title: Human 58K oligonucleotide chip

status: Public on Sep 30 2012

city: Odense C

first: Nete

middle: Vinstrup

last: Michelsen

address: Sdr Boulevard 29

department: Dept of Clinical Genetics

country: Denmark

institute: Odense University Hospital

organism: Homo sapiens

technology: spotted oligonucleotide

distribution: non-commercial

manufacturer: Human MicroArray Centre, University of Southern Denmark.

manufacture_protocol: A human oligonucleotide library composed of 29,134 oligonucleotide targets (60mers) recognising 28,830 genes was purchased from Sigma-Genosys (The Woodlands, TX) and designed by Compugen (Compugen Ltd., Jamesburg, NJ) with a 5´ amino linker modification. The oligonucleotides have been designed to include known genes, expressed sequence tags, the majority of known alternative splice variants (http://www.labonweb.com/oligo), and spike targets.  According to the CodeLinkTM protocol, oligonucleotide targets were solubilized in 150 mM sodium phosphate buffer (pH 8.5) and divided into a single aliquot and applied to 76 384-well source plates using an Eppendorf epMotion 5070 robot (Radiometer, DK) at a final concentration of 20pmol/µl. Oligonucleotide targets were arrayed in duplicate by a spotting robot (Virtek ChipWriter Pro (ESI)) onto 75 slides in a controlled environment with a humidity of 38 % inside the spotting compartment. 12 SMP 2.5 stealth pins (TeleChem International Inc., Sunnyvale, USA) were used for printing. After printing, slides were incubated overnight and blocked as recommended by the manufacturer. Dried microarray slides were stored in a desiccated environment at room temperature.


title: AbC_ELTE_human_432_v1

city: Budapest

first: Krisztian

last: Papp

address: 1/C Pazmany P.

country: Hungary

institute: MTA-ELTE Immunology Research Group

organism:
Homo sapiens
Sus scrofa
Bos taurus
Capra hircus
Oryctolagus cuniculus

technology: spotted peptide or protein

manufacturer: Eotvos Lorand University, Budapest, Hungary

manufacture_protocol: Antigens were spotted in five fold serial dilution (2-5 point) onto Fast Slide nitrocellulose chip. Dilutions were carry out in 0.05% azide containing PBS. BioOdyssey Calligrapher (Bio-Rad) was used for the printing with the programm detailed in the "platform_protocol.txt" file linked as a supplementary file at the foot of this record.


title: Cryptococcus neoformans JEC21 whole genome array from Wash. U.

status: Public on Sep 29 2012

city: Newark

first: Chaoyang

last: Xue

state: NJ

address: 225 Warren Street

country: USA

institute: University of Medicine and Dentistry of New Jersey

organism: Cryptococcus deneoformans JEC21

manufacture_protocol: spotted oligonucleotide


title: Nanostring nCounter Human microRNA Expression Platform

status: Public on Sep 28 2012

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol: See manufacturer's website


title: Illumina HiSeq 2000 (Schistocerca gregaria)

last: GEO

organism: Schistocerca gregaria

technology: high-throughput sequencing

distribution: virtual


title: GEArray Express Mouse Stem Cell Microarray (EMM-405)

city: Frederick

first: SuperArray

last: Bioscience Corporation

address: Suite 101, 7320 Executive Way

institute: Technical Support

organism: Mus musculus

distribution: commercial

manufacture_protocol: The details are provided by the manufacturer at www.sabiosciences.com -- 60-mer oligonucleotides are spotted onto positively charged nylon membranes.


title: Agilent-029585 BosTaurus_AlHV-1_60K_v1.0

status: Public on Mar 20 2013

city: Liege

first: Leonor

last: Palmeira

address: Bd Colonster 20

department: Faculty of Veterinary Medicine

country: Belgium

institute: University of Liege

organism:
Bos taurus
Alcelaphine gammaherpesvirus 1

description: The microarray was custom designed for Agilent 8x60K slides. It targets both AlHV-1 by tiling array and Bos taurus transcripts: the AlHV-1 tiling has a 15bp sliding step between each 60-mer probe; Bos taurus transcripts were targeted with all 60-mer probes from Agilent's B. taurus (Bovine) Oligo Microarray v2_1. Probe design was performed by Agilent.

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


title: Affymetrix GeneChip Rat Genome 230 2.0 Array [custom CDF: Rat2302_Rn_ENSG_14.1.0]

city: Brussels

first: Tatyana

last: Doktorova

state: Belgium

address: Laarbeeklaan 103, building G

department: FAFY

institute: VUB

organism: Rattus norvegicus

description: Brainarray custom CDF Rat2302_Rn_ENSG_14.1.0

manufacture_protocol: see manufacturer's web site


title: Illumina HumanOmni2.5-4v1_B BeadChip [hg19]

status: Public on Sep 26 2012

city: South San Francisco

first: Peter

last: Haverty

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

technology: oligonucleotide beads

description: Please see http://www.illumina.com/technology/infinium_hd_assay.ilmn


title: Illumina Genome Analyzer II (Gossypium hirsutum)

status: Public on Sep 25 2012

organism: Gossypium hirsutum


title: Illumina HiSeq 2000 (Cynoglossus semilaevis)

organism: Cynoglossus semilaevis


title: Solanum lycopersicum  385K 4-plex array 4x72K array

city: Rehovot

first: Dagan

last: Sade

address: Hertzel

country: Israel

institute: Hebrew University of Jerusalem

organism: Solanum lycopersicum

description:
NimbleGen design name 101115_Czosnek_tomato_expr X4 expression design for Solanum lycopersicum, sequences from customer; used modified tiling procedure: 2 60mer probes selected from the 1500 bases at the 3' end (i0w1501), max_matches=1, for sequences with no match1 probes, allow up to 10 matches; empty features on array filled with randomly generated probes of comparable length and G+C content.
101115_Czosnek_tomato_expr.ndf
101115_Czosnek_tomato_expr.ngd

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


title: Agilent-018257 NematodeNet_Ascaris suum_42K_v1.0

city: St. Louis

first: Makedonka

last: Mitreva

state: Missouri

address: 4444 Forest Park Ave

institute: The Genome Institute

organism: Ascaris suum

last: Gao

manufacture_protocol:
Agilent 4x44K format chips were used for this genome-wide expression array. The Agilent gene expression custom array for A. suum was designed in Agilent eArray:
4x44K
Design ID 018257
The final array contains 42,212 customized probes, each derived from a single predicted A. suum gene. We also included 1,591 spike control spots of ten probes, each targeting a different Arabidopsis thaliana gene that did not have homology to known non-plant sequences currently in public databases (SpotReport@-10 Array Validation System, Stratagene).


title: Agilent-031749 Hp695 3 probes [Probe Name version]

city: Los Angeles

first: David

last: Scott

address: 11301 Wilshire Blvd

institute: UCLA/VA GLAHS

organism: Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504 = JCM 12093

description:
Arrays of this design have barcodes that begin with 16031749 or 2531749.
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.

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


title: NimbleGen Micrococcus luteus 4x72K array v1.0 - Design ID 12568

status: Public on Sep 24 2012

city: Emeryville

first: Ee-Been

last: Goh

address: 5885 Hollis St, 4th Floor

department: Fuels Synthesis Division

institute: Joint BioEnergy Institute

organism: Micrococcus luteus NCTC 2665

description: NimbleGen design name 080219_M_luteus_LBNL_Beller_expr_X4.  A 4x72K expression design for 2,374 ORF based on the draft genome sequence of Micrococcus luteus annotated by JGI. There are ten 60-mer probe pairs (PM/MM) per ORF and each probe is replicated 3 times in the array.  The design includes random GC and other control probes. Design ID is 12568.


title: Illumina HiSeq 2000 (Cleome hassleriana)

organism: Tarenaya hassleriana


title: YaleLu Mouse miRNA v1.0

city: New Haven

first: Brian

last: Adams

state: CT

address: 10 Amistad Street; Rm214K

department: Genetics

institute: Yale University

manufacture_protocol: Refer to [Lu, J., Guo, S., Ebert, B. L., Zhang, H., Peng, X., Bosco, J., Pretz, J., Schlanger, R., Wang, J. Y., Mak, R. H., et al. (2008). MicroRNA-mediated control of cell fate in megakaryocyte-erythrocyte progenitors. Dev Cell 14, 843–853]  for miRNA plate capture and luminex detection protocols.


title: Illumina MiSeq (Mycoplasma penetrans)

status: Public on Sep 20 2012

organism: Malacoplasma penetrans


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

status: Public on Sep 21 2012

city: Tianjin

first: baocun

last: sun

address: Qixiangtai Road No.22, Heping District

country: China

institute: Tianjin Medical University

manufacture_protocol: see manufacturer's website


title: NimbleGen Rice 3'-Tiling Microarray

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: Oryza sativa

description:
The Rice 3'-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.dna.affrc.go.jp/).

The following NimbleGen native array files are linked below as supplementary files:
2006-11-14_ggb_rap1_3tile_101706.ndf
2006-11-14_ggb_rap1_3tile_101706.pos

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


title: Illumina Genome Analyzer II (Taphozous melanopogon)

status: Public on Sep 19 2012

organism: Taphozous melanopogon


title: Illumina Genome Analyzer II (Miniopterus fuliginosus)

organism: Miniopterus fuliginosus


title: NimbleGen_Junco hyemalis_Expression Array_12x135k_All Probes [DesignID 537583]

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

organism: Junco hyemalis

description:
This is a song bird (Junco hyemalis) whole-genome expression array in HD2 12x135K format manufactured by Roche NimbleGen.
DESIGN_ID : 537583
native array description file : 100702_Jhye_JL_exp.ndf
native array description file : 100702_Jhye_JL_exp.txt
Peterson MP, Whittaker DJ, Ambreth S, Sureshchandra S, Buechlein A, Podicheti  R, Choi JH, Lai Z, Mockatis K, Colbourne J, Tang H, Ketterson ED. De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system. BMC Genomics. 2012 Jul 9;13:305. PubMed PMID: 22776250. doi:10.1186/1471-2164-13-305


title: Illumina Genome Analyzer II (Rousettus leschenaultii)

organism: Rousettus leschenaultii


title: Illumina Genome Analyzer II (Hipposideros armiger)

organism: Hipposideros armiger


title: Illumina HiSeq 2000 (Invertebrate iridescent virus 6)

organism: Invertebrate iridescent virus 6


title: Agilent-028103 Aggregatibacter actinomycetemcomitans Pangenome Microarray [Gene centered version]

city: Seattle

first: Weerayuth

last: Kittichotirat

state: WA - Washington

address: 960 Republican st

department: Microbiology

institute: University of Washington

organism: Aggregatibacter actinomycetemcomitans

description:
This array is designed based on AaHa GeneTable 100728 (http://expression.washington.edu/genetable/script/gene_table_viewer?organism=aa_ha&build=10_07_28)
Arrays of this design have barcodes that begin with 16028103 or 2528103.
This is the Gene-cenetered version of GPL15712

first: Roger

last: Bumgarner

first: Casey

last: Chen


title: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655star)

status: Public on Sep 27 2012

last: GEO


title: Illumina Genome Analyzer II (Eonycteris spelaea)

organism: Eonycteris spelaea


title: Illumina Genome Analyzer IIx (Dunaliella viridis)

organism: Dunaliella viridis


title: Illumina Genome Analyzer II (Rhinolophus affinis)

organism: Rhinolophus affinis


title: [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [Alternative CDF: MBNI Entrez Gene version 11]

first: Ayush

last: Raman

state: WA

address: 401 Terry Avenue North

department: Computational Dept.

institute: Institute for Systems Biology

organism: Mus musculus

description: This Platform is identical to GPL6096 but a custom cdf environment was used to extract data. The cdf can be found at the link below.

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

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


title: AB SOLiD 4hq System (Mus musculus)

status: Public on Sep 18 2012


title: IHB miR Zebrafish 14 0.3K

status: Public on Sep 17 2012

city: Wuhan

first: Yanyan

last: Zhao

address: Donghu South Road 7

institute: Institute of Hydrobiology

organism: Danio rerio

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: Agilent-036031 Schizosaccharomyces pombe sp10b [ProbeName version]

status: Public on Sep 15 2012

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

country: Australia

institute: The Australian National University

organism: Schizosaccharomyces pombe

description:
S.p. 10 bp res

Arrays of this design have barcodes that begin with 16036031 or 2536031.


title: AB 5500xl Genetic Analyzer (Mycobacterium tuberculosis CDC1551)

organism: Mycobacterium tuberculosis CDC1551


title: Agilent-036227 Schizosaccharomyces pombe sp40c [ProbeName version]

description:
Tm optimized 75C

Arrays of this design have barcodes that begin with 16036227 or 2536227.


title: PBMC gene expression RT-PCR assay

city: Kuopio

first: Otto

middle: Taavetti

last: Mykkänen

address: Yliopistonranta 1

department: Public Health and Clinical Nutrition

country: Finland

institute: University of Eastern Finland

organism: Homo sapiens

technology: RT-PCR

description: RT-PCR (TaqMan® Gene Expression Assay)


title: Synechocystis cDNA microarray ver. 2.0

city: Guangzhou

first: Gu

last: CHEN

address: 381 Wushan Road

institute: South China University of Technology

organism: Synechocystis sp. PCC 6803

technology: spotted DNA/cDNA

manufacture_protocol: This microarray covered 3,076 of the 3,264 open reading frames of the Synechocystis genome [Kaneko, T. et al.:DNA Res., 3, 109-136 (1996)]. Description of each ID can be obtained from CyanoBase (http://genome.kazusa.or.jp/cyanobase).


title: Agilent-031109 Schizosaccharomyces pombe sp40a 029798 [ProbeName version]

description: Arrays of this design have barcodes that begin with 16031109 or 2531109.


title: Agilent-012694 Whole Mouse Genome G4122A v.2 (Feature Number version)

status: Public on Sep 13 2012

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

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. Conten

Arrays of this design have barcodes that begin with 16012694 or 2512694.

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 is assigned accession number GPL7042, GPL2872 and GPL6585.


title: Illumina Genome Analyzer II (Myotis laniger)

organism: Myotis laniger


title: 454 GS 20 (Coprinopsis cinerea)

status: Public on Sep 10 2012

organism: Coprinopsis cinerea


title: Scsie_Univ Valencia_Saccaromyces cerevisiae_ver.4

city: A Coruña

first: M Esperanza

last: Cerdan

state: A Coruña

address: Campus de A Zapateira

department: Biología Celular y Molecular

country: Spain

institute: Universidad de A Coruña

organism: Saccharomyces cerevisiae

manufacturer: DNA-Chips Services from Univ. Valencia. Spain

first: Angel

last: Vizoso-Vázquez

first: Mónica

last: Lamas-Maceiras

first: Manuel

last: Becerra

first: M

middle: I

last: González-Siso

first: Esther

last: Rodríguez-Belmonte

middle: E

last: Cerdán

first: Jose

last: Perez-Ortin

last: Garcia-Martinez


title: Illumina Genome Analyzer IIx (Homo sapiens; Mus musculus)

status: Public on Sep 14 2012

organism:
Homo sapiens
Mus musculus


title: Mouse EG4000 CustomArray ver.3

city: Toyonaka

first: Yoshinobu

last: Ohira

state: Osaka

address: 1-17 Machikaneyama-cho

department: Applied Physiology

country: Japan

institute: Osaka University

description: oligo DNA (35 to 40-mer)


title: Bos taurus QTL of female fertility region Tiling Array 385K Nimblegen

status: Public on Sep 11 2012

city: Jouy-en-Josas

first: Sylvain

last: Marthey

address: Domaine de Vilvert Bat 320

department: Animal Genetics

country: France

institute: INRA

organism: Bos taurus

description: The 385k Fertility Tiling Array was designed in both orientations to cover one of female fertility QTL on chr3. Target regions was gotten from UCSC database on Oct 2007 release (bosTau4). The 385k Fertility Tiling Array contains 171581 forward experimental probes, 171581 reverse experimental probes and 45961 randomly generated probes.

manufacture_protocol: Maskless array synthesis was used to construct isothermal arrays. An isothermal format (Tm=76oC) and probe length constraint between 50 and 75 bp were used for probe synthesis. Each probe overlapped its neighbor by about 40 base pairs.


title: C. elegans 12 x 135K Gene Expression Array

city: Kunming

first: Cheng Gang

last: Zou

state: Yunnan

address: No. 2,North of Cuihu Road

institute: Yunnan University

organism: Caenorhabditis elegans

description: NimbleGen 12x135K microarrays for gene expression analysis enable you to conveniently and simultaneously hybridize 12 samples on each slide.

manufacture_protocol: NimbleGen 12x135K microarrays for gene expression analysis, Source: Wormbase, Build: WS190,Probe Length: 60mer,Genes: 23,187, Probes/Target: 6


title: Illumina HiSeq 2000 (Metarhizium robertsii)

last: GEO

organism: Metarhizium robertsii


title: NimbleGen Human ChIP-chip 2.1M Economy Whole-Genome Tiling - Array 2 of 4 [100718_HG18_Economy_02_HX1]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
Format: 2.1M
Source: UCSC
Build: HG18
designname: 100718_HG18_Economy_02_HX1


title: NimbleGen Human ChIP-chip 2.1M Economy Whole-Genome Tiling - Array 3 of 4 [100718_HG18_Economy_03_HX1]

description:
Format: 2.1M
Source: UCSC
Build: HG18
designname: 100718_HG18_Economy_03_HX1


title: NimbleGen Human ChIP-chip 2.1M Economy Whole-Genome Tiling - Array 1 of 4 [100718_HG18_Economy_01_HX1]

description:
Format: 2.1M
Source: UCSC
Build: HG18
designname: 100718_HG18_Economy_01_HX1


title: AB SOLiD 3 Plus System (Danio rerio)


title: NimbleGen Human ChIP-chip 2.1M Economy Whole-Genome Tiling - Array 4 of 4 [100718_HG18_Economy_04_HX1]

description:
Format: 2.1M
Source: UCSC
Build: HG18
designname: 100718_HG18_Economy_04_HX1


title: Illumina HiSeq 2000 (Apis mellifera)

organism: Apis mellifera


title: NimbleGen Human DNA Methylation 385K Promoter Plus CpG Island Array [2006-11-02_HG18_CpG_Promo]


title: University of Groningen Lactococcus lactis MG1363 amplicon/oligo 2 X 2.5K v2

status: Public on Sep 12 2012

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

organism: Lactococcus cremoris subsp. cremoris MG1363

manufacture_protocol: eneral Microgrid II spotting protocol on superamine slides


title: SABiosciences human T cell anergy and tolerance PCR assay panel

city: Dresden

first: Anke

last: Theil

address: Fetscherstr. 105

country: Germany

institute: CRTD

description:
Human T cell anergy and tolerance gene panel
SABiosciences RT² Profiler panel of PCR assays.


title: Illumina HiSeq 2000 (Beauveria bassiana)

organism: Beauveria bassiana


title: SMD Print_980 LC-46

status: Public on Sep 06 2012

city: Stanford

last: Stanford Microarray Database

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: AB 5500xl Genetic Analyzer (Arabidopsis thaliana)

organism: Arabidopsis thaliana


title: Genotypic Technology Private Limited designed Custom Mus musculus 1 million ChIP-on-chip Array (AMADID-024567)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

organism: Mus musculus

description: Probe coordinates based on NCBI37/mm9 mouse genome assembly.

first: Mugasimangalam

middle: C

last: Raja


title: Nimblegen D. yakuba custom 385K array (2007_06_22)

status: Public on Sep 05 2012

city: Iowa City

first: Ana

last: Llopart

address: 469 Biology Building

institute: University of Iowa

organism: Drosophila yakuba

description:
Nimblegen Drosophila yakuba custom design array (385K) for expression in D. yakuba, D. santomea and hybrids.  An average of 10 array element probes per gene were selected without-bias vis-a-vis position within the gene model.  Protein coding gene predictions were obtained from final genome assemblies (Comparative Assembly Freeze 1 CAF1, http://rana.lbl.gov/drosophila/caf1.html) and genome annotations in D. yakuba (GLEANR set, http://rana.lbl.gov/~venky/AAA/freeze_20061030/protein_coding_gene/GLEANR/annotation).  See details of arrays see Llopart (2012).
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.


title: AECOM Human 28K HH5 series

city: Bronx

first: Antonia

last: Patsialou

state: NY

address: 1301 Morris Park Ave

department: Anatomy and Structural Biology

institute: Albert Einstein College of Medicine

manufacturer: Albert Einstein College of Medicine Microarray Facility

manufacture_protocol: Information about the AECOM custom-printed chips can be found in http://microarray1k.aecom.yu.edu/.  Unique Genome Systems human full lenght cDNAs from the I.M.A.G.E. consortium were used for printing on glass slides.  The arrays were printed under rigorous clean-room conditions and quality control is employed all along the way, starting with preparation of the printing material as well as during the actual printing and finally with post-printing tests that include a sample chip hybridization. The microarray printer consists of a three-axis robot mounted on a Newport Vibration Isolation Workstation table with a research-grade laser tabletop.  The three-axis mechanical slides are from THK and are selected to provide the best combination possible of precision and speed consistent with the design objectives. The Pen Tip Assembly consists of a proprietary design having 12 pen tips contained within a precision-machined housing that is supported by the moving block on the Z-axis slide.  The mechanical slides are positioned with motors and servo amplifiers from Yaskawa. The robot can spot 12 points every 1/2 second, or, 100 slides with 12 spots each in under 60 seconds.   The resulting slides of the HH5 series had the following configuration: HUMAN 27K gene chips: 48 grids, 26 columns X 23 rows each.


title: SMD Print_980 LC-46

first: Claudia

last: Macaubas

department: Pediatrics

institute: SUMC


title: Illumina HiSeq 2000 (Fusarium oxysporum f. cubense)

status: Public on Sep 04 2012

organism: Fusarium oxysporum f. sp. cubense


title: Illumina HumanHT-12 V3.0 expression beadchip

status: Public on Sep 01 2012

city: Rochester

first: Virginia

middle: Bartleson

last: Hebl

state: MN

address: 200 1st St. SW

institute: Mayo Clinic

manufacture_protocol: See the manufacturer's website.


title: Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Gene Symbol Version)

first: GEO

last: admin

state: MD

description:
This multi-pack (4X44K) formatted microarray represents a compiled view of the human genome as it is understood today. The sequence information used to design this product was derived from a broad survey of well known sources such as RefSeq, Goldenpath, Ensembl, Unigene and others. The resulting view of the human genome covers 41K unique genes and transcripts which have been verified and optimized by alignment to the human genome assembly and by Agilent's Empirical Validation process.

*** 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 GPL4133

relation:
Alternative to: GPL4133
Alternative to: GPL6480


title: Ion Torrent PGM (Saccharomyces cerevisiae)

status: Public on Sep 07 2012


title: Agilent-019497 MMLv2.0 [Probe Name version]

first: Junfang

last: Zhang

address: 37 Convent Dr.

department: NCI-CCR

institute: NIH

description:
Myb-MML-Hbsl1 version 2.0
Arrays of this design have barcodes that begin with 16019497 or 2519497.
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-019859 MMLv2.1 [Probe Name version]

description:
Updated version of MML array, with properly designed probes using numbering from old 2006 version of genome.
Arrays of this design have barcodes that begin with 16019859 or 2519859.
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-020349 MMLv2.2  [Probe Name version]

description:
MML chip - for CTCF
Arrays of this design have barcodes that begin with 16020349 or 2520349.
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-021202 MMLv3 [Probe Name version]

description:
MMLv3.0
Arrays of this design have barcodes that begin with 16021202 or 2521202.
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: 081014_Styp_LT2_EXP_X4

city: Vicksburg

first: Dawn

last: Hancock

state: Mississippi

address: 3909 Halls Ferry Road

department: Engineer Research and Development Center

institute: DEPARTMENT OF DEFENSE Army Corps of Engineers

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

description:
NimbleGen design name 081014_Styp_LT2_EXP_X4, NimbleGen design ID 081014.  An expression design for 4,504 genes from Salmonella typhimurium LT2 with seven 45 to 60-mer probe pairs per gene. Each probe is replicated twice.
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.


title: Bacillus subtilis WGD14 platform

city: Houston

first: Jue

middle: D.

last: Wang

state: TX

address: 1 Baylor Plaza, Rm T932

department: Molecular and Human Genetics

institute: Baylor College of Medicine

organism: Bacillus subtilis

manufacture_protocol: Please read Britton et al. Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis.  J Bacteriol. 2002 Sep;184(17):4881-90


title: Urocitellus parryii 9.6k

city: New York

first: Yichi

last: Xu

address: 1275 York Avenue

institute: MSKCC

organism: Urocitellus parryii

first: Chunxuan

last: Shao

first: Vadim

middle: B

last: Fedorov

first: Anna

middle: V

last: Goropashnaya

first: Brian

middle: M

last: Barnes

first: Jun

last: Yan

manufacture_protocol: cDNA spot array on nylon membrane http://www.wistar.org/research_facilities/facilities/genomics/review.html


title: Agilent-028966 UTHORT Eustoma_EST v.1 (Feature Number version)

city: Bunkyo-ku

first: Saneyuki

last: Kawabata

state: Tokyo

address: 1-1-1 Yayoi

institute: University of Tokyo

organism: Eustoma russellianum

description:
Arrays of this design have barcodes that begin with 16028966 or 2528966.

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 Streptomyces hygroscopicus var. jinggangensis 15K [Agilent-025874] [Probe version]

city: shanghai

first: hang

last: wu

address: Huashan Road

institute: sjtu

organism: Streptomyces hygroscopicus subsp. jinggangensis

description: Arrays of this design have barcodes that begin with 16025874 or 2525874.


title: Agilent-023844_Dreissena_IDAEA_15k

status: Public on Jan 22 2012

city: Barcelona

last: Navarro Cuenca

state: Barcelona

address: C/Jordi Girona 18-26

department: Environmental Toxicology

institute: IDAEA-CSIC

organism: Dreissena polymorpha

description:
Arrays of this design have barcodes that begin with 16023844 or 2523844.
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.

last: Navarro

first: Bruno

last: Campos

manufacture_protocol:
The array for Dreissena polymorpha was designed using the eArray tool from Agilent (https://erray.chem.agilent.com/erray/).
A total of 4057 sequences were compiled from the GeneBank using the EBI website (European Bioinformatic Institute, http://srs.ebi.ac.uk).
From these sequences, 3253 belongs to Dreissena rostriforme, 705 to D. polymorpha and the rest to other bivalve species.
An 8x15 Array (a slide with 8 arrays with 15000 probes) was designed using primers of 60 nucleotides.
Three probes for each sequence were designed following a position criteria zone (5’, center, and 3’), using the eArray software from Agilent.
Three extra probes were also designed from each gene, based in the criteria of non self-complementation and low redundancy. After eliminating redundant probes, the array included from four to six probes for each gene sequenced


title: Agilent Custom Antirrhinum majus Gene Expression 8x15k designed by Genotypic Technology Pvt. Ltd. (AMADID:016341)

status: Public on Aug 31 2012

first: Genotypic

last: technology

organism: Antirrhinum majus

description: Some of the  probes representing  by "PUT-157a-Antirrhinum_majus" were taken from: http://www.antirrhinum.net/

first: Mugasimangalam

last: Raja


title: Agilent-025620 wasabiearray1

status: Public on Aug 24 2012

city: Helsinki

first: Martin

last: Broberg

address: Viikinkaari 5D

department: Biosciences

institute: University of Helsinki

organism: Pectobacterium wasabiae

description: strain SCC3193

manufacture_protocol: Agilent 60mer


title: Illumina HumanOmni2.5-Quad BeadChip

status: Public on Mar 22 2011

city: Bethesda

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Homo sapiens

description:
common and rare SNP content from the 1kGP (MAF>2.5%) for diverse world populations
build: hg18
=optimized tag SNP content from recently released 1000 Genomes Project pilot data

manufacture_protocol: See manufacturer's website


title: Custom Agilent Saccharomyces cerevisiae 8x15K Yeast_LH_03

status: Public on May 01 2010

city: Ottawa

first: Linda

middle: J

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

organism: Saccharomyces cerevisiae

manufacture_protocol: SurePrint technology: Custom commercial microarrays are manufactured using a non-contact industrial inkjet printing process, in which oligo monomers are deposited uniformly onto specially-prepared glass slides. This in situ synthesis process prints 60-mer length oligonucleotide probes, base-by-base, from digital sequence files. The precise inkjet process enables the delivery of extremely small, accurate volumes (picoliters) of the chemicals to be spotted. Standard phosphoramidite chemistry used in the reactions allows for very high coupling efficiencies to be maintained at each step in the synthesis of the full-length oligonucleotide. Precise quantities are reproducibly deposited “on the fly” and is achieved without stopping, to make contact with the slide surface and without introducing surface-contact feature anomalies.


title: UCSF Mouse BAC 3K array

status: Public on Jan 14 2010

city: San Francisco

first: Bing

last: Huey

state: CA

address: 1450 Third Street

department: Helen Diller Comprehensive Cancer Center

institute: University of California at San Francisco

description: The clones are ordered by position in the genome (UCSC draft genome sequence, May 2004 freeze) beginning at chromosome 1 and ending with chromosome X.

manufacture_protocol:
Isolation of BAC/P1 DNA. We inoculated 0.1ul of a glycerol stock of BAC or P1 containing bacteria into 5 ml LB media containing chloramphenicol (10 ug/ml) or kanamycin (50 ug/ml) for BACs or P1s, respectively and incubated the cultures overnight (~16 h) at 37 degrees C with agitation at 225 rpm. We prepared larger cultures for DNA isolation, by inoculating 25 ml LB media, containing the appropriate antibiotic with 200 ul of the previously grown overnight culture and incubating in a shaking incubator at 37 degrees C at 225 rpm overnight (~16 h). We monitored bacterial growth by measuring the OD of a 1:10 dilution, which preferably ranged between 0.25 and 0.35 at a wavelength of 600 nm. We used the Qiagen Plasmid Mini kit to isolate DNA, following a modified version of the Qiagen Plasmid Mini Purification protocol. We transferred the 25 ml cultures into 50 ml tubes and centrifuged them for 15 min at 4000 rcf at 4 degrees C to pellet the bacteria. We re-suspended the pellet in Qiagen buffer P1 (1.5 ml), containing RNase A at the manufacturer’s recommended concentration and then added buffer P2 (1.5 ml). We mixed the tubes extremely gently by inversion and incubated at room temperature for 5 min. Then, we added buffer P3 (1.5 ml), again mixed very gently by inversion and incubated on ice for 10 min. We inverted each tube once and centrifuged at 4000 rpm at 4 degrees C until the supernatant became clear (45 to 60 min). We filtered the supernatant through a 35-micron nylon mesh prior to loading onto Qiagen-tip 20 columns, which had been equilibrated following the manufacturer’s protocol. We followed the manufacturer’s protocol for the DNA isolation steps with the exception that the elution buffer QF was heated to 65 degrees C before it was added to the column. After elution, we added 0.56 ml isopropanol to the DNA and incubated overnight at 4 degrees C. We collected the DNA pellet by centrifugation for 45 min at 14000 rpm at 4 degrees C. After aspirating the supernatant, we allowed the pellet to dry in air for at most 30 min before re-suspending the DNA in 50 ul of H2O. We determined the DNA concentration using a fluorometer. The yield typically ranged between 60-100 ng/ul (i.e. 3-5 ug per isolation). To ascertain DNA purity, we digested each BAC (200 ng) with HindIII and electrophoresed the digest through a 0.75% agarose gel. We discarded DNA preparations that showed a significant contamination with host bacterial DNA, seen as a background smear of degraded DNA in the gel.

Preparation of BAC/P1 DNA representations by ligation-mediated PCR. We digested the DNA with MseI by incubating overnight at 37 degrees C in a 5 ul reaction containing 1.5 ul DNA (20 to 600 ng), 0.4 U/ul MseI (New England Biolabs), and 0.4x One-Phor-All-Buffer-Plus (Amersham). For ligation of adapters, we diluted 1 ul of each digest to a final concentration of 1 ng/ul with H2O and then mixed 1 ng of the digested DNA with 0.5 ul One-Phor-All-Buffer-Plus (10x, Amersham), 0.5 ul of 100 uM Primer 1 (TAACTAGCATGC), 0.5 ul of 100 uM Primer 2 (5’ aminolinker AGTGGGATTCCGCATGCTAGT) and 5.5 ul H2O. We incubated the mixture at 65 degrees C for 1 min after which we ramped the temperature down to 15 degrees C with a ramp-speed of 1.3 degrees C per minute. When the temperature reached 15 degrees C, we added 1 ul of 10 mM ATP and 1 ul T4-DNA ligase (5 U/ul, Gibco BRL) and continued incubation at 15 degrees C overnight. To initiate the first round of PCR amplification, we added a 40 ul mixture, consisting of 3 ul PCR Buffer 1 (Expand Long Template PCR System, Roche), 2 ul of a mixture of each nucleotide (10 mM) and 35 ul H2O to the ligation reaction. Before we started the PCR program, we incubated the reaction at 68 degrees C for 4 min and then added 1 ul DNA polymerase (3.5 U/ul, Expand Long Template PCR System, Roche). We carried out thermal cycling in a Perkin-Elmer Gene Amp PCR System 9700 block as follows: 94 degrees C for 40 s, 57 degrees C for 30 s, 68 degrees C for 1.25 min for 14 cycles, followed by, 94 degrees C for 40 s, 57 degrees C for 30 s, 68 degrees C for 1.75 min for 34 cycles and 94 degrees C for 40 s, 57 degrees C for 30 s and 68 degrees C for 5 min for the final cycle. We electrophoresed 3.5 ul of the PCR product through a 1% agarose gel to determine the size range of the amplified DNA, which ideally ranged from 100 to 2000 bp. To make the DNA for spotting on the arrays, we carried out a second round of amplification in a 100 ul reaction containing 1 ul of the primary PCR product, 4 uM Primer 2, TAQ-buffer II (1x; Perkin Elmer), 0.2 mM dNTP mix, 5.5 mM MgCl2 (Perkin Elmer), 2.5 U Amplitaq Gold (Perkin Elmer) and H2O. We carried out an initial incubation at 95 degrees C for 10 min in a MJ Research Peltier Thermal Cycler 225, followed by 95 degrees C for 30 s, 50 degrees C for 30 s and 72 degrees C for 2 min for 45 cycles and finally 7 min at 72 degrees C. This reaction yields ~10 ug of DNA, with each fragment containing a 5’ amino linker.

Preparation of DNA spotting solutions. We evaporated the amplification reaction (100 ul) to a final volume of 50 ul by incubation at 45 degrees C in a hybridization oven (Techne, Hybridizer HB-1D) for approximately 75 min and then added 2.5 volumes of ice-cold ethanol and 0.1 volumes of 3 M NaOAc to precipitate the DNA. (The use of ethanol precipitation proved superior to isopropanol precipitation.) We inverted the tubes and chilled them at –20 degrees C for 15 min before collecting the precipitate by centrifugation at 1699 rcf for 90 min. We washed the pellets with 70% ethanol (150 ul) and collected them by centrifugation at 1699 rcf for 45 min. We air-dried the pellets for approximately 60 to 90 min and then re-suspended them in 12 ul of 20% DMSO in H2O (~0.8 ug/ul). We transferred the DNA solutions into 864 well microtitre plates for robotic arraying. Previously, we prepared DNA for spotting in 80% DMSO and 0.3 ug/ul nitrocellulose. However, we subsequently evaluated spotting solutions containing various concentrations of dimethyl formamide, formamide or DMSO, with or without nitrocellulose. We determined that nitrocellulose was not required for spotting DNA prepared by PCR using primers with 5’amino linkers and that spotting solutions made with 20% DMSO performed well. We have also generated representations of large insert clones for arraying by using degenerate oligonucleotide primed PCR and by amplification of mixtures of subclones from BACs, but found the ligation-mediated PCR procedure to be superior.

Array printing. We used a custom built printer, employing a 4 x 4 array of quartz capillary tubes spaced on 3 mm centers to print ~70-100 μm diameter spots on 130 μm centers. We printed each DNA solution in triplicate to create an array of ~7500 elements in a 12 mm square area. We printed the arrays on chromium coated microscope slides (PTI or Nanofilm) for these studies, but also routinely print the arrays on glass slides (Corning GAPs). We allowed the printed slides to dry overnight, then exposed the slides to UV light (65 mJ) in a UV Stratalinker 2400 (Stratagene). We hybridized to these slides without additional treatment, except for the pre-hybridization slide blocking described below. We found no indication of DNA loss from the spots at any stage of the procedure when we performed hybridization in formamide buffers at 37 °C.


title: "Dehalococcoides ethenogenes" strain 195 with Mixed Community Sequences

status: Public on Aug 20 2010

city: Ithaca

first: Cresten

last: Mansfeldt

address: 220 Hollister Hall

institute: Cornell University

organism: Dehalococcoides mccartyi 195

description: "Dehalococcoides ethenogenes" strain 195 with additional community members and luciferase. Arrays of this design have barcodes that begin with 16023019 or 2523019. Orientation:  Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent. 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: Ruth

last: Richardson

first: Annie

middle: R

last: Rowe

first: Laura

last: Hug

first: Gretchen

last: Heavner

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


title: Xylella fastidiosa 9a5c Biochip v.2.0

status: Public on Dec 21 2006

city: Santo André

first: Luiz

middle: R.

last: Nunes

state: SP

address: Rua Santa Adélia 166

department: Centro de Ciências Naturais e Humanas

country: Brazil

institute: UFABC - Universidade Federal do ABC

organism: Xylella fastidiosa

description: Xylella fastidiosa, isolate 9a5c

manufacturer: Laboratório de Genômica Estrutural e Funcional - Núcleo Integrado de Biotecnologia - Universidade de Mogi das Cruzes

first: Regina

last: Oliveira

manufacture_protocol: The array consists of DNA amplicons from ~2300 ORFs from the genome of the phytobacterium Xylella fastidiosa 9a5c. The amplicons were PCR amplified with specifically designed primer pairs and purified with the QiaQuick 96 PCR purification system (Qiagen), dried in a Savant speed-vac, resuspended in 50 % DMSO at a final concentration of 100-200 mg/ml and spotted onto CMT-GAPS Coated Slides (25 x 75 mm, Corning) using an Affimetrix 427 arrayer. Those interested in obtaining the X. fastidiosa microarrays, please contact lnunes@umc.br or reginaco@umc.br for further details.


title: Paracoccidioides brasiliensis microarray v1

status: Public on Aug 26 2005

organism: Paracoccidioides brasiliensis

description: Paracoccidioides brasiliensis isolate 18

first: Daniela

last: Leite

first: Vivian

middle: S

last: da Silva

first: Gustavo

middle: H

last: Goldman

first: Francisco

middle: G

last: Nóbrega

first: Marina

middle: P

first: Maria

first: Rosana

last: Puccia

last: Travassos

manufacture_protocol: The array consists of cDNA inserts from representative ESTs from 4,692 expressed genes that were functionally classified by similarity to known genes. These inserts were PCR amplified with the M13 forward and reverse primers and the amplified products were purified with the QiaQuick 96 PCR purification system (Qiagen), dried in a Savant speed-vac, resuspended in 50 % DMSO at a final concentration of 100-200 mg/ml and spotted onto CMT-GAPS Coated Slides (25 x 75 mm, Corning) using an Affimetrix 427 arrayer. Those interested in obtaining the P. brasiliensis microarrays, please contact lnunes@umc.br or ggoldman@usp.br for further details


title: Illumina MiSeq (Escherichia coli)

status: Public on Sep 20 2012

last: GEO

organism: Escherichia coli