title: IFTC Rattus norvegicus 1152

status: Public on Feb 24 2009

city: Hannover

first: Cornelia

last: Repenning

address: Callinstr 5

country: Germany

institute: Institut fuer Technische Chemie

organism: Rattus norvegicus

technology: spotted oligonucleotide

distribution: non-commercial

first: Thomas

last: Scheper

first: Frank

last: Stahl

manufacture_protocol: Oligonucleotide design and synthesis: 50mer oligonucleotides with a 5' aminolink were designed and synthesised by MWG (Ebersberg, Germany). Spotting protocol: To produce microarrays silylated slides were purchased from TeleChemTM International Inc. (Sunnyvale, CA, USA) and the printing of the oligonucleotides was performed by using an AffymetrixTM 417 arrayer. Oligonucleotide solutions were prepared in 96-well-plates containing each 30 µl. The concentration of the printed oligonucleotides was 50 µM in 1x ArrayItTM Microarray Spotting Solution Plus. After spotting, the slides were incubated at 80 °C for 2 h. Slides were blocked in SSC containing 1% BSA (Sigma) for 45 min and rinsed with water for 5 min.


title: Zebrafish 12kb promoter 44K array_slide 5 of 9

status: Public on Feb 19 2009

city: Cambridge

first: Fiona

last: Wardle

address: Downing Street

department: Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

organism: Danio rerio

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol: As described at www.agilent.com


title: Nimblegen 2006-08-02_GRI4489_HG18_ChIP array

status: Public on Feb 27 2009

city: Bristol

first: Anthony

last: Dallosso

address: University Walk

department: School of Cellular & Molecular Medicine

institute: University of Bristol

organism: Homo sapiens

manufacture_protocol: see manufacturer's website


title: BRC Mus musculus 3K

status: Public on Feb 23 2009

city: Szeged

first: Agnes

last: Zvara

address: Temesvari krt 62

country: Hungary

institute: Biological Research Center

organism: Mus musculus

technology: spotted DNA/cDNA

manufacturer: Biological Research Center of the Hungarian Academy of Sciences

manufacture_protocol: 4x4 format, MicroGridII


title: Affymetrix GeneChip N. gonorrhoeae Genome Array

city: Iowa City

first: Megan

middle: L.

last: Falsetta

state: IA

address: 51 Newton Road

department: Microbiology

country: USA

institute: University of Iowa

organism: Neisseria gonorrhoeae

description: This is a custom Affymetrix GeneChip (MPAUT1a520274F) for studying global transcriptional changes in Neisseria gonorrhoeae.  The N. gonorrhoeae probe sets are specific to the FA1090 Oklahoma sequence strain.  This array contains probes for 1744 N. gonorrhoeae open reading frames.  The MPAUT1a520274F GeneChip also contains probe sets for other organisms, including Neisseria meningitidis and Haemophilus influenza.

first: David

middle: W

last: Dyer

first: Robert

middle: J

last: Belland

middle: S

last: Munson

first: Michael

middle: A

last: Apicella


title: Tursiops truncatus cDNA Microarray version 2.0

status: Public on Feb 21 2009

city: Charleston

first: Marine

last: Genomics

state: SC

address: 331 Ft. Johnson Road

institute: Medical University South Carolina

organism: Tursiops truncatus

manufacturer: Hollings Marine Laboratory, Genomics Core

first: Annalaura

last: Mancia

first: Mats

last: Lundqvist

first: Greg

last: Warr

manufacture_protocol: as described by Mancia et al.


title: NimbleGen DMEL ChiP Set 3 of 3

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

organism: Drosophila melanogaster

distribution: commercial


title: Illumina Mouse Ref-6 V1

status: Public on Jan 01 2008

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

technology: oligonucleotide beads


title: NimbleGen DMEL ChiP Set 1 of 3


title: CATMA version 2 TIGR 8.0

status: Public on Feb 25 2009

city: Amsterdam

first: Mark

middle: de

last: Jong

address: Kruislaan 318

country: Netherlands

institute: University of Amsterdam

organism: Arabidopsis thaliana

manufacturer: Utrecht University - Molecular Genetics Group

manufacture_protocol:
Production of the Complete Arabidopsis Transcriptome MicroArray (CATMA)

CATMA (Complete Arabidopsis Transcriptome MicroArray) is a spotted microarray of Arabidopsis thaliana gene specific tags (GSTs). Production took place in a cooperative effort of 12 European research groups [1]. Each group produced part of the 21120 Gene Specific Tags (GSTs), while spotting took place at each individual laboratory. Using a high-resolution spotter enabeled our group to produce all CATMA GSTs on one slide.

GST and primer design

CATMA consists of 21120 GSTs. In order to design these GSTs, a proprietary gene annotation of the Arabidopsis nuclear genome was made with EuGene software [2]. For each annotated gene, a specific region in the first exon was selected and for that region a specific primer pair was designed. Each primer carries a gene-specific 3-prime domain and a 5-prime extension which allowed re-amplification using a small set of extension primers. GST selection and primer design were performed with SPADS software [3].

Amplification

Where possible GSTs were amplified from a collection of IGF[4] and TAMU[5] BAC DNAs. Genomic Col-0 DNA was used if this proved to be impossible. The PCR products were examined by agarose gel electrophoresis, and were only accepted if a single clear band of the correct size was observed. Moreover the sequences of a random selection of BAC-amplified GSTs and in addition all GSTs amplified from genomic DNA were determined. Of 1400 GSTs checked, no incorrect sequences were found. All GSTs were purified, quantified and normalised to 200 ng / µl before spotting.

Spotting

The GSTs are spotted on GAPSII glass slides (Corning) with 48 pins (type 10K) using a MicroGrid II TAS spotter (BioRobotics). A spot size of less than 100 micrometer, and a spot distance of 100 micrometer allows for a total number of 30.000 spots on each slide. Spotting quality is ensured by sampled analysis of deposited buffer salt chrystals, ethidium bromide staining and test hybridisations.

Batch-wise processing

To track the quality of each slide, bar codes are used to administer the spotting runs, and the manufacturers production batch. This provides the ability to quickly recognise series of slides with spotting defects and even the ability to recall certain groups of slides.

Conclusion

The CATMA microarray consists of GSTs that are based on modern gene annotation software which provide a minimal level of sequence overlap. Production of the slides takes place under stringent conditions ensuring high quality and reproducability over a wide range of experiments.

Remarks

1. The general homepage with the contributing groups can be found at www.catma.org
2. Schiex, T, Moisan, A, and Rouzé, P (2001), EUGENE: An Eukaryotic Gene Finder That Combines Several Sources of Evidence, Lecture Notes in Computer Sciences 2066: 111-125
3. SPADS is available on the internet: genoplante-info.infobiogen.fr/spads/
4. Mozo T, Fischer S, Shizuya H, Altmann T (1998) Construction and characterization of the IGF Arabidopsis BAC library, Molecular and General Genetics 258(5):562-70
5. TAMU BAC DNA: hbz.tamu.edu/bac.html


title: Affymetrix GeneChip Rat Genome 230 2.0 Array [CDF:Rn230_Rn_ENTREZG]

city: RTP

first: Johannes

middle: M

last: Freudenberg

state: NC

address: 111 TW Alexander Dr

department: Biostatistics Branch

institute: NIEHS

description: This platform is identical to GPL1355 but a custom CDF environment was used to extract data. We used CDF: Rn230_Rn_ENTREZG (version 10). The CDF can be found at the Web link below.

relation: Alternative to: GPL1355 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: EBT_UA_Daphnia magna_2.3K_version1

city: Antwerp

first: Tine

last: Vandenbrouck

address: Groenenborgerlaan 171

department: Department of Biology

country: Belgium

institute: University of Antwerp

organism: Daphnia magna

manufacturer: Laboratory for Ecophysiology, Biochemisty and Toxicology, University of Antwerp

first: Anneleen

last: Soetaert

first: Wim

last: De Coen

manufacture_protocol:
This microarray is composed of 3 cDNA libraries which are the result of 3 SSH procedures. One SSH was performed with adult vs juvenile gene pools, one with ecdyson exposed vs control organisms and one with starved vs well fed organisms (Soetaert et al., 2006; 2007). In general, the differentially expressed genes were ligated in a TA-vector system using the pGEM-T easy vector (Promega, USA). Escherichia coli competent cells (JM109, Promega) were transformed through heat shock. Clones were amplified with vector specific primers (M13 forward and M13 reverse) and purified by an exosap reaction.
In preparation for spotting, cDNA-inserts of the clones were, amplified using adaptor specific primers (nested primers, Clontech), purified by Montage PCR Plate (Millipore, USA) and loaded into 384-well plates (Genetix, UK) in 50% dimethylsulfoxide at ~150 ng/µl. A Qarray Mini Robot (Genetix) with 16-solid pin-head was used to spot each clone in triplicate onto aminosilane coated glass slides (Generoma microarray slides; Asper Biotech, Estonia). In addition, a set of artificial genes control genes (Lucidea Universal Scorecard, Amersham Biosciences, UK) was spotted in 20 replicates spread over each array: 10 calibration controls, 8 ratio controls and 2 negative controls. After rehydration and drying, the slides were fixated by UV-radiation at 300mJ (UV Stratalinker 2400; Stratagene, USA).


title: Zebrafish 12kb promoter 44K array_slide 2 of 9

first: Fiona

last: Wardle


title: Agilent Human Promoter ChIP-on-Chip Set 244K, combined Microarray (slides 1 and 2) HG18 build

city: Los Angeles

first: Wei

last: Xie

state: CA

address: 611 Young Dr. East, Boyer Hall Rm 332, UCLA

institute: UCLA

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


title: ZB/SBS-NTU Plasmodium falciparum 3D7 10.4K v1.0

city: Singapore

first: Bernardo

last: Foth

email: bfoth@gmx.net, ZBozdech@ntu.edu.sg

address: 60 Nanyang Drive

department: SBS

country: Singapore

institute: Nanyang Technological University

organism: Plasmodium falciparum

first: Guangan

last: Hu

first: Zbynek

last: Bozdech

first: Manuel

last: Llinás

first: Jingguang

last: Li

first: Peter

middle: R

last: Preiser

manufacture_protocol:
Long oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350.
The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biology 2003, 4:R9.


title: Sentrix Mouse-6 Expression BeadChip

status: Public on Aug 02 2006

description: The Sentrix Mouse-6 BeadChip can be used to study expression of over 47,000 transcripts. Array content is based largely on the MEEBO set. The MEEBO content represented on the BeadChips is supplemented with more than 11,000 probes for additional targets from RIKEN FANTOM2 and the NCBI RefSeq transcript databases. 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.

first: Boris

last: Greber


title: Miyajma mouse 10K 1.0

city: Tokyo

first: Chen

last: Yenrong

address: yayoi 1-1-1, bunkyo_ku

country: Japan

institute: the university of Tokyo

manufacturer: Incyte Pharmaceuticals, Inc., Palo Alto, CA


title: Zebrafish 12kb promoter 44K array_slide 6 of 9


title: Human Agilent-016332 custom array

status: Public on Feb 28 2009

city: Bangalore

first: Tapas

middle: Kumar

last: Kundu

state: Karnataka

address: Jakkur

department: Molecular Biology and Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced scientific Research

first: Selvi

last: BR

manufacture_protocol: Refer Manufacturer's Website


title: Zebrafish 12kb promoter 44K array_slide 3 of 9


title: Illumina humanRef-8 v2.0 expression beadchip

status: Public on Dec 07 2007

first: GEO

last: admin


title: INRS-Institut Armand-Frappier Agilent-011868 Rat Oligo Microarray G4130A

status: Public on Feb 20 2009

city: Laval

first: Patrick

last: Devine

state: QC

address: 531 boulevard des Prairies

department: INRS-Institut Armand-Frappier

country: Canada

institute: Institut national de la recherche scientifique

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


title: Mus musculus spotted antigen array

city: La Jolla

first: Gregg

last: Silverman

address: 9500 Gilman Dr

department: Medicine

institute: UC San Diego School of Medicine

technology: spotted peptide or protein

manufacturer: Whatman FAST slides, proteins spotted in Silverman Lab, UCSD School of Medicine

first: Kathy

last: Andrews

first: Liudmila

last: Kulik

first: Michael

middle: V

last: Holers

first: Sherry

middle: D

last: Fleming

first: Chantal

last: Moratz

first: Jason

last: Reuter

first: Aleksey

last: Novikov

first: Kuan

last: Chen

first: Adam

last: Markaryan

first: Richard

last: Quigg

first: George

middle: C

last: Tsokos

manufacture_protocol:
Microarray Printing Protocol
1.	Load Q soft microarray program/ turn on the microarray machine- do not turn it off while the program is on.
2.	Load the 2005916 dual profile.
3.	Click on "change head" icon.
4.	Remove the pins once the machine moves the printing head.
5.	Wash the printing pins using aQuclean diluted to 2% solution with DI water.  Place the pins on four corners of  pin container. Pour 2% aQuclean solution into the sonicator then submerge the printing head into the sonicator for 15 minutes then 5 minutes in DI water with the sonicator on.
It is recommended to "de-gas" without the printing head in the sonicator- run the sonicator with 2% aQuclean without the printing head. (Sonicator runs for 5 minutes per cycle, therefore you have to run the cycle 3 times)
6.	Flush the tube every once in a while.
7.	Water and ethanol tanks fit 5L. Fill the water tank with nano pure water from the back room.
Turn on the filter by pressing the green button on top left. "17" or better is adequate for use.
For ethanol(not actualy ethanol but tween solution), clean out the tank with DI water first then measure 4L nano pure water  in cylinder. Pour the nano pure water into a plastic tank. Use     serological pipette to measure 2mL tween (Tween BP276500 Fischer), place it in plastic tank with the 4L nano pure water.
8.	Drain out waste tank before running the microarray machine.
9.	In room 120, check the clean printing pins under microscope for dirt, or anything that might be
      lodged in between the small space at the tip of the pins.
      - Clean the glass with kimwipe using 70% EtOH.
- Clean the pins with kimwipe then wipe excess moisture.
- Keep the orientation of the pins constant at all times- this may allow us to pinpoint the    problematic pin in printing error.
10.	Dump out aQuclean solution in the sonicator then rinse with DI water. Fill the sonicator with
nano pure water and let the sonicator run for a while without the printing pins in it. Run the sonicator with the printing tips for 5 minutes.
11.	Clean and wipe the machine with 70% EtOH using kimwipes. Wipe in between the panels, back
      of the panel, etc. Also use the ethanol wash bottle to clean the pins.
12.	Place 3 epoxy slides on bottom right most corner for "pre-printing." Place 50 Whatman slides (item# 10485317) on the panel, ensuring that the slides are touching the top & right corners of each printing panels. Cover the last printing panel as all printing panels must be covered in order for the vacuum to work. Keep same lot # for all the slides printed together. Close the lid.
13.	Find sample plates from the refrigerator with "REVCO" sticker. Centrifuge the array sample for compression. Balance the sample plate using a plate that is of same weight. (can be found in cabinet next to the GS-6R centrifuge) Use two green weight to balance the plates.
Centrifuge at speed ~1800 for a minute or so.
14.	After the centrifuge, peel off the aluminum from the sample plate then place the sample plate in
Platform right next to the raised black wash station on the right-hand side of the miroarray machine. Turn on the machine, ensure that the vacuum is on auto. Pour nano pure water into nebulizer, then tightly seal the opening.
15.	Open Qsoft microarraying program. Loading 2005916 Dual. Turn on chiller and vacuum, then
humidity, using icons in the program.
16.	Place the pins in the right most 4 corners. Click on "run"- type: normal, no change in head-yes: Go ahead
17.	Fill out the information on slide batches- mark date and slide lot # and list slide barcode #s.
18.	The machine runs for ~ 5 hours.
GAL File Generation Protocol 3/3/08 (see attached example file for further clarification):
1.	Open data tracking template in Excel
a.	Input Names of Antigens
b.	Input ZZZ for barcode, accession number, and comments for column 2, 4 and 6
c.	Assign Unique name to library name, column 1
2.	Save as CSV (comma-separated values) format in excel
3.	Open CSV file in Notepad and copy all
4.	Re-open excel and paste. All data will now be on one column
a.	Save as .txt (Tab-delimited) file
b.	Reopen file in notepad and make sure that the format is as below:
i.	"20060801_hu array_20061002,zzz,PLATE LOCATION,zzz,SAMPLE NAME ,zzz"
ii.	Make sure that there are NO QUOTES in the first four lines
iii.	Make sure that there are no commas within any given field for the rest of the lines, otherwise you will have to manually find this and delete the commas later
5.	Copy .txt file onto Qarray laptop
6.	Open QArray DataTracking
7.	Tools->Import Process File -> Our .txt file
a.	Next, next, finish…
8.	Open QArray Mini, Load the current routine from which the slides were printed
9.	Data Tracking Tab
a.	Make sure that the export data check mark is checked
b.	Set a file name for your gal file
c.	File format: Gal 4.1 or Gal
d.	Double click groups
i.	Double click the current routine within groups
ii.	Click the Library Manager import entry
iii.	Add the entry that we have made earlier, in step 7
iv.	Delete any other entries within this group
10.	Go to Start Tab
a.	Run Type -> Data Tracking Export Only
b.	Run
c.	The .xml file will be saved in the same directory as your .txt file that you loaded in step 7
d.	The .gal file will be saved in “C:/Program Files/Genetix/QArray/Logs/”, as the filename you gave it
11.	Transfer this file to the scanner computer or the other Dell desktop to perform Spot ID protocol.


title: Zebrafish 12kb promoter 44K array_slide 7 of 9

first: Fiona

last: Wardle


title: Zebrafish 12kb promoter 44K array_slide 9 of 9


title: NimbleGen DMEL ChiP Set 2 of 3

first: Marek

last: Bartkuhn


title: Zebrafish 12kb promoter 44K array_slide 4 of 9


title: Zebrafish 12kb promoter 44K array_slide 8 of 9


title: Mouse Human T15 Apoptotic Cell protein array

status: Public on Feb 22 2009

organism:
Homo sapiens
Mus musculus

first: Ekta

last: Patel

first: Yong-Beom

last: Park

first: Yifang


title: Sentrix HumanRef-8 v2 Expression BeadChip

status: Public on Apr 17 2008

first: GEO

last: admin


title: Zebrafish 12kb promoter 44K array_slide 1 of 9


title: Streptococcus pneumoniae whole genome tiling array

status: Public on Feb 10 2009

city: starkville

first: Ranjit

last: Kumar

state: MS

address: 240 Wise Center Drive,PO Box 6100

department: Dept of Basic Science

institute: MSU

organism: Streptococcus pneumoniae

description: Maskless Array Synthesizer (MAS) technology

first: Pratik

last: Shah

first: Ed

last: Swiatlo

first: Bindu

last: Nanduri

first: Shane

last: Burgess

first: Mark

middle: L

last: Lawrence

manufacture_protocol: Available at manufacturer's website: www.nimblegen.com


title: Broad NimbleGen 385k Phytophthora infestans

status: Public on Feb 16 2009

city: Cambridge

first: Brian

last: Haas

state: MA

address: 7 Cambridge Center

institute: Broad Institute

organism:
Solanum lycopersicum
Phytophthora infestans

first: Liliana

last: Cano

first: Chad

last: Nusbaum

first: Sophien

last: Kamoun

manufacture_protocol:
Roche NimbleGen’s proprietary Maskless Array Synthesis (MAS) technology uses digital light processing and rapid, high-yield photochemistry to synthesize
long oligo, high-density DNA microarrays with extreme flexibility.  Approximately seven 60mer oligo probes were designed for each target on the array.  Targets include 46,098 Phytopthora infestans genome features (annotated genes, pseudogenes, ab initio gene predictions, genomic regions with homology to known proteins), 2,147 P. infestans reference mobile element sequences, and an additional 7,215 tomato expressed genes.


title: IAH/VLA/CEFAS Virus Detection Array 6K VA3

status: Public on Feb 17 2009

city: Roslin

first: Michael

middle: Bryan

last: Watson

state: Midlothian, EH25 9PS

address: Roslin Biocentre

department: ARK-Genomics

institute: The Roslin Institute

organism: Viruses

description: Microarray for the detection of viruses, produced by the IAH, the VLA and CEFAS.

first: P

last: Britton

first: D

middle: P

last: King

first: A

last: Abu-Median

first: J

last: Dukes

first: M

last: Banks

last: Dastjerdi

last: Stone

manufacture_protocol:
Oligos were synthesised commercially and spotted to Epoxy-coated glass slides using a Migrogrid II robot (Biorobotics) using previously published protocol [1]
1. Burton, J.E., et al., Development of a multi-pathogen oligonucleotide microarray for detection of Bacillus anthracis. Mol Cell Probes, 2005. 19(5): p. 349-57.


title: FAP-Human-4.8K03

status: Public on Feb 13 2009

city: São Paulo

first: Alex

middle: Fiorini

last: Carvalho

address: Rua Professor Antonio Prudente, 211

country: Brazil

institute: Fundação Antonio Prudente

middle: F

manufacture_protocol: Bacteria were grown in LB (Luria-Bertani) medium containing ampicillin (250mg/ml). Inserts were amplified by PCR using M13 reverse and forward primers and products were submitted to 1% agarose gel stained in ethidium bromide for quality control. cDNA clones with single amplicons were purified by filtration in Sephadex G50 (GE Healthcare), following the manufacturer’s directions, printed onto Corning glass slides (Corning) and fixed by UV crosslink.


title: STv7bE(2)ws_MMCC

status: Public on Feb 12 2009

city: Irvine

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

organism: Salmonella enterica

description: whole slide version of STv7E(2)

first: Steffen

last: Porwollik

first: Pui

last: Cheng

first: Xiao-Qin

last: Xia

manufacture_protocol: custom made Salmonella PCR product array


title: Arizona Arabidopsis thaliana 29K v1.0 version 02_07_02

status: Public on Feb 15 2009

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

manufacturer: Arizona Arabidopsis Oligonucleotide Microarray

first: María

last: Busi

middle: E

last: Gomez-Lobato

first: Sebastián

last: Rius

first: E

last: Zabaleta

first: Diego

last: Gómez-Casati

first: Alejandro

last: Araya

manufacture_protocol: The arrays were printed using the Operon Arabidopsis Genome Oligo Set Version 2.0 (02_07_02). This set comprised 26,000 oligonucleotides.  Print Format 2 (which is used currently) involves one array printed using 48 pins.  It comprises 12 metarows and 4 metacolumns, and the subarrays comprise 24 columns and 25 rows.


title: INRArray 01.4

status: Public on Feb 19 2009

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

manufacturer: Laboratoire de Pharmacologie-Toxicologie INRA UR66, Toulouse, France

manufacture_protocol: Genes were identified from  the literature and from microarray screenings of liver RNA extracted from mice treated with RXR (LG100268) or PPARalpha (fenofibrate) pharmacological activators. PCR primers were selected to amplify a specific fragment of 295 selected cDNAs. The amplified cDNAs were cloned into pCR 2.1 TOPO vector (Invitrogen). The list of all cDNA fragments and their sizes are available at www.inra.fr/internet/Centres/toulouse/pharmacologie/lpt.htm. In addition, a set of 13 yeast cDNAs (spikes) were identified by hybridizing mouse liver, kidney and intestine total RNAs to a yeast macroarray and selecting spotted yeast cDNAs that did not yielded a significant signal. These yeast cDNAs were cloned into pCR 2.1 TOPO to produce the spotted probes and into pSP64(polyA) vector (Promega) to produce the corresponding mRNAs to be spiked into the samples before labeling. Twelve of the Yeast mRNAs (one was used as negative control) were produced by in vitro transcription, assayed and controlled on a Bioanalyzer 2100 (Agilent) before being mixed together. The absence of cross-hybridization of the spiked-in yeast mRNAs with the spots corresponding to mouse genes on INRArray was also controlled. All cDNAs (mouse and yeast) were then amplified using common PCR primers targeting the pCR 2.1 cloning vector at both sides of the inserts. PCR amplicons were assayed and diluted at 200 ng/µL in 50% DMSO before being spotted onto nylon membranes (Millipore) using a VersArray Chipwriter Pro (Biorad) at the GenoToul biochip facility (http://biopuces.genotoul.fr/). During spotting, wells containing 50% DMSO without amplicons were systematically inserted between wells containing amplicons to assess background signal on the whole surface of the arrays. The final macroarrays contained 768 spots (4 x 12 pins each spotting a 4x4 subgrid).


title: IPPE Rice MPSS

status: Public on Feb 02 2009

city: Shanghai

first: Hong-Wei

last: Xue

address: 300 Fenglin Road

country: China

institute: Institute of Plant Physiology and Ecology,Shanghai Institutes of Biological Sciences

organism: Oryza sativa

technology: MPSS

description: All MPSS was performed as described by Mineno et al.(Nucleic Acids Res. 2006 1765:1771).

distribution: virtual

first: Liang-Jiao

first: Jing-Jing

last: Zhang


title: Food Safety Potato cDNA Microarray 1.0

status: Public on Feb 01 2009

city: Wageningen

first: Jeroen

last: van Dijk

address: Bornsesteeg 45

institute: RIKILT, institute of food safety

organism:
Solanum tuberosum
Solanum phureja

first: Kok

middle: J

last: Esther

first: Katarina

last: Cankar

manufacture_protocol: PCR fragments were purified through Sephadex G-50 columns (Sigma-Aldrich, USA) and precipitated by overnight incubation with of 1/10 V 3M sodium acetate (pH 5.2) and 1 V of isopropanol. The pellets were washed with 70% ethanol, air-dried, redissolved in 12 μl 5 x SSC and used for spotting. Microarrays were spotted on sylilated slides (CELAssociates, USA) at 19°C and 55% relative humidity using Microgrid instrument (Apogent technologies, USA) in 6 blocks containing 26 x 26 spots. As positive controls three different luciferase fragments corresponding to the 5', middle and 3' part of the cDNA, as well as the entire luciferase cDNA were spotted seven times in each block of the array as well as a Salmonella gene fragment as a negative control. Microarrays were dried and stored at room temperature until use. Spotting quality was assessed for two of the spotted arrays in the series by staining the slides with 0.2 μM cyanine nucleic acid dye POPO-3 (Molecular probes, USA). Prior to hybridisation free aldehyde groups were blocked with NaBH4.


title: Illumina Mouse v2 MicroRNA expression beadchip

status: Public on Feb 11 2009

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

description:
The mouse miRNA v1 panel targets 656 mouse miRNAs (> 96% coverage of miRBase release 12).

Please use the GEO Data Submission Report Plug-in v1.0 for Gene Expression which may be downloaded from https://icom.illumina.com/icom/software.ilmn?id=234 to format the normalized and raw data.  These should be submitted as part of a GEOarchive.  Instructions for assembling a GEOarchive may be found at http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html

manufacture_protocol: see manufacturer's website


title: Agilent_Dm_4.3_112_tiling_b

status: Public on Feb 07 2009

city: Durham

first: David

last: MacAlpine

address: Box 3813 DUMC

department: Pharmacology and Cancer Biology

institute: Duke University Medical Center

description: ChIP resolution tiling array for modENCODE. Average probe spacing of 112 bp for Drosophila genome (5.1). 2 of 4 array set.

manufacture_protocol: Agilent Technologies


title: FAP-Human-4.8K03 ver01

first: Alex

last: Carvalho


title: ULB-Erasme_MGE_Staphaureus_v2.00

city: Brussels

first: Ricardo

middle: Luis

last: De Mendonca

address: Route de Lennik 808

institute: ULB - Hôpital Erasme

organism: Staphylococcus aureus

description: 1326 probes recognize 403 target genes located on the accessory or core variable genome. Target genes encode antimicrobial resistance factors (35 %), virulence factors (28 %) and adhesins (31%).Controls:A total of  102 controls are included in the set. This encompasses:Negative controls:  84 buffer only and 6 probes corresponding to human actin and gapdh genes were positioned throughout the array to assist in determining background. Each human negative control was spotted in triplicatePositive controls:  12 probes corresponding to two distinct 23S rRNA genes and two distinct 16S rRNA genes. Each control was spotted in triplicate.

first: Farid

last: El Garch

first: Marie

last: Hallin

first: Marc

last: Daukandt

manufacture_protocol: Custom made commercial DNA-microarray selectively target 403 staphylococci genes. 60-mer oligonucleotides were designed to specifically target those genes by using the Array Designer 4.0 software (Eurogentec, Liège, Belgium - www.eurogentec.com/product/research-oligonucleotide-design.html). A local BLAST database containing the eight complete S. aureus genomes was used to ensure probe specificity. Oligonucleotide probes were synthesized (http://www.eurogentec.com/product/research-oligonucleotide-synthesis-and-quality-control.html), then printed in triplicate on UltraGaps glass slides (Corning) with the VersArray® ChipWriter Pro System (Bio-Rad)


title: Lactococcus lactis subsp. lactis 15K 60-mer array, Version 1, our ID KF147_IL1403

city: Amsterdam

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

institute: Vrije Universiteit Amsterdam

organism: Lactococcus lactis subsp. lactis

description: This array contains 60-mer probes that are designed for L. lactis strains KF147 and IL1403. The sequence of strain IL1403 is present in public databases, Acc. Nr. AE005176.


title: Illumina Mouse v1 MicroRNA expression beadchip

description:
The mouse miRNA v1 panel contains 380 mouse microRNAs described in miRBase v9.1.

Please use the GEO Data Submission Report Plug-in v1.0 for Gene Expression which may be downloaded from https://icom.illumina.com/icom/software.ilmn?id=234 to format the normalized and raw data.  These should be submitted as part of a GEOarchive.  Instructions for assembling a GEOarchive may be found at http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html


title: Eurogentec AG S. pombe ORF array 11k (spD080C)

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

organism: Schizosaccharomyces pombe

description:
Schizosaccharomyces pombe
4976 ORFs spotted in duplicate on glass slide
Keywords = yeast ORF DNA microarray
Reference:    Xue Y, Haas SA, Brino L, Gusnanto A et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 2004 Jan 15;21(1):25-39. PMID: 14745780

first: Yongtao

last: Xue-Franzen

first: Anna

last: Johnsson

manufacture_protocol:
Primary PCR: The PCR reactions are performed using tagged genome specific primers in the presence of genomic DNA (provided by your laboratory). We normally achieve a success rate of 93 % of PCR reactions. For the failed PCR reactions we perform three different protocols of PCR conditions, which include different MgCl2 concentrations and different Taq polymerase. We should normally get an additional 2 % working and reach a success rate of 95 % in total. We check 5 % of the total oligos by Mass Spectrometry and will re-synthesize maximum 2 % of the oligos based on a newly designed primer. We will perform the PCR reactions with the new designed oligonucleotides with the standard PCR protocol. Following this process we reach usually 97 % success rate.
Secondary PCR: amplifications will be performed using a single pair of primers annealing to tag sequences introduced on primary PCR primers. These PCR amplifications will also be controlled by agarose gel electrophoresis and repeated if required reaching a minimum of 95 % success rate. The final PCR products will contain an amino group at their 5' end to promote the attachment of the predicted gene coding DNA strand to the treated glass slides.


title: JCVI PFGRC Fusobacterium nucleatum 21K v3 array designed primarily based on strain ATCC10953

status: Public on Jan 27 2009

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Fusobacterium nucleatum

description: This set includes 4230 oligonucleotides, has 21168 spots distributed in 48 blocks.

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


title: SLA/Immune Response/NRSP8 Pig 70 mers Oligonucleotides 3.8K + 13.3K v1

city: Jouy-en-Josas

first: Sylvain

last: Marthey

address: Domaine de Vilvert Bat 320

department: Animal Genetics

institute: INRA

organism: Sus scrofa

description: The oligos set used for this microarray is a mix of the 13,3k generic set from Operon and a 3.8K SLA/Immune response specific set designed by Yu Gao (LREG-INRA) and synthetised by Operon.

manufacture_protocol:
1-1. Oligos from 13K set are arrayed by Operon in Genetix 384-well V-bottom plates. Each well contains 600 pmol of 70-mer oligo.
1-2. Resuspend oligos in water(20µM).
1-3. Incubate at room temperature during a night shaking plates to aid resuspension of DNA.
1-4. Deep freeze and defrost centrifuging plates at 1000 rpm for 16 minutes then 2000 rpm for 3 minutes.
1-5. Take 5 µl of oligos solution and put it in new Genetix polypropylene v-bottom plates (cat# X7022)
1-6. Add 5 µL of 1X Corning Printing Buffer to each well and mix.
2-1. Oligos from 3.8K SLA/Immune response set are arrayed by Operon in Genetix 384-well V-bottom plates. Each well contains 200 pmol of 70-mer oligo.
2-2. Resuspend oligos in water(20µM).
2-3. Incubate at room temperature during a night shaking plates to aid resuspension of DNA.
2-4. Deep freeze and defrost centrifuging plates at 1000 rpm for 16 minutes then 2000 rpm for 3 minutes.
2-5. Add 5 µL of 1X Corning Printing Buffer to each well and mix.
3-1. cDNA from Lucidea microarray Scorecard (GE Healthcare) are resuspended in water (100ng/µl).
3-2. Incubate at room temperature during a night shaking plates to aid resuspension of DNA.
3-3. Deep freeze and defrost centrifuging tubes at 1000 rpm for 16 minutes then 2000 rpm for 3 minutes.
3-4. Take 5 µl of solution and put it in new Genetix polypropylene v-bottom plates (cat# X7022). Each cDNA Lucidea scorecard are put 4 times.
3-5. Add 5 µL of 1X Corning Printing Buffer to each well and mix.
4. Centrifuge plates at 2000 rpm for 3 minutes.
5. Oligos are ready for spotting.
6. Spotting on glass slides (Corning, Ultragaps), with 48 Microspotting pins Stealth 3 on Chipwriter (Virtek), with control of humidity (45-50%).
7. Fixation of the oligos slides with UV (600 mJoules).
8. Storage the slides in a vacuum.
9. After the print run is completed, cover oligos plates with seals and deepfreeze them at -20°C in a protected environment.


title: Illumina human-6 v2.0 expression beadchip (extended)

status: Public on Jan 13 2009

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Homo sapiens

first: Felix

last: Engel

first: Frederic

last: Blond


title: Agilent_Dm_4.3_112_tiling_a

organism: Drosophila melanogaster

description: ChIP resolution tiling array for modENCODE. Average probe spacing of 112 bp for Drosophila genome (5.1).  1 of a 4 array set.


title: University of Washington - Rathod Lab - Plasmodium falciparum - 7665 - v1.0

status: Public on Nov 20 2008

city: Notre Dame

first: Michael

last: Ferdig

state: IN

address: 280 Galvin Life Science

institute: University of Notre Dame

manufacturer: Pradipsinh Rathod Lab; University of Washington

first: Joseph

last: Gonzales

first: Pradipsinh

middle: K

last: Rathod

middle: T

manufacture_protocol: Microarrays contained 7665 70mer oligonucleotide probes representing 5150 Plasmodium falciparum ORFs kindly provided by Dr. Joseph DeRisi (University of California, San Francisco; San Francisco, California). The majority of the oligonucleotides for printing the array corresponded to the Qiagen Operon set (Operon Biotechnologies, Inc.; Huntsville, Alabama), but some additional sequences matched ORFs in the original P. falciparum sequence reads. The oligonucleotides were printed on polylysine-coated slides using a new generation, ultra fast, linear servo driven DeRisi microarrayer.


title: Agriculture and Agri-Food Canada B. napus Westar 15K v1.0

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

organism: Brassica napus

description: 2 spots printed for each probe

manufacture_protocol: The B. napus 50-mer oligo array was developed by Agriculture and Agri-Food Canada using the collection of approximately 150,000 3′ and 5′ B. napus ESTs derived from cDNA libraries representing a range of vegetative tissues of the homozygous line DH12075. A custom unigene set of sequences identified from the collection was used for oligo design with the aim of developing a resource with the potential to detect differential expression between members of closely related multi-gene families within the polyploid B. napus genome. A full description of the development of the set of 15,000 50-mer oligos will be published separately (Sharpe et al., in preparation). The oligos were synthesized by Illumina (San Diego) and printed onto epoxide slides (Corning Inc. Lovell, MA, USA) using a 48-pin GeneMachines arrayer at the University of Alberta Microarray Facility (Edmonton, AB, Canada) Microarray Facility. Each one of the 48 sub-arrays were designed with 26 columns × 25 rows for a total capacity of 31,200 features. Each of the 15,000 oligos were replicate spotted within each sub-array. The Stratagene Alien oligo set (La Jolla, CA, USA) and phosphate buffer blanks were added as controls.


title: Agilent-014707 Human Promoter ChIP-on-Chip Set 244K, Microarray 2 of 2 G4489A (Probe name version)

status: Public on Feb 09 2009

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Human Promoter ChIP-on-Chip Set 244K 2 of 2

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 GPL4125.

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


title: Agilent-014706 Human Promoter ChIP-on-Chip Set 244K, Microarray 1 of 2 G4489A (Probe name version)

description:
Human Promoter ChIP-on-Chip Set 244K 1 of 2

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 GPL4124.


title: Mouse Genome 430 2.0 Array [ENSG build 46 (v10) CDF]

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

organism: Mus musculus

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

manufacture_protocol: This is identical to GPL1261 but a custom cdf environment was used to extract data. We used custom chip definition files (CDF) based on Ensembl gene annotation from build 46 rather than Affymetrix annotation (Dai et al., PMID: 16284200).


title: UHN Homo Sapiens cDNA microarray 10K

city: Toronto

first: Susan

last: Done

address: 610 University Ave

institute: Ontario Cancer Institute

manufacturer: University Health Network Microarray Centre, Toronto, Canada, www.microarrays.ca


title: mouse-6 v1.1 (Illumina)

status: Public on Feb 11 2008

description:
This platform represents the commercially-available Illumina mouse-6 v1.1 expression beadchip, but is not intended for general use.
Please contact the GEO staff if you need help submitting Illumina data.


title: University of Missouri Illumina mouseRef-8 23K

status: Public on Dec 22 2008

description: The Mouse-8 BeadChip can be used to study expression of over 24,000 mouse transcripts based on MEEBO, RefSeq and RIKEN FANTOM2 content. researchers can generate whole-genome expression profiles for 8 samples in parallel on a single BeadChip.


title: HumanRef-8 v2 Expression BeadChip

status: Public on Jun 01 2007

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.

first: Fumiaki

last: Sato

first: Tetsuo

last: Ito

first: Stephen

last: Meltzer


title: Illumina Human v1 MicroRNA expression beadchip

last: Illumina Inc.

description:
The human v1 miRNA panel, containing 735 microRNAs, was designed against miRBase v9.1 and potential miRNAs identified in a RAKE analysis study.

Please use the GEO Data Submission Report Plug-in v1.0 for Gene Expression which may be downloaded from https://icom.illumina.com/icom/software.ilmn?id=234 to format the normalized and raw data.  These should be submitted as part of a GEOarchive.  Instructions for assembling a GEOarchive may be found at http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html


title: Sentrix Mouse-6 Expression BeadChip (2)

status: Public on Apr 12 2008


title: HumanRef-8 v2 Expression BeadChip ( 2 )

status: Public on Oct 16 2007

first: Leon

last: Wescombe


title: P.stutzeri A1501

status: Public on Apr 20 2007

city: Beijing

first: yongliang

last: yan

address: zhongguancun south 12th

institute: CAAS

organism: Stutzerimonas stutzeri A1501

manufacturer: Biotechnology research institute of China academy of agricultural sciences

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


title: Sentrix® HumanRef-8RD BeadChip

status: Public on Aug 08 2005

description: The Sentrix® HumanRef-8RD BeadChip is an early-access version of a multi-sample, gene expression microarray with content derived from the NCBI RefSeq database. Designed to interrogate over 23,000 transcripts per array, probe content was optimized prior to commercial release and the first-generation research product (8RD) was subsequently replaced by the HumanRef-8 BeadChip.  Researchers can generate genome-wide expression profiles for eight samples in parallel on the BeadChip.  Each array on the BeadChip is composed of 3-micron features with 30-fold average feature redundancy.  Every features is quality-controlled during array manufacturing.  Probes are fully screened, full-length 50-mers.  Assay requires 50-100ng of total RNA input.


title: Illumina HumanHap550 Genotyping BeadChip v1

status: Public on Feb 05 2008

description: Version 1, Illumina Sentrix HumaHap550 Genotyping BeadChip

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


title: HumanHap300-2 v2.0 Genotyping BeadChip

status: Public on Jul 31 2007

description:
HumanHap300-2 v2.0 Genotyping BeadChip provides genome-wide coverage using >318,000 tag SNPs chosen from the International HapMap Project.

The HumanHap300-Duo BeadChip is a two-sample format and contains:
• >318,000 tag SNPs derived from the Phase I and II HapMap data, >42,000 of these from Phase II HapMap data.
• A higher density of tag SNPs in regions of the genome within 10kb of a gene or in evolutionarily conserved regions.
• Approximately 7,300 nsSNPs (non-synonymous amino-acid changing SNPs).
• A higher density of SNPs across Major Histocompatibility Complex (MHC) regions.
• Higher genomic coverage with fewer SNPs compared to wholegenome genotyping strategies that use randomly selected SNPs.
• Approximate 5kb median SNP spacing, providing unprecedented resolution for detecting chromosomal aberrations.
• The ability to analyze matched (paired) samples for LOH and DNA copy number analysis applications.
• Over 52,000 SNPs in reported copy number variant (CNV) regions1.

first: Jonathan

last: Pevsner

manufacture_protocol: other


title: JCVI PFGRC Fusobacterium nucleatum 21K v3 array designed primarily based on strain ATCC 25586

first: PFGRC

last: JCVI


title: NIAID Cgaa -- Candida glabrata 6K

status: Public on Feb 13 2009

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

organism: Nakaseomyces glabratus

manufacturer: NIAID, Genomic Technologies Section (NIH)

first: Guojian

last: Jiang

manufacture_protocol: Microarrays were printed with an Omnigrid robotic arrayer by Genomic Solutions ( http://www.genomicsolutions.com ) that is fitted with a printhead and 32 SMP3 print tips from Telechem ( http://www.arrayit.com ). Candida glabrata expression oligonucleotide probes were purchased from Institut Pasteur. An additional 384 well plate containing control oligos was also included. Oligonucleotide probes in 384-well polypropylene plates (Genetix, 384 micro array) were dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normalized 25 micromolar concentration. Spot density was 240 microns (center-to-center). The microarrays were printed on Epoxy Slides from Corning (Catalog # 40042) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.