title: NimbleGen/RIKEN Aspergillus fumigatus 4x72K array

status: Public on Jun 30 2010

city: Wako

first: Takayuki

last: Motoyama

state: Saitama

address: 2-1 Hirosawa

country: Japan

institute: RIKEN

organism: Aspergillus fumigatus Af293

technology: in situ oligonucleotide

description:
Species: Aspergillus fumigatus
Strain: Af293
Type of array: Eukaryotic Expression(4plex)
Number of targets: 9,887
Length of probes: 60-mer
Number of probes per target: 7 pairs
Replicate: 1

Oligonucleotide sequences are available in the '2009-01-07_RDKK143_Afum_60mer_expr.ndf' supplementary file.

distribution: custom-commercial

first: Hiroyuki

last: Osada

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


title: Chiton 4x2K array

status: Public on Jun 25 2010

city: Pacific Grove

first: Luke

last: Gardner

state: California

address: 120 Ocean View Blvd, Hopkins Marine Station

country: USA

institute: Stanford University

organism: Liolophura hirtosa

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


title: ISU_Minion_Mhyo_IG-oligo_v1.0

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

organism: Mesomycoplasma hyopneumoniae

technology: spotted oligonucleotide

distribution: non-commercial

manufacturer: Chris Minion Laboratory at Iowa State University

first: F

middle: C

first: Stuart

middle: W

manufacture_protocol: Probes were designed for the intergenic regions of Mycoplasma hyopneumoniae. Intergenic regions were defined as noncoding DNA sequences between annotated genes in the M. hyopneumoniae genome sequence (GenBank accession # AE017332). Intergenic regions larger than 50 bp were considered for analysis, and those between 125-450 bp were considered for PCR-based probes. Oligonucleotides were designed for some intergenic regions based on the inability to produce PCR products or the length of the region (50-125 bp). Oligonucleotides ranged in size from 50 to 60-mers and were synthesized by Integrated DNA Technologies, Inc. (IDT, Coralville, IA). Oligonucleotides were resuspended to 100 pmol/μl in nuclease free water and then 9 μl were vacuum dried and diluted to 30 μM in IDT Epoxide spotting buffer. These oligonucleotides were spotted to Corning Epoxide substrates in triplicate.


title: Plant virus detection microarray

city: Beijing

first: Yongjiang

last: Zhang

country: China

institute: Chinese Academy of Inspection and Quarantine

organism:
Sobemovirus
Carlavirus
Capillovirus
Potexvirus
Potyvirus
Tobamovirus
Comovirus
Nepovirus
Tobravirus
Cucumovirus
Ilarvirus
Pomovirus
Orthotospovirus

description: 70mer probes were designed to detect plant viruses infection in genus level. This microarray platform is able to detect 169 plant virus species of 13 virus genera.

first: Jun

last: Yin

first: Shuifang

last: Zhu

manufacture_protocol: The 70-mer oligonucleotide arrays were synthesized on 75-mmx25-mm glass slides using a SmartArrayer system (CapitalBio, China). All probes were spotted three times on the microarray. The reverse complementary sequences of the Capillovirus and Tospovirus probes were synthesized to analyze the probe strand effect. Three types of control probes were spotted. The 5¡¯ amino-linker oligonucleotide (5¡¯- TTTTTTTTTTTTTTTCTCATGCCCATGCCGATGC -3¡¯) was used as the positive control. This positive control was a random sequence which did not hybridize with any virus sequences. It was mixed with the samples before hybridization, and used to monitor the hybridization of the microarray. The spotting buffer was used as the negative control. The internal control was 5¡¯ Hex-linker oligonucleotide (5¡¯- GTCACATGCGATGGATCGAGCTCCTTTATCATCGTTCCCACCTTAATGCA -3¡¯). The internal control was spotted on the microarray to monitor the ligation of probes to the chips. Spotted slides were air dried for 10 min and then fixed by UV exposure at 240mJ/cm2. After being incubated in a 0.5% sodium dodecyl sulfate solution at 60¡æ for an hour, slides were rinsed in 100 mM Tris (pH 8.0) for 5 min, and kept moist at 4¡æ for use.


title: Agilent-022820 Homo sapiens 44K TET2 and 7q

city: Salisbury

first: Andy

last: Chase

address: Salisbury District Hospital

country: United Kingdom

institute: Wessex Regional Genetics Laboratory

organism: Homo sapiens

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


title: DGRC-Drosophila melanogaster-DGRC1-15552 15k cDNA array_v5

status: Public on Jun 24 2010

city: Guangzhou

first: TIAN

last: TANG

address: Xingangxi Rd. #135

institute: Sun Yat-Sen University

organism: Drosophila melanogaster

technology: spotted DNA/cDNA

manufacturer: Drosophila Genomics Resource Center (DGRC)

manufacture_protocol: DGRC-1 amplicon transcriptome microarrays are spotted with DNA fragments amplified from genomic DNA of the Oregon R strain of Drosophila melanogaster using gene-specific oligonucleotide primer pairs made by Incyte Genomics. The primers were designed against release 1 of the annotated genome sequence and were selected to amplify fragments which have minimal sequence similarity to other genes, size range between 100-600 bp, and location biased towards the 3'-end of transcripts. The array also contains the following controls: a ubiquitously expressed gene (actin 5C), a spotting buffer-only control (3XSSC plus 1.5M Betaine), exogenous(non-Drosophila) probes (7 from Arabidopsis and 8 Ambion array control PCR spots from bacteria that can be used with spiking RNAs), and three exogenous markers: GAL4, lacZ, and FLP. The DGRC arrays are printed using an Omnigrid 300 contact-printing instrument and 48 silicon split-pins on Corning GAPS II slides.


title: AB SOLiD System (Saccharomyces cerevisiae)

status: Public on Jun 22 2010

last: GEO

organism: Saccharomyces cerevisiae

technology: high-throughput sequencing

distribution: virtual


title: Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Hs133P_Hs_UG_8.cdf]

city: Melbourne

first: Victoria

middle: Mary

last: Perreau

state: Victoria

address: Parkville

department: Center for Neuroscience

country: Australia

institute: University of Melbourne

description: This array is identical to GPL570, but a custom, remapped CDF environment is used to extract data. The CDF file (Hs133P_Hs_UG_8.cdf) was created by the Microarray Lab at the Molecular and Behavioral Neuroscience Institute at the University of Michigan.

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


title: Illumina Genome Analyzer II (Geobacter sulfurreducens PCA)

organism: Geobacter sulfurreducens PCA


title: BCCRC 27K SMRT array

status: Public on Jun 26 2010

city: Vancouver

first: Ivy

last: Tsui

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre


title: Affymetrix Human Genome U133 Plus 2.0 Array [individual probe level version]

city: Turku

first: Henna

last: Kallionpää

address: P.O. Box 123

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

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

Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts
All probe sets represented on the GeneChip Human Genome U133 Set are identically replicated on the GeneChip Human Genome U133 Plus 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz Golden-Path human genome database (April 2001 release).
In addition, there are 9,921 new probe sets representing approximately 6,500 new genes. These gene sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from the UniGene database (Build 159, January 25, 2003) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the NCBI human genome assembly (Build 31).

This platform represents all the individual probes (not probesets) on the Affymetrix Human Genome U133 Plus 2.0 Array. Individual probes are named with the probeset ID (AFFY_ID) plus the number of the probe.

distribution: commercial

relation: Alternative to: GPL570 (ProbeSet Version [official])

manufacture_protocol: see manufacturer's web site


title: ISU_Minion_Mhyo_IG_v1.0

description: Corning UltraGAPS substrates (catalog #40016)

manufacture_protocol: Probes were designed for the intergenic regions of Mycoplasma hyopneumoniae. Intergenic regions were defined as noncoding DNA sequences between annotated genes in the M. hyopneumoniae genome sequence (GenBank accession # AE017332). Intergenic regions larger than 50 bp were considered for analysis, and those between 125-450 bp were considered for PCR-based probes. PCR primers were designed using the Primer3 online software program. PCRs were performed in 96-well plate format in a MJ Research Dyad thermocycler (Bio-Rad Laboratories, Inc. Waltham, MA) in 100 μl reactions using the following conditions: 1X MgCl2-free PCR buffer (Invitrogen); 3.5 mM MgCl2; 0.2 mM each dATP, dTTP, dGTP, and dCTP (NEB); 200 pmol of each primer (IDT); 2 units Taq polymerase (Invitrogen); and 100 ng M. hyopneumoniae strain 232 chromosomal DNA obtained via phenol-chloroform extraction. Thermocycler conditions started with a denaturation at 95ºC for 5 minutes followed by 30 cycles of denaturation at 94ºC for 1 minute, annealing at 56ºC for 1 minute, and elongation at 68ºC for 30 seconds and ending with a final elongation at 68ºC for 10 minutes. Products were confirmed by 1.2% agarose gel electrophoresis and purified via Mobio’s UltraClean PCR Clean-Up Kit according to manufactures protocol. Purified PCR products were quantified by visual inspection, dried via vacuum centrifugation, and resuspended to approximately 200 ng per μl in Corning spotting buffer (Corning). Products suspended in spotting buffer were electrophoresis in 1.2% agarose gels to confirm purity and concentration of each product. The PCR product microarrays were spotted to Corning UltraGAPS glass substrates in triplicate by the University of Iowa DNA facility.


title: WashU-Virgin gHV68 44k v1.0

status: Public on Jun 28 2010

city: St. Louis

first: Steven

last: Johnson

state: MO

address: 660 S. Euclid

department: Department of Pathology and Immunology

institute: Washington University-School of Medicine

organism: Murid gammaherpesvirus 4


title: Agilent Whole_genome_Podospora anserina_v.2_4X44K (oligonucleotides microarray development)

city: Orsay

first: Frederique

last: Bidard

address: Bâtiment 400

department: SIGNAL TRANSDUCTION, REPRODUCTION & DEGENERATIVE PROCESSES

country: France

institute: Institut de Génétique et Microbiologie UMR 8621

organism: Podospora anserina

description:
Podospora anserina Oligonucleotide Microarray by Agilent Technologies. Intermediate microarray with 4 different probes per CDS used to select one probe per CDS to develop a custom expression microarray. Barecodes of arrays with this design are 251636610001 to 251636610005.
See Podopora anserina database's web site at http://podospora.igmors.u-psud.fr/padb/index.php

first: Sandrine

last: Imbeaud

first: Nancie

last: Reymond

first: Robert

last: Debuchy

first: Herve

last: Delacroix

first: Veronique

last: Berteaux

first: Olivier

last: Lespinet

first: Philippe

last: Silar

first: Corinne

last: Clavé


title: Illumina Genome Analyzer II (Trypanosoma brucei)

organism: Trypanosoma brucei


title: PIQOR (TM) Immunology Microarray, human, antisense (614) 1.1K

status: Public on Jun 27 2010

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

country: Germany

institute: Miltenyi Biotec GmbH

description: The PIQOR (TM) Immunology Microarray is composed of 1076 human specific cDNAs. These cDNAs include for each array four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer, respectively. All features are spotted in quadruplicate. The Platform data table reflects a condensed representation of the quadruplicate features.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

manufacture_protocol: Defined 200-400 bp fragments of selected cDNAs were generated by RT-PCR, cloned and sequence-verified. Amplified and purified cDNA inserts were spotted in quadruplicate on PIQOR slides using a proprietary piezoelectric spotter. The PIQOR slides were coated in a 2 step process generating a surface which covalently binds DNA molecules.


title: [Canine] Affymetrix Canine Genome 1.0 Array

status: Public on Jul 12 2006

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Canis lupus familiaris

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

Array has been discontinued by Affymetrix

first: Caroline

last: Ojaimi

first: Khaled

last: Qanud

first: Thomas

middle: H

last: Hintze

first: Fabio

middle: A

last: Recchia

manufacture_protocol: Probe sets for over 21,700 transcripts provide comprehensive coverage of the Canis familiaris genome. Sequence information for the GeneChip Canine Genome Array includes public content from GenBank® (release 137.0, August 2003), dbEST (October 2003), and proprietary beagle sequence content licensed from LION bioscience AG. LION bioscience sequence information was derived from sequences in cDNA libraries for the following eleven tissues: testis, ovary, brain, embryo, liver, spleen, kidney, muscle, aorta, uterus, and jejunum.


title: UCSD Nimblegen Geobacter sulfurreducens 381K Tiling Array 2007 (ORF)

city: La Jolla

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

description: NimbleGen design name 2007-10-02_Gsulf_Palsson_Tiling, NimbleGen design ID 6481.  A tiling array design for Geobacter Sulfurreducens PCA with 50-mer probe spaced 20bp apart across the genome.  This design also contains control probes.


title: PIQOR (TM) Rheuma Microarray, human, antisense (469) 0.9K

description: The PIQOR (TM) Rheuma Microarray is composed of 906 human specific cDNAs. These cDNAs include for each array four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer, respectively. All features are spotted in quadruplicate. The Platform data table reflects a condensed representation of the quadruplicate features.


title: Pfu gamma array v1.0

status: Public on Sep 01 2006

city: College Park

first: Jocelyne

last: DiRuggiero

state: MD

address: 3221 H.J. Patterson Hall

department: Cell Biology and Molecular Genetics

institute: University of Maryland

organism: Pyrococcus furiosus

first: Todd

last: Lowe

first: Ernest

last: Williams

manufacture_protocol: The P. furiosus full-genome microarray represented 2065 protein encoding genes. DNA fragments for spotting were produced by PCR. The array was constructed by designing oligonucleotide primers to span the most unique portions of each gene, averaging 350 nucleotides in length. A custom Perl program was written to select primers with the most desirable thermodynamic conditions possible for each gene using the Whitehead Institute's Primer3 program (version 3.09) as its core analysis engine. The polymerase chain reaction was performed in 100 µl reactions with 1µM of each primer, 2mM MgCl2, 1.0 mM dNTPs, 1.75 U AmpliTaq DNA polymerase (Applied Biosystems, Foster City, CA) 1x AmpliTaq buffer, and 20ng genomic DNA for 30 cycles (94°C 30 sec, 50°C 1 min, 72°C 2 min). All PCR products were checked by agarose gel electrophoresis and failures were repeated or new primers designed. Each PCR amplicon was spotted on poly-L-lysine coated glass slides twice, each time by a different print pin (print plates were rotated 180 degrees for second spotting) using a 16-pins ArrayMaker Version 1.0 (http://cmgm.stanford.edu/pbrown/mguide/index.html).


title: Arabidopsis thaliana 0.3K Sanger miRBase release 12.0 + custom probes

city: Brisbane

first: Shazia

last: Iram

state: Queensland

address: John Hines building # 62

department: School of Biological Sciences

institute: University of Queensland

organism: Arabidopsis thaliana

description: A Microfluidic Array Platform was used with μParafloTM Microfluidics Chip by LC Sciences employing the µParaflo® technology.


city: Toronto

first: Patricia

last: Reis

state: Ontario

address: 610 University Avenue

department: Applied Molecular Oncology

institute: University Health Network

technology: RT-PCR

manufacture_protocol: Generation of miR expression data was a two-step process involving a reverse transcription reaction followed by a quantitative real-time polymerase chain reaction (qRT-PCR).  The reverse transcription reaction was carried out according to the manufacturer’s instructions including 1 mM dNTPs (including TTP), 50U MultiScribe Reverse Transcriptase, 3.8U RNase inhibitor, and 1x Reverse Transcription buffer.  The manufacturer suggests the use of 10-100ng/ul of input RNA for each reverse transcription reaction. TaqMan stem-loop primers for 365 individual miRs and 3 endogenous controls were used in the reverse transcription reaction.  Conditions for the reverse transcription reaction were as follows: 16˚C for 30 minutes, 42˚C for 30 minutes, 85˚C for 5 minutes, then hold at 4˚C.  cDNA samples were stored at -20˚C overnight prior to application on the TaqMan Human MicroRNA Array v1.0 (Early Access).  Reverse transcription reaction products were diluted (62.5x, 30x, 15x, or 5x) prior to adding an equivalent volume of TaqMan 2x Universal PCR Master Mix, No AmpErase UNG.  A minimum of 5x cDNA dilution is required to obtain the necessary volume for application to the TaqMan Human MicroRNA Array. The entire mixture was then added to individual ports of the TaqMan Human MicroRNA Array v1.0 (Early Access); the array was centrifuged at 1,200 rpm twice for 1 minute each, and then run on an Applied Biosystems 7900HT Fast Real-Time PCR system for 40 cycles.


title: Nimblegen Mouse 25K MM5_HELP_Promoter array

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

organism: Mus musculus

description:
2006-10-26_MM5_HELP_Promoter (design id=4803)
Custom DNA methylation microarray for the HELP assay, designed to cover 25,720 HpaII-amplifiable fragments around promoter regions and imprinted regions of the mouse genome. Based on the May 2004 release (NCBI Build 33, UCSC mm5) of the mouse genome.
While the data probes are the same for both the 2006-10-26_MM5_HELP_Promoter array (design id=4803) and the 2005-07-20_MM5_HELP_Promoter array (design id=2371), they differ in the number of random probes included.
The sequences of the oligonucleotides are available in the .ndf file, which is linked as a supplementary file.

middle: E

first: Ari

middle: M

last: Melnick

first: John

last: Greally

manufacture_protocol: See Roche NimbleGen website.


title: LC Human_Mouse_Rat miRNA Array (MRA-1030)

status: Public on Jun 23 2010

city: Jefferson

first: Zhiguang Li

state: AR

address: HFT130, 3900 NCTR Road

department: Division of Genetic an Reproductive Toxicology

institute: National Center for Toxicological Research

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description:
Name: HumanMouseRat miRNA Array
Version: miRHumanMouseRat_12.0_080901
Platform table annotations based on miRBase release 12.

first: Zhiguang

last: Li

first: Tao

last: Chen

manufacture_protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the microfluidic chip, each detection probe consisted 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 were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  The hybridization melting temperatures were balanced by chemical modifications of the detection probes.


title: Porphyromonas gingivalis version 2

city: Sheffield

first: graham

last: stafford

address: School of Clinical Dentistry

institute: University of Sheffield

organism: Porphyromonas gingivalis

manufacturer: Pathogen Functional Genomics Resource Center

middle: p


title: NimbleGen Mus musculus MM8 25.6K 60mer

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

description: Expression design for Mouse from mm8.

middle: L

manufacture_protocol: Nimblegen


title: Affymetrix Human Exon 1.0 ST Array [CDF: HuEx_1_0_st_v2_main_A20071112_EP.cdf]

city: New York

first: Barry

middle: Stephen

last: Taylor

state: NY

address: 1275 York Avenue, Box #460

institute: Memorial Sloan-Kettering Cancer Center

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

manufacture_protocol: See manufacturer's website.


title: Agilent-018343 Whole Podospora anserina Genome Microarray v.3 4x44K

first: Frederique

last: Bidard

description:
Podospora anserina 60 mers Oligonucleotide Microarray by Agilent Technologies : microarray with a unique probe per CDS. The final array design contained 10,539 probes for nuclear CDS and 17 mitochondrial CDS probes. Each probe was replicated four times on each 44K array.
See Podopora anserina database's web site at http://podospora.igmors.u-psud.fr/padb/index.php

first: Sandrine

last: Imbeaud

first: Nancie

last: Reymond

first: Robert

last: Debuchy

first: Herve

last: Delacroix

first: Veronique

last: Berteaux

first: Philippe

last: Silar

first: Corinne

last: Clavé


title: Geobacter sulfurreducens 3.5K

city: Amherst

first: Ashley

middle: Edwin

last: Franks

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV North

department: Microbiology

institute: University of Massachusetts Amherst

organism: Geobacter sulfurreducens

manufacture_protocol: Purchased custom Affymetrix array


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [CDF: Brainarray Version 11.0.1, HuEx10stv2_Hs_ENTREZG]

city: Adelaide

first: Stephen

middle: Martin

last: Pederson

state: SA

address: North Terrace

department: Biological Sciences

institute: University of Adelaide

description: Probe set data extracted from custom CDF [Brainarray Version 11.0.1, HuEx10stv2_Hs_ENTREZG]

manufacture_protocol: See manufacturer's web site


title: Mouse/human oligo array from MWG version FJ

status: Public on Jun 18 2010

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

institute: L'institut du thorax

organism:
Homo sapiens
Mus musculus

first: Catherine

last: Chevalier

first: Isabelle

last: Guisle

manufacture_protocol: Oligos (MWG/Ocimum) spotted on the Amersham Lucidea spotter. Epoxyslide. Hygrometry=65%


title: UCSD Nimblegen Geobacter sulfurreducens 381K Tiling Array 2007 (Probe)

first: Bernhard

last: Palsson

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


title: Illumina Genome Analyzer (Pan troglodytes)

status: Public on Jun 16 2010

last: GEO

organism: Pan troglodytes


title: Agilent-025993 biofilm_v2

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism:
Bacillariophyta
Chlorophyta
Chlamydomonas
Tetradesmus obliquus

description:
probes for chlamydomonas genome, EST sequences of Scenedesmus obliquus and functional genes for diatoms and green algae

Arrays of this design have barcodes that begin with 16025993 or 2525993.

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: Illumina Genome Analyzer II (Pongo pygmaeus)

organism: Pongo pygmaeus


title: Ion Channel specific Human Oligo Array

status: Public on Jun 17 2010

city: Hamburg

first: Christoph

last: Ogrodowczyk

address: Falkenried 94

department: Institute for Neural Signal Transduction

institute: ZMNH

organism: Homo sapiens

manufacture_protocol:
1.Oligos are arrayed in Greiner 384-well flat-bottom plates, resuspended in betaine spotting-buffer (3x SSC, 1.5M Betaine). Vortex vigourously
2. Place plate into spotting roboter (Tecan). Each Oligo was printed onto a lysine-coated glas slide in replication (4x).
3. After printing slides were placed in vacuum for 2h. Drying was followed by crosslinking with a total energy of 60mJ.
4. Printing process was controlled by sybr-green staining (s. Battaglia, 2000 Analysis of DANN Microarrays by non-destructive fluorescent staining using sybr-green II).


title: Illumina Genome Analyzer (Clonorchis sinensis)

status: Public on Jun 11 2010

organism: Clonorchis sinensis


title: Phalanx Escherichia coli 0.155 K Custom Small RNA Array

status: Public on Jun 15 2010

city: Hsin-Chu

first: Chi-Dung

last: Yang

address: No 75, St. Po-Ai

department: Department of Biological Science and Technology

country: Taiwan

institute: National Chiao Tung University

organism: Escherichia coli

description: Phalanx Escherichia coli Custom Small RNA Array is 1 in. X 3 in. (25 mm x 75 mm) standard-format glass slide. Probe is spotted onto the array in a highly consistent manner using an innovative non-contact spotting technology adapted and perfected by Phalanx Biotech for microarray manufacturing.

first: Yih-Wei

last: Ju

first: Hsi-Yuan

last: Huang

first: Hsien-Da

first: Ching-Ping

last: Tseng

manufacture_protocol:
The sequence of sRNAs and control genes were selected from Ecocyc and Ecogene Database. All of the 50 mer oligonucleotide sequences were design and determined by by ArrayDesign 4.2. Each of the probes was a perfect match to the corresponding E.coli chromosomal sequences. The 155 Probes small RNA array was made by Phalanx Biotech Group. The pre-synthesized DNA oligonucleotides with 5’ amine modification (Biosearch, CA, USA) were spotted and fixed onto the 1’x3’ standard glass by amide formation. To ensure the accuracy, each tri-spot was arranged in a stagger format to form a 9 replication in an 8.7mm*21.1mm printing area. Each glass slide contained 2 such printing areas for any experimental pair.
See http://www.phalanxbiotech.com/ for updated protocols


title: NimbleGen 25-mers oligo flax microarray

city: Villeneuve d'Ascq

first: Stephane

last: Fenart

address: Cité Scientifique

department: Biology

institute: University Lille 1

organism: Linum usitatissimum

description:
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.
native array description file: 090121_Lusi_BT_exp.ndf
native array description file: 090121_Lusi_BT_exp.ngd


title: Agilent-022270 Tomato Gene Expression Microarray (Probe Name version)

status: Public on Jun 21 2010

organism: Solanum lycopersicum

description:
S. lycopersicum (Tomato) Oligo Microarray

*** The ID column represents the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL10570.


title: Agilent custom rat miRNA array v2

status: Public on Jun 12 2010

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

institute: Kaohsiung Chang Gung Memorial Hospital

organism: Rattus norvegicus

manufacture_protocol: see manufacturer's website


title: NimbleGen 385k whole genome tiling 2006-07-12_galGal3_WG_CGH

city: Nashville

first: Xiaofei

last: Wang

state: TN

address: 3500 John A Merritt blvd

institute: Tennessee State University

organism: Gallus gallus

description: UCSC May 2006 chicken (Gallus gallus) v2.1 draft assembly

manufacture_protocol: Whole genome CGH design for chicken (galGal3). Whole genome tiled at 50 bp interval spacing using dual mode (Tm 76; 148 cycles). Whole genome CGH probes selected at 2000 bp interval spacing, using 500 bp window. Used 15mer frequency of 30 for final filtering. Interval spacing stats: 2557 bp (mean); 2586 bp (median). 4357 random probes added.


title: SMD Print_1115 Francisella tularensis

status: Public on Jun 09 2010

city: Stanford

first: Kaitian

last: Peng

address: 299 Campus Drive, Fairchild, D327

institute: Stanford University

organism: Francisella tularensis

manufacturer: Stanford Functional Genomics Facility, Stanford School of Medicine

manufacture_protocol: Material is transferred from microtiter plate wells to the slide surface by an automated print head


title: Illumina Genome Analyzer (Hypophthalmichthys nobilis)

status: Public on Jun 08 2010

organism: Hypophthalmichthys nobilis


title: Illumina Genome Analyzer (Hypophthalmichthys molitrix)

organism: Hypophthalmichthys molitrix


title: SMD Print_1492 Francisella tularensis


title: SMD Print_1298 Saccharomyces cerevisiae, Saccharomyces paradoxus

first: Gavin

last: Sherlock

address: 300 Pasteur Drive

department: Genetics

organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus


title: SMD Print_1603 Saccharomyces cerevisiae, Saccharomyces paradoxus


title: SMD Print_1604 Saccharomyces cerevisiae, Saccharomyces paradoxus


title: Illumina Genome Analyzer (Saccharomyces kluyveri NRRL Y-12651)

organism: Lachancea kluyveri NRRL Y-12651


title: Illumina Genome Analyzer (Yarrowia lipolytica)

organism: Yarrowia lipolytica


title: SMD Print_1664 Bacillus subtilis

first: Sharon

last: Hoover

address: 337 Campus Drive, Lokey 105

department: Department of Biology

organism: Bacillus subtilis

manufacture_protocol: Array Design Name: bs1


title: Illumina Genome Analyzer (Kluyveromyces lactis)

organism: Kluyveromyces lactis


title: Nimblegen HG18 WG CGH 1 of 4

city: Ames

first: Zuo-Wei

last: Wu

address: 1113 Veterinary Medicine Bldg

institute: Iowa state university


title: Nimblegen HG18 WG CGH 4 of 4


title: Nimblegen HG18 WG CGH 2 of 4


title: Illumina Genome Analyzer (Debaryomyces hansenii)

organism: Debaryomyces hansenii


title: Illumina Genome Analyzer (Candida glabrata)

organism: Nakaseomyces glabratus


title: Illumina Genome Analyzer (Lachancea waltii)

organism: Lachancea waltii


title: Genotypic Designed Human Whole genome gene expression profiling microarray 4x44k

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

organism: Homo sapiens

first: Rohit

middle: N

last: Shukla

first: Shruti

last: Sinha

first: Raja

last: Mugasimangalam

manufacture_protocol: Refer to www.opengenomics.com


title: Nimblegen HG18 WG CGH 3 of 4

state: IA


title: Rosetta human miRNA qPCR array

city: Boston

first: Julja

last: Burchard

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

manufacture_protocol: LNA-containing primers were designed as in: Raymond CK, Roberts BS, Garrett-Engele P, Lim LP, Johnson JM. (2005) Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs.  RNA 11:1737-44.  Oligonucleotides were purchased from Proligo LLC.


title: Agilent-017164 Homo sapiens

city: Bethesda

first: Douglas Scott

last: Merrell

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

institute: Uniformed Services University

manufacture_protocol: Agilent


title: Illumina Genome Analyzer (Saccharomyces mikatae)

last: GEO

organism: Saccharomyces mikatae


title: UMich_Proteus mirabilis_v1.0 3.7k array

status: Public on Jun 07 2010

city: Ann Arbor

first: Melanie

last: Pearson

state: MI

address: 1150 W Medical Center Dr

department: Microbiology and Immunology

institute: University of Michigan Medical School

organism: Proteus mirabilis HI4320

manufacture_protocol: 70mer oligos corresponding to 3719 predicted ORFs in the Proteus mirabilis HI4320 genome were designed by Operon Biotechnologies, Inc.  The average GC% of all gene sequences was 39.618% and the Tm corresponding to this GC% was 74.0 C.  Test runnings suggest that this is optimal Tm for this species.  Out of 3719 sequences, 3714 have the oligos that meet the design criteria.  Oligos were suspended in NaPO4 buffer and spotted in triplicate onto Corning UltraGAPS slides by Microarrays, Inc.


title: AB SOLiD System 2.0 (Xenopus laevis)

status: Public on Jun 04 2010

organism: Xenopus laevis


title: Illumina Genome Analyzer II (Solanum lycopersicum)

organism: Solanum lycopersicum


title: Custom NimbleGen Aedes aegypti Expression Array [Design 6336]

status: Public on Jun 05 2010

city: NOTRE DAME

first: David

last: Severson

state: IN

address: Galvin Life Science

department: Dept. of Biological Sciences

institute: University of Notre Dame

organism: Aedes aegypti

first: Susanta

middle: K

last: Behura

manufacture_protocol: See NimbleGen Website


title: HPI-AG KSHV 15k v. 3.0

status: Public on Jun 06 2010

first: Thomas

last: Guenther

department: Mechanisms of Antiviral Defense

institute: Heinrich-Pette-Institut

organism: Human gammaherpesvirus 8

manufacture_protocol: Custom high-resolution KSHV microarrays were designed by shifting a sequence window of 60 nt. across both strands of the prototypic type P KSHV sequence (NC_009333) and the terminal repeat unit (KSU86666). Probes with a length between 45 and 60 nucleotides were selected from these windows such that their melting temperature was close to the optimal Tm of  80°C. To also ensure complete coverage of type M KSHV strains, the resulting probesets were aligned to the type M reference sequence (genbank accession NC_003409) and additional probes were designed in an identical manner for all regions which were not already covered by the original probeset. The length of all probes was subsequently adjusted to 60 nucleotides using sequences from a common linker (ATAACCGACGCCTAA), and each probe was synthesized in duplicate on Agilent 8x15k custom microarrays. For normalization purposes, the array also contains probesets which were generated in an identical manner to cover the adenovirus type 5 genome (AY339865) as well as the pCR2.1 plasmid (Invitrogen).


title: Custom SFGF HEEBO Human Set v1.00 Array

first: Judy

last: Yen

address: 620 Albany St., Rm 401H

department: NEIDL/Microbiology

institute: Boston University School of Medicine

description:
Probes include:
Constitutive Exonic Probes (30,718): that will recognize all known transcripts of a gene.
Alternatively Spliced / Skipped Exonic Probes (8,441): will recognize exons that are present in some, but not all transcripts of a gene.
Non Coding RNA Probes (196): recogning non-protein coding transcripts (ribosomal RNAs, miRNAs).
BCR / TCR Genic / Regional Probes (372): recognizing transcripts from genes that undergo somatic rearrangement.
Other Human Probes (843): recognizing human mitochondrion derived DNA sequences.
Viral or bacterial probes (1152): recognizing transcripts from viral and bacterial genes
Controls include:
A total of 4,189 controls are included in the set, including
Negative Controls (398 and 194 buffer only): Buffer only and 410 random sequences are positioned throughout the set to assist in determining background.
Positive Controls (864): recognizing a small subset of human transcripts.
Doped Controls (1,384): recognizing non-human sequences that can be spiked into RNA samples

manufacture_protocol: The Human Exonic Evidence Based Oligonucleotide (HEEBO) array was developed by a group of researchers from Stanford University with collaborators from UCSF, Rockefeller, Basel, and the Stowers Institute. This custom microarray utilizes the HEEBO human oligonucleotide set which includes a subset of viral and bacterial probes. This set consists of 47,814 70mer probes that were designed using a transcriptome-based annotation of exonic structure for genomic loci.


title: Illumina Genome Analyzer (Citrus trifoliata)

status: Public on Jun 02 2010

organism: Citrus trifoliata


title: Illumina Genome Analyzer II (Acer pseudoplatanus; Aesculus hippocastanum; Betula pendula; Fagus sylvatica; Fraxinus excelsior; Quercus robur; Tilia platyphyllos)

status: Public on Jun 01 2010

organism:
Betula pendula
Acer pseudoplatanus
Fagus sylvatica
Fraxinus excelsior
Quercus robur
Aesculus hippocastanum
Tilia platyphyllos


title: Custom Agilent Escherichia coli 4 x 44k Gene Expression Array

city: Houston

first: Jue

middle: D.

last: Wang

state: TX

address: 1 Baylor Plaza, Rm T932

department: Molecular and Human Genetics

institute: Baylor College of Medicine

organism: Escherichia coli str. K-12 substr. MG1655

manufacture_protocol: Please refer to the manufacturer's web site at http://www.agilent.com/


title: 3D-Gene Rat Oligo chip 12k

status: Public on Jun 03 2010

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

organism: Rattus norvegicus

description: Ultra sensitive DNA chip for rat genome wide gene expession analysis

manufacture_protocol: See manufacturer's web site


title: Illumina Genome Analyzer II (Acer pseudoplatanus; Corylus avellana; Fagus sylvatica; Tilia platyphyllos; Ulmus glabra)

organism:
Acer pseudoplatanus
Corylus avellana
Fagus sylvatica
Tilia platyphyllos
Ulmus glabra


title: Illumina Genome Analyzer (Canis lupus familiaris)

organism: Canis lupus familiaris


title: Illumina Genome Analyzer (Monodelphis domestica)

organism: Monodelphis domestica


title: HMS/SomeroLab-Mytilus-105K array-v1.0

city: Pacific Grove

first: Brent

last: Lockwood

state: CA

address: 120 Oceanview Blvd.

institute: Hopkins Marine Station of Stanford University

organism:
Mytilus californianus
Mytilus galloprovincialis

description:
HMS/Somero-Mytilus-105K_Agilent-v1.0
To accurately compare the transcriptomes of Mytilus galloprovincialis and M. trossulus, we chose to develop a common microarray format that could be used for both species. This microarray design consisted of probe sequences generated from the out-group species, M. californianus. M. trossulus and M. galloprovincialis are approximately 30 million years divergent from M. californianus, yet only 3.5 million years divergent from each other (Seed, 1992). Therefore, heterologous hybridization to the microarray allowed us to compare transcriptional responses of M. galloprovincialis and M. trossulus without the inherent sequence biases that would result from a microarray that was designed from sequences of either M. galloprovincialis or M. trossulus. A limited number of sequences (556) from ESTs from M. galloprovincialis that matched M. californianus ESTs were included on the microarray to test for the effects of sequence mismatches. To further control for sequence biases only probes that were present in all hybridizations of all 84 samples of both M. galloprovincialis and M. trossulus were used in our analyses.
The Platform data table reflects a condensed representation of the array's replicate features.  The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.

manufacture_protocol:
Microarrays were designed using approximately 26,000 publicly available ESTs from M. californianus (ES7325872 - ES738966; ES408175 - ES387463; (Gracey et al., 2008)) and M. galloprovincialis (AJ623313  - AJ626468; AJ516092 - AJ516921; (Venier et al., 2003)). Both sets of ESTs were sequenced from libraries constructed using Suppression Subtractive Hybridization (SSH) (Diatchenko et al., 1996) to enrich for transcripts expressed in response to various stressors.
Sequences for each species were separately screened for vector contamination, clustered, assembled, and loaded into a PostgresQL database using the PartiGene bioinformatics pipeline (Parkinson et al., 2004), yielding a total of 12,961 and 1,688 putative gene transcripts (clusters) for M. californianus and M. galloprovincialis sequences, respectively. Clusters were annotated for identity against the UniRef 90 protein database using NCBI Blast, with an e-value cutoff of 10-8. Clusters were also annotated for Gene Ontology (GO) and enzyme classification (EC) using the program annot8r (Schmid and Blaxter, 2008), again with an e-value cutoff of 10-8.
Long oligo (60-mer) probes were designed against the M. californianus clusters using the probe design program YODA (Nordberg, 2005) under default parameters, with a maximum of 5 probes per cluster. This yielded 43,969 total unique probes to 11,506 clusters, with a mean of 2.6 probes per cluster. To measure the effects of interspecific sequence variation on probe performance, the above probes were compared to M. galloprovincialis clusters using BLAST. Probes designed to the M. californianus library that successfully aligned with the smaller M. galloprovincialis library had counterparts designed using the M. galloprovincialis sequence. This resulted in 556 pairs of probes that had matched M. californianus and M. galloprovincialis sequences, with a mean number of 4.6 divergent nucleotide bases per probe. Altogether, there were 44,524 unique probes that were duplicated or triplicated randomly to fill a 105,000-feature microarray and in-situ synthesized by Agilent Technologies, Inc. (Santa Clara, CA, USA).


title: CLI/Metagenomics_GUT_739_v4

status: Public on Mar 01 2010

city: Brisbane

first: Seungha

last: Kang

state: QLD

address: 306 Carmody road

institute: CSIRO

organism:
Bacteria
Archaea

first: Christopher

middle: S

last: McSweeney

manufacture_protocol: A custom phylogenetic microarray consisting of eubacterial and archaebacterial probes was designed based on 16S rRNA sequences from gastrointestinal bacteria. Initially, a search for bacterial sequences previously identified as gastrointestinal microbes was performed on the Entrez Nucleotide database. Individual probes were then designed using the GoArray oligonucleotide program. In addition, probes obtained by way of a literature search of published papers were included, as well as several reference probes which served as internal standards and for normalization of the data. The reference probes targeted different sequences within the rrs human mitochondrial gene (positive controls), while probes which targeted sequences outside this region acted as negative controls for determining the level of background signal. Furthermore, the probes were also checked for specificity using the ‘Probe Match’ function of ARB software. Thus, the oligonucleotide probes designed for the microarray represented diverse taxonomic groups, with specificities ranging from species to phylum levels but the majority were species specific. The final oligonucleotide probes, as well as several negative and quality control probes were synthesized onto a 4 X 2K custom microarray by Combimatrix (Mukilteo WA, USA) with three replicates of each probe randomly distributed across the array to reduce biases caused by spatial variations.


title: Custom Agilent/Univ Antwerp Human H295R 1.9K

city: Antwerp

first: Caroline

last: Vanparys

address: Groenenborgerlaan 171

country: Belgium

institute: University of Antwerp

manufacture_protocol: In situ printing of 60-mer oligonucleotides.


title: Nimblegen/NCSU Zymomonas mobilis array

status: Public on May 05 2010

city: Raleigh

first: Stan

last: Martin

state: NC

address: 1404 Crete Dr.

institute: Science Apps, L3C

organism: Zymomonas mobilis

manufacture_protocol: Nimblegen proprietary.


title: CNRS Mouse 432 GPCR1 v1.0

status: Public on Dec 01 2009

city: Montpellier

first: Laurent

last: Journot

address: 141 rue de la Cardonille

institute: MGX - Montpellier GenomiX

organism: Mus musculus


title: Arabidopsis thaliana genome tiling 1.0R array

status: Public on Feb 01 2009

city: Los Angeles

first: matteo

last: Pellegrini

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

organism: Arabidopsis thaliana

description: The Arabidopsis tiling array has 2.8 million probes, spaced 35 bases apart, with one 25 base probe within each window. Tiles most of the Arabidopsis genome.

first: Matteo

first: Yana

middle: V

last: Bernatavichute

first: Xioayu

last: Zhang

first: Steve

last: Jacobsen

first: Shawn

middle: J

last: Cokus

manufacture_protocol: Standard Affymetrix manufacturing process


title: UCSD/Ideker Candida glabrata 44k v1.0 (13568)

city: La Jolla

first: Dwight

last: Kuo

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

organism: Nakaseomyces glabratus

manufacture_protocol: see Agilent for details


title: BYU Adams H. bacteriophora 15K EST array

city: Provo

first: Chin-Yo

last: Lin

state: UT

address: 753 WIDB

department: Microbiology and Molecular Biology

institute: Brigham Young University

organism: Heterorhabditis bacteriophora

description:
NimbleGen Design ID: 7867. NimbleGen Design Name:  080714_H_bacterio_BYU_CYL_expr. Four-plex expression design for Heteroorhabditis bacteriophora. 4 probes per target, no replicates.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf files is linked below as a supplementary file.
080714_H_bacterio_BYU_CYL_expr.ndf
Platform_probe_seq_ID.txt

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


title: CLI/Metagenomics_Gut_739_v5

status: Public on Jan 01 2010


title: JCVI PFGRC Helicobacter pylori 13K v3 array designed primarily based on strain J99

status: Public on Nov 19 2008

city: Rockville

first: PFGRC

last: JCVI

state: MD

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Helicobacter pylori

description: This set includes 2561 oligonucleotides, has 13872 spots distributed in 48 blocks.

manufacture_protocol: 3QHP, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Helicobacter pylori 13K v3 array designed primarily based on strain 26695


title: Illumina Genome Analyzer (Drosophila virilis)

last: GEO

organism: Drosophila virilis


title: Rana pirica tadpole-stage cDNA 3k array

status: Public on Jun 15 2009

city: Fujisawa

first: Tsukasa

last: Mori

state: kanagawa

address: Kameino 1866

department: Nihon University College of Bioresource Sciences

institute: Nihon University

organism: Rana pirica

description:
Tadpole Rana pirica cDNA microarray
Keywords = Tadpole Rana pirica
Keywords = cDNA array
Keywords = gene expression

first: Hiroko

last: Kawachia

first: Chiharu

last: Imaia

first: Manabu

last: Sugiyama

first: Youichi

last: Kurata

first: Osamu

last: Kishida

first: Kinya

last: Nishimura

manufacture_protocol: Inserts in the pCRII-TOPO vector (Invitogen) from the subtraction experiments were amplified with PCR using primers from sequences flanking the cloning site.  The PCR products (1020 clones) were visualized on 0.8% agarose gel to ensure adequate PCR amplification prior to being robotically printed onto glass slides (DNA Chip Research Inc).  After electrophoresis, PCR products were performed isopropanol precipitation without salt and glycogen.  These PCR products were spotted in triplicate onto the glass slide.


title: C. elegans 385K ChIP03

status: Public on Oct 20 2008

city: Chapel Hill

first: Christina

last: Whittle

address: 406 Fordham Hall, CB#3280

department: Biology

institute: University of North Carolina-Chapel Hill

organism: Caenorhabditis elegans

description:
C. elegans whole genome tiling array (3 array set) at 86bp resolution, 385K features per array, 1.15M total features.

WormBase Release WS120.

first: Jason

middle: D

last: Lieb

first: Leo

last: Iniguez

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


title: C. elegans 385K ChIP02


title: MLRG_Droso_15K_V1.1

status: Public on Sep 06 2006

first: Laurent

last: Journot

organism: Drosophila melanogaster

description: The Drosophila melanogaster Genome Oligo Set contains 14,593 70mer probes representing 13,664 genes and 17,899 transcrits. All probes are designed from gene transcript sequences from the Gadfly release 3.1 database.

manufacturer: Montpellier Génopole Microarray core facility

first: Dany

last: Severac

first: Cindy

last: Aknin

first: Christelle

last: Dantec

manufacture_protocol:
Manufacturing microarrays
The Drosophila Qiagen/Operon Array Ready oligo set Version 1.1  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. After printing, the slides were stored at room temperature in a dessicator.


title: MLRG Human 21K V12.0

status: Public on Apr 10 2007

organism: Homo sapiens

description:
The Human Genome Oligo Set Version 2.0 contains
21,329 70mers representing 21,329 genes obtained
from the UniGene Database Build Hs 147 and the Human
RefSeq Database, both developed and maintained at the
National Center of Biotechnology Information
(www.ncbi.nlm.nih.gov/UniGene). The set also includes
12 unique positive and 12 unique negative controls
provided in 16 replicates in a 384-well plate.

manufacture_protocol:
Manufacturing microarrays
The Human Qiagen/Operon Array Ready oligo set Version 2.0 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. After printing, the slides were stored at room temperature in a dessicator.


title: NimbleGen Human CGH 385K Whole-Genome Tiling Array v1.0

status: Public on Dec 03 2009

city: Cambridge

last: Curtis

address: Robinson Way

department: Computational Biology/Oncology

institute: University of Cambridge

description:
Genome build: hg18
NimbleGen description file: 2006-07-27_HG18_WG_CGH.ndf
NimbleGen description file: 2006-07-27_HG18_WG_CGH.pos
DESIGN_ID: 4366
DESIGN_NAME: 2006-07-27_HG18_WG_CGH
Version: 1.0
Probe Length: 50-75mer
Median Probe Spacing: 6270bp
Catalog number: B4366-00-01

Single array CGH design for whole human genome (hg18; NCBI Build 36). Probes selected from hg18_tiling database using 6000 bp interval and 250 bp window. Isothermal probes with min length of 50 bp and max length of 75 bp and target Tm of 76C. Cycle restricted to 148 synthesis cycles. Interval spacing: 6253 bp (mean); 6270 bp (median). 3553 random probes added. Includes pseudo-autosomal regions from chrX and chrY, though the counts for those regions have been changed to 1 to allow standard analysis.

manufacture_protocol: see manufacturer's website