title: Rice 44K

status: Public on May 30 2007

city: Tsukuba

first: Hiroshi

last: Takatsuji

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

country: Japan

organism: Oryza sativa

technology: in situ oligonucleotide

distribution: custom-commercial

first: Masaki

last: Shimono

first: Akira

last: Nakayama

manufacture_protocol:
Probe Length:  	60 bases
Probe Orientation:  	Sense
genes/microarray: 44000
Content Source: Japan - National Institute of Agrobiological Sciences, Dr. Shoshi Kikuchi
Feature size:  115 microns


title: CodeLink UniSet Human 20K I Bioarray

status: Public on Jul 31 2007

city: Berkeley

first: Terumi

last: Kohwi-shigematsu

state: CA

address: 1 Cyclotron road

department: Life Science

country: USA

institute: LBNL

organism: Homo sapiens

technology: spotted oligonucleotide

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


title: NimbleGen Thermotoga maritima Tmar_Design_v2

status: Public on Jul 02 2012

city: Logan

first: Daniel

middle: R

last: Hyduke

state: UT

address: 4105 Old Main Hill ENGR 402S

department: Biological Engineering

institute: Utah State University

organism: Thermotoga maritima MSB8

description:
NimbleGen tiling array for Thermotoga maritima MSB8 (ATCC: 43589).
High-density four-plex oligonucleotide tiling arrays consisting of 4 x 71,548 probes of variable length spaced across the whole Thermotoga maritima genome.
Native array description file: Tmar_Design_v2.ndf
Native array description file: Tmar_Design_v2.ngd

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


title: DPMB/AG Lab Agilent Rice array (4x44K) AMADID No. 15241

status: Public on May 31 2012

city: New Delhi

first: Anil

last: Grover

state: Delhi

address: Benito Juarez Road

department: Plant Molecular Biology

country: India

institute: University of Delhi South Campus

technology: spotted DNA/cDNA

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


title: CDMC_Drosophila_7k3

status: Public on Oct 01 2004

city: Mississauga

first: Zak

last: Razak

state: ON

address: 3359 Mississauga Road

department: Zoology Department

country: Canada

institute: University of Toronto

organism: Drosophila melanogaster

description:
The CDMC_Drosophila_7k3 array is a primarily cDNA-based Drosophila melanogaster glass microarray.  The array features 5,756 Berkeley Drosophila genome Project cDNAs, 1,078 NIH Testis cDNAs (Andrews et al., 2000) and 546 gene fragments that were amplified from genomic DNA, together representing approximately 50% of the predicted genes in D. melanogaster.  The array is produced by the Canadian Drosophila Microarray Centre, located at the University of Toronto, and is available for distribution to academic labs.

The arrays are printed on CMT-GAPS II substrates (Corning Inc., Acton, MA) using a SpotArray 72 microarrayer (Perkin Elmer, Boston, MA).  The array features 16,896 spots in total, representing ~6,900 unique genes and numerous controls.  The spots are approximately 125 microns in diameter and are spaced at 180 micron centre-to-centre distances.  Printing conditions and post-print treatments are as described earlier (Neal et al., 2003).
Keywords = CDMC
Keywords = Drosophila
Keywords = Microarray
Keywords = cDNA

distribution: non-commercial

first: Scott

middle: J

last: Neal

first: Meredith

middle: L

last: Gibson

first: Anthony

middle: K

last: So

first: J

middle: T

last: Westwood

first: Jianming

last: Pei

first: Huafen

last: Li


title: MCI Human HEEBOChip 42k oligo array

status: Public on Oct 07 2008

city: Zürich

first: Keith

middle: S

last: Hoek

address: private

country: Switzerland

institute: Currently unaffilliated

description: Human Exonic Evidence-Based Oligonucleotide Chip (HEEBOChip), 70mer oligos.

manufacturer: This array was assembled by/for researchers at the Mitchell Cancer Institute (MCI) of the University of South Alabama.

manufacture_protocol: Stanford Functional Genomics Facility (SFGF) standard protocol.


title: AB SOLiD System 3.0 (Dictyostelium discoideum)

last: GEO

organism: Dictyostelium discoideum

technology: high-throughput sequencing

distribution: virtual


title: Illumina Genome Analyzer IIx (Acinetobacter oleivorans)

status: Public on May 30 2012

organism: Acinetobacter oleivorans


title: MERH03-S1-0002 (Rhodococcus sp. RHA1 22K)

status: Public on Jun 27 2006

city: Vancouver

first: Shawn

last: Anderson

address: The Prostate Centre at Vancouver General Hospital, 2660 Oak Street

department: Urological Sciences

institute: University of British Columbia

organism: Rhodococcus jostii RHA1

manufacturer: The Microarray Facility of the Prostate Centre at Vancouver General Hospital

middle: A

first: Melanie

last: Lehman

first: Bruce

last: Dangerfield

manufacture_protocol: Oligonucleotides are consolidated into 384-well plates, lyophilized by speed-Vac, and resuspended in 3x SSC to a printing concentration of 30uM. Oligos are printed on aminosilane slides (Erie, Hudson, NH, USA) with a Biorobotics Microgrid II microarray printer (Genomic Solutions). Microspot 10K quill pins (Biorobotics) in a 48-pin tool were used to deposit <0.5 nL per spot onto the slide. The resulting microarrays have a 4 x12 subgrid layout with 392 spots per subgrid, each spot having approximate diameter and pitch of 90 µm and 190µm, respectively. A 280-bp GFP (green fluorescent protein) oligo was printed in subgrid corners to assist in placing on the grid. The slides were crosslinked in a UV Stratalinker 2400 (Stratagene) at 300mJ. Array quality was assessed by visual inspection and hybridization of representative slides from a print run by dye-labelled random 9-mer oligonucleotides. The quality control images were aquired via the ScanArray Express from Perkin Elmer at a 10 micron resolution and quantified with the Imagene 6.0 software suite.


title: Agilent-016555 Human NR3C1 locus tiling array

city: Montreal

first: Moshe

last: Szyf

state: Quebec

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

department: Pharmacology

institute: McGill University

description:
The oligonucleotide microarray is composed of 45055 45-60mer oligonucleotides from the Agilent's eArray ChIP probe database. The probes include those that tile the 6.5 million base pair region of human chromosome 5 centered at the NR3C1 gene at 100 bp spacing.

Coordinates based on human genome build hg18.

manufacture_protocol: Agilent high-density ink-jet.


title: Canis familiaris V1.0.1 AROS Operon

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

organism: Canis lupus familiaris

manufacture_protocol: see manufacturer`s website


title: Exiqon miRPlus_V9.0_300107

city: BERKELEY

first: Patty

middle: B

last: Garcia

address: 439 LSA

institute: UC BERKELEY

organism: synthetic construct

manufacture_protocol:
See manufacturer's website
Homo sapiens; Mus musculus; Rattus norvegicus; Human herpesvirus 1;Human herpesvirus 5; Murid herpesvirus 1; Human herpesvirus 4; BK polyomavirus; JC polyomavirus; Simian virus 40; Human immunodeficiency virus 1; Murid herpesvirus 4; Human herpesvirus 8


title: Okazaki Fly 22k Microarray v2

status: Public on Sep 19 2006

city: Okazaki

first: Shuji

last: Shigenobu

state: Aichi

address: Nishigonaka 38, Myodaiji

institute: National Institute for Basic Biology

first: Satoru

last: Kobayashi

manufacture_protocol: see manufacture's website


title: Dmel_arrayplatform

status: Public on Jul 24 2003

city: New Haven

first: Tong-Ruei

state: CT

address: 333 Cedar St. Rm#NSB386

department: Department of Genetics

institute: Yale University School of Medicine

description:
Spotted array using PCR fragments of approximately 95% of the genes in the D. melanogaster BDGP genome.

We followed a sequence of decreasingly stringent tests to pick optimal primer pairs for the PCR fragments on the arrays.  For each gene, we looked for (first) a 500b to 2kb sequence at the 3’ end and, failing this, (second) two 200b to 500b sequences in:(1) coding sequence, completely within an EST clot, and unduplicated (BLAST<=10^-4); (2) coding sequence, partially within an EST clot, unduplicated; (3) coding sequence, unduplicated; (4) exon, completely within an EST clot, unduplicated; (5) exon, partially within an EST clot, unduplicated; (6) exon, unduplicated; (7) sequence less than 2kb at the 3’ end.  See above for the other details about making these arrays.

first: Kevin

middle: P

last: White


title: bthetaa511044F

status: Public on Mar 30 2005

city: Saint Louis

first: Justin

middle: L.

last: Sonnenburg

state: MO

address: 4444 Forest Park

department: Center for Genome Sciences

institute: Washington University

organism:
Bacteroides thetaiotaomicron
Bifidobacterium longum

description: Antisense genome array (GeneChip) querying 99% of Bacteroides thetaiotaomicron ORFs and tRNAs.

first: Jian

last: Xu

first: Douglas

middle: D

last: Leip

first: Chien-Huan

last: Chen

first: Benjamin

last: Westover

first: Jeremy

last: Weatherford

last: Buhler

first: Jeffrey

middle: I

last: Gordon


title: NimbleGen Saccharomyces cerevisiae 385K [2006-08-18_TI4932_60mer]

city: Hiroshima

first: Kozo

last: Ochi

state: Hiroshima

address: 2-1-1 Miyake, Saeki-ku

department: Food Sciences and Biotechnology

institute: Hiroshima Institute of Technology

organism: Saccharomyces cerevisiae S288C

description: Design Name : 2006-08-18_TI4932_60mer  Format : 385K (Arrays Per Slide: 1, Probes Per Array: 385,000, Feature Size: 16um x 16um, Slide Size: 1 x 3 (25 x 75mm))  Accession Numbers :   Target Genes : 5,868  Probes per target : 20  Replicates : 3

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


title: Illumina Genome Analyzer IIx (Triticum aestivum)

last: GEO

organism: Triticum aestivum


title: Illumina Genome Analyzer II (Neurospora crassa)

organism: Neurospora crassa


title: AB SOLiD System 2.0 (Photobacterium profundum)

status: Public on May 25 2012

organism: Photobacterium profundum


title: Agilent custom Chironomus riparius 1M array

status: Public on May 26 2012

city: Amsterdam

first: Wim

last: de Leeuw

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

organism:
Chironomus tentans
Aedes aegypti
Anopheles gambiae
Culex quinquefasciatus
Anopheles darlingi
Anopheles funestus
Chironomus riparius

description: We sampled extensively covering all C. riparius developmental stages as well as toxicant exposed larvae and obtained from a normalized cDNA library 1.5M NGS reads totalling 501 Mbp. For this platform we designed 844k probes directly on the NGS reads, as well as, 76k probes targeting expressed sequence tags of related species.

first: Marino

last: Marinković

middle: C

first: Mark

last: de Jong

first: Michiel

middle: H

last: Kraak

last: Admiraal

first: Timo

middle: M

last: Breit

first: Martijs

last: Jonker


title: Illumina HiSeq 2000 (Vriesea carinata)

organism: Vriesea carinata


title: Illumina HiSeq 2000 (Eugenia uniflora)

status: Public on May 24 2012

organism: Eugenia uniflora


title: NimbleGen K. pneumoniae MGH78578 array

city: Ulsan

first: Donghyuk

last: Kim

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

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578

description: The .ndf, .ngd, and .pos files are linked below as supplementary files.


title: Illumina Genome Analyzer II (Citrullus lanatus subsp. vulgaris)

status: Public on May 23 2012

organism: Citrullus lanatus


title: Murine Array Ready Oligo Set (AROS) long oligo array version 4.0

city: Hyderabad

first: Tushar

last: Vaidya

address: Uppal Road Habshiguda

institute: Centre for Cellular and Molecular Biology

organism: Mus musculus

manufacture_protocol:
1. Each well contains 600 pmol of 70-mer oligo.
2. Oligos are resuspended in a proprietary spotting buffer.
3. Oligos are spotted onto Schott Nexterion E substrate.
4. Post-processing is complete and microarrays shipped ready-to-use.
5. Shelf life is date of post-processing plus 9 months.


title: Illumina Genome Analyzer II (Lagenaria siceraria)

organism: Lagenaria siceraria


title: Illumina Genome Analyzer II (Cucurbita pepo)

organism: Cucurbita pepo


title: Illumina Genome Analyzer II (Cucurbita moschata)

organism: Cucurbita moschata


title: Illumina HiSeq 2000 (human gut metagenome)

organism: human gut metagenome


title: Agilent-022922 Bacillus methanolicus MGA3_1

city: Trondheim

first: Tonje

middle: Marita Bjerkan

last: Heggeset

address: Postboks 4760 Torgarden

department: Industry

country: Norway

institute: SINTEF

organism: Bacillus methanolicus

description:
1st design (based on the first annotation of the Bacillus methanolicus strain MGA3 genome)

Some identifiers which do not correlate to any coding sequences in the final genome sequence were annotated with the text "Excluded in final annotation".

Arrays of this design have barcodes that begin with 16022922 or 2522922.

DesignID: 022922

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: Citrus 20K cDNA

status: Public on May 22 2012

city: wuhan

first: Qiu

last: wen-ming

state: hubei

address: shizishan street

country: China

institute: Key Laboratory of Horticultural Plant Biology (Ministry of Education)

organism: Citrus reticulata

description: Annotations are based on the Uniprot database

manufacture_protocol: About 40 microlitre of PCR products were re-precipitated by adding 100 μl of anhydrous ethanol and were dissolved in EasyArrayTM spotting solution (CapitalBio Corp, China) at a final concentration of 0.1-0.5 μg/μl and then printed on amino-silaned glass slides with a SmartArrayerTM microarrayer (CapitalBio Corp). Each clone was printed triplicate.


title: Illumina Genome Analyzer (Aeromonas veronii)

status: Public on May 21 2012

organism: Aeromonas veronii


title: Agilent_029535 Univ. of Sao Paulo-FCFRP/Mol Biol Lab Aspergillus nidulans 4X44K v.1.0

city: Ribeirao Preto

first: Wagner

middle: Rodrigo

last: de Souza

state: Sao Paulo

address: Av do Cafe

department: Pharmaceutical Sciences

country: Brazil

institute: University of Sao Paulo

organism: Aspergillus nidulans

manufacture_protocol: in situ oligonucleotide were synthesized directly on the glass microarray surface according to SurePrint Technology (Agilent Technologies), as described in manufacturer's protocol. Basically, in situ oligonucleotides were synthesized base by base on a solid glass surface, one layer at a time, based on standard phosphoramadite chemistry.


title: Illumina Genome Analyzer II (Glycine soja)

status: Public on May 20 2012

organism: Glycine soja


title: Illumina Genome Analyzer IIx (Capsicum annuum)

status: Public on May 16 2012

organism: Capsicum annuum


title: NimbleGen Streptococcus pyogenes NZ131 intergenic array [090910_MF_S_pyo_NZ131_expr]_gene-level version

city: Chicago

first: Michael

last: Federle

state: IL

address: 900 S Ashland Ave. MC870

department: Microbiology & Imm. / Cntr Pharm Biotech

institute: University of Illinois at Chicago

organism: Streptococcus pyogenes NZ131

description: Expression array including select intergenic region tiles of S. pyogenes NZ131


title: Linum usitatissimum 385K (60-mer)

status: Public on May 15 2012

city: Villeneuve d'Ascq

first: Lucau

last: Anca

address: Cité scientifique

country: France

institute: University Lille 1

organism: Linum usitatissimum

description:
The 60-mers array utilized 4 duplicate, 60 bp-long oligonucleotides for 46,589 contigs.
The .ndf and .ngd files are linked below as supplementary files.

manufacture_protocol: 60-mers high-density flax microarrays based on the Nimblegen design format (Nimblegen Systems, Inc., Madison, WI, USA)


title: 022125-Agilent Mycobacterium tuberculosis H37Ra 8x15K (Feature Number version)

city: Hefei

first: Yuzhi

last: Hong

state: Anhui Province

address: 3 Feixi Road

department: Modern Experiment Technology Center

institute: Anhui University

organism: Mycobacterium tuberculosis H37Ra

first: Haihong

last: Fang

first: Baolin

last: Sun

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


title: Rosetta/Merck Rat RSTA Custom Affymetrix 1.0 microarray

status: Public on May 18 2012

city: Seattle

first: Amit

middle: V

last: Kulkarni

state: WA

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

organism: Rattus norvegicus

description:
Oligonucleotide array on glass.
Contains 60-mer probes (60-mer).

first: John

last: Castle

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


title: Linum usitatissimum 385K (25-mer)

description:
The 25-mers array utilized 8 distinct, 25 bp-long oligos for each of the 48,021 contigs.
The .ndf and .ngd files are linked below as supplementary files.

manufacture_protocol: 25-mers high-density flax microarrays based on the Nimblegen design format (Nimblegen Systems, Inc., Madison, WI, USA)


title: Toxoplasma gondii ME49 ChIP-chip genome-wide tiling array 2 of 2

city: Tampa

first: Kami

state: FL

address: 3720 Spectrum Blvd, Suite 304

department: Internal Medicine Medicine

institute: University of South Florida

organism: Toxoplasma gondii ME49

description:
Tiling microarray encompassing 63 Mb of Toxoplasma gondii genome (reference genome strain ME49; chromosomes Ia, Ib, II, III, IV, V, VI, VIIa, VIIb, VIII, IX, X, XI and XII, and unmapped contigs).
The genome wide chip was designed using the Nimblegen isothermal protocol design based upon Release 4.1 of the T. gondii ME49 genome (www.toxodb.org). The "target Tm" for all probes is 76 C. There are 392,074 probes total on each array for a total of 784,148 probes, including controls. Of these, 366,336 are T. gondii specific probes on each of two slides, Tiling1 and Tiling2 for a total of 732,672 toxo specific probes. The design name for each chip is 2007-05-02_Toxo_WG_tiling1 and 2007-05-02_Toxo_WG_tiling2.
Genomic sequence available at: http://toxodb.org/common/downloads/release-4.1/
Native NimbleGen files (ndf, pos) are linked below as supplementary files.

manufacture_protocol:
NimbleGen manufactures custom, high-density DNA arrays based on its proprietary Maskless Array Synthesizer (MAS) technology. The MAS system is a bench top, solid-state, high-density DNA array fabrication instrument comprised of a maskless light projector, a reaction chamber, a personal computer, and a DNA synthesizer. NimbleGen builds its arrays using photo-mediated synthesis chemistry with its MAS system.
At the heart of the system is a Digital Micromirror Device (DMD), similar to Texas Instruments' Digital Light Processor (DLP), employing a solid-state array of miniature aluminum mirrors to pattern up to 786,000 individual pixels of light. The DMD creates "virtual masks" that replace the physical chromium masks used in traditional arrays.
These "virtual masks" reflect the desired pattern of UV light with individually addressable aluminum mirrors controlled by the computer. The DMD controls the pattern of UV light projected on the microscope slide in the reaction chamber, which is coupled to the DNA synthesizer. The UV light selectively cleaves a UV-labile protecting group at the precise location where the next nucleotide will be coupled. The patterns are coordinated with the DNA synthesis chemistry in a parallel, combinatorial manner such that up to 786,000 unique probe features are synthesized in a single array.


title: Toxoplasma gondii ME49 ChIP-chip genome-wide tiling array 1 of 2


title: CSHL-Human-MOMA2 368K CpG tiling array

city: Cold Spring Harbor

first: Kazimierz

middle: O.

last: Wrzeszczynski

state: NY

address: One Bungtown Rd.

institute: Cold Spring Harbor Laboratory

organism: Homo sapiens

manufacture_protocol: Our approach to map genome-wide methylation involves tiling all the predicted CpG islands. All annotated CpG islands were obtained from the UCSC genome browser. These islands were predicted using the published Gardiner-Garden and Frommer definition and involves the following criteria: length >= 200bp, %GC >= 50%, observed/expected CpG >= 0.6. There are 27,325 CpG islands in the range represented by 159,436 MspI fragments on the array. Arrays were manufactured by Nimblegen Systems Inc using the 390K format to the following specifications. The CpG island annotation from human genome build 35 (hg17) was used to design a 50 mer tiling array. The 50 mers were shifted on either side of the island sequence coordinates to evenly distribute the island. The 390K format has 367,658 available features which would not fit all islands with a 50 mer tiling. Therefore we made a cutoff on the islands to be represented based on size, with only CpG islands of size 200b-2000b being assayed. The array represents classical CpG islands and does not include imprint control regions or other non-island promoters known to be methylated. Background hybridization signal could be high with probes of high GC content since by definition these probes will be. Therefore, control probes which are not in a MspI representation were designed to represent background signal, and these probes were used to calculate signal to noise.


title: Illumina Genome Analyzer II (Spodoptera frugiperda)

status: Public on May 11 2012

last: GEO

organism: Spodoptera frugiperda


title: Illumina Genome Analyzer IIx (Solanum lycopersicum)

status: Public on May 17 2012

organism: Solanum lycopersicum


title: Pleiss Lab_S.cerevisiae_Q-PCR Screen Library

city: Ithaca

first: Jeffrey

last: Pleiss

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

organism: Saccharomyces cerevisiae

technology: other

first: Laura

last: Albulescu

manufacture_protocol: The S. cerevisiae strains from Open Biosystems were arrayed onto 14 384-well growth plates. Another set of temperature senzitive strains from Phil Hieter's lab were arrayed on the 15th 384-well plate together with conditional alleles derived from the Guthrie lab. RNA was extracted from these strains in a high-throughput manner, followed by cDNA synthesis and Q-PCR. The set comprises about 5500 mutants.


title: Agilent-019451 Papilio xuthus

status: Public on May 12 2012

city: Tsukuba

first: Ryo

last: Futahashi

address: Central6, Higashi 1-1-1

institute: National Institute of Advanced Industrial Science and Technology

organism: Papilio xuthus

description: 019451 Papilio

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


title: Rodent TaqMan® Low Density miRNA Arrays A v2.0 (TLDA, Life Technologies)

city: Sydney

first: Richard

last: Bagnall

address: Missenden Road

department: Molecular Cardiology

country: Australia

institute: Centenary Institute

organism: Mus musculus

technology: RT-PCR

description: RT-PCR quantification of mature microRNAs

manufacture_protocol: see manufacturer's website


title: Agilent-029890 NJND_apricot_01 [Probe name version]

status: Public on May 13 2012

city: Nanjing

first: Jinggui

address: tongwei road 6

department: college of Horticulture

institute: Nanjing Agricultural University

organism:
Prunus persica
Prunus armeniaca
Prunus salicina
Prunus mume

description:
Arrays of this design have barcodes that begin with 16029890 or 2529890.

The ID column represents the Agilent Probe name.


title: NimbleGen MM9/HG18 Chimeric Array [110330_MM9_HuMA_M]

city: Philadelphia

first: Renato

middle: V.

last: Iozzo

state: PA

address: 1020 Locust St. Rm 336

department: Pathology, Anatomy, and Cell Biology

institute: Thomas Jefferson University

organism:
Homo sapiens
Mus musculus

description:
NimbleGen Design name: 110330_MM9_HuMA_M
NimbleGen Design ID: 550681
Genome builds: Human hg18, Mouse mm9

HX3 expression design for mm9 sequences; a sister design to 550671; contains the same probes as 550671 except the HG180902_prime3_best_5_probes set is replaced by Selected_5_mouse_from_090310_HG18_MM9_expr, and the mouse_*_expr_probes are replaced by humanliver_*_expr_probes. Two copies of each experimental probe, one copy of each random probe on the array. Because there are fewer probes on this array than 550671, there are some empty features.

first: Simone

last: Buraschi

first: Thomas

last: Neill

first: Rick

last: Owens

first: Leonardo

last: Iniguez

first: George

middle: E

last: Purkins

first: Raj

last: Vadigepalli

first: Liliana

last: Schaefer

first: Stephen

last: Peiper

first: Z

middle: X

last: Wang

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


title: SMD Print_910 MMZ

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: CapitalBio 4.3K Xcc cDNA array

status: Public on May 10 2012

city: Beijing

first: jun

last: tao

address: Beichen west road

institute: institute of microbiology, Chinese academy of sciences

organism: Xanthomonas campestris pv. campestris

manufacture_protocol: as described in National Engineering Research Center for Beijing Biochip Technology(CapitalBio Corporation) manual


title: Human miRNA 1K

city: Guangzhou

first: Rongrong

last: wei

address: 651 Dongfeng East Road

department: cancer center

institute: Sun-Yat Sen university

manufacture_protocol: The probes (40 μM final concentration) mixed with printing buffer were printed onto slides in duplicate using SmartArrayer™ 136 printer (CapitalBio Inc, Beijing, China). 2.5 μg of total RNA was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16 ℃ overnight. The labeled RNAs were mixed and hybridized to the array with a 2×hybridization solution (final concentration: 5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46 ℃ for 12 to 16 hours. After washing, the microarray was scanned with a LuxScan™ 10K Microarray Scanner (CapitalBio Inc, Beijing, China) at PMT 800. The scanned image was gridded using the GenPix Pro 6.0 software (Axon Instruments, Foster City, CA, U.S.A.).


title: SUWHR Lipids 104 v2.0

status: Public on May 09 2012

first: William

last: Robinson

address: 269 Campus Drive

institute: Stanford University

organism:
Pseudomonas aeruginosa
Escherichia coli
Staphylococcus aureus
Streptococcus pyogenes
Bacillus subtilis
Mycobacterium tuberculosis
Homo sapiens
Sus scrofa domesticus
Bos primigenius
Salmonella enterica subsp. enterica serovar Typhimurium

description: Spotted lipids.

manufacturer: WHRobinson Lab, Stanford University School of Medicine

manufacture_protocol:
Making the arrays: 1. Cut one sandwich of PVDF membrane into six equal-sized pieces. PVDF Membrane Filter Paper Sandwich, (0.2 uL Pore Zie, #LC2002, Invitrogen). Trim the vertical edges of the membrane first to eliminate excess cover paper; 2. Using two pieces of double-sided 3M Scotch tape, tape each membrane onto the middle of a pre-cleaned microscope slide, (Gold Seal Microslides, Cat#3050). Avoid tape overlap and ensure that tape meets the edge of the membrane; 3. Align the membrane using an old slide as a guide; 4. Trim extra membrane or tape portions off the edge of the slide.

Printing the arrays: CAMAG Automatic TLC Sampler 4 (ATS4) robot. 1. Turn on the nitrogen gas by turning the large silver knob to the left. Gas is usually set to 65-75 psi, so other knobs should not have to be adjusted; 2. Turn on arrayer by pushing the button on the back left-hand side of the machine. Arrayer display should read "ATS4 System Ready."; 3. Check the "Rinse" (right, methanol) and "Waste" (left) bottles. Refill or empty as necessary; 4. Rinse the system by hitting "End" (display will read “this job clean rinse unit”), and then “Enter.”; 5. Obtain and organize 0.01 ml lipid aliquots from cold room and 4C fridge; 6. Mark slides using pencil with the array number and the date of the print. Check the arrays for cracks in the glass, and to make sure the PVD membrane goes to the edge of the slide and line up with membranes from the other slides; 7. Place each slide in appropriate slot on arrayer. Push down on the slide to make sure it is secured in place. For slides that are loose, push towards lower left-hand corner of the slot. Once all slides are in place, run finger down the end of each to secure again; 8. Push platform up (back) and left, and lock with lever on right-hand side; 9. For each aliquot, remove all black caps with decrimper and push on the plastic orange caps; 10. Place aliquots in machine, giving each a slight shake to make sure they are thawed; 11. Close lid of arrayer; 12. On Desktop, Open “Wincats.”; 13. Enter Login ID and password; 14. Under Instruments, select ATS4 “Freemode”; 15. Select File, then Open “8x11x12partA50” **The Arrayer uses two program files to spot each slide: 8x11x12partA50 (lipids 1-25) and 8x11x12partB50 (lipids 26-50). The Arrayer will spot program A on all twelve slides in each run and then spot program B; 16. Under Dosage, select Start. The arrayer will begin printing; 17. Watch arrayer carefully to note any problems. Once Program A is complete, the arrayer will make a sound and the screen backdrop will turn blue. Switch to Program B at this time (Select File, then Open “8x11x12partB50” then select Dosage, “Start”); 18. After each print run (every 12 slides), check aliquot levels and substitute fresh aliquots if need be. Repeat Steps 6-11, and 15-17 for each run; 19. At the end of the printing, being a Rinse cycle (hit “End”); 20. Turn off machine and store printed arrays appropriately.


title: Illumina Genome Analyzer IIx (Cryptococcus neoformans var. grubii H99)

last: GEO

organism: Cryptococcus neoformans H99


title: SUWHR Lipids 104 v1.0

description: Spotted lipids.

manufacture_protocol:
Making the arrays: 1. Cut one sandwich of PVDF membrane into six equal-sized pieces. PVDF Membrane Filter Paper Sandwich, (0.2 uL Pore Zie, #LC2002, Invitrogen). Trim the vertical edges of the membrane first to eliminate excess cover paper; 2. Using two pieces of double-sided 3M Scotch tape, tape each membrane onto the middle of a pre-cleaned microscope slide, (Gold Seal Microslides, Cat#3050). Avoid tape overlap and ensure that tape meets the edge of the membrane; 3. Align the membrane using an old slide as a guide; 4. Trim extra membrane or tape portions off the edge of the slide.

Printing the arrays: CAMAG Automatic TLC Sampler 4 (ATS4) robot. 1. Turn on the nitrogen gas by turning the large silver knob to the left. Gas is usually set to 65-75 psi, so other knobs should not have to be adjusted; 2. Turn on arrayer by pushing the button on the back left-hand side of the machine. Arrayer display should read “ATS4 System Ready.”; 3. Check the “Rinse” (right, methanol) and “Waste” (left) bottles. Refill or empty as necessary; 4. Rinse the system by hitting “End” (display will read “this job clean rinse unit”), and then “Enter.”; 5. Obtain and organize 0.01 ml lipid aliquots from cold room and 4C fridge; 6. Mark slides using pencil with the array number and the date of the print. Check the arrays for cracks in the glass, and to make sure the PVD membrane goes to the edge of the slide and line up with membranes from the other slides; 7. Place each slide in appropriate slot on arrayer. Push down on the slide to make sure it is secured in place. For slides that are loose, push towards lower left-hand corner of the slot. Once all slides are in place, run finger down the end of each to secure again; 8. Push platform up (back) and left, and lock with lever on right-hand side; 9. For each aliquot, remove all black caps with decrimper and push on the plastic orange caps; 10. Place aliquots in machine, giving each a slight shake to make sure they are thawed; 11. Close lid of arrayer; 12. On Desktop, Open “Wincats."; 13. Enter Login ID and password; 14. Under Instruments, select ATS4 “Freemode”; 15. Select File, then Open “8x11x12partA50” **The Arrayer uses two program files to spot each slide: 8x11x12partA50 (lipids 1-25) and 8x11x12partB50 (lipids 26-50). The Arrayer will spot program A on all twelve slides in each run and then spot program B; 16. Under Dosage, select Start. The arrayer will begin printing.; 17. Watch arrayer carefully to note any problems. Once Program A is complete, the arrayer will make a sound and the screen backdrop will turn blue. Switch to Program B at this time (Select File, then Open “8x11x12partB50” then select Dosage, “Start”); 18. After each print run (every 12 slides), check aliquot levels and substitute fresh aliquots if need be. Repeat Steps 6-11, and 15-17 for each run; 19. At the end of the printing, being a Rinse cycle (hit “End”); 20. Turn off machine and store printed arrays appropriately.


title: AB SOLiD System 3.0 (Saccharomyces cerevisiae)

status: Public on May 08 2012


title: Illumina Genome Analyzer IIx (Danio rerio)

organism: Danio rerio


title: Illumina Genome Analyzer IIx (Vitis vinifera)

status: Public on May 03 2012

organism: Vitis vinifera


title: SUWHR Lipids 104 v3.0

description: Spotted lipids.

manufacture_protocol:
Making the arrays: 1. Cut one sandwich of PVDF membrane into six equal-sized pieces. PVDF Membrane Filter Paper Sandwich, (0.2 uL Pore Zie,  #LC2002, Invitrogen). Trim the vertical edges of the membrane first to eliminate excess cover paper; 2. Using two pieces of double-sided 3M Scotch tape, tape each membrane onto the middle of a pre-cleaned microscope slide (Gold Seal Microslides, Cat#3050). Avoid tape overlap and ensure that tape meets the edge of the membrane; 3. Align the membrane using an old slide as a guide; 4. Trim extra membrane or tape portions off the edge of the slide.

Printing the arrays: CAMAG Automatic TLC Sampler 4 (ATS4) robot. 1. Turn on the nitrogen gas by turning the large silver knob to the left. Gas is usually set to 65-75 psi, so other knobs should not have to be adjusted; 2. Turn on arrayer by pushing the button on the back left-hand side of the machine. Arrayer display should read “ATS4 System Ready.”; 3. Check the “Rinse” (right, methanol) and “Waste” (left) bottles. Refill or empty as necessary; 4. Rinse the system by hitting “End” (display will read “this job clean rinse unit”), and then “Enter.”; 5. Obtain and organize 0.01 ml lipid aliquots from cold room and 4C fridge; 6. Mark slides using pencil with the array number and the date of the print. Check the arrays for cracks in the glass, and to make sure the PVD membrane goes to the edge of the slide and line up with membranes from the other slides; 7. Place each slide in appropriate slot on arrayer.  Push down on the slide to make sure it is secured in place. For slides that are loose, push towards lower left-hand corner of the slot. Once all slides are in place, run finger down the end of each to secure again; 8. Push platform up (back) and left, and lock with lever on right-hand side; 9. For each aliquot, remove all black caps with decrimper and push on the plastic orange caps; 10. Place aliquots in machine, giving each a slight shake to make sure they are thawed; 11. Close lid of arrayer; 12. On Desktop, Open “Wincats.”; 13. Enter Login ID and password; 14. Under Instruments, select ATS4 “Freemode”; 15. Select File, then Open “8x11x12partA50” **The Arrayer uses two program files to spot each slide: 8x11x12partA50 (lipids 1-25) and 8x11x12partB50 (lipids 26-50). The Arrayer will spot program A on all twelve slides in each run and then spot program B; 16. Under Dosage, select Start. The arrayer will begin printing; 17. Watch arrayer carefully to note any problems. Once Program A is complete, the arrayer will make a sound and the screen backdrop will turn blue. Switch to Program B at this time (Select File, then Open “8x11x12partB50” then select Dosage, “Start”); 18. After each print run (every 12 slides), check aliquot levels and substitute fresh aliquots if need be. Repeat Steps 6-11, and 15-17 for each run; 19. At the end of the printing, being a Rinse cycle (hit “End”); 20. Turn off machine and store printed arrays appropriately.


title: GU_rainbowtrout_15k_v3.0

city: Gothenburg

first: Marija

last: Cvijovic

address: Chalmers Tvärgata 3

country: Sweden

institute: Chalmers Univeristy of Technology

organism: Oncorhynchus mykiss

first: Erik

last: Kristiansson

first: Filip

last: Cuklev

first: Lina-Maria

last: Gunnarsson

first: Joakim

last: Larsson

manufacture_protocol: An oligonucleotide microarray was designed for the Geniom platform, which is fully automated system with in situ synthesized probes (Febit, Heidelberg, Germany). Probes for all eelpout transcripts were generated in a two-stage process. First, a preemptive clustering step, where very similar transcripts were grouped into single entities, was used to avoid losing good probes due to presumed cross-hybridization to splice variants and isogenes. Next, probes were designed using OligoArray 2.1 which is an algorithm using thermodynamic approach  to calculate specificity and to predict secondary structures. The probe design were run using the following parameters: the probe length were set to 50 nucleotides, Tm-range to 90°–95°, GC-content to 45%–55%, folding temperature to 70° and cross-hybridization temperature to 50°. The default settings were kept for all other parameters and no specificity check was done between transcripts within the same cluster. For sequences where no satisfactory probe could be found, a second run with a slightly less strict GC-content (45%–60%) were done. Since massively parallel pyrosequencing is dependent on a fragmentation step, where the mRNA is randomly cut into processable pieces, the strand orientation is lost and thus the direction of transcription for the generated reads and, ultimately, for the assembled contigs. We therefore designed probes for all assembled transcripts and the corresponding reverse complements resulting in 39,618 (74%) and 39,733 (74%) probes respectively. In total, 117,316 probes were used and distributed over eight separate microarrays. Each array contained 15,648 spots, including controls, and were synthesized in situ on one single biochip using the 5' standard synthesis set for Geniom.


title: NimbleGen Human ChIP-chip 2.1M Deluxe Promoter Array [100718_HG18_Deluxe_Promoter_HX1]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
Design ID: 535383
Design name: 100718_HG18_Deluxe_Promoter_HX1
Genome build: HG18

distribution: commercial

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


title: Phalanx Human miRNA OneArray Ver 3 (miRBase Release 17)

status: Public on May 06 2012

city: Hsinchu

first: Sean

last: Chang

address: 6F, NO.6 Technology Road 5

department: R&D

country: Taiwan

institute: PhalanxBiotech Group

description: Human miRNA microarray designed and annotated based on Sanger's miRBase release 17.

manufacture_protocol: See http://www.phalanxbiotech.com/ for updated protocols


title: Illumina Genome Analyzer IIx (Tetrahymena thermophila)

status: Public on May 01 2012

organism: Tetrahymena thermophila


title: NimbleGen_BIOMA_Zymomonas mobilis_array [DesignID 549081]

city: Chengdu

first: Mingxiong

last: He

state: Sichuan

address: Section 4-13, Renming Nanlu

department: Biomass Energy Technology Research Centre

institute: Biogas Institute of Ministry of Agriculture

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

description:
BIOMA_Zymomonas mobilis ATCC31821_furfural stress_arra

Zymomonas mobilis subsp. mobilis ZM4 chromosome, complete genome [BUILD 1102]

DESIGN_ID: 549081

designname: 110218_ZmobilisZM4_YR_exp

native array description file: 110218_ZmobilisZM4_YR_exp.ndf
native array description file: 110218_ZmobilisZM4_YR_exp.ng

manufacture_protocol: CapitalBio Corporation


title: Phalanx Rat miRNA OneArray Ver 4 (miRBase Release 18)

organism: Rattus norvegicus

description: Rat miRNA microarray designed and annotated based on Sanger's miRBase release 18


title: Phalanx Mouse miRNA OneArray Ver 4 (miRBase Release 18)

description: Mouse miRNA microarray designed and annotated based on Sanger's miRBase release 18


title: Beaudet mouse PWS/AS strand-specific microarray

city: Houston

first: Linyan

last: Meng

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Agilent eArray online tool was used to design the array (SurePrint G3 Custom CGH Microarray 8x60K, 60-mer). High quality Agilent probes from chr7:65,910,585-67,600,789 (Snrpn-Ube3a, mm9), chr6:125,111,870-125,115,601 (Gapdh), chrX:103,382,463-103,399,038 (Pgk1), chr16:32,609,107-32,632,876 (Tfrc), and chr5:143,664,795-143,668,403 (Actb) were selected by eArray to generate probe group 1 (representing high quality probes). Genomic tilling probes for the Snrpn-Ube3a region were also generated to form probe group 2 ( named with "CUST", representing low quality probes). The default Agilent probes are from the plus strand. These two probe groups were then used to generate the reverse-complementary probes named with "RC" followed by their original probe name. These are the probes from the minus strand.

first: Richard

last: Person


title: Illumina HiSeq 2000 (Equus caballus)

organism: Equus caballus


title: Agilent 034318 Schizosaccharomyces pombe 44K

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

organism: Schizosaccharomyces pombe

description: Custom 60mer oligonucleotide array that represents alternately the plus and minus strands tiling a large portion of chromosome 2 and small segments of chromosome 1 and 3 at 50bp resolution. Included are following sections: chromosome 2  from position 1000000 to 3049820 and from 4491831 to 4541531 and small sections of chromosome 1 and 3.

manufacture_protocol: Agilent's in situ synthesis printing; for details visit manufacturer's web site www.chem.agilent.com


title: arrayTAG LION Bioscience cDNA array

city: Lund

first: Ulrike

last: Nuber

address: Klinikgatan 26

institute: Lund University

description: spotted PCR products

manufacturer: Max Planck Institute for Molecular Genetics, Berlin, Germany

manufacture_protocol: Purified PCR products were resuspended in 8 μl of 3× SSC and printed on Corning GAPS II slides by using a robotic spotting device (SDDC-2 MicroArrayer, ESI, Toronto, Canada/ChipWriter Pro, Bio-Rad, Munich, Germany) with SMP3 pins from TeleChem International (Sunnyvale, CA).


title: Exiqon miRCURYTM LNA Array Version 9.2

first: Yangjin

last: Bae

department: Molecular Human Genetics

description: LNA Array microRNA Profiling

manufacture_protocol: LNA Array Power labeling kit used for labeling of microRNAs. Tecan hybridization stations used for hybridization.


title: Rodrigues_S.baltica_30K

city: Arlington

first: Sealy

last: Hambright

address: 701 S. Nedderman Dr.

department: Biology

institute: UT Arlington

organism: Shewanella baltica

description:
Phosphoramidite synthesis. Non-spotted.
http://www.mycroarray.com/index.html

middle: S

first: Jorge

last: Rodrigues


title: Agilent-023057 Genotypic Technology designed Custom Mycobacterium tuberculosis h37Rv Whole Genome 8x15k GE Microarray

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

organism: Mycobacterium tuberculosis H37Rv

first: Mugasimangalam

last: Raja


title: Agilent-017202 whole mouse genome (mm8) custom 2×105k array

first: Robert

middle: A

last: Waterland

address: 1100 Bates St.,


title: microRNA array v10 four genome

status: Public on May 02 2012

city: Chapel Hill

first: Scott

last: Hammond

state: NC

department: Dept Cell and Developmental Biology

institute: University of North Carolina

organism:
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

first: Michael

last: Thomson

first: Keith

last: Woods

first: Martin

last: Newman

manufacture_protocol:
Oligonucleotide probes to mouse, human, rat, and Danio Rerio microRNA genes were designed, antisense to the mature sequence as reported in the Sanger microRNA registry (4/1/07). Probes were spotted at 40 uM on Corning GAPS-II slides in 3X SSC, dried, and crosslinked by 600mJ UV. Slides were prehybridized in 3x SSC, 0.1% SDS, 0.2% BSA for 45 minutes, hybridized for 2h at 37C in 400mM Na2HPO4 pH 7.0, 0.8% BSA,
5% SDS, 12% formamide.


title: microRNA array v10 mouse

organism: Mus musculus

manufacture_protocol:
Oligonucleotide probes to 198 mouse microRNA genes were designed, antisense to the mature sequence as reported in the Sanger microRNA registry (4/1/07). Probes were spotted at 40 uM on Corning GAPS-II slides in 3X SSC, dried, and crosslinked by 600mJ UV. Slides were prehybridized in 3x SSC, 0.1% SDS, 0.2% BSA for 45 minutes, hybridized for 2h at 37C in 400mM Na2HPO4 pH 7.0, 0.8% BSA,
5% SDS, 12% formamide.


title: 3.7k LUMC BAC array

status: Public on Sep 12 2011

city: Leiden

first: Els

last: Robanus-Maandag

address: Einthovenweg 20

department: Human Genetics

institute: LUMC

organism: Homo sapiens

manufacture_protocol: The array contains 3700 probes spotted in triplicate on glass slides. The BAC set is distributed by the Welcome Trust Sanger Institute (Hinxton, UK), and comprises of 1 mb spaced probes, a set of subtelomeric sequences for each chromosome arm, and a few hundred probes selected for their involvement in oncogenesis. Reference: Knijnenburg J, Szuhai K, et.al. Am J Med Genet A. 2005 Jan 1;132(1):36-40. Insights from genomic microarrays into structural chromosome rearrangements.


title: [Mouse4302_Mm_EntrezG] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Brainarray Version 14]

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

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 14, Mouse4302_Mm_ENTREZG]. CDF and other files can be downloaded at: (see web link below).


title: University of Groningen Lactococcus lactis MG1363 amplicon/oligo 5K

status: Public on Jul 02 2011

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

organism: Lactococcus cremoris subsp. cremoris MG1363

technology: mixed spotted oligonucleotide/cDNA

last: de Jong

first: Siger

last: Holsappel

manufacture_protocol: General Microgrid II spotting protocol on superamine slides


title: Illumina HumanHap650Yv2 Genotyping BeadChip (HumanHap650Y_v2-0_GenotypingBC_11237679_A)

city: Toronto

first: Ekaterina

last: Rogaeva

address: 6 Queen’s Park Crescent West

institute: Tanz Centre for Neurodegenerative Diseases

technology: oligonucleotide beads

description:
Descriptor File Name(s),HumanHap650Y_v2-0_GenotypingBC_11237679_A.bpm
Assay Format,Infinium II
SNP Count,662841

manufacture_protocol: See manufacturer's website


title: Agilent-023462 Desert and Migratory Locust EST Array

status: Public on Nov 25 2011

city: Leuven

first: Jozef

last: Vanden Broeck

address: Naamsestraat 59

department: Animal Physiology and Neurobiology

country: Belgium

institute: KU Leuven

organism:
Locusta migratoria
Schistocerca gregaria

description:
We recently developed an 'expressed sequence tag' (EST) database derived from the desert locust (Schistocerca gregaria) central nervous system [Badisco L, Huybrechts J, Simonet G, Verlinden H, Marchal E et al. (2011) Transcriptome analysis of the desert locust central nervous system: production and annotation of a Schistocerca gregaria EST database. PLoS One 6: e17274.]. The microarray platform contains probes corresponding to all these S. gregaria EST sequences and to all available GenBank S. gregaria transcript sequences. The migratory locust (Locusta migratoria) is a species related to the desert locust for which EST sequence information is also available [Ma ZY, Yu J, Kang L (2006) LocustDB: a relational database for the transcriptome and biology of the migratory locust (Locusta migratoria). BMC Genomics 7: 11.]. Therefore, the S. gregaria transcript sequences included in the microarray design were complemented with all L. migratoria EST sequences having no blastn orthologue (blastn hits producing E < 1E-10 were considered orthologs) in the S. gregaria set.
The locust microarrays were designed by means of the eArray system (Agilent Technologies). Probes were designed according to the following criteria: (i) probe length: 60 nucleotides, (ii) two probes per target sequence (best probe methodology) and (iii) probe orientation: sense. Other parameters were set at default settings. In total 20,755 unique locust transcript sequences (12,783 S. gregaria and 7,972 L. migratoria sequences) were represented on the arrays.
(EST sequences are publically available in GenBank.)

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


title: Phalanx Mouse OneArray Ver 2

first: Sean

last: Chang

description:
Annotation is based on two databases:
. NCBI RefSeq release 52
. Ensembl release 66 cDNA sequences and
Ensembl_core_66_3 annotations


title: CCDTM Mm-CCDTM36k (derived from GPL5960)

status: Public on Oct 22 2011

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

manufacturer: NIH Clinical Center, Dept. of Transfusion Medicine, Immunogenetics Section (NIH/CC/DTM)

manufacture_protocol: The Operon mouse Array-Ready Oligo Set (AROS™) V 4.0 contains 35,852 long 70mer probes representing 25,000 genes and about 38,000 gene transcripts and also includes 380 controls. The oligo design is based on the Ensembl Mouse Database release 26.33b.1, Mouse Genome Sequencing Project, NCBI RefSeq, Riken full-length cDNA clone sequence, and other GenBank sequence (http://www.operon.com/). The oligonucleotide probes were purchased in 384-well polypropylene plates (Genetix, 384 micro array) and resuspend in 3XSSC print buffer at a concentration of 25uM. The microarray is composed of 48 blocks and one spot is printed per probe per slide. The spot size is 100 micron and spot distance is 157.5 microns (center-to-center). The microarrays were printed on SuperChip™ Epoxysilane MicroArray Slides (C50-5588-M20, Thermo Fisher Scientific Co) post-processed according to manufacture protocol.


title: Agilent-031546 PBANKA1_X8

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

organism: Plasmodium berghei ANKA

description:
Arrays of this design have barcodes that begin with 16031546 or 2531546.

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 Lactuca sativa 44K

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

organism: Lactuca sativa

manufacture_protocol: see manufacturer's website


title: NCI/ATC Mm-MEEBO 38K

status: Public on Sep 28 2011

city: Bethesda

first: Daekwan

last: Seo

state: MD

address: 37 Convent Dr. Rm 4140

department: NCI

country: USA

institute: NIH

description:
NCBI mouse genome Build 37 (UCSC mm9).
Derived from GPL4200.

manufacturer: Advanced Technology Center Microarray Facility (NIH/NCI/CCR/ATC)

manufacture_protocol: Microarrays are printed with GeneMachines robotic arrayer from Genomic Solutions (http://www.genomicsolutions.com) that is fitted with a printhead containing 48 SMP2.5 printing pins from Telechem International (http://www.arrayit.com). The mouse long oligonuleotide probe set contains 38,467 optimized 70mers (plus NCI Spotplate #4 controls) obtained from Invitrogen (http://www.invitrogen.com/). The long oligonucleotide probes were purchased in 384-well polypropylene plates (Genetix, 384 microarray) and dissolved print buffer of sodium phosphate (150mM) at ph 8.5 and 4% sodium sulphate at a concentration of 20-30 uM. The microarray spots are printed with 160 micron column x 155 microns row spacing, and one spot is printed per probe per slide. The microarrays were printed on Corning Expoxide slides and post-processed according to the manufacturer's protocol.


title: Agilent custom Human 14K Oligo Microarray

status: Public on Oct 01 2010

city: Taipei

first: Men-Luh

last: Yen

address: No.1, Sect. 1, Jen-Ai Road

institute: National Taiwan University

description: This is a custom array designed for 11,000 genes from the 'Agilent-012391 Whole Human Genome Oligo Microarray G4112A' array contained in GEO as GPL6848.


title: NimbleGen mouse tiling array (100723_MM8_GS_Meth_03)

status: Public on Jan 01 2012

city: Rennes

first: Aurelien

last: Serandour

address: Bâtiment 13, Campus de Beaulieu

department: UMR CNRS 6290

institute: Université de Rennes 1

description:
Design_ID: 531891

Custom MM8 Meth. order for 3 regions provided by the customer (chr11, chr17, and portions of chr4).

Mouse genome mm8 (NCBI Build 36).

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


title: NimbleGen Streptococcus pyogenes NZ131 intergenic array

status: Public on Nov 15 2010

city: Chicago

middle: J

last: Federle

address: 900 S Ashland Ave. MC870

department: Microbiology & Imm. / Cntr Pharm Biotech

institute: University of Illinois at Chicago

organism: Streptococcus pyogenes NZ131

description: Expression array including select intergenic region tiles of S. pyogenes NZ131


title: JCVI PFGRC Enterococcus faecalis 14K v1 array (condensed)

status: Public on Dec 20 2011

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

organism: Enterococcus faecalis

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


title: NCI/ATC Mm-MEEBO ver. 07/27/09 (derived from GPL4200)

status: Public on Aug 01 2010

first: Snorri

last: Thorgeirsson

address: 37 Convent Dr. # 4146

department: Laboratory of Experimental Carcinogenesis

institute: National Cancer institute/NIH


title: Affymetrix IST_IBB Burkholderia 15K v1.0 (GeneChip BCC1sa520656F)

status: Public on Aug 22 2011

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

organism:
Burkholderia cenocepacia J2315
Burkholderia multivorans ATCC 17616

relation: Alternative to: GPL15600 (Alternative CDF)

manufacture_protocol:
see manufacturer's web site
The parameters chosen for the custom array design were as follows: 11-micron feature size, standard 12.8-mm array format, prokaryotic antisense target type, perfect-match probes only, full length sequence for probe selection, and eight as the minimum acceptable probes per sequence.


title: JCVI PFGRC Enterococcus faecalis 14K v1 array designed primarily based on strain OG1RF

status: Public on Mar 18 2010

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

description: This set includes 6600 oligonucleotides, has 14688 spots distributed in 48 blocks.


title: Affymetrix Rice Genome Array (custom CDF)

status: Public on Dec 25 2010

city: Blacksburg

first: Andy

last: Pereira

state: VA

address: Washington Street MC0477

department: Virginia Bioinformatics Institute

institute: Virginia Tech

organism: Oryza sativa

description: The custom CDF was built by uniquely mapping 442,810 probe sequences to 35,161 rice gene-based probe sets in the following manner: (i) probes that have perfect sequence identity with a single target gene were selected, (ii) probes mapping to reverse complements of genes were annotated separately as antisense probes (not used in the above counts), and finally, (iii) probes were grouped into probe sets, each corresponding to a single gene, and probe sets having at least 3 unique sequences were retained (>98% probe sets have >=5 probes). Note that these stringent criteria used to construct the CDF make it possible to reliably measure expression values of members of multigene families (free from cross-hybridization between paralogs showing high sequence similarity).

manufacture_protocol: see manufacturer's web site


title: NimbleGen Rana muscosa/sierrae 12-plex Oligo Custom Expression Array [100211_RM_MS_EXP]

city: Berkeley

first: Thomas

last: Poorten

address: 54 Mulford Hall

department: Environmental Science, Policy, and Management

institute: UC Berkeley

organism:
Rana muscosa
Rana sierrae

description:
The microarray contained 127,867 60-mer probes representing a possible 29,259 expressed transcripts (probe sets). Probe sets were defined as all probes that mapped to a single transcript, which in turn mapped to a single gene.
Probe sequences within the ndf file.
SLIDE_LAYOUT_NAME: NimbleChip_HX12
DESIGN_NAME: 100211_RM_MS_EXP
DESIGN_ID: 11375


title: CCDTM miRNA700-V3 (H. sapiens and EBV subset; condensed)

status: Public on Mar 11 2010

organism:
Homo sapiens
human gammaherpesvirus 4

description:
Derived from GPL6773 04/01/09 - H. sapiens and EBV subset.
This is a condensed representation of the full array in Platform GPL6773.

manufacture_protocol: Oligos sythesized by Operon with 3' amine modification and purified by desalting. Oligos are adjusted to the same concentration and resuspend in 2mM phosphate buffer at 25mM oligo concentration and spotted on CodeLink(TM) Activated Slides (GE Healthcare) using an Omnigrid robotic arrayer (Genomic Solutions).


title: CCDTM miRNA 850 version 4.1

status: Public on Dec 05 2009

organism:
Homo sapiens
Mus musculus
Rattus norvegicus
human gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus macacae

description: Derived from GPL7089 - CCDTM miRNA850-version 4


title: CCDTM miRNA850-version 4 (H. sapiens and EBV subset; condensed)

status: Public on Jun 21 2010

description:
Derived from GPL7089 07/29/09 - CCDTM miRNA850-version 4
This is a condensed representation of the full array in Platform GPL7089.


title: CCDTM Hs_CCDTM17.5k version 2

status: Public on Oct 04 2007

manufacture_protocol: Microarrays are printed with GeneMachines robotic arrayer from Genomic Solutions (http://www.genomicsolutions.com) that is fitted with a printhead containing 32 SMP2.5 printing pins from Telechem International (http://www.arrayit.com). The human cDNA probe set is based on RG_HsKG_031901 8k clone set and 9k clones from the RG_Hs_seq_ver_070700 40k clone set from Research Genetics (http://clones.invitrogen.com). The set includes 12,072 uniquely named genes, 875 duplicates of named genes and all remainder consisted of expression sequence tags (about 4053 EST). In addition, 194 selected cDNA clones from Stratgene and 218 custom designed 60mer oligo representing transcripts with immunological function were added to the probe set. The cDNA probes were amplified by PCR and distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in 3XSSC print buffer at a concentration of 50-100 ug/ml. The microarray spot densities are 280 microns (center-to-center), and one spot is printed per probe per slide. The microarrays are printed on Fisher Premium microscope slides (cat# 12-544-1) coated with poly-L-lysine and post-processed according to the procedures on the NCI website http://madb.nci.nih.gov/.


title: Agilent-022857 Helicobacter pylori microarray

status: Public on Mar 15 2011

city: BANGALORE

first: RITESH

last: KUMAR

address: DEPARTMENT OF BIOCHEMISTRY, INDIAN INSTITUTE OF SCIENCE

country: India

institute: INDIAN INSTITUTE OF SCIENCE

organism: Helicobacter pylori

manufacture_protocol: refer to Agilent Web site


title: [Mm35b_P04R] Affymetrix Mouse Tiling 2.0R Set, Array 4

status: Public on Feb 01 2008

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

description:
Tiling array submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The GeneChip® Mouse Tiling 2.0R Array Set is designed for chromatin immunoprecipitation (ChIP) experiments. This set of seven arrays contains approximately 45 million oligonucleotide probes to interrogate the mouse genome. Each array in the set contains over 6.5 million perfect match probes to specifically interrogate genomic regions.
Sequences used in the design of the Mouse Tiling 2.0R Array Set were selected from NCBI mouse genome assembly (Build 33). Repetitive elements were removed by RepeatMasker. The Mouse Tiling 2.0R Array Set is available either as a whole-genome set of seven arrays (P/N 900852), or individual arrays from the set may be purchased separately.
Probes are tiled at an average resolution of 35 base pairs, as measured from the central position of adjacent 25-mer oligos, leaving a gap of approximately 10bp between probes. Oligonucleotide probes are synthesized in situ complementary to each corresponding sequence.

BPMAP and other files can be downloaded from the Affymetrix Web site below.

manufacture_protocol: See manufacturer's web site


title: University of Padova Sparus aurata 40k array version 1

status: Public on Feb 20 2009

city: Legnaro

first: Luca

last: Bargelloni

state: PD

address: Viale dell'Università 16

department: Dept. Sanità Pubblica, Patologia Comparata ed Ig. Veterinaria

country: Italy

institute: Agripolis

organism: Sparus aurata

description: GE 4x44k oligo microarray that covers 19,715 unique transcripts of the gilthead sea bream (Sparus aurata). Oligonucleotides, 60-mer plus a “linker”, are synthesized directly on glass slide using the Agilent’s SurePrint Tecnology; oligo design was carried out by Agilent and two non overlapping probes were designed for each ESTs cluster. The number of transcripts represented by two probes is 19,664 while 51 targets have only one probe; the total number of target probes in the platform is 39379. Both independent probes designed for the same transcript are named with an univocal ID and distinguished by suffix _1 or _2. Sequence and description of each gene (cluster) are available in the SAPD database (http://enne.cribi.unipd.it:5555/biomart/martview), where cluster ID corresponds to probe ID on the array. (Access to SAPD database will be free after publication. Login and password are now required and will be provided upon request).

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


title: Applied Biosystems Human Taqman MicroRNA Array v3.0

status: Public on Sep 15 2011

city: Baltimore

first: Kenneth

middle: W

last: Witwer

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

description: qRT-PCR TaqMan Low-Density Array

manufacture_protocol: see manufacturer's website: http://www.appliedbiosystems.com/


title: CCDTM Mm-CCDTM36k

last: Marincola

institute: Sidra Medical and Research Center


title: CCDTM miRNA700-V3

description: This is a full representation of the condensed array in Platform GPL8377.


title: MMV

status: Public on Jan 25 2006

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: [GenomeWideSNP_5] Affymetrix Genome-Wide Human SNP 5.0 Chromosome 1

status: Public on Dec 03 2009

city: Cambridge

first: Christina

last: Curtis

address: Robinson Way

department: Computational Biology/Oncology

country: United Kingdom

institute: University of Cambridge

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

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

Contains SNPs on NC_000001.9
Annotations correspond to hg18 (NCBI 36.1)


title: NCI S. pombe 44K C50

status: Public on Aug 24 2009

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

organism: Schizosaccharomyces pombe

description: Custom 60mer oligonucleotide array that represents alternately the plus and minus strands tiling a large portion of chromosome 2 and small segments of chromosome 1 and 3 at 50bp resolution. Included are following sections: chromosome 2  from position 1000000 to 3049820 and from 4491831 to 4541531 and small sections of chromosome 1 and 3.

manufacture_protocol: Agilent's in situ synthesis printing; for details visit manufacturer's web site www.chem.agilent.com


title: 3.7k full genome LUMC BAC array

status: Public on Jul 21 2006

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

first: Karoly

last: Szuhai

manufacture_protocol: The array contains 3700 probes spotted in triplicate on glass slides. The BAC set is distributed by the Welcome Trust Sanger Institute (Hinxton, UK), and comprises of 1 mb spaced probes, a set of subtelomeric sequences for each chromosome arm, and a few hundred probes selected for their involvement in oncogenesis. Reference: Knijnenburg J, Szuhai K, et.al. Am J Med Genet A. 2005 Jan 1;132(1):36-40. Insights from genomic microarrays into structural chromosome rearrangements.


title: NCI/ATC Mm-MEEBO

status: Public on Aug 22 2006

city: Gaithersburg

first: David

last: Petersen

address: 8717 Grovemont Circle

relation:
Affiliated with: GPL9027
Affiliated with: GPL14634


title: Illumina HumanOmni1-Quad BeadChip

status: Public on Jul 27 2009

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

manufacture_protocol: See manufacturer's website


title: URGV Arabidopsis thaliana 25K CATMA_v2.2

status: Public on Sep 22 2006

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

institute: INRA

organism: Arabidopsis thaliana

description: Corning Ultra-GAPS (TM) slides are spotted with 64 pins (8x8) therefore the spotted area is divided into 3 metablocks, each containning 64 blocks of 144 spots (12x12)

first: Jean-Pierre

last: Renou

first: Frédérique

first: Ludivine

last: Taconnat

first: Vincent

last: Thareau

first: Pierre

last: Hilson

manufacture_protocol:
A.thaliana genes were predicted with Eugene software (Foissac S. et al., Nucleic Acids Res., 2003) and gene-specific sequence tags were automatically designed (Thareau et al. Bioinformatics, 2003 Nov 22). Two rounds of PCR were performed and PCR products were finally purified and dissolved in 50% DMSO in TE at concentrations ranging between 50-200ng/ul and re-arrayed in 1536 microtiter plates. The pins are washed in 0.1% SDS at 50 °C then three times in bi-distilled water. Spotter settings are 45-55% humidity, and a pitch = 180 um. The room temperature is set between 19 and 21 degrees Celsius and below 40 % humidity. The microtiter plates are placed in the biobank. The four trays are cleaned and 100-120 slides placed on them (30 slides per tray). The spotting lasts 25 hours. The slides are stored in the dark in a dry-cabinet for 3 days and UV-cross-linked at 300 mJ. After crosslinking, the slides are stored in the dark in a dry-cabinet.
- 24576 Gene Specific Tags (GST)
- 615 Chloroplastic and Mitochondrial Tilling array probes
- 48 Non Protein Coding (NPC)