title: Affymetrix Human Gene ST 1.0 Custom RefSeq CDF version 12 [CDF: HuGene10stv1_Hs_REFSEQ]

status: Public on Dec 31 2010

city: San Francisco

first: Jun

middle: S

last: Song

state: CA

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

country: USA

institute: UCSF

organism: Homo sapiens

technology: in situ oligonucleotide

description: Annotation file for the custom RefSeq CDF HuGene10stv1_Hs_REFSEQ from the University of Michigan.

distribution: custom-commercial

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

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


title: Agilent Daphnia magna 4x44k oligonucleotide array

city: Boston

first: Helen

middle: C

last: Poynton

state: MA

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

organism: Daphnia magna

description:
AMDID#:020740
ONLY CLONES OF INTEREST HAVE BEEN IDENTIFIED WITH GENBANK ACCESSION NUMBER.

manufacture_protocol: see manufacturer's website for details: https://earray.chem.agilent.com/earray/


title: Mouse ChIP 2.1M WG-T Set-10 (3 of 10)

city: Worcester

first: Richard

middle: E

last: Baker

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

organism: Mus musculus

description:
cat# 05340659001
NCBI build 36 (mm8)

manufacture_protocol: see manufacturer's website


title: Incyte Genomics Human UniGene 1 9.1K Microarray

city: Catania

first: Vincenza

last: Barresi

address: V.le A Doria, 6

country: Italy

institute: University of Catania

technology: spotted DNA/cDNA

manufacturer: IncyteGenomics, St. Louis, Missouri, USA

manufacture_protocol: Human UniGene 1 Microarray was manufactured by IncyteGenomics (St. Louis, Missouri, USA) and  contains a set of 9128 human cDNA clones corresponding to 8524 unique genes/EST clusters.


title: Agilent-026570 Custom BCM-Beaudet Human 180K V8.1 Superfinal aCGH Array

city: Houston

first: April

middle: Burant

last: Hall

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description:
array Comparative Genomic Hybridization (arrayCGH)
180K array with 30kb backbone coverage and exon by exon coverage for 1714 genes reported to be associated with or cause disease
V8.1 Superfinal
Arrays of this design have barcodes that begin with 16026570 or 2526570.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

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


title: RayBio Homo sapiens 0.1K apoptosis array

city: Newark

first: David

middle: M.

last: Lukac

state: NJ

address: 225 Warren St.; ICPH E350C; PO Box 1709

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers Univ./NJ Medical School

technology: antibody

description:
Principle of the Assay
With RayBio® Human Apoptosis Antibody Array kit, researchers can now simultaneously detect the relative level of 43 apoptosis related proteins in cell lysates. By monitoring the changes in protein levels in different experimental model systems, researchers can study pathway activation without spending excess time and effort in performing immunoprecipitations and/or Western Blotting.
With RayBio® Human Apoptosis Antibody Array kit, each of the capture antibodies is printed on the membranes, and then treated or untreated cell lysate is added into antibody array membranes. After extensive washing, the membranes are incubated with a cocktail of biotin-conjugated anti-apoptotic protein antibodies. After incubation with	HRP-Streptavidin,	 the signals	are	visualized	by chemiluminescence

first: Sophia

last: Spadavecchia

first: Kyla

last: Driscoll Carroll

first: Diana

last: Palmeri

middle: M


title: Mouse ChIP 2.1M WG-T Set-10 (1 of 10)

description:
cat# 05340659001
NCBI build 36 (mm8)


title: Mouse ChIP 2.1M WG-T Set-10 (4 of 10)

description:
cat# 05340659001
NCBI build 36 (mm8)


title: Illumina Genome Analyzer (Tomato yellow leaf curl China virus)

status: Public on Dec 30 2010

last: GEO

organism: Tomato yellow leaf curl China virus

technology: high-throughput sequencing

distribution: virtual


title: Mouse ChIP 2.1M WG-T Set-10 (8 of 10)

description:
cat# 05340659001
NCBI build 36 (mm8)


title: Mouse ChIP 2.1M WG-T Set-10 (5 of 10)

description:
cat# 05340659001
NCBI build 36 (mm8)


title: [RaEx-1_0-st] Affymetrix Rat Exon 1.0 ST Array [CDF: ENTREZG 10]

city: Singapore

first: Chui Sun

last: Yap

address: 8, College Road

country: Singapore

institute: Duke-NUS

organism: Rattus norvegicus

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

relation: Alternative to: GPL6194 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site


title: Mouse ChIP 2.1M WG-T Set-10 (6 of 10)

description:
cat# 05340659001
NCBI build 36 (mm8)


title: Xenopus Gene Expression Microarray (AMADID: 015066)

city: Shizuoka

first: Akinori

last: Ishihara

country: Japan

institute: Shizuoka University

organism: Xenopus laevis

manufacture_protocol: Please see manufacturer's web site.


title: NimbleGen/Broad Puccinia graminis 385k Expression Array

city: Cambridge

first: Christina

middle: A

last: Cuomo

address: 7 Cambridge Center

institute: Broad Institute

organism: Puccinia graminis f. sp. tritici

description:
A Nimblegen custom microarray was designed based on the predicted gene set of Puccinia graminis f. sp. tritici.
NimbleGen design name: 080215_PG_CC_EXP.
NimbleGen design id: 7123.
A custom expression design for 20,228 genes from Puccinia graminis f. sp tritici, based on the first Broad annotation of this genome [Puccinia triticina genome project: http://www.broadinstitute.org/annotation/genome/puccinia_group/MultiHome.html]. Additional probes on the array match 558 ESTs without overlapping predicted gene calls, and 41 wheat and barley genes.

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology.


title: JCVI PFGRC Salmonella typhimurium 6K version 2

city: Dallas

first: Palmy

middle: R

last: Jesudhasan

department: Microbiology

institute: University of Texas Southwestern Medical Center

organism: Salmonella enterica subsp. enterica serovar Typhimurium

technology: spotted oligonucleotide

description:
Microarray: Version 2
Number of Grids: 48
Oligonucleotides Designed:  6780
Replicate Oligo Printings:  2x, 4X, 6X

distribution: non-commercial

first: Suresh

middle: D

last: Pillai

manufacture_protocol: Spot replicates -Some genes are printed 2X, 4X and 6X.


title: Exiqon Human MicroRNA Array [208000V8.1]

city: Xi'an

first: An-Gang

last: Yang

address: No.17,Changle West Road

country: China

institute: Fourth Military Medical University

description:
Product No. = 208000V8.1-208001V8.1-208002V8.1
miRBase Release 8.1


title: HCI Human TReg Chip

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

manufacturer: German Research Centre for Biotechnology (GBF), Array Facility

manufacture_protocol: Amino-modified 50-mer oligonucleotides are printed onto CodeLink activated slides (Amersham) using a MicroGrid TAS II spotter.


title: sciTracer_Staphylococcus_aureus_N315_Scienion2002

status: Public on Mar 11 2013

city: Bonn

first: Peter

last: Sass

state: NRW

address: Sigmund-Freud-Straße 25

department: Institute for Microbiology (IMMIP)

institute: University of Bonn

organism: Staphylococcus aureus subsp. aureus N315

manufacture_protocol: The sciTRACER S. aureus contains 2338 PCR products from all 2593 ORFs in the annotated genome (Ref ID: NC_002745), arranged in unique and second sequences: since the ORFs sizes range from 51 bp (e.g.: 13700427) up to 2kb (e.g.: 13701232), additional second PCR products have been developed. As unique sequences, 2333 PCR products and as second sequences, 333 PCR products are immobilized from which 5 are not in the group of unique gene fragments. All unique products cover 90 % of all ORFs. All PCR fragments are purified, concentration normalized, dissolved in spotting solution and spotted robotically onto modified glass slides. They are represented twice (duplicates) on each array. Controls are usually spotted in the last row of each subarray block forming the control area and comprising controls for spiking and endogenous controls. The SCIENION control set consists of positive, negative and multifunctional elements. All references/controls are spotted in a special pattern enabling functional monitoring of the entire experimental process. The glass slides are processed and ready for hybridization reaction. For easy correlation of gene names to their spot position on the slide the “Spot Identification Pattern-Table” (gal-file) is available. Information source: The genes represented on sciTRACER S. aureus are selected from order requests derived from the University of Würzburg, Infectious Biology Group (Head: Prof. Dr. Jörg Hacker) at the Institut für Molekulare Infektionsbiologie. Generation of sequences: 1. The PCR fragments derive mostly from regions at the last 500 nt from the 3’ end and have an average size of 355 bps. In case that the predicted ORF displayed a size unsuitable for appropriate amplicon generation, the primer design was extended towards flanking regions in order to cover the desired ORF. 2. All selected sequences are designed to provide the highest specificity and display minimal similarity to other mRNA and DNA sequences within the specified host genome. 3. In order to obtain strong and comparable sensitivity and signal specificity, all fragments are designed to feature similar lengths, comparable G/C-contents and optimized melting temperatures. 4. Based on algorithmic and manual revisions of the predicted sequences, the designed PCR fragments are well suited for the generation of highly reliable gene expression data. Quality controls: All sequences are validated in silico and approved by size control and sequence verification. The spot morphology is checked by automated optical control and hybridization of labeled RNA or SyBRGreenI® assay. Functional tests are performed by complex hybridization with labeled reference RNA for each batch. Source Organism: Staphylococcus aureus N 315 (NC_002745, contig BA000018) Microarray mapping: Each SCIENION microarray consists of two regions: the hybridizing region and the identifier region. The identifier region carries a sticker showing the name of the product, the date of production, batch number and the ID of the array. This region also serves to grasp the slide. The DNA microarray is in the center of the hybridizing region. Spot distance and feature size: The spot distance (center to center) is 375 µm. The array size is approximately 54 mm x 18 mm (height x broadness). Each array consists of 48 blocks and each block comprises 12 x 11 spots. These blocks are separated by a blank line and display a defined order. to Product description: The sciTRACER S. aureus contains 2338 PCR products from all 2593 ORFs in the annotated genome (Ref ID: NC_002745), arranged in unique and second sequences: since the ORFs sizes range from 51 bp (e.g.: 13700427) up to 2kb (e.g.: 13701232), additional second PCR products have been developed. As unique sequences, 2333 PCR products and as second sequences, 333 PCR products are immobilized from which 5 are not in the group of unique gene fragments. All unique products cover 90 % of all ORFs. All PCR fragments are purified, concentration normalized, dissolved in spotting solution and spotted robotically onto modified glass slides. They are represented twice (duplicates) on each array. Controls are usually spotted in the last row of each subarray block forming the control area and comprising controls for spiking and endogenous controls. The SCIENION control set consists of positive, negative and multifunctional elements. All references/controls are spotted in a special pattern enabling functional monitoring of the entire experimental process. The glass slides are processed and ready for hybridization reaction. For easy correlation of gene names to their spot position on the slide the “Spot Identification Pattern-Table” (gal-file) is available. Information source: The genes represented on sciTRACER S. aureus are selected from order requests derived from the University of Würzburg, Infectious Biology Group (Head: Prof. Dr. Jörg Hacker) at the Institut für Molekulare Infektionsbiologie. Generation of sequences: 1. The PCR fragments derive mostly from regions at the last 500 nt from the 3’ end and have an average size of 355 bps. In case that the predicted ORF displayed a size unsuitable for appropriate amplicon generation, the primer design was extended towards flanking regions in order to cover the desired ORF. 2. All selected sequences are designed to provide the highest specificity and display minimal similarity to other mRNA and DNA sequences within the specified host genome. 3. In order to obtain strong and comparable sensitivity and signal specificity, all fragments are designed to feature similar lengths, comparable G/C-contents and optimized melting temperatures. 4. Based on algorithmic and manual revisions of the predicted sequences, the designed PCR fragments are well suited for the generation of highly reliable gene expression data. Quality controls: All sequences are validated in silico and approved by size control and sequence verification. The spot morphology is checked by automated optical control and hybridization of labeled RNA or SyBRGreenI® assay. Functional tests are performed by complex hybridization with labeled reference RNA for each batch. Source Organism: Staphylococcus aureus N 315 (NC_002745, contig BA000018) Microarray mapping: Each SCIENION microarray consists of two regions: the hybridizing region and the identifier region. The identifier region carries a sticker showing the name of the product, the date of production, batch number and the ID of the array. This region also serves to grasp the slide. The DNA microarray is in the center of the hybridizing region. Spot distance and feature size: The spot distance (center to center) is 375 µm. The array size is approximately 54 mm x 18 mm (height x broadness). Each array consists of 48 blocks and each block comprises 12 x 11 spots. These blocks are separated by a blank line and display a defined order.


title: Mouse ChIP 2.1M WG-T Set-10 (9 of 10)

description:
cat# 05340659001
NCBI build 36 (mm8)


title: Agilent-024196 Whole Rat Genome Microarray 4x44K (Feature Number version)

status: Public on Dec 06 2010

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: With a focus on well known rat genes and homologues to human and mouse genes with useful annotation, Agilent's Whole Rat Genome Oligo – 4X44K microarray provides researchers with a new tool for modeling human biology in the rat model organism. For researchers, this means they now have access to a microarray made up of relevant content that has been empirically validated by Agilent.


title: Mouse ChIP 2.1M WG-T Set-10 (10 of 10)

last: Baker

description:
cat# 05340659001
NCBI build 36 (mm8)


title: Agilent-026378 Genotypic Designed Candida Glabrata 16K Whole Genome Gene Expression Profiling Microarray

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

organism: Nakaseomyces glabratus CBS 138

first: Raja

last: Mugasimangalam

first: Rohit

middle: N

last: Shukla

first: Shruti

last: Sinha

manufacture_protocol: Refer to www.opengenomics.com


title: OSU-CCC MicroRNA Microarray Version 2.0 [condensed version]

city: Evry

first: stefano

last: cairo

address: 4 rue Pierre Fontaine

country: France

institute: Xentech

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

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


title: Mouse ChIP 2.1M WG-T Set-10 (7 of 10)

first: Richard

description:
cat# 05340659001
NCBI build 36 (mm8)


title: Illumina ratRef-12 v1.5.0.34 expression beadchip

status: Public on Jan 07 2009

technology: oligonucleotide beads

distribution: commercial


title: Mouse ChIP 2.1M WG-T Set-10 (2 of 10)

description:
cat# 05340659001
NCBI build 36 (mm8)


title: University of Gothenburg Rainbow trout 15.5K microarray version 2

status: Public on Aug 22 2011

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

country: Sweden

institute: Chalmers University of Technology

organism: Oncorhynchus mykiss

manufacture_protocol: Probes were designed according to Cuklev et al 2010. Oligonucleotides were then synthesized in situ on one single biochip using the 5’ standard synthesis set for Geniom Instrument (http://www.febit.com/go/en/).


title: NimbleGen Bos taurus UMD3.0 2.1M WG HD CGH

status: Public on May 22 2011

city: Beltsville

first: George

last: Liu

address: 10300 Baltimore Ave

institute: United States Department of Agriculture

organism: Bos taurus

description:
This array was designed based on Btau_UMD3.0.
The Btau_UMD3.1 assembly is identical in almost all respects to UMD3.0. All chromosomes are unchanged. For additional information, see http://www.cbcb.umd.edu/research/bos_taurus_assembly.shtml .
The supplementary file 'GPL11314_Btau_4.0.txt' contains the results of LIFTOVER (default setting) to convert the positions of probes from UMD3.0 to Btau_4.0. About 95% (~2,066,000) of the probes were converted successfully.

manufacture_protocol: Maskless array synthesis was used to construct isothermal arrays. 2.1M high density probes were selected with an approximate probe spacing of 1.2 kb. Probes were synthesized using an isothermal format (Tm = 76°C) and varied in length from 50 to 75 bp.


title: LC_MRA-1002_miRMouse_12.0_080901 [condensed version]

city: DUNDEE

first: Claire

last: Monk

address: James Black Centre, University of Dundee, Dow Street

country: United Kingdom

institute: University of Dundee

description:
Mouse miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 12.0
This array represents a condensed version of GPL8529.

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


title: Agilent/OGT Escherichia coli APECO1 15K

city: Birmingham

first: Chrystala

last: Constantinidou

department: School of Biosciences

institute: University of Birmingham

organism: Escherichia coli APEC O1

manufacture_protocol:
In-situ synthesized 60mer 8x15k oligonucleotide arrays.
Multiple probes per gene designed by OGT were screened by UBEC using RNA and genomic DNA hybridizations. Optimal probe per gene was selected and arrays were synthesized by Agilent.


title: JCVI PFGRC Campylobacter jejuni v2 array designed primarily based on strain 81-176 [full array]

status: Public on Dec 28 2010

city: Ames

first: Haihong

last: Hao

state: IA

address: 1600 Christensen Drive

institute: Iowa State University

organism: Campylobacter jejuni

description:
Microarray Version:2;
Number of Grids:48;
Element Type:70mer Oligonucleotide;
Surface Coating:Aminosilane;
Oligonucleotides Designed:6987;
Replicate Oligo Printings:3x;
Controls:500 Arabidopsis thaliana 70mers

manufacturer: Pathogen Functional Genomics Resource Center

first: Zonghui

last: Yuan

first: Qijing

last: Zhang

manufacture_protocol:
see manufacturer's web site
http://pfgrc.jcvi.org/index.php/microarray/protocols.html


title: Illumina Genome Analyzer II (Callorhinchus milii)

status: Public on Dec 21 2010

last: GEO

organism: Callorhinchus milii


title: HIS/SIBS Human 15K cDNA array

city: Shanghai

first: wentao

last: yang

address: chong qing nan lu #225

department: Institute of Health Science

institute: Shanghai Institute for Biological Sciences,China Academy of Science

manufacture_protocol:
1. cDNA are arrayed in Greiner 384-well Microplates(cat# 784101). Each well contains 50-100 ng/ul cDNA .
2. Incubate at RT for 30 minutes to aid resuspension of cDNA.
3. Shake plates near maximum rotational speed on flat-bed shaker for 1 minute.
4. Centrifuge plates at 2000 rpm for 3 minutes.
5. Remove seals and cover with plate lids. Place in appropriate location of plate cassette. This should be done with first plates just before print run is started to minimize evaporation time before printing.
6. Make sure plates rest behind both holding clips in the cassettes. Push plates back into the cassettes as far as they will go, putting them in the proper position for the server arm.
7. After the print run is completed,the chips are ready for hybridization.


title: Agilent-028081 Human Genome CGH + SNP Microarray (Probe Name version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
028081_D_20100413

Agilent human genome CGH + SNP 420K microarray design, April 2010

Arrays of this design have barcodes that begin with 16028081 or 2528081.

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


title: Agilent-019439 Escherichia coli 15K array (Gene Name version)

status: Public on Dec 29 2010

city: BANGALORE

first: RITESH

last: KUMAR

address: DEPARTMENT OF BIOCHEMISTRY, INDIAN INSTITUTE OF SCIENCE

institute: INDIAN INSTITUTE OF SCIENCE

organism: Escherichia coli

description: Custom Gene Expression E. coli  8x15k (AMADID: 19439)


title: Illumina Genome Analyzer II (Scyliorhinus canicula)

organism: Scyliorhinus canicula


title: BPI Silkworm ncRNA Array

status: Public on Dec 22 2010

city: Nanyang

first: Yunchao

last: Kan

state: Henan

address: Wolong road 1638

institute: China-UK-NYNU-RRes Joint Libratory of insect biology

organism: Bombyx mori

description: Bombyx mori strain Dazao P50

manufacture_protocol: see manufacturer's web site


title: TingM Mouse 1.5K Operon Print 1

city: Chapel Hill

first: June

last: Brickey

state: NC

address: 450 West Drive

institute: UNC

manufacturer: Duke University Microarray Facility (Duke Institute for Genome Sciences & Policy)

manufacture_protocol:
Oligos are arrayed in Greiner 384-well flat-bottom plates. Each well contains 600 pmol of 70-mer oligo.
GeneMachines Omnigrid arrayer is used to spot the oligos
4 replicate oligos spotted per array
16 blocks of spotted oligos, each with 20 rows x 21 columns and feature diameter of 110 microns
Oligos are obtained originally from Operon Biotechnologies, Inc. (Huntsville, AL)


title: DOME_Dsv.halophilus_900_v1

city: Vienna

first: Doris

last: Steger

state: Vienna

address: Althanstrasse 14

department: Department of Microbial Ecology

country: Austria

institute: University of Vienna

organism: Pseudodesulfovibrio halophilus

manufacturer: Department of Microbial Ecology, University of Vienna

first: Alexander

last: Loy

manufacture_protocol: A published 16S rRNA-targeted oligonucleotide probe, DVHO831 (S-*-Dv.h.o-0831-a-A-18, 5’-GAA CCC AAC GGC CCG ACA-3’), synthesized by MWG Biotech (Ebersberg, Germany), was used for microarray spotting. The 5’ end of the oligonucleotide was tailed with 12 dTTPs (T-spacer) and the terminal dTTP was aminated to enable covalent coupling of the oligonucleotide to aldehyde group-coated VSS-25 glass slides (CEL Associates). The probe concentration was adjusted to 50 pmol/µl in 50% dimethyl sulfoxide. Microarrays were printed with a single split pin (MicroSpot 2500, Zinsser Analytic GmbH) using a BioRobotics MicroGrid spotter (Genomics Solutions) at 20°C and greater than 50% humidity. Square arrays of identical spots (approximate diameter 150 µm) were produced (30 x 30 spots). Spotted microarrays were incubated overnight at room temperature in a wet chamber and processed with sodium borohydride, as described previously.


title: UCSF MouseArray1.5

status: Public on Dec 23 2010

city: San Francisco

first: David

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

organism: Mus musculus

manufacture_protocol: Isolation of BAC/P1 DNA. We inoculated 0.1ul of a glycerol stock of BAC or P1 containing bacteria into 5 ml LB media containing chloramphenicol (10 ug/ml) or kanamycin (50 ug/ml) for BACs or P1s, respectively and incubated the cultures overnight (~16 h) at 37 degrees C with agitation at 225 rpm. We prepared larger cultures for DNA isolation, by inoculating 25 ml LB media, containing the appropriate antibiotic with 200 ul of the previously grown overnight culture and incubating in a shaking incubator at 37 degrees C at 225 rpm overnight (~16 h). We monitored bacterial growth by measuring the OD of a 1:10 dilution, which preferably ranged between 0.25 and 0.35 at a wavelength of 600 nm. We used the Qiagen Plasmid Mini kit to isolate DNA, following a modified version of the Qiagen Plasmid Mini Purification protocol. We transferred the 25 ml cultures into 50 ml tubes and centrifuged them for 15 min at 4000 rcf at 4 degrees C to pellet the bacteria. We re-suspended the pellet in Qiagen buffer P1 (1.5 ml), containing RNase A at the manufacturer’s recommended concentration and then added buffer P2 (1.5 ml). We mixed the tubes extremely gently by inversion and incubated at room temperature for 5 min. Then, we added buffer P3 (1.5 ml), again mixed very gently by inversion and incubated on ice for 10 min. We inverted each tube once and centrifuged at 4000 rpm at 4 degrees C until the supernatant became clear (45 to 60 min). We filtered the supernatant through a 35-micron nylon mesh prior to loading onto Qiagen-tip 20 columns, which had been equilibrated following the manufacturer’s protocol. We followed the manufacturer’s protocol for the DNA isolation steps with the exception that the elution buffer QF was heated to 65 degrees C before it was added to the column. After elution, we added 0.56 ml isopropanol to the DNA and incubated overnight at 4 degrees C. We collected the DNA pellet by centrifugation for 45 min at 14000 rpm at 4 degrees C. After aspirating the supernatant, we allowed the pellet to dry in air for at most 30 min before re-suspending the DNA in 50 ul of H2O. We determined the DNA concentration using a fluorometer. The yield typically ranged between 60-100 ng/ul (i.e. 3-5 ug per isolation). To ascertain DNA purity, we digested each BAC (200 ng) with HindIII and electrophoresed the digest through a 0.75% agarose gel. We discarded DNA preparations that showed a significant contamination with host bacterial DNA, seen as a background smear of degraded DNA in the gel. Preparation of BAC/P1 DNA representations by ligation-mediated PCR. We digested the DNA with MseI by incubating overnight at 37 degrees C in a 5 ul reaction containing 1.5 ul DNA (20 to 600 ng), 0.4 U/ul MseI (New England Biolabs), and 0.4x One-Phor-All-Buffer-Plus (Amersham). For ligation of adapters, we diluted 1 ul of each digest to a final concentration of 1 ng/ul with H2O and then mixed 1 ng of the digested DNA with 0.5 ul One-Phor-All-Buffer-Plus (10x, Amersham), 0.5 ul of 100 uM Primer 1 (TAACTAGCATGC), 0.5 ul of 100 uM Primer 2 (5’ aminolinker AGTGGGATTCCGCATGCTAGT) and 5.5 ul H2O. We incubated the mixture at 65 degrees C for 1 min after which we ramped the temperature down to 15 degrees C with a ramp-speed of 1.3 degrees C per minute. When the temperature reached 15 degrees C, we added 1 ul of 10 mM ATP and 1 ul T4-DNA ligase (5 U/ul, Gibco BRL) and continued incubation at 15 degrees C overnight. To initiate the first round of PCR amplification, we added a 40 ul mixture, consisting of 3 ul PCR Buffer 1 (Expand Long Template PCR System, Roche), 2 ul of a mixture of each nucleotide (10 mM) and 35 ul H2O to the ligation reaction. Before we started the PCR program, we incubated the reaction at 68 degrees C for 4 min and then added 1 ul DNA polymerase (3.5 U/ul, Expand Long Template PCR System, Roche). We carried out thermal cycling in a Perkin-Elmer Gene Amp PCR System 9700 block as follows: 94 degrees C for 40 s, 57 degrees C for 30 s, 68 degrees C for 1.25 min for 14 cycles, followed by, 94 degrees C for 40 s, 57 degrees C for 30 s, 68 degrees C for 1.75 min for 34 cycles and 94 degrees C for 40 s, 57 degrees C for 30 s and 68 degrees C for 5 min for the final cycle. We electrophoresed 3.5 ul of the PCR product through a 1% agarose gel to determine the size range of the amplified DNA, which ideally ranged from 100 to 2000 bp. To make the DNA for spotting on the arrays, we carried out a second round of amplification in a 100 ul reaction containing 1 ul of the primary PCR product, 4 uM Primer 2, TAQ-buffer II (1x; Perkin Elmer), 0.2 mM dNTP mix, 5.5 mM MgCl2 (Perkin Elmer), 2.5 U Amplitaq Gold (Perkin Elmer) and H2O. We carried out an initial incubation at 95 degrees C for 10 min in a MJ Research Peltier Thermal Cycler 225, followed by 95 degrees C for 30 s, 50 degrees C for 30 s and 72 degrees C for 2 min for 45 cycles and finally 7 min at 72 degrees C. This reaction yields ~10 ug of DNA, with each fragment containing a 5’ amino linker. Preparation of DNA spotting solutions. We evaporated the amplification reaction (100 ul) to a final volume of 50 ul by incubation at 45 degrees C in a hybridization oven (Techne, Hybridizer HB-1D) for approximately 75 min and then added 2.5 volumes of ice-cold ethanol and 0.1 volumes of 3 M NaOAc to precipitate the DNA. (The use of ethanol precipitation proved superior to isopropanol precipitation.) We inverted the tubes and chilled them at –20 degrees C for 15 min before collecting the precipitate by centrifugation at 1699 rcf for 90 min. We washed the pellets with 70% ethanol (150 ul) and collected them by centrifugation at 1699 rcf for 45 min. We air-dried the pellets for approximately 60 to 90 min and then re-suspended them in 12 ul of 20% DMSO in H2O (~0.8 ug/ul). We transferred the DNA solutions into 864 well microtitre plates for robotic arraying. Previously, we prepared DNA for spotting in 80% DMSO and 0.3 ug/ul nitrocellulose. However, we subsequently evaluated spotting solutions containing various concentrations of dimethyl formamide, formamide or DMSO, with or without nitrocellulose. We determined that nitrocellulose was not required for spotting DNA prepared by PCR using primers with 5’amino linkers and that spotting solutions made with 20% DMSO performed well. We have also generated representations of large insert clones for arraying by using degenerate oligonucleotide primed PCR and by amplification of mixtures of subclones from BACs, but found the ligation-mediated PCR procedure to be superior. Array printing. We used a custom built printer, employing a 4 x 4 array of quartz capillary tubes spaced on 3 mm centers to print ~70-100 μm diameter spots on 130 μm centers. We printed each DNA solution in triplicate to create an array of ~7500 elements in a 12 mm square area. We printed the arrays on chromium coated microscope slides (PTI or Nanofilm) for these studies, but also routinely print the arrays on glass slides (Corning GAPs). We allowed the printed slides to dry overnight, then exposed the slides to UV light (65 mJ) in a UV Stratalinker 2400 (Stratagene). We hybridized to these slides without additional treatment, except for the pre-hybridization slide blocking described below. We found no indication of DNA loss from the spots at any stage of the procedure when we performed hybridization in formamide buffers at 37 °C.


title: Applied Biosystems TaqMan Human MicroRNA A Cards v1.0

status: Public on Dec 16 2010

city: Lausanne

first: Eric

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

organism: Homo sapiens

technology: RT-PCR


title: Human JAK / STAT Signaling Pathway PCR Array

first: Marta

last: Catalfamo

state: Maryland

department: Laboratory of Immunoregulation

institute: NIAID, NIH

description: The Human JAK / STAT Signaling Pathway RT² Profiler™ PCR Array profiles the expression of 84 genes related to Jak- and Stat-mediated signaling. The array represents all known Jak and Stat family members, the receptors that activate them, nuclear co-factors and co-activators associated with the Stat proteins, Stat-inducible genes, and negative regulators of the pathway. Using real-time PCR, you can easily and reliably analyze expression of a focused panel of genes related to the Jak / Stat Signaling Pathway with this array.

manufacture_protocol: see manufacturer's website


title: JCVI PFGRC Campylobacter jejuni v2 array designed primarily based on strain NCTC_11168 [full array]

description:
Microarray Version:2
Number of Grids:48
Element Type:70mer Oligonucleotide
Surface Coating:Aminosilane
Oligonucleotides Designed:6987;
Replicate Oligo Printings:3x;
Controls:500 Arabidopsis thaliana 70mers


title: Agilent-029830 Human Genome CGH + SNP Microarray (Probe Name version)

description:
029830_D_20100817

ISCA plus CGH+SNP 180K Microarray

Arrays of this design have barcodes that begin with 16029830 or 2529830.


title: AB SOLiD System (Tribolium castaneum)

status: Public on Dec 13 2010

organism: Tribolium castaneum


title: Illumina Genome Analyzer II (Leucoraja erinacea)

organism: Leucoraja erinaceus


title: Illumina Genome Analyzer II (Medicago truncatula)

organism: Medicago truncatula


title: Laval/Sirard bovine embryo 3K V3.0

status: Public on Dec 15 2010

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

manufacturer: Marc-André Sirard' laboratory, Laval University.

manufacture_protocol: cDNA was obtained by SSH experiments (Clontech). The substractions were done on embryos from GV stage to Blastocyst stage. Each clone was amplified by PCR, purified, dry-down and resuspended in H20/DMSO(50:50). The clones were spotted using a chipwritter (Virtek) on ultra-glass slides (Corning). The slides were UV treated occording to the manufacturer's protocole.


title: CapitalBio human imsRNA expression profile array

city: Beijing

first: Shunmin

last: He

address: 15 Datun Road, Chaoyang District

department: National Laboratory of Biomacromolecules

institute: Institute of Biophysics, Chinese Academy of Sciences

manufacture_protocol:
A human genome oligonucleotide set consisting of 5’ amino acid-modified 50-mer probes and representing 327 characterized Homo sapiens ncRNAs was synthesized from Invitrogen.

The oligonucleotides were dissolved in EasyArrayTM spotting solution (CapitalBio Corp) at 40M concentration, and printed on PolymerSlide, in which the surface is covered by a thin layer of aldehyde group modified three-dimensional polymer chain (CapitalBio Corp.).


title: Multi-species (Bovine, Mouse, Frog) oocyte 14k array

city: Quebec

first: Eve-Lyne

last: Sylvestre

address: 2440 Boul Hochelaga

organism:
Xenopus laevis
Bos taurus
Mus musculus

description: Bos taurus (clones 1-1249), Mus musculus (clones 1250-2399), Xenopus Laevis (clones 2400-3552).

manufacture_protocol: Pools of total RNA (1 μg) from bovine, mouse and xenopus oocytes and somatic tissues were used for cDNA production. The mRNAs were reverse transcribed, and the cDNAs were amplified using the BD SMART PCR cDNA Synthesis Kit (BD Biosciences, Mississauga, ON, Canada) according to the manufacturer's instructions. The SSH was performed with the PCR Select cDNA Subtraction Kit (BD Biosciences) as described by the manufacturer. Briefly, the pools consisted of oocytes for the tester and  somatic tissues for the driver. The PCR was performed in a ThermoHybaid Hybrid MultiBlock System (Bio-Rad, Mississauga, ON, Canada). The subtracted PCR products generated by SSH were cloned into the TOPO Cloning 5-min PCR Cloning Kit (Invitrogen) and then transformed into DH5-α-T1 Max Efficiency cells (Invitrogen).Purified PCR products were speedvac-evaporated (SPD SpeedVac ThermoSavant), resuspended in a mixture of equal parts 3× SSC (1× SSC: 0.15 M sodium chloride and 0.015 M sodium citrate with dimethyl sulfoxide), and spotted in four replicates on GAPS II glass slides (Corning, Corning, NY) using a VersArray Chip WriterPro robot (Bio-Rad). (bovine: 1076 clones, mouse: 1086 clones, frog:1086 clones). Full detailed procedure is described in : Vallee M,Gravel C,Palin MF,Reghenas H,Stothard P,et al. (2005) Identification of novel and known oocyte-specific genes using complementary DNA subtraction and microarray analysis in three different species. Biol Reprod 73: 63-71.


title: PFGRC Burkholderia mallei/pseudomallei 9.9K oligo array v2

status: Public on Dec 14 2010

city: Maung

first: THANATCHAPORN

last: BARTPHO

state: Khon Kaen

address: 123 Mitthaphap

country: Thailand

institute: Meliodosis Research Center, Faculty of Medicine, Khon Kaen University

organism:
Burkholderia mallei
Burkholderia pseudomallei

manufacturer: Pathogen Functional Genomics Resource Center (PFGRC) at the JCVI

first: Thanatchaporn

last: Bartpho

first: Thidathip

last: Wongsurawat

first: Surasakdi

last: Wongratanacheewin

first: Adel

last: Talaat

first: Nitsara

last: Karoonuthaisiri

first: Rasana

middle: W

last: Sermswan

manufacture_protocol: The array contains a total of 9,826 oligo probes (70-mer) consisting 5,174 oligos from B. mallei, 3,261 from B. pseudomallei 1710b and 1,391 from B. pseudomallei K96243 to which the design target belongs. These oligos correspond to a 100% sequence identity and 100% length hit with the locus given as the design target (more than one locus from different strains used in the design). Oligos are designed based on ORF sequence across all genomes for a given chip. All oligos represent multiple strains and/or species (5,440 ORFs of B. mallei, 5,854 ORFs of B. pseudomallei K96243 and 6,348 ORFs of B. pseudomallei 1710b). Each probe was spotted in duplication. There are more than one oligo from different strains many locus from many strain (the oligos that have multiple hits with 90-99.99 % identity correspond to any locus) that can be used a replicate and they were averaged their target. All arrays contained 48 grids (12 x 4 configurations). Each block has 21 rows and 22 columns. Surface coating is aminosilane. The receipt slides were stored in a humidity-controlled cabinet until used.


title: Agilent-020127 Lactobacillus reuteri 100-23 Agilent 4x44k format

status: Public on Dec 11 2010

city: Oak Ridge

first: Charlotte

last: Wilson

state: Tennessee

address: 1 Bethel Valley Road

department: Biosciences Bldg 1520

country: New Zealand

institute: ORNL

organism: Limosilactobacillus reuteri subsp. rodentium

first: Gerald

last: Tannock

first: Paul

last: O'Toole

manufacture_protocol: Chemical In-situ oligonucleotide synthesis.


title: Agilent-023971 Genotypic designed Custom Bacillus cereus 8x15k gene expression microarray

city: Bangalore

first: Genotypic

last: technology

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

institute: Genotypic Technology

organism: Bacillus cereus

first: Raja

last: Mugasimangalam

first: Rohit

last: Shukla

first: Shruthi

last: Sinha


title: Agilent Caenorhabditis elegans Alternative Splicing 244K Array

city: Toronto

first: Qun

last: Pan

address: 160 College St.

institute: University of Toronto

organism: Caenorhabditis elegans

first: John

last: Calarco

first: Arun

middle: K

last: Ramani

first: Sepand

last: Mavandadi

first: Ying

last: Wang

first: Andrew

last: Nelson

first: Leo

middle: J

last: Lee

first: Morris

last: Quaid

first: Benjamin

last: Blencowe

first: Mei

last: Zhen

middle: G

last: Fraser

manufacture_protocol: 60-mer ink-jet Agilent microarray.


title: Agilent-015067 Canine 4x44K Microarray (Probe Name version)

last: Agilent Technologies

organism: Canis lupus familiaris

description:
Agilent-015067
015067_D_20060913

manufacture_protocol: See manufacturer's website.


title: NimbleGen Soybean 700K CGH array (design 091113_Gmax_RS_CGH_HX3)

city: Saint Paul

first: Robert

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

organism: Glycine max

first: Carroll

middle: P

last: Vance

first: Gary

last: Stacey

manufacture_protocol: Roche 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. Roche 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 786,000 to 4.2 million 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 385,000 to 2.1 million unique probe features are synthesized in a single array.


title: Illumina Genome Analyzer (Paralichthys olivaceus)

status: Public on Dec 10 2010

last: GEO

organism: Paralichthys olivaceus


title: Agilent Technologies Custom microarray (SurePrint G3 Custom CGH, 8 Å~ 60 K)

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

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


title: PICME Oak 20K

status: Public on Dec 09 2010

city: Seibersdorf

first: Dieter

last: Kopecky

address: Campus Seibersdorf

department: Biogenetics/Natural Resources

institute: Austrian Research Centers GmbH - ARC

organism:
Quercus petraea
Quercus robur

description:
This platform represents all slides of Series 1, i.e. 1_1, 1_2, 1_3 and 1_4, which are fully identical in their properties except the lot number.
PICME Oak 20K 1_2 uses lot number: 17508000(Barcode# 139*); 02508000 (Barcode# 138)
PICME Oak 20K 1_3 uses lot number: 17508000(Barcode# 139*); 02508000 (Barcode# 138)
PICME Oak 20K 1_4 uses lot number: 07609000
Support: Corning GAPS II/Amplislide Amine (Genewave); Coating: Gamma Amino Propyl Silane
Number of spots: 19.968
Number of pins/blocks: 48
Spottdistance in µm: 200
Recurrances spots/slide: 1
Number of spots vertical: 21
Number of spots horinzontal: 20
Vertical offset of first block in µm: 1200
Horizontal offset of first block in µm: 3150

manufacturer: AIT - Austrian Institute of Technology GmbH

first: Silvia

last: Fluch

first: Antoine

last: Kremer

first: Christophe

last: Plomion

manufacture_protocol:
Spottingbuffer: 3xSSC+ 1,5MBetain
Spottingplate setting: Biozym 10µl
Arrayer Hardware: GeneMachines Omnigrid II
Arrayer Software: OmniGrid Gridder 2.2.13
Humidity: 50%
Dipping time in sec: 1


title: Bluegnome human Cytochip_1[1].1_4

status: Public on Dec 08 2010

city: Meldola

first: Chiara

last: Molinari

state: FC

address: via Maroncelli 40

department: Bioscience Laboratories

institute: IRST(Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori)


title: hoptag02A, abridged

city: Baltimore

first: Jef

last: Boeke

address: 733 N BROADWAY # 339

institute: Johns Hopkins U

organism: Saccharomyces cerevisiae

description:
Comprehensive array (June 2002) of all 6018 UpTag/DnTag pairs incorporated into deletion constructs in the Yeast Knockout strain collection
Same as GPL1444, but with one gene per table row

manufacturer: Agilent Technologies (no longer available)

first: Daniel

last: Yuan

manufacture_protocol: In-situ synthesis using inkjet printing technology


title: hoptag07A, abridged

description:
Comprehensive array (March 2007) of the sequence TAGs ("barcodes") incorporated into deletion constructs in the Yeast Knockout strain collection
Same as GPL6266, but with one gene per table row

manufacture_protocol: Proprietary "Maskless Array Synthesizer" based on a "Digital Micromirror Device" for light-controlled in-situ oligonucleotide synthesis. See http://www.nimblegen.com/technology/manufacture.html


title: Bluegnome human Cytochip_1[1].1_5


title: Bluegnome human Cytochip_1.1_3


title: Illumina Genome Analyzer (Populus euphratica)

status: Public on Dec 01 2010

organism: Populus euphratica


title: GreenGene/Operon/Galbraith lab Rice 60K Oligo Array

status: Public on Dec 07 2010

city: Suwon

first: Myoung Ryoul

last: Park

address: 126 Suin-ro

country: South Korea

institute: National Institute of Crop Science

organism: Oryza sativa

first: Myoung-Ryoul

first: Ki-Young

last: Kim

first: Benildo

last: Reyes

first: Song-Joong

last: Yun

manufacture_protocol: The 60K Microarray was designed to represent all the genes in rice. In total, 60,727 oligomers were designed from gene-specific regions of both japonica and indica subsp. These include 58,417 from known and predicted genes and 66 randomized DNA. Among these, 2,310 genes were also designed as antisense oligomers. Oligomer sequences were extracted by Qiagen-Operon (Cologne, Germany) based on rice genome information from Beijing Genomics Institute (Yu et al., 2002). Oligomers were synthesized and purified by Qiagen-Operon and spotted on SuperAmine slide using facilities of the Dr. David Galbraith lab at the University of Arizona. A set of Rice 60 K Microarray is composed of 2 slides and has a total of 64,896 spot addresses. Each slide is formatted with 48 (12 × 4) blocks with addresses composed of 676 (26 × 26) spots. Blank spots (4,099) were also included for easy alignment of scanning format. Each oligomer, 70 nucleotides long and average melting temperature of 78℃, was printed in each spot address with a diameter of 100 ㎛.


title: MIT-Gifford-mouse-Hox-244K-v1.0

status: Public on Dec 06 2010

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

organism: Mus musculus

description: Data table annotations based on genome build mm8.

manufacture_protocol: Custom designed 244K 60mer probes. Manufactured by Agilent.


title: Corynebacterium glutamicum ATCC 13032 11K

status: Public on Dec 02 2010

city: Bielefeld

first: Jung-Won

last: Youn

address: Universitaetsstrasse 25

department: Genetics of Prokaryotes

institute: Bielefeld University

organism: Corynebacterium glutamicum ATCC 13032

description:
Degussa (Frankfurt, Germany) as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532
spotted PCR-Fragments
C. glutamicum ATCC 13032, based on the genome sequence entry NC_006958

manufacture_protocol: spotted with amplified PCR-Fragments


title: Montastraea faveolata G2 array

city: Thuwal

first: Christian

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

organism: Orbicella faveolata

first: Shinichi

last: Sunagawa

first: Michael

last: DeSalvo

first: Monica

last: Medina

first: Collin

last: Closek

manufacture_protocol: PCR-amplified clones were printed in duplicate on Poly-L-Lysine coated slides


title: Porphyromonas gingivalis W83 genomic tiling array mapped format

city: Cambridge

first: Tsute

last: Chen

state: MA

address: 245 First Street

department: Microbiology

country: USA

institute: The Forsyth Institute

organism: Porphyromonas gingivalis W83

description: The probe set printed on the array consists of 380,000 unique oligonucleotide sequences. On this particular platform, all the 380k unique probes were mapped to all the matched loci of the reference genome, thus each unique probe sequence may appear multiple times due to the repeated probe sequence found in the genome.

first: Hedda

last: Høvik

first: Wen-Han

last: Yu

manufacture_protocol:
The probes were synthesized on the Nimblgen 385K arrays using Nimblegen's proprietary Maskless Array Synthesizer (MAS) technology.
The probes were designed based on an algorithm published by Høvik & Chen (BMC Bioinformatics. 2010; 11: 82).


title: Bluegnome human Cytochip_v2

first: Chiara

last: Molinari

country: Italy

organism: Homo sapiens


title: Illumina Genome Analyzer (Gossypium barbadense)

last: GEO

organism: Gossypium barbadense


title: NimbleGen human hg18 array (2007-06-15_WiCell_HG18_p14)

status: Public on Dec 03 2010

city: Madison

first: Igor

last: Slukvin

state: WI

address: 1220 Capitol Court

department: Department of Pathology and Laboratory Medicine

institute: University of Wisconsin

description: The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features. The .ndf file, which is linked below as a supplementary file, includes the oligonucleotide sequences.

manufacture_protocol: Customized NimbleGen maskless array synthesis for 60-mer hg18 gene expression array.


title: Eukaryotic gene expression array_Sacchromyces cerevisiae_385K 1-plex arrays

city: Bethesda

first: Eun-Hee

last: Park

address: 6 Center Dr.

department: NICHD

institute: NIH

description:
2006-08-18_TI4932_60mer Catalog design for Saccharomyces cerevisiae (Taxonomy Id: 4932) covering NC_001133, NC_001134, NC_001135, NC_001136, NC_001137, NC_001138, NC_001139, NC_001140, NC_001141, NC_001142, NC_001143, NC_001144, NC_001145, NC_001146, NC_001147, NC_001148, NC_001224. Probes selected for 5868/5869 sequences. Median number of probes/sequence is 20 with an average of 19.98. Each probe will be replicated 3 times on the chip. Probes are randomly distributed over the surface of the array. Unused features have been filled with randomly generated probes of comparable GC content. (cat# A4345001-00-01)
native array description file: 2006-08-18_TI4932_60mer.ndf
native array description file: 2006-08-18_TI4932_60mer.ngd

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


title: Multi-species 1.1K miRNA array

city: Minneapolis

first: Xiaoxiao

last: Zhang

address: 312 Church St. SE

organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

manufacturer: Biomedical Genomics Center Microarray Facility at the University of Minnesota

manufacture_protocol: A miRNA probe set was purchased from Invitrogen, which was designed based on the Sanger miRBase Sequence Database, Release 9.0.  The set contains approximately 1,140 oligonucleotides of 34 to 44 nt long as probes.  They are complementary to C. elegans, Drosophila, zebrafish, mouse, rat, and human miRNAs, and also include a number of internal and negative control probes.  The oligonucleotides were dissolved in 3 x SSC and quadruply printed on Corning® GAPSTM II coated slides  using a BioRobotics Microgrid II spotter


title: Oryza sativa 60-mer Oligonucleotide Platform

city: New Delhi

first: Nandula

last: Raghuram

email: raghuram98@hotmail.com, ravipathak@aol.in, pathakster@gmail.com, navjyoti.chakraborty@gmail.com

state: Delhi

address: Dwarka, Sector -16C

department: School of Biotechnology

institute: Guru Gobind Singh Indraprastha University

first: Ravi

last: Pathak

manufacture_protocol: Both catalog and custom microarrays are manufactured using a proprietary non-contact industrial inkjet printing process, in which oligo monomers are deposited uniformly onto specially-prepared glass slides. This in situ synthesis process prints 60-mer length oligonucleotide probes, base-by-base, from digital sequence files. The precise inkjet process enables the delivery of extremely small, accurate volumes (picoliters) of the chemicals to be spotted.


title: Phalanx OneArray Mouse miRNAs v1.0

city: Houston

first: Guohui

last: Wan

state: TX

address: 7777 Knight Road

department: Cancer Biology

institute: The University of Texas M.D. Anderson Cancer Center

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


title: SMD Print_1329 Saccharomyces cerevisiae

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

institute: Swiss Federal Institute of Technology

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: STv7bEws_MMCC

city: Irvine

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

organism: Salmonella enterica

description: whole slide version of STv7E

first: Steffen

last: Porwollik

first: Pui

last: Cheng

first: Xiao-Qin

last: Xia

manufacture_protocol: custom made Salmonella PCR product array


title: Agilent custom ME and HK design array [9mer]

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

organism: synthetic construct

description: 9mer sequence depicted below is not the sequence represented on the array, but the targeted sequence. Please see the two array design files attached below for array probe sequences.

manufacture_protocol: This protein binding microarray (PBM) involved binding GST-tagged proteins to custom-designed, double-stranded 44K Agilent microarrays in order to determine their sequence preferences. The method is described in Berger et al., Nature Biotechnology 2006.


title: Illumina Genome Analyzer (Rattus norvegicus)

organism: Rattus norvegicus


title: Kluyveromyces lactis ChIP tiling 240k array

city: San Francisco

first: Lauren

last: Booth

address: 600 16th Street, N374

department: Micobiology and Immunology

institute: University of California, San Francisco

organism: Kluyveromyces lactis NRRL Y-1140

description:
Design ID: 018173
GenBank accession numbers: NC_006037-0067042
GenBank release date:  07/2004
Downloaded: 05/2006

manufacture_protocol: see manufacturer's website


title: Applied Biosystems TaqMan human microRNA_Array v1.0 early access

city: NEW-YORK

first: christelle

last: borel

state: NY

address: 14250 madison avenue

department: genetics and genomic sciences

institute: mount sinai school of medicine

manufacture_protocol: see manufacturer's web site


title: CapitalBio Cotton 12K cDNA Array v1.0

city: Nanjing

first: miao

last: weiguo

address: Weigang

institute: Nanjing Agricultural Uiversity

organism: Gossypium hirsutum

manufacture_protocol: as described in CapitalBio Corporation Manual


title: Agilent-023001 Bacillus Subtilis strain 168 43k array

city: Nottingham

first: Panos

last: Soultanas

state: Nottinghamshire

address: University Park

department: School of Chemistry

institute: University of Nottingham

organism: Bacillus subtilis subsp. subtilis str. 168

description:
Agilent DesignID: 023001, Project-0273-001
Universal Bacillus Subtilis array
Arrays of this design have barcodes that begin with 16023001 or 2523001.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

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


title: Miltenyi Biotec miRXplore miRNA Microarray (717)

city: louisville

first: Guy

last: Brock

state: KY

address: 485 E. Gray St

department: Bioinformatics and Biostatistics

institute: University of Louisville

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description:
Mus musculus (ICR).
Each spot occurs in quadruplicate.
Supplementary file 717.HQR contains the metadata describing each spot position on the chip.

manufacture_protocol: protocol according to Miltenyi Biotec


title: Miltenyi Biotec miRXplore miRNA Microarray (653)

description:
Mus musculus (ICR).
Each spot occurs in quadruplicate.
Supplementary file 653.HQR contains the metadata describing each spot position on the chip.


title: NimbleGen/UCL human 388K tiling array

city: London

first: Gareth

last: Wilson

address: 23 Huntley Street

institute: UCL Cancer Institute

description:
Annotation from NCBI human build 36.
Tiling of various regions on NCBI human build 36 (hg18), including selected regions designated as controls by the customer. Probes (control and experimental) selected from hg18_tiling at int50win25.  Mean probe spacing at 74bps for both sets.

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


title: ICGEB_Homo sapiens_35K_operon oligo_ver4.0

first: Shahid

last: Jameel

address: Aruna Asaf Ali Marg

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

manufacturer: Department of Biomarker Discovery, PLSL, Mumbai

manufacture_protocol:
Oligos are arrayed in Greiner 384-well flat-bottom plates. Each well contains 600 pmol of 70-mer oligo.
Before printing, add 40 µL of 50% DMSO to each well.
Seal plates with Corning seals.
Incubate at 37°C for 30 minutes to aid resuspension of DNA.
Shake plates near maximum rotational speed on flat-bed shaker for 1 minute.
Centrifuge plates at 2000 rpm for 3 minutes.
Remove seals and cover with plate lids. Place in appropriate location of plate cassette.
Printed with 48 SMP3 pins on aminosilane slides under 50% RH and 25 degree centigrade


title: Cribi Mouse Operon v1.1 13.4K

status: Public on Oct 29 2009

city: Chieti

first: Rosa

last: Mancinelli

state: Chieti

address: via Dei Vestini 29

department: Dept. Basic and Applied Medical Sciences

institute: University "G. d'Annunzio" Chieti-Pescara, Chieti

description: Mouse oligonucleotide array consists of 13,443 70mer oligonucleotides (Operon version 1.1)

manufacture_protocol: Details of the design of the slide and sequence selection can be found at the manufacturer’s website (http://microcribi.cribi.unipd.it/e-index.htm)


title: Agilent-020623 Dinoroseobacter shibae DFL 12 15k Oligo Microarray (Feature Number version)

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

organism: Dinoroseobacter shibae DFL 12 = DSM 16493

description: Custom array.


title: NCI Mouse MMEB Array [Mm-MEEB-V1.2p18]

city: Augusta

first: Kebin

last: Liu

state: GA

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Medical College of Georgia

manufacture_protocol: see NCI Microarray Core Facility website https://madb.nci.nih.gov/


title: Agilent Escherichia coli 15K array

status: Public on Jun 20 2009

city: Mumbai

first: Shamlan

last: Reshamwala

address: Powai

institute: Indian Institute of Technology Bombay

organism: Escherichia coli

manufacture_protocol: Agilent's E. coli Custom Array (8*15k)(AMADID: 19439).


title: GGSIU Agilent 4x44k Array

status: Public on Dec 31 2008

first: Nandula

last: Raghuram

organism: Oryza sativa

first: Ravi

last: Pathak

last: raghuram

manufacture_protocol: 60-mer technology


title: CEINGE_Exiqon_Human miRNA Microarray [208002V8.1]

status: Public on Sep 10 2008

city: Baronissi (SA)

first: Rosanna

last: Martinelli

address: Via Allende

department: Medicine and Surgery

institute: Salerno University

description:
Exiqon design 208002V8.1 Lot: 20393.03
http://www.exiqon.com

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


title: Stanford Affymetrix Caulobacter crescentus 16.6K CauloHi1

status: Public on Mar 10 2010

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

organism: Caulobacter vibrioides

manufacture_protocol: This is a custom commercial array designed by Affymetrix and the Harley McAdams and Lucy Shapiro Labs at Stanford University using the Caulobacter crescentus strain CB15 genome annotation of 2001 (Proc Natl Acad Sci USA. 98:4136-4141).  The construction of this Affymetrix GeneChip has been described by McGrath et. al., 2007. Nat Biotechnol. 25:584-592.


title: Arborea spruce 11K cDNA microarray

city: Edmonton

first: Chelsea

last: Ju

state: Alberta

address: CW 405, Biological Sciences Centre

department: Biological Sciences

institute: University of Alberta

organism: Picea glauca

manufacturer: Project Arborea, Centre d'Etude de la Foret, Université Laval, Québec, Québec, Canada

first: Nathalie

last: Pavy

first: Brian

last: Boyle

first: Colleen

last: Nelson

first: Charles

last: Paule

first: Isabelle

last: Giguère

first: Sébastien

last: Caron

first: Lee

middle: S

last: Parsons

first: Nancy

last: Dallaire

first: Frank

last: Bedon

first: Hugo

last: Bérubé

first: Janice

last: Cooke

first: John

last: Mackay

manufacture_protocol: The 11K microarray was designed based on the white spruce (Picea gluca [Moench.] Voss) expressed sequence tag (EST) assembly. This assembly comprised 16600 unique contigs sequenced from 17 cDNA libraries, which represented different tissues at a diverse developmental stages and growing conditions.  10400 nonredundant sequences were selected and printed as double, side-by-side on the microarray slide with 4X12 subgrid layout and 132 spots per subgrid.  Details of the microarray manufacture and quality control are described in Pavy et al. (2008) (PMID 18811621).


title: WJC hsa mmu miRNA v7.1 01

status: Public on Feb 27 2008

city: Copenhagen

first: Mads

last: Bak

address: Blegdamsvej 3

country: Denmark

institute: University of Copenhagen

organism:
Homo sapiens
Mus musculus

manufacturer: Wilhelm Johannsen Center for Functional Genome Research, University of Copenhagen

first: Sakari

last: Kauppinen

first: Niels

last: Tommerup

first: Mette

last: Christensen

first: Asli

last: Silahtaroglu

manufacture_protocol:
Locked nucleic acid modified oligonucleotide probes were purchased from Exiqon.
Probes were dissolved in printing buffer (150 mM sodium phosphate, pH 8.5) to a final concentration of 25 µM and printed in quadruples onto CodeLink slides (GE-Healthcare) using a MicroGridII (Biorobotics) at 50 % relative humidity. Printed slides were post-processed according to the slide manufacturer's instructions.


title: CodeLink™ UniSet Mouse 20K I Bioarray

status: Public on Oct 12 2007

city: Seoul

first: Min Joo

last: Lee

address: Hyochangwon-gil 52, Yongsan-ku

department: Department of Biological Science

institute: Sookmyung Women's University

organism: Mus musculus

first: M

first: E

last: Park

first: J


title: E. coli K12, Sakai and EDL933 genes (MGW oligonucleotide)

status: Public on Nov 13 2008

city: Montreal

last: Faucher

state: QUEBEC

address: C.P. 6128 Succ. Centre-Ville

department: Microbiology and Immunology

institute: University of Montreal

manufacturer: Genomics Core Facility, National Microbiology Laboratory, Canadian Science Centre for Human and Animal Health, Public Health Agency of Canada.

manufacture_protocol: Oligo set used is the E. coli O157 set commercially provided by MWG-Biotech and supplemented with 104 additional oligos requested by Vic Gannon's group. All were 50'mers resuspended in fresh 50%DMSO to a final concentration of 50uM using a Biomek 2000 robotic liquid handler (Beckman Coulter Inc). Print plates were sealed and stored at -20C when not in use. Prior to printing arrays the oligo plates were allowed to come to room temperature then heated for 5min at 60C. Once cooled they were centrifuged for 3min at 3000rpm to collect all liquid prior to arraying. Arrays were printed on Corning UltraGAPS slides using Telechem SMP3 pins in a BioRad ChipWriter Pro arrayer. Arrays were printed at room temperature (21-23C) and at 58-60% relative humidity. Arrays were printed with 24 pins in a 4x6 arrangement such that each subgrid contains 18x16 spots with an interspot distance of 245 microns centre to centre and a spot diameter of 100 microns. Duplicate supergrids were created lengthwise across the slide so that two spots per oligo exist at separate locations on the array. When spotting was complete, the chamber humidification was turned off and the arrays were allowed to "dry" in the print chamber for a minimum of 6 hours. The slides were then cross-linked at 600mJ and packaged in the original slide holders that they were received in from Corning. For shipping, arrays were packaged with dessicant in foil heat sealed bags.


title: JCVI PFGRC Staphylococcus aureus 16K v9 array designed primarily based on strain USA300

status: Public on Jul 01 2010

city: Rockville

first: PFGRC

last: JCVI

state: MD

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Staphylococcus aureus

description: This set includes 4528 oligonucleotides, has 16416 spots distributed in 48 blocks.

manufacture_protocol: 9QSA, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: NimbleGen Homo sapiens HG18 60mer expr 4plex (4x72k)

status: Public on Jul 31 2009

city: Madison

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Homo sapiens

description: This is a whole human genome array in 4-plex format provided by nimblegen. See manufacturer's website at http://www.nimblegen.com/.

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


title: Hitachisoft AceGene Human Oligo Chip 30K 1 Chip Version

status: Public on Jun 18 2004

last: Hitachi Software Engineering Co.

country: Japan

institute: Hitachi Software Engineering Co., Ltd.

manufacture_protocol: see manufacturer's web site