title: Vandy NIA Mouse 20k

status: Public on Jul 08 2006

city: Cincinnati

first: Bruce

middle: J

last: Aronow

institute: Cincinnati Children's Hospital Medical Center

description: Spotted NIA mouse 15K cDNA clones - This  has clones from several early embryonic cDNA libraries, including blastocyst, preimplantation, embryonic stem cells, trophoblast stem cells, embryonic germ cells, and others.

manufacture_protocol: Spotted NIA 15k cDNA clones


title: Mouse Prostate MPEDB cDNA Array v2

status: Public on Sep 01 2006

city: Seattle

first: Denise

last: Mauldin

state: WA

address: 1100 Fairview Ave N D4-100

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Research Center

organism: Mus musculus

technology: spotted DNA/cDNA

distribution: non-commercial

first: Peter

middle: S

last: Nelson

first: Colin

last: Pritchard

middle: E

last: Abbott

first: Ruth

last: Dumpit

manufacture_protocol: As cited


title: Institute of Cancer Research 5808-spot slide_version3

status: Public on Jun 29 2006

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

organism: Homo sapiens

description: cDNA

manufacture_protocol: as described in Institute Labs manual


title: GE Healthcare/Amersham Biosciences CodeLink UniSet Rat I Bioarray, layout EXP5280X2-584

status: Public on Jun 23 2007

city: Mountain View

first: Jeremy

last: Gollub

state: CA

address: 325 E. Middlefield Rd.

institute: Iconix Biosciences

organism: Rattus norvegicus

technology: spotted oligonucleotide

description: layout EXP5280X2-584

distribution: custom-commercial

manufacture_protocol: see product literature


title: Mouse Compugen oligo array

city: Potomac Falls

first: Agnieszka

middle: Maria

last: Lichanska

state: VA

institute: Tessarae, LLC

manufacture_protocol: unknown


title: GE Healthcare/Amersham Biosciences CodeLink UniSet Rat I Bioarray, layout EXP5280X2-613

description: layout EXP5280X2-613


title: Whole Genome, Alternative Splicing Drosophila Chip v2

status: Public on Jun 22 2006

city: Gainesville

first: Lauren

middle: M.

last: McIntyre

state: FL

department: Dept. of Molecular Genetics and Microbiology

institute: University of Florida

organism: Drosophila melanogaster

middle: M

manufacture_protocol: Oligonucleotide probes were designed using


title: DKFZ_LION Mouse 20k cDNA array

status: Public on Jun 10 2006

city: Heidelberg

first: Hendrik

last: Reuter

department: Moleculare Genetics B060

country: Germany

institute: DKFZ

first: Meinhard

last: Hahn

last: Lichter

manufacture_protocol: Spotted cDNA array produced using the commercially available 20K library arrayTAG; LION bioscience AG, Heidelberg, Germany. Inserts were amplified using the M13 primers 5 -TCG AGC GGC CGC CCG GGC AGG T-3  and 5 -Amino(C6)-AGC GTG GTC GCG GCC GAG GT-3  (Biospring, Frankfurt, Germany). For each cDNA clone, 1  l bacterial suspension of an overnight culture was used as template in a 40 ul PCR reaction containing 10 mM Tris-HCl (pH 8.3 at 20°C), 50 mM KCl, 1.5 mM MgCl2, 0.4  M of each primer, 0.2 mM of each dNTP and 1.2 U AmpliTaq DNA polymerase (Applied Biosystems). The amplification reaction was performed in a Primus HT Multiblock PCR-System (MWG Biotech, Ebersberg, Germany): an initial denaturation step at 94°C for 2 min was followed by 33 cycles of denaturation at 94°C for 15 sec, annealing at 68°C for 30 sec and extension at 72°C for 50 sec, with a final extension step at 72°C for 5 min. Purity and quantity of the PCR products were analysed by electrophoresis on 1.2% 96-well-Ready-to-Run-Agarose-Gels (Amersham Biosciences) according to the manufacturer's instructions. For a subset of the clones, DNA quality and concentration were evaluated by absorption spectroscopy between 220 and 320 nm (1 OD260 = 50  g/ml dsDNA). PCR products were purified by ethanol precipitation (2.5 vol. 100% ethanol; 1/10 vol 3 M sodium acetate, pH 5.2), followed by a washing step with 70% (v/v) ethanol. Pellets were dried, dissolved in 20  l of 3xSSC, 1.5M betaine and transferred to 384-well-microtiter plates applying the robotic liquid handling system MultiProbe II EX (Packard Bioscience, Dreieich, Germany). Dissolved PCR products were spotted as array duplicates using epoxy-silane coated glass slides (Schott Nexterion) and stainless steel split pins (SMP3, Telechem) at 20°C and 40% rH. Slides were dried (60' @ 60°C) and DNA was UV-crosslinked with 240 mJ/cm2 @ 254 nm. Slides were stored, sealed airtight and dry, at 4°C.


title: Nimblegen Human 1.5 kb promoter

status: Public on Jun 06 2006

city: Davis

first: Sharon

last: Squazzo

address: 4617 GBSF, 451 E. Health Sci. Dr.

department: Pharmacology

institute: UC Davis Genome Center

technology: in situ oligonucleotide

manufacture_protocol: 100 bp oligos tiled from 1.3 kb upstream to 200 bp downstream of 24,000 promoter regions


title: YUSM (K. White) D. melanogaster cDNA array

status: Public on Jun 01 2006

city: La Jolla

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

description: PCR fragment array for Drosophila melanogaster

manufacturer: Dr. Kevin P. White Lab at Yale University School of Medicine

first: Jin

last: Xue

first: Kevin

middle: P

last: White

first: Gabriel

middle: G

last: Haddad

manufacture_protocol: PCR fragments of ~95% of the genes in D. melanogaster BDGP release 4.0 were spotted.  Array has 8 rows of 4 blocks each, numbered 1-32 starting in the upper left and ending in the lower right. 16 pins used to print.


title: Mergen Expresschip Mouse MO3

city: Boston

first: Winston

middle: Patrick

last: Kuo

state: MA

address: 188 Longwood Avenue

department: Genetics

institute: Harvard Medical School

description: A mouse array with 9248 features, in 32 zones, with 8902 biosequences representing 9248 reporters and 0 composite sequences

manufacture_protocol: The ExpressChip™ arrays are pre-spotted with oligonucleotide sequences designed to interrogate the expression of target genes with the highest specificity. The arrayed oligos are all 30 mers that are BLAST-tested for specificity and carefully designed with stringent specifications including Tm/GC content, nucleotide repetition, and gene location. Oligo sequences are chosen to target known genes and current ExpressChip™ versions include chips for human, mouse, or rat genomes. Total number of features of Mouse MO3: 9248


title: Nimblegen Mouse 1.5 kb promoter array [2006-11-16_MM5_min_promoter]

manufacture_protocol: tiling array


title: MGH Long Oligonucleotide array

manufacture_protocol:
   1.   Oligos are arrayed in Greiner 384-well flat-bottom plates. Each well contains 600 pmol of 70-mer oligo.
   2. Resuspend oligos in water to 20 uM and rearray 5 µL into 384-well, Genetix polystyrene V-bottom plates (cat# X6004).
   3. Allow Genetix plates to dry through passive water evaporation in a protected environment (e.g., chemical hood).
   4. Before printing, add 5 µL of 1X Printing Buffer to each well. This can be done the night before a print run is started.
   5. Seal plates with Corning seals.
   6. Incubate at 37°C for 30 minutes to aid resuspension of DNA.
   7. Shake plates near maximum rotational speed on flat-bed shaker for 1 minute.
   8. Centrifuge plates at 2000 rpm for 3 minutes.
   9. Remove seals and cover with plate lids. Place in appropriate location of plate cassette. This should be done with first plates just before print run is started to minimize evaporation time before printing. For second and third cassettes, wait until 30 minutes before next cassette is needed to begin centrifugation.
  10. Make sure plates rest behind both holding clips in the cassettes. Push plates back into the cassettes as far as they will go, putting them in the proper position for the server arm.
  11. After the print run is completed, allow plates to dry through passive evaporation in a protected environment.
  12. For each subsequent preparation of these plates for a print run, add water to the wells instead of sodium phosphate buffer. The amount of water should be decreased by 0.25 µL per print run, as this is the amount drawn up by the pin capillary during each dip.


title: Rosetta/Merck (C57BL/6J X C3H/HeJ)F2 on ApoE null backgrounds 75K oligio array 1

status: Public on Jul 07 2006

city: Los Angeles

first: Leslie

last: Ingram-drake

department: Medicine/MIMG/Human Genetics

institute: UCLA

description: Oligonucleotide array on glass.  Contains 60mer probes designed against 23,000+ mouse genes arrayed on Agilent ink-jet arrays. Keywords=mouse genetics gene expression oligonucleotide

first: Susanna

last: Wang

first: Nadir

last: Yehya

first: Hui

first: Eric

last: Schadt

first: Thomas

middle: A

last: Drake

first: Aldons

last: Lusis


title: CCDTM Hs_CCDTM17.5k

status: Public on Jun 23 2006

city: Doha

first: Francesco

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

manufacturer: NIH Clinical Center, Dept. of Transfusion Medicine, Immunogenetics Section (NIH/CC/DTM)

manufacture_protocol: Microarrays are printed with GeneMachines robotic arrayer from Genomic Solutions (http://www.genomicsolutions.com) that is fitted with a printhead containing 32 SMP2.5 printing pins from Telechem International (http://www.arrayit.com). The human cDNA probe set is based on RG_HsKG_031901 8k clone set and 9k clones from the RG_Hs_seq_ver_070700 40k clone set from Research Genetics (http://clones.invitrogen.com). The set includes 12,072 uniquely named genes, 875 duplicates of named genes and all remainder consisted of expression sequence tags (about 4053 EST). The cDNA probes were amplified by PCR and distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in 3XSSC print buffer at a concentration of 50-100 ug/ml. The microarray spot densities are 280 microns (center-to-center), and one spot is printed per probe per slide. The microarrays are printed on Fisher Premium microscope slides (cat# 12-544-1) coated with poly-L-lysine and post-processed according to the procedures on the NCI website http://madb.nci.nih.gov/.


title: NCI Mus musculus 10K FCRF UniGEM2

status: Public on May 17 2006

city: Genoa

first: Paolo

last: Fardin

address: Largo G. Gaslini 5

department: Molecular Biology

country: Italy

institute: Istiuto Giannina Gaslini

manufacturer: NCI-Frederick/LMT Microarray Research Facility

manufacture_protocol: The custom arrays are manufactured by the NCI Frederick Laboratory of Molecular Technology Microarray Facility (NIH/NCI/SAIC/LMT). Microarrays are printed with BioRobotics TAS II robotic arrayer from Genomic Solutions that is fitted with a printhead containing 32 SMP3 printing pins from Telechem International. The mouse cDNA probe set is based on 9984 PCR products from Incyte's mouse UniGEM 2.0 library. The set includes 9234 Unique GenBank Accessions; 8882 mapped into Mm UniGene Build #1201; 8656 Unique UniGene Clusters; 3463 EST clusters; 5193 Named clusters. The cDNA probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in 3XSSC print buffer at a concentration of 50-100 ug/ml. The microarray spot densities are 235 microns (center-to-center), and one spot is printed per probe per slide. The microarrays are printed on Fisher Premium microscope slides (cat# 12-544-1) coated with poly-L-lysine and post-processed according to the procedures on the mAdb NCI website.


title: population genetic approach to host patheogen response

status: Public on May 26 2006

city: Albuquerque

first: John

middle: Joseph

last: Rushton

state: NM

address: MSC10 5550, 1 University of New Mexico

department: Internal Medicine

institute: University of New Mexico, School of Medicine

manufacturer: University of New Mexico Experimental Biology Laboratory

first: C.

middle: R

last: Lyons

manufacture_protocol: Oligonucleotide printing, microarray slide preparation and processing :Oligonucleotide libraries are printed on poly L Lysine coated microscope slides which are blocked prior to hybridization. Prior to printing, the microscope slides (Gold Seal, VWR, So. Plainfield, NJ) are cleaned with 2.5 M NaOH in 61% ethanol, washed thoroughly, and then coated with 0.01% poly l lysine (Sigma, St. Louis, MO) in filtered 10% phosphate buffered saline without calcium or magnesium (Hyclone, Logan, UT). After coating, excess poly l lysine is rinsed off and the slides are vacuum dried and stored at least 2 weeks prior to printing. The mouse ver 1.1 library of 70mer oligonucleotides (Operon, Alameda,  CA) is resuspended at 40uM in 3xSSC in 384 well v bottom plates (Genetix, Beaverton, OR) prior to printing 100 slides on an OmniGrid Microarray printer (GeneMachines, San Carlos, CA). In brief, the printing conditions are 60% humidity, 16 Majer pins (Majer Precision Engineering, Tempe, AZ), 24 column by 22 row subarrays,  8448 features per array including controls, duplicate arrays per slide, 0 millisecond print time, and 22  384 well plates per print run.  Between each sample, pins are cleaned with two loops of 3 second sonication, 2 second washing and 4 second drying per loop.  Printed controls include 70mer oligonucleotides specific for constitutively expressed housekeeping genes (e.g. actin, 28s rRNA), 3xSSC printing buffer, blanks, murine genomic DNA, and B. subtilis gene pcr products (American Type Culture Collection, Rockville MD).  After printing, the microarray slides are rehydrated, snap dried at 105oC,  UV crosslinked at 65 mjoules (Stratalinker, Stratagene, LaJolla, CA) and blocked with 43mM sodium borate (Fisher, Fair Lawn, NJ) and 157mM succinic anhydride (Aldrich, Milwaukee, WI) in 1-methyl 2-pyrolidinone (Aldrich, Milwaukee, WI).


title: GE Healthcare/Amersham Biosciences CodeLink™ UniSet Rat I Bioarray, layout EXP5280X2-648

first: Jeremy

last: Gollub

description: layout EXP5280X2-648


title: UAF Arctic Ground Squirrel Illumina BeadArray 2A

status: Public on Aug 03 2006

city: Fairbanks

first: Jun

last: Yan

state: AK

address: 311 Irving Building

department: Institute of Arctic Biology

institute: University of Alaska Fairbanks

organism:
Urocitellus parryii
Ictidomys tridecemlineatus
Callospermophilus lateralis

technology: oligonucleotide beads

description: This array (2A) contains the second 707 genes designed from the mixed sequences of three close-related ground squirrel species: golden-mantled ground squirrel; thirteen-lined ground squirrel; arctic ground squirrel. Two 50bps probes were designed for each gene.

first: Franziska

last: Kohl

first: Brian

last: Barnes

last: Marr


title: UNM Human Operon 18K version 3 slide 1 array format

status: Public on Apr 18 2006

manufacturer: University of New Mexico, School of Medicine EBL

first: Clifford


title: FHCRC Human Prostate PEDB cDNA Array v3

status: Public on Jul 14 2006

first: Denise

last: Mauldin

first: Peter

last: Nelson

first: Ilsa

last: Coleman

last: Abbott

first: Ruth

last: Dumpit

manufacture_protocol: DNA spotted onto polylysine-coated glass microscope slides


title: Eurogentec S. pombe ORF array (D040E)

status: Public on Mar 28 2006

city: Gothenburg

first: Claes

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

organism: Schizosaccharomyces pombe

description: 11520 ORFs were spotted in duplicate on glass slide

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.


title: Iyer Lab Human 46K cDNA microarray

status: Public on Apr 12 2006

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

manufacture_protocol: Human 46K cDNA microarray


title: SLRI_Zebrafish_3.5k_v1

status: Public on Mar 16 2006

city: Toronto

first: Chi-Yip

last: Ho

state: Ontario

address: 600 University Ave. rm-981

department: Research

country: Canada

institute: SLRI/Mount Sinai Hospital

organism: Danio rerio

manufacturer: SLRI/Mount Sinai Hospital, Toronto, Ontario, Canada

first: Chi-Kin

last: Chan

manufacture_protocol: This microarray is printed in triplicate with Operon's the Zebrafish Genome Oligo Set Version 1.0 contains 3,479 70mer probes representing 3,479 Danio rerio genes. The set of 3,479 probes represents cloned Zebrafish genes and some expressed sequence tags (ESTs). For our probe design we use state-of-the-art methodology and proprietary software. All probes are designed from the UniGene Database Build Dr 41, and the Zebrafish Reference Sequence (RefSeq) database, developed and maintained at the National Center of Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov). For the oligo set design, we selected 1,206 sequences, representing well-annotated genes, and 2,273 ESTs with high or moderate homology to known genes. The probes are Tm normalized to 78ºC (±5ºC) and have a 5' amino linker. The concentration of all probes are normalized to 40 micromolar and printed on NUNC poly-L-lysine coated slides using BioRad VersArray Chipwriter Pro.


title: SLRI_Mouse_13.5k_v1

manufacture_protocol: This microarray is printed in duplicate with the Operon's Mouse Genome Oligo Set Version 1 consists of 13443 70mer probes representing 11107 genes and about 13904 gene transcripts. The design is based on the Ensembl Mouse Database, Mouse Genome Sequencing Project, NCBI RefSeq, Riken full-length cDNA clone sequence, and other GenBank sequence. The probes are Tm normalized to 78ºC (±5ºC) and have a 5' amino linker. All probes concentrations are normalized to 40 micromolar. The array is printed on NUNC poly-L-lysine coated slides using BioRad VersArray Chipwriter Pro.


title: SLRI_Worm20k_Singlet_v1

status: Public on Mar 09 2006

organism: Caenorhabditis elegans

manufacture_protocol: This microarray is printed in singlet with the Operon's C. elegans Genome Oligo Set Version 1 consists of 19,873 70mer probes representing 20,445 Caenorhabditis elegans gene transcripts plus 12 controls. The probes were designed from the WormPep DNA Release 75 database, maintained and developed by the Sanger Institute (Cambridge, UK) (www.sanger.ac.uk). The probes are Tm and concentration normalized to 76ºC (±5ºC) and 40 micromolar and have a 5' amino linker. The array is printed on NUNC poly-L-lysine coated slides using BioRad VersArray Chipwriter Pro.


title: Human 12K cDNA clones, print AgB3

status: Public on Sep 21 2007

city: Phoenix

first: Michael

last: Bittner

state: AZ

address: 445 N. 5th Street

department: Computational Biology

institute: Translational Genomics Research Institute

description:
Agilent Technologies inkjet print (same technique as platform GPL875) of custom content
custom print for National Human Genome Resarch Institute

manufacture_protocol: Agilent procedure, same technique as platform GPL875


title: Chromosome coordinates of S. pombe DNA microarray (Eurogentec AR-ScPGS-1)

status: Public on Jan 30 2006

city: Seattle

first: Bonita

last: Brewer

department: Genome Sciences

institute: University of Washington

description:
Chromosome coordinates for this commercial array were determined idependently using Sanger and NCBI. There are about 500 out of 5,000 spots that are not used in our final calculations.  In both datasets, about 170 spots the majority of which were the same spots were flagged during the data extraction process. There are also about 330 spots that are either controls or those with names that cannot be matched in the pombe gene database. Due to the fact that pombe genes contain a significant number of introns, the pombe gene database gives coordinates for each exon.  However, the database does not distinguish between different exons in the nomenclature.  Consequently, there are multiple entries of coordinate information for a given ORF sharing the same name.  For example, the following ORF is listed twice in the pombe genome database with different coordinates (we calculated the midpoint ourselves).

ORF           Start(bp)   End(bp)     Mid(kb)
SPAC977.06     39431      39848       39.6395
SPAC977.06     39899      40050       39.9745

Our program uses the first entry (39.6395) as the coordinate for a given ORF.  In hindsight, we should have taken the average of all the exons.  As it stands, our coordinates do contain a 5' bias for every ORF.  However, we assessed the difference between the midpoint of the first exon and the midpoint of the whole ORF and the overwhelming majority of the ORFs show less than 2kb difference with only 34 out of 4,500 greater than 2kb.

first: Wenyi

last: Feng

first: Dave

last: Collingwood

first: Mosur

middle: K

last: Raghuraman

manufacture_protocol: see manufacturer's website


title: S. cerevisiae Whole-Genome PCR Array, ORF and Intergenic

status: Public on Jan 15 2006

city: Santa Cruz

first: Carrie

middle: Anne

last: Davis

address: 412 Sinsheimer Labs

department: MCD Biology

institute: UC Santa Cruz

organism: Saccharomyces cerevisiae

description: Whole-Genome S. cerevisiae Microarray made up of spotted PCR products representing every annotated open reading frame and intergenic region -based on the 1999 SGD annotation

first: Manuel

last: Ares Jr

manufacture_protocol: Spotted PCR products


title: SLRI_Yeast_6.4K_v1

manufacture_protocol: This microarray is printed in duplicate with Operon's The Yeast Genome Oligo Set Version 1.0 contains 6,388 70mer probes representing 6,388 Saccharomyces cerevisiae open reading frames (ORFs). All probes were designed from the Saccharomyces Genome Database (SGD) at Stanford University (Palo Alto, CA, USA) (http://genome-www.stanford.edu/Saccharomyces/). The probes are Tm normalized to 73ºC (±5ºC) and have a 5' amino linker. The concentration of all probes are normalized to 40 micromolar and printed on NUNC poly-L-lysine coated slides using BioRad VersArray Chipwriter Pro.


title: UCSF 11Mm Mouse v.2 Oligo Array

status: Public on Jan 10 2006

city: San Francisco

middle: E.

last: Salazar

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

manufacture_protocol: MGuide / ArrayMaker


title: Spotted RIKEN cDNA array 20-40K

status: Public on Dec 20 2005

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: spotted cDNA


title: Duke University Murine Operon v.2.0 Spotted Array

status: Public on Dec 06 2005

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

institute: Duke University

description: Protocol for Preparing Poly-Lysine Slides for Microarrays page 1 Basics: -The following protocol is for coating 180 slides with poly-l-lysine. -Be sure slide racks are bent slightly inwards in the middle to hold slides more securely. -DO NOT use powdered gloves at any time during this protocol. -To avoid dust, try to keep slides covered or submerged in solution at all times. -It is recommended that at least two batches of poly-lysine slides are prepared per printing. 1. Prepare wash solution for 180 slides: 200 g NaOH pellets 1200 ml 95% EtOH 800 ml H2O 2. Mix wash solution until NaOH pellets are completely dissolved. 3. Rinse slide dishes completely with H2O. Add one rack of Gold Seal Microslides(30 slides/rack) per slide dish. Pour wash solution over slides and cover. 4. Shake slides gently for 2 hours in wash solution. Although the slides come “pre-washed” the are still significant amounts of oils and debris. This basic wash is necessary to completely clean the slides before applying the poly-lysine. 5. Rinse slides with several liters of Milli-Q H2O. I like to fill a large container with H2O so that I can vigorously dump the rinse over the slides. Let the slides sit in the water while you prepare the poly-lysine solution. 6. Prepare poly-lysine solution (**use only plastic-ware when preparing poly-lysine): 180 slides: 1500 ml H2O 205 ml 1XPBS (filtered) 352 ml poly-l-lysine 7. Mix ingredients on stir plate in plastic beaker in order listed above. 8. Before adding poly-lysine, dump H2O from slides. Immediately after adding poly-lysine pour solution over slides. 9. Let slides shake gently in poly-lysine for 30 minutes. 10. Rinse slides again with Milli-Q H2O in same fashion as described above. 11. Immediately spin slides in tabletop at 600 rpm until dry. 12. To ensure slides are completely dry, place racks in 50°C vacuum oven for at least 5 min. Protocol for Preparing Poly-Lysine Slides for Microarrays page 2 13. Store slides in a clean plastic slide box. Slides MUST be stored for at LEAST 14 days before spotting DNA. We do not recommend using slides that are more than 4 months old as degradation of poly-lysine has been observed. **Poly-lysine solution can be reused if you expect to prepare a large volume of slides. To do so, filter lysine solution after step 9 and store at 4°C in a plastic container. When ready to use, distribute solution to slide dishes and add an additional 10-15 ml of new poly-lysine to each dish. This should be repeated a maximum of 6 times. After slides are preparred they are spotted with Operon olgionucleotides, for details see weblink below.

middle: C

first: Andrea

last: Amalfitano

first: Anne

last: Kiang

manufacture_protocol: The Operon mouse oligonucleotide library,version 3.0, comprised of 70-mer oligonucleotides representing 24,878 unique mouse genes, was printed on poly-L-lysine-coated glass slides. The library also included sets of positive and negative controls that were used for quality control purposes. Oligonucleotides were spotted using a GeneMachines Omnigrid arrayer by the Duke University Microarray facility. Details can be found at http://mgm.duke.edu/genome/dna_micro/core/spotted.htm.


title: UC Human 22K v2.2 Operon 70-mer oligo array

status: Public on Sep 24 2005

city: Chennai

first: Rajkumar

last: T

state: Tamilnadu

address: Adyar

department: Molecular Oncology

country: India

institute: Cancer Institute (WIA)

description: Human 70-mer oligo library (V2.2):  Representing a total of 22,102 annotated genes.

manufacturer: Genomics and Microarray Laboratory, University of Cincinatti Medical Center

manufacture_protocol:
Aminosilane-coated slides (Cell Associates, Cat#CSA-100 C) are used.
Printing
1. The Operon 70-mer oligonucleotides were  suspended in 3XSSC.  The DNA is printed on aminosilane-coated slides (Cell Associates, Cat.# CSA-100 C).

UV-Crosslinking and storage
1. Lay slides array-side-up in a Stratalinker and irradiate at 6000 (x100) mjoules (600mJ).
2. Store slides at room temperature under vacuum.
Notes:  The 70 mer oligonucleotides are spotted at 22ºC and 65-85% relative humidity at ~100 mm center-spacing using a high-speed robotic machine (OmniGrid-100; GeneMachines; San Carlos, CA) using Stealth pins (SMP3 pins) from TeleChem (Sunnuvale, CA), mounted on a 48-pin head.  Spot volumes are 0.5 nl and spot diameters are 75-85 mm.


title: Chinnaiyan Human 20K Hs3

status: Public on Jan 02 2006

city: Ann Arbor

first: Scott

last: Tomlins

state: MI

address: 1400 E. Medical Center Dr., 5410 CCGC

department: Pathology

institute: University of Michigan

description: This 20,000 element (32 blocks, 25 columns and rows per block) array contains spotted cDNA clones (version Hs3)

first: Arul

last: Chinnaiyan


title: Yeast nitric oxide platform

status: Public on Nov 17 2005

first: Joseph

last: DeRisi

institute: UCSF

manufacturer: UCSF Aaron Sarver Joe Derisi Genomics Core

first: Aaron

middle: L

last: Sarver

manufacture_protocol: spotted cdna micorarray


status: Public on Oct 15 2005

last: Hitachi Software Engineering Co.

country: Japan

institute: Hitachi Software Engineering Co., Ltd.

description:
Hitachisoft Hypergene Yeast Chip Ver. 3.0
ID is made by connecting BlockX, BlockY, SpotX and SpotY.
Keywords = S. cerevisiae
Keywords = cDNA microarray

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: 20K RIKEN cDNA array


title: S. pombe 10K long oligonucleotide array

status: Public on Dec 31 2005

city: Singapore

first: Jianhua

last: Liu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description:
Spotted long oligonucleotide array on glass
This set includes 9,858 oligonucleotides that represent 4,929 genes based on S. pombe genome (Sanger Center, UK, November 2001)
Keywords = Spotted, 50-mer oligonucleotides

first: Lance

middle: D

last: Miller

first: Juntao

last: Li


title: UIUC Cattle 7,872-element cDNA - alternate version

city: Urbana

first: Harris

last: Lewin

state: IL

address: 1201 West Gregory Drive

department: Animal Sciences

institute: University of Illinois

organism: Bos taurus

description: The 7,872 cDNAs used in this microarray were obtained from normalized and subtracted cattle placenta and spleen cDNA libraries (see Band et al., 2002 Anim. Biotechnol. 13:163-172; Everts et al., 2005 Vet. Immunol. Immunopathol. 105:235-245). Positive controls include beta actin (ACTB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and hypoxanthine phosphoribosyltransferase (HPRT). Exogenous spiking controls are the soybean genes chlorophyll ab binding protein (CAB), Rubisco small chain 1 (RBS1), and major latex protein (MSG). Negative controls are Cot1 DNA, genomic DNA, spotting buffer, poly-A, and water. All PCR products were printed in duplicate on the array.  This is an alternative version of GPL2108.  Keywords: cDNA, cow, bovine, microarray

manufacturer: W.M. Keck Center, University of Illinois Urbana-Champaign

first: Robin

middle: E

last: Everts

first: Mark

last: Band

first: Lewis

middle: Z

first: Charu

last: Kumar

first: Lei

first: Juan

middle: J

last: Loor

first: Rosane

last: Oliveira

manufacture_protocol: cDNAs were printed in 3xSSC/1.5M betaine on amino-silane coated slides.


title: Rosetta (Merck) GEL Breast Tumor Profiles

status: Public on Jun 28 2006

first: Chang-Kyu

last: Lee

address: 401 Terry Ave N.

department: Informatics

institute: Rosetta Inpharmatics

description:
Oligonucleotide array on glass.
Contains 60-mer probes (60-mer).
Submitted to Cancer Research for publication by Dai et al.

first: Hongyue

last: Dai

first: Laura

last: van t Veer

first: John

last: Lamb

first: Yudong

last: He

first: Mao

last: Mao

first: Bernard

middle: M

last: Fine

first: Rene

last: Bernards

first: Marc

last: ven de Vijver

first: Paul

last: Deutsch

first: Alan

last: Sachs

first: Roland

last: Stoughton

first: Stephen

middle: H

last: Friend

manufacture_protocol: RT/IVT


title: Sigma Mouse oligo set I LGTC

status: Public on Sep 20 2005

city: Leiden

first: Ellen

last: Sterrenburg

address: Wassenaarseweg 72

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

description:
7.5 K sigma mouse oligo set I
printed in duplicate


title: Sigma Mouse oligo set II LGTC

description: 15 K sigma mouse extension oligo set II


title: Human 6k Transcriptionally Informative Gene Panel for DASL

status: Public on Jan 07 2008

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center


title: Muscle-related 4K cDNA array

status: Public on Sep 15 2005

description:
IMAGE cDNA clones
muscle related

first: Rolf

last: Turk


title: Nitricyeast

status: Public on Jul 22 2005

first: Joseph

last: DeRisi

first: Aaron

last: Sarver

manufacture_protocol: pin transfer from 96 well plate using automated arrayer


title: MWG rat 10k oligo set

status: Public on Sep 13 2005

city: Stillwater

first: Zhongming

last: Chen

state: OK

address: 264 McElroy Hall

department: Deptment of Physiological Sciences

institute: Oklahoma State University

description:
Normal rat transcriptomes of six organs: lung, heart, kidney, liver, spleen and brain were obtained using a novel DNA microarray hybridization system. In this system, six organs were hybridized simultaneously on one glass slide.
Keywords = Transcriptome
Keywords = parallel hybridization
Keywords = microarray

first: Jiwang

first: Tingting

last: Weng

first: Lin

last: Liu


title: Agilent-012799 Mouse Developmental Microarray 44K G2519A Option 002 (Feature Number version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
The Mouse Development Oligo Microarray 44K array represents the first commercial whole mouse genome microarray based on the NIA (National Institute on Aging) Mouse Gene Index, which is optimized for stem cell and developmental research.

Arrays of this design have barcodes that begin with 16012799 or 2512799.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7273.

relation:
Alternative to: GPL7273
Alternative to: GPL11531

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


title: Hitachisoft Hypergene Yeast Chip Ver. 0

status: Public on Jul 26 2005

last: Hitachi Software Engineering Co.

description:
Hitachisoft Hypergene Yeast Chip Ver. 0
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


title: human 10K D

status: Public on Aug 20 2005

city: Epalinges

first: Eugenia

last: Migliavacca

state: Vaud

address: Ch des Boveresses 155

country: Switzerland

institute: ISREC

manufacture_protocol: cDNA arrays were spotted using the OmniGrid 300 microarrayer from Genomic Solutions


title: NIA Mouse 44K Microarray v2.0 (Whole Genome 60-mer Oligo)

status: Public on Jun 21 2005

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: The Agilent's Mouse Development Oligo Microarray 44K is formatted on a 1x3 inch (25mm x 75mm) glass slide.  Each 44,290-feature microarray contains 42,291 (60-mer) probes representing all empirical and predicted mouse genes and transcripts from the NIA Mouse Gene Index.  The sequence and associated annotation information is based on the NIA Mouse Gene Index 4.0 http://lgsun.grc.nia.nih.gov/geneindex4, which combines genome assembly sequences from public databases (RefSeq, Ensembl, Riken), and the NIA collection of public EST libraries derived from stem cells and early stage of mouse embryos, along with human-curated genetic databases to form structure models of over 40,000 genetic loci4.  Furthermore, a set of synthetic spike-in control probes are included to control variations in target labeling and hybridization, and to provide more quantitative information on transcripts5.

manufacture_protocol: As descripted by Agilent manuals under Platform_web_link


title: FHCRC Yeast Oligo Array v1.1

status: Public on Sep 02 2005

first: Ryan

last: Basom

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

manufacture_protocol: Operon Version 1.1 of the Yeast Genome Oligo Set, containing 6388 70mer probes representing 6388 Saccharomyces cerevisiae ORFs, was mechanically "spotted" onto glass microscope slides using an OmniGrid high-precision robotic gridder (Genomic Solutions, Ann Arbor, MI).  All probes were designed from the Saccharomyces Genome Database (SGD) at Stanford University.


title: Zacharewski-Mouse Array

status: Public on Jul 20 2005

city: East Lansing

first: Joshua

last: Kwekel

address: 224 Biochemistry

department: Biochemistry and Molecular Biology

institute: Michigan State University

first: Darrell

last: Boverhof

first: Cora

last: Fong

first: Tim

last: Zacharewski


title: NIA Mouse 44K Microarray v2.1 (Whole Genome 60-mer Oligo)

description: The Agilent's Mouse Development Oligo Microarray 44K is formatted on a 1x3 inch (25mm x 75mm) glass slide.  Each 44,290-feature microarray contains 41,034 (60-mer) probes representing all empirical and predicted mouse genes and transcripts from the NIA Mouse Gene Index.  The sequence and associated annotation information is based on the NIA Mouse Gene Index 4.0 http://lgsun.grc.nia.nih.gov/geneindex4, which combines genome assembly sequences from public databases (RefSeq, Ensembl, Riken), and the NIA collection of public EST libraries derived from stem cells and early stage of mouse embryos, along with human-curated genetic databases to form structure models of over 40,000 genetic loci4.  Furthermore, a set of synthetic spike-in control probes are included to control variations in target labeling and hybridization, and to provide more quantitative information on transcripts5.


title: SHFB

status: Public on Mar 01 2006

city: Stanford

first: Howard

last: Chang

state: CA

address: CCSR 2142

department: Dermatology

institute: Stanford University

manufacturer: Joan,,Hebert; SFGF, 2255, CCSR, Stanford, Ca, USA, 94025; 650-736-0075; jhebert@genome.Stanford.edu

manufacture_protocol: Joan,,Hebert


title: KI Schizosaccharomyces pombe 10K IGR+ORF

city: Gothenburg

first: Claes

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

institute: Gothenburg University

description: 10752 IGRs were spotted in duplicate on glass slide

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: Stanford 44k

status: Public on Jul 05 2005

city: SG

first: Amit

last: Aggarwal

department: Cellular and Molecular Research

institute: National Cancer Centre of Singapore

description: Stanford 44k


title: NIA Mouse 22K Microarray v2.0 (Development 60-mer Oligo)

description: NIA Mouse 22K Microarray v2.0 contains 21,052 60-mer oligonucleotides representing over 20,000 known and predicted mouse genes. The sequence annotation information is based on the NIA Mouse Gene Index 4.0 http://lgsun.grc.nia.nih.gov/geneindex4, which combines genome assembly sequences from public databases (RefSeq, Ensembl, Riken), and the NIA collection of public EST libraries derived from stem cells and early stage of mouse embryos, along with human-curated genetic databases to form structure models of over 40,000 genetic loci4.


title: SRC-MUSCGEN22K

status: Public on Jun 19 2005

first: Sean

last: Grimmond

state: QLD

institute: Institute of Molecular Bioscience, Uni of QLD

description: Standard gene content of IMB SRC Mouse Compugen 22K long oligo arrays


title: Saccharomyces cerevisiae ORFs

status: Public on Jun 15 2005

city: Boston

first: Kevin

last: Struhl

state: MA

address: 240 Longwood Ave.

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description: Saccharomyces cerevisiae ORFs

first: Edward

last: Sekinger

first: Zarmik

last: Moqtaderi


title: human 10K E


title: Oncochip v.2

city: Barcelona

first: Moises

middle: Burset

last: Albareda

state: Barcelona

address: Cartagena, 340-350

department: Molecular biology

country: Spain

institute: Fundacio Puigvert

description: Grid with 27648 positions (106 controls and 11663 different clones mainly from IMAGE consortium). Designed to study cancer related genes. http://grupos.cnio.es/genomica/arrays/reports/ochip_v2.xls

manufacturer: Centro Nacional de Investigaciones Oncologicas

manufacture_protocol: Clones were spotted in consecutive pairs onto Ultra-GAPS-II slides. Microarrays were spotted with PCR products in 50% DMSO. Spotted slides were fixed by UV crosslinking and stabilized in sodium borohydride presoaking reagent.


title: Eurogentec S. pombe ORF array (F010D)

status: Public on Aug 11 2005

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

institute: Karolinska Inst

description: 11520 ORFs were spotted in duplicate on glass slide

first: K

first: A

middle: P

last: Wright

first: D

last: Talibi

first: S

last: Hass

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.


title: Human 2.6K cDNA array

status: Public on Jul 30 2005

first: Syed

middle: S

last: Ahmed

address: 715 Albany Street

department: Medicine

institute: Boston University School of Medicine

description:
cDNA grid (composed of 4 panels) spotted in triplicate on glass
This set includes a 2,635 feature cDNA microarray based on the gene set available from Research Genetics (Huntsville, AL)
Keywords = spotted, triplicate cDNA grids


title: YaleNIA15k cDNA microarray

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: spotted NIA 15k cDNA clones

middle: A

first: Chenhao

last: Fan

first: Sanda

first: Gabriel

middle: G

last: Haddad

manufacture_protocol: spotted NIA 15k cDNA clones


title: Eurogentec S. pombe IGR+ORF array (B160E)

description: 22176 IGRs and ORFs were spotted in duplicate on a glass slide


title: SHFD

status: Public on Jun 08 2005

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Support: glass
Coating: unknown_surface_type
Manufacturer: Stanford Functional Genomics Facility,  Stanford School of Medicine


title: Cardiac Allograft Rejection Detection Microarray, 24K designB

status: Public on Jun 01 2005

city: South San Francisco

first: Expression

last: Diagnostics

address: 750 Gateway Boulevard, Suite H

institute: XDx Inc

description:
50-mer oligonucleotides (Sigma) spotted on 1x3 glass slides (Superarmine, Telechem)
Keywords = Transplantation
Keywords = Allogeneic
Keywords = Graft Rejection
Keywords = Heart Transplantation
Keywords = Biological Markers
Keywords = Immunologic
Keywords = Immune Response Genes
Keywords = Immunologic Monitoring
Keywords = Gene Expression Profiling

first: XDx

last: Inc


title: Mouse Genomic Long Oligo Array (AECOM)

status: Public on Jul 21 2005

city: La Jolla

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

manufacturer: Microarray Core Facility of Albert Einstein College of Medicine

manufacture_protocol: Facility's Description


title: Zacharewski-Rat Array

first: Joshua

last: Kwekel


title: Cardiac Allograft Rejection Detection Microarray, 24K designA

description:
General Design: 50-mer oligonucleotides (Sigma) spotted on 1x3 glass slides (Superamine, Telechem)
Keywords = Transplantation
Keywords = Allogeneic
Keywords = Graft Rejection
Keywords = Heart Transplantation
Keywords = Biological Markers
Keywords = Immunologic
Keywords = Immune Response Genes
Keywords = Immunologic Monitoring
Keywords = Gene Expression Profiling


title: Cardiac Allograft Rejection Detection Microarray, 16K design

description: 50mer oligonucleotides (Sigma) spotted on 1x3 glass slides (Superamine, Telechem)


title: NIA Mouse 44K Microarray v1.0 (Development-Toxicology 60-mer Oligo)

first: Minoru

last: Ko

description: NIA Mouse 44K Microarray v1.0 combines two 22K Agilent arrays: "NIA Mouse 22K Microarray v2.0 (Development 60-mer Oligo)"  and  "Agilent Mouse Oligo Microarray (G4121A)" into one 44K chip. 44K array is formatted on a 1x3 inch (25mm x 75mm) glass slide.  Each 44,176-feature microarray contains 41,920 (60-mer) probes representing empirical and predicted mouse genes and transcripts.  The annotation information is based on the NIA Mouse Gene Index 4.0 http://lgsun.grc.nia.nih.gov/geneindex4, which combines genome assembly sequences from public databases (RefSeq, Ensembl, Riken), and the NIA collection of public EST libraries derived from stem cells and early stage of mouse embryos, along with human-curated genetic databases to form structure models of over 40,000 genetic loci4.


title: FHCRC Human 18K Array

status: Public on May 17 2005

city: Seattle

first: Pavel

last: Sova

address: 325 9th Avenue

department: Department of Pathology

institute: University of Washington

description: Microarray construction and hybridization protocols were modified from DeRisi, J.L., V.R Iyer, and P.O. Brown. Science 278:680-686, 1997. The microarrays were constructed using a set of more than 17000 sequence-verified clones from Research Genetics (UniGene Build 136). The cDNA inserts were amplified from replica plate cultures by PCR, purified and mechanically spotted onto polylysine-coated microscope slides using an OmniGrid robotic spotter (GeneMachines, San Carlo, CA).

first: Qinghua

last: Feng

first: Gary

middle: K

last: Geiss

first: Troy

middle: R

last: Wood

first: Robert

last: Strauss

first: Vania

last: Rudolf

first: Andre

last: Lieber

first: Nancy

middle: B

last: Kiviat


title: FlyChip003 cDNA Array

status: Public on May 05 2005

city: Cambridge

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

institute: University of Cambridge

description: cDNA array generated from DGC v1.0

first: Steven

last: White

first: Ian

last: Birch-Machin

first: Shan

last: Gao

first: David

last: Huen

first: Richard

last: McGirr


title: 18k cDNA chip NCCS

status: Public on May 03 2005

first: Amit

last: Aggarwal

description: cDNA chip printed at National Cancer Centre of Singapore in 2001

first: Patrick

last: Tan


title: PBRC Mouse Oligo_M6+ series (Operon 19K)

status: Public on May 16 2005

city: Baton Rouge

first: Leslie

middle: DeBardeleben

last: McLaughlin

state: LA

address: 6400 Perkins Road

department: Department of Experimental Obesity

institute: Pennington Biomedical Research Center

description:
Mouse Oligonucleotide (70 mer) probes designed and manufactured by Operon (mouse library version 2.0, QIAGEN Operon, Inc., Alameda, CA) were solubilized in 45% DMSO and printed onto poly-L-lysine slides.  This library contains 19,200 oligos representing 17,280 unique genes.  Slides were printed using a Genomic Solutions (Gene Machine) OmniGrid equipped with Telechem SMP4 Stealth Micro Spotting pins by the Genomics Core Facility at the Pennington Biomedical Research Center.  Additional information concerning gene specifics can be located on the Operon website (http://omad.operon.com/mouse2/index.php)
Keywords = mouse 19K oligonucleotide

first: Jennifer

middle: W

last: McClaine

first: Dawn

last: Graunke

last: Koza

first: Christpher

last: Faulk

first: John

last: Bearden


title: Human 7.5K cDNA chip (eGenomix)

status: Public on Feb 26 2005

city: Taipei

first: Yuan-Chii

middle: Gladys

last: Lee

department: Graduate Institute of Medical Informatics

country: Taiwan

institute: Taipei Medical University

description: This non-commercial 7500 cDNA microarrays representing approximately 7411 distinct human transcripts. Fluorescence intensities for Cy3 and Cy5 targets were measured and scanned separately using a GenePix 4000B Array Scanner (Axon Instruments; Foster City, CA).

first: Chin-Tarng

last: Lin

first: Chi-Ying

middle: F

last: Huang

manufacture_protocol: not available


title: AECOM-11M cDNA spotted microarray

status: Public on Jan 14 2005

city: New York

first: Weijia

last: Zhang

state: NY

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

description: Each slide contained an unbiased, random collection of 9,568 cDNA probe elements derived from the sequence-verified GEM1 clone set (Incyte Genomics Inc., Palo Alto, CA).

first: K

last: Susztak

first: EP

last: Bottinger

first: A

last: Novetsky

first: D

last: Liang

first: Y

last: Zhu

first: E

last: Ciccone

last: Wu

first: S

last: Dunn

first: P

last: McCue

last: Sharma


title: Iyer Lab_Human promoter microarray

status: Public on Jan 01 2005

first: Jonghwan

last: Kim

address: 1 Blackfan circle Karp-7

institute: HMS/CHB

description: Human 13K promoter microarray.


title: SAN1 platform

status: Public on Jan 19 2005

first: Daniel

last: Gottschling

address: 1100 Fairview Avenue N., Mailstop A3-025

department: Division of Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Custom microarray platform for san1 data

first: Richard

last: Gardner

first: Zara

last: Nelson

middle: E


title: FHCRC Human Oligo Array v2.1

status: Public on Mar 18 2005

first: Ryan

last: Basom

address: 1100 Fairview Ave N

description: Operon Version 2.1 of the Human Genome Oligo Set containing 21,329 70mer probes representing 21,329 genes.  A majority of the probes (21,322) were designed from the UniGene Database Build Hs147 (February 2002) and the Human Reference Sequence (RefSeq) Database with the exception of 7 probes designed from the UniGene Database Build Hs 152.


title: Agilent AMADID012719

status: Public on Dec 10 2004

city: Palo Alto

first: Svetlana

last: Shchegrova

institute: Agilent Technologies, Inc

description:
This design includes 1900 60-mer insitu synthesized oligonucleotides
Orientation: Barcode location: Left; Scan Side: Back
Keywords = Agilent

middle: V


title: CEA_SGF:AHC

status: Public on Mar 31 2005

city: Evry

first: Cyrille

last: Petat

address: 2, rue Gaston Crémieux

department: DSV/DRR

country: France

institute: CEA

description:
Chip contains 10752 features (probes and controls):
2304 PCR products from cDNA matrix using primers specific of genes involved in important biological process (apoptosis, cell cycle, stress response).
5760 PCR products from cDNA clones from human infant brain library (Soares et al. 1994).
1536 PCR products from lymphocytes library.
1152 control reporters and pseudo-features.


status: Public on Apr 09 2005

last: Hitachi Software Engineering Co.

institute: Hitachi Software Engineering Co., Ltd.

description:
Hitachisoft Hypergene Yeast Chip Ver. 1.1 (48block).
ID is made by connecting BlockX, BlockY, SpotX and SpotY.
Keywords = S. cerevisiae
Keywords = cDNA microarray


title: SHCE

status: Public on Feb 21 2005

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description:
Support: glass
Coating: unknown_surface_type
Manufacturer:  = Joan,,Hebert; SFGF, 2255, CCSR, Stanford, Ca, USA, 94025; 650-736-0075; jhebert@genome.Stanford.edu


title: DOT4/UBP10 platform

status: Public on Feb 25 2005

description: Custom microarray platform data for dot4/ubp10 data


title: dmyc overexpression

status: Public on Dec 15 2004

first: Ling

last: Li

address: 1100 Fairview Ave. N.

department: Basic Sciences

description: cDNA spotted microarrays were constructed from release 1 of the Drosophila Gene Collection (Rubin et al. 2000 ) and 430 additional cDNA and genomic sequences. ). Microarray analyses were performed on samples ar 7 or 14h after dMyc induction.  Total RNA was isolated from wondering third instar larvae (120 h after egg deposition, AED) which were heat shocked at 37°C for 2 h.

first: Savraj

last: Grewal

first: Amir

last: Orian

first: Robert

middle: N

last: Eisenman

first: Bruce

last: Edgar


title: Yeast 70mer oligos

status: Public on Feb 19 2005

city: Albuquerque

first: Sushmita

last: Roy

state: NM

institute: Biology, University of New Mexico

description:
Spotted long oligonucleotide array on glass.
This set includes 6400 oligonucleotides
Keywords = spotted, long oligonucleotide

first: Anthony

middle: D

last: Aragon

first: Margaret

middle: C

last: Werner-Washburne


title: AECOM_H9_cDNA

status: Public on Dec 03 2004

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

description:
Albert Einstein College of Medicine, New York; Microarray Facility; Research Genetics cDNA-derived PCR products on aminosilane-coated glass platform; 9K clone series
Keywords = glomerular podocyte
Keywords = differentiation

first: I

last: Witherden

first: J

last: Zavadil

last: Sanday

first: R

last: Lennon

first: L

last: Ni

first: E

last: Bottinger

first: P

last: Mundel

last: Mathieson

first: M

last: Saleem


title: AECOM Mouse 27k cDNA array

status: Public on Nov 12 2004

first: Dumitru

last: Iacobas

state: TX

institute: Prairie View A&M University

description:
These cDNA microarrays were obtained from the Albert Einstein College of Medicine Functional Genomics Facility. Each array was spotted in staggered pattern (48 blocks) with 27400 sequence verified mouse clones and 192 bacterial controls on Corning glass slides. 8968 clones were in MGEM1.0 plates from Incyte, 14208 clones in MNCI-V1 plates from NCI (http://lgsun.grc.nia.nih.gov/cDNA/15k.html ) and 4224 clones in MIMP-V1 plates from Research Genetics.
Gene annotation was performed at 01/13/2004 using http://genome-www5.stanford.edu/cgi-bin/source//sourceBatchSearch.

first: Aldo

last: Massimi


title: Yeast Deletions DownTag array (Rosetta Inpharmatics)

status: Public on Nov 05 2004

city: Baltimore

first: Xuewen

last: Pan

address: 733 N. Broadway, Room 331

department: Department of Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description:
Array of Down (3') Tags as designed by the Yeast Deletion Project, in triplicate
Keywords = yeast, deletion, knockout, tag, barcode, synthetic, oligonucleotide

first: Daniel

last: Shoemaker


title: MJArray Fly

status: Public on Nov 01 2004

city: Karlsruhe

first: Michael

middle: J.

last: Pankratz

department: Institute of Genetics

institute: Forschungszentrum Karlsruhe

description:
The array was assembled using amplicons that were obtained using the Incyte primer set. The set is identical to the one used to produce platform GPL20, primer sequences can be viewed in that platform. We included a reference to the ID of GPL20. The amplicons represent approximately 93% of the genes predicted in version 1.0 of the Drosophila genome from sequences released by the Berkeley Drosophila Genome Project and Celera Genomics in March 2000. The amplicons represent approximately 75% of the genes predicted in the January 2003 release 3.1 Drosophila genome annotation update.

The regions amplified to build the array ranged in size from 150 to 600 bp with an average size of 410 bp. PCR fragments were amplified and each amplicon was quality control tested for DNA concentration, purity, and fragment size. A total of 11,796 reactions led to a single product of correct size and sufficient amount (marked as ok in column GENE_NAME). The 675 reactions that produced multiple products were run on a gel again and the band of the correct size was excised cloned into pCR TOPO 2.1 (Invitrogen). The 2034 reactions where no band was visible was also subjected to a 'blind' clone-attempt. Those 2709 cloning-reactions led to 2033 positive clones, that were included on the array and marked as 'clone!' in column GENE_NAME. Non sequence-verified clones were not included in the current study. A mixture of all these 2033 clones was used to make a titration dilution as a hybridisation control (Incyte Amplification Titration Standard, IATS) that is included in each of the 48 blocks of our array.
Arrays were spotted with a Omnigrid 100 (GeneMachines) with 24 SMP3 pins (Telechem). By having two identical subarrays next to each other on each slide, we obtain 48 blocks with 26 rows and 26 columns each. Spot to spot spacing is 150 micron, average spot diameter is 100 micron.

first: Joerg

last: Katzenberger

first: Matthias

last: Bauer

middle: J


last: Hitachi Software Engineering Co.

description:
Hitachisoft Hypergene Yeast Chip Ver. 1.1 (32block).
ID is made by connecting BlockX, BlockY, SpotX and SpotY.
Keywords = S. cerevisiae
Keywords = cDNA microarray


title: EPA mouse gal V3

status: Public on Apr 21 2005

city: RTP

first: Edward

last: Karoly

state: NC

address: MD 58D

department: HSD

institute: U.S. EPA

description: Probes were from an Array-Ready Oligo set for the mouse genome version 2 (Qiagen Operon, Valencia CA) consisting of 16,423 70mer oligonucleotide probes, 24 positive and negative controls and additional in house derived specific probes.  Total number of probes= 17,388.

first: E.

middle: S

last: Hunter


title: Eurogentec AG S. pombe ORF array

status: Public on May 01 2005

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

institute: Karolinska Inst

description:
Schizosaccharomyces pombe

4976 ORFs spotted in duplicate on glass slide
Keywords = yeast ORF DNA microarray

first: Yongtao

last: Xue

first: Stefan

middle: A

last: Haas

first: Laurent

last: Brino

first: Arief

last: Gusnato

first: Mark

last: Reimers

first: Driss

last: Talibi

first: Martin

last: Vingron

first: Anthony

middle: P

last: Wright


title: UCSF-MMC-Fantom

status: Public on Feb 26 2005

city: San Francisco

middle: Scott

last: German

address: 513 Parnassus, HSW 1090

department: Diabetes Center

institute: University of California San Francisco

description:
Custom cDNA slides produced by the Mouse Microarray Consotium at UCSF.
Include PCR products from the Fantom-1 set of clones from RIKEN Japan as well as custom UCSF clones.
Keywords = MMC UCSF Fantom

first: Caroline

last: Mrejen

last: Maibaum


title: NIAID - Mmad

status: Public on Oct 21 2004

city: Bethesda

last: Wilson

address: 50 South Drive, Room 5509

department: Division of Intramural Research

description:
Printing by NIAID / Microarray Research Facility
Surface type: non-adsorptive, polylysine-coated glass
Attachment: covalent, (UV-treated polylysine)
Array description: The custom microarrays are manufactured by the Microarray Research Facility of the National Institute of Allergy and Infectious Diseases (NIH/NIAID). Microarrays are 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 ). The mouse microarray (Mmad) probe set is based on 70mer oligonucleotides from Qiagen's Mouse Genome Oligo Set V1.0 (http://oligos.qiagen.com/arrays/omad.php ) -- version 1.0 contains oligo IDs M000001_01 through M006868_01 of the version 1.1 set listed at this URL. Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in 4XSSC print buffer at a normalized 25 micromolar concentration. The Mmad microarray spot densities are 190 microns (center-to-center).  Each probe is printed in duplicate as side-by-side features.  The microarrays are printed on Fisher Premium microscope slides (cat# 12-544-1) coated with poly-L-lysine and post-processed according to the procedures on the Stanford website: http://cmgm.stanford.edu/pbrown/protocols/index.html .


title: FHCRC Human 18K v1.0

status: Public on Feb 17 2005

first: Ryan

last: Basom

description: Microarray construction and hybridization protocols were modified from DeRisi, J.L., V.R Iyer, and P.O. Brown. Science 278:680-686, 1997. The microarrays were constructed using a set of more than 17000 sequence-verified clones from Research Genetics (UniGene Build 133). The cDNA inserts were amplified from replica plate cultures by PCR, purified and mechanically spotted onto polylysine-coated microscope slides using an OmniGrid robotic spotter (GeneMachines, San Carlo, CA).


title: University of Goettingen TAL UniGene_Set_RZPD2_mm2 pattern 06102003

status: Public on Jan 31 2005

city: Göttingen

first: Bettina

last: Spielbauer

address: Humboldtallee 23

department: Neuro and Sensory Physiology

institute: University of Goettingen

description:
Preparation of high-density cDNA microarrays. PCR-based cDNA amplification (Hedge et al., 2000 PMID: 10997270) was used to generate DNA from a murine cDNA clone library (Mouse Unigene Set RZPD 2) purchased from the RZPD (http://www.rzpd.de). This murine library contained 21,826 non-redundant clones from diverse tissues. After fully automated PCR-amplification and ultrafiltration-based purification using a Beckman-Coulter cDNA-production unit, control gel electrophoresis was perfomed showing that 95% of the products were clonally amplified. Non clonal or failed PCR-products were excluded from data analysis. The PCR-products were spotted on epoxy-coated glass slides (Schott Nexterion) using the BioRad spotter "Virtek Chip-Writer Pro" with 48 split pins (purchased from Telechem, www.arrayit.com). The arrays were prepared for hybridisation using surface blocking as described by the slide manufacturer.
Keywords = cDNA, microarray, spotted, PCR-products

first: Jobst

last: Landgrebe


title: Agilent AMADID012717

status: Public on Dec 10 2004

first: Svetlana

last: Shchegrova

description:
This design includes 1900 60-mer insitu synthesized oligonucleotides
Orientation: Barcode location: Left; Scan Side: Back
Keywords = Agilent


title: Barbry cDNA

status: Public on May 21 2004

city: Sophia Antipolis

first: Chimene

last: Moreilhon

institute: CNRS

description:
cDNA microarray
All probes (i) had a normalized length of 250 bp ± 19 bp; (ii) had a normalized GC content of 52 % ± 8 %; (iii) were specific for a unique human gene.
Each gene is spotted 4 times on the slide.


title: CEA_SGF:ABU

status: Public on May 19 2004

first: Cyrille

last: Petat

description:
Chip contains 2400 features (probes and controls):
1632 PCR products from cDNA clones from the I.M.A.G.E consortium (Research Genetics collection).
480 PCR products from rat cDNA clones of a substractive bank (old versus normal kidney).
288 control reporters and pseudo-features.


title: CEA_SGF:ALE

status: Public on Apr 16 2004

description:
Chip contains 10496 features (probes and controls):
2304 PCR products from cDNA matrix using primers specific of genes involved in important biological process (apoptosis, cell cycle, stress response).
5760 PCR products from cDNA clones from human infant brain library (Soares et al. 1994).
1536 PCR products from lymphocytes library.
896 control reporters and pseudo-features.


title: Hitachisoft AceGene Mouse Oligo Chip 30K Subset B

status: Public on Jun 18 2004

last: Hitachi Software Engineering Co.


title: CCF Cancer cDNA Array

status: Public on Aug 14 2004

city: Cleveland

first: Wenliang

last: Li

state: OH

address: 9500 Euclid Ave

department: Department of Cancer Biology

institute: Lerner Research Inst., The Cleveland Clinic

description: The Cancer cDNA Array contains probes for 9241 cDNA clones corresponding to ~4900 unigenes or unclustered ESTs relevant to cancer biology. These include:  1) 1800 genes implicated in metastasis or tumor development in general from the literature and Affymetrix cancer G110 array (www.affymetrix.com/analysis/index.affx); 2) 1809 genes involved in kidney development (golgi.ana.ed.ac.uk/kidhome.html) or showing more than 3-fold variation of expression among 4 primary Wilms tumors and fetal kidney in our previous Affymetrix GeneChip experiments (unpublished data); 3) 1400 potential downstream targets of p53 transcriptional regulation; 4) 950 genes with AU-rich elements in their 3’ and/or 5’ UTR; 5) 1245 cytokine responsive genes, genes for zinc finger proteins or genes implicated in apoptosis.

first: Bryan

last: Williams


title: SuperArray GEArray Q series Mouse p53 Signaling Pathway Gene Array

status: Public on Apr 09 2004

city: Frederick

first: SuperArray

last: Bioscience Corporation

address: Suite 101, 7320 Executive Way

institute: Technical Support

description:
GEArray Q series Mouse p53 Signaling Pathway Gene Array is designed to profile gene expression of a panel of 96 key genes involved in the p53 pathways. These genes are grouped into two major categories: p53 upstream signaling and p53 downstream signaling. The genes regulating p53 is sub-grouped according to their functional relationship to p53 protein. The genes regulated by p53 are divided into the functional clusters that are implicated in cell cycle arrest, apoptosis, DNA repair, and blood vessel formation. Through a simple side-by-side hybridization, you can determine simultaneously the expression synopsis of these 96 genes interconnected in the p53 network.
Catalog number MM-027 (Superarray, Frederick, MD)
Platform_weblink: http://www.superarray.com/home.php


title: Agilent Oligo Yeast

status: Public on Dec 01 2004

city: Leiden

first: Paul

last: van Heusden

address: Wassenaarseweg 64

institute: Institute of Biology

description:
Microarray Profile
Agilent's Yeast Oligo Microarray contains 60-mer oligonucleotide probes to 6,256 annotated ORFs in the 25-May-2002 ORF list for the S288C strain of Saccharomyces cerevisiae. The ORF list was downloaded from the Saccharomyces Genome Database (SGD weblink below) at Stanford University. This public domain site maintains the official database of the molecular biology of the yeast Saccharomyces cerevisiae, as well as the Gene Name Registry for this organism.

Probe Design
Powerful probe selection algorithms designed by Agilent were used to select unique probes that maximize probe sensitivity and minimize the potential for cross hybridization. Agilent's SurePrint Technology was employed to synthesize the oligos directly on the microarray's surface in an iterative, flexible manner.


title: Leatherwood/Futcher pombe 09_2004 annotated

status: Public on Sep 30 2004

city: Stonybrook

first: Adam

middle: Phillip

last: Smith

address: 130 Life Sciences

department: Molecular Genetics and Microbiology

institute: Stonybrook University

description:
Leatherwood and Futcher pombe PCR product mechanically spotted arrays.
Stonybrook University
redgreengene.com

last: Rosebrock

first: Bruce

last: Futcher

first: Janet

middle: K

last: Leatherwood

first: Anna

last: Oliva

first: Francisco

last: Ferrezuelo


title: CEA_SGF:ACI

status: Public on Apr 07 2004

institute: CEA

description:
Chip contains 4800 features (probes and controls):
2016 PCR products from cDNA matrix using primers specific of genes involved in important biological process (apoptosis, cell cycle, stress response).
1632 PCR products from cDNA clones from the I.M.A.G.E consortium (Research Genetics collection).
480 PCR products from rat cDNA clones of a substractive bank (old versus normal kidney).
672 control reporters and pseudo-features.


title: Agilent Mouse mucosal/immuno

status: Public on Sep 16 2004

city: Berlin

last: Walduck

address: Schumanstrasse 21/22

department: Molecular Biology

description:
Oligonucleotide array printed with 8015 unique 60-mer oligos derived from Unigene clusters (Unigene Build#148).
Array is a custom design developed at the Max-Planck Institute for Infection Biology, in Berlin, Germany.
Genes were selected to preferentially represent those expressed  in the gut  (intestine, stomach), lung and immune system.

first: Hans

last: Mollenkopf

first: Stefan

middle: H

last: Kaufmann

first: Thomas

last: Meyer


title: Hitachisoft AceGene Mouse Oligo Chip 30K Subset A

institute: Hitachi Software Engineering Co., Ltd.


title: UCSF 10Mm Mouse v.2 Oligo Array

first: Michael

middle: E.

last: Salazar

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

description:
Spotted long oligonucleotide array on glass.
Keywords = spotted, long oligonucleotide


title: UCSF Gladstone 18K Mouse v.2 Oligo Array


title: SuperArray GEArray Q series Human p53 Signaling Pathway Gene Array

description:
GEArray Q series Human p53 Signaling Pathway Gene Array is designed to profile gene expression of a panel of 96 key genes involved in the p53 pathways. These genes are grouped into two major categories: p53 upstream signaling and p53 downstream signaling. The genes regulating p53 is sub-grouped according to their functional relationship to p53 protein. The genes regulated by p53 are divided into the functional clusters that are implicated in cell cycle arrest, apoptosis, DNA repair, and blood vessel formation. Through a simple side-by-side hybridization, you can determine simultaneously the expression synopsis of these 96 genes interconnected in the p53 network.
Catalog number HS-027 (Superarray, Frederick, MD)
Platform_weblink: http://www.superarray.com/home.php


title: CEA_SGF:ACH

last: Petat


title: RNG-MRC_MM25k_NICE

status: Public on Oct 05 2004

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

last: Le Brigand

first: Pascal

last: Barbry


title: CEA_SGF:AFU

status: Public on Apr 02 2004

city: Villejuif

first: Dalila

last: Sekkai

department: hematopoiesis and stem cell

institute: IGR

description:
Chip contains 9216 features (probes and controls):
2014 PCR products from cDNA matrix using primers specific of genes involved in important biological process (apoptosis,  cell cycle, stress response).
1684 PCR products from cDNA clones from the I.M.A.G.E consortium (Research Genetics collection).
2014 PCR products from mouse cDNA clones of a substractive bank (myodistrophic versus normal muscle).
1800 PCR products from rat cDNA clones of a substractive bank (atrophied versus normal muscle).
1704 control reporters.


title: NCI/LMT Mm_FCRF_UniGEM2

status: Public on Oct 27 2004

first: Lisa

middle: M

last: Gangi

address: 915 Tollhouse Ave

department: LMT-Frederick

institute: NCI

description:
Printing by the NCI-Frederick/LMT Microarray Research Facility
Surface type: non-adsorptive, polylysine-coated glass
Attachment: covalent, (UV-treated polylysine)
Array description:  The custom arrays are manufactured by the NCI Frederick Laboratory of Molecular Technology Microarray Facility (NIH/NCI/SAIC/LMT).  Microarrays are printed with BioRobotics TAS II robotic arrayer from Genomic Solutions (http://www.genomicsolutions.com) that is fitted with a printhead containing 32 SMP3 printing pins from Telechem International (http://www.arrayit.com).  The mouse cDNA probe set is based on 9984 PCR products from Incyte's mouse UniGEM 2.0 library (http://www.incyte.com).  The set includes 9234 Unique GenBank Accessions; 8882 mapped into Mm UniGene Build #1201; 8656 Unique UniGene Clusters; 3463 EST clusters; 5193 "Named" clusters. The cDNA probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in 3XSSC print buffer at a concentration of 50-100 ug/ml.  The microarray spot densities are 235 microns (center-to-center), and one spot is printed per probe per slide.  The microarrays are printed on Fisher Premium microscope slides (cat# 12-544-1) coated with poly-L-lysine and post-processed according to the procedures on the NCI website http://nciarray.nci.nih.gov/ .


title: NIAID - Mmac

status: Public on Feb 11 2004

last: Wilson

description:
Printing by NIAID / Microarray Research Facility
Surface type: non-adsorptive, polylysine-coated glass
Attachment: covalent, (UV-treated polylysine)
Array description: The custom microarrays are manufactured by the Microarray Research Facility of the National Institute of Allergy and Infectious Diseases (NIH/NIAID). Microarrays are 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 ). The mouse microarray (Mmac) probe set is based on 70mer oligonucleotides from Qiagen's Mouse Genome Oligo Set V1.1 (http://oligos.qiagen.com/arrays/omad.php ).  A comprehensive gene list is also available at http://madb.niaid.nih.gov

Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in 4XSSC print buffer at a normalized 25 micromolar concentration. The Mmac microarray spot densities are 190 microns (center-to-center).  The microarrays are printed on Fisher Premium microscope slides (cat# 12-544-1) coated with poly-L-lysine and post-processed according to the procedures on the Stanford website: http://cmgm.stanford.edu/pbrown/protocols/index.html .


title: VIB Mouse 5K 1

status: Public on Nov 25 2003

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
[1]. Array Description:
This microarray contains 4608 array elements spotted in duplicate.
Since the microarray spotter is equipped with 12 capillary pins,
the spots are arrayed over the entire length of the slide
in 1 column of 12 blocks each containing 32x12 unique spots.
The duplicates spots are printed in an identical column next to the first one. Spotting time to print 36 slides takes approximately 4 hours.

[2]. Array protocol description:
Equipment: 1. Generation III microarray spotter (Amersham Biosciences, Buckinghamshire, UK). 2. 384 microtiter plates (Amersham Biosciences, Buckinghamshire, UK). 3. UV-crosslinker (Biolink, BLX-254, Vilber Lourmat, France). 4. Type VII silane coated slides (cat#: RPK0174, Amersham BioSciences, Buckinghamshire, UK). Spotting: 1. Dissolve cDNA array elements in 50% DMSO at concentrations ranging between 100-200ng/µl and array in 384 microtiter plates. 2. Set spotter settings for 4608 spots in duplicate: normal mode, 55% humidity, spot diameter: 250, spot buffer: 30, and pen deflection:0.508mm. 3. Make sure room temperature is between 20-24 degrees Celsius. 4. Place microtiter plates in the plate hotel with A1 in upper right corner. 5. Place 36 slides on the slide-deck and perform 2 manual pin-washes. 6. After spotting, let slides dry at 55% humidity for 3 hours and cross-link at 50 mjoules. 7. Block slides in %SSPE for 30 minutes at room temperature rinse in water and dry in centrifuge. 8. Slides can be stored for at least 6 months in a dry-cabinet.

last: Van Hummelen


title: M15K array

status: Public on Jul 29 2004

city: La Jolla

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

country: USA

institute: University of California, San Diego, School of Medicine

description: The M15K array contains cDNAs from the NIA Mouse 15K cDNA clone collection. The array slides are produced by Keck DNA Microarray Resource at Yale University School of Medicine.

first: Jin

last: Xue

first: Orit

last: Gavrialov

first: Gabriel

middle: G

last: Haddad


title: Hitachi AceGene subset A

status: Public on Sep 29 2003

city: Tokyo

first: Motoyuki

last: Otsuka

department: Department of Gastroenterology

institute: University of Tokyo

description: Spotted oligonucleotide array on glass. This set includes 10800 oligonucleotides, mostly 50-mers, designed based upon representative sequences in the human UniGene database.


title: Hitachisoft AceGene Mouse Oligo Chip 30K Subset C

last: Hitachi Software Engineering Co.


title: NIAID - Mmaa

status: Public on Sep 04 2003

description:
Printing by NIAID / Microarray Research Facility
Surface type: non-adsorptive, polylysine-coated glass
Attachment: covalent, (UV-treated polylysine)
Array description: The custom microarrays are manufactured by the Microarray Research Facility of the National Institute of Allergy and Infectious Diseases (NIH/NIAID). Microarrays are 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 ). The mouse microarray (Mmaa) probe set is based on 70mer oligonucleotides from Qiagen's Mouse Genome Oligo Set V1.0 (http://oligos.qiagen.com/arrays/omad.php ) -- version 1.0 contains oligo IDs M000001_01 through M006868_01 of the version 1.1 set listed at this URL. Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in 4XSSC print buffer at a normalized 25 micromolar concentration. The Mmaa microarray spot densities are 190 microns (center-to-center).  Each probe is printed in duplicate as side-by-side features.  The microarrays are printed on Fisher Premium microscope slides (cat# 12-544-1) coated with poly-L-lysine and post-processed according to the procedures on the Stanford website: http://cmgm.stanford.edu/pbrown/protocols/index.html .


title: MWG Yeast Array

status: Public on Oct 07 2003

city: High Point

last: MWG Biotech

address: 4170 Mendenhall Oaks Parkway, Suite 160

institute: MWG Biotech

description: 6250 gene specific oligonucleotide probes represent the complete Saccharomyces cerevisiae genome on one single slide.


title: LC-20

status: Public on Jun 17 2003

city: Stanford

first: Xin

last: Chen

department: Biochemistry

institute: Stanford University

description:
Tip Configuration: Standard 48 tip
Columns per Sector: 28
Rows per Sector: 28
Column Spacing: 157
Row Spacing: 157


title: NIAID - Hsaa

status: Public on Mar 03 2004

description:
Printing by NIAID / Microarray Research Facility
Surface type: non-adsorptive, polylysine-coated glass
Attachment: covalent, (UV-treated polylysine)
Array description: The custom microarrays are manufactured by the Microarray Research Facility of the National Institute of Allergy and Infectious Diseases (NIH/NIAID). Microarrays are 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 ). The human microarray (Hsaa) probe set is based on 70mer oligonucleotides from Qiagen's Human Genome Oligo Set V1.0 (http://oligos.qiagen.com/arrays/omad.php ) -- version 1.0 contains oligo IDs H000001_01 through H013971_01 of the version 1.1 set listed at this URL. Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in 4XSSC print buffer at a normalized 25 micromolar concentration. The Hsaa microarray spot densities are 190 microns (center-to-center).  The microarrays are printed on Fisher Premium microscope slides (cat# 12-544-1) coated with poly-L-lysine and post-processed according to the procedures on the Stanford website: http://cmgm.stanford.edu/pbrown/protocols/index.html .


title: AECOM 9K mouse array; 6M-8M print series

status: Public on Sep 22 2003

city: Bronx

first: Weijia

last: Zhang

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

description: cDNA spotted microarray; 8,976 cDNAs from Incyte GEM1 mouse cloneset; chip layout in 4(tips)X51(columns)X44(rows).

first: Yaw-Ching

last: Yang

first: Ester

last: Piek

first: Jiri

last: Zavadil

last: Liang

first: Donglu

last: Xie

first: Joerg

last: Heyer

first: Paul

last: Pavlidis

first: Raju

last: Kucherlapati

first: Anita

middle: B

last: Roberts

first: Erwin

last: Bottinger


title: BIOGEM Array

status: Public on Jan 08 2003

first: Richard

last: Rouse

address: 9500 Gilman Drive

institute: UCSD

description:
This array is designed to measure the stoicheometry of sample - array feature interaction.
Keywords = natural units, absolute abundance

first: Katrine

last: Verdun

first: Hannes

last: Niedner

first: Gary

last: Hardiman


title: RNG-MRC_HU25k_NICE

status: Public on Sep 23 2004

first: Kevin

last: Lebrigand

last: Le Brigand

first: Pascal

last: Barbry


title: Incyte Drosophila LifeArray v1.0

status: Public on Nov 14 2001

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description:
The array was assembled using amplicons representing approximately 93% of the genes predicted in version 1.0 of the Drosophila genome from sequences released by the Berkeley Drosophila Genome Project and Celera Genomics in March 2000.  The amplicons represent approximately 75% of the genes predicted in the January 2003 release 3.1 Drosophila genome annotation update.

Incyte in-house algorithms were used to develop gene-specific primers averaging 20 nucleotides in length that were used to PCR amplify one exon or exon fragment from every predicted gene in the fly genome. The regions amplified to build the array ranged in size from 150 to 600 bp with an average size of 410 bp.  PCR fragments were amplified and each amplicon was quality control tested for DNA concentration, purity, and fragment size.  A total of 13,856 unique Drosophila elements are included on the array.  Each element was spotted in duplicate(some are spotted multiple times) for a total of 29,222 elements which were distributed on two separate glass slides designated subarrays A and B.  In addition to the Drosophila elements, both halves of the array contain non-Drosophila controls elements that serve to orient the arrays, function to correct for background and to provide calibration standards.  The total number of elements (Drosophila transcripts and controls) is 31,464.  Each array element includes an area of 150 micron diameter with a center to center separation of 170 microns.  Adhesion to glass was facilitated by UV crosslinking at 120,000 mj/cm2.
Qualification of the arrays was examined by dying representatives of each print run with Syto 61 dye. Dyed slides were read with a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm.
The April 2007 platform update is based on the Dmel_RELEASE 4.1 re-annotation result from DGRC (https://dgrc.cgb.indiana.edu/microarrays/annotation.html).

first: Pamela

last: Edwards


title: UCSD BIOGEM Core Human Array

status: Public on May 09 2002

description: This array was printed using the Amersham GenIII spotter on type 7 star slides. The sequence of the clone ID can be found on our website.


title: NIAID - Hsab

first: Michael

last: Wilson

description:
Printing by NIAID / Microarray Research Facility
Surface type: non-adsorptive, epoxy-coated glass
Attachment: covalent
Array description: The custom microarrays are manufactured by the Microarray Research Facility of the National Institute of Allergy and Infectious Diseases (NIH/NIAID). Microarrays are 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 ). The human microarray (Hsab) probe set is based on 70mer oligonucleotides from Qiagen's Human Genome Oligo Set V1.0 (http://oligos.qiagen.com/arrays/omad.php ) -- version 1.0 contains oligo IDs H000001_01 through H013971_01 of the version 1.1 set listed at this URL.  A comprehensive gene list is also available at http://madb.niaid.nih.gov/
Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved to a normalized 25 micromolar concentration in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl).  The Hsbb microarray spot densities are 190 microns (center-to-center).  The microarrays are printed on MWG Epoxy Slides (MWG Biotech Inc., # 1150-000000) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.