title: Illumina Genome Analyzer II (Anopheles funestus)

status: Public on May 24 2010

last: GEO

country: USA

organism: Anopheles funestus

technology: high-throughput sequencing

distribution: virtual


title: BMFZ Mouse 40K V.1 part 1

status: Public on May 31 2010

city: Duesseldorf

first: Antje

last: Lindecke

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: Universitaet Duesseldorf

organism: Mus musculus

technology: spotted oligonucleotide

description: spotter = QArray (Genetix)

distribution: non-commercial

manufacturer: BMFZ Heinrich Heine University Düsseldorf

first: Jürgen

last: Mehrens

first: Karl

last: Köhrer

manufacture_protocol:
1. Oligos are purchased from Operon (AROS Mus Musculus V.4.0, plate 1-48 + control plate and buffer plate) arrayed in Genetix V-bottom 384-well plates. Each well contains 300 pmol of 70-mer oligo.
2. A day before printing oligos were resuspend in 15 µl Amino-Spotting-Buffer ((Genetix Ltd., Hampshire, UK)
3. Centrifuge plates at 1000 rpm for 5 minutes.
4. Plates were sealed and store at 8°C over night
5. Centrifuge plates at 1000 rpm for 5 minutes.
6. Remove seals and cover with plate lids. Place in appropriate location of plate cassette.
7. After the print run is completed, allow plates to dry through passive evaporation in a protected environment.
8. For each subsequent preparation of these plates for a print run, add water to the wells instead of spotting buffer. The amount of water should be decreased by 0.5 µL per print run, as this is the amount drawn up by the pin capillary during each print run.


title: Virus 45K Microarray - Agilent 2517771

city: New York

first: Omar

last: Jabado

state: NY

address: 722 W 168 Street 17th Fl

department: Epidemiology

institute: Columbia University

organism: Viruses

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol: see manufacturer's website


title: Virus 45K Microarray - Agilent 25161471


title: AB SOLiD System 3.0 (Rattus norvegicus)

status: Public on May 27 2010

organism: Rattus norvegicus


title: BMFZ Mouse 40K V.1 part 2

description: spotter = QArray (Genetix)

manufacture_protocol:
1. Oligos are purchased from Operon (AROS Mus Musculus V.4.0, plate 49-95 + control plate and buffer plate) arrayed in Genetix V-bottom 384-well plates. Each well contains 300 pmol of 70-mer oligo.
2. A day before printing oligos were resuspend in 15 µl Amino-Spotting-Buffer ((Genetix Ltd., Hampshire, UK)
3. Centrifuge plates at 1000 rpm for 5 minutes.
4. Plates were sealed and store at 8°C over night
5. Centrifuge plates at 1000 rpm for 5 minutes.
6. Remove seals and cover with plate lids. Place in appropriate location of plate cassette.
7. After the print run is completed, allow plates to dry through passive evaporation in a protected environment.
8. For each subsequent preparation of these plates for a print run, add water to the wells instead of spotting buffer. The amount of water should be decreased by 0.5 µL per print run, as this is the amount drawn up by the pin capillary during each print run.


title: The Hebrew university Human 105k v1

status: Public on May 25 2010

city: Jerusalem

first: Itamar

last: Simon

address: Ein Karem Campus

department: Molecular Biology

country: Israel

institute: The Hebrew university

organism: Homo sapiens

manufacture_protocol: Agilent Technologies has developed an in situ synthesized DNA microarray platform that offers flexible custom design, high quality DNA microarrays. Probes are synthesized directly on the surface of the microarray in a maskless manufacturing process, using standard DNA phosphoramidite chemistry (Beaucage and Caruthers,1981).


title: Custom Agilent Homo sapiens 4x44k aCGH containing 34,966 HD probes covering LSAMP

status: Public on May 12 2011

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

first: Francesca

last: Scrimieri

first: Jack

first: Paul

middle: S

last: Meltzer

manufacture_protocol: Custom Agilent 4x44k  aCGH containing 34,966 HD probes covering LSAMP and the surrounding 5’ region. The interested region was 1.5 Mb. The average spatial resolution between the probes was 200bp.


title: AWRI_Oenoccocus_oeni_105kv1.0_016965

city: Urrbrae

first: Anthony

middle: R

last: Borneman

state: South Australia

address: Paratoo Rd

country: Australia

institute: The Australian Wine Research Institute

organism: Oenococcus oeni

first: Eveline

middle: J

last: Bartowsky

first: Jane

last: McCarthy

last: Chambers

manufacture_protocol: Ink jet in situ oligonucleotide synthesis.


title: Nimblegen 385K custom array (Human tiling array of hg16 at 50bp resolution (chr17q, chr20q, etc)).

first: Yidong

last: Chen

first: Sean

last: Davis

manufacture_protocol: Custom-designed oligonucleotides spaced approximately every 50 base pairs, covering partial non-repetitive human genome (hg16), were synthesized in situ. Details on the manufacture protocol can be found on http://www.nimblegen.com/.


title: Bulgac Calbicans 12.4K Combimatrix v2

city: Atlanta

first: Hong

last: Qin

state: GA

address: 350 Spelman Ln SW, Box 1183

department: Biology

institute: Spelman College

organism: Candida albicans

description: The probes are designed based on annotation (version 19) of Candida Genome Database (http://www.candidagenome.org/).

manufacture_protocol: Combimatrix


title: Bulgac Calbicans 12.4K Combimatrix v1


title: NimbleGen_Homo Sapiens_720k_080530_HG18_WG_CGH_v2_HX3

status: Public on May 28 2010

city: Cardiff

first: Duncan

last: Baird

address: Heath Park

department: School of Medicine

country: United Kingdom

institute: Cardiff University

description:
hg18
native array description file: 080530_HG18_WG_CGH_v2_HX3.ndf
native array description file: 080530_HG18_WG_CGH_v2_HX3.pos
native array description file: 080530_HG18_WG_CGH_v2_HX3_probe_locations.gff

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


title: Voskuil Lab Mycobacterium tuberculosis Operon Microarray

status: Public on May 22 2010

city: Aurora

first: Ryan

middle: William

last: Honaker

state: CO

department: Microbiology

institute: University of Colorado Denver

organism: Mycobacterium tuberculosis

first: Voskui

last: Martin

manufacture_protocol:
1. Oligos are arrayed in Whatman 384-well V-bottom plates. Each well contains 600 pmol of 70-mer oligo.
2. Oligos are suspended in 3xSSC to 20 uM and centrifuged at 500 rpm for 2 minutes.
3. Plates are stored at 4oC overnight.
4. Incubate at RT for 30 minutes and shakern for 5 min to aid resuspension of DNA.
5. Centrifuge plates at 500 rpm for 2 minutes.
6. Remove seals
7. Print
8. After completion of print, allow slides to dry through passive evaporation in a protected environment.


title: Mouse metabolomics mass spec data

city: Vancouver

first: L. Caetano

middle: M.

last: Antunes

state: BC

department: Michael Smith Laboratories

country: Canada

institute: The University of British Columbia

technology: MS

manufacture_protocol: Not applicable.


title: Swegene H_v2.1.1_20k

status: Public on May 29 2010

city: Lund

first: Anna

middle: Isinger

last: Ekstrand

address: Barngatan 2b

department: Oncology

country: Sweden

institute: Clinical Sciences

manufacture_protocol: Arrays were produced by the Swegene DNA micro array resource center at Lund University by using probes from Operon. Probes were recovered in Corning Universal Spotting Solution and printed on amino-silane-coated glass slides (UltraGAPS from Corning) using a MicroGrid2 robot (BioRobotics).


title: Custom NimbleGen Tribolium castaneum expression array

city: Arlington

first: Jeff

last: Demuth

email: jpdemuth@uta.edu, eprince@uta.edu

state: TX

address: Box 19498 501 S. Nedderman Dr

institute: The University of Texas at Arlington

organism: Tribolium castaneum

first: Jeffery

middle: P

first: Eldon

middle: G

last: Prince

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


title: The Hebrew university Mouse 105k v1

first: Itamar

last: Simon


title: Illumina HumanRef-6 Expression BeadChip

first: Yuelin

last: Zhu

technology: oligonucleotide beads

description: The Sentrix Human-6 BeadChip can be used to study expression of over 47,000 human transcripts. Researchers can generate whole-genome expression profiles for 6 samples in parallel on a single BeadChip. Array is composed of 3 micron features with average feature redundancy of 30-fold . All features are QCed by sequential hybridizations process called array decoding. Probes are fully screened all-full-length 50-mers. Assay requires 50-100ng of total RNA input. Array content is based on RefSeq and additional space is occupied by targets selected from Unigene build 163 and Gnomon databases.


title: IOLR_Cherax quadricarinatus_5.755K_v1.0

city: Haifa

first: Moshe

last: Tom

department: Marine Biology and Biotechnology

organism: Cherax quadricarinatus

technology: spotted DNA/cDNA

description: The array was printed on 2.5 x 7.5 cm glass slides (GAPS II, Corning) on an area less than 6 x 2 cm. The grid system includes 4 x 12 sub-arrays, each containing 16 rows and 16 columns, a total of 12288 spots. The printing pattern included two complete and separate sets of the transcriptome, in the upper and lower part of the slide, respectively. Empty spots which include only the printing buffer were taken out of the data table but their position on the slide can be identified (designated "XX") in the GPR files accompanied each experiment-related dataset.

manufacturer: Moshe Tom's laboratory - Israel Oceanographic and Limnological Research, Haifa, Israel.

first: Yana

last: Yudkovski

first: Assaf

last: Shechter

first: Lilah

last: Glazer

first: Amir

last: Sagi

manufacture_protocol:
X Organ – Sinus Gland complex was bi-laterally extirpated from several C. quadricarinatus males to induce molting initiation. The molt cycle stage was monitored by gastrolith size, maxillar setae appearance and in some individuals the presence of new cuticle under the old one. Gastrolith disks were dissected from sacrificed males 10 days post-extirpation. Several hepatopancreatic lobes, hypodermis layered beneath the carapace or new hypodermis already formed, muscle tissue and the entire Y organ pair were dissected from sacrificed males 13 or 14 days post-extirpation. RNA was extracted from the dissected tissues. Dissected muscle served as a reference organ, whereas the molt-related gastrolith disks, hepatopancreas, hypodermis and Y-organ were the target organs. The cDNA assemblage was constructed in two stages: (1) SMART (Switching Mechanism At 5' end of the RNA Transcript), aimed at amplification of reverse transcribed cDNAs using a universal primer, linked to both ends of the template cDNA during the reverse transcription stage (Clontech, manufacturer instructions). (2) SSH (Subtractive-Suppression Hybridization method; Diatchenko et al. 1999; PCR-select, Clontech), aimed at T-A cloning of a roughly equally represented cDNAs from the target organs into an expression plasmid (pGEM-Teasy, Promega) biased towards genes differentially expressed in the target tissues in comparison to the reference one. The cloned cDNAs were transfected into E. coli, and 5755 bacterial colonies were isolated, amplified and frozen at -70C. A subset of the clones were successfully sequenced and assembled by the CAP3 software (Huang and Madan, 1999), to identify unique sequences. All the 5755 clones were amplified by standard PCR from 1 µl bacterial culture templates (5’ at 95C; 32 cycles of 0.5’ at 95C, 0.5’ at 68C and 1.5’ at 72C; a final incubation of 4’ at 72C). PCR products were precipitated from the PCR solution by one volume of isopropanol at room temperature. The dry DNA was dissolved in printing buffer at final concentration of 50% DMSO and 0.3 x SSC and was printed on a glass slide (GAPS II slides, Corning; MGII robot-printer, BioRobotics) in duplicates. The amplification efficiency was tested by running the PCR products on a 1% agarose gel concurrent with a DNA mass ladder. The platform is a broadening of a previous platform designated by GEO accession number GPL4786 (Yudkovski et al., 2007), with updated annotations.

References:

Diatchenko, L., Lukyanov, S., Lau, Y.F.C. Siebert, P.D. (1999) uppression subtractive hybridization: A versatile method for identifying differentially expressed genes. In: cDNA Preparation and characterization, Meth. Enzymol. 303: 349-380.

Huang, X. and Madan, A. (1999) CAP3: A DNA sequence assembly program. Gen Res 9: 868-877.

Yudkovski, Y., Shechter, A., Chalifa-Caspi, V., Auslander, M., Ophir, R., Dauphin-Villemant, C., Waterman, M., Sagi, A. & Tom, M. (2007). Hepatopancreatic multi-transcript expression patterns in the crayfish Cherax quadricarinatus during the moult cycle. Insect Mol. Biol. 16, 661-674.


title: Illumina HumanRef-8 Expression BeadChip

description: The Sentrix® HumanRef-8 BeadChip can be used to study expression of over 23,000 human transcripts from the NCBI RefSeq database. Researchers can generate whole-genome expression profiles for 8 samples in parallel on a single BeadChip. The array is composed of 3 micron features with average feature redundancy of 30-fold. All features are quality controlled by sequential hybridizations process called array decoding. Probes are fully screened, full-length 50-mers. Assay requires 50-100ng of total RNA input.


title: Applied Biosystems Human and Rodent TaqMan Low Denisty microRNA Microarray

status: Public on May 30 2010

city: Camperdown

first: Nicole

last: Schonrock

state: New South Wales

address: 100 mallett street

department: Medicine

institute: Brain and Mind Research Institute, University of Sydney

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

technology: RT-PCR


title: Univ Freiburg Sinorhizobium meliloti Sm6kPCR

status: Public on May 20 2010

city: Napoli

first: Carmen

last: Bianco

address: Via p. Castellino 111

country: Italy

institute: IGB-CNR

organism: Sinorhizobium meliloti 1021

manufacturer: Anke Becker - Molekulare Genetik, Institut für Biologie III, Albert-Ludwigs-Universität Freiburg, Schänzlestr. 1 D-79104 Freiburg

manufacture_protocol: PCR fragments and oligonucleotides were printed onto 3-aminopropyltrimethoxysilane-coated SA-1 glass slides (Asper Biotech, Tartu, Estonia) using the MicroGrid II 600 spotter (BioRobotics, Cambridge, UK) equipped with 48 SMP3 stealth pins (TeleChem International, Sunnyvale, CA, USA). DNA was cross-linked to the surface by incubation of the slides for 3 h at 80◦ C. Unbound DNA was removed by two washes in 0.1% (w/v) SDS for 2 min at 42◦C and two washes in distilled water for 2 min at 20◦C. After denaturation at 100◦ C for 3 min in distilled water, slides were dunked into ethanol and dried by centrifugation.


title: IFR_Salmonella_5.6k_v1.0

city: Western Bank

first: Matthew

middle: D

last: Rolfe

state: Sheffield

address: Firth Court

department: Department of Molecular Biology and Biotechnology

institute: University of Sheffield

organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. DT104
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Salmonella enterica subsp. enterica serovar Enteritidis
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

first: Arthur

last: Thompson

first: Sacha

last: Lucchini

first: Jay

middle: C

last: Hinton

manufacture_protocol:
PCR product microarray of ORF's from S. Typhimurium LT2, S. Typhimurium SL1344, S. Typhimurium DT104 and S. Enteritidis PT4. For the description of PCR amplification and printing procedures see:
Clements et al., (2002) PNAS 99(13): 8784-8789;
Nagy et al., (2006) Infect. Immun. 74(10):5914-5925


title: Illumina Genome Analyzer (Triticum aestivum)

last: GEO

organism: Triticum aestivum


title: BIOTEC UniShrimpChip

status: Public on May 26 2011

city: Pathumthani

first: nitsara

last: karoonuthaisiri

state: Pathumthani

address: Paholyothin

department: Central

country: Thailand

institute: BIOTEC

organism: Penaeus monodon

first: Rungnapa

last: Leelatanawit

first: Umaporn

last: Uawisetwathana

first: Thidathip

last: Wongsurawat

first: Sarawut

last: Wongphayak

first: Nitsara

last: Karoonuthaisiri

first: Sirawut

last: Klinbunga

manufacture_protocol:
Array Design:
Amplification
Approximately 5000 sequences will be amplified either from plasmids of EST clones or from the first strand cDNA template. For amplification from EST clones, PCR reactions were optimized considering the following parameters: (1) amounts of template, (2) types of Taq DNA polymerase, (3) units of Taq DNA polymerase, and (4) MgCl2 concentrations.  In all experiments, the reactions were performed using purified plasmids as templates in a 96-well format PCR plate (Axygen) with final concentrations of the following components: 0.3 mM dNTPs, 1X buffer, 0.4 uM each primer (LM13F: CAC GAC GTT GTA AAA CGA CGG CCA G and LM13R: CAT GGT CAT AGC TGT TTC CTG T, BioBasic). Amplification was carried out for 35 cycles at the following settings: 94C for 30 sec, 600C for 30 sec, 72C for 3 min.
For amplification from first strand cDNA, PCR reactions were optimized considering the following parameters: (1) amounts of template, (2) MgCl2 concentrations, (3) units of Taq DNA polymerase, and (4) reaction volumes.  In all experiments, the reactions were performed using cDNA as templates in a 96-well format PCR plate (Axygen) with final concentrations of the following components: 0.4 mM dNTPs, 1X buffer, 0.6 uM each gene-specific primer (designed as described below; IDT, Singapore). Amplification was carried out for 38 cycles at the following settings: 940C for 30 sec, 570C for 60 sec, 720C for 3 min. The resulting amplicons were electrophoretically analyzed on 1.5% agarose gel prepared in 0.5X TBE buffer.
Purification
The PCR products were purified using Multiscreen PCR 96 well purification plate (Millipore, #MSNU03050). Briefly, PCR products were thoroughly loaded to the purification plate and placed under a vacuum manifold. The bound DNA on the plate will be washed with sterile water once in vacuo until completely dried. To collect the purified products, sterile water was added to the Millipore plate and let stand for 5-10 min before resuspended into a polysterene V-shape 96-well plate (Corning, CoStar # 3897)
Microarray fabrication
Fifteen plates of 384-well print plates were used as source plates for microarray fabrication. Source plates were resuspended in 7 uL of 3xSSC buffer (Invitrogen, cat no.15557-044) and incubated at 4C overnight before printing. The cDNA microarrays were fabricated using Nanoprint LM210 microarray spotter (ArrayIt, USA) fitted with a 24-pin head on GAPS II amino-silane coated slides (CORNING, cat no.40005). A 11,136 spots/array pattern was designed by 24 X 20 spots per block, containing a total of 24 arrays. Each amplicon was spotted in replicate. The printed slides were UV-crosslinked at 200 mJ of energy (GS Gene Linker UV chamber, BIO-RAD) and stored at room temperature in a dry incubator.


title: OSU-CCC Homo sapiens 0.9K microRNA microarray v4

status: Public on Feb 28 2011

city: Columbus

first: Amy

middle: M

last: Hayes

state: OH

address: 1925 Coffey Rd

department: Veterinary Biosciences

institute: Ohio State University

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.   Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions (http://www.genomicsolutions.com ) that is fitted with a printhead and 16 SMP3 print tips from Telechem (http://www.arrayit.com). The microRNA microarray probe set is based on 40mer oligonucleotides from Sigma-Genosys.   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: NimbleGen Matzkin Drosophila mojavensis 70K array v1.0.

status: Public on May 21 2010

city: Huntsville

first: Luciano

middle: Matias

last: Matzkin

state: Alabama

address: 301 Sparkman Drive

department: Biological Sciences

institute: University of Alabama in Huntsville

organism: Drosophila mojavensis

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


title: HOMIM-v.03

city: Boston

first: Bruce

last: Paster

state: MA

address: 140 Fenway

institute: The Forsyth Institute

organism: Bacteria

manufacturer: Michigan State University Research Technology Support Facility

manufacture_protocol: 16S rRNA-based oligonucleotide reverse capture probes were custom synthesized with a 5’-(C6)-amine modified base, eight spacer thymidines and 18 to 20-nucleotides of target sequence, and printed on 25 x 76 mm aldehyde-coated glass slides


title: SMD Print_1259 Mycobacterium tuberculosis

city: Guadalajara

first: Mario

middle: A

last: Flores Valdez

state: Jalisco

address: Av. Normalistas No. 800

department: Col. Colinas de la Normal

country: Mexico

institute: Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco, A.C.

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 (Equus caballus)

organism: Equus caballus


title: Agilent human chip6 017851 (Agilent-022109)

city: Rehovot

first: Einat

last: Sitbon

address: 10 Plaut St

institute: Rosetta Genomics

description: miRBase 12 sequences, deep sequencing and predicted miR sequences.

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


title: Agilent_Escherichia coli_15K

status: Public on May 18 2010

city: Singapore

first: Hua

last: Ling

address: 62 Nanyang Drive

department: Department of Chemical and Biomolecular Engineering, SCBE

country: Singapore

institute: Nanyang Technological University

organism: Escherichia coli

description:
Design ID: Agilent-020097
8 x 15K

manufacture_protocol: Agilent 60-mer SurePrint technology


title: CLI Bovine innnate immune array

city: St Lucia

first: Ylva

last: Strandberg-Lutzow

state: Queensland

address: 306 Carmody Road

department: Livestock Industries

institute: CSIRO

organism: Bos taurus

first: Laurelea

last: Donaldson

first: Tony

last: Vuocolo

first: Christian

last: Gray

last: Strandberg

first: Antonio

last: Reverter

first: Sean

last: McWilliam

first: Yonhong

last: Wang

first: Keren

last: Byrne

first: Ross

last: Tellam

manufacture_protocol: Microarray printing was performed at the Machines for Genes Laboratory, CSIRO Livestock Industries (Geelong, Vic). Of the 20 384-well source plates, 19 were printed in duplicate side-by-side, whilst the 384-well control plate was printed in duplicate at both the top and bottom of each printed block, giving a total of 16,128 printed elements. Elements were spotted on Corning UltraGAPS slides using a BioRobotics MicroGrid II TAS using MicroSpot 2500 pins. These pins produce a spot size of approximately 100 μm diameter with a pitch of 220 μm between spots. Each amplified DNA fragment was printed in duplicate adjacent to each other. The pin configuration was arranged in 4 columns and 12 rows yielding 48 subarrays of 19 × 19 spots. Elements were printed in a 150 mM sodium phosphate printing buffer (pH 8.5). The spots were then fixed to the slide by baking for two hours at 80°C. To ensure DNA spotting was uniform across the slides, samples were taken from each batch of microarrays and probed with Panomer™ 9 random oligodeoxynucleotide conjugated with Alexa Fluor® 532 (Molecular Probes, Invitrogen). Reproducibility was visually assessed between spot duplicates and between slides within a printing batch.


title: SMD Print_580 Mycobacterium tuberculosis

first: Martin

middle: I

last: Voskuil


title: SMD Print_498 Mycobacterium tuberculosis


title: Homo sapiens 2.3K oncogene and clock gene oligo array

status: Public on May 16 2010

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

description: This array contains a total of 2304 features, including transcripts as well as buffers, controls and empty spots. The genes on the array were selected inter alia with a focus on inflammation, regulation of inflammatory processes. Furthermore 20 clock genes and 70 clock-associated genes are interrogated. Every feature was printed at least in duplicate. The array contains 880 genes in total.

first: Derek

last: Zieker

first: Katharina

last: Buck

manufacture_protocol: 65mer Oligos were designed by Sigma Aldrich. Oligos were spotted using a Affymetrix 417 spotter.


title: Illumina Genome Analyzer II (Bacteroides thetaiotaomicron VPI-5482; Blautia hydrogenotrophica DSM 10507)

status: Public on May 19 2010

last: GEO

organism:
Bacteroides thetaiotaomicron VPI-5482
Blautia hydrogenotrophica DSM 10507


title: Illumina Genome Analyzer II (Escherichia coli str. K-12 substr. MG1655)


title: Agilent-027065 SurePrint G3 Rat CGH Microarray 1x1M

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

organism: Rattus norvegicus

description:
Arrays of this design have barcodes that begin with 16027065 or 2527065.

Data table annotations based on genome build UCSC rn4 (Baylor HGSC Build 3.4), November 2004.

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.

distribution: commercial

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


title: SuperArray GEArray Mouse Neurogenesis and Neural Stem Cell Microarray [cat# OMM-404]

city: Frederick

first: SuperArray

last: Bioscience Corporation

address: Suite 101, 7320 Executive Way

institute: Technical Support

organism: Mus musculus

manufacture_protocol: see manufacturer's website


title: Illumina Genome Analyzer II (Blautia hydrogenotrophica DSM 10507)

organism: Blautia hydrogenotrophica DSM 10507


title: Illumina Genome Analyzer II (Bacteroides thetaiotaomicron VPI-5482)

organism: Bacteroides thetaiotaomicron VPI-5482


title: Agilent Mus musculus proximal promoter 185k array slide 2

status: Public on May 13 2010

city: Cambridge

first: Kenzie

last: MacIsaac

address: 77 Massachusetts Ave.

institute: MIT

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


title: Lactobacillus casei ATCC 334 5.1K

city: Logan

first: Jeff

last: Broadbent

state: UT

department: NFS

institute: Utah State University

organism:
Lactobacillus helveticus
Lacticaseibacillus paracasei ATCC 334

first: Rebecca

middle: L

last: Larsen

first: Virginia

last: Deibel

first: James

last: Steele

manufacture_protocol: The DNA is printed, spotted, or actually synthesized directly onto the support. The whole process is based on hybridization probing, a technique that uses fluorescently labeled nucleic acid molecules as "mobile probes" to identify complementary molecules, sequences that are able to base-pair with one another.


title: 454 GS (Mus musculus)


title: Agilent Mus musculus proximal promoter 185k array slide 1


title: NSF45K_UCD_slide_a

status: Public on May 17 2010

city: Davis

first: Ki-hong

last: Jung

address: one shields

department: Plant pathology

institute: UC DAVIS

organism: Oryza sativa

first: Ki-Hong

first: Pamela

last: Ronald

first: Patrick

last: Schnable

first: Robin

last: Buell

first: David

last: Rocke

first: Hui-Hsien

last: Chou

first: Peijian

last: Cao

manufacture_protocol: vist http://www.ricearray.org


title: SFGF HEEBO Human Set v1.00 with custom orthopox oligos

first: Judy

last: Yen

address: 620 Albany St., Rm 401H

department: NEIDL/Microbiology

institute: Boston University School of Medicine

organism: Homo sapiens

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 a set of orthopox (vaccinia virus, monkeypox virus, and variola) 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 inlcudes the HEEBO human oligonucleotide set with a custom set of probes for orthopox (vaccinia, variola, and monkeypox) genes. This set consists of 47,814 70mer probes that were designed using a transcriptome-based annotation of exonic structure for genomic loci.


title: Ocimum Biosolutions Yeast OciChip

city: Hyderabad

first: Ocimum

last: Biosolutions

email: govind.a@ocimumbio.com, sandhya.p@ocimumbio.com, hazira.b@ocimumbio.com, anwaruddin.m@ocimumbio.com

state: Andhra Pradesh

address: Banjara Hills Road No., 1 VI Floor Reliance Classic

department: Bioinformatics

country: India

institute: Ocimum Biosolutions

organism: Saccharomyces cerevisiae

description: epoxide

first: Govind

last: Rao

first: Rashmi

last: Sharma

first: Sandhya

last: Pemmasani

first: Hazira

last: Begum

manufacture_protocol:
Array Design and Printing
Yeast OcichipTM  consists of 6368 spots printed on Corning® epoxy coated  glass slides using Omnigrid (Gene Machines). Chip has been printed using 4x4 SMP4 pins on 75.5x 25.5x1.3 mm microarray glass slides with a spot area of 1.8 x3.6 cm. The origin offset values were 0 for X direction and 15000 for Y direction. The dot to dot distance is 290 mm; distance between subarrays is 500 mm in horizontal direction and 200 in vertical direction and no of dots per array is 15x15=225 in subarray 1-16 and 15x12=163 in subarray 17-20. Oligos were printed using spotting buffer A from Ocimum Biosolution at 50% humidity and temperature at 22°C. The time taken by the robotic gridder to print yeast altogether was 16 hrs. Each probe was checked for its performance by standard QC process followed at Ocimum Biosolutions. Printed slides were stored in a light-tight box in a bench-top dessicator, with desiccant and were kept at 4°C until they were used for hybridization.


title: Ocimum Biosolutions S. pneumoniae OciChip

organism: Streptococcus pneumoniae R6

description: epoxide

manufacture_protocol:
Array Design and Printing
S. pneumoniae OcichipTM  consists of 2048 spots printed on Corning® epoxy coated  glass slides using Omnigrid (Gene Machines). Chip has been printed using 4x4 SMP4 pins on 75.5x 25.5x1.3 mm microarray glass slides with a spot area of 1.8x 1.8cm. The origin offset values were 0 for X direction and 10000 for Y direction. The dot to dot distance is 350 mm for x axis and 350 mm for y axis; distance between subarrays is 150 mm and no of dots per array is 12x12=144. Oligos were printed using spotting buffer A from Ocimum Biosolution at 50% humidity and temperature at 22°C. The time taken by the robotic gridder to print yeast altogether was 5 hrs. Each probe was checked for its performance by standard QC process followed at Ocimum Biosolutions. Printed slides were stored in a light-tight box in a bench-top dessicator, with desiccant and were kept at 4°C until they were used for hybridization.


title: SU Homo sapiens 912

city: Lecce

first: Oscar

middle: Fernando

last: D'Urso

state: Lecce

address: provinciale Monteroni

department: Department of biological science

institute: Salento University

first: Pietro

middle: F

first: Pasqualino

last: Ciappetta

manufacture_protocol: Probe set relative to 912 gene features were designed by means of ArrayDesigner4. Probes were purchased dry in 384 well plate and resuspended in 3X SSC as spotting buffer. Spotting was performed by means of SpottArray 428 (Perkin Elmer), under humidity range of 50%-60% with optimum setted to 55%. All probes were spotted in duplicate. After printing procedure slides were incubated in a 95% humidity chamber for 30'. After dry to 60° for 20 minutes slides were stored dry and light protected upon usage


title: NSF45K_UCD_slide_b

first: Ki-hong

middle: S

manufacture_protocol: Visit http://www.ricearray.org


title: Institut Pasteur de Lille Human MMP & ADAM long oligo array

status: Public on May 12 2010

city: Lille

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

country: France

institute: Institut Pasteur de Lille

description: Spotted long oligonucleotides.

manufacturer: Transcriptomics and Applied Genomics Laboratory, Institute Pasteur of Lille

manufacture_protocol:
1. Oligo were purchased at MWG-biotech In 96-well plates (Abgene 1058). Each oligo was resustended in QMT2 buffer (Corning) at 50 µM final
2. Oligo solutions were spotted using Affymetrix 427 pin-and-ring arrayer on aldehyde fonctionnnalised slides (Genetix) at 22°C and 60-70% relative humidity.
3. Glass slides were hydrated in saturated humidity chamber at 42°C overnight. Glass slides were then treated in 132mM NaBH4 in PBS containing 25% ethanol at 42°C during 8h.
4. Glass slides were washed once in 0.2% SDS at 42°C during 2 minutes and twice in distilled water and finally dried by centrifugation.
5. Slides were pre-hybridized with 15µl of hybridization buffer at 42°C during 1h just before hybridization.


title: Ocimum Biosolutions Mouse Inflammation 0.16K OciChip

status: Public on May 07 2010

description: epoxide

last: Kiran

manufacture_protocol:
Array Design and Printing
Mouse inflammation OcichipTM  consists of 160 spots in duplicate printed on Corning® epoxy coated  glass slides using Omnigrid (Gene Machines). Chip has been printed using 2x2 SMP4 pins on 75.5x 25.5x1.3 mm microarray glass slides with a spot area of 0.8x 1.45 cm. The origin offset values were 4000 for X direction and 14000 for Y direction. The dot to dot distance is 500 mm; distance between subarrays is 1500 mm and no of dots per array is 8x5=40. Oligos were printed using spotting buffer A from Ocimum Biosolution at 50% humidity and temperature at 22°C. The time taken by the robotic gridder to print yeast altogether was 3 hrs. Each probe was checked for its performance by standard QC process followed at Ocimum Biosolutions. Printed slides were stored in a light-tight box in a bench-top dessicator, with desiccant and were kept at 4°C until they were used for hybridization.


title: SMD Print_1034 Mus musculus

city: Ann Arbor

first: Jun

last: Li

state: MI

address: 5789A Medical Science II, Box 5618

institute: University of Michigan

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


title: Microarray lab/BRI-NRC Solanum chacoense 7.7K V1.0 array

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

institute: CHU Québec

organism: Solanum chacoense

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

manufacture_protocol: PCR products were resuspended in 10 µl of 50% DMSO and arrayed from 384 well microtiter plates onto UltraGAPSTM slides (Corning incorporated, Corning, NY, USA). A total of 7741 ESTs spotted in duplicate along with a variety of controls.


title: [S_pneumoni530157] Affymetrix Streptococcus pneumoniae TIGR4 Array

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Streptococcus pneumoniae TIGR4

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

manufacture_protocol: see manufacturer's web site


title: Ocimum Biosolutions Human Inflammation 0.16K OciChip

description: epoxide

manufacture_protocol:
Array Design and Printing
Human OcichipTM  consists of 160 spots in duplicate printed on Corning® epoxy coated  glass slides using Omnigrid (Gene Machines). Chip has been printed using 2x2 SMP4 pins on 75.5x 25.5x1.3 mm microarray glass slides with a spot area of 0.8x 1.45 cm. The origin offset values were 4000 for X direction and 14000 for Y direction. The dot to dot distance is 500 mm; distance between subarrays is 1500 mm and no of dots per array is 8x5=40. Oligos were printed using spotting buffer A from Ocimum Biosolution at 50% humidity and temperature at 22°C. The time taken by the robotic gridder to print yeast altogether was 3 hrs. Each probe was checked for its performance by standard QC process followed at Ocimum Biosolutions. Printed slides were stored in a light-tight box in a bench-top dessicator, with desiccant and were kept at 4°C until they were used for hybridization.


title: 454 GS (Homo sapiens)

status: Public on May 06 2010

last: GEO


title: Ocimum Biosolutions H. pylori 1.9K OciChip

organism: Helicobacter pylori

description: epoxide

manufacture_protocol:
Array Design and Printing
H. Pylori OcichipTM  consists of 1920 spots on Corning® epoxy coated  glass slides using Omnigrid (Gene Machines). Chip has been printed using 4x4 SMP4 pins on 75.5x 25.5x1.3 mm microarray glass slides with a spot area of 1.8x 1.8cm. The origin offset values were 0 for X direction and 10000 for Y direction. The dot to dot distance is 540 mm for x axis and 285 mm for y axis; distance between subarrays is 150 mm and no of dots per array is 15x 8=120. Oligos were printed using spotting buffer A from Ocimum Biosolution at 50% humidity and temperature at 22°C. The time taken by the robotic gridder to print yeast altogether was 2.5 hrs. Each probe was checked for its performance by standard QC process followed at Ocimum Biosolutions. Printed slides were stored in a light-tight box in a bench-top dessicator, with desiccant and were kept at 4°C until they were used for hybridization.


title: SNI_human_MPSS

city: Seattle

first: Biaoyang

last: Lin

state: WA

address: 550 17th Ave, James Tower suite 550

department: Swedish Neuroscience Institute

institute: Swedish Medical Center

technology: MPSS

manufacture_protocol: The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634. Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library. The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.


title: UHN Mouse 22.4K v1.0

status: Public on May 02 2010

city: Windsor

first: Alan

last: Morettin

state: ON

address: 401 Sunset Ave.

institute: University of Windsor


title: LC_MRA-1002_miRMouse_11.0_080411 (miRNA ID version)

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

description: Mouse miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 11.0

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-027414 SurePrint G3 Mouse CGH Microarray 1x1M

last: Agilent Technologies

description:
Arrays of this design have barcodes that begin with 16027414 or 2527414.

Data table annotations based on NCBI Build 37 (UCSC mm9), July 2007.

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 (Lateolabrax japonicus)

organism: Lateolabrax japonicus


title: Trichophyton rubrum cDNA microarray 3

status: Public on May 04 2010

city: Beijing

first: Qi

last: Jin

state: Beijing

address: No.6 Rongjing East Street, BDA

country: China

institute: National Institute for Viral Disease Control and Prevention

organism: Trichophyton rubrum

manufacturer: State Key Laboratory for Molecular Virology and Genetic Engineering

first: Lingling

last: Wang

first: Li

last: Yang

manufacture_protocol: PCR  fragments used  for  printing  the microarray  chip were amplified  from  the EST library  in  96-well  plates  using  vector-PCR  amplification  with  T7  and  SP6  universal primers  on  the GeneAmp  PCR  system  9600  (Perkin Elmer,  Foster City, CA).  PCRs were initiated with DNA denaturation (5 min at 96 oC) followed by annealing for 30 s at 55 oC and extension  (1 min and 30 s at 72 oC)  steps carried out  for 35 cycles. PCR products were puried and dried  and  then  resuspended  with  a concentration of 100 ng/ μL. The positive control came from T. rubrum PCR product and the negative control came from the SpotReport-10 cDNA Array Validation System (Stratagene). The PCR products were mixed with equal volumn of 60%DMSO, then printed to CMT-GAPII slides(Corning).


title: Trichophyton rubrum cDNA microarray 2

manufacture_protocol: PCR  fragments used  for  printing  the microarray  chip were amplified  from  the EST library  in  96-well  plates  using  vector-PCR  amplification  with  T7  and  SP6  universal primers  on  the GeneAmp  PCR  system  9600  (Perkin Elmer,  Foster City, CA).  PCRs were initiated with DNA denaturation (5 min at 96 ºC) followed by annealing for 30 s at 55 ºC and extension  (1 min and 30 s at 72 ºC)  steps carried out  for 35 cycles. PCR products were puried and dried  and  then  resuspended  with  a concentration of 100 ng/ μL. The positive control came from T. rubrum PCR product and the negative control came from the SpotReport-10 cDNA Array Validation System (Stratagene). The PCR products were mixed with equal volumn of 60%DMSO, then printed to CMT-GAPII slides(Corning).


title: UoL-LMF Zebrafish 17K v1.0

city: Liverpool

first: Ashley

last: Sawle

address: Crown Street

department: Biosciences

institute: University of Liverpool

organism: Danio rerio

manufacturer: Liverpool Microarray Facility, University of Liverpool, UK

manufacture_protocol: The oligonucleotide arrays were printed in-house by the Liverpool Microarray Facility. The probes included on the array were 65 base pair oligonucleotides from the Zebrafish OligoLibrary™ designed by Compugen (Jamesburg) and an additional 400 customs probes designed at the labs of Professor Charles Tyler, University of Exeter, and Dr. Peter Kille, Cardiff University. The oligos were synthesised by Sigma-Genosys (The Woodlands). These together with control and blank spots were printed onto Nexterion® HiSens E slides (Schott, U.S.A.) with a BioRobotics TAS contact-printing robot (Genomic Solutions, Huntingdon, UK) giving a total of 16578 features.


title: Trichophyton rubrum cDNA microarray 1

description:
The PCR product were  spotted  onto  CMT-GAPSII-coated  slides
(Corning  Glass).

manufacture_protocol:
PCR  fragments used  for  printing  the microarray  chip were amplified  from  the EST library  in  96-well  plates  using  vector-PCR  amplification  with  T7  and  SP6  universal primers  on  the GeneAmp  PCR  system  9600  (Perkin Elmer,  Foster City, CA).  PCRs were initiated with DNA denaturation (5 min at 96 ºC) followed by annealing for 30
s at 55 ºC and extension  (1 min and 30 s at 72 ºC)  steps carried out  for 35 cycles. PCR products were puried and dried  and  then  resuspended  with  a concentration of 100 ng/ μL.


title: WCFS yoghurt arrays, TB1_8, Version 1

status: Public on May 05 2010

city: Ede

first: Sander

last: Sieuwerts

address: Kernhemseweg 2

department: Health

country: Netherlands

institute: NIZO Food Research

organism:
Streptococcus thermophilus CNRZ1066
Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365

manufacture_protocol: The oligomers were designed using the algorithm described in Appl Environ Microbiol 73:1753-1765. Spotting the probes was performed according to Agilent's standards


title: Febit Sus Scrofa miRNA Custom 0.8K

city: Berlin

first: Soroush

last: Sharbati

address: Oertzenweg 19b

department: Institute of Veterinary Biochemistry

institute: Freie Universitaet Berlin

organism: Sus scrofa

description: Based on miRDeep predicted porcine miRNAs.

manufacture_protocol:
MicroRNAs (miRNAs) are endogenous, non-coding RNAs that play a fundamental role in gene regulation and have critical functions across various biological processes. Pairing to mRNAs of protein-coding genes, they direct posttranscriptional repression by altering the stability or translational efficiency of their target mRNAs.
Recent studies indicate that miRNAs are involved in the development of human malignancies, suggesting that they represent a promising new class of cancer biomarkers. Identifying miRNAs involved in specific cancers could provide useful diagnostic information, allow disease classification and reveal potential treatment targets.
MPEA: On-Chip Labeling for Highest Sensitivity
Enzymatic labeling assay requires minimal sample amount
In addition to the standard hybridization of pre-labeled RNA, the microfluidic Geniom Biochip enables a highly sensitive enzymatic labeling protocol.
MPEA benefits
* Higher sensitivity and specificity
* miRNA hybridization without preceding treatment like enrichment, PCR -based amplification or labeling eliminates potential bias
* High discriminatory power
* Minimal amount of sample RNA needed (more than or equal 20 ng total RNA)
* Easy to use protocol for Geniom RT Analyzer
The unique Microfluidic Primer Extension Assay (MPEA) uses unlabeled miRNAs for hybridization. In a second step, Klenow fragment of DNA polymerase I is added directly into the channels of the microfluidic chip, where the specific elongation of the bound miRNAs takes place.
The method combines the specificity of a hybridization assay with the discriminatory power of an enzymatic extension and reduces the required sample amount to a minimum.
Details provided at www.febit.com


title: Febit Homo Sapiens and Sus Scrofa 1.1K miRBase 13.0

description: Based on Sanger miRBase Release 13.0 and deep sequencing data.

first: Sharbati

last: Soroush


title: NimbleGen agrsci porcine 2.1M v1

status: Public on May 01 2010

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

description:
Annotation in this record based on the porcine pre genome assembly, version 6
native array description files:
Sscorfa_U_Aarhus_CB_cgh_HX1.ndf
Sscorfa_U_Aarhus_CB_cgh_HX1.pos

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


title: Affymetrix GeneChip Mouse Genome 430 2.0 Array [CDF: Mm_Unigene_10]

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

description:
CDF file was created by Microarray Lab at the Molecular and Behavioral Neuroscience Institute at the University of Michigan.
After probe sequences are BLASTed against the latest UniGene Build and genome sequence, a series of filtering and grouping criteria are applied for different CDF files.
A probe must hit only one genomic location.
Probes that can be mapped to the same target sequence in the correct direction are grouped together in the same probe set;
Each probe set must contain at least three oligonucleotide probes and probes in a set are ordered according to their location in the corresponding exon;

first: Stephanie

last: Hirner

relation: Alternative to: GPL1261 (Alternative CDF [official])

manufacture_protocol: This is identical to GPL1261 but a custom cdf environment was used to extract data. The custom CDF (Mm_Unigene_10) can be found at the Web link below and also as a supplementary file at the foot of the record.


title: Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Gene Name version)

city: Oslo

first: Hilde

last: Johnsen

address: Montebello

department: Genetics

country: Norway

institute: Norwegian Radium Hospital

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


title: NimbleGen/Yamaga Streptococcus pyogenes 7k ID_2222

city: Honolulu

middle: Francis

last: Garcia

state: Hawaii

address: 651 Ilalo Street

department: Tropical Medicine, Medical Microbiology and Pharmacology

country: USA

institute: John A Burns School of Medicine

organism: Streptococcus pyogenes

description:
NimbleGen design name 2005-08-12_B_fragilis_24mer, NimbleGen design ID 2451. A 1:2 expression design for 4,302 genes from Bacteroides fragilis NCTC 9343 and associated plasmid pBF9343 with fourteen 24-mer probe pairs (PM/MM) per gene. Each probe is replicated 3 times. The design includes random GC and other control probes.
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.
1:2 design of 5 strains of S. pyogenes specified by customer. Each probe replicated 2x on chip. DRU update of design 1369.
Streptococcus pyogenes (M1_GAS NC_002737; MGAS10394 NC_006086; MGAS315 NC_004070; MGAS5005 NC_007297; MGAS6180 NC_007296; MGAS8232 NC_003485; SSI-1 NC_004606)

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


title: Affymetrix Human Genome U133 Plus 2.0 Array [MBNI v12 Entrez Gene ID CDF]

status: Public on May 11 2010

city: Grand Rapids

first: Karl

last: Dykema

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Custom CDF environment (version 12 Entrez Gene ID CDF) created by The Molecular & Behavioral Neuroscience Institute (MBNI), University of Michigan.

relation: Alternative to: GPL570 (Alternative CDF [official])

manufacture_protocol: See the Affymetrix website (www.affymetrix.com).


title: Agilent-019314 UW_Lidstrom_2008 Methylobacterium extorquens AM1 11k array

status: Public on Feb 22 2010

first: Ludmila

last: Chistoserdova

address: 616 NE Northlake Place

department: Chemical Engineering

institute: University of Washington

organism: Methylorubrum extorquens AM1

description:
Methylobacterium extorquens strain AM1
Platform annotation based on June 2002 annotation (genome sequencing done by Integrated Genomics, http://www.integratedgenomics.com/genomereleases.html).

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


title: Affymetrix Human Genome U133 Plus 2.0 Array [CDF: HGU133Plus2_Hs_REFSEQ_11.0.1]

city: Yokohama

first: Mariko

last: Okada

address: W518, 1-7-22, Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN RCAI

description: Custom CDF (BrainArray HGU133Plus2_Hs_REFSEQ v11.0.1).

manufacture_protocol: See manufacturer's web site.


title: Agilent Potato bacteria scabturg 15K array

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

organism:
Streptomyces scabiei
Streptomyces turgidiscabies

manufacture_protocol: Agilent 60mer


title: PFGRC Trypanosoma cruzi Oligonucleotide Array v2

city: Athens

first: Todd

last: Minning

state: GA

address: Rm 310 Coverdell

department: CTEGD

institute: University of Georgia

organism: Trypanosoma cruzi

description: There are 192 spot differences between GPL8132 (ie, version 1) and the version 2 array.  Column 'Corresponding v1 ID' identifies the 192 divergent array features.

manufacturer: PFGRC - Pathogen Functional Genomics Resource Center

manufacture_protocol: sense strand


title: LC_MRA-1002_miRMouse_11.0_080411

status: Public on May 19 2009

first: Christoph

last: Eicken

organism: Mus musculus

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: NRC-IBS_human-mouse_miRNA_422

status: Public on Apr 11 2009

city: Ottawa

first: Brandon

last: Smith

state: Ontario

address: 1200 Montreal Road

department: Institute for Biological Sciences

institute: National Research Council Canada

organism:
Homo sapiens
Mus musculus

description: 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.

first: Julie

last: Treadwell

first: Dongling

last: Zhang

first: Iain

last: McKinnell

first: Dao

last: Ly

first: Roy

last: Walker

first: Marianna

last: Sikoska

manufacture_protocol: Oligonucleotide probes (synthesized by MWG-Biotech, High Point, NC and Sigma-Genosys, Saint Louis, MO) were resuspended in Nexterion Spot II buffer (Schott Nexterion, Louisville, KY) at a concentration of 40µM and printed in triplicate onto Nexterion Slide E epoxy-coated glass slides with an Affymetrix 417 Arrayer (Affymetrix, Santa Clara, CA) in a pattern of four 20×18 sub-arrays with 350µm spacing between spots. The spotted “trimeric concatamer” probes were complementary to the mature miRNA sequences concatenated three times, such that a 22 nt miRNA was represented on the array by a 66 nt probe.


title: WUSTL Yersinia pestis 15K array

status: Public on Feb 06 2010

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

organism: Yersinia pestis

manufacturer: Genome Sequencing Center, Washington University School of Medicine

manufacture_protocol: Oligos were synthesized using standard methods by Illumina (San Diego, CA). The oligonucleotides were dissolved at a concentration of 50 μM in 3X SSC with 0.75M betaine and were printed in triplicate on Corning Epoxy slides by a locally constructed linear servo arrayer.


title: LC_MRA-1002_miRMouse_12.0_080901

status: Public on May 11 2009

description: Mouse miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 12.0


title: LC_MRA-1001_miRHuman_13.0_090309

status: Public on Apr 01 2009

organism: Homo sapiens

description: Human miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 13.0


title: [Sc03b_MF] Affymetrix GeneChip S. cerevisiae Tiling 1.0F Array

status: Public on Sep 04 2008

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Saccharomyces cerevisiae

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

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

manufacture_protocol:
Designed for identifying novel transcripts, mapping sites of protein/DNA interaction in chromatin immunoprecipitation (ChIP) experiments, and other whole-genome experiments

Single array comprised of over 3.2 million perfect match/mismatch probe pairs tiled through the complete Saccharomyces cerevisiae genome.

The array also contains probes to interrogate a 2-µm circle plasmid (NCBI Accession J01347).

Probes are tiled at an average of 5 base pair resolution, as measured from the central position of adjacent 25-mer oligos, creating an overlap of approximately 20 base pairs on adjacent probes.


title: NimbleGen Homo sapiens 386K HG18 RefSeq promoter 2006-07-18

status: Public on May 16 2010

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

manufacture_protocol: Roche NimbleGen has developed a proprietary hybridization system, including protocols, buffers, hybridization cassettes, hardware, and temperature control instrumentation that generate highly reproducible and sensitive hybridizations. These protocols have been optimized to require minimum amounts of sample, while providing a hybridization volume that can be continually mixed over the time-course of the incubation. This method generates arrays with extremely high inter-array reproducibility (up to r2>0.99) and very low intra-array coefficient of variation (cv < 12%) across the array surface.


title: Applied Biosystems Human Taqman MicroRNA Array v2.0

status: Public on Dec 31 2009

city: La Jolla

first: Erick

middle: T

last: Tatro

address: 9500 Gilman Dr

department: Psychiatry

institute: University of California San Diego

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


title: Biomphalaria glabrata 70-mer oligo array version 1

status: Public on Jan 01 2010

city: Albuquerque

first: Patrick

last: Hanington

state: NM

address: 1 University of New Mexico

department: Department of Biology, University of New Mexico

institute: Center for Evolutionary and Theoretical Immunology

organism: Biomphalaria glabrata

first: Coen

last: Adema

first: Eric

last: Loker

manufacture_protocol: The 1152 oligonucleotides supplied by IDT, originally provided at a 6nM concentration were resuspended in deionized water to a concentration of 100μM. They were further diluted into 50% water and 50% ESB (Epoxide Spotting Buffer, Integrated DNA Technologies, Coralville, IA) to a final concentration of 40μM for spotting on the microarray. Twenty microliters of each oligonucleotide was transferred to 384 well microarray plates (Genetix, Queensway, New Milton, Hampshire, UK). A total of 300 Epoxide-coated glass slides (Corning Life Sciences, Lowell, MA) were spotted using the QArray Max (Genetix, Queensway, New Milton, Hampshire, UK) and dried for one hour at 80% humidity and then overnight at 60% humidity. A 24 pin microarraying head was used to print the slides. The plate type selected was for a 10μl calibration even though there was 20μl of sample per slide. Eight landing lights (consisting of 5μM Cy5 labeled oligo, 5μM Cy3 labeled oligo, 40μM of unlabeled oligo (GCF3), and ESB) were printed on every subarray for orientation. The printing conditions consisted of 630 stamps/ink and 1 stamp/spot. The stamp time for each spot was 20ms (milliseconds) and the total inking time was 9999ms. A total of 2 touch-offs per inking were used and lasted 4000ms. The sterilization cycle used included 10000ms wash time and 35000ms dry time. All samples were printed first and the markers printed last.Three replicates of each oligo were printed in each field, resulting in 6 replicate spots per slide. Replicates were spotted so that they were not adjacent to each other. A total of 48 subarrays with dimensions 12 x 13 spots were printed on each slide resulting in a 7,488 feature array. All slides were stored in a dessicated mircro array cabinet until use.