title: SAGE:17:NlaIII:Trypanosoma brucei brucei

status: Public on Jul 03 2007

last: GEO

country: USA

organism: Trypanosoma brucei brucei

technology: SAGE NlaIII

description: This is a virtual platform for SAGE libraries generated for Trypanosoma brucei brucei using NlaIII as an anchor enzyme.

distribution: virtual


title: AECOM Melnick Nimblegen 12 plex array

status: Public on Jul 07 2007

city: Bronx

first: Ari

last: Melnick

state: NY

address: 1300 Morris Park Ave - Chanin 302

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

organism: Homo sapiens

technology: in situ oligonucleotide

description: Genomic array containing whole locus of custom selected genes, based on Human May 2004 Assembly (NCBI Build 35).

distribution: custom-commercial


title: NimbleGen_S.cerevisiae_tiling_array

status: Public on Jul 31 2007

city: Cambridge

first: Antonis

last: Kirmizis

state: England

address: Gurdon institute, Tennis Court Rd

country: United Kingdom

institute: Antonis Kirmizis

organism: Saccharomyces cerevisiae

description: 379K element tiling array based on sacCer1 build of the yeast genome. The array contains 50-mer oligonucleotides, positioned at every 64 basepairs (bp) throughout the yeast genome representing both DNA strands.

first: Helena

last: Santos-Rosa

first: Christopher

middle: J

last: Penkett

first: Michael

middle: A

last: Singer

first: Michiel

last: Vermeulen

first: Matthias

last: Mann

first: Jurg

last: Bahler

first: Roland

middle: D

last: Green

first: Tony

last: Kouzarides

manufacture_protocol: Tiling array; see NimbleGen website


title: DKFZ CpG Island Chip

city: Heidelberg

first: Stefan

middle: M

last: Pfister

address: INF 580

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center

technology: spotted DNA/cDNA

description: Corning GAPSII

distribution: non-commercial

first: Christof

last: Schlaeger

first: Bernhard

last: Radlwimmer

first: Peter

last: Lichter

manufacture_protocol: Whole-genome CpG Island-array. CpG Island clones were amplified by colony-PCR and reamplified with the same primer pair. PCR products were dissolved in 3xSSC, 1.5M betaine and spotted as triplicates on aminosilane-coated slides.


title: NeuroTrans_UMR7637

status: Public on Jul 30 2007

city: Paris

first: Luce

last: Dauphinot

address: 47 boulevard de l'hôpital

department: ICM

country: France

institute: INSERM U1127-CNRS UMR7225-UPMC

organism: Mus musculus

technology: spotted oligonucleotide

first: MC

last: Potier

first: L

first: G

last: Golfier

first: F

last: Richard

manufacture_protocol:
50-mers oligonucleotide primers synthesized by EuroGentec.
spotting realized on CodeLink® activated glass slides (GE Healthcare) using a MicroGrid II spotter (Biorobotics) by the society Genescore.


title: Hitachisoft AceGene Mouse Oligo Chip 30k 1 Chip Version

status: Public on Jun 18 2004

last: Hitachi Software Engineering Co.

country: Japan

institute: Hitachi Software Engineering Co., Ltd.

description: Hitachisoft AceGene Mouse Oligo Chip 30K 1 Chip Version

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: VMSR Mus 20K version 2

status: Public on Jul 12 2007

city: Los Angeles

first: Mark

middle: H.

last: Chin

state: CA

address: 650 Charles E. Young Dr

department: Human Genetics

institute: UCLA

first: Shawn

middle: W

last: Levy

first: Vicky

last: Amann

first: Braden

last: Boone

manufacture_protocol:
1. Microarrays containing 22,172 cloned genes from the National Institute on Aging 15k cDNA clone set, mouse sequence-verified clones from Research Genetics and several control genes were generated by the Vanderbilt Microarray Shared Resource.
2. Briefly, all cDNA clones were amplified (Hegde, P, et. al., Biotechniques, 29, 548-562.) and verified by gel electrophoresis.
3. The dried PCR products were then resuspended in 40 ml VMSR buffer A [Vanderbilt Microarray Shared Resource, Nashville, TN] resulting in an average concentration of 400 – 700 mg/ml per product.
4. The PCR products were then transposed to 384 well plates and robotically arrayed using a BioRobotics MicroGrid II microarray printing robot (Apogent Discoveries, Hudson, NH) onto amine-coated  glass slides (TeleChem International, Sunnyvale, CA).
5. The microarrays were then crosslinked using  80mjoules of ultraviolet energy (Stratgene Stratalinker, LaJolla, CA).
6. Following crosslinking, the arrays were baked for two hours at 70°C in a standard oven and stored under low humidity conditions until use.


title: ARK-Genomics G. gallus 20K v1.0

status: Public on Jul 11 2007

city: Roslin

last: Fell

state: Midlothian

address: Roslin Institute

department: Bioinformatics

institute: ARK-Genomics@Roslin Institute

organism: Gallus gallus

description: This is an oligo array containing 20460 elements. Oligos were designed using gene predictions from Ensembl and TIGR, together with full-length cDNAs from the BBSRC UMIST ChickEST database (http://chick.umist.ac.uk/) and chicken bursal EST sequences from Jean-Marie Buerstedde's DT40 database. Sequences from these resources were aligned together and oligos were designed against regions in common to more than one dataset. Oligos were then designed using OligoArray2.0.

manufacturer: ARK-Genomics, Roslin Institute, Roslin, Midlothian, EH25 9PS, United Kingdom

first: Wilfrid

last: Carre

first: Richard

last: Talbot

first: Andy

last: Law

first: John

last: Young

first: Pete

last: Kaiser

manufacture_protocol:
Oligos were resuspended in Corning Pronto Epoxide spotting solution to
give a final concentration of 20uM. DNA was printed on Corning Epoxide
slides using a Genomic Solutions MicroGrid II arrayer and the MicroSpot
10K pins, according to manufacturer's instructions. All printing was
carried out in conditions of constant humidity (52% RH) and temperature
(20C) in a room supplied with HEPA filtered air. Prior to printing the
pins were cleaned by ultra-sonication in water and if necessary 50mM
potassium hydroxide. A test print of all pins was carried out by
printing Cy3 streptavidin conjugate dye in printing buffer onto epoxide
slides and printing 100 features per pin. When all pins were printing
consistent size spots for more than 80 features they were accepted as
ready to print. The MicroGrid II was then programmed for the array print
run, with a grid layout file prepared to allow duplicate printing at
random within a patch. At the end of the print run the slides were
removed following the program instructions in preparation for post
processing.
Slides dessicated overnight and then transferred to a humid chamber (45%
humidity, 42C) for 8 hours. The slides were then washed in 0.2% SDS
(room temperature) for 2 minutes with agitation before being rinsed in
three water washes (30seconds, 30 seconds, 1 minute) with agitation.
After these steps the slides were then incubated in water at 50C for 20
minutes before spin drying. The slides were then stored in a desiccator
in the dark ready for use.


title: Escherichia coli 5K oligo microarray

status: Public on Jul 16 2007

city: Bucheon

first: Pil

last: Kim

state: Gyunggi

address: 43-1 Yokkok2-dong

country: South Korea

institute: Catholic Univ. of Korea

organism: Escherichia coli

description: Escherichia coli 5K oligo microarray produced by Digital Genomics, Inc. Seoul, Korea.

first: SUNG-HAN

last: KIM

first: DONG-YOON

last: PARK

first: LANG-HO

last: LEE

first: HAN-YONG

first: YOON-JUNG

last: NAM

first: HYE-YOUNG

last: JEONG

first: DONG-SOO

last: RYU


title: IMP Vienna microarray facility Murine 23K cDNA array version 20.1

status: Public on Jul 13 2007

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohr-Gasse 7

country: Austria

institute: Research Institute of Molecular Pathology

manufacture_protocol:
Arraying
1. Transfer PCR reactions to 96-well V-bottom tissue culture plates (Costar).Add 1/10 vol. 3M sodium acetate (pH 5.2) and equal volume isopropanol. Store at -20 C for a 2 hours.
2. Centrifuge in Sorvall at 3500 RPM for 45 min. Rinse with 70% EtOH, centrifuge again and dry.
2. Resuspend DNA in 12ul 3X SSC for a 4 hours and transfer to flexible U-bottom printing plates.
4. Spot DNA onto poly-l-lysine slides with an arrayer.
Post processing.
1. Rehydrate arrays by suspending slides over a dish of warm ddH2O. (~1 minute)
2. Snap-dry each array (DNA side up) on a 100°C hot plate for 3 seconds.
3. UV X-link DNA to the glass by using a Stratalinker set for 60 milliJoules
4. Dissolve 5g of succinic anhydride (Aldrich) in 315mL of n-methyl-pyrrolidinone.
5. To this, add 35mL of 0.2M NaBorate pH 8.0 (made by dissolving boric acid in water and adjusting the pH with NaOH), and stir until dissolved.
6. Soak arrays in this solution for 15 minutes with shaking.
7. Transfer arrays to 95°C water bath for 2 minutes
8. Quickly transfer arrays to 95% EtOH for 1 minute.
9. Remove excess liquid from slides by spinning the rack of slides on microtiter plate carriers at 500rpm.


title: Hitachisoft AceGene Human Oligo Chip 30K Subset A

last: Hitachi Software Engineering Co.


title: Hypertension Microarray Platform

city: Phildelphia

first: Rishi

last: Khan

state: PA

address: 1020 Locust Street Room 381

department: Pathology

institute: Thomas Jefferson University

organism: Rattus norvegicus

middle: L

first: Hester

last: Liu

manufacture_protocol: Microarray Manufacture. Microarrays were fabricated using a rat clone set (GF200; ResGen Huntsville, AL, and Invtrogen, Carlsbad, CA) for cDNA microarrays consisting of approximately 8,800 sequence-verified non-redundant (as of Unigene build 150). The cDNA clones from all rat cDNA targets were prepared from freshly grown overnight bacterial cultures by PCR amplification using GF200 primers (Invitrogen, Carlsbad, California). PCR products were purified and verified by agarose gel electrophoresis, and the yield was determined spectrophotometrically (NanoDrop Inc., Wilmington, DE). cDNAs were mixed with an equal volume of DMSO (10-70 ng/ul) and printed onto Corning cDNA slides (Corning, Corning, NY) using a MicroGrid II arrayer (Genomic Solutions, Ann Arbor, MI). Microarrays were air dried for 30 min and cross-linked by UV irradiation. We printed arrays of 18,240 spots representing ~9000 clones in adjacent duplicate spots. The arrays used in the present study had approximately 5,300 annotated genes based on the Entrez Gene database.


title: Zebrafish 33K (Compugen, MWG, Operon)

status: Public on Jul 20 2007

city: Bethesda

first: Benjamin

last: Feldman

state: MD

address: 35 Convent Drive

institute: National Institutes of Health

organism: Danio rerio

description:
The zebra fish 35k chip is a combination of 16,399 60 mer oligos from Compugen http://www.labonweb.com/oligo/libraries.htm
14,067 50 mers from MWG. http://www.ocimumbio.com/web/arrays/oligo_zebrafish.asp
and 3500 70 mer oligos from Operon. http://www.operon.com/arrays/oligosets_zebra.php
To look for the genes in the Compugen/MWG original list, click here (http://magic2.nhgri.nih.gov/mcore/zebrafish_genelist.txt)
General questions or comments about this specific platform please direct to:
Abdel G. Elkahloun: abdel@mail.nih.gov (tel. 301-402-3170 )
Settara Chandrasekharappa: chandra@mail.nih.gov (tel. 301-402-2344)

manufacturer: National Human Genome Research Institute / National Institutes of Health (NHGRI/NIH)

first: Wuhong

last: Pei

first: Houtan

last: Noushmehr

first: Abdel

middle: G

last: Elkahloun

manufacture_protocol: Microarray preparation.  The 33K Zebra fish oligo array consist of three oligo sets: Compugen (with 16,512 60mers), MWG (with 14,240 50mers) and Operon (3,479 70mers). The set includes 170 positive (known house keeping gene) and 244 negative control oligos (Random sequences) to control the homogeneity and specificity of the hybridization.  The 5' amine modified oligos were resuspended in 3xSSC and printed on Epoxy slides from Corning Life Sciences.


title: Missouri Gallus gallus 21k

status: Public on Jul 26 2007

city: columbia

first: lakshmi

middle: praveena

last: yarru

state: MO

address: 920 east campus dr

department: Division of Animal science

institute: University of Missouri

manufacturer: Genomic Research Laboratory, University of Arizona

first: LAKSHMI

middle: P

last: YARRU

first: ERIC

last: ANTONIOU

first: DAVID

middle: R

last: LEDOUX

manufacture_protocol: long oligo library manufactured under a custom design


title: SLA_PrV porcine DNA/cDNA microarray

city: Jouy en Josas

first: Laurence

last: Flori

address: Domaine de Vilvert

department: Génétique Animale

institute: INRA

organism: Sus scrofa

description: Two identical networks per slide were spotted. A network contains 16 blocks with 12 rows and 12 columns for each block.

manufacturer: LREG, CRB_GADIE, INRA Jouy en Josas, France, F_78350

first: Claire

last: Rogel-Gaillard

first: Karine

last: Hugot

first: Patrick

last: Chardon

manufacture_protocol: The SLA/PrV microarray, composed of cDNA and sub-cloned exons, is a dedicated array containing porcine and PrV probes. This microarray was constructed in the CRB-GADIE (Centre de Ressources Biologiques-Génomique des Animaux Domestiques et d'Intérêt Economique, LREG, INRA, Jouy-en Josas, France). The list of genes present in the human SLA orthologous region (6p21-p23) was drawn up using the human sequence draft (May 2004) on UCSC web site (http://genome.ucsc.edu/). Corresponding porcine  cDNA clones were selected when they were available in the AGENAE library  or in 2 American libraries MARC1PIG and MARC2PIG constructed in US by the United States Departement of Agriculture (USDA). When no porcine cDNA clone was found, exons were identified by comparison between ESTs and genomic DNA using ICCARE comparison mapping tool (http://genopole.toulouse.inra.fr/Iccare/). Primers were designed with Primer 3 (http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi).PrV amplicons (80) targeting 70 genes an pig exons were amplified by PCR and subcloned (PGEMT easy plasmid, Promega and XXX). cDNA and sub-cloned exons were amplified by PCR (Taq PCR Master Mix Kit, Qiagen) with universal primers located in the vector (35 cycles:30 sec at 94°C, 30 sec at 60°C and 2 min at 70°C). After purification (Multiscreen-PCR plates, Millipore), PCR products were checked on 1% agarose gel, quantified (Fluoroscan), evaporated and pellets were resuspended in 13µl SSC3X. Forty six control spots were added on the slide (Lucidea Universal scorecard, Amersham Biosciences). Two identical arrays were spotted on slides (25x75 mm, UltraGAPS Coated Slides, Corning) with a 16 needles spotter (Microarraywriter Pro,Virtek). After spotting, slides were first treated with steam to homogenise spots hydratation. Then spotted DNA was denatured (5 sec at 100°C) and UV fixed (300 mJ). Slides were stored in dry atmosphere before use.  All the SLA and immune clones spotted on the SLA/PrV slides were sequenced. Sequence homology was checked by multi-alignement (BLAST) against human and pig EST database (NCBI and VEGA). The SLA/PrV microarray probes were reannotated taking into account the most significant BLAST results and his final geneID file was used in the analysis.


title: Compugen 16K Zebrafish Spotted Oligo Array

status: Public on Jul 28 2007

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute for Molecular Bioscience, Uni of Qld

manufacture_protocol:
All relevant protocols are provided at the website:
http://www.microarray.adelaide.edu.au/


title: SAGE:17:NlaIII:Schistosoma mansoni

last: GEO

organism: Schistosoma mansoni

description: This is a virtual platform for SAGE libraries generated for Schistosoma mansoni using NlaIII as an anchor enzyme.


title: USDA Bradyrhizobium japonicum 8.5K (BJ_USDA110_Oligo_Array)

status: Public on Jul 15 2007

city: Arlington

first: Woo-Suk

last: Chang

state: TX

address: 501 S. Nedderman Dr. , Life Science Building 216

department: Biology

institute: University of Texas at Arlington

organism: Bradyrhizobium japonicum

first: Gary

last: Stacey

first: David

last: Emerich

first: Michael

last: Sadowsky

first: Dong

last: Xu

manufacture_protocol: 1. Unique 70-mer oligonucleotides were designed and synthesized for each of the predicted ORFs by Operon Biotechnologies, Inc. (Huntsville, AL). 2. Arrayer pre-printing setup - Remove any large objectives that would obstruct the arrayer's path from the deck. - Clean the pins for 15 min with warm (40 celsius) water followed by washing with 0.5% SSC. - Dry the pins. 3. Microarray printing: Oligonucleotides were printed onto Corning® epoxy coated slides (Corning Inc., Lowell, MA) at the Washington University Genome Sequencing Center (St. Louis, MO). - Arraymaker 2 software was used. - Set up: 2X wash to 4500 msec. - Remove the orange rubber strips and wipe off the columns needed to print on the deck with a 95% isopropanol swipe and allow it to dry. - Place orange rubber strip, located next to the deck, over all other unused columns on the deck. - Place the slides in their appropriate slide locations. - Place the first 384 well plate into the centrifuge and spin it at 1,500 rpm for 1 minutes at room temperture. - Place the spun down plate in the holder with appropriate position. Make sure the plate is sitting flat. - Make sure all the slides are moved toward the left of the column and to the top of their columns for uniformity of printing. - Plug in the pump for the deck. - Click on the "START" button. 4. Post processing slides Ultra GAPS - Put the printed slides into a slide box and store them in a dessicant cabinet for 48 hrs. - Add 1.5 L of MilliQ water to a pyrex container and heat the water until steaming. - Take out a slide and hold it over the steaming water, element slide down, and allow the slide to cover with steam for 8-10 seconds. - Immediately place the slide, element up, on the heat block for 8-10 seconds to allow the slide to snap dry. - After rehydration, place them in the UV stratalinker. - Turn on the machine and press in "3000". Make sure 3000 appears on the digital screen (300mJ). - Press energy button and then press the start button. - After crosslinkin, scribe each slide with a diamond scribe and place the slides in a slide box. - Store them in a dessicant cabinet.


title: Ciona intestinalis 44k Oligoarray ver.2

status: Public on Jul 27 2007

city: Kyoto

first: Nori

last: Satoh

address: Sakyo-ku

department: Department of Zoology

institute: Kyoto University

organism: Ciona intestinalis

first: Yutaka

last: Satou

manufacture_protocol:
The microarray was manufactured by Agilent Technologies. The details can be found in their web site
http://www.chem.agilent.com/Scripts/PCol.asp?lPage=494


title: PulseChip

status: Public on Jul 24 2007

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Bldg 223, Level 1, Plenty Road

department: Biotechnology & Environmental Biology

institute: RMIT University

organism:
Cicer arietinum
Lathyrus sativus
Lens culinaris

manufacturer: RMIT University, School of Applied Sciences, Bundoora AUSTRALIA

first: Rebecca

last: Ford

first: Tristan

middle: E

last: Coram

first: Edwin

last: Pang

manufacture_protocol:
Coram TE and Pang ECK. 2006. Expression profiling of chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Published in Plant Biotechnology Journal.
A total of 715 ESTs, 41 RGA DNA sequences, and 12 controls were used in the construction of 768-feature microarrays according to minimum information about a microarray experiment guidelines (MIAME). Of the 715 ESTs, 516 were obtained from a previously synthesized and characterized EST collection constructed from cDNA of the ascochyta blight resistant ICC3996 chickpea genotype. Briefly, 1021 ESTs were generated from stem/leaf tissue of ICC3996 harvested after inoculation with A. rabiei spores, and assembled into 516 unigenes employed in the construction of this microarray. A single clone was selected to represent each contig. A further 43 chickpea cDNAs whose sequencing reactions had previously failed were also included in this microarray. The remaining 156 ESTs represent potential defence-related ESTs from a grasspea (Lathyrus sativus) cDNA library constructed from the Mycosphaerella pinodes resistant genotype ATC80878. Finally, the 41 RGA sequences were isolated from lentil (Lens culinaris) genotypes ILL6002 (A. lentis susceptible) and ILL7537 (A. lentis resistant). The 12 controls included negative, printing, and blank buffer controls. All samples were dried in 384-well plates before being resuspended in 10 µL 50% (v/v) dimethylsulphoxide:water at 250 ng/µL, and arrayed onto amino-silanized slides (Corning Incorporated Life Sciences, Acton, MA) using a BioRobotics® MicroGrid II Compact (Genomic Solutions, Ann Arbor, MI) with four Microspot 2500 pins (Genomic Solutions, Ann Arbor, MI). Blank buffer spots, digested vector and PCR primer were also incorporated as negative controls, as well as Cy5-10T as a printing control. Each element was deposited six times with a volume of approximately 6 nL and diameter of 200 µm. Slides were pre-hybridised by blocking in 5X SSC, 0.1% SDS, 25% Formamide, 1% BSA for 45 min at 42ºC, rinsed in distilled water and dried.


title: TIGR PFGRC Aspergillus nidulans version 1 array designed primarily based on strain FGSC A4

status: Public on Jul 25 2007

city: Ribeirão Preto

first: Gustavo

middle: Henrique

last: Goldman

state: São Paulo

address: Av do Café, s/n

country: Brazil

institute: Faculty of Pharmaceutical Sciences of Ribeirão Preto

organism: Aspergillus nidulans

description:
This set includes 11481 oligonucleotides (ss oligo 70 mer), has 23962 spots (2x oligo replicates) distributed in 48 blocks.

The condensed array layout file (ie, 1x representation of oligos) is linked below as a supplementary file.

manufacturer: TIGR PFGRC (The Pathogen Functional Genomics Resource Center)

manufacture_protocol: Arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: UPenn Homo sapiens 6K BAC array (1MB interval spacing)

first: Mitchell

last: Guttman

state: MA

address: 7 Cambridge Center

institute: Broad Institute

first: Don

last: Baldwin

first: Katarzyna

last: Dudycz-Sulicz

first: Carolyn

last: Mies

manufacture_protocol: We created our 6,912-probe microarray using a human BAC clone set spaced at 1-Mb intervals throughout the genome. The clone were spotted in-house on Corning Ultra-Gap slides (Corning, USA)


title: SHFM

status: Public on Jul 14 2007

city: Stanford

first: Dejan

last: Juric

address: 269 Campus Drive

department: Medicine, Oncology

institute: Stanford University School of Medicine

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: NHICU Human 19K v1.0

status: Public on Jul 01 2007

city: Glebe

first: Benjamin

middle: Man Piu

last: Tang

state: NSW

address: 12/29 Cook Street

department: Intensive Care Medicine

institute: Nepean Hospital

description: See www.microarray.adelaide.edu.au for more details.

manufacture_protocol:
CompuGen Human OligoLibrary V1.0 (cat# HUMLIB384) comprising 18,861 60-mers representing 18,664 unique genes + 197 controls. Each oligo has a 5' C6-amino linker enabling covalent attachment to the substrate. An additional locally made control plate was also spotted. Probes were arrayed onto Corning Epoxide slides using 32 (8x4) tungsten pins in a Versarray Chipwriter Pro robot. Each pin printed an array of 625 spots arranged in 25 rows by 25 columns (20000 features per array).

Support  Coated-glass
Coating  Epoxide


title: SAGE:17:NlaIII:Emiliania huxleyi CCMP1516

status: Public on Jul 04 2007

last: GEO

organism: Emiliania huxleyi CCMP1516

description: This is a virtual platform for SAGE libraries generated for Emiliania huxleyi CCMP1516 using NlaIII as an anchor enzyme.


title: ARK-Genomics G. gallus 13K v4.0

first: Mark

last: Fell

description: This is a chicken multi-tissue cDNA microarray with 12752 elements. It comprises clones from chicken EST collections generated by BBSRC, University of Delaware and the Fred Hutchinson Cancer Research Center. Sequence information is available from GenBank for all features on the array.

first: Joan

last: Burnside

first: Richard

last: Talbot

first: Jeff

last: Delrow

manufacture_protocol:
The clone-set was amplified in 96 well plates and re-arrayed into a 384-well Montage (Millipore) filtration plate to isolate the amplified DNA products. These products were checked by agarose gel electrophoresis and quantified using a Picogreen DNA quantitation assay. All single band PCR products were re-arrayed, in fresh barcoded 384 well pates (Genetix 7022), at a concentration of 150ng per microlitre in 0.1M sodium phosphate buffer pH 8 containing 0.01% SDS, ready for printing. All re-arraying was done with Multiprobe II (Perkin Elmer) liquid handling robot. DNA was printed onto aminosilane coated glass slides (Corning GAPS II) using a Genomic Solutions MicroGrid II arrayer and the MicroSpot pins according to the manufacturers instructions. All printing was carried out in conditions of constant humidity (52% RH) and temperature (20oC) in a room supplied with HEPA filtered air. Prior to printing the pins were cleaned by ultra-sonication in water and if necessary 50mM potassium hydroxide. A test print of all pins was carried out by printing Cy3 streptavidin conjugate dye in printing buffer onto poly lysine slides and printing 100 features per pin. When all pins were printing consistent size spots for more than 80 features they were accepted as ready to print.
The MicroGrid II was then programmed for the array print run, with a grid layout file prepared to allow duplicate printing at random within a patch. At the end of the print run the slides were removed following the program instructions in preparation for post processing. The slides are processed to bind the DNA to the slide, denature the DNA, and prevent non-specific binding during hybridisation. Slides were transferred from the printer into stainless steel slide staining racks before baking at 80oC for 4 hours in an oven.
The slides were blocked after they had returned to room temperature. Blocking was carried out in a fume hood. Once in solution, the blocking agents do not remain active for long, so it is important to prepare fresh solutions and use them immediately. Dissolve 0.75g succinic anhydride completely in 125ml 1-methyl-2-pyrrolidinone. Immediately mix in 125ml of 0.2M boric acid pH 8.0. The slides were plunged into the solution and vigorously agitated for 15 minutes using a magnetic stirrer. The slides were then transferred to a stirred water bath containing MilliQ water maintained at 95 oC and plunged up and down and side to side for 2 minutes to denature the DNA to single strands. The slides were then transferred to a trough containing 96% ethanol for 1 minute. The slides were then transferred to microscope slide boxes and dried by centrifugation. Slides were then stored in a desiccator in the dark at room temperature until use.


title: Zebrafish 34K (Compugen, MWG, Operon)

last: Feldman

department: National Human Genome Research Institute

first: Jamie

last: Boorech

first: Houtan

last: Noushmehr

first: Martha

last: Kirby

first: Abdel

last: Elkahloun

manufacture_protocol: Microarray preparation. The 33K Zebra fish oligo array consist of three oligo sets: Compugen (with 16,512 60mers), MWG (with 14,240 50mers) and Operon (3,479 70mers). The set includes 170 positive (known house keeping gene) and 244 negative control oligos (Random sequences) to control the homogeneity and specificity of the hybridization. The 5' amine modified oligos were resuspended in 3xSSC and printed on Epoxy slides from Corning Life Sciences.


title: Virtual Institute of Microbial Stress and Survival- Desulfovibrio vulgaris Hildenborough - 3368

status: Public on Jul 03 2007

city: Calgary

first: Sean

middle: Michael

last: Caffrey

state: Alberta

address: 2500 University Dr NW

department: Biological Scineces

country: Canada

institute: University of Calgary

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

manufacture_protocol: 70-mer oliognucleotide


title: IMP Vienna microarray facility Murine 28K cDNA array version 18.1

first: Meinrad

last: Busslinger


title: SMChum8400A cDNA Array

status: Public on Jul 17 2007

city: Beaverton

first: Alejandro

last: Lomniczi

state: OR

address: 505 NW 185th Ave

department: Neuroscience

institute: Oregon National Primate Research Center - OHSU

manufacturer: Oregon Health and Science University Spotted Microarray Core

first: Robert

last: P. Searles

first: Julie

last: Patch

first: Aaron

last: Kabb

first: David

last: Lee

manufacture_protocol:
1.  PCR products were derived from the first 88 plates of the Research Genetics distribution of the I.M.A.G.E. Consortium Human cDNA library.  The link for the I.M.A.G.E. Consortium is http://image.llnl.gov/.
2.  cDNAs were amplified by PCR using DynaZyme Ext polymerase (MJResearch) using 0.5 units of enzyme per reaction.  Amplification protocol was 94 C for 45 sec, 55 C for 45 sec, and 72 C for 2 min 30 sec for 32 cycles.  Amplifications were performed in an MJResearch PTC-225 Thermal Cycler fitted with four 96-well heads.
3.  PCR products were separated from unincorporated nucleotides using Millipore Multiscreen PCR filter plates and recovered from the filter in 100 ul of water.  2 microliter aliquots were removed and run on 0.8% agarose gels for quality control. Purified PCR products were reduced from 98 microliters to dryness in a LabConCo CentriVap concentrator.  Dried DNA was resuspended in 30 microliters of 50% DMSO and stored frozen at -20C.
4.  Three microliters of each PCR product were transferred to Whatman 384-well microtiter plates for printing.  Printing plates were used up to 7 times.  Plates were stored at -20 C between print runs.  Prior to each print run, thawed plates were spun at 3000 rpm in a Sorvall RT7plus tabletop centrifuge for 10 minutes.
5.  Arrays were printed on Corning UltraGAPS slides using a Cartesian PixSys 5500XL array printer with a Pegasus plate handler attachment.  The plate handler chamber was maintained at 70% relative humidity; the print chamber was maintained at 50% relative humidity.  Printing was done with 16 Telechem CMP-2 array printing pins.  Printing used twenty-two 384-well microtiter plates and took approximately 24 hours.  Printed arrays were baked at 80 C for 3.5 hours in a baking oven.  Arrays were stored in the dark in a sealed desiccator until use.  Prior to use, arrays were blocked for 1 hour at 55 C in 5X SSC, 1.0% SDS, and 2.0% BSA.


title: ORNL-ESD Geobacter metallireducens 70mer oligo-array

city: Knoxville

first: Qiang

last: He

state: TN

address: 57A Perkins Hall

department: Civil and Environmental Engineering

institute: The University of Tennessee

organism: Geobacter metallireducens GS-15

description: In total, 4129 probes were designed based on an early version of the gene model (2003) and printed on the microarray, among which 3727 probes have 1 perfect match with one single ORF; 98 probes have more than 1 perfect matches with more than 1 ORFs; 261 probes have at least 1 perfect match with the genome, but not with an ORF; and 43 probes have no perfect match with the genome.

manufacturer: Microbial Ecology and Functional Genomics Laboratory, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN

first: Zhili

first: Jizhong

last: Zhou

manufacture_protocol: All 70mer oligonucleotides were commercially synthesized without modification by MWG Biotech Inc. (High Point, NC). The concentration of oligonucleotides was adjusted to 100 pmol/µl. Oligonucleotide probes were prepared in 50% vol/vol DMSO (Sigma-Aldrich, St. Louis, MO) and spotted onto UltraGAPS glass slides (Corning Life Sciences, Corning, NY) using a BioRobotics Microgrid II microarrayer (Genomic Solutions, Ann Arbor, MI). Each oligonucleotide probe had two replicates on a single slide. After printing, the oligonucleotide probes were fixed onto the slides by UV cross-linking (600 mJ of energy) according to the protocol of the manufacturer of the UltraGAPS glass slides (Corning Life Science, Corning. NY).


title: Bacillus subtilis WGD11 platform

status: Public on Jul 02 2007

city: Cambridge

first: Alan

middle: D.

last: Grossman

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

address: 31 Ames Street, 68-530

institute: MIT

organism: Bacillus subtilis

last: Britton

first: Elke

last: Kuester-Schoeck

first: Thomas

last: Auchtung

manufacture_protocol: See Britton RA et al. J Bacteriol. 2002 Sep;184(17):4881-90.


title: SAGE:21:NlaIII:Homo sapiens

status: Public on Jul 19 2007

last: GEO

organism: Homo sapiens

description: This is a virtual platform for SAGE libraries generated for Homo sapiens using NlaIII as an anchor enzyme.


title: Bacillus subtilis WGD3 platform


title: AFFY Human Phase3 v1.0 - C85

status: Public on May 25 2007

city: Santa Clara

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

manufacture_protocol:
Affymetrix standard array manufacture protocol.
Please refer to http://www.affymetrix.com/technology/manufacturing/index.affx for details.


title: AFFY Human Phase3 v1.0 - C89


title: AFFY Human Phase3 v1.0 - C86


title: AFFY Human Phase3 v1.0 - C90


title: AFFY Human Phase3 v1.0 - C87


title: AFFY Human Phase3 v1.0 - C88


title: Custom Genome PCR Tiling Array of the Igf2r Imprinted Gene Cluster

city: Vienna

first: Denise

middle: P.

last: Barlow

address: Dr. Bohrgasse 9/4

department: Austrian Academy of Sciences

institute: Center of Molecular Medicine (CeMM)

manufacturer: Biooptics Department, Research Institute of Molecular Pathology (IMP), Vienna, Austria

first: Kakkad

last: Regha

first: Mathew

last: Sloane

first: Ru

last: Huang

first: Florian

last: Pauler

first: Katarzyna

last: Warczok

first: Balázs

last: Melikant

first: Martin

last: Radolf

first: Joost

middle: H

last: Martens

first: Gunnar

last: Schotta

last: Jenuwein

manufacture_protocol:
The tiling array contained only single copy sequence (exons, introns and intergenic regions) from the Igf2r imprinted gene cluster on mouse chromosome 17. Repeat elements were excluded by RepeatMasker (www.repeatmasker.org). PCR primers were designed with Primer3 (http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi) to amplify all unique single copy mouse sequence. The PCR products were overlapping with an average size of 430bp. The manufacture protocol was adapted from "Diehl, F. et al. (2001). Manufacturing DNA microarrays of high spot homogeneity and reduced
background signal. Nucleic Acids Research: 29(7), e38" with the exception of using 1-methyl 2-pyrrolidone instead of 1,2-dichlorethane. Each PCR product was spotted in 8 positions on Nexterion slides (Schott) with a Promedia Associates Inc. printer (Model PA-MP2000) using SMP3 printing tips (Telechem).


title: ConPath Chip

status: Public on Jun 08 2007

city: Yokohama

last: DNA Chip Research Inc.

institute: DNA Chip Research Inc.

description: DNA Chip Research Inc. ConPath Chip

manufacture_protocol: see Manufacture's web site


title: AFFY Human Phase3 v1.0 - C82


title: AFFY Human Phase3 v1.0 - C81


title: AFFY Human Phase3 v1.0 - C84


title: AFFY Human Phase3 v1.0 - C79


title: AFFY Human Phase3 v1.0 - C76


title: AFFY Human Phase3 v1.0 - C83


title: AFFY Human Phase3 v1.0 - C78


title: AFFY Human Phase3 v1.0 - C80


title: AFFY Human Phase3 v1.0 - C75


title: University of London Streptococcus pneumoniae TIGR4/R6 Array v1

city: Adelaide

first: Uwe

last: Stroeher

state: South Australia

address: North Terrace

department: School of Molecular and Biomedical Science

institute: University of Adelaide

organism: Streptococcus pneumoniae

description: The S.pneumoniae array was designed using the TIGR4 strain as a base strain with annotation described in Tettelin et al (2001) Science 293: 498-506. PCR primers were designed and products ampilifed to 2236 target genes. The genes extra to strain R6 where identified from the annotation described in Hoskins et al (2001) J. Bacteriol. 183: 5709-5717. PCR primers were thus designed to 117 R6 target genes and added to the array

manufacturer: The Bacterial Microarray Group at St George's, University of London (BµG@S)

first: James

middle: C

last: Paton

manufacture_protocol: See the website of The Bacterial Microarray Group at St George's, University of London


title: AFFY Human Phase3 v1.0 - C74


title: AFFY Human Phase3 v1.0 - C73


title: AFFY Human Phase3 v1.0 - C91


title: AFFY Human Phase3 v1.0 - C71


title: AFFY Human Phase3 v1.0 - C72


title: AFFY Human Phase3 v1.0 - C70


title: AFFY Human Phase3 v1.0 - C69


title: AFFY Human Phase3 v1.0 - C77


title: AFFY Human Phase3 v1.0 - C67


title: AFFY Human Phase3 v1.0 - C64


title: AFFY Human Phase3 v1.0 - C61


title: AFFY Human Phase3 v1.0 - C60


title: AFFY Human Phase3 v1.0 - C68


title: AFFY Human Phase3 v1.0 - C57


title: AFFY Human Phase3 v1.0 - C66


title: AFFY Human Phase3 v1.0 - C65


title: AFFY Human Phase3 v1.0 - C56


title: AFFY Human Phase3 v1.0 - C63


title: AFFY Human Phase3 v1.0 - C59


title: AFFY Human Phase3 v1.0 - C54


title: AFFY Human Phase3 v1.0 - C55


title: AFFY Human Phase3 v1.0 - C53


title: AFFY Human Phase3 v1.0 - C58


title: AFFY Human Phase3 v1.0 - C50


title: AFFY Human Phase3 v1.0 - C52


title: AFFY Human Phase3 v1.0 - C51


title: AFFY Human Phase3 v1.0 - C62


title: AFFY Human Phase3 v1.0 - C47


title: AFFY Human Phase3 v1.0 - C45


title: AFFY Human Phase3 v1.0 - C46


title: AFFY Human Phase3 v1.0 - C44


title: AFFY Human Phase3 v1.0 - C49


title: AFFY Human Phase3 v1.0 - C48


title: AFFY Human Phase3 v1.0 - C43


title: AFFY Human Phase3 v1.0 - C42


title: AFFY Human Phase3 v1.0 - C39


title: AFFY Human Phase3 v1.0 - C40


title: AFFY Human Phase3 v1.0 - C41


title: AFFY Human Phase3 v1.0 - C38


title: AFFY Human Phase3 v1.0 - C35


title: AFFY Human Phase3 v1.0 - C37


title: AFFY Human Phase3 v1.0 - C34


title: AFFY Human Phase3 v1.0 - C36


title: AFFY Human Phase3 v1.0 - C33


title: AFFY Human Phase3 v1.0 - C31


title: AFFY Human Phase3 v1.0 - C24


title: AFFY Human Phase3 v1.0 - C29


title: AFFY Human Phase3 v1.0 - C30


title: AFFY Human Phase3 v1.0 - C32


title: AFFY Human Phase3 v1.0 - C26


title: AFFY Human Phase3 v1.0 - C28


title: AFFY Human Phase3 v1.0 - C25


title: AFFY Human Phase3 v1.0 - C27


title: AFFY Human Phase3 v1.0 - C20


title: AFFY Human Phase3 v1.0 - C23


title: AFFY Human Phase3 v1.0 - C22


title: AFFY Human Phase3 v1.0 - C18


title: AFFY Human Phase3 v1.0 - C13


title: AFFY Human Phase3 v1.0 - C21


title: AFFY Human Phase3 v1.0 - C09


title: AFFY Human Phase3 v1.0 - C19


title: AFFY Human Phase3 v1.0 - C03


title: AFFY Human Phase3 v1.0 - C04


title: Mature Human miRNA Array

status: Public on Apr 01 2007

city: Singapore

first: Meng Ling

last: Choong

address: 31 Biopolis Way, #03-01 Nanos

department: Drug Discovery

country: Singapore

institute: Experimental Therapeutics Centre

description: The complete platform showing three replicates per miRNA on the chip

first: MengLing

first: Henry

last: Yang

first: Ian

last: McNiece

manufacture_protocol: Probeset was obtained from Ambion. Construction of the probeset, printing of probset on to array, hybridization and detection protocols can be obtained from Ambion.


title: AFFY Human Phase3 v1.0 - C01

first: Thomas

last: Gingeras


title: AFFY Human Phase3 v1.0 - C17


title: AFFY Human Phase3 v1.0 - C14


title: AFFY Human Phase3 v1.0 - C11


title: AFFY Human Phase3 v1.0 - C12


title: AFFY Human Phase3 v1.0 - C15


title: AFFY Human Phase3 v1.0 - C10


title: AFFY Human Phase3 v1.0 - C08


title: AFFY Human Phase3 v1.0 - C05


title: AFFY Human Phase3 v1.0 - C07


title: WRAIR Homo sapiens 9k array

status: Public on Mar 29 2006

city: Silver Spring

first: Rasha

last: Hammamieh

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

manufacturer: Walter Reed Army Institute of Research (WRAIR)

manufacture_protocol: Custom array


title: Ambion Human_Mouse_Rat mirVana miRNA Bioarray_1566V1

status: Public on Feb 18 2006

city: Austin

first: Lakshmi

middle: V.

last: Madabusi

address: 2130 Woodward St

department: Ambion Services

institute: Ambion Inc

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description:
Manufactured using GE Healthcare’s CodeLink (TM) 3-D Gel Matrix Technology
Surface type: non-adsorptive
Attachment: covalent
The mirVana miRNA Bioarrays are an Ambion product that is manufactured by GE Healthcare and incorporates the CodeLink™ 3-D Gel Matrix slide surface. This aqueous environment elevates the probes away from the surface of the slide, allowing for maximum interaction between the probes and targets.

manufacture_protocol:
CodeLink(tm) Activated Slides are designed to covalently immobilize amine-modified DNA for microarrays. They are easy to use and are compatible with most available arraying and scanning instruments. CodeLink Activated Slides are coated with a novel 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.

Technical specifications:
Slide dimensions: 25 × 75 × 1 mm
1× Printing buffer: 50 mM sodium phosphate at pH 8.5

Codelink slides are manufacured by SurModics and were formally sold as 3D-Link(tm) Activated Slides.


title: Hitachisoft AceGene Premium Human

status: Public on Jul 21 2006

last: Hitachi Software Engineering Co.

institute: Hitachi Software Engineering Co., Ltd.

description: Hitachisoft AceGene Premium Human

manufacture_protocol: see manufacturer's web site


title: NMC Human 15K duplicate cDNA microarray

status: Public on Feb 03 2006

city: Trondheim

first: Tom

middle: Even

last: Wheeler

address: Olav Kyrresgt. 3

department: Department of cancer research and molecular medicine

country: Norway

institute: Norwegian University of Science and Technology, NTNU

description:
30000 spots printed with 48 pins:
12759 genes, of which
117 with DNR-numbers
10 spikes, plus 1 "empty", "1 Neg_BC" and 1 "Neg_HS"
Multippel spots:
9893 genes are spotted twice
261 genes are spotted three times
1745 genes are spotted four times
1 gene is spotted five times (47359: "endothelin 1")
1 gene is spotted six times (345935: "MAD (mothers against decapentaplegic, Drosophila) homolog 3")
13 genes are spotted 48 times (Spikes 1-10, Neg_BC, Neg_HS, " ")
1 gene is spotted 972 times (empty: "")

first: Bjorn

last: Kristiansen

first: Signe

last: Hagen

first: Ola

last: Myklebost

manufacture_protocol: The 15k human cDNA duplicate arrays were prepared from a collection of 40k cDNAs purchased from Research Genetics (Huntsville, AL) (see Invitrogen website for the manual: Sequence-Verified cDNA Clones, Catalog nos. 97002.V, 97001.V, 97002.MmV, Version C, February 3, 2003, 25-0627). Plasmids were isolated from overnight bacterial cultures in 96-well plates and cDNA inserts amplified by PCR using M13 primers 5'-ctg caa ggc gat taa gtt ggg taa c and 5'-gtg agc gga taa caa ttt cac aca gga aag a. The PCR products were purified with Montage PCR purification kit (Millipore) and quality and concentration was assessed by agarose gel electrophoresis. The purified PCR products were dissolved in 50% DMSO (about 50-200 ng/ l) and spotted in duplicate onto 25 x 75mm amino-silane coated CMT-GAPS glass slides (Corning, NY) using a MicroGrid II printing robot (BioRobotics; Cambridge, UK). The arrays were spotted with 48 pins and contained 4 x 12 blocks of 25 x 25 spots. The probes were fixed to the slide surface by UV irradiation (200 mJ). The 15k cDNA arrays represent 14018 unique probes, all printed in duplicates. In addition, a few in-house cDNA probes and a set of positive and negative control elements including 10 different PCR products of exogenous DNA from SpotReport™ cDNA Array Validation System (Stratagene, La Jolla, CA) were printed on the arrays. Totally, each array contained 30000 elements including duplicates and controls.


title: AFFY Human Phase3 v1.0 - C06


title: AFFY Human Phase3 v1.0 - C02


title: ENCODE NimbleGen hg16 tiling array

status: Public on Jan 01 2007

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

description: 388K element tiling array based on NCBI34 build of the human genome (hg16) and contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

first: Nathaniel

middle: D

last: Heintzman

first: Rhona

middle: K

last: Stuart

first: Gary

last: Hon

first: Yutao

last: Fu

first: Christina

middle: W

last: Ching

first: David

last: Hawkins

first: Leah

middle: O

last: Barrera

first: Sara

middle: V

last: Calcar

first: Chunxu

last: Qu

first: Keith

middle: A

first: Wei

last: Wang

first: Zhiping

last: Weng

first: Roland

last: Green

first: Gregory

last: Crawford

manufacture_protocol: Tiling array; see NimbleGen website. Contains one 50-mer every 38 nts.


title: Physcomitrella patens high-throughput small RNA sequencing

status: Public on Aug 15 2006

city: University Park

first: Michael

middle: J

last: Axtell

address: 280 Mueller Lab

institute: Pennsylvania State University

organism: Physcomitrium patens

technology: other

description:
Endogenous small RNAs from Physcomitrella patens were sequenced using pyrosequencing as described in Axtell et al. (2006) A two-hit trigger for siRNA biogenesis in plants.  Cell 127: 565-577.
UPDATED JULY 9, 2007 TO INCLUDE SEQUENCED RNAS THAT DO NOT HAVE AN EXACT MATCH IN THE GENOME

middle: P

last: Bartel


title: AFFY Human Phase3 v1.0 - C16

first: Thomas

middle: R

last: Gingeras