title: Agilent-018261 Coupland Lab (MPIPZ)-Arabidopsis/Arabis-244K

status: Public on May 27 2013

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

country: Germany

institute: Max Planck Institute

organism: Arabidopsis thaliana

technology: in situ oligonucleotide

description: Custom Arabidopsis array for heterologuos hybridization studies.

distribution: custom-commercial

manufacture_protocol: Oligos were designed using the eArray application based on the Arabidopsis DNA sequence starting from the less conserved 3´ end and going in the direction of the 5´ end of every gene. Up to 10 oligos / Arabidopsis gene were designed against the DNA sequence (oligo-set). Total of 244K array. The calculated median distance between the end and the start of two consecutive oligos was 27 nt. In situ synthesized 60 mer long oligoes according to stadard Agilent manufacture protocol.


title: HuGene1_0_genecentric

status: Public on Apr 15 2013

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

country: USA

institute: Icahn School of Medicine at Mount Sinai

organism: Homo sapiens

relation: Alternative to: GPL6244 (alternative CDF [official])

manufacture_protocol: see Affymetrix protocol


title: Agilent-031272 Aspergillus nidulans expression array V5

status: Public on Apr 03 2013

city: Kgs. Lyngby

first: Mikael

middle: R

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.

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.


title: UCM_Apal_10622_G3_Sra subset

status: Public on Nov 21 2012

city: Thuwal

first: Christian

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

organism: Acropora palmata

technology: spotted DNA/cDNA

distribution: non-commercial

first: Manuel

last: Aranda

first: Michael

last: DeSalvo

first: Till

last: Bayer

first: Monica

last: Medina

relation:
Alternative to: GPL15442
Alternative to: GPL15443

manufacture_protocol: printer with DeRisi arrayer on Poly-L-lysine coated glass slides


title: Agilent-028674 BGC_NTHI_86_028NP

status: Public on Feb 04 2013

city: Columbus

first: Alistair

last: Harrison

state: OH

address: 700 Children's Drive

department: Center for Microbial Pathogenesis

institute: The Research Institute at Nationwide Children's Hospital

organism: Haemophilus influenzae 86-028NP

description:
Agilent Gene Expression array for non-typeable Haemophilus influenzae 86-028NP (NC_007146).

Arrays of this design have barcodes that begin with 16028674 or 2528674.

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: UCM_Apal_12550_G3_Acer subset

relation:
Alternative to: GPL15442
Alternative to: GPL15444


title: UCM_Apal_10776_G3_Mfav subset

description: cDNA microarray Montastraea faveolata

relation:
Alternative to: GPL15444
Alternative to: GPL15443


title: 020310-Agilent Micropterus salmoides 15K

status: Public on Aug 31 2012

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

organism: Micropterus salmoides

technology: spotted oligonucleotide

first: Nancy

last: Denslow

manufacture_protocol: SurePrint G3 Gene Expression Microarrays


title: Affymetrix Human Genome U133 Plus 2.0 Array [CDF:gahgu133plus2_2.2.0]

status: Public on Mar 31 2013

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Custom definition files for Affymetrix HG-U133 Plus 2.0 array

first: F.

last: Ferrari

first: S.

last: Bortoluzzi

first: A.

last: Coppe

last: Sirota

first: M.

last: Safran

last: Shmoish

first: D.

last: Lancet

first: GA.

last: Danieli

last: Bicciato

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

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


title: Illumina Genome Analyzer II (Methylacidiphilum fumariolicum)

last: GEO

technology: high-throughput sequencing

distribution: virtual


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

status: Public on Nov 07 2012

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

description: The Platform data table reflects a condensed representation of the array's replicate features. The full array layouts (2 versions) representing all of the individual features are linked as supplementary files at the foot of this record.

manufacture_protocol: Oligonucleotides (with C6 amino linker) were suspended at 50pmoles/ul in spotting buffer and spotted onto SuperEpoxy2 substrate glass slides using 946MP3 Micro Spotting Pins.


title: EcoArrayBass-4x44K-001 [ProbeName version]

city: Alachua

first: Barbara

middle: Joan

last: Carter

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

organism:
Micropterus salmoides
Micropterus dolomieu

description:
This is the ProbeName version of GEO Platform GPL7799
Our bass microarray contains genes for both largemouth (Micropterus salmoides) and smallmouth (Micropterus dolomieu) bass.  It was constructed by assembling over 40,000+ sequences to identify non-overlapping, unique sequences (singlets and contigs) in both species.  These data include our own proprietary sequences obtained from suppressive subtraction hybridizations and library construction plus sequence information licensed from the University of Florida.  Homology searches (Blast) were performed on these sequences in order to provide annotation (gene name) and ontology (gene function) information where present.  A total of 19,308 contigs were assembled.  Probes, 60-bases in length, were designed using Agilent’s web-based E-Array program.  The content of our bass microarray is located on our web site and contains 19,308 sequences.

manufacturer: Applied Food Technologies/EcoArray, Agilent

middle: J

manufacture_protocol: EcoArray selected Agilent Technologies as the manufacturer of our microarrays for environmental toxicology.   Probes are synthesized in situ using Agilent’s inkjet based “SurePrint” technology.  These arrays are manufactured on superior quality 1” x 3” (24.2 mm x 76.2 mm) treated glass slides for overall excellent performance.  This process minimizes variability across each production lot (batch to batch) and provides the highest consistency in slide-to-slide comparisons.  These glass slide microarrays are designed for either a one- or two-color  (cyanine-3 and cyanine-5) labeling reaction, the most reliable and sensitive methods for detecting differentially expressed genes.  Agilent's Feature Extraction software, when used with a high resolution (5 micron) scanner, provides QA metrics for each indivdual microarray, ensuring quality results.  Each slide contains four individual 44K arrays.


title: Agilent-14262 MSKCC Human custom 15K

city: Chapel Hill

first: Joel

last: Parker

state: NC

address: 5109 B Bioinformatics Building

department: Genetics

institute: UNC - CH

manufacture_protocol: see  manufacturer's website


title: [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [CDF: Brainarray Version 11.0.1, MoEx10stv1_Mm_ENSG]

city: Edmonton

first: Eliana

last: Lucchinetti

address: HMRC 408

country: Canada

institute: University of Alberta

organism: Mus musculus

relation: Alternative to: GPL6096 (Alternative CDF [official])

manufacture_protocol: This is identical to GPL6096 but a custom cdf environment was used to extract data. Microarray analysis was performed using customCDF from Brainarray (Brainarray Version 11.0.1, MoEx10stv1_Mm_ENSG). The custom cdf is linked below as a supplementary file.


title: Illumina Genome Analyzer IIx (Didelphis virginiana)

status: Public on Aug 30 2012

organism: Didelphis virginiana


title: AB SOLiD 4 System (Trichophyton rubrum)

status: Public on Aug 28 2012

organism: Trichophyton rubrum


title: Illumina HiSeq 2000 (Thalassiosira pseudonana CCMP1335)

organism: Thalassiosira pseudonana CCMP1335


title: PIQOR (TM) custom_583, rat (583)

status: Public on Aug 29 2012

first: Bernhard

last: Gerstmayer

address: Stockheimer Weg 1

institute: Miltenyi Biotec GmbH

organism: Rattus norvegicus

description: The PIQOR (TM) custom Microarray CTID583 is composed of 636 rat specific cDNAs, 99 mouse-specific probes with similarity to rat orthologous sequences and 40 undisclosed probes derived from differential display experiments  These cDNAs include for each array five rat house-keeping genes(ACTA2, ACTB, GAPDH, HPRT, TUBA) 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: 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: E. coli Oligo Set v1.03 MSU 13K

city: Boston

first: Deborah

middle: R.

last: Yoder-Himes

state: MA

address: 77 Louis Pasteur Ave, 1038 NRB

department: Microbiology and Molecular Genetics

institute: Harvard Medical School

organism: Escherichia coli

manufacture_protocol: 70-mer oligos spotted in duplicate onto Corning UltraGaps slides.


title: PIQOR (TM) custom_370, rat (370)

description: The PIQOR (TM) custom Microarray CTID370 is composed of 638 rat specific cDNAs, 99 mouse-specific probes with similarity to rat orthologous sequences and 49 undisclosed probes derived from differential display experiments  These cDNAs include for each array five rat house-keeping genes(ACTA2, ACTB, GAPDH, HPRT, TUBA) 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.


title: Agilent Custom Arabidopsis thaliana Gene Expression 4x44k designed by Genotypic Technology Pvt. Ltd. (AMADID:015226)

status: Public on Aug 24 2012

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

first: Mugasimangalam

middle: C

last: Raja


title: miRXplore TM Microarray (878)

status: Public on Aug 25 2012

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: The miRXplore TM Microarray is composed of 5884 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 1374 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 1374 miRNA sequences covered sequence verified miRNAs of the species human (859) mouse (622) and rat (428) as well as viral miRNAs (129) as deposited in the miRBase sequence database version 12.0. The 97 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (43 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 36 positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 13 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences. Microarrays were manufactured by Miltenyi Biotec.

manufacture_protocol: 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides in quadruplicates using a customized piezoelectric spotter.


title: JCVI/PFGRC Salmonella Typhimurium LT2 genome microarray version 4

status: Public on Aug 21 2012

city: College Station

first: Bhimanagouda

middle: S

last: Patil

state: TX

address: 1500 Research Pkwy, Ste A120

institute: Texas A&M University

organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Salmonella enterica subsp. enterica serovar Typhi str. CT18

manufacturer: Pathogen Functional Genome Resource Center

manufacture_protocol: Please refer to webpage http://pfgrc.jcvi.org/index.php/microarray/array_description/salmonella_typhimurium/version4.html


title: SMD Print_1540 hoaf Homo sapiens

status: Public on Aug 23 2012

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

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: Illumina Genome Analyzer IIx (Pseudomonas aeruginosa PAO1)

organism: Pseudomonas aeruginosa PAO1


title: Agilent-037580 Plecoglossus altivelis SweetFishGene 50K

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

organism: Plecoglossus altivelis

manufacture_protocol: The same as the manufacture protocol of Agilent gene expression Microaray Kit. See manufacturer's web site at http://www.agilent.com/


title: Illumina Genome Analyzer IIx (Aspergillus flavus)

status: Public on Aug 17 2012

organism: Aspergillus flavus


title: JCVI PFGRC Streptococcus mutans UA159 array version 3

status: Public on Aug 22 2012

city: Ithaca

first: Guoping

last: Feng

address: 262 Stocking Hall

department: Food Science

institute: Cornell University

organism: Streptococcus mutans UA159

manufacturer: The Pathogen Functional Genomic Resource Center (PFGRC)

first: Hyun

last: Koo

manufacture_protocol: Glass slides with aminosiane coating, 5X replicate oligo printing of 1948 70-mer oligonucleotide


title: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)


title: Exiqon Mouse microRNA v11.0.

status: Public on Aug 20 2012

city: Little Rock

first: Jeanne

last: Wei

address: 4301 West Markham Street

department: Geriatrics

institute: University of Arkansas for Medical Sciences

description: Exiqon's miRCURY LNA™ microRNA Array system is a complete system for global microRNA expression profiling. The system is based on the LNA™-technology, which offers unique advantages in the specific and sensitive detection of short RNA sequences.

manufacture_protocol: The following is the claim of Exiqon Inc.:  Our array platform is the most sensitive platform on the market. Due to the incorporation of LNA™ in the capture probes, more than 90% of our probes have a detection limit of less than 10 amol. This enables us to perform microRNA profiles with very low levels of total RNA input. All our capture probes are Tm-normalized to ensure uniform and high quality performance across the array


title: Human Exon 1.0 ST Array [CDF: Brainarray Version   9.0.1, HsEx10stv2_Hs_REFSEQ]

city: Vienna

first: Stefan

last: Kastner

address: Dr. Boehringer-Gasse 5-11

country: Austria

institute: Boehringer Ingelheim RCV

organism: Homo sapiens

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

manufacture_protocol: see manufacturer's website


title: Illumina HiSeq 2000 (Beauveria bassiana ARSEF 2860)

last: GEO

organism: Beauveria bassiana ARSEF 2860


title: MRA-1004 miR Zebrafish 10.1

status: Public on Aug 18 2012

city: Houston

first: Christoph

last: Eicken

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism: Danio rerio

description: Zebrafish miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 10.1

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


title: [Mouse4302_Mm_ENTREZG] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Brainarray Version 15.1.0]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

relation: Alternative to: GPL1261 (Alternative CDF [official])

manufacture_protocol: This is identical to GPL1261 but a custom CDF environment was used to extract data [Brainarray Version 15.1.0, Mouse4302_Mm_ENTREZG].


title: SMD Print_1392 hos Homo sapiens


title: NimbleGen Human DNA Methylation 385K RefSeq Promoter Array [2006-07-18_HG18_RefSeq_promoter]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
Design name: 2006-07-18_HG18_RefSeq_promoter
Design_ID: 4226


title: NimbleGen Petromyzon marinus 53K 081218_Pmar_JS_CGH

status: Public on Aug 19 2012

city: Lexington

first: Jeramiah

last: Smith

state: KY

address: 101 T.H. Morgan Building

department: Biology

institute: University of Kentucky

organism: Petromyzon marinus

description: covers ~1% of the lamprey genome, in fragments.

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


title: Agilent-028680 SurePrint G3 Human Exon 2x400K Microarray (Feature Number version)

description:
Human2x400KExon

Arrays of this design have barcodes that begin with 16028680 or 2528680.

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.

Includes probes for exons from 35 to 60 bp, using stilts for exons under 50 bp Targets 5' and 3' UTRs in addition to gene exons, 96 ERCC control probes, and 32 E1A spike-in control probes

Design based on RefSeq Build 36.3, Ensemble Release 52, Unigene Build 216,GenBank (April 2009)

relation: Alternative to: GPL15950 (Probe Name version)

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


title: Kanazawa Univ. Human Liver chip 10k

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

country: Japan

institute: Kanazawa University

description: In addition to in-house cDNA microarray slides consisting 1080 cDNA clones as previously described（Gastroenterology. 2001 Mar;120(4):955-66, we made a new cDNA microarray slide for detailed analysis of the signaling pathway of metabolism and enzyme function in liver disease. Besides cDNA microarray analysis, a total of 256 550 tags were obtained from hepatic SAGE libraries (derived from normal liver, CH-C, CH-C related HCC, CH-B, CH-B related HCC respectively), including 52 149 unique tags. Among these, 16 916 tags expressing more than two hits were selected to avoid the effect of sequencing errors in the libraries. From these candidate genes, 9,614 non-redundant clones were obtained from Incyte Genomics (Incyte Corporation, Beverly, MA, USA), Clontech (Nippon Becton Dickinson, Tokyo, Japan), and Invitrogen (Invitrogen Japan K.K., Tokyo, Japan). Each clone was sequence validated and PCR amplified by Dragon Genomics (Takara Bio, Otsu, Japan), and the cDNA microarray slides (Liver chip 10k) were constructed using SPBIO 2000 (Hitachi Software, Fukuoka, Japan) as described previously.

manufacturer: First Department of Internal Medmme, Kanazawa University


title: Illumina HiSeq 2000 (Prunus mume)

status: Public on Aug 16 2012

organism: Prunus mume


title: Agilent-030893 Rainbow_trout_60KV2 [Probe Name version]

status: Public on Aug 27 2012

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

country: France

institute: Institut National de la Recherche Agronomique

organism: Oncorhynchus mykiss

description:
Arrays of this design have barcodes that begin with 16030893 or 2530893.

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.


title: AB 5500 Genetic Analyzer (Drosophila melanogaster)

organism: Drosophila melanogaster


title: Agilent-028680 SurePrint G3 Human Exon 2x400K Microarray (Probe Name version)

description:
Human2x400KExon

Arrays of this design have barcodes that begin with 16028680 or 2528680.

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 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 GPL15949.

Includes probes for exons from 35 to 60 bp, using stilts for exons under 50 bp Targets 5' and 3' UTRs in addition to gene exons, 96 ERCC control probes, and 32 E1A spike-in control probes

Design based on RefSeq Build 36.3, Ensemble Release 52, Unigene Build 216,GenBank (April 2009)

relation: Alternative to: GPL15949 (Feature Number version)


title: Illumina Genome Analyzer IIx (Gorgonia ventalina)

organism: Gorgonia ventalina


title: PacBio RS (Bacillus cereus)

status: Public on Aug 15 2012

organism: Bacillus cereus


title: PacBio RS (Vibrio breoganii)

organism: Vibrio breoganii


title: PacBio RS (Campylobacter jejuni)

organism: Campylobacter jejuni


title: SAGE:17:NlaIII:Cryptococcus neoformans var. grubii H99

organism: Cryptococcus neoformans H99

technology: SAGE NlaIII

description: This is a virtual platform for SAGE libraries generated for Cryptococcus neoformans var. grubii H99 using NlaIII as an anchor enzyme.


title: Agilent-026636 Prueba Lp IFI 021109

organism: Lactiplantibacillus plantarum WCFS1

description:
Genoma Total Lp WCFS1

Arrays of this design have barcodes that begin with 16026636 or 2526636.

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: PacBio RS (Geobacter metallireducens)

organism: Geobacter metallireducens


title: Agilent-014850 FIVI_Human-mRNA_44k_v01

city: Valencia

first: Jose

middle: Antonio

last: Martinez-Conejero

address: C/ Guadassuar 1, bajo

country: Spain

institute: iGenomix

first: Aymara

last: Mas

first: Irene

last: Cervello

first: Claudia

last: Gil-Sanchis

first: Amparo

last: Faus

first: Jaime

last: Ferro

first: Antonio

last: Pellicer

first: Carlos

last: Simon

manufacture_protocol: See manufacturer's website.


title: PacBio RS (Chromohalobacter salexigens)

organism: Chromohalobacter israelensis


title: UWAPG GPL9529 Saccharomyces cerevisiae v1.0 [ORF centered]

first: David

middle: B

last: Berry

address: 3456 Genetics Biotech. Building

department: Laboratory of Genetics

institute: University of Wisconsin: Madison

organism: Saccharomyces cerevisiae

description:
This is an ORF-centered version of GPL9529 "UW-Madison Saccharomyces cerevisiae 380K tiling array 51mer oligos 2006-10-12" Platform.

Please see GPL13254_Scer_Probe_Mapping.txt file for mapping probes to the ORFs.

manufacture_protocol: Standard NimbleGen synthesis procedures.


title: Illumina Genome Analyzer IIx (Oxytricha trifallax)

status: Public on Aug 13 2012

organism: Oxytricha trifallax


title: TaqMan® Array Human MicroRNA Set Cards v2.0

status: Public on Aug 11 2012

city: Tampa

first: jianguo

last: tao

address: 12902 Magnolia Dr

institute: H Lee Moffitt Cancer Center

organism: Homo sapiens

technology: RT-PCR

description: reverse transciped with Megaplex™ RT Primers, Human Pool Set v2.0


title: Illumina Genome Analyzer IIx (Chlorella pyrenoidosa)

status: Public on Aug 10 2012

last: GEO

organism: Auxenochlorella pyrenoidosa


title: Illumina HiSeq 2000 (Chlorella pyrenoidosa)


title: ICDC Streptococcus suis GZ1 tilling arrays (MAP01, MAP02)

status: Public on Aug 09 2012

first: Xiao

last: Zheng

address: Liuzi five hao

institute: China CDC

organism: Streptococcus suis GZ1

description:
Annotation in this record is based on Streptococcus suis GZ1 (GenBank accession number CP000837).

Customized tilling arrays were generated by using 29-mer oligonucleotide probes spaced every seven bases across the reference genome on both strands. Arrays MAP01 and MAP02 are represented by this Platform record.

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


title: NTU Bambusa oldhamii spotted array

city: Taipei

first: Mong-Hsun

last: Tsai

address: 4F, No. 81, Chang-Xing St.

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

organism: Bambusa oldhamii

manufacturer: Center of Genomic Medicine, National Taiwan University

first: Mong

first: Ai

middle: Y

last: Wang

manufacture_protocol: The microarray contained 298 Bambusa oldhamii cDNA clones in triplicate, 9 actin internal controls, and 273 empty spots (7-by-7 probes in each of the 24 blocks). All probes were spotted onto poly-L-lysine-coated slides according to Eisen & Brown (Eisen, M. B., and Brown, P. O. DNA arrays for analysis of gene expression. Methods Enzymol., 303: 179-205, 1999) using an OmniGrid arrayer (GeneMachines, San Carlos, CA).


title: SA Biosciences Jak/STAT Signal Transduction PCR Array

city: San Antonio

first: Sarah

middle: E

last: Hardison

state: Georgia

address: One UTSA Circle

institute: University of Texas at San Antonio

organism: Mus musculus

description:
PCR assay
SABiosciences RT² Profiler panel of PCR assays.


title: SA Biosciences Toll-like Receptor PCR Array


title: EXIQON miRCURY™ V8.1 LNA array [miRbase 12]

status: Public on Aug 08 2012

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

description: Each array was printed twice on one slide.

manufacturer: Division of Pathway Medicine, University of Edinburgh

manufacture_protocol: The miRCury miRNA probe set version 8.1 (Exiqon) was printed onto Codelink slides (GE Healthcare) with each probe printed in triplicate per array.


title: Loblolly pine 26K cDNA array v3.0, PtGen3

city: Athens

first: Adam

middle: W.

last: Barb

address: 180 E. Green Street

department: Biochemistry and Molecular Biology

institute: University of Georgia

organism: Pinus taeda

manufacturer: Dr. Jeff Dean Laboratory, Warnell School of Forestry and Natural Resources, University of Georgia

manufacture_protocol: Plasmid DNAs that had been propagated in the EST sequencing pipeline were re-arrayed and consolidated into new plates to using a BioMek 2000 liquid handling robot (Beckman Coulter, Fullerton, CA).  Samples were then diluted five-fold in millipure dH20 (mp dH20) and 5uL was transferred to a 96-well plate (ABgene AB-0900, Thermo Fisher Scientific Inc. Waltham, MA) for PCR amplification.  PCR reactions were performed in a 100uL volume containing 10 mM Tris (pH 8.8), 3.5 mM MgCl2, 25 mM KCl, 0.25 mM (ea.) dNTP, 0.4 uM pSLFOR2 primer {5'-AAAACGACGGCCAGTGCCAAG-3'}, 0.4uM pSLREV2 primer {5'-GCTTCCGGCTGCTATGTTGTGTGG-3'}, and 1 uL of homemade Taq polymerase.  PCR reactions were incubated at 95oC for 3 min., followed by 30 amplification cycles (95oC for 30 sec., 58oC for 1 min., 72oC for 2.5 min.) and then incubated at 72oC for 7 min.  Each reaction product was verified by agarose gel electrophoresis prior to samples being vacuum desiccated in a Savant Speed Vac Plus Model SC210A (Thermo Fisher Scientific Inc., Waltham, MA).  Samples were resuspended in 30 uL spotting buffer (150mM PO4 1.5M Betaine, 0.001% SDS) with a Robbins Scientific HydraTM96 liquid handling robot and 15uL was transferred to 384 well Corning Costar spotting plates 07-200-747(Corning Inc., Corning, NY).  Printing was done at Microarray Inc. (HudsonAlpha Institute - Suite 3300, 601 Genome Way, Huntsville, AL 35806).  cDNAs were spotted onto Corning UltrGAPS slides (Corning Inc., Corning, NY) and printed using a proprietary microarray gridder equipped with a 48 pin print head.  The PtGen3 platform is simply a re-print of PtGen2 (GEO accession GPL11184) using a different gridding instrument.  Because the print geometry could not be matched to the print from the instrument used to generate PtGen2, a new platform accession is necessary.


title: Candida tropicalis 12.5K v1.0

status: Public on Aug 14 2012

city: Providence

first: Richard

last: Bennett

state: RI

address: 171 Meeting St

department: Molecular Microbiology and Immunology

institute: Brown University

organism: Candida tropicalis

description: 8 x 15k array

first: Allison

middle: M

last: Porman

first: Bennett

last: Richard

manufacture_protocol: Default Agilent protocol


title: Invitrogen NCode Human miRNA Microarray V3 (MIRAH305)

city: Doylestown

first: Rasha

last: Elbaz

address: 3805 Old Easton Road

institute: Drexel University College Of Medicine

description: Based on miRBase 10.0.


title: Human 32k tiling BAC array

city: Beaverton

first: Lucia

last: Carbone

state: Oregon

address: 505 NW 185th ave

institute: Oregon Health & Science University

description: This set includes 32462 BAC clones, amplified by DOP-PCR, selected by fingerprint mapping to cover the entire human genome in a tiling fashion.

manufacture_protocol: as described in MFN manual


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene10stv1_Mm_REFSEQ_13.0.0]

first: GEO

last: admin

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

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/refseq.asp


title: Illumina Genome Analyzer (Human herpesvirus 4)

organism: human gammaherpesvirus 4


title: 454 GS FLX (Litopenaeus stylirostris)

organism: Penaeus stylirostris


title: Illumina HiSeq 2000 (Schistosoma mansoni)

organism: Schistosoma mansoni


title: Agilent-023710 DM15k_01_Of_1

status: Public on Aug 05 2012

city: Boston

first: Helen

last: Poynton

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

organism: Daphnia magna

description:
Arrays of this design have barcodes that begin with 16023710 or 2523710.

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: 2006-11-02_HG18_CpG_Promo

status: Public on Aug 06 2012

first: Hung-Cheng

last: Lai

address: No.250, Wuxing St.

department: Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,

institute: Taipei Medical University


title: IMP Genomics Mouse 35MM

city: Vienna

first: Harald

last: Scheuch

state: Vienna

address: Dr. Bohrgasse 7

department: Core Facilities

institute: Research Institute of Molecular Pathology (IMP)

manufacture_protocol:
Prepare in house spotted  DNA Microarrays
PCRs and Printing Dilution plates:  Prepare 96 well pates and label them ( eg. 1130 Dil)  Aliquot 95 µl dd water into each well (roboter “95µl verteilen”)  Pipette 5µl from the copy plate into the Dilution plate (roboter “dilution plate”).  (If you do not perform immediately:  Heat for 10 min at 94°C ( PCR machine)  Spin down  Freeze away or perform PCR reaction)  PCRmix for a 96 well plate:550µl 10x buffer (100mM Tris.HCl pH8.3, 500mM KCl)  11µl UNI-primer (1µg/µl CCCAGTCACGACGTTG)  11µl REV-primer (1µg/µl CACAGGAAACAGCTATG)  11µl 1M MgCl2 (has to be adjusted to Taq used)  44µl 25mM dNTPs  110µl Taq  1887µl dd water  2514µl 3M Betaine  5138µl total Volume (45µl per well)
PCR Reaction:  Transfer 5µl of the working dilution (see bacteria growth) to PCR-plate (MJResearch, skirted plate) containing 45µl PCRmix, seal plate with sealing sheet (ABGene AB-0558)  Spin down  PCR program: 94°C 1min, 35X 94°C 30sec 52°C 30sec  72°C 1min 30sec, 72°C 5min
Load 5µl PCR product on a 1% agarose gel for quality control  Preparation for printing the PCR products:  Concentrate PCR products in a Speedvac (Determine time until no further reduction of volume is seen, in our case it is at least 4 hours when using 8 plates per batch, final volume is approximately 6-7 µl)  Add 6µl 6xSSC  Shake vigorously up to 3 hours at 4°C (we use a modified vortex,  probably mixing with pipetting robot before transfer into 384 well plates will do)  Transfer into 384 well plates  Store PCR-plates at –80°C  Spot onto Schott Nexterion A slides
Slide Blocking:  Fixation: Put slides 30 min on 80°C heating plate and cross link with 600mJ(Schott) or 60mJ with Poly-lysine slides  Blocking: Dissolve 1.37 g Succinic Anhydride in 90ml N-Methyl - Pyrrolidone, Add 2.5 ml N-methylimidazol (FLUKA), Immediately pour it into a slide chamber and incubate slides for 1 hour with slight agitation, transfer slide into 0.1 % SDS for 20sec, transfer into H2O for 20sec.
Denature: Slides are briefly washed in water (or DCE) and incubated for 4 min in a boiling water bath, After a brief rinse in 95% EtOH spin slides 4 min 1200rpm for drying  For 30 slides in a big chamber with 300 ml blocking solution:(4,11 g SA in 270 ml NMP and 7,5 ml NMI)


title: IMP Genomics Mouse 40MM


title: Illumina HiSeq 2000 (Scylla paramamosain)

status: Public on Aug 07 2012

organism: Scylla paramamosain


title: IMP Genomics Mouse 41MM


title: NimbleGen Mouse gene expression array [100718_MM9_EXP] (probe-level version)

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
DESIGN_ID: 534493
DESIGN_NAME:100718_MM9_EXP
SLIDE_LAYOUT_NAME: NimbleChip_HX12


title: IMP Genomics Mouse 43MM


title: NimbleGen Fusarium_tiling_300k_V1

status: Public on Aug 03 2012

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

organism: Fusarium graminearum

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


title: NimbleGen Nitrosomonas europaea 24mer 2.6k custom array v1.0  [2005-07-14_FIG_N_europaea_mod]

city: Cambridge

first: Paul

last: Berube

address: 15 Vassar Street

department: Civil and Environmental Engineering

institute: Massachusetts Institute of Technology

organism: Nitrosomonas europaea ATCC 19718

description:
NimbleGen design name 2005-07-14_FIG_N_europaea_mod, NimbleGen design ID 2358.  A catalogue Nitrosomonas europaea expression array modified to include an additional 176 24-mer probes targeting intergenic regions adjacent to a selection of ammonia oxidation, carbon fixation, regulatory, and housekeeping genes.  The design includes random GC and other control probes.
designname=2005-07-14_FIG_N_europaea_mod
designid=2358


title: Rocky Mountain Regional Center for Excellence Francisella tularensis full genome array (FTT version)

status: Public on Aug 04 2012

city: Fort Collins

first: Luke

last: Kingry

state: CO

address: 2025 IDRC at Foothills Campus Delivery

institute: Colorado State University

organism: Francisella tularensis subsp. tularensis SCHU S4

middle: A

last: Slayden


title: LC Sciences Sus scrofa BST_miRPig_15

city: Beijing

first: Ang

last: Li

address: Tian Tan Xi Li No.4

institute: Capital Medical University School of Stomatology

organism: Sus scrofa

description:
Part No.: MRA-2001
Name: Pig miRNA Array
Version No.: miRPig_15_BST_100720

No. of Unique Pig Probes: 188; No. of Repeats: 4

Based on Sanger miRBase Release 15.

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


title: Illumina HiSeq 2000 (Solenopsis invicta)

last: GEO

organism: Solenopsis invicta


title: Agilent-016772 G. max (Soybean) Oligo Microarray 4x44K (Probe Name version)

city: Bethesda

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Glycine max

description:
G. max (Soybean) Oligo Microarray 4x44K

Arrays of this design have barcodes that begin with 16016772 or 2516772.

*** 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 GPL15668

relation: Alternative to: GPL15668 (Feature Number version)


title: Rocky Mountain Regional Center for Excellence Francisella tularensis full genome array


title: Illumina Genome Analyzer II (Rosa hybrid cultivar)

organism: Rosa hybrid cultivar


title: Illumina Genome Analyzer II (Staphylococcus aureus)

organism: Staphylococcus aureus


title: 8x15K custom made zebrafish miRNA microarray [Agilent-024479]

status: Public on Aug 02 2012

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

institute: Woods Hole Oceanographic Institution

organism: Danio rerio

description:
Arrays of this design have barcodes that begin with 16030294 or 2530294.

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: Matthew

last: Jenny

first: Mark

last: Hahn


title: OSU-CCC MicroRNA Microarray Version 2

status: Public on Aug 01 2012

first: Aaron

last: Schetter

address: 37 Convent Drive, Building 37, Room 3050

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

organism:
Homo sapiens
Mus musculus

manufacturer: Microarray Shared Resource, Comprehensive Cancer Center, The Ohio State University (OSU-CCC)

manufacture_protocol: Manufacured using GE Healthcare's CodeLink (TM) 3-D Gel Matrix Technology. CodeLink(tm) Activated Slides are designed to covalently immoblize amine-modified DNA for microarrays. The slides are coated with a 3-D surface chemistry comprised of a long-chain, hydrophilic polymer containing amine-reactive groups. This polymer is covalently crosslinked to itself and to the surface of the slide. The crosslinked polymer, combined with end-point attachment, orients the immobilized DNA, and holds it away from the surface of the slide. The 1x printing buffer consists of 50 mM sodium phosphate at pH 8.5. Codelink slides are manufactured by SurModics and were formally sold as 3D-Link(tm) Activated Slides. ¹ Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions that is fitted with a printhead and 16 SMP3 print tips from Telechem. The microRNA microarray probe set is based on 40mer oligonucleotides from Sigma-Genosys. ¹ Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normalized 25 micromolar concentration. The miRNA microarray spot densities are 200 microns (center-to-center). The microarrays are printed on Codelink Activated Slide (PN300011)) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: Agilent-015933 Bombyx mori 015933_D_20070204 [ProbeName version]

city: Mishima

first: Hiromasa

last: Ono

state: Shizuoka

address: National Institute of Genetics, Yata 1111

department: Database Center for Life Science (DBCLS)

institute: Research Organization of Information and Systems

organism: Bombyx mori

description:
User Design

Arrays of this design have barcodes that begin with 16015933 or 2515933.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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


title: Agilent-029152 Unrestricted Mouse miRNA v15.0 Microarray 028772 (Probe Name version)

organism: Mus musculus

description:
Mouse miRBase 15.0

Arrays of this design have barcodes that begin with 16029152 or 2529152.

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 PROBE_NAME


title: Illumina Genome Analyzer II (Rosa rugosa)

organism: Rosa rugosa


title: NimbleGen Anabaena variabilis ATCC 29413 Gene Expression Array [2006-07-27_TI240292_60mer]

city: Madison

organism: Trichormus variabilis ATCC 29413

description:
Design name: 2006-07-27_TI240292_60mer
DESIGN_ID: 4385


title: UCSF HUMAN 1.14 v4

city: Pamplona

first: Vicente

middle: Jose

last: Fresquet

state: Navarra

address: Av Pio XII 55

department: Division of Oncology

institute: Center for Applied Medical Research (Cima)

organism: Homo sapiens

description:
The arrays contain 2462 BAC clones printed as triplicated spots.
The array was used for genome wide measurement of DNA copy number.

manufacturer: University of California, San Francisco (UCSF).

manufacture_protocol: Production and validation of the array, hybridization methods and analytical procedures have been described elsewhere: Snijder AM, Nowak N, Segraves R, et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet. 2001;29:263-264.


title: miRNAChip_human_V2

city: Aveiro

first: Patrícia

middle: Matos

last: Pereira

address: Campus Universitário de Santiago

country: Portugal

institute: University of Aveiro

manufacturer: National DNA-Microarray Facility located at the University of Aveiro, Portugal

manufacture_protocol: The arrays contained a total of 1175 probes spotted in quadruplicate. Each array was printed with optimized probe sequences targeting all of the 703 known human mature miRNAs deposited in the Sanger miRBase Sequence Database, Release 10.0 (http://microrna.sanger.ac.uk), as well as 393 novel human miRNAs discovered through deep sequencing and validated by qRT-PCR and array profiling (NCode™ Human miRNA microarray probe set V3 from Invitrogen). The probe set also includes mismatch controls for screening 1- and 2-base sequence mismatches for monitoring hybridization specificity, as well as the NCode™ Positive Control for labeling quality control and easier spot finding. These unmodified oligonucleotides, which are 34–44 bases in length, were dissolved in 150 mM phosphate buffer pH 8.5 at a concentration of 20 µM and printed onto Nexterion E slides (SCHOTT) using a MicroGrid II compact spotter. Printed slides were further processed according to manufacturer's recommendations. The library is provided in 384-well plates in lyophilized form.  LIQUID HANDLING: The goal was 20 uM oligos in 150 mM phosfate buffer in 384-well plates (Genetix X-6004) ready for robotic spotting.  1. Lyophilized oligos (500 pmol in 384-well plates) were resuspended in 150 mM phosphate buffer to a concentration of 20 uM using a liquid handling station (Sciclone LH 3000, Caliper).  2. Shaking overnight at 4 ºC, at 100 rpm. The 384-well plate was stored at -80 ºC ready for spotting.  3. The remaining stock in 384-well plates was air dried at room temperature and stored at -80 ºC. When necessary, milliQ water was used to resuspend the oligos accounting for lost volume.  SPOTTING:  1. The 34-44mer probes were transfered in quadruplicate from the 384-well plates and printed on Nexterion E slides (SCHOTT) with a BioRobotics MicroGrid Compact II spotter (Genomic Solutions) in an environment controlled room. Humidity was 60% ± 2%. Temperature was 21 ºC in the spotter. Quill Pins type MicroSpot2500 (BioRobotics) were used for spotting.  2. For probe fixation, the printed slides were incubated in a humidity chamber at room temperature, overnight.  3. Slides were stored in a desiccator-cabinet (Nalgene, with blue Silica (Sigma)) ready to use (continue with our hybridization protocol).


title: Agilent-028465/UniversityPadova Ruditapes decussatus 4x44K v1.0 (Feature Number version)

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

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

institute: University of Padova

organism: Ruditapes decussatus

description: Target sequences to be included in the R.decussatus microarray were obtained from the assembly of two sets of libraries (MGE011, 122,471 reads; cDN18 327,209  reads) making a  total of 449,680 reads were sequenced  using  normalized cDNA libraries constructed with a mixture of adult tissues and another containing gonadal tissue and larvaes. The same libraries were been used to obtain 2434 and 2077 ESTs with traditional Sanger sequencing respectively. Assembly perfromed by MIRA3 grouped these seqeunces and reads into 41,119 contigs. The array included all annotated sequences with a blast hit to vertebrates and invertebrates.Probe design started with selection of target sequences to be represented onto the R. philippinarum microarray. All annotated entries (12,479) were included whereas non annotated transcripts were considered only if sequence length was ≥400 bp and average Phred sequence quality was ≥31, yielding 21,900 target sequences. For each contigs two probes with opposite orientation (sense and antisense) were designed. A total of 43,758 out of 43,800 (99.9%) probes were successfully obtained, representing 21,887 R. decussatus transcripts.

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


title: [PhyloChip] Affymetrix G2 PhyloChip

city: San Francisco

first: Susan

last: Lynch

address: 513 Parnassus Ave, S357D

department: Medicine

institute: University of California at San Francisco

organism:
Bacteria
Archaea

description:
16S PhyloChip
Probes target 16S rRNA genes. Probesets represent operational taxonomic units (OTUs).

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


title: Voskuil Lab Mycobacterium tuberculosis Operon Microarray

city: Aurora

first: Martin

middle: I

last: Voskuil

department: Microbiology

institute: University of Colorado Denver

organism:
Mycobacterium tuberculosis CDC1551
Mycobacterium tuberculosis H37Rv

first: Voskui

last: Martin

manufacture_protocol:
1. Oligos are arrayed in Whatman 384-well V-bottom plates. Each well contains 600 pmol of 70-mer oligo.
2. Oligos are suspended in 3xSSC to 20 uM and centrifuged at 500 rpm for 2 minutes.
3. Plates are stored at 4oC overnight.
4. Incubate at RT for 30 minutes and shakern for 5 min to aid resuspension of DNA.
5. Centrifuge plates at 500 rpm for 2 minutes.
6. Remove seals
7. Print
8. After completion of print, allow slides to dry through passive evaporation in a protected environment.


title: Genotoul/Biopuces Eurogentec Yarrowia lipolytica 6.4K oligonucleotide array v2007

status: Public on May 05 2011

city: Thiverval-Grignon

first: Nicolas

last: Morin

address: Av. Lucien Bretignières

department: UMR 1319 Micalis

institute: INRA

organism: Yarrowia lipolytica

manufacture_protocol: 4x8 pin head, each pin has spotted a block of 22x19 spots. Each well is spotted in duplicate.


title: LC_MRA-1001_miRHuman_13.0_090309 (miRNA ID version)

status: Public on May 14 2010

city: Houston

first: Christoph

last: Eicken

address: 2575 W. Bellfort

institute: LC Sciences, LLC

description: Human miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 13.0

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


title: NimbleGen HD2 Human whole genome custom array 2.1M [090310_LP_til_HX1]

status: Public on Dec 31 2010

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description:
Custom made nimblegen array
NimbleGen file 090310_LP_til_HX1.ndf linked below as supplementary file.
Platform table annotations based on NCBI36 build.

manufacture_protocol: See manufacturer's website


title: URMC_Dunman_Brucella_abortus_v1.0

status: Public on Jun 15 2012

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

organism: Brucella abortus

description: Affymetrix 11 micron 100-3660 array format GeneChip

first: R

last: Roop

manufacture_protocol: This is a custom-made B. abortus GeneChip based off of strain 2308 genome.  The array was manufactured by Affymetrix.


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) custom CDF: HuEx10stv2_Hs_VEGAG.cdf (v10)]

status: Public on May 23 2011

city: Paris

first: Claire

last: Vandiedonck

address: 10 avenue de Verdun

department: Faculte de Medicine Villemin

institute: Inserm U958, Universite Paris Denis Diderot - Paris 7

description: Chip description file: HuEx10stv2_Hs_VEGAG.cdf (v10)

manufacture_protocol: See manufacturer's web site


title: Agilent-016772 G. max (Soybean) Oligo Microarray 4x44K

status: Public on Jul 31 2012

city: Fuchu

first: Shin

last: OKAZAKI

state: Tokyo

address: 3-5-8 Saiwaicho

institute: Tokyo University of Agriculture and Technology

description:
G. max (Soybean) Oligo Microarray 4x44K

Arrays of this design have barcodes that begin with 16016772 or 2516772.

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: GPL15901 (Probe Name version)

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


title: Kyoto Univ. Invitrogen NCode Human miRNA Microarray V3

status: Public on May 14 2009

city: Kyoto

first: Akira

last: Myomoto

address: Yoshida-Shimoadachi

institute: Kyoto Univ.

first: F

last: Sato

first: S

last: Tsuchiya

first: K

last: Terasawa

first: G

last: Tsujimoto

manufacture_protocol: Efficient Profiling of Global miRNA Expression Patterns with Novel miRNA Content -The NCode™ Human miRNA Microarray V3 contains optimized probes targeting nearly all of the known human mature miRNAs in mirBase 10.0 along with 380 novel human miRNAs discovered through deep sequencing. The probes are spotted in triplicate on Corning Glymo epoxide slides.


title: Arraystar Human lncRNA array version 1

status: Public on Dec 03 2010

city: Rockville

first: Panos

last: Pan

address: 9430 Key West Avenue

institute: Arraystar Inc.

description: This array contains ~19000 RefSeq coding genes and ~21000 long non-coding RNAs (lncRNA).


title: KRIBB Hansenula 11K

status: Public on Nov 12 2008

city: Daejeon

first: Min Jeong

last: Sohn

address: 52 Eoeun-dong, Yuseong-gu

department: Protein therapeutics research center

institute: Korea Research Institute of Bioscience and Biotechnology

organism: Ogataea angusta

first: MinJeong

first: HyunAh

last: Kang

first: Ohsuk

last: Kwon

first: Doo-Byoung

last: Oh

first: YunWi

first: YongKyung

last: Kim

first: SangKi

last: Rhee

first: Gerd

last: Gellissen

manufacture_protocol: DNA spotted onto aldehyde-coated galss slides


title: JCVI Synechococcus sp. WH 8102 19K v2.0

status: Public on Jun 15 2009

city: Sydney

first: Ian

last: Paulsen

state: NSW

address: Macquarie University

department: Department of Chemistry and Biomolecular Sciences

country: Australia

institute: Macquarie University

organism: Parasynechococcus marenigrum WH 8102

technology: mixed spotted oligonucleotide/cDNA

first: Brian

last: Palenik

first: Katherine

last: Phillippy

first: Daniel

last: Johnson

manufacture_protocol: Primers were designed to yield 2142 PCR amplicons of approximately 800 base pairs, and 70-mer oligonucleotides were designed for another 389 genes that were less than 200 base pairs in length or could not be amplified by PCR.  PCR amplicons and oligonucleotides were suspended in 50% DMSO and spotted onto Corning UltraGAPS slides using an Intelligent Automation Systems arrayer.  Each gene is represented six times on the array.  Negative controls include 50% DMSO / 50% DI water and air.  A mixture of PCR amplicons, Arabidopsis spike-in controls, and Arabidopsis 70-mer oligonucleotides were used as positive controls.  Slides were air dried for at least 30 minutes after printing.  DNA was irreversibly cross-linked to the slides with 250 mJ/cm^2 UV energy by using a Stratagene Stratalinker.  Slides were stored at room temperature in a dessicator.


title: Loblolly pine 26K cDNA array v2.0, PtGen2

status: Public on Jan 26 2011

city: Athens

first: Adam

last: Barb

state: GA

address: 180 E. Green Street

department: Biochemistry and Molecular Biology

country: USA

institute: University of Georgia

organism: Pinus taeda

manufacture_protocol: Plasmid DNAs that had been propagated in the EST sequencing pipeline were re-arrayed and consolidated into new plates to using a BioMek 2000 liquid handling robot (Beckman Coulter, Fullerton, CA).  Samples were then diluted five-fold in millipure dH20 (mp dH20) and 5mL was transferred to a 96-well plate (ABgene AB-0900, Thermo Fisher Scientific Inc. Waltham, MA) for PCR amplification.  PCR reactions were performed in a 100mL volume containing 10 mM Tris (pH 8.8), 3.5 mM MgCl2, 25 mM KCl, 0.25 mM (ea.) dNTP, 0.4 mM pSLFOR2 primer {5’-AAAACGACGGCCAGTGCCAAG-3’}, 0.4mM pSLREV2 primer {5’-GCTTCCGGCTGCTATGTTGTGTGG-3’}, and 1 mL of homemade Taq polymerase.  PCR reactions were incubated at 95oC for 3 min., followed by 30 amplification cycles (95oC for 30 sec., 58oC for 1 min., 72oC for 2.5 min.) and then incubated at 72oC for 7 min.  Each reaction product was verified by agarose gel electrophoresis prior to samples being vacuum desiccated in a Savant Speed Vac Plus Model SC210A (Thermo Fisher Scientific Inc., Waltham, MA).  Samples were resuspended in 30mL spotting buffer (150mM PO₄ 1.5M Betaine, 0.001% SDS) with a Robbins Scientific HydraTM96 liquid handling robot and 15mL was transferred to 384 well Corning Costar spotting plates 07-200-747(Corning Inc., Corning, NY).  Printing was done at the Vanderbilt Microarray Shared Resource (VMSR) facility.  cDNAs were spotted onto Corning UltrGAPS slides (Corning Inc., Corning, NY) and printed with a BioRobotics Microgrid II (Genomic Solutions, Ann Arbor, MI) with a 48 pin print head


title: JCVI Synechococcus sp. CC9311 21k v1.0

status: Public on Jun 30 2009

organism: Synechococcus sp. CC9311

middle: T

manufacture_protocol: Unique 70-mer oligonucleotides were designed for 2892 genes of the Pseudomonas fluorescens Pf-5 genome. Oligonucleotides were suspended in 50% DMSO and spotted onto Corning UltraGAPS slides using an Intelligent Automation Systems arrayer. Each gene is represented six times on the array. Negative controls include 50% DMSO / 50% DI water and air. Arabidopsis spike-in controls and Arabidopsis 70-mer oligonucleotides were used as positive controls. Slides were air dried for at least 30 minutes after printing. DNA was irreversibly cross-linked to the slides with 250 mJ/cm^2 UV energy by using a Stratagene Stratalinker. Slides were stored at room temperature in a dessicator.


title: [FDA_ECSGa520423F] Affymetrix Escherichia coli and Shigella 23K

status: Public on Jul 25 2011

city: Baltimore

first: David

last: Rasko

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

organism:
Escherichia coli
Shigella

manufacture_protocol: see manufacturer's website


title: Agilent-029152 Unrestricted Mouse miRNA v15.0 Microarray 028772 (Feature Number version)

status: Public on Dec 07 2011

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

description:
Mouse miRBase 15.0

Arrays of this design have barcodes that begin with 16029152 or 2529152.

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: GPL15169 (miRNA_ID version)


title: Agilent-012694 Whole Mouse Genome G4122A (Probe Name version)

status: Public on Jul 10 2008

description:
Designed to truly represent all known genes in the mouse genome and their resulting transcripts, Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts. Content for this microarray was generated from leading public databases, including RefSeq, RIKEN, NIA, Ensembl, RIKEN, UCSC Goldenpath, and Unigene

*** 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 GPL2872.


title: 080922_modEncode_Caenorhabditis elegans_2M tiling chip_HX1

status: Public on Jun 05 2009

city: Chapel Hill

first: Everett

last: Zhou

state: NC

address: 1000 Manning Dr.

institute: UNC

organism: Caenorhabditis elegans

description: Native NimbleGen files (ndf, pos) are linked below as supplementary files.

first: Jason

last: Lieb

manufacture_protocol: Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR,Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol. 1999 Oct;17(10):974-8. PMID: 10504697


title: FZ_IBG-1_Goxydans_10K_Ver1 array

status: Public on Aug 01 2012

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

organism: Gluconobacter oxydans 621H

description:
spotted with 70-mer oligonucleotides obtained from Operon (Cologne, Germany)
G.oxydans 621H, based on the genome sequence entry NC_006677

manufacturer: Operon (Cologne, Germany) and Microarrays Inc. (Huntsville, USA)