing

first: Dong

last: Haibo

institute: Nanjing Agricultural University

description:
Arrays of this design have barcodes that begin with 16041492 or 2541492.

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 (synthetic construct)

status: Public on Sep 25 2013

last: GEO

organism: synthetic construct


title: CYL Calbicans 2.0

status: Public on Mar 15 2012

city: Hsinchu

first: Yu-Ting

last: Chen

address: No.101, Sec. 2, Guang-Fu Rd.

department: Institute of Molecular and Cellular Biology

institute: National Tsing Hua University, Taiwan

organism: Candida albicans

manufacturer: DNA Microarray Core Laboratory, Institue of Plant and Microbial Biology,  Academia Sinica, Taiwan.

manufacture_protocol: Probes were dissolved in 3X SSC at a concentration of 40 μM. The microarrays were printed on UltraGAPS-coated slide (Corning) with a GeneMachines OmniGrid 100 Microarrayer (Diglab) using CMP#3 pin (TeleChem) according to the manufacturer’s instructions. The slides post-proceed according to Corning’s protocol. GeneMachines OminGrid operation software was used to track where samples have been printed on the slides and to exprot the Gene Array list (GAL) file.


title: Illumina Genome Analyzer IIx (Zea mays)

status: Public on Jul 27 2011


title: NIMBLE_MMCCSAL07_14028_380k [MMCCSAL07_100416_SP_CGH]

status: Public on Dec 06 2011

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

description:
design name: MMCCSAL07_100416_SP_CGH
This set includes 374328 46~50mer oligonucleotides that hit both Typhimurium LT2 and Typhimurium 14028s, complemented with 10451 oligos that are specific for 14028s (and 100 duplicate spots). The probes were designed based on the Salmonella typhimurium LT2 (NC_003197.1) and 14028s (CP001363.1: complete genome and CP001362.1: plasmid) genomes, with a moving window of about 12 bases. All probes (including control oligos) are represented in this file.

first: Fred

last: Long

first: Steffen

last: Porwollik

manufacture_protocol: in situ oligonucleotide


title: Exiqon miRCURY LNA microRNA array v.11.0 Extended Version

status: Public on Jun 10 2011

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

description: Array represents miRBase version 11.0 with additional features.

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


title: Print_1216

status: Public on Sep 25 2009

city: Seattle

first: Nina

middle: Reda

last: Salama

state: WA

address: 1100 Fairview Ave. N

department: Division of Human Biology

country: USA

institute: Fred Hutchinson Cancer Research Center

organism: Helicobacter pylori

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine

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


title: Maize oligo array version 1.9 array B

status: Public on Jun 29 2007

city: Rockville

first: Jia

last: Liu

address: 9712 Medical Center Drive

institute: Plant Genomics

description: Spotted oligo array on glass. The whole maize array set 1.9 version contains 56310 unique probes from maize and array B contains 28470 of them. The number of total spots including empty and controls is 32448.

first: C

last: Buell

manufacture_protocol:
REHYDRATION AND PRINTING OF THE OLIGONUCLEOTIDE MICROARRAYS
1.Add 15 uL of 3XSSC to each well of the 300 pM oligonucleotide set to make a 20 μM oligonucleotide solution.
2.Transfer onto an orbital shaker for 1 h at RT at 100 rpm. The oligonucleotides are now ready for printing.
3.The Arabidopsis oligonucleotide microarrays are printed on aminosilane-coated “Superamine” slides (Telechem) or “Powermatrix” slides (Full Moon Biosystems), using Telechem Type SMP3 printing pins.
4.Printing conditions:
Single array element printed per oligonucleotide, 48 pins in the print head, 31% relative humidity, redipping after every 50 slides.  The print head Z- velocity is set to a maximum of 10 mm/sec.
5.Bake slides for 2h at 80oC. Store dry and in darkness at RT.
The microarrays are sent out to recipient scientists at this point.  Prior to hybridization, these next steps should be followed:
IMMOBILIZATION OF THE OLIGONUCLEOTIDE ARRAY ELEMENTS

1.Rehydrate the microarray slide over 50oC water for 5-10 seconds; snap-dry on a 65oC heating block for 5 seconds.  Repeat this step 4-6 times, examining the slides under a dissection microscope (or using red reflectance imaging) to verify complete re-hydration of all the spots.  If re-hydration is not complete, repeat the process several more times.
2.Crosslink the oligonucleotides to the slide surface by exposing the DNA-side of the microarray to UV irradiation.  We employ a Stratalinker set at an energy level of 180 mJ.

Re-hydration and UV cross linking can be done well in advance before microarray hybridization, and the slides can be stored at room temperature for several months.  However we do not recommend storage of washed microarray slides.
3.Wash the slides in 1% SDS dissolved in sterile ddH2O for 5 min at RT.
4.Rinse the slides by plunging 10 times into sterile ddH2O.
5.Rinse in 100% ETOH for 30 seconds to 5 min, with gentle shaking.
6.Spin dry the slides in a centrifuge at 1000 rpm for 2 min.
7.Store the slides in a light-proof box under cool dry conditions.


title: Dictyostelium discoideum cDNA Microarray 6000

status: Public on Apr 22 2005

city: Cologne

first: Ludwig

last: Eichinger

address: Joseph-Stelzmann-Strasse 52

institute: Institute for Biochemistry 1

organism: Dictyostelium discoideum

description:
Spotted cDNAs array on glass.
The current Dictyostelium DNA microarray carries approximately 5,400 non-redundant ESTs from the Dictyostelium cDNA project, partial sequences of 450 known genes and appropriate positive and negative controls"


title: Maize oligo array version 1.9 array A

description: Spotted oligo array on glass. The whole maize array set 1.9 version contains 56310 unique probes from maize and array A contains 29270 of them. The number of total spots including empty and controls is 32448.


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray HGU133Plus2_Hs_ENTREZG 14.0.0]

status: Public on Nov 21 2012

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

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

status: Public on Apr 24 2012

city: Madison

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Drosophila melanogaster

description:
Design name: 090828_Dmel_exp
Design ID: 10545
Source: Flybase
Build: DM5.7
Probe Length: 60mer
16637 target genes (exemplars), 21051 CDS sequences.

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


title: GE Healthcare/Amersham Biosciences CodeLink™   UniSet Human 20K I Bioarray

status: Public on Sep 29 2005

city: Tempe

first: Randall

last: Lockner

state: AZ

address: 7700 S River Parkway

department: Bioinformatics

institute: GE Healthcare Life Sciences

description:
CodeLink UniSet Human Bioarray content was based on the public UniGene and RefSeq databases, and sequences for design were derived from Incyte LifeSeq™ Gold and Foundation databases. Well-annotated mRNA or coding sequences were chosen to ensure usefulness for a large range of applications in basic research, biotechnology, and drug development. Each sequence was carefully screened to ensure high quality, specific probe design, and to reduce redundancy of gene targets. Every probe was functionally validated against multiple tissues to ensure best representation of the gene so that the results will be biologically relevant. Every bioarray is also functionally validated during production to further ensure quality performance.

CodeLink users can submit data to GEO by exporting tab-delimited text files from the CodeLink software. The "Feature_id" header will need to be renamed to "ID_REF", and the "Normalized_intensity" header to "VALUE" before uploading the exported tables.

In addition, users are encouraged to include additional raw data columns in their data uploads. These additional columns do not need to be renamed.


title: Nimblegen/NCSU Zymomonas mobilis array (gene name version)

status: Public on Sep 04 2013

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821


title: Agilent-042453 Bursaphelenchus xylophilus array [Probe name version]

status: Public on Sep 03 2013

first: Jianren

last: Ye

address: Long Pan Road

country: China

institute: Nanjing Forestry University

organism: Bursaphelenchus xylophilus

description: The ID column represents the Agilent Probe name.


title: Agilent-014810 Yeast Whole Genome ChIP-on-Chip Microarray 4x44K (G4493A) [Probe Name version]

status: Public on Sep 16 2010

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Saccharomyces cerevisiae

description: *** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL4131.


title: Agilent-031272 Aspergillus nidulans expression array V5 (Feature Number version)

status: Public on Sep 01 2013

city: Kgs. Lyngby

first: Mikael

last: Andersen

address: Søltofts plads, bygn 223

department: BioCentrum-DTU

country: Denmark

institute: Technical University of Denmark

organism: Aspergillus nidulans FGSC A4

description:
DTU-Anidulans-44K-V5
4x44K

Arrays of this design have barcodes that begin with 16031272 or 2531272.

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: Probes designed using the OligoWiz 2.0 software (Workman et al., 2002) from the CDS sequences of predicted ORFs from the genome sequence of A. nidulans FGSC A4 using version 5 of the A. nidulans gene annotation, downloaded from the Aspergillus Genome Database (aspgd.org). For each gene, a maximum of 3 non-overlapping perfect-match 60-mer probes were calculated by using the OligoWiz standard scoring of cross-hybridization, melting temperature, folding, position preference, and low complexity. A position preference for the probes was included in the computations. Pruning of the probe sequences was done by removing duplicate probe sequences. The arrays were manufactured according to the current standards for Agilent 4x44K arrays.