title: Pisum sativum 12K array

status: Public on Oct 26 2009

city: Parkville

first: Chui

middle: E

last: WONG

state: Victoria

address: University of Melbourne

department: Land and Food

country: Australia

institute: University of Melbourne

organism: Lathyrus oleraceus

technology: in situ oligonucleotide

distribution: custom-commercial

first: Dacheng

last: Liang

last: Wong

first: Mohan

middle: B

last: Singh

first: Belinda

last: Phipson

first: Gordon

last: Smyth

first: Prem

middle: L

last: Bhalla

manufacture_protocol:
Please refer to the manufacture's website for the complete protocol
http://www.combimatrix.com/tech_microarrays.htm


title: miRXploreTM microarrays (856)

status: Public on Oct 27 2009

city: Bergisch Gladbach

first: Ute

last: Bissels

state: NRW

address: Friedrich-Ebert-Str. 68

department: R&D

country: Germany

institute: Miltenyi Biotec GmbH

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

technology: spotted DNA/cDNA

description:
Each microarray contained a total of 5308 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 2012 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 2012 miRNA sequences covered sequence verified miRNAs of the species human (849) mouse (616) and rat (426) as well as viral miRNAs (121) as deposited in the miRBase sequence database version 11.0. The 97 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (43 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 36 positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 13 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences. Microarrays were manufactured by Miltenyi Biotec. Briefly, 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides in quadruplicates using a customized piezoelectric spotter.
Each microarray contained a total of 5308 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 2012 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 2012 miRNA sequences covered sequence verified miRNAs of the species human (849) mouse (616) and rat (426) as well as viral miRNAs (121) as deposited in the miRBase sequence database version 11.0. The 97 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (43 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 36 positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 13 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences. Microarrays were manufactured by Miltenyi Biotec. Briefly, 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides in quadruplicates using a customized piezoelectric spotter.

distribution: commercial

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

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


title: UCM-Medina-Apalmata-2058-v4

status: Public on Oct 31 2009

city: San Francisco

first: Michael

last: DeSalvo

state: CA

department: Department of Anesthesia

country: USA

institute: UC San Francisco

organism: Acropora palmata

distribution: non-commercial

manufacture_protocol: cDNA microarray containing 2,059 genes of the Caribbean Elkhorn coral Acropora palmata


title: miRXploreTM microarrays (865)

description: Each microarray contained a total of 5504 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 2036 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 2036 miRNAs sequences covered sequence verified miRNAs of the species human (872) mouse (634) and rat (427) as well as viral miRNAs (130) as deposited in miRBase version 12.0. The 97 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (43 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 36 internal positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 13 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences. Microarrays were manufactured by Miltenyi Biotec. Briefly, 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted four times on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides using a customized piezoelectric spotter.


title: Illumina Genome Analyzer (Prunus persica)

last: GEO

organism: Prunus persica

technology: high-throughput sequencing

distribution: virtual


title: Illumina Genome Analyzer (Prunus persica var. nucipersica)

organism: Prunus persica var. nucipersica


title: Grossman Lab BSS1-3

status: Public on Oct 16 2009

city: Cambridge

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

state: MA

address: 31 Ames Street, 68-530

department: Biology

institute: MIT

organism: Bacillus subtilis

technology: spotted oligonucleotide

middle: D

first: Catherine

middle: A

last: Lee

manufacture_protocol:
Oligonucleotide library of B. subtilis from Sigma-Genosys (catalog number BACLIB96, consisting of 4106 annotated genes in the Subtilist genome data release R16.1) and five additional custom oligonucleotides designed by Grossman lab spotted on Corning GAPS II slides using Genetix Q-Array Mini Printer. The sequences for the five Grossman lab custom probes are as follows:

dnaN2
GGAGTATCCTTTACAGGGAGTGACTCAGATATTTCTATTGAATCCTTCATTCCAAAAGAAGAAGG

dnaN3
CAGTATTTGACGATTATCCGTTCTGGTAAAGCTGAATTTAATCTAAACGGACTGGATGCTGATGA

pep1
ATGAAAAAGGCTTATAAGAAACCTCGTCTTTTTGAACTGCGCCGTGCTGTAGCAGCTGGCGGCCAT

pep2
ATGAAAAAAGCTTATAAGAAACCTCGCCTTTTTGAACTGCGCCGTGCTGTAGCAGCTGGCGGCCAT

pep3
ATGAAAAAAGCTTATAAGAAACCTCGCCTTTTTGAATTGCGCCGCGCTGTAGCAGCTGGCGGTCAT


title: SBO_LAB_2k_version1

status: Public on Oct 20 2009

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

organism:
Leuconostoc mesenteroides
Oenococcus oeni
Pediococcus acidilactici
Pediococcus pentosaceus
Staphylococcus aureus
Streptococcus thermophilus
Enterococcus faecalis
Enterococcus faecium
Enterococcus hirae
Lactococcus lactis
Lactobacillus acidophilus
Levilactobacillus brevis
Lentilactobacillus buchneri
Lacticaseibacillus casei
Weissella confusa
Lactobacillus delbrueckii
Lactobacillus helveticus
Lentilactobacillus hilgardii
Lactiplantibacillus pentosus
Lactiplantibacillus plantarum
Lactobacillus gasseri
Lacticaseibacillus paracasei
Limosilactobacillus reuteri
Latilactobacillus sakei
Companilactobacillus alimentarius
Lactobacillus amylovorus
Companilactobacillus farciminis
Limosilactobacillus fermentum
Fructilactobacillus fructivorans
Fructilactobacillus sanfranciscensis
Bifidobacterium
Brevibacterium linens
Latilactobacillus curvatus
Lactobacillus johnsonii
Leuconostoc citreum
Leuconostoc pseudomesenteroides
Limosilactobacillus pontis
Enterococcus casseliflavus
Mammaliicoccus lentus
Limosilactobacillus panis
Lacticaseibacillus rhamnosus
Lactobacillus crispatus
Enterococcus mundtii
Lactiplantibacillus paraplantarum
Companilactobacillus paralimentarius
Limosilactobacillus frumenti
Lentilactobacillus parabuchneri
Companilactobacillus mindensis
Furfurilactobacillus rossiae

description:
This species-independent microarray for Lactic Acid Bacteria (LAB) enables to assess the expression  of genes that play a key role in the production of sugar carbolites, bacteriocins, exopolysaccharides, and aromas, in probiotic and biosafety characteristics, and in stress response.
The array design contains 11,520 features (30-mer oligonucleotides) printed in a layout of 12 meta rows and 4 meta columns; consisting out of 16 rows and 15 columns per block.  The array measures the expression of 2,269 functional genes, spotted with four duplicates.
A second group of oligos consists out of 96 identification oligos, also added with each four duplicates, resulting in 384 spots.
The Lucidea Universal ScoreCard Controls (Amersham Biosciences Buckinghamshire, UK) are added. We added 10 probes, that assess the dynamic range and 8 ratio controls.  Each control was spotted in 16 block with 4 copies per block (i.e., 16x4=64 copies); making a total of 1,152 control spots on the chip.
A set of 908 spots remained empty.
The platform data table reflects a condensed representation of the array.  The complete array layout file representing the replicated features as well is linked as a supplementary file.

first: Stefan

last: Weckx

first: Joke

last: Allemeersch

first: Roel

last: Van der Meulen

first: Gino

last: Vrancken

first: Luc

last: De Vuyst

first: Paul

last: Van Hummelen

manufacture_protocol: All oligos were obtained from Isogen Life Science BV (Ijsselstein, The Netherlands) and diluted to 25 µM in 100 mM Na-Phosphate buffer plus 0.000675% sarcosyl (Sigma-Aldrich). A MicroGrid II spotter (Genomic Solutions, Huntingdon, United Kingdom) was used to spot the oligos using 10K pins on CodeLink™ Activated Slides (GE Healthcare, Bucks, United Kingdom). After spotting, the CodeLink™ Activated Slides were placed in a humid chamber containing saturated NaCl for minimal 24 h. Unused active groups were blocked with preheated blocking solution (50 mM ethanolamine, 0.1M Tris pH=9.0) at 50 °C for 30 min. Slides were rinsed twice with MilliQ water and washed with preheated 4xSSC, 0.1% SDS at 50 °C for 30 min in a shaking water bath. Slides were rinsed with MilliQ water and dried by centrifugation at 800 rpm for 3 min.


title: NimbleGen Drosophila 385k array rel.5 10 bp in 18 containers

status: Public on Oct 15 2009

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

organism: Drosophila melanogaster

description:
FlyBase release 5
18 regions distributed over all chromsome arms, including pericentric heterochromatin of 2R and HOX gene clusters.
080423_Dmel5_LP_Tiling.ndf

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


title: Radiata pine 18K cDNA microarrays

city: Canberra

first: Xinguo

last: Li

state: ACT

address: Building 602, Black Mountain Laboratories

department: Plant Industry

institute: CSIRO

organism: Pinus radiata

manufacture_protocol: A total of 18,432 purified PCR products were spotted on the GAP II coated slides (Corning Incorporated, NY) using the SDDC2 arrayer (ESI, Toronto, Canada) and Chipmaker 3 pins (Telechem International, CA) at 20 °C and humility 60 %.


title: NimbleGen Nitrosomonas europaea ATCC 19718 [080303_TI228410 60mer expr X4]

status: Public on Oct 23 2009

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Nitrosomonas europaea ATCC 19718

description:
NimbleGen design name 080303 TI228410 60mer expr X4, NimbleGen Catalog Number A7306-00-01.  A 1:2 expression design for 2,368 genes from Nitrosomonas europaea (ATCC 19718) with 4 X 72,000  60-mer 14 probe pairs per gene, with two-fold technical redundancy.
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.

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


title: Adelaide microarray facility Exiqon LNA miRNA microarray_version8.1

city: Adelaide

first: Anna

last: Tsykin

state: SA

address: Frome Road

department: Hanson Institute

institute: SA Pathology

organism:
Arabidopsis thaliana
Saccharomyces cerevisiae
Caenorhabditis elegans
Drosophila melanogaster
Gallus gallus
Macaca mulatta
Homo sapiens
Bos taurus
Mus musculus
Rattus norvegicus

description: The actual (physical) array contains duplicate spots, 1487 x 2 + empty -> 3072 spots

first: Mark

last: van der Hoek

manufacture_protocol: please request from Adelaide microarray facility.


title: Affymetrix GeneChip Dentala520298F

city: Oklahoma City

first: Justin

last: Merritt

state: OK

address: 975 NE 10th St BRC364

department: Oral Biology

institute: University of Oklahoma Health Sciences Center

organism: Fusobacterium nucleatum


title: miRXploreTM microarrays (872)

first: Ute

last: Bissels

description: Each microarray contained a total of 5504 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 2063 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 2063 miRNA sequences covered sequence verified miRNAs of the species human (871) mouse (634) and rat (426) as well as viral miRNAs (132) as deposited in the miRBase sequence database version 12.0. The 97 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (43 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 36 positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 13 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences. Microarrays were manufactured by Miltenyi Biotec. Briefly, 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides in quadruplicates using a customized piezoelectric spotter.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

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


title: PICME Capsicum 10K

city: Seibersdorf

first: Dieter

last: Kopecky

address: Campus Seibersdorf

department: Biogenetics/Natural Resources

country: Austria

institute: Austrian Research Centers GmbH - ARC

organism:
Populus trichocarpa x Populus deltoides
Capsicum annuum
Solanum tuberosum
Ipomoea batatas
Triticum aestivum
Zea mays
Homo sapiens
Pinus pinaster
Populus euphratica
Populus tremula x Populus alba

description:
Support: Corning GAPS II; Coating: Gamma Amino Propyl Silane
Number of spots: 10.800
Number of pins/blocks: 48
Spottdistance in µm: 220
Recurrances spots/slide: 2
Number of spots vertical: 15
Number of spots horinzontal: 15
Vertical offset of first block in µm: 2350
Horizontal offset of first block in µm: 3250

first: Heidemarie

last: Sziderics

first: Ildiko

last: Matusikova

first: Friederike

last: Trognitz

first: Steffen

middle: J

last: Rodewald

first: Silvia

last: Fluch

manufacture_protocol:
Spottingbuffer: 3xSSC+ 1,5MBetain
Spottingplate setting: Biozym 10µl
Arrayer Hardware: GeneMachines Omnigrid II
Arrayer Software: OmniGrid Gridder 2.2.13
Humidity: 40%
Dipping time in sec: 1


title: miRXploreTM microarrays (781)

description: Each microarray contained a total of 3632 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 1479 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 1479 miRNA sequences covered miRNAs of the species human (549) mouse (466) and rat (369) as well as viral miRNAs (95) as deposited in the miRBase sequence database version 10.0. The 97 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (43 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 36 positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 13 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences. Microarrays were manufactured by Miltenyi Biotec. Briefly, 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides in quadruplicates using a customized piezoelectric spotter.


title: Institute of Nuclear-Agricultural Sciences Deinococcus radiodurans 3166 array [condensed version]

status: Public on Oct 22 2009

city: Hangzhou

first: Yuejin

last: Hua

state: Zhejiang

address: 268 KaiXuan Road

country: China

institute: Zhejiang University

organism: Deinococcus radiodurans

manufacturer: The Bioinformatics and Molecular Regulation Laboratory, Zhejiang University

first: Xiaoting

first: Hu

last: Wang

manufacture_protocol: The oligonucleotides designed to represent the respective predicted ORFs of Deinococcus radiodurans ((NC_001263, NC_001264, NC_000958, NC_000959) are synthesized and purified by hydrophobic column on HPLC. The oligonucleotides are deposited on to poly-L-Lysine slide in duplicate. There are 32 blocks on the array. In each blocks there were 18 columns and 17 rows. Details can also be found in (Huan Chen, Guangzhi Xu, Ye Zhao, Bing Tian, Huiming Lu, Xiaoming Yu, Songnian Hu, Yuejin Hua*, A Novel OxyR Sensor and Regulator of Hydrogen Peroxide Stress with One Cysteine Residue in Deinococcus radiodurans, PLoS One, 2008, 3 (2): e1602.)


title: Cornell Cdifficile_630 3.8K Genome array

city: Brookings

first: Joy

last: Scaria

state: SD

department: Veterinary and Biomedical Sciences

institute: South Dakota State University

organism: Clostridioides difficile 630

first: Tavan

last: Tanvilisri

first: Yung-Fu

last: Chang

manufacture_protocol: This array consists of 60mers representing each CDS in Clostridium difficile 630 genome. Probes were designed using Agilent technologies E-array (http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/gp50660.aspx) expression algorithm. One probe was designed for each CDS and each probe was printed in triplicate using Agilent Sureprint technology.


title: Hox Tiling Array Agilent-018523 (ChIP)

city: Kansas City

first: Pengfei

state: MO

address: 1000 E. 50th Street

institute: Stowers Institute

organism: Mus musculus

manufacture_protocol: Mouse hox regions A,B,D were identified and 60-mer probes were created that overlapped by 20 (probes were taken from both strands). The worst 3% of probes were removed to avoid cross-hybridization. Probes were uploaded to agilent using earray (http://earray.chem.agilent.com) and arrays were ordered from agilent. This design is identical to 018680 in all but modified IDs.


title: miRXploreTM microarrays (834)

description: Each microarray contained a total of 5288 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 1977 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 1977 miRNA sequences covered sequence verified miRNAs of the species human (738) mouse (588) and rat (426) as well as viral miRNAs (150) and further mammalian species (75) as deposited in the miRBase sequence database version 10.1. The 97 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (43 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 36 positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 13 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences. Microarrays were manufactured by Miltenyi Biotec. Briefly, 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides in quadruplicates using a customized piezoelectric spotter.


title: IMTSSA/UMR-MD3/UNIVMED - Plasmodium falciparum - 2x11k v1.0

city: MARSEILLE

first: Charles

last: Chapus

address: Allée du Médecin colonel Eugène Jamot

country: France

institute: IMTSSA

organism: Plasmodium falciparum 3D7

first: Daniel

last: Parzy

first: Natalie

last: Wurtz

first: Jérôme

last: Desplans

first: Marylin

last: Madamet

first: Yannick

last: Le Priol

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


title: Sus scrofa Swine Leucocyte Antigen region Tiling Array 385K Nimblegen

city: Jouy-en-Josas

first: Sylvain

last: Marthey

address: Domaine de Vilvert Bat 320

department: Animal Genetics

institute: INRA

organism: Sus scrofa

description: The 385k SLA Tiling Array was designed in both orientations to cover the SLA complex. The sequence from olfactory receptor gene OLF42 to BTNL6 on SSC7 p arm that belong to Class I and III regions was gotten from VEGA database on 16 May 2007 release (http://vega.sanger.ac.uk/Sus_scrofa/index.html) including 1,795,000 nt, and the sequence from centromeric sequences to RING1 on SSC7 q arm that belong to Class II region was gotten from VEGA database on 16 May 2007 release and SBAB BACs including 974,684 nt. The tiling array also covered the sequence belonging to centromeric/pericentromeric region and it was gotten from SBAB BACs, which were derived from a Large White boar homozygous for the H01 haplotype including 241,770 nt.

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: Emory University Custom Breast Cancer DASL Panel

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

organism: Homo sapiens

technology: oligonucleotide beads

first: Brian

middle: R

last: Leyland-Jones

manufacture_protocol:
Sentrix® Array Matrix
The sophisticated Sentrix Array Matrix (SAM) platform is a fiber-optic assembly composed of 96 individual arrays arranged in an 8-by-12 format, matching the well spacing of a standard microwell plate. Each individual array in the matrix holds 1,536 different oligonucleotide probe sequences (IllumiCode sequences), in turn attached to 3-micron beads assembled into microwells at the end of the optical fiber bundle. Because the microwells outnumber probe sequences, multiple copies of each bead type are present in the array. This built-in redundancy further improves robustness and measurement precision. The SAM manufacturing process includes hybridization-based quality control for each array feature, allowing consistent production of high-quality, reproducible arrays.


title: Hox Tiling Array Agilent-018680 (ChIP)

manufacture_protocol: Mouse hox regions A,B,D were identified and 60-mer probes were created that overlapped by 20 (probes were taken from both strands). The worst 3% of probes were removed to avoid cross-hybridization. Probes were uploaded to agilent using earray (http://earray.chem.agilent.com) and arrays were ordered from agilent.


title: Illumina Genome Analyzer (Sulfolobus solfataricus P2)

status: Public on Oct 19 2009

last: GEO

organism: Saccharolobus solfataricus P2


title: NimbleGen Drosophila 385k array rel4 300bp

first: Bas

last: van Steensel

description:
60mer oligo probes
FlyBase release 4.3
Non-repetitive portion of FlyBase release 4.3, 1 Mb high density on arm 2L
Native NimbleGen files (ndf, pos) are linked below as supplementary files.


title: HML L. vannamei 15k cDNA array v1.1

city: Charleston

first: Marine

last: Genomics

state: SC

address: 331 Ft. Johnson Road

institute: Medical University South Carolina

organism: Penaeus vannamei

manufacturer: Hollings Marine Laboratory, Genomics Core

manufacture_protocol: contact spotting of L. vannamei cDNA clones using a Q-ArrayMax (Genetix) machine, baked for 2 h at 80 ºC, and stored under vacuum until used


title: Streptococcus pneumoniae, multi strain 7k version7 (condensed)

status: Public on Oct 18 2009

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

organism: Streptococcus pneumoniae

technology: mixed spotted oligonucleotide/cDNA

description: The Platform data table reflects a condensed representation of the array's replicate features.

manufacture_protocol: ArrayIt superamine slides spotted with a Genpak-array21 spotter.


title: Illumina Genome Analyzer II (Schizosaccharomyces pombe)

organism: Schizosaccharomyces pombe


title: Illumina Genome Analyzer II (NC10 bacterium 'Dutch sediment')

status: Public on Oct 13 2009


title: MacLeod custom equine cartilage 10K cDNA microarray version 3

status: Public on Oct 14 2009

city: Dublin

first: Beatrice

middle: Ann

last: McGivney

state: Dublin

address: Belfield

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

organism: Equus caballus

description: The 9,322 cDNAs spotted on this microarray were obtained from a normalized and subtracted cDNA library generated from the total RNA of articular cartilage from a 15-month old equine Thoroughbred gelding. In addition, cDNAs from 28 plasmids used within the lab were spotted; 2 plasmids have been submitted to GenBank. Positive control spots include Elongation Factor Tu (EFTu) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Negative control spots are Invitrogen oligos from Arabidopsis thaliana genes CAD1 and GAPC. The original negative control soybean genes chlorophyll ab binding protein (CAB - SPOT_ID: ABbinding) and Rubisco small chain 1 (RBS1 - SPOT_ID: Rubisco) were contaminated prior to spotting with Bos taurus cDNA and thus might show hybridization. Other spots might be identified as empty of buffer. Keywords: cDNA, equine, articular cartilage, microarray

manufacturer: W.M. Keck Center, University of Illinois Urbana-Champaign

first: J

middle: N

last: MacLeod

first: M

last: Band

first: Q

last: Sun

last: Mienaltowsk

first: S

last: Coleman

manufacture_protocol: The cDNAs were spotted in 3x SSC buffer supplemented with 1.5 M betaine


title: 3D-Gene Human miRNA Oligo chip v12

city: Kamakura

first: Satoko

last: Takizawa

state: Kanagawa

address: 6-10-1 Tebiro

department: New Frontiers Research Laboratories

country: Japan

institute: TORAY Industries, Inc.

manufacture_protocol: See manufacturer's web site


title: Agilent Eisenia fetida 15K oligo array sense

status: Public on Oct 12 2009

city: Vicksburg

first: Ping

last: Gong

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: US Army ERDC

organism: Eisenia fetida

description:
Arrays of this design have barcodes that begin with 16016423 or 2516423.
Orientation: assuming sense
Features are numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner, i.e., 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, i.e., barcode on the bottom, DNA on the front surface
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions

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


title: Oligo GEArray Human Extracellular Matrix and Adhesion Molecules Microarray OHS-013

status: Public on Oct 09 2009

city: Frederick

first: SuperArray

last: Bioscience Corporation

state: MD

address: Suite 101, 7320 Executive Way

institute: Technical Support

description: Catalog number OHS-013

manufacture_protocol: see manufacturer's web site


title: 454 GS (Chlamydomonas reinhardtii)

organism: Chlamydomonas reinhardtii


title: Yeast Protoarray 082004_YeastProtoArrayKSP

city: Durham

first: Matthew

last: Foster

state: NC

address: Box 2612 Research Dr.

department: Medicine

institute: Duke University

organism: Saccharomyces cerevisiae

technology: spotted peptide or protein

middle: W

first: Michael

middle: T

last: Forrester

first: Jonathan

middle: S

last: Stamler

manufacture_protocol: GST-tagged yeast proteins spotted on glass slide suitable for kinase substrate identification (KSI)


title: 454 GS (Arabidopsis suecica)

status: Public on Oct 08 2009

organism: Arabidopsis suecica


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array [CDF: Hs133P_Hs_REFSEQ_10]

city: Boston

first: Xiaobo

last: Xia

address: 44 Binney St, Mayer 649

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: This is identical to GPL570 but a custom CDF environment (Hs133P_Hs_REFSEQ_10) was used to extract data. The CDF can be found at the link below.


title: 454 GS FLX (Xenopus laevis)

last: GEO

organism: Xenopus laevis


title: 454 GS (Arabidopsis arenosa)

organism: Arabidopsis arenosa


title: Illumina Genome Analyzer II (Xenopus laevis)


title: 454 GS FLX (Xenopus (Silurana) tropicalis)

organism: Xenopus tropicalis


title: AB SOLiD System 2.0 (Rattus norvegicus)

organism: Rattus norvegicus


title: Illumina Genome Analyzer II (synthetic construct)

organism: synthetic construct


title: 454 GS FLX (Rattus norvegicus)


title: Illumina Genome Analyzer (Bacillus anthracis)

organism: Bacillus anthracis


title: AB SOLiD System (Bacillus anthracis)


title: Illumina Genome Analyzer II (Youcai mosaic virus)

organism: Youcai mosaic virus


title: Illumina Genome Analyzer (Xenopus (Silurana) tropicalis)


title: 454 GS (Arabidopsis thaliana)

status: Public on Oct 07 2009

organism: Arabidopsis thaliana


title: Illumina Genome Analyzer (Flock house virus)

organism: Flock House virus


title: Illumina Genome Analyzer II (Pyrococcus furiosus)

organism: Pyrococcus furiosus


title: Campylobacter NCTC 11168 ORF-based array printed at IFR (second type)

city: Norwich

first: Bruce

middle: MacKenzie

last: Pearson

state: Norfolk

address: Colney Lane

department: Food Safety

country: United Kingdom

institute: Institute of Food Research

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

description: Corning barcoded GAPSII slides used

middle: M

first: Kathryn

last: Holmes

manufacture_protocol: PCR product array of ORF's from Campylobacter jejuni subsp. jejuni NCTC 11168. For description of PCR amplification see Pearson et al., FEBS Letters 554(2003) 224-230.


title: Blomberg Lab Pig Pre-implantation Embryo 40K oligo array

city: Beltsville

first: Le Ann

last: Blomberg

address: 10300 Baltimore Ave

department: ANRI

institute: USDA-ARS

organism: Sus scrofa

description:
Agilent-016936 Blomberg Swine
porcine embryo

Arrays of this design have barcodes that begin with 16016936 or 2516936.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

first: LeAnn

first: Lori

last: Schreier

first: Robert

last: Li


title: SMD Print_1597 Macaca mulatta

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism: Macaca mulatta

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: SMD Print_1259 Mycobacterium tuberculosis

organism: Mycobacterium tuberculosis


title: 454 GS (Cocksfoot streak virus)

organism: Cocksfoot streak virus


title: Illumina Genome Analyzer II (Gallus gallus)

organism: Gallus gallus


title: 454 GS (Turnip mosaic virus)

organism: Turnip mosaic virus


title: Illumina Genome Analyzer II (Dictyostelium purpureum)

organism: Dictyostelium purpureum


title: 454 GS FLX (Watermelon mosaic virus)

organism: Watermelon mosaic virus


title: 454 GS FLX (Tomato yellow leaf curl virus)

organism: Tomato yellow leaf curl virus


title: 454 GS FLX (Melon necrotic spot virus)

organism: Melon necrotic spot virus


title: Illumina Genome Analyzer II (Dictyostelium discoideum)

organism: Dictyostelium discoideum


title: Illumina Genome Analyzer (Vitis vinifera)

organism: Vitis vinifera


title: 454 GS FLX (Cymbidium ringspot virus)

organism: Cymbidium ringspot virus


title: Illumina Genome Analyzer II (Pan troglodytes)

organism: Pan troglodytes


title: 454 GS FLX (Pepper mild mottle virus)

organism: Pepper mild mottle virus


title: 454 GS FLX (Potato virus X)

organism: Potato virus X


title: Illumina Genome Analyzer II (Petunia x hybrida)

organism: Petunia x hybrida


title: 454 GS FLX (Cucumber mosaic virus)

organism: Cucumber mosaic virus


title: Illumina Genome Analyzer (Tetrahymena thermophila)

organism: Tetrahymena thermophila


title: 454 GS FLX (Turnip mosaic virus)


title: Illumina Genome Analyzer (Drosophila pseudoobscura)

organism: Drosophila pseudoobscura


title: AB SOLiD System 2.0 (Physcomitrella patens)

organism: Physcomitrium patens


title: Illumina Genome Analyzer (Drosophila simulans)

organism: Drosophila simulans


title: Illumina Genome Analyzer (Physcomitrella patens)


title: Illumina Genome Analyzer (Crassostrea gigas)

organism: Magallana gigas


title: 454 GS FLX (Drosophila melanogaster)

status: Public on Oct 01 2009

organism: Drosophila melanogaster


title: Agilent/FIMM Human 95K Array

status: Public on Oct 05 2009

city: Helsinki

first: Maija

middle: K

last: Wolf

address: Biomedicum Helsinki 2U, Tukholmankatu 8,

country: Finland

institute: Institute for Molecular Medicine Finland (FIMM)

organism: Homo sapiens

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


title: Illumina Genome Analyzer II (Candidatus Kuenenia stuttgartiensis)

organism: Candidatus Kuenenia stuttgartensis


title: VUMC MACF Human 30k oligo v62

status: Public on Oct 06 2009

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

description: hydrophilic polymer containing N-hydroxysuccinimide (NHS) ester reactive groups

manufacture_protocol: The Human Release 2.0 oligonucleotide library, containing 60-mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). The oligonucleotides were dissolved at 10 uM concentration in 50 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink slides (Amersham Biosciences), using an OmniGrid 100 microarrayer (Genomic Solutions, Ann Arbor, MI, USA) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). After printing slides were processed and blocked prior to use according to the manufacturer's protocol.


title: 454 GS FLX (Tobacco rattle virus)

organism: Tobacco rattle virus


title: Barley cell wall microarray

city: Glen Osmond

first: Ute

last: Baumann

address: Hartley Grove

department: Australian Centre for Plant Functional Genomics

institute: University of Adelaide

organism: Hordeum vulgare


title: Atlas Plastic Human 12K Microarray (Cat.#7931-1)

city: Madrid

first: Teresa

last: Bellón

state: Madrid

address: Pº Castellana 261

department: Research Unit

country: Spain

institute: Hospital La Paz

manufacture_protocol: Oligonucleotides were immobilized in duplicate dots on a plastic support by UV radiation


title: Solea senegalensis 5k oligo microarray

status: Public on Oct 02 2009

city: Talence

first: angela

last: tingaud-sequeira

address: avenue des Facultés

institute: Université Bordeaux 1

organism: Solea senegalensis

manufacture_protocol:
10,185 high-quality sequences were obtained from 10 tissue(or stage of development)-specific libraries and were submitted to GenBank (accession numbers: FF281814-FF291996)
The final array design contained 5,087 gene specific Solea senegalensis probes, as well as positive and negative control probes (maize expansin, ZmMYB42, and xyloglucan endo-transglycosylase), a total of 700 per array. These were used to assess detection limits and range, to verify spatial homogeneity, and to determine experimental within-array variation.
Microarray slides, each containing two microarrays, were synthesized by Agilent using ink-jet printing and in situ oligonucleotide synthesis.


title: Washington University School of Medicine Microarray Core Brugia malayi microarray V.2

city: Oshkosh

last: Griffiths

address: 800 Algoma Blvd

department: Biology and Microbiology

institute: University of Wisconsin Oshkosh

organism: Brugia malayi

first: George

last: Mayhew

first: Rebecca

last: Zink

first: Sara

last: Erickson

first: Jeremy

last: Fuchs

last: Christensen

first: Colleen

last: McDermott

first: Michelle

last: Michalski

manufacture_protocol:
The Brugia malayi Version 2 (V.2) array contains 18,153 oligonucleotides, 878 based on W. bancrofti ESTs, 1,016 based on O. volvulus gene indices, 804 from the Wolbachia complete genome, and the remaining 15,455 based on B. malayi ESTs, TIGR gene indices, TIGR gene models, and L3 ESTs.
Oligonucleotide selection:
We patterned our oligo selection algorithm after PICK70 (J. DeRisi, personal communication).  The algorithm utilizes two input files in oligo selection: the first is a fasta format file of all genes to be used for oligo selection and the second is a fasta format file of the entire genome sequence. For the input gene sequences, we bias selection of oligos to the 3’-most 1000 bases of sequence (for genes greater than 1000 bp in length) by pre-masking all sequences upstream of this cutoff.  The initial portion of the oligo selection routine is designed to mask out any repetitive sequence elements or any highly similar portions (e.g. to other genes) of the input gene sequences.  This masking is accomplished by BLAST comparison of genes to genome, using a stringent cut-off to mask out any sequence with 70% or greater similarity to any other sequence in the genome that extends over 66% of the desired oligo length.  Once the input gene sequences are masked, they are subjected to the oligo selection algorithm.  Here, the algorithm examines each sequence one at a time, starting from base number one and looking at the first contiguous 65 bases (or whatever the input desired oligo length is) with respect to the following parameters, in order:
1.Ensures that all of the bases being considered are either A, C, G or T (e.g. no N’s or masked bases are contained in the putative oligo sequence).  If all bases do not conform, the algorithm shifts to base two of the sequence and reiterates the check.
2.If all bases conform, examines the input bases for whether they collectively fall in the desired G/C range of the oligo. If not, the sequence is rejected and the algorithm shifts to base two of the input sequence and reiterates step one, etc.
3.If all bases and the G/C range conform, the algorithm examines the input bases for whether they collectively fall in the desired Tm range of the oligo.  If not, the sequence is rejected and the algorithm shifts to base two of the input sequence and reiterates step one.  The Tm calculation currently used is nearest-neighbor calculation.
For the next series of checks, the algorithm assigns “scores” for the input oligo, rather than outright rejection of non-conforming sequence. The score assigned indicates the relative deviation of the oligo from the desired parameter, where a score of zero means that the oligo conforms to the parameter.
4.If the bases conform to the Tm range desired, then the algorithm examines the oligo for percentage of G/C content across the oligo, using a sliding window.  If any window has a G/C content that deviates from the average G/C content of all windows by more than a specified amount (the default is 10% of the overall oligo Tm) the oligo score is incrementally increased.  This ensures uniformity of G/C content across the oligo.
5.Once the sequence G/C uniformity is scored, the algorithm examines the oligo for homopolymers greater in length than the cut-off length set by the user (we typically stipulate that the same base cannot occur more than 4 times in a row or the oligo score is increased from zero).  The number of homopolymer runs in the oligo greater than the cut-off length and the total number of bases encompassed by these runs is also determined and stored.
6.Once the homopolymer content is assessed, the algorithm calculates secondary structure potential.  This is done using a fasta comparison of the sequence to itself.  The optimal score of the fasta alignment is used here as the score reported for the oligo.  An optimal fasta score of zero indicates no potential for self-annealing.  The optimal score increases as more regions of potential self-alignment are found.  Our examination of many such alignments indicates that oligos with a reverse fasta score lower than 100 lack significant secondary structure.
7.If the algorithm passes through all these checks with the oligo starting at base one of the input sequence, it writes that oligo and its scores to a temporary database and starts over with the next input oligo (bases 2-66 in this example).  The algorithm reiterates over the entire input gene and then passes to the next gene.
8.In some stretches of input sequence, multiple oligos will result that differ by only one base in succession, but all conform to the desired oligo parameters.  In these cases, the algorithm selects the best scoring sequence for all parameters and selects it as the best oligo sequence representing a particular region.
9.In some input genes, the algorithm may not find any oligos within the desired Tm range.  In these cases, the algorithm will lengthen or shorten the oligo length according to the length range input, and re-iterate at each length to determine whether the desired Tm range can be met. If not, the algorithm selects the best oligo that falls outside the range, with the corresponding Tm appearing in the final output file.
10.The final output of the algorithm is a text document containing the optimal oligo for each gene examined, including the oligo names (gene name plus oligo start position as an extension) and sequences, followed by the output of all parameter scores for that sequence (see Appendix for an example).
For genes that do not result in an oligo selection, we manually examine the input sequences and then relax certain algorithmic parameters in order to select an oligo (typically we relax the constraint on similarity in the initial masking step, up to 80% identity). In some instances, no oligo that uniquely represents a gene can be found since no sufficient length of the gene sequence is left unmasked due to gene family similarities at the nucleotide level.
Oligos were synthesized from the consensus sequence of selected clusters (n=3569) by standard methods by Illumina (San Diego, CA). The oligonucleotides (50nM in 3x SSC with 0.75M betaine) were printed in duplicate on MWG Epoxy slides (MWG Biotech Inc, High point, NC) by a locally constructed linear servo arrayer


title: Illumina Genome Analyzer (Listeria monocytogenes)

last: GEO

organism: Listeria monocytogenes


title: EMBL/CodeLink Mouse 0.4K miCHIP v9.2

city: Heidelberg

first: Mirco

last: Castoldi

address: Im Neuenheimer Feld 156

department: Department of Pediatric Oncology, Hematology and Immunology

institute: University of Heidelberg

organism: Mus musculus

description:
miChip array are spotted on CodeLink, GE Life Science, cat. no. 30001100). Codelink glass slides are coated with N-hydroxysuccinimide

NOTE: Probe sequences used in this array are proprietary, belonging to Exiqon.

manufacturer: Array were spotted by the Genomics Core Facility, EMBL, Germany. LNA-modified capture probes were manufactured by Exiqon, Denmark

first: Benes

last: Vladimir

first: Sabine

last: Schimidt

first: Martina

middle: U

last: Muckenthaler

first: Matthias

last: Hentze

manufacture_protocol:
LNA-modified oligonucleotide (Exiqon) capture probes are designed to have a close to uniform Tm of 72 Celsius against their complementary targets. This is achieved by adjustment of LNA content and length of capture probes (miRCURY Array probes, Exiqon, http://www.exiqon.com). A C6-amino linker is added to the 5'-end of all capture probes. The desiccated capture probe set is available in a 384-well plate format. Capture probes are printed onto N-hydroxysuccinimide glass surfaces (Codelink, GE Healthcare Life Science) using the Lucidea Array Spotter (GE Healthcare Life Science).
Additional material required for array preparation:
post-coupling blocking solution [50 mM ethanolamine, 0.1 M Tris (pH 9)], post-coupling washing solution (4 XSSC, 0.1% SDS), a water bath (50 C) and a tabletop centrifuge (Eppendorf, 5810R) fitted with rotor (A4-62) adaptors for microplate carriers or for 50 ml tubes.
miRCURY Array probes (Exiqon) are diluted to a final concentration of 20 uM in 3X printing buffer [(150 mM sodium phosphate (pH 8.5)] prior to spotting. Probe set are spotted on CodeLink, (GE Healthcare Life Science), where slides are printed using the Lucidea array spotter (GE Healthcare Life Science) with 65% humidity and a temperature of 21 C.
Each spot measures about 120 um in diameter with a center-to-center spacing between spots of 300 um. To obtain a reliable read out each capture probe is printed in quadruplicate using a re-dip after four slides. Spotted glass slides are subjected to post processing as recommended by the manufacturer. In brief, CodeLink slides are designed to covalently immobilize amine-modified oligonucleotides for microarrays. However, the reactive groups are moisture sensitive and slides must be stored desiccated, hence the coupling of C6-amino linker oligonucleotides to the surface takes place in a humid environment following printing. Consequently, following printing, arrays are collected and introduced into bottom-sealed racks (e.g. microscope slide racks) that are placed in boxes containing a saturated solution of sodium chloride.
(Note. To prepare a saturated solution of sodium chloride, add as much solid NaCl to water as needed to form a 1 cm deep slurry in the bottom of the box). Boxes are sealed with saran wrap or airtight lids, and stored overnight at room temperature. Next Day, printed arrays are transferred into glass racks and residual reactive groups on the CodeLink surface are inactivated by incubation with post-coupling blocking solution (pre-warmed to 50 C) for 30 min in the water bath (50 C). Then the slides are rinsed twice with deionized water and a third time with post-coupling washing solution (pre-warmed to 50 C) for 30 min on the shaker. Slides are then briefly rinsed with deionized water. Subsequently, the racks are placed into microplate carriers, and centrifuged for 2 min at 1500 rpm.
Ready-to-hybridize slides can be stored for up to 6 month at room temperature in a dessicator.


title: University of Queensland Human SSH19kv4

status: Public on Sep 24 2009

city: St Lucia

first: Rosemarie

middle: Lotte

last: Kryger

state: Qld

address: Sir Fred Schonell Drive

department: Biochemistry

institute: University of Queensland

manufacture_protocol:
1. DNA are arrayed in Greiner 384-well v-bottom (source) plates. Each well contains 0.1ug/ul to 0.25ug/ul
2. Source plates are dried in SpeedVac
3. DNA is resuspended in 6 ul of printing buffer.
4. Source plates are Incubated at room temperature for 30 minutes to aid resuspension of DNA.
5. Source plates are sealed with Corning seals and stored at 4°C
6. Before printing, source plates are centrifuged at 1500 rpm for 5 minutes.
7. Remove seals and cover with plate lids and place source plates for printing in the robotic fixture.
8. After the print run is completed, plates are sealed and stored at 4°C.


title: Tiling Array for TNFa induced genes

status: Public on Sep 19 2007

city: Komaba

first: Shuichi

last: Tsutsumi

institute: The University of Tokyo

first: Tatsuhiko

last: Kodama

first: Hiroyuki

last: Aburatani

first: Sigeo

last: Ihara


title: University of Groningen Bacillus Cereus ATCC14579 11kv1

status: Public on Apr 07 2009

city: Groningen

first: Anne

last: Jong

address: Nijenborgh 7

institute: university of Groningen

organism: Bacillus cereus ATCC 14579

description: Replicates indicated as _rep1 and _rep2

last: de Jong


title: 454 GS (Oryza sativa)

organism: Oryza sativa


title: Illumina Genome Analyzer (Gossypium hirsutum)

organism: Gossypium hirsutum


title: EMBL/CodeLink Human 0.56K miCHIP v9.2

first: Vladimir

last: Benes

manufacture_protocol:
LNA-modified oligonucleotide (Exiqon) capture probes are designed to have a close to uniform Tm of 72 Celsius against their complementary targets. This is achieved by adjustment of LNA content and length of capture probes (miRCURY Array probes, Exiqon, http:// www.exiqon.com). A C6-amino linker is added to the 5'-end of all capture probes. The desiccated capture probe set is available in a 384-well plate format. Capture probes are printed onto N-hydroxysuccinimide glass surfaces (Codelink, GE Healthcare Life Science) using the Lucidea Array Spotter (GE Healthcare Life Science).
Additional material required for array preparation: post-coupling blocking solution [50 mM ethanolamine, 0.1 M Tris (pH 9)], post-coupling washing solution (4 XSSC, 0.1% SDS), a water bath (50 C) and a tabletop centrifuge (Eppendorf, 5810R) fitted with rotor (A4-62) adaptors for microplate carriers or for 50 ml tubes
miRCURY Array probes (Exiqon) are diluted to a final concentration of 20 uM in 3X printing buffer [(150 mM sodium phosphate (pH 8.5)] prior to spotting. Probe set are spotted on CodeLink, (GE Healthcare Life Science), where slides are printed using the Lucidea array spotter (GE Healthcare Life Science) with 65% humidity and a temperature of 21 C.
Each spot measures about 120 um in diameter with a center-to-center spacing between spots of 300 um. To obtain a reliable read out each capture probe is printed in quadruplicate using a re-dip after four slides. Spotted glass slides are subjected to post processing as recommended by the manufacturer. In brief, CodeLink slides are designed to covalently immobilize amine-modified oligonucleotides for microarrays. However, the reactive groups are moisture sensitive and slides must be stored desiccated, hence the coupling of C6-amino linker oligonucleotides to the surface takes place in a humid environment following printing. Consequently, following printing, arrays are collected and introduced into bottom-sealed racks (e.g. microscope slide racks) that are placed in boxes containing a saturated solution of sodium chloride.
(Note. To prepare a saturated solution of sodium chloride, add as much solid NaCl to water as needed to form a 1 cm deep slurry in the bottom of the box). Boxes are sealed with saran wrap or airtight lids, and stored overnight at room temperature. Next Day, printed arrays are transferred into glass racks and residual reactive groups on the CodeLink surface are inactivated by incubation with post-coupling blocking solution (pre-warmed to 50 C) for 30 min in the water bath (50 C). Then the slides are rinsed twice with deionized water and a third time with post-coupling washing solution (pre-warmed to 50 C) for 30 min on the shaker. Slides are then briefly rinsed with deionized water. Subsequently, the racks are placed into microplate carriers, and centrifuged for 2 min at 1500 rpm.
Ready-to-hybridize slides can be stored for up to 6 month at room temperature in a desiccator.


title: EMBL/CodeLink Rat 0.28K miCHIP v9.2

organism: Rattus norvegicus

description:
miChip array are spotted on CodeLink, GE Life Science, cat. no. 30001100). Codelink glass slides are coated with N-hydroxysuccinimide.

NOTE: Probe sequences used in this array are proprietary, belonging to Exiqon.

manufacture_protocol:
LNA-modified oligonucleotide (Exiqon) capture probes are designed to have a close to uniform Tm of 72 Celsius against their complementary targets. This is achieved by adjustment of LNA content and length of capture probes (miRCURY Array probes, Exiqon, http://www.exiqon.com). A C6-amino linker is added to the 5'-end of all capture probes. The dessicated capture probe set is available in a 384-well plate format. Capture probes are printed onto N-hydroxysuccinimide glass surfaces (Codelink, GE Healthcare Life Science) using the Lucidea Array Spotter (GE Healthcare Life Science).
Additional material required for array preparation: post-coupling blocking solution [50 mM ethanolamine, 0.1 M Tris (pH 9)], post-coupling washing solution (4 XSSC, 0.1% SDS), a water bath (50 C) and a tabletop centrifuge (Eppendorf, 5810R) fitted with rotor (A4-62) adaptors for microplate carriers or for 50 ml tubes.
miRCURY Array probes (Exiqon) are diluted to a final concentration of 20 uM in 3X printing buffer [(150 mM sodium phosphate (pH 8.5)] prior to spotting. Probe set are spotted on CodeLink, (GE Healthcare Life Science), where slides are printed using the Lucidea array spotter (GE Healthcare Life Science) with 65% humidity and a temperature of 21 C.
Each spot measures about 120 um in diameter with a center-to-center spacing between spots of 300 um. To obtain a reliable read out each capture probe is printed in quadruplicate using a re-dip after four slides. Spotted glass slides are subjected to post processing as recommended by the manufacturer. In brief, CodeLink slides are designed to covalently immobilize amine-modified oligonucleotides for microarrays. However, the reactive groups are moisture sensitive and slides must be stored desiccated, hence the coupling of C6-amino linker oligonucleotides to the surface takes place in a humid environment following printing. Consequently, following printing, arrays are collected and introduced into bottom-sealed racks (e.g. microscope slide racks) that are placed in boxes containing a saturated solution of sodium chloride.
(Note. To prepare a saturated solution of sodium chloride, add as much solid NaCl to water as needed to form a 1 cm deep slurry in the bottom of the box). Boxes are sealed with saran wrap or airtight lids, and stored overnight at room temperature. Next Day, printed arrays are transferred into glass racks and residual reactive groups on the CodeLink surface are inactivated by incubation with post-coupling blocking solution (pre-warmed to 50 C) for 30 min in the water bath (50 C). Then the slides are rinsed twice with deionized water and a third time with post-coupling washing solution (pre-warmed to 50 C) for 30 min on the shaker. Slides are then briefly rinsed with deionized water. Subsequently, the racks are placed into microplate carriers, and centrifuged for 2 min at 1500 rpm.
Ready-to-hybridize slides can be stored for up to 6 month at room temperature in a dessicator.


title: Illumina Genome Analyzer II (Zea mays)

organism: Zea mays


title: NimbleGen Xylella fastidiosa 2K

status: Public on Oct 03 2009

city: Berkeley

first: Nabil

last: Killiny

address: University of California

department: Environmental science, policy and management

institute: UC-Berkeley

organism: Xylella fastidiosa

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


title: Penn State Physcomitrella SOLiD sequencing

city: University Park

first: Michael

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

organism: Physcomitrium patens

technology: MPSS

description: Processed degradome signatures representing the 5' ends of uncapped, polyA+ mRNAs. AB SOLiD System 2.0

first: Charles

last: Addo-Quaye

first: JoAnn

last: Snyder


title: Nimbelgen Mouse 35K Array

status: Public on Oct 04 2009

city: Bronx

first: Laureen

last: Ojalvo

state: NY

address: Chanin 607, 1300 Morris Park Avenue

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

last: Whittaker

first: John

last: Condeelis

first: Jeffrey

last: Pollard

manufacture_protocol: Details on the manufacture protocol can be found on http://www.nimblegen.com/technology/index.html


title: CSIR Eucalyptus grandis 20060210 15K v1.0

city: Pretoria

first: Eugenia

last: Barros

state: Gauteng

address: Meiring Naude Rd

department: Building 20

country: South Africa

institute: CSIR

organism: Eucalyptus grandis

manufacturer: CSIR and ACGT Microarray Facility, University of Pretoria, Pretoria, South Africa

manufacture_protocol:
1. cDNA clones with no prior sequence information were transferred to Genetix X7022 384-well plates for arraying.
2. Each well contained a final concentration of 20 µM cDNA in 50% DMSO spotting solution (v/v).
3. Between printing runs the plates were stored at -20°C.
4. Prior to printing the plates were incubated at room temperature for 30 min to aid temperature equilibration.
5. Plates were centrifuged at 2000 x g for 5 minutes prior to printing.
6. Printing was performed on the Molecular Dynamics Generation III spotter.
7. Seals were removed and plates placed in the spotter immediately prior to initiating the printing process to prevent unnecessary evaporation.
8. A relative humidity of 50% was maintained in the spotter cabinet during printing runs.
9. Following completion of the printing run, the plates were sealed with a new Abgene adhesive plate seal and stored at -20°C.


title: Illumina/Rockerfeller human 44k array

city: New York

first: Edgar

middle: D.

last: Charles

address: 1230 York Avenue, Box 64

department: Virology and Infectious Disease

institute: Rockefeller University

manufacture_protocol: See manufacturer's website.


title: BIOTEC Penaeus monodon_ReproArray_Printrun2_3

city: Pathumthani

first: nitsara

last: karoonuthaisiri

state: Pathumthani

address: Paholyothin

department: Central

country: Thailand

institute: BIOTEC

organism: Penaeus monodon

first: Nitsara

last: Karoonuthaisiri

first: Kanchana

last: Sittikankaew

first: Rachanimuk

last: Preechaphol

first: Thidathip

last: Wongsurawat

first: Umaporn

last: Uawisetwatthana

first: Sergey

last: Kalachikov

first: James

last: Russo

first: Jingyue

last: Ju

first: Sirawut

last: Klinbunga

first: Kanyawim

last: Kirtikara

manufacture_protocol:
EST Library construction
The P. monodon testes and ovary libraries were previously constructed using a ZAP-cDNA synthesis and cloning kit (Strategene, #200400, La Jolla, CA).  Briefly, cDNAs with fragments length at least 500 bp were cloned into dephosphorylated EcoRI/XhoI-digested Uni-ZAP XR and transfected into E.coli XL1-Blue MRF’.  The resulting lambda library was converted into a pBluescript library by in vivo excision according to the manufacturer’s protocol.  The ovary library was further normalized to remove abundant transcripts.  In addition, subtractive ovary libraries between mature and immature ovaries were successfully constructed (Leelatanawit et al., 2004).
Amplication of cDNAs and microarray construction
Amplification
cDNA inserts were amplified via polymerase chain reactions (PCRs) in 96-well plates using GeneAmp PCR system 9700 (ABI, Foster City, CA).  For the testes library, templates were replicated from cultures grown in 96-well plates containing 160 l liquid 2x YT with 7.5% glycerol and 100 g/ml Ampicilin at 370C, covered with AirPore membranes (Qiagen, #19571, Valencia, CA) while shaking  for 16-18 hrs.  For the ovary library, plasmid stocks (approx. 10 ng each) were used as templates.  A PCR reagent master mix consisting of 0.2mM dNTPs, 1x PCR buffer, 1.5 mM MgCl2, 0.5 mM each primer (LM13F: CAC GAC GTT GTA AAA CGA CGG CCA G and LM13R: CAT GGT CAT AGC TGT TTC CTG T), and 4.5 U Taq polymerase was aliquoted to each well.  The PCR reactions were carried out using the following conditions: denaturation at 940C for 3 min, 35 cycles at the following settings: 940C for 25 sec, 600C for 25 sec, 720C for 3 min, and a final extension of 720C for 7 min.  The resulting amplicons were electrophoretically analyzed on 1% agarose gel prepared in 1x TBE buffer.
Purification
Purification of the amplicons was performed using GF/B filter 96-well purification plates (Whatman, #7700-1303, Florham Park, NJ).  Briefly, equal volumes of binding buffer (7M Guanidine-HCL; 200mM MES Buffer, pH 5.6) and PCR product were thoroughly mixed before transferred to the purification plate and placed under a vacuum manifold.  The bound DNA on the plate was washed with 200 l of 80% ethanol twice under vacuum until dried.  Ethanol trace was further removed by centrifuging at 1,500 rpm for 10 min.  To elute the purified products, a new standard 96-well plate was placed underneath before adding 200 l of water to the purification plate and let stand for 5-10 min before centrifuged at 1,500 rpm for 10 min.  The concentrations and yields of the purified products were assessed by agarose gel electrophoresis and quantified using a spectrophotometer.  A typical yield after purification was 2-4 g per reaction.
The purified PCR products in 96-well plates were air-dried until complete absence of liquid.  The plates were resuspended with 8 l 3xSSC, covered tightly with foil and left in 40C overnight.  The resuspended products were transferred from 96-well plates to 384-well plates, covered tightly with foil left in 40C a day prior to microarray fabrication.
Microarray fabrication
The 4,992 PCR products (1920 and 3072 products from the ovary and testes libraries, respectively) were spotted onto aminosilane UltraGAPS slides (Corning, #40017, Big Flats, NY) using an automatic spotter, SpotArray 72 (PerkinElmer, Waltham, MA).  All arrays contained 16 blocks (4 x 4 configurations) of spots.  Each block had 15 rows and 21 columns.  The fabricated slides were stored in a humidity-controlled cabinet until used.
DNA Sequencing and Analysis of testes library
For the testes library, the purified amplicons from the colony PCR were sequenced unidirectionally using an automated ABI 3730 DNA sequencer (GE Healthcare, Foster City, CA).  Nucleotide sequences were analyzed using ESTplus, an integrative system for comprehensive and customized EST Analysis and proteomic data matching (Pacharawongsakda et al., 2008).  Briefly, the sequences were compared by BLASTX with the GenBank nr database.  Significant probabilities of matched nucleotides were considered when E-value was < 10-5.  Blast2GO was used to analyze gene ontology further.
Microarray Post-Processing
Prior to hybridization, the arrays were post-processed according to the recommended protocol by Corning for UltraGAPS slides.  Briefly, rehydration by passing the slide over water steam for 3 sec and snap drying on a 700C heat block allowed denaturing spotted double-stranded probes to evenly spread within their spotted areas.  The arrays were immobilized by a UV cross-linker before blocking the unused surfaces.  The arrays were immersed in blocking solution (5x SSC, 0.1% SDS, and 0.1 mg/mL BSA) at 420C for 45-60 minutes before washing with 0.1x SSC at room temperature for two times and final rinsing with MiliQ-water for 30 sec.  The arrays were dried by centrifugation at 1,600 rpm for 2 min.
Test Hybridizations
Quality and spot morphology of arrays from different locations from the same and different print-runs were tested using a DNA probe amplified from pBluescript using LM13F and LM13R primers.  The probe was labeled with AlexaFluor® 546 using ARES DNA labeling kit (Invitrogen, #A21667, Carlsbad, CA).  The probe was resuspended in hybridization solution (50% Formamide; 5x SSC; 0.1% SDS; 1 mg/ml Human Placental DNA; 10mM Tris, pH 7.5) and placed onto the post-processed slides.  The slides were hybridized at 420C for 16 hrs before they were washed according to Corning’s protocol.


title: TIGR Potato 10k cDNA array version 3 (condensed version)

city: Madison

first: Lara

middle: Colton

last: Kramer

state: WI

address: 1575 Linden Drive

department: Horticulture

institute: University of Wisconsin - Madison

organism: Solanum tuberosum

manufacture_protocol:
Spotted PCR amplified cDNA array on glass.
This version 3 set includes PCR products amplified from 15264 potato EST clones.
Each PCR product is duplicated on the slide. The number of total spots including empty and controls is 32448. This is a condensed version (duplicates removed) of platform GPL1902.


title: Helmholtz Centre Streptococcus mutans UA159 6k array (uncondensed)

status: Public on Jul 26 2006

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

organism: Streptococcus mutans UA159

description: A condensed version of this array is represented in Platform GPL9332.

manufacturer: Helmholtz Centre for Infection Research, Array Facility

first: Helena

last: Sztajer

first: Georg

last: Conrads

manufacture_protocol:
1957 oligonucleotides were deposited onto CodeLink activated slides (Amersham Biosciences) at a concentration of 25 µM in 1.5 x sodium phosphate buffer in a contact-dependent manner using a MicroGrid TAS II spotter (BioRobotics, Freiburg, Germany). All 50-mers were amino-modified at the 5’-end enabling covalent linkage to reactive ester groups provided by the glass surface. Coupling of DNA was ensured by overnight incubation in a saturated sodium chloride chamber and blocking residual reactive groups was done as recommended by the manufacturer (Amersham biosciences). Until they were used, slides were maintained in a desiccated environment. To ensure complete spotting, SYBR-Green staining of three randomly selected microarrays of each printing batch was performed.
The S. mutans UA159 chip consists of 1952 oligonucleotides probing genes specific for ORFs at genomic scale and five Arabidopsis thaliana sequences served as hybridization controls and were used for grid finding. Altogether, three replicates were immobilized per oligonucleotide and array. Two arrays were placed on one slide.


title: Keasling Lab_In-house spotted 70-mer oligo_E. coli array

city: Emeryville

last: Dahl

address: 5885 Hollis St, JBEI

department: Chemical Engineering

institute: University of California-Berkeley

organism: Escherichia coli

manufacture_protocol:
1.  70-mer oligos (Operon - v.1.0.2) representing each ORF of E. coli were arrayed in 384 well plates, total of 600 pmol in each well.
2.  Oligos were suspended in water to 40 uM, and 5 uL were transferred to a new 384 well plate.
3.  The print plates were dried down in a speedvac and resuspended in 5 uL 3x SSC buffer, the day before printing.
4.  Plates were sealed until just before use to prevent evaporation.
5.  Super Amine 2 substrates (Telechem) were arrayed on a robotic spotter (Gene Machines).
6.  The print run was designed to print each gene on a slide 3 times.
7.  After printing, the print plates were dried in a speed-vac and stored at -80 C for storage.  For future printing, the plates were re-suspended in water.
8.  Printed slides were rehydrated over water and UV cross-linked with 150 mJ/cm2.


title: INRA Vitis vinifera 14k oligo array version 2.0

status: Public on Mar 21 2008

city: Ljubljana

first: Kristina

last: Gruden

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

organism: Vitis vinifera

manufacturer: Montpellier GenomiX, Institut de Genomique Fonctionnelle, France

first: Nancy

last: Terrier

first: Dany

last: Severac

manufacture_protocol:
1. Oligoset Array-Ready Oligo Set™ for the Grape (Vitis vinifera)  Genome Version 1 1.0 (Operon)
2. The Vitis vinifera oligo set were spotted using the Amersham Biosciences Lucidea Array spotter on aminosilane-coated mirror glass slides (7 Star, Amersham Biosciences). Negative and positive control oligo were also printed into 24 different sectors of each slide.
3. After printing, the slides were stored at room temperature in a dessicator.


title: miRNA microarrays (676)

status: Public on Oct 27 2009

city: Bergisch Gladbach

first: Ute

last: Bissels

state: NRW

address: Friedrich-Ebert-Str. 68

department: R&D

institute: Miltenyi Biotec GmbH

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: Each microarray contained a total of 256 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 22 miRNA sequences (standard), 29 different variants of oligonucleoties and 13 controls. All probes were spotted in quadruplicates. The 22 miRNA sequences covered sequence verified miRNAs as deposited in the miRBase sequence database version 10.0. The 29 different variant oligonucleotides were chosen as follows: 9 different oligonucleotide variants for miR-122a and miR-16, including probes with (a) spacer sequences (6, 12 or 18 nucleotides in length named SP6, SP12 and SP18); (b) variants with omitted linker named NO-LINK; (c) dimer (DI) and trimer (TRI) variants and (d) oligo variants with adjusted TM (MELT). Oligo variants with adjusted TM were added for seven further miRNAs besides miR-16 and miR-122a. The 13 controls presented 10 positive and 3 negative controls.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

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