title: Amersham BioSciences CodeLinkTM Uniset Human 20K I Bioarray

status: Public on Jul 04 2004

city: Jerusalem

first: Ofer

last: Mandelboim

department: The Lautenberg Center for General and Tumor Immunology

country: Israel

institute: The Hebrew University of Jerusalem

organism: Homo sapiens

technology: spotted DNA/cDNA

description: CodeLink™ UniSet Human 20K I targets approximately 20 000 of the most well-annotated human genes published in public databases, derived from the public UniGene and RefSef databases, and sequences for design were derived from Incyte™ LifeSeq™ Gold and Foundation databases.

distribution: custom-commercial

first: Jacob

last: Hanna


title: UTSW Human 22k Oligo spotted array

status: Public on Aug 19 2004

city: Stillwater

first: Patricia

middle: J

last: Ayoubi

state: OK

address: 246 NRC

department: Biochemistry and Molecular Biology

country: USA

institute: Oklahoma State University

technology: spotted oligonucleotide

description: Construction and Preparation of Human Oligo 22K Spotted Microarrays by UTSW:  Operon Human Genome Oligo Set (Version 2) (70mers) representing 21,329 human genes in 150mM Sodium Phosphate (pH8.3) plus 1xSSC at 30 µM were spotted singly onto polymer-coated glass slides (Full Moon Biosystems) using BioRobotics MicroGrid II spotter (Genomic Solutions) fitted with 4x12 Microspot 2500 quill pins at 20-23°C and 60-65% RH.  Spot are arranged with 22x22 spots per block (48 total blocks) and spot centers are 200 µm apart.  Printed slides were subjected to a UV-cross-linking at a dose of 650mJ cm2 for probe immobilization. Slides with immobilized probes were then stored in slide holders and placed in a desiccator at room temperature.

distribution: non-commercial

first: Anwu

last: Zhou


title: Ips_pini-midgut.3

status: Public on Nov 13 2003

city: Reno

first: Christopher

middle: Ian

last: Keeling

state: NV

address: 1664 North Virginia Street

department: Department of Biochemistry/Mail Stop 330

institute: University of Nevada, Reno

organism: Ips pini

description:
The Ips_pini-midgut.3 array is a cDNA-based glass microarray produced for Dr. Claus Tittiger's laboratory by the Nevada Genomics Center at the University of Nevada, Reno. The array features 1920 spots representing 574 tentatively unique genes chosen from an Ips pini (the North American pine engraver beetle) EST project of anterior midgut tissue from juvenile hormone III treated (20 h) males (Eigenheer, A. L., et al., Gene 316:127-136, 2003 PMID:14563559).  Pheromone biosynthesis occurs de novo in this tissue.  cDNA was amplified using vector specific primers from selected clones.  PCR products were resuspended in Micro Spotting Solution Plus (Arrayit) and spotted onto SuperAmine microarray substrates (Arrayit) using a Virtek SDDC2 Microarrayer with a 1 x 8 array of SMP5B Stealth Micro Spotting pins (Arrayit) printing subarrays of 8 x 10 spots with 550 µm spacing.  Spotting was replicated in triplicate on each substrate with replicate spots 6 mm apart.  DNA was bound to substrate by first rehydrating the array, flash drying on a hot plate, crosslinking with 120 mJ of UV light (Stratagene UV Stratalinker 1800), and then baking for 60 min at 80°C.  Clones were chosen to represent the longest clone of a cluster-contig.
Keywords = North American pine engraver beetle
Keywords = anterior midgut
Keywords = juvenile hormone
Keywords = pheromone biosynthesis
Keywords = Coleoptera
Keywords = Scolytidae

middle: I

first: Claus

last: Tittiger


title: RAT_6K_OligoArray

status: Public on Feb 11 2004

city: San Antonio

first: Phillip

last: Bowman

state: TX

address: 3400 Rawley E. Chambers Ave

institute: Institute of Surgical Research

organism: Rattus norvegicus

description:
Spotted 70mer oligonucleotide
The Rat Genome Oligo Set Version 1.1 (Qiagen) contains 5,705 70mer probes representing 5,677 Rattus norvegicus genes plus 24 controls oligonucleotides. The oligo set represents most cloned rat genes and some expressed sequence tags (ESTs).
All probes are designed from the UniGene Database Build Rn 90(Version 1.0), UniGene Database Build Rn 108 (Upgrade), and the Rat RefSeq database, developed and maintained at the National Center of Biotechnology Information (NCBI).

Keywords = spotted
Keywords = 70mer oligonucleotide

middle: D

first: Baiteng

last: Zhao


title: Dmel.testis.1.0

status: Public on Oct 08 2000

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

organism: Drosophila melanogaster

description:
The array was assembled using 1,681 testes ESTs, representing 1,527 Drosophila melanogaster EST sequences and 144 anonymous clones from the bs collection (CLONE_ID).
An aliquot of the same DNA preparation used in the sequencing reactions (GB_ACC), diluted 2/50 in TE, provided material for the PCRs.
Inserts were PCR amplified (1X PCR buffer [Life Technologies], 1.5 mM MgCl2, 0.2 mM dNTPs, 1 µM T7 22-mer primer, 1 µM T3 20-mer primer, 2 µl of plasmid DNA dilution [approximately 10 ng], 0.035 U/µl recombinant Taq DNA polymerase [Life Technologies], in a volume of 100 µl, cycled 94C 2 min, 30X[94 C 0.5 min, 55 C 0.5 min, 2.5 min 72 C], 10 min 72 C in a PTC-225 DNA Engine Tetrad [MJ Research]), and successful amplification was confirmed by agarose gel electrophoresis (PCR-QC:  passed = product present, failed = no product).
Samples of approximately 5 nl of 250 µg/ml DNA, in 0.1 N NaOH were printed in 300 µm spots in subarrays (SUB-ARRAY) of 12 x 12 clones (ROW and COLUMN indicated) at 665 µm spacing on Supercharge nytran membranes (Schleicher & Schuell) using a GMS 417 arrayer (Genetic Microsystems).
Subarrays were printed in duplicate (DUPLICATE a or b).
Printing was validated (SPOT_QC) by hybridization of one array with the short vector sequence common to all amplicons (pBluescript SK, 626-791 bp).
SPOT_QC values are hybridization intensity.  BEST-HIT and associated E value for ESTs aligned with the nr database are given.
Keywords = germline sex testis, membrane, filter

first: B

first: J

last: Andrews

first: G

middle: G

last: Bouffard

first: C

last: Cheadle

last: Lu

first: K

last: Becker


title: Human Skeletal Muscle Array

status: Public on Sep 30 2005

city: Bern

first: Silvia

last: Schmutz

country: Switzerland

institute: University of Bern

description: Nylon, custom-designed human cDNA array produced by Clontech, BD Biosciences. The cDNA fragments (200-600 bp) are PCR-amplified using gene-specific primers, and are selected so that they lack repetitive elements and have minimal homology with other genes on the array.

first: Martin

last: Flück

first: Hans

last: Hoppeler


title: Human Unigene I, part 1

status: Public on May 31 2001

city: Heidelberg

first: Wolfgang

last: Huber

address: Im Neuenheimer Feld 280

department: Molecular Genome Analysis

country: Germany

institute: German Cancer Research Center

description:
Human cDNA filter from the Resource Centre of the German Human Genome Project. Each of the two parts (GPL9 and GPL10) contains half of 31,488 PCR amplificates of human cDNAs selected as representatives of UniGene clusters (Build #17, NCBI)

Selection of a Global Human Clone Set:

In order to generate a non-redundant human clone set, we postprocessed the UniGene clusters (Build 17, NCBI), which represent a large number of human genes. All processing steps are part of the GeneNest software (Haas et al., 2000), that additionally provides an interactive graphical interface to the postprocessed UniGene database (http://www.dkfz.de/tbi/services/GeneNest/index). To identify the most reliable, representative clone from each cluster, we analyzed the following criteria (sorted according to their importance): (1) Availability of clones at the RZPD. (2) Quality of cDNA library of origin. (3) Presence of more than one read of the same clone in a cluster, ensuring a higher confidence in the sequence - clone relationship. (4) Calculated insert size, selecting for larger inserts. (5) Presence of a polyA signal. We used a fuzzy logic based rule system to combine all clone selection criteria in order to obtain a quality measure of each clone in the entire UniGene set. For each cluster we selected the clone with the highest quality as representative. To estimate the redundancy of the global clone set, we re-sequenced over 2,700 clones of the set and found 12.8% wrongly assigned clones. All of these belonged to clusters that were already represented by another clone. Therefore, the overall redundancy of the clone set was estimated to be 1.44-fold, and the 31,500 clones on the cDNA array represent an estimated 21,875 different transcripts.

31,500 Clone Human cDNA Array:

From the Human UniGene 1 clone set, cDNA inserts of the clones from the 82 first 384-well microtiter plates were amplified by PCR in a 384-well format (MJ Research, Boston, Massachusetts) using M13 forward (5'-CGTTGTAAAACGACGGCCAGT-3') and reverse primers (5'-TTTCACACAGGAAACAGCTATGAC-3'). The 31,488 PCR products were transferred in a 4x4 pattern onto a set of two 22x22 cm Hybond N+ nylon membranes (Amersham Pharmacia Biotech, Uppsala, Sweden) soaked in 0.4 M NaOH using a Picking-Spotting-Robot (Linear Drives  LDT, Essex, UK) with 400 µm pins (Genetix, Hampshire, UK). After  spotting the arrays were carefully floated for 2 minutes on 0.4 M  NaOH and 5 x SSC (pH 7.5) successively, air dried and cross-linked  by UV. Every 4x4 block contained one spot with PCR product from the  bacterial kanamycin resistance gene to serve as a guide spot in automated image analysis, one empty spot to serve as background measurement and DNA from seven clones spotted in duplicate. On each filter, a  control plate containing putative housekeeping genes and positive and negative controls was spotted. To assure even quality between subsequent rounds of hybridization, cDNA arrays were pre-stripped before their first use (Hauser et al., 1998). To check for filter quality, M13 forward oligonucleotide hybridizations were carried out.
Keywords = membrane, filter

first: Judith

last: Boer

first: Holger

last: Sueltmann

first: Friederike

last: Wilmer

first: Anja

last: von Heydebreck

first: Stefan

last: Haas

first: Bernhard

last: Korn

first: Andreas

last: Vente

last: Vingron

first: Annemarie

last: Poustka


title: Yeast non-coding RNA microarray

status: Public on Oct 28 2005

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

country: Canada

institute: Best Institute

organism: Saccharomyces cerevisiae

technology: in situ oligonucleotide

manufacture_protocol: In situ oligosynthesized


title: Bacillus_anthracis_CGH

status: Public on May 01 2003

city: Rockville

first: David

last: Rasko

address: 9712 Medical Center Drive

department: Microbial Genomics

institute: The Institute for Genomic Research

organism: Bacillus anthracis

description:
Amplicons representing 79 of 217 and 41 of 122 genes from pXO1 and pXO2 respectively, and 3601 of 5753 chromosomal genes as predicted by Glimmer 30 ( and see supplemental methods) were arrayed onto glass microscope slides (Telechem, Inc). Redundant genes were generally represented once or a few times on the array.
NOTE: N/A indicates that during the completion of the sequencing and annotation project these coding regions were removed.
Annotation is not provided for plasmid genes as these genes were not annotated by TIGR.
All spots that are included have primer sequences included.
Amplicon sequences are included only where the amplicon was contained within the final coding region and matched the sequence exactly.
Keywords = Bacillus anthracis, Bacillus cereus, Comparative Genomic Hybridization

first: Timothy

last: Read

first: Scott

middle: N

last: Peterson

first: Nicolas

last: Tourasse

first: Les

middle: W

last: Baillie

first: Ian

middle: T

last: Paulsen

first: Karen

middle: E

last: Nelson

first: Hervé

last: Tettelin

first: Derrick

last: Fouts

first: Jonathan

last: Eisen

first: Steven

middle: R

last: Gill

first: Erik

middle: K

last: Holtzapple

first: Ole Andreas

last: Økstad

first: Erlendur

last: Helgason

first: Jennifer

last: Rilstone

last: Wu

first: James

middle: F

last: Kolonay

first: Maureen

last: Beanan

first: Robert

last: Dodson

first: Lauren

middle: M

last: Brinkac

first: Michele

last: Gwinn

last: DeBoy

first: Ramana

last: Madpu

first: Sean

middle: C

last: Daugherty

first: A. Scott

last: Durkin

first: Daniel

middle: H

last: Haft

first: William

first: Jeremy

first: Mihai

last: Pop

first: Hoda

last: Khouri

first: Diana

last: Radune

middle: L

last: Benton

first: Yasmin

last: Mahamoud

first: Lingxia

last: Jiang

first: Ioana


title: ResGenHs15K_DIO

status: Public on Oct 27 2005

city: Madrid

first: Luis

middle: Andres

last: Lopez-Fernandez

state: Madrid

address: Darwin 3

department: Immunology and oncology

country: Spain

institute: CNB-CSIC

description: Array is 4 x 12 (48 subarrays). Each subarray is 18 x 18.

middle: A

first: Manuel

last: Muñoz

manufacture_protocol: The Research Genetics 40K sequence-verified clone human cDNA library (http://www.resgen.com/products/SVHcDNA.php3) was used to generate cDNA arrays, as described (Guerra, S., L. A. López-Fernandez, A. Pascual-Montano, M. Muñoz,  K. Harshman, and Esteban, M. (2003) J. Virol. 77: 6493-6506.).  Slides contained 15,360 cDNAs, of which 13,295 correspond to known genes and 2,257 to control genes.  The cDNA resuspended in 50%DMSO was printed on CMT-GAPS II slides (Corning) with a Microgrid II (BioRobotics)


title: GAP_M_I

status: Public on Jan 15 2003

city: Raleigh

first: Ahmad

last: Fakhoury

state: NC

department: Plant Pathology

institute: North Carolina State University

organism: Aspergillus flavus

description:
PCR products were generated using approximately 5 ng plasmid DNA isolated from unique cDNA clones. T3 and T7 primers were used to generate amplicons. PCR products were then purified by isopropanol precipation followed by a 70% ethanol wash. The presence of amplicons was verified by agarose gel electrophoresis.
PCR products at approximately 250 ng/ul in 50% DMSO were spotted in triplicate onto Telechem SuperAldehyde slides (Sunnyvale, CA) using an Affymetrix 417 Arrayer (Santa Clara, CA). Spots were allowed to air dry before being fixed following manufacturer’s recommendation.
Keywords = aspergillus, aflatoxin

first: Gregory

last: OBrian

first: Gary

last: Payne


title: Sentrix HumanRef-8 Expression BeadChip

status: Public on Jul 30 2005

city: San Diego

last: Illumina Inc.

state: CA

address: 9885 Towne Centre Drive

institute: Illumina Inc.

technology: oligonucleotide beads

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

distribution: commercial


title: mKIAA oligonucleotide microarray

status: Public on Apr 19 2005

city: Kisarazu

first: Kazuhide

last: Imai

state: Chiba

address: 2-6-7 Kazusa-Kamatari

country: Japan

institute: Chiba Industry Advancement Center

organism: Mus musculus

description:
Description of KIAA and FLJ genes; Since 1994, a human cDNA project to accumulate information regarding the protein-coding sequences (CDSs) of unidentified human genes (at least the time they were sequenced) was initiated in Kazusa DNA Research Institute. They have focused their sequencing efforts on human long cDNAs encoded large proteins which might uncover unknown general aspects of the biological roles of these proteins.  As an outcome of this human cDNA sequencing project, we have reported the cDNA sequences of more than 2000 identified human genes (Nagase, T., et.al., 2001, DNA Res., 8, 319-327). The information regarding KIAA has been shared with the research community worldwide through the HUGE database (http://www.kazusa.or.jp/huge).
Description of mKIAA and mFLJ genes; Since 2001, To relieve from legal and ethical restrictions on the use of human materials, we selected the mouse as a model organism to perform functional characterization of KIAA genes. For the first step, we began to isolate and characterize cDNA clones encoding mouse counterparts of human KIAA and FLJ proteins. We have already reported the cDNA sequences of approximately 1500 mouse KIAA-homologues (mKIAA genes) and 110 mouse FLJ-homologues (mFLJ genes) (Okazaki, N., et.al., 2004, DNA Res., 11, 205-218).The information regarding mKIAA and mFLJ genes has been shared with the research community worldwide through the ROUGE database (http://www.kazusa.or.jp/rouge/index.html).
Description of mKIAA oligonucleotide microarray; "mKIAA oligonucleotide microarray" were spotted 511 long oligonucleotides on glass, consisting of 486 mKIAA genes, 3 mKIAA-paralogous genes, 1 mFLJ gene, 7 positive controls (housekeeping genes), and 14 negative controls (plant chloroplast genes: 1 spot of psaA, 1 spot of psbB, and 12 spots of rbcL). The oligonucleotides were designed according to four conditions: 1) lengths were between 65 and 75 bases; 2) melting temperatures were between 70 and 80°C; 3) GC contents were between 45 and 65%; and 4) representative unique sequences against 87,543 entries in mouse UniGene database (Build #113) were designed  by ProbeQuest software (Dynacom, Kanagawa, Japan).
Keywords = Mouse
Keywords = Long oligonucleotide
Keywords = KIAA
Keywords = mKIAA


title: NMC_Rat_5k_cDNA_Ser2

status: Public on Mar 07 2003

city: Trondheim

first: Fekadu

last: Yadetie

address: Olav Kyrres gt 3

department: Cancer Research and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

description: The 5k rat cDNA arrays used here are part of a larger collection of 14k cDNAs purchased from Research Genetics (Huntsville, AL).   (http://nova.idi.ntnu.no/MCF/products.html). 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 prepared in 50% DMSO (about 50-200 ng/ l) and spotted onto 25 x 75mm amino-silane coated CMT-GAPS glass slides (Corning, NY) using a printing robot built in-house in collaboration with NEMKO (Trondheim, Norway) after a prototype developed at the National Human Genome Research Institute (NHGRI), (http://www.nhgri.gov/DIR/LCG/15K(HTML/). The arrays were spotted with 8 pins and contained 2 x 4 blocks of 31 x 31 spots. The probes were fixed to the slide surface by UV irradiation. The 5k cDNA probes represent 4908 unique UniGene clusters, of which 2511 cDNAs (51%) were 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 7688 elements including duplicates and controls.

first: Astrid

last: Laegreid

first: Ingunn

last: Bakke

first: Waclaw

last: Kusnierczyk

first: Jan

last: Komorowski

first: Helge

last: Waldum


title: HumArray 1.14

status: Public on Feb 12 2002

city: San Francisco

first: Donna

last: Albertson

department: Comprehensive Cancer Center

institute: University of California San Francisco

description:
This array was designed for copy-number assessments across the human genome.  We printed 2,460 BAC and P1 clones in triplicate (approx. 7,500 elements) in a 12mm X 12mm square.  Each clone contains at least one STS, allowing linkage to the genome sequence.  Cytogenetic mapping indicated that 2,298 of the arrayed clones are single copy;  this array thus provides average resolution of approximately 1.4 Mb across the genome.

Protocol from Nat Genet 2001 Nov;29(3):263-4 web supplement:
Genomic clones. We selected the majority of the clones for the arrays from the set of cytogenetically mapped BACs reported previously4 and obtained these clones from the Roswell Park Cancer Institute.  We obtained additional clones mapping near the telomeres of each chromosome5 and clones containing certain named genes from J. Flint, D. Ledbetter, C. Lese and Vysis, Inc.  We included P1 clones used previously on arrays of chromosome 20 (ref. 1,2).  We also used additional clones from the DuPont A library, including RMC01P052 (163D7), RMC01P057 (213C4), RMC07P014 (548H7), RMC07P025 (1128F4), RMC07P028 (252B4) and RMC07P038 (1429E1.c2), as well as RMC17P041 (75D7), RMC17P069 (88H6) and RMCXP002 (124A3) from the DuPont B library.  The array provides only minimal coverage of the Y chromosome, since only one clone unique to the Y chromosome is included on the array in addition to the telomeric clones that are shared between the X and Y chromosomes.
Isolation of BAC/P1 DNA.  We inoculated 0.1l of a glycerol stock of BAC or P1 containing bacteria into 5 ml LB media containing chloramphenicol (10 g/ml) or kanamycin (50 g/ml) for BACs or P1s, respectively and incubated the cultures overnight (~16 h) at 37 C with agitation at 225 rpm.  We prepared larger cultures for DNA isolation, by inoculating 25 mlLB media, containing the appropriate antibiotic with 200 l of the previously grown overnight culture and incubating in a shaking incubator at 37 C at 225 rpm overnight (~16 h).  We monitored bacterial growth by measuring the OD of a 1:10 dilution, which preferably ranged between 0.25 and 0.35 at a wavelength of 600 nm.  We used the Qiagen Plasmid Mini kit to isolate DNA, following a modified version of the Qiagen Plasmid Mini Purification protocol.  We transferred the 25 ml cultures into 50 ml tubes and centrifuged them for 15 min at 4000 rcf at 4 C to pellet the bacteria.   We re-suspended the pellet in Qiagen buffer P1 (1.5 ml), containing RNase A at the manufacturer's recommended concentration and then added buffer P2 (1.5 ml).  We mixed the tubes extremely gently by inversion and incubated at room temperature for 5 min. Then, we added buffer P3 (1.5 ml), again mixed very gently by inversion and incubated on ice for 10 min.  We inverted each tube once and centrifuged at 4000 rpm at 4 C until the supernatant became clear (45 to 60 min).  We filtered the supernatant through a 35-micron nylon mesh prior to loading onto Qiagen-tip 20 columns, which had been equilibrated following the manufacturer's protocol.  We followed the manufacturer's protocol for the DNA isolation steps with the exception that the elution buffer QF was heated to 65 C before it was added to the column.  After elution, we added 0.56 ml isopropanol to the DNA and incubated overnight at 4 C.  We collected the DNA pellet by centrifugation for 45 min at 14000 rpm at 4 C.  After aspirating the supernatant, we allowed the pellet to dry in air for at most 30 min before re-suspending the DNA in 50 l of H2O.  We determined the DNA concentration using a fluorometer.  The yield typically ranged between 60-100 ng/l (i.e. 3-5 g per isolation). To ascertain DNA purity, we digested each BAC (200 ng) with HindIII and electrophoresed the digest through a 0.75% agarose gel.  We discarded DNA preparations that showed a significant contamination with host bacterial DNA, seen as a background smear of degraded DNA in the gel.
Preparation of BAC/P1 DNA representations by ligation-mediated PCR.  We digested the DNA with MseI by incubating overnight at 37 C in a 5 l reaction containing 1.5 l DNA (20 to 600 ng), 0.4 U/l MseI (New England Biolabs), and 0.4x One-Phor-All-Buffer-Plus (Amersham).  For ligation of adapters, we diluted 1 l of each digest to a final concentration of 1 ng/l with H2O and then mixed 1 ng of the digested DNA with 0.5 l One-Phor-All-Buffer-Plus (10x, Amersham), 0.5 l of 100 M Primer 1 (TAACTAGCATGC), 0.5 l of 100 M Primer 2 (5' aminolinker AGTGGGATTCCGCATGCTAGT) and 5.5 l H2O. We incubated the mixture at 65 C for 1 min after which we ramped the temperature down to 15 C with a ramp-speed of 1.3 C per minute.  When the temperature reached 15 C, we added 1 l of 10 mM ATP and 1 l T4-DNA ligase (5 U/l, Gibco BRL) and continued incubation at 15 C overnight.  To initiate the first round of PCR amplification, we added a 40 l mixture, consisting of 3 l PCR Buffer 1 (Expand Long Template PCR System, Roche), 2 l of a mixture of each nucleotide (10 mM) and 35 l H2O to the ligation reaction.  Before we started the PCR program, we incubated the reaction at 68 C for 4 min and then added 1 l DNA polymerase (3.5 U/l, Expand Long Template PCR System, Roche).  We carried out thermal cycling in a Perkin-Elmer Gene Amp PCR System 9700 block as follows: 94 C for 40 s, 57 C for 30 s, 68 C for 1.25 min for 14 cycles, followed by, 94 C for 40 s, 57 C for 30 s, 68 C for 1.75 min for 34 cycles and 94 C for 40 s, 57 C for 30 s and 68 C for 5 min for the final cycle.   We electrophoresed 3.5 l of the PCR product through a 1% agarose gel to determine the size range of the amplified DNA, which ideally ranged from 100 to 2000 bp.  To make the DNA for spotting on the arrays, we carried out a second round of amplification in a 100 l reaction containing 1 l of the primary PCR product, 4 M Primer 2, TAQ-buffer II (1x; Perkin Elmer), 0.2 mM dNTP mix, 5.5 mM MgCl2 (Perkin Elmer), 2.5 U Amplitaq Gold (Perkin Elmer) and H2O. We carried out an initial incubation at 95 C for 10 min in a MJ Research Peltier Thermal Cycler 225, followed by 95 C for 30 s, 50 C for 30 s and 72 C for 2 min for 45 cycles and finally 7 min at 72 C.  This reaction yields ~10 g of DNA, with each fragment containing a 5' amino linker.
Preparation of DNA spotting solutions.  We evaporated the amplification reaction (100 l) to a final volume of 50 l by incubation at 45 C in a hybridization oven (Techne, Hybridizer HB-1D) for approximately 75 min and then added 2.5 volumes of ice-cold ethanol and 0.1 volumes of 3 M NaOAc to precipitate the DNA.  (The use of ethanol precipitation proved superior to isopropanol precipitation.)  We inverted the tubes and chilled them at 20 C for 15 min before collecting the precipitate by centrifugation at 1699 rcf for 90 min.  We washed the pellets with 70% ethanol (150 l) and collected them by centrifugation at 1699 rcf for 45 min.  We air-dried the pellets for approximately 60 to 90 min and then re-suspended them in 12 l of 20% DMSO in H2O (~0.8 g/l).  We transferred the DNA solutions into 864 well microtitre plates for robotic arraying.  Previously, we prepared DNA for spotting in 80% DMSO and 0.3 g/l nitrocellulose.  However, we subsequently evaluated spotting solutions containing various concentrations of dimethyl formamide, formamide or DMSO, with or without nitrocellulose.  We determined that nitrocellulose was not required for spotting DNA prepared by PCR using primers with 5'amino linkers and that spotting solutions made with 20% DMSO performed well.  We have also generated representations of large insert clones for arraying by using degenerate oligonucleotide primed PCR and by amplification of mixtures of subclones from BACs, but found the ligation-mediated PCR procedure to be superior.
Array printing.  We used a custom built printer, employing a 4 x 4 array of quartz capillary tubes spaced on 3 mm centers to print ~70-100 µm diameter spots on 130 µm centers.  We printed each DNA solution in triplicate to create an array of ~7500 elements in a 12 mm square area.  We printed the arrays on chromium coated microscope slides (PTI or Nanofilm) for these studies, but also routinely print the arrays on glass slides (Corning GAPs).  We allowed the printed slides to dry overnight, then exposed the slides to UV light (65 mJ) in a UV Stratalinker 2400 (Stratagene).  We hybridized to these slides without additional treatment, except for the pre-hybridization slide blocking described below.  We found no indication of DNA loss from the spots at any stage of the procedure when we performed hybridization in formamide buffers at 37 °C.
Keywords = comparative genomic hybridization, CGH, array

first: Antoine

last: Snijders

first: Norma

last: Nowak

first: Richard

last: Segraves

first: Stephanie

last: Blackwood

first: Nils

last: Brown

first: Jeffery

last: Conroy

first: Greg

last: Hamilton

first: Anna

last: Hindle

first: Bing

last: Huey

first: Karen

last: Kimura

first: Sindy

last: Law

first: Ken

last: Myambo

first: Joel

last: Palmer

first: Bauke

last: Ylstra

first: Jingzhu

middle: P

last: Yue

first: Joe

last: Gray

first: Ajay

last: Jain

first: Daniel

last: Pinkel


title: Wistar Institute Mus musculus 9.6k MA11 array

status: Public on Oct 18 2005

city: Philadelphia

first: Louise

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

first: Michael

first: Wenhwai

last: Horng

manufacture_protocol:
cDNA spot array on nylon membrane.
http://www.wistar.org/research_facilities/facilities/genomics/review.html


title: Human Array 1.0

status: Public on Jul 28 2005

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Human Array 1.0 was constructed arraying on glass slides PCR-amplified cDNAs obtained from our archive of recombinant bacterial clones. This archive consists of 2688 different cDNA clones collected after systematic sequencing of human skeletal muscle cDNA libraries that contain only the 300-500 bp long 3’-portions of muscle transcripts.

manufacturer: C.R.I.B.I. Biotechnology Center (University of Padova)

first: Stefano

last: Campanaro

first: Beniamina

last: Pacchioni

first: Silvia

last: Trevisan

first: Paolo

last: Laveder

first: Cristiano

last: De Pittà

manufacture_protocol: 2688 different cDNA inserts were PCR amplified directly from bacterial cultures. Bacterial clones were inoculated in 96-well, 2 ml Assay Block (Corning), containing 600 µl LB/Ampicillin (50 µl /ml) and incubated at 37 °C for 16 hrs. Approximately 1µl of culture suspension was transferred in 96 well plate (Corning), loaded in each single well with 100 µl of the following solution: 1X PCR buffer, 1.5 mM MgCl2, 0.15 mM for each of the four dNTPs, 0.2 µM for each of primer A and B, 0.02U/µl of Taq Polimerase (New England Biolabs). PCR buffer and unincorporated nucleotides were removed by filtering through 96-well multiscreen filter plates (Millipore, Bedford, MA, USA). The purification protocol was automated using the 96 channel robotic workstation Multimek (Beckman) to avoid errors due to the manual handling of large number of samples. Quality control and quantification of the amplified products was done by separation of 3 µl samples on agarose gels containing EtBr and gel image analysis with Chemi Doc UV transilluminator equipped with the Quantity One software (Bio-Rad, Hercules, CA, USA). PCR products were then lyophilized and plates were sealed using thermowell sealers (Corning) and stored at –20°C. For microarray printing, PCR products were dissolved in 15 µl of Micro Spotting Solution (ArrayIt, Telechem, Sunnyvale, CA, USA) by vigorous shaking of plates for 4-5 hrs at 4°C, and transferred in 384 well plates. Spotting was performed using the robotic system Genpak Array 21 (Genetix, Hampshire, UK) equipped with 32 Stealth Micro Spotting Pins SMP 3B (ArrayIt) settled to obtain spots with an average diameter of 120 µm. Samples were spotted in duplicate on derivatized glass slides (MICROMAX Glass Slides: SuperChip™ I, PerkinElmer, Wellesley, MA, USA) to obtain more consistent fluorescence measures. Spotting was performed at 50% relative humidity to obtain the best spot morphology and to reduce the plate evaporation. Microarrays were then processed in a UV cross linker (Stratagene, La Jolla, CA, USA) (total power of 300 mJoules) for the binding the DNA to the slides. Microarrays were finally processed to remove any unbound PCR product, dried and stored under vacuum at room temperature in sealed boxes.


title: Amersham Biosciences CodeLink UniSet Mouse I Bioarray

status: Public on May 07 2004

city: Atlanta

first: Hanjoong

last: Jo

state: GA

department: Biomedical Engineering

institute: Emory University

description:
CodeLink UniSet Mouse I Bioarray contains single-stranded oligonucleotide probes derived from a large majority of publicly available, well-annotated mRNA sequences found in the Mouse UniGene set of unique clusters. Each bioarray contains probes for an independent assay of all 10,000 genes in the set.

* ~10 000 mouse genes — 1 specific, prescreened probe per gene, functionally validated

* one set of housekeeping genes that may be used for baseline normalization

* 18 bacterial positive control probes from 6 genes with 6 corresponding spikes included in the cDNA Synthesis Kit to monitor
Keywords = http://www1.amershambiosciences.com/APTRIX/upp01077.nsf/Content/codelink_uniset_mouse1_bioarray?OpenDocument&hometitle=codelink


title: QtsA cDNA clones

status: Public on Nov 11 2002

city: Tokyo

first: Naoki

last: Osada

state: Tokyo

address: 1-23-1, Toyama-cho, Shinjuku-ku

institute: National Institute of Infectious Diseases

organism: Macaca fascicularis

description:
We determined 512 full-insert sequences of cDNAs derived form cynomolgus monkey testis.  An aliquot of the same DNA preparation used in the 5’-end-sequencing reactions provided material for the PCRs.  Inserts were amplified by PCR using 5’-CTTCTGCTCTAAAAGCTGCG-3’ as a forward primer and 5’-CGACCTGCAGCTCGAGCACA-3’ as a reverse primer, in a volume of 100 µl.  Successful amplification was confirmed by agarose gel electrophoresis.  When the first PCR failed to amplify enough products, the first PCR products were amplified again.  Samples of approximately 300 µg /ml DNA in 2 x Solution-T reagent (Takarabio) were printed on duplicate glass-slides with a GMS 417 arrayer (Genetic MicroSystems).
Keywords = cynomolgus monkey, testis, QtsA

first: Munetomo

last: Hida

first: Jun

last: Kusuda

first: Reiko

last: Tanuma

first: Makoto

last: Hirata

first: Yumiko

last: Suto

first: Momoki

last: Hirai

first: Keiji

last: Terao

first: Sumio

last: Sugano

first: Katsuyuki

last: Hasihmoto


title: Human Unigene I, part 2

first: Wolfgang

last: Huber

description:
Human cDNA filter from the Resource Centre of the German Human Genome Project. Each of the two parts (GPL9 and GPL10) contains half of 31,488 PCR amplificates of human cDNAs selected as representatives of UniGene clusters (Build #17, NCBI).

Selection of a Global Human Clone Set:

In order to generate a non-redundant human clone set, we postprocessed the UniGene clusters (Build 17, NCBI), which represent a large number of human genes. All processing steps are part of the GeneNest software (Haas et al., 2000), that additionally provides an interactive graphical interface to the postprocessed UniGene database (http://www.dkfz.de/tbi/services/GeneNest/index). To identify the most reliable, representative clone from each cluster, we analyzed the following criteria (sorted according to their importance): (1) Availability of clones at the RZPD. (2) Quality of cDNA library of origin. (3) Presence of more than one read of the same clone in a cluster, ensuring a higher confidence in the sequence - clone relationship. (4) Calculated insert size, selecting for larger inserts. (5) Presence of a polyA signal. We used a fuzzy logic based rule system to combine all clone selection criteria in order to obtain a quality measure of each clone in the entire UniGene set. For each cluster we selected the clone with the highest quality as representative. To estimate the redundancy of the global clone set, we re-sequenced over 2,700 clones of the set and found 12.8% wrongly assigned clones. All of these belonged to clusters that were already represented by another clone. Therefore, the overall redundancy of the clone set was estimated to be 1.44-fold, and the 31,500 clones on the cDNA array represent an estimated 21,875 different transcripts.

31,500 Clone Human cDNA Array:

From the Human UniGene 1 clone set, cDNA inserts of the clones from the 82 first 384-well microtiter plates were amplified by PCR in a 384-well format (MJ Research, Boston, Massachusetts) using M13 forward (5'-CGTTGTAAAACGACGGCCAGT-3') and reverse primers (5'-TTTCACACAGGAAACAGCTATGAC-3'). The 31,488 PCR products were transferred in a 4x4 pattern onto a set of two 22x22 cm Hybond N+ nylon membranes (Amersham Pharmacia Biotech, Uppsala, Sweden) soaked in 0.4 M NaOH using a Picking-Spotting-Robot (Linear Drives  LDT, Essex, UK) with 400 µm pins (Genetix, Hampshire, UK). After  spotting the arrays were carefully floated for 2 minutes on 0.4 M  NaOH and 5 x SSC (pH 7.5) successively, air dried and cross-linked by UV. Every 4x4 block contained one spot with PCR product from the bacterial kanamycin resistance gene to serve as a guide spot in automated image analysis, one empty spot to serve as background measurement and DNA from seven clones spotted in duplicate. On each filter, a  control plate containing putative housekeeping genes and positive and negative controls was spotted. To assure even quality between subsequent rounds of hybridization, cDNA arrays were pre-stripped before their first use (Hauser et al., 1998). To check for filter quality, M13 forward oligonucleotide hybridizations were carried out.
Keywords = membrane, filter

first: Judith

last: Boer

first: Holger

last: Sueltmann

first: Friederike

last: Wilmer

first: Anja

last: Heydebrec

first: Stefan

last: Haas

first: Bernhard

last: Korn

first: Andreas

last: Vente

first: Martin

last: Vingron

first: Annemarie

last: Poustka


title: WRAIR Homo sapiens 10k fatty acid binding proteins in prostate cancer

status: Public on Oct 29 2005

city: Silver Spring

first: Rasha

last: Hammamieh

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

first: Marti

last: Jett

manufacture_protocol: Custom array


title: Rice indica whole genome tiling array OS_18730

status: Public on Oct 15 2005

city: New Haven

first: Xing-Wang

last: Deng

state: CT

address: 165 Prospect

department: MCD Biology

institute: Yale University

organism: Oryza sativa

description:
Oligo nucleotides 36mer in length are designed to represent sense and antisense strands of the nonrepetitive DNA of the indica rice genome.
The probes were selected from the August 1, 2003 indica sequence (Annotated by Beijing Genomics Institue).

first: Lei

last: Li

first: Xiangfeng

last: Wang

first: Viktor

last: Stolc

first: Xueyong

first: Dongfen

last: Zhang

first: Ning

last: Su

first: Waraporn

last: Tongprasit

first: Songgang

first: Zhukuan

last: Cheng

first: Jun

first: XingWang

manufacture_protocol: Microarrays containing these oligos are synthesized on glass with Expedite DNA synthesizers (Applied Biosystems, Foster City, CA) in conjunction with Maskless Array Synthesis units (NimbleGen Systems, Madison, WI).


title: Rice indica whole genome tiling array OS_18711


title: Rice indica whole genome tiling array OS_18733


title: Rice indica whole genome tiling array OS_18735


title: UOregonJohnsonLab092004 Drosophila melanogaster 26k array

status: Public on Oct 21 2005

city: Eugene

first: Eric

last: Johnson

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular biology

institute: University of Oregon

first: Guowen

last: Liu

first: Julianne

last: Roy

first: Jason

last: Carriere

manufacture_protocol:
Incyte Genomics primer set
and DGC r2 cDNA clones
DeRisi-design printer made at Oregon
Spotted in SSC/betaine


title: HCI Yeast Lucidea 18 Plate Layout

city: Salt Lake City

first: Robert

middle: J

last: Crisp

state: UT

address: 30 North Medical Drive

department: Dep't of Pathology

institute: University of Utah


title: NIA Mouse 15K Custom Array

status: Public on Oct 25 2005

city: Tucson

first: Kevin

last: Greer

state: AZ

institute: University of Arizona

description: Custom cDNA array containing the mouse NIA 15K Cloneset plus additional unidentified clones.

first: Heddwen

last: Brooks

first: McReynold

last: Matt

manufacture_protocol: Standard protocol.


title: Rice indica whole genome tiling array OS_18654

first: Xing-Wang

first: Lei

first: Xiangfeng

first: Viktor


title: Rice indica whole genome tiling array OS_18924

first: Xueyong

first: Dongfen

first: Ning

first: Waraporn


title: Rice indica whole genome tiling array OS_18923

first: Songgang

first: Zhukuan

first: Jun

first: XingWang


title: Galbraith Laboratory Operon Long Oligonucleotide Microarray version 3.0 (ATv303.02.Z)

status: Public on Oct 26 2005

first: David

middle: William

last: Galbraith

address: 303 Forbes Building

department: Plant Sciences and Bio5 Institute

organism: Arabidopsis thaliana

description: This oligonucleotide array is produced from the Operon Version 3.0 Array-Ready Oligo set (AROS), which comprises 29,110 70-mer oligonucleotides representing 26,173 protein-coding genes, and 28,964 protein-encoding gene transcripts, and 87 microRNA gene precursors.  AROS design is based on ATH1 release 5.0 of the TIGR Arabidopsis genome annotation database, and Release 4.0 of the miRNA Registry at the Sanger Institute.  Various additional elements are printed as controls.  Microarrays can be ordered from the Galbraith laboratory. This platform represents slides ATv303.02.001-ATv303.02.300 (http://www.ag.arizona.edu/microarray).

manufacturer: The Galbraith Lab, University of Arizona

manufacture_protocol: GeneMachines Omnigrid 300


title: Rice indica whole genome tiling array OS_18925

last: Deng


title: The Use of a Soybean cDNA Microarray to Assess for Differential Gene Expression in Vicia Species: A Mixed Model Approach

status: Public on Oct 30 2005

city: Fort Collins

first: Kathleen

last: Yeater

state: CO

address: 2150 Centre Avenue

institute: USDA-ARS

organism:
Glycine max
Vicia villosa
Vicia pannonica

manufacturer: Telechem Superamine Slides printed at Keck Center, University of Illinois, Urbana-Champaign

first: A. Lane

last: Rayburn

first: M. Javed

last: Iqbal

first: Donald

middle: G

last: Bullock

first: Sandra

last: Rodriguez-Zas

first: German

last: Bollero

manufacture_protocol:
Printer was a Cartesian Pyxis 5500

PCR primers:

F NIA-M13F CCAGTCACGACGTTGTAAAACGAC
R NIA-M13R GTGTGGAATTGTGAGCGGATAACAA

PCR condition:
50 ul reactions
95oC 10 min
35 cycles of 95oC 40 sec, 65oC 40 sec, 72oC 3 min
72oC 5 min
4oC 1 min

All products were run out on 1.5% agarose gels. Failed reactions were rerun and replaced. The entire reaction was cleaned on Sephadex columns in Whatman filter plates, transferred to a 384 well plate,
dried down in a speedvac and resuspended in printing buffer.

There was one grid, double spotted with 185 x 185 micron spacing. 8 columns and 39 rows.


title: Maize Unigene 1-02-01

status: Public on Oct 20 2005

city: Ames

first: Hongwu

last: Jia

state: IA

address: 1407 Agronomy Hall

department: Agronomy

institute: Iowa State University

organism: Zea mays

manufacturer: Dr. David Galbraith's lab at the University of Arizona


title: MMRRC

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: 9600 cDNA IMAGE consortium clones were obtained from Incyte Genomics. After amplification, they were arrayed on Corning or Fullmoon sialized slides with a GMS 417 arrayer. Cy3 and cy5 labels were scanned with a GSI Lumonics Scanarray4000XL or GenePix4000B.

first: Cheryl

last: Eifert

first: Tiffany

last: Devine

first: Marcy

last: Kuentzel

first: Ana

last: Perez

first: Paulette

last: McCormick


title: 16S and 23S rRNA Gel Pad Microarray

status: Public on Oct 22 2005

city: Louvain-la-Neuve

first: Laurent

last: Eyers

address: Place Croix du Sud 2/19

department: Unit of bioengineering

country: Belgium

institute: Catholic University of Louvain

organism: unidentified

description: Probes targeting the 16S and 23S rRNA of various organisms (mainly Bacteria)

manufacture_protocol: Gel-Pad microarrays consisted of 100 x 100 x 20 µm polyacrylamide gel pads photopolymerised to a glass slide with a center-to-center distance of 300 µm (Guschin et al. 1997, Anal. Biochem. 250:203-211). After activation of gel pads (Proudnikov et al. 1998, Anal. Biochem. 259:34-41), oligonucleotide probes were spotted (2 pmol deposited) on each gel pad by Schiff base coupling to aldehyde groups within the gel pads (Bavykin et al. 2001, Appl. Environ. Microbiol. 67:922-928). The coupling was stabilised by reduction with NaCNBH3 (Proudnikov et al. 1998, Anal. Biochem. 259:34-41). The design of oligonucleotide probes targeting rRNA molecules was done as described previously (El Fantroussi et al. 2003, Appl. Environ. Microbiol. 69:2377-2382). Gel-Pad microarrays contained 29 different perfect match oligonucleotide probes (13-25 nucleotides in length) that were complementary to universal, domain, species, and phylogenetic group specific rRNA sequences. In addition to perfect match probes, single mismatch probes were printed on the Gel-Pad microarray. Design of single mismatch probes was based on several criteria: i) GC content was not changed (e.g., substitution of G to C (c-MM probes) or C to G (g-MM probes)), ii) mismatches at terminal positions were avoided (Urakawa et al. 2002, Appl. Environ. Microbiol. 68:235-244), iii) non-complementarity of MM probes to any microorganism was checked by comparing MM probe sequences to the 1999 alignment of 16S rRNA sequences with ARB software (http://www.mikro.biologie.tu-muenchen.de) and the GenBank database (http://www.ncbi.nih.gov/Genbank), and iv) approximately 4°C differences in theoretical Tds between PM and c-MM and about 6°C differences between PM and g-MM were chosen.


title: Rice indica whole genome tiling array OS_18788

first: Xing-Wang

first: Lei

last: Li

first: Xiangfeng

last: Wang

first: Viktor

last: Stolc

first: Xueyong

first: Dongfen

last: Zhang

first: Ning

last: Su

first: Waraporn

last: Tongprasit

first: Songgang

first: Zhukuan

last: Cheng

first: Jun


title: Rice indica whole genome tiling array OS_18789

last: Deng

first: XingWang


title: Rice indica whole genome tiling array OS_18792


title: Rice indica whole genome tiling array OS_18791


title: Rice indica whole genome tiling array OS_18780


title: Rice indica whole genome tiling array OS_18787


title: Rice indica whole genome tiling array OS_18809


title: Rice indica whole genome tiling array OS_18928


title: Rice indica whole genome tiling array OS_18926


title: Rice indica whole genome tiling array OS_18778


title: Rice indica whole genome tiling array OS_18768


title: Rice indica whole genome tiling array OS_18922


title: Rice indica whole genome tiling array OS_18767


title: Rice indica whole genome tiling array OS_18769


title: Rice indica whole genome tiling array OS_18682


title: Rice indica whole genome tiling array OS_18757


title: Rice indica whole genome tiling array OS_18786


title: Rice indica whole genome tiling array OS_18740


title: Rice indica whole genome tiling array OS_18779


title: Rice indica whole genome tiling array OS_18766


title: Rice indica whole genome tiling array OS_18758


title: Rice indica whole genome tiling array OS_18741


title: Rice indica whole genome tiling array OS_18826


title: Rice indica whole genome tiling array OS_18743


title: Rice indica whole genome tiling array OS_18756


title: VDX_Homo_sapiens_Breast_2

city: San Diego

first: Tim

last: Jatkoe

institute: Veridex

manufacture_protocol: Affymetrix Protocol


title: Rice indica whole genome tiling array OS_18739


title: UCSF_Gross_Ecoli_v12.txt

status: Public on Oct 13 2005

first: Virgil

middle: Arthur

last: Rhodius

address: Genentech Hall, 600 16th Street

department: Microbiology and Immunology

institute: UCSF

organism: Escherichia coli

description:
A microarray with 5376 spot features.
Tip configuration: Standard 16-tip
Column per Sector: 24
Rows per Sector: 14
Column spacing: 183 um
Row spacing: 183 um

manufacture_protocol: PCR products for 4110 ORFs representing 95.8% of the Escherichia coli K12 MG1655 ORFs were prepared according to Richmond et al (1999; Nucleic Acids Res. 27:3821-35). The products were spotted onto glass slides to make DNA arrays as described in MGUIDE at http://cmgm.stanford.edu/pbrown/mguide/index.html and protocols on http://www.microarrays.org/


title: Human Stress Chip Rev. 1.0

status: Public on Oct 04 2005

city: Tuebingen

first: Janko

last: Dietzsch

address: Sand 14

department: ZBIT (Center for Bioinformatics Tuebingen)

institute: University Tuebingen

description: cDNA microarray of genes which are related to inflammation, apoptosis and stress response

first: Derek

last: Zieker

first: Judith

last: Fliegner

first: Elvira

last: Fehrenbach

first: Peter

last: Gebicke-Haerter

first: Hinnak

last: Northoff


title: Wistar Institute Mus musculus 9.6k MA08 array

status: Public on Oct 08 2005

first: Louise

last: Showe

first: Michael

first: Wenhwai

last: Horng


title: UCSF_Gross_Ecoli_v7.txt

description:
A microarray with 6384 spot features.
Tip configuration: Standard 16-tip
Column per Sector: 19
Rows per Sector: 21
Column spacing: 200 um
Row spacing: 200 um


title: Wistar Institute Mus musculus 9.6k MA10 array


title: UCSF_Gross_Ecoli_v8.txt

description:
A microarray with 5776 spot features.
Tip configuration: Standard 16-tip
Column per Sector: 19
Rows per Sector: 19
Column spacing: 200 um
Row spacing: 200 um


title: Phage Epitope Microarrays

city: Ann Arbor

first: Xiaoju

last: Wang

state: MI

address: 1500 E. Medical Center Drive

institute: University of Michigan

technology: other

description: Phage epitope microarrays contain individual phage clones immobilized on membrane coated glass slides. These phage clones were selected from an affinity enriched prostate cancer cDNA phage display library. Patient sera and normal control sera were screened on the epitope chip to identify humoral immune reponse signatures. Multiplex epitope profiling was used to ditinguish prostate cancer samples from control subjects.


title: NCI Pombe 44K v1.0

status: Public on Aug 31 2005

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

organism: Schizosaccharomyces pombe

description: Agilent 60mer oligo arrays tiling entire S. pombe genome across 3 chromsomes at 300bp interval alternately from the plus and minus strand.

first: Hugh

last: Cam

first: Tomoyasu

last: Sugiyama

first: Ee

middle: S

last: Chen

first: Xi

last: FitzGerald

middle: I

manufacture_protocol: Custom 60mer oligonucleotide microarrays based upon Agilent’s non-contact in situ synthesis process.


title: Wistar Institute Mus musculus 9.6k MA07 array

status: Public on Sep 30 2005

city: Philadelphia

institute: The Wistar Institute


title: TJU-DBI Rat array v1

city: Phildelphia

first: Rishi

last: Khan

address: 1020 Locust Street Room 381

department: Pathology

institute: Thomas Jefferson University

description:
ResGen clones for Rat
Tip Configuration: Standard 48 tip
Columns per Subarray: 20
Rows per Subarray: 19
Column Spacing: 225
Row Spacing: 225

first: James

last: Schwaber

first: Gregory

last: Gonye


title: Focused Phage Epitope Microarray

description: 180 phage clones were spotted on the membrane coated slide to make small focused epitope array. Each spot on the chip represents a different phage clone.


title: Center for Functional Analysis of Human Genome Human KUGI 24K (liver cancer)

status: Public on Oct 06 2005

city: Daejeon

first: Heun-Sik

last: Lee

address: 52 Eoeun-dong, Yuseong-gu

country: South Korea

institute: Korea Reaearch Institute of Bioscience and Biotechnology

manufacturer: The Center for Functional Analysis of Human Genome

manufacture_protocol: cDNA microarrays were fabricated in our core facility using a robotic arrayer (PixSYS 5500, Cartesian; Ann Arbor, MI). The 24K microarray contains 24,288 genes from KUGI unigene library (http://21cgenome.kribb.re.kr/html/2004_new/genome_php/cdna/cdna_list.htm). All the clones were verified by sequencing in our facility. The cDNA inserts were amplified by PCR, and after purification, spotted onto silylated glass slides (CSS-100; Telechem, Sunnyvale, CA). Each microarray slide contained control genes to normalize the effect of different fluorescent dyes.


title: ABC Human 8K

status: Public on Aug 02 2005

city: Taipei

first: Yi-Ming

state: Taiwan

address: 155, Li-Noun St., Sec. 2

department: AIDS Prevention and Research Center

country: Taiwan

institute: National Yang-Ming University

description: It’s a commercial 7500 human cDNA microarray chip (ABC Human UniversoChip 8K; Asia BioInnovations Corporation, Taipei).

first: Cheng-Ming

first: Shih-Yin

first: Yuan-Chii

first: Chi-Ying

last: Huang


title: Pfu gamma v1

status: Public on Jul 02 2005

city: College Park

first: Jocelyne

last: DiRuggiero

address: 3221 H.J. Patterson Hall

department: Cell Biology and Molecular Genetics

institute: University of Maryland

organism: Pyrococcus furiosus

description:
P. furiosus full-genome microarray numbered 2065 protein encoding genes, and 108 RNA genes (transfer RNAs, ribosomal RNAs, small RNAs). In addition, all "intergenic" regions of 60 nucleotides or larger were represented on the array (602 total).  DNA fragments for spotting were produced by PCR. The array was constructed by designing oligonucleotide primers to span the most unique portions of each gene, averaging 350 nucleotides in length.  A custom Perl program was written to select primers with the most desirable thermodynamic conditions possible for each gene using the Whitehead Institute's Primer3 program (version 3.09) as its core analysis engine. Primers for intergenic regions and RNAs were designed to cover the entire target region. The polymerase chain reaction was performed on 100 µl reactions with 1µM of each primer, 2mM MgCl2, 1.0 mM dNTPs, 1.75 U Amplitaq DNA polymerase, 1x Amplitaq buffer, and 20ng genomic DNA for 30 cycles (94°C 30 sec, 50°C 1 min., 72°C 2 min.) to generate DNA fragments.  All PCR products were checked by agarose gel electrophoresis, and failures were repeated or new primers designed.   Each PCR amplicon was spotted on poly-L-lysine coated glass slides twice, each time by a different print pin (print plates were rotated 180 degrees for second spotting) using a 16-pins ArrayMaker Version 1.0 (http://cmgm.stanford.edu/pbrown/mguide/index.html).
Keywords = archaea
Keywords = gamma
Keywords = DNA repair
Keywords = extremophile

first: Ernest

last: Williams

first: Todd

last: Lowe

first: Jeffrey

last: Savas


title: coffee nylon arrays

status: Public on Aug 15 2005

city: Campinas

first: Jorge

middle: Maurício Costa

last: Mondego

state: SP

address: Cidade Universitária Zeferino Vaz s/n

department: Genetics and Evolution

country: Brazil

institute: UNICAMP

organism: Coffea hybrid cultivar

description: Nylon membranes containing coffee ESTs from subtracted cDNA librares. Plasmid clones were used. A set of sixteen 96-well plates was spotted on two nylon filters (85 mm x 125 mm) in a 4 x 4 array configuration, with a 96 pins hand-held array tool

first: Oliveiro

last: Guerreiro-Filho

first: Mário Henrique

last: Bengtson

first: Rodrigo

middle: D

last: Drummond

first: Juliana

last: Felix

first: Melina

last: Duarte

first: Daniel

last: Ramiro

first: Miriam

last: Maluf

first: Mari

last: Sogayar

first: Marcelo

last: Menossi


title: Diagnostic miniarray of childhood acute lymphoblastic leukemia (ALL)

status: Public on Jul 05 2005

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

organism: Homo sapiens

description:
Miniarray is a diagnostic platform to recognize different subtypes of ALL. It was constructed arraying on glass slides PCR-amplified cDNAs of 30 genes best discriminating ALL-B and ALL-T patients, 10 tags that are differentially expressed in all leukemia samples and 9 housekeeping genes used as hybridization controls. PCR products are printed in quadruplicate in each miniarray and each slide contains four miniarrays.
cDNA inserts were PCR amplified directly from bacterial cultures. Bacterial clones were inoculated in 96-well, 2 ml Assay Block (Corning), containing 600 µl LB/Ampicillin (50 µl /ml) and incubated at 37 °C for 16 hrs. Approximately 1µl of culture suspension was transferred in 96 well plate (Corning), loaded in each single well with 100 µl of the following solution: 1X PCR buffer, 1.5 mM MgCl2, 0.15 mM for each of the four dNTPs, 0.2 µM for each of primer A and B, 0.02U/µl of Taq Polimerase (New England Biolabs). PCR buffer and unincorporated nucleotides were removed by filtering through 96-well multiscreen filter plates (Millipore, Bedford, MA, USA). Spotting was performed using the robotic system Genpak Array 21 (Genetix, Hampshire, UK) equipped with 32 Stealth Micro Spotting Pins SMP 3B (ArrayIt) settled to obtain spots with an average diameter of 120 µm. Samples were spotted in quadruplicate on derivatized glass slides (MICROMAX Glass Slides: SuperChip™ I, PerkinElmer, Wellesley, MA, USA) to obtain more consistent fluorescence measures. Spotting was performed at 50% relative humidity to obtain the best spot morphology and to reduce the plate evaporation. Microarrays were then processed in a UV cross linker (Stratagene, La Jolla, CA, USA) (total power of 300 mJoules) for the binding the DNA to the slides. Microarrays were finally processed to remove any unbound PCR product, dried and stored under vacuum at room temperature in sealed boxes.

Keywords = childhood leukemia
Keywords = gene expression profiling
Keywords = miniarray

first: Lucia

last: Tombolan

first: Cristiano

last: De Pittà

first: Silvia

last: Carnio

first: Stefano

last: Cagnin

first: Beniamina

last: Pacchioni


title: Human 22K long oligo array

status: Public on Oct 01 2005

city: Beijing

first: yong

last: guo

state: Beijing

address: Qinghuayuan

department: Medical Systems Biology Research Center

country: China

institute: Tsinghua University

description: This set includes 22k oligonucleotides, mostly 70-mers, designed based upon representative sequences in the human UniGene database."

first: Yong

last: Guo

first: Liang

last: Zhang

manufacture_protocol: as described in CapitalBio Labs manual


title: Euphorbiaceae chip1

status: Public on Jun 15 2005

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

organism:
Manihot esculenta
Euphorbia esula

manufacturer: International Center for Tropical Agriculture

first: James

last: Anderson

first: Mauricio

last: Soto-Suárez

manufacture_protocol:
López, C., M. Soto-Suárez, S.Restrepo, B.Piegu, R.Cooke, M.Delseny, J.Tohme,
and V.Verdier 2005. Global transcriptome analysis of cassava responses
to Xanthomonas axonopodis pv. manihotis infection using a cassava cDNA
microarray. Plant Molecular Biology. (in press).


title: FHCRC Arabidopsis Intergenic Array

status: Public on Aug 11 2005

city: Seattle

first: Ryan

last: Basom

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

manufacture_protocol: To obtain the 240 random single-copy loci, nonoverlapping 1-kb segments were selected at random from a database consisting of available contigs for A. thaliana chromosomes 1, 3, and 5 and complete chromosomes 2 and 4 from GenBank (August 2, 2000).  The Primer3 program running on a SUN Solaris workstation was applied with default settings to select 17-bp candidate primers with Tm > 50°C that encompass 700 ± 25 bp fragments. To stringently avoid redundant loci, each fragment was then searched against the database using blastn (word SIZE = 20, match SCORE = 1, mismatch SCORE = -50, gap open PENALTY = 50, gap extension PENALTY = 50, and no filtering), reporting only those hits with E value < 0.15, except for the first hit to itself.  Custom oligonucleotide primers were obtained in 96-well microtiter plates from MWG-Biotech and were used for PCR amplification with Ex-Taq polymerase (Fisher/Panvera Labs).  Microarrays were constructed by mechanically spotting PCR amplification products onto poly-lysine-coated microscope slides using an OmniGrid high-precision robotic gridder (GeneMachines). All loci were present in duplicate on the microarray.


title: EDGE Liver Microarray version 1

status: Public on Sep 07 2005

city: Madison

first: Aaron

last: Vollrath

state: WI

address: 1400 University Ave

institute: McArdle Laboratory

manufacture_protocol: For the liver microarray, clones were selected from a minimally redundant set of liver-derived EST and full-length cDNAs to create a minimally redundant set of clones. This was accomplished by screening them against the RefSeq database of known gene products. This set of clones was then fortified with cDNAs representing toxicologically relevant genes such as drug-metabolizing enzymes (e.g., cytochromes P450), inflammatory responsive genes (e.g., serum amyloid a1), and genes that we have previously identified as useful in classification of chemicals. All clones were then sequence verified from both 3' and 5' directions. These cDNAs were then amplified through PCR and purified using the Millipore Ultra-Screen system (Millipore Corporation, Billerica, MA). The cDNAs were then dried and resuspended in a 50/50 H2O/DMSO solution. Six replicates of each cDNA were printed on each array using a Microgrid II (Genomic Solutions, Ann Arbor, MA) at a pitch of 180 µm for a total of 27,648 features per chip. The slides were then baked at 80°C for 3 h and stored in a desiccator until their use.


title: RNG-MRC_HU25k_STRASBOURG

status: Public on Apr 09 2005

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

first: Kévin

last: Le Brigand

first: Pascal

last: Barbry


title: Populus 2.0

city: Davis

first: Andrew

last: Groover

state: CA

address: 1100 West Chiles Rd

department: Institute of Forest Genetics

institute: USDA Forest Service

organism: Populus trichocarpa

description: This array has probes designed from gene models taken from the Joint Genome Institute Populus trichocarpa genome sequence, as well as probes designed using aspen ESTs.

first: SP

last: DiFazio

first: AM

last: Brunner

first: P

last: Dharmawardhana

first: KJ

last: Munn

manufacture_protocol: Propriety in situ oligonucleotide synthesis.


status: Public on Apr 07 2005

city: Shanghai

first: Zhengjun

last: Chen

state: Shanghai

address: 320 Yueyang Road

institute: Institute of Biochemistry and Cell Biology

technology: MS

description:
Proteomic analysis of pervanadate-induced tyrosine-phosphorylated proteins in hepatocellular carcinoma WRL 68 cells
Protein tyrosine phosphorylation plays critical roles in modulating biological processes such as cellular proliferation, differentiation, migration, apoptosis and metabolism. To profile tyrosine phosphorylated (pTyr) proteins as well as search novel pTyr proteins as cross-talk points among different cellular pathways, we developed a rapid and efficient approach to identify cellular pTyr proteins and their complexes by a combination of subcellular proteomics approach with signal transduction strategies. Human hepatocytic cells from WRL68 cell line were treated with pervanadate (POV), subfractionated into four fractions and then subjected to immunoaffinity purification with anti-pTyr antibody. The eluted mixtures of the anti-pTyr purification were identified by LC-MS/MS.
Subcellular fractionation and affinity purification of tyrosine-phosphorylated proteins:
WRL68 cells were first grown to 80% confluence in MEM complete medium and then the medium replaced with serum free media. After 15 h, the cells were either untreated or stimulated with 0.1 mM pervanadate (1 mM sodium orthovanadate, 3 mM H2O2) for 10 min. 150-mm cultures of WRL 68 cells were rinsed twice with 4? PBS and then scraped from the dish in 750?l of hypotonic buffer (10 mM Tris, 1 mM NaF, 10 mM IAA, pH 7.5) containing a cocktail of protein inhibitors. After a 20-min incubation on ice, the cells were passed about five times through a 25-g needle. The resulting lysate was subjected to a 15min centrifugation at 1000 rpm at 4?, after which the pellet was resuspended in 250?l of hypotonic buffer and re-extracted by a second round of the trituration and centrifugation. The supernatants of the first and second spins were combined, adjusted to 0.25 M NaCl, and separated into cytosolic (supernatant) and membrane (pellet) fractions bycentrifugation at 19,000 rpm (43,000 g) for 90 min at 4?. All the pellets and total cell lysate were resuspended in RIPA buffer (50 mM Tris-HCl, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid sodium) containing 1mM pervanadate with a cocktail of protein inhibitors with sonication aid. Cleared cell lysates were incubated overnight at 4? with 30?l monoclonal anti-phosphotyrosine-agrose (Sigma). Precipitated immune complexes were washed three times with 1×HNTG (20 mM HEPES, 150 mM NaCl, 0.1% Triton X-100, 10% Glycerol, pH 7.5) and then eluted with 100 mM phenyl phosphate (Sigma) in lysis buffer at 4?.
Enzyme digestion, mass spectrometry and protein identification:
The sample was digested according to the published method. Chromatography was performed using a surveyor LC system (Thermo Finnigan,SanJose,CA) on C18 reverse phase column(RP, 180 µm x 150 mm, BioBasic® C18, 5 µm, Thermo Hypersil-Keystone). The pump flow rate is split 1:100 for a colum flow rate of 1.5 µL/min.The column effluent is directly electrosprayed using the orthogonal metal needle source without further splitting.Mobile phase A is 0.1% formic acid in water,and the B mobile phase is 0.1% formic acid in acetonitrile. The separation of peptides obtained by enzymatic digest of bile sample was achieved with a gradient of 2-80% B over 360 min.The column effluent from the reverse phase column was analyzed by LCQ Deca XP ion-trap mass spectrometer.The micro-electrospray interface uses a 30 µm metal needle that is orthogonal to the inlet of the LCQ.The mass spectrometer was set that one full MS scan was followed by three MS/MS scans on the three most intense ion from the MS spectrum with the following Dynamic Exclusion™ settings: repeat count, 1; repeat duration, 0.5 min; exclusion duration, 3.0 min. The acquired MS/MS spectra were automatically searched against protein database for human proteins (SWISS-PROT/TrEMBL) using the TurboSEQUEST program in the BioWorks™ 3.0 software suite. An accepted SEQUEST result had to have a ?Cn score of at least 0.1 (regardless of charge state) and Xcorr (one charge?1.5, two charges?2.0, three charges?2.5). Single peptides that alone identify a protein were manually validated after meeting the above criteria.
Bioinformatics analysis:
The pI and MW of the proteins were analyzed using ExPASy proteomics tools accessed from http://cn.expasy.org/tools/#proteome. The grand average hydropathicity (GRAVY) values were determined according to Kyte-Doolittle. The protein subcellular location annotation was from SwissProt &TrEMBL protein database (http://us.expasy.org/sprot/). The protein function family was categorized according to Gene Ontology (GO) annotation terms extracted by InterPro (http://www.ebi.ac.uk./interpro/). The annotation of protein phosphorylation was from SwissProt &TrEMBL protein database (http://us.expasy.org/sprot/) and PhosphoSite (http://www.phosphosite.org). The kinases were annotated according to human kinome.

distribution: virtual

first: Yiguo

last: Wang

first: Dan

last: Du

first: Longhou

last: Fang

first: Rongxia

last: Li

first: Haixin

last: Yuan

first: Guang

last: Yang

first: Rong

last: Zeng

first: Friedrich

last: Lottspeich

first: Axel

last: Ullrich


title: Human_1_20K_Chip

status: Public on Aug 22 2005

city: Manassas, VA

first: Francesco

last: Gorreta

state: VA

address: 10900 University Blvd

institute: George Mason University

description: Human_1_20K_Chip was constructed from approximately 20,000 human cDNA clones purchased from Research Genetics (Huntsville, AL, USA). cDNA inserts were amplified directly from clones in culture using GF200F (5’-CTGCAAGGCGATTAAGTTGGGTAAC) and GF200R (5’-GTGAGCGGATAACAATTTCACACAGGAAACAGC).

first: Luca

last: Del Giacco

first: Amy

last: VanMeter


title: Human 58K oligonucleotide chip

status: Public on Aug 19 2005

city: Odense

first: Mads

last: Thomassen

address: Soender Boulevard 9

department: Clinical Genetics (KKA)

country: Denmark

institute: Odense University Hospital

description: 29,134 oligonuclaotides recognising 28,800 genes or EST designed by Compugene and produced by Sigma

manufacturer: Human MicroArray Centre, University of Southern Denmark

first: Vibe

last: Skov

first: Freyja

last: Eiriksdottir

first: Qihua

last: Tan

first: Kirsten

last: Jochumsen

first: Niels

last: Fritzner

first: Jesper

last: Dahlgaard

first: Klaus

last: Brusgaard

first: Torben

last: Kruse

manufacture_protocol:
A human oligonucleotide library composed of 29,134 oligonucleotide targets (60mers) recognising 28,830 genes was purchased from Sigma-Genosys (The Woodlands, TX) and designed by Compugen (Compugen Ltd., Jamesburg, NJ) with a 5´ amino linker modification. The oligonucleotides have been designed to include known genes, expressed sequence tags, the majority of known alternative splice variants (http://www.labonweb.com/oligo), and spike targets.
According to the CodeLinkTM protocol, oligonucleotide targets were solubilized in 150 mM sodium phosphate buffer (pH 8.5) and divided into a single aliquot and applied to 76 384-well source plates using an Eppendorf epMotion 5070 robot (Radiometer, DK) at a final concentration of 20pmol/µl. Oligonucleotide targets were arrayed in duplicate by a spotting robot (Virtek ChipWriter Pro (ESI)) onto 50 slides in a controlled environment with a humidity of 38 % inside the spotting compartment. Duplicate spots were 9 mm apart. 24 SMP 2.5 stealth pins (TeleChem International Inc., Sunnyvale, USA) were used for printing and each spot were about 100 µm in diameter and spot centres were 124 µm apart. After printing, slides were incubated overnight at 70% humidity and blocked as recommended by the manufacturer. Dried microarray slides were stored in a desiccated environment at room temperature.


title: FHCRC Mouse 15K v1.0

status: Public on Mar 18 2005

first: Ryan

last: Basom

description: 15,341 feature cDNA array consisting of the NIA Mouse 15K clone set, along with 94 'control' spots.


title: mKIAA cDNA microarray ver2.0

status: Public on Jun 14 2005

city: Kisarazu

first: Kazuhide

last: Imai

state: Chiba

address: 2-6-7 Kazusa-Kamatari

institute: Chiba Industry Advancement Center

manufacture_protocol: Description of mKIAA cDNA microarray ver2.0: Description of mKIAA cDNA microarray: 1707 duplicated mKIAA (1612) and mFLJ cDNA (95) clones and several controls  (e.g., house keeping genes, negative controls, artificial external control plasmids) are spotted on  nylon membrane microarray (18´55 mm). The plasmid DNA was amplified using the TempliPhi DNA amplification kit (Amersham, Piscataway, NJ) in twin.tec PCR plate 384 (eppendorf, Hamburg, Germany). Ampliphied DNA mixture was dried and then disolved in 80% formamide, 20mM EDTA (see detail of  the method in Yamakawa, H., et.al., 2004, DNA Res., 11, 353-360). The mixture were spotted onto a nylon membrane (Biodyne Plus; Pall, East Hills, NY) attached to a slide glass using GeneTac RA1 microarrayer (Genomic Solutions, Ann Arbor, MI).


title: Human cDNA array

status: Public on Jul 01 2005

city: Trondheim

first: Vidar

last: Fykse

address: Olav Kyrres gt 3

department: Cancer Research and Molecular Medicine

institute: NTNU

first: Kristin

last: Nørsett

first: Turid

last: Follestad

last: Beisvåg

first: Helge

last: Waldum

first: Arne

middle: K

last: Sandvik


title: Pinus taeda cDNA microarray Platform 2

status: Public on Feb 25 2005

city: Raleigh

first: Debbie

middle: Ross

last: Craig

state: NC

address: 840 Main Campus Drive

department: Forestry

institute: North Carolina State University

organism: Pinus taeda

description: The microarray contains ESTs selected from 6 Xylem libraries: 1. NXCI - ESTs from juvenile compression wood of Pinus taeda (loblolly pine) 2. NXLV - ESTs from transitional/mature late wood of Pinus taeda (loblolly pine) 3. NXNV - ESTs from mature normal wood of Pinus taeda (loblolly pine) 4. NXPV - ESTs from transitional planings wood of Pinus taeda (loblolly pine) 5. NXRV - ESTs from root wood of Pinus taeda (loblolly pine) 6. NXSI - ESTs from juvenile side wood of Pinus taeda (loblolly pine) , a Pollen Cone library, and a Shoot tip library. The ESTs were PCR amplified, purified, denatured in 50% DMSO and printed on Corning GapsII amino-silane coated slides.

first: Johan

last: Wadenbäck

first: David

last: Clapham

first: Deborah

first: Ron

last: Sederoff

first: Gary

middle: F

last: Peter

first: Sara

last: von  Arnold

first: Ulrika

last: Egertsdotter


title: Galbraith Laboratory Operon Long Oligonucleotide Microarray version 3.0 (ATv302.01.Z)

status: Public on Apr 02 2005

city: Tucson

last: Galbraith

state: AZ

address: 303 Forbes Building

department: Plant Sciences and Bio5 Institute

institute: University of Arizona

description: This oligonucleotide array is produced from the Operon Version 3.0 Array-Ready Oligo set (AROS), which comprises 29,110 70-mer oligonucleotides representing 26,173 protein-coding genes, and 28,964 protein-encoding gene transcripts, and 87 microRNA gene precursors.  AROS design is based on ATH1 release 5.0 of the TIGR Arabidopsis genome annotation database, and Release 4.0 of the miRNA Registry at the Sanger Institute.  Various additional elements are printed as controls.  Microarrays can be ordered from the Galbraith laboratory. This platform represents slides ATv302.01.001-ATv302.01.300 (http://www.ag.arizona.edu/microarray).

middle: W


title: cDNA microarray Trymanosoma cruzi - v.1

status: Public on Mar 04 2005

city: São Paulo

first: Ricardo

last: Vêncio

address: Av. Prof. Lineu Prestes, 748 - Butantã

department: Departamento de Bioquímica

institute: Instituto de Química da Universidade de São Paulo

organism: Trypanosoma cruzi

description: DNA microarrays were constructed with 710 ESTs obtained from non-normalised and normalised cDNA libraries of CL Brener epimastigotes . Polymerase chain reaction (PCR) amplification of the ESTs (average length 800 bp) was obtained with T3 and T7 primers using DNA polymerase (BIOLASE). The amplification products were purified with Multiscreen plates (Millipore). Inserts representing 20 cloned T. cruzi coding and non-coding genes , control sheared DNAs and oligonucleotides  were also immobilised on the glass slides with Generation III Microarray System spotter (Molecular Dynamics) according to manufacturer's instructions. The DNA probes were distributed in 10 sub-arrays, containing 288 spots each. Each sub-array was spotted in duplicate (left and right side of the slide) resulting in at least 6 and at most 60 replicates depending on probe. Detailed spotting map is available at supplemental web-site. After immobilisation, DNA was UV-irradiated at 254 nm (Stratagene lamp) with 50 mJ total energy.

first: Cássio

last: Baptista

middle: Z

first: Sarah

last: Abdala

first: Maria Paula

last: Valadares

first: Camila

last: Martins

first: Carlos Alberto

middle: B

last: Pereira

first: Bianca

last: Zingales


title: Pinus taeda cDNA

status: Public on Dec 01 2004

first: Frederick

middle: O

last: Asiegbu

first: Åke

last: Olson

first: Guosheng

last: Li

first: Aleksandra

last: Adomas

first: Tzu-Ming

last: Chu

first: Gregory

last: Heller

first: Magnus

last: Karlsson

first: Jarmila

last: Nahalkova

first: Len

last: van Zyl

first: Russ

last: Wolfinger

first: Ralph

middle: A

last: Dean

first: Roger

last: Finlay

first: Jan

last: Stenlid


title: VV1_0_1

status: Public on Mar 16 2005

city: Seoul

first: Dae-Kyun

last: Park

address: Sinsoo-dong 1

department: Department of Life Science

institute: Sogang University

organism: Vibrio vulnificus

description:
The PCR products were purified using Qiagen PCR purification kit, and printed on Corning GAPS II coated slide in quadriplicate using a DNA arrayer, Affimatrix 427.
This set includes 160 genes, DNA fragment spanning about a 700-bp region of the 3¡Çend portion of each gene was prepared by PCR using primers specific to DNA nucleotide sequence of each gene designed based on the genome sequences of V. vulnificus in the GenBank (Accession numbers NC_004459 and NC_004460)
Keywords = Vibrio vulnificus, cyclic dipeptide

first: Ko-Eun

last: Lee

first: Saet-Byoul

first: Chang-Ho

last: Baek

first: Won

last: Hwang

first: Jung-Im

last: Shim

first: Byung-Soo

last: Kim

first: Kun-Soo


title: the shrimp cDNA array of 3114 clone

status: Public on Jan 14 2005

city: Qingdao

first: Wang

last: Bing

state: Shandong

institute: Institute of Oceanology

organism: Penaeus chinensis

description:
A total of 3136 cDNA targets including 1578 unique genes from the cDNA library, 1536 cDNA clones from reverse and forward Subtractive Suppression Hybridization (SSH) libraries plus 14 negative and 8 blank control clones were spotted onto the NH2-modified glass slides with an area of 18×18mm.
Keywords = Fenneropenaeus chinensis
Keywords = WSSV
Keywords = microarray
Keywords = SSH library
Keywords = EST
Keywords = cDNA library

first: WANG

first: LI

last: Fuhua

first: XIANG

last: Jianhai


title: 2nd 7.5K of NIA-NIH 15K Mouse cDNA set

status: Public on Dec 16 2004

city: Bar Harbor

first: Ioannis

middle: M

last: Stylianou

state: ME

address: 600 Maine Street

institute: The Jackson Laboratory

organism: Mus musculus

description:
2nd 7.5K of NIA-NIH 15K Mouse cDNA set
pre/peri implation mouse cDNA
Ref:
Tanaka, T. S., et al. Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. Proc.Natl.Acad.Sci.U.S.A 97: 9127-9132, 2000.
Keywords = Fob3
Keywords = Fob3b
Keywords = QTL
Keywords = congenic

first: Michael

last: Clinton

first: Clare

last: Pritchard

first: Zuzzana

last: Lallane

first: Lutz

last: Bünger

first: Grahame

last: Bulfield

first: Simon

last: Horvat


title: FHCRC Yeast Amplicon v1.0

status: Public on Mar 08 2005

first: Ryan

last: Basom

organism: Saccharomyces cerevisiae

description: Yeast ORF microarrays were constructed employing a set of 6229 ORF-specific PCR primer pairs (Research Genetics, Huntsville, AL).  Individual PCR products were verified as unique via gel electrophoresis, purified, and mechanically “spotted” onto poly-L-lysine coated microscope slides using an OmniGrid high-precision robotic gridder (GeneMachines, San Carlo, CA).


title: 1st 7.5K of NIA-NIH 15K Mouse cDNA set

description:
1st 7.5K of NIA-NIH 15K Mouse cDNA set
pre/peri implation mouse cDNA
Ref:
Tanaka, T. S., et al. Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. Proc.Natl.Acad.Sci.U.S.A 97: 9127-9132, 2000.
Keywords = Fob3
Keywords = Fob3b
Keywords = QTL
Keywords = congenic


title: GAP_M_Ia

status: Public on Jan 01 2005

city: Lynchburg

last: Price

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

organism: Aspergillus flavus

description:
PCR products were generated using approximately 5 ng plasmid DNA isolated from unique cDNA clones. T3 and T7 primers were used to generate amplicons. PCR products were then purified by isopropanol precipation followed by a 70% ethanol wash. The presence of amplicons was verified by agarose gel electrophoresis.
PCR products at approximately 250 ng/ul in 50% DMSO were spotted in triplicate onto Corning GAPSII slides (Corning, NY) using an Affymetrix 417 Arrayer (Santa Clara, CA). Spots were allowed to air dry before being fixed following manufacturer’s recommendation.
Keywords = aspergillus
Keywords = aflatoxin

first: Ahmad

last: Fakhoury

first: Gregory

middle: R

last: OBrian


title: HHV8/KSHVvo1

city: Bethesda

last: Lu

address: 10 Center Drive, Blg. 10, Rm 10S255

department: HIV and AIDS Malignancy Branch

institute: National Cancer Institute

organism:
Homo sapiens
Human gammaherpesvirus 8

description:
Printing by the National Cancer Institute/Advanced Technology Center Microarray Facility
Surface type: poly-L lysine coated glass slides
Attachment: UV cross-linked at 600 mJ
Array description: The long oligo (60-65 nt) custom arrays were manufactured at the Advanced Technology Center Microarray Facility (NIH/NCI/CCR/ATC).  Microarrays were printed with a GeneMachines robotic arrayer from Genomic Solutions (http://www.genomicsolutions.com) that was fitted with a printhead containing four (4) SMP3 printing pins from Telechem International (http://www.arrayit.com).  In addition to the KSHV probes, the array included human housekeeping genes for normalization purposes.  The human housekeeping 65 nt oligomer set (Cat # HUMLIBST) probing for 96 cellular genes is commercially available from Compugen (http://www.labonweb.com).  The HHV-8 60-65 nt oligomer set was custom designed by Compugen or in-house based on available genomic or cDNA sequence attainable from GenBank or additional published information, particularly for alternatively spliced messages (see Lu et al, publication data to be inserted). The human housekeeping and KSHV oligomer probe sets were distributed into 384-well polypropylene plates (Nalge Nunc Intl, 384 micro array) and dissolved in 3XSSC print buffer at a concentration of 200 ng/µl or 10µM.  The 384-well plate contained either 3 wells with each housekeeping gene probe and 1 well with each KSHV probe, or duplicate wells for each housekeeping probe and duplicate wells for each KSHV probe.  The microarray spot densities were 250 microns (center-to-center).  Duplicate spots were printed per probe in two separate regions of each slide.  The microarrays are printed on locally produced poly-L lysine coated slides and post-processed according to DNA microarrays: a molecular manual, 2003 edited by D. Bowtell and J. Sambrook, CSHL Press, Cold Spring Harbor, NY.
Keywords = Human Herpesvirus-8
Keywords = HHV-8
Keywords = Kaposi's sarcoma-associated herpesvirus
Keywords = KSHV
Keywords = long oligomer microarray

first: Jacqueline

last: Suen

first: Carolina

last: Frias

first: Ruth

last: Pfeiffer

first: Mong-hsun

last: Tsai

first: Eric

last: Chuang

first: Steven

middle: L

last: Zeichner


title: Custom-made oligonucleotide array for activated human monocytes

status: Public on Mar 11 2005

city: Vandoeuvre

first: Dan

last: Longrois

institute: INSERM U684

description: This array contains 250 genes known to be expressed by activated human monocytes.

first: Didier

last: Hanriot

first: Gaelle

last: Bello

first: Armelle

last: Ropars

first: Carole

last: Seguin-Devaux

first: Gael

last: Poitevin

first: Sandrine

last: Grosjean

first: Véronique

last: Latger-Cannard

first: Yvan

last: Devaux

first: Faiez

last: Zannad

first: Paul-Michel

last: Mertes

first: Ketsia

last: Hess


title: GAP_M_II

first: Michael

last: Price

description:
PCR products were generated using approximately 5 ng plasmid DNA isolated from unique cDNA clones. T3 and T7 primers were used to generate amplicons. PCR products were then purified by isopropanol precipation followed by a 70% ethanol wash. The presence of amplicons was verified by agarose gel electrophoresis.
PCR products at approximately 250 ng/ul in 50% DMSO were spotted in triplicate onto Corning UltraGAPS slides (Corning, NY) using a Genetix Qarray Mini array printer (Genetix Limited, Hampshire, UK). Spots were allowed to air dry before being fixed following manufacturer’s recommendation.
Keywords = aspergillus
Keywords = aflatoxin

first: Kimberly

last: Schwartzburg

first: Gary

last: Payne


title: GAP_MAF1

status: Public on Dec 09 2004

first: Ahmad

last: Fakhoury

department: Plant Pathology

description:
PCR products were generated using approximately 5 ng plasmid DNA isolated from unique cDNA clones. T3 and T7 primers were used to generate amplicons. PCR products were then purified by isopropanol precipation followed by a 70% ethanol wash. The presence of amplicons was verified by agarose gel electrophoresis.
PCR products at approximately 250 ng/ul in 50% DMSO were spotted in triplicate onto onto Corning CMT-GAPS glass slides (Corning, NY), using an Affymetrix 417 Arrayer (Santa Clara, CA). Spots were allowed to air dry before being fixed following manufacturer’s recommendation.


title: Zebrafish nucleotide array

status: Public on Dec 21 2004

city: Leiden

first: Christoph

middle: Peter

last: Bagowski

country: Netherlands

institute: Leiden University

organism: Danio rerio

description: Microarrays of the MWG 14k Zebrafish Oligonucleotide Set were produced using the facilities of the Leiden Genome Technology Center (http://www.lgtc.nl). Oligonucleotides were dissolved in 150mM phosphate buffer (pH 8.5) to a concentration of 20 µM. With Omnigrid 100 (Genemachines) oligonucleotides were spotted on Codelink activated slides (Amersham Biosciences) according to the Amersham Codelink protocol and as described in (‘t Hoen et al 2003 and Meijer et al 2004). Microarrays were spotted according to the MIAME guidelines with 15.532 unique zebrafish oligonucleotides from the MWG oligonucleotide set. Ambion’s arraycontrol oligonucleotides (8 sense oligos) and 3 custom designed oligonucleotides were spotted together with the MWG oligonucleotide set. Spotted Codelink activated slides were treated with blocking solution and washed according to the manufacturer’s instructions.

middle: P

first: David

last: van der Meer

first: Jelani

middle: T

last: Leito


title: Cell Wall Chip cwchv02

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

institute: Facultad de Farmacia (UCM)

description:
8 subarrays (spots organised in 8 rows and 14 columns per subarray) distributed in 4 rows and 2 columns of subarrays. Controls are LAC, BLANK, SOPB and emp. Most of genes printed in this slide are cell wall related

Keywords = Saccharomyces cerevisiae
Keywords = cell wall
Keywords = cell wall chip

first: Jose

last: Rodríguez-Peña

first: Rosa

last: Pérez-Díaz

first: Sara

last: Alvarez

first: Clara

last: Bermejo

first: Raúl

last: García

first: Catalina

last: Santiago

first: César

last: Nombela


title: Human 36mer genome tiling array HS_24906

status: Public on Oct 29 2004

city: New Haven

first: Paul

last: Bertone

state: CT

institute: Yale University

description:
Maskless photolithographic synthesis oligonucleotide array on glass
This series of microarrays is designed to represent sense and antisense strands of the nonrepetitive DNA of the human genome with 36mer oligonucleotide probes, positioned every 46nt on average. The probes were selected from the November 14, 2002 human genome sequence assembly (NCBI Build 31/hg13).
Microarrays were constructed with Expedite DNA synthesizers (Applied Biosystems, Foster City, CA) in conjunction with Maskless Array Synthesis (MAS) units (NimbleGen Systems, Madison, WI).
Arrays containing approximately 390,000 oligonucleotide features in a 14 × 17.4 mm square area were fabricated with photolabile phosophoramidites (NPPOC-dAdenosine (N6-tac) -Cyanoethylphosphoramidite, NPPOC-dCytidine (N4-Isobutyryl) -Cyanoethylphosphoramidite NPPOC-dGuanosine (N2-ipac) -Cyanoethylphosphoramidite, NPPOC-dThymidine-Cyanoethylphosphoramidite) obtained from Proligo (Boulder, CO). Following MAS synthesis, base-protecting groups were removed in a solution of ethylenediamine:ethanol (1:1 v/v) (Aldrich, St. Louis, MO) for 2 hours. The arrays were rinsed with water, dried and stored desiccated until use.
Keywords = genomic tiling, maskless photolithography


title: Human 36mer genome tiling array HS_20282


title: Human 36mer genome tiling array HS_17996


title: Human 36mer genome tiling array HS_24610


title: Cell Wall Chip cwchv01

description:
8 subarrays (spots organised in 7 rows and 14 columns per subarray) distributed in 4 rows and 2 columns of subarrays. Controls are LAC, BLANK, SOPB and emp. Most of genes printed in this slide are cell wall related
Keywords = Saccharomyces cerevisiae
Keywords = cell wall
Keywords = cell wall chip


title: Human 36mer genome tiling array HS_17918


title: Human 36mer genome tiling array HS_19824


title: Human 36mer genome tiling array HS_20338


title: Human 36mer genome tiling array HS_20289


title: Human 36mer genome tiling array HS_20275


title: Human 36mer genome tiling array HS_17913


title: Human 36mer genome tiling array HS_20344


title: Human 36mer genome tiling array HS_17911


title: Human 36mer genome tiling array HS_14317


title: Human 36mer genome tiling array HS_14313


title: Human 36mer genome tiling array HS_14311


title: Human 36mer genome tiling array HS_18601


title: Human 36mer genome tiling array HS_20266


title: Human 36mer genome tiling array HS_14307


title: Human 36mer genome tiling array HS_18517


title: Human 36mer genome tiling array HS_18373


title: Human 36mer genome tiling array HS_14297


title: Human 36mer genome tiling array HS_14293


title: Human 36mer genome tiling array HS_17915


title: Human 36mer genome tiling array HS_16306


title: Human 36mer genome tiling array HS_14284


title: Human 36mer genome tiling array HS_17916


title: Human 36mer genome tiling array HS_14280


title: Human 36mer genome tiling array HS_14278


title: Human 36mer genome tiling array HS_14318


title: Human 36mer genome tiling array HS_14273


title: Human 36mer genome tiling array HS_14326


title: Human 36mer genome tiling array HS_14276


title: Human 36mer genome tiling array HS_14272


title: Human 36mer genome tiling array HS_14270


title: Human 36mer genome tiling array HS_14274


title: Human 36mer genome tiling array HS_14267


title: Human 36mer genome tiling array HS_14309


title: Human 36mer genome tiling array HS_14316


title: Human 36mer genome tiling array HS_14308


title: Human 36mer genome tiling array HS_14310


title: Human 36mer genome tiling array HS_14262


title: Human 36mer genome tiling array HS_14269


title: Human 36mer genome tiling array HS_14294


title: Human 36mer genome tiling array HS_14288


title: Human 36mer genome tiling array HS_14292


title: Human 36mer genome tiling array HS_14289


title: Human 36mer genome tiling array HS_13243


title: Human 36mer genome tiling array HS_13107


title: Human 36mer genome tiling array HS_13051


title: Human 36mer genome tiling array HS_12869


title: Human 36mer genome tiling array HS_18605


title: Human 36mer genome tiling array HS_14287


title: Human 36mer genome tiling array HS_12859


title: Human 36mer genome tiling array HS_14285


title: Human 36mer genome tiling array HS_12866


title: Human 36mer genome tiling array HS_12813


title: Human 36mer genome tiling array HS_14277


title: Human 36mer genome tiling array HS_12803


title: Human 36mer genome tiling array HS_12801


title: Human 36mer genome tiling array HS_12783


title: Human 36mer genome tiling array HS_14271


title: Human 36mer genome tiling array HS_11703


title: Human 36mer genome tiling array HS_11693


title: Human 36mer genome tiling array HS_12610


title: Human 36mer genome tiling array HS_11691


title: Human 36mer genome tiling array HS_11692


title: Human 36mer genome tiling array HS_14263


title: Human 36mer genome tiling array HS_11650


title: Human 36mer genome tiling array HS_14259


title: Human 36mer genome tiling array HS_14261


title: Human 36mer genome tiling array HS_13289


title: Human 36mer genome tiling array HS_13254


title: Human 36mer genome tiling array HS_13242


title: Human 36mer genome tiling array HS_52441


title: Human 36mer genome tiling array HS_13111


title: Human 36mer genome tiling array HS_52361


title: Human 36mer genome tiling array HS_52358


title: Human 36mer genome tiling array HS_12867


title: Human 36mer genome tiling array HS_52395


title: Human 36mer genome tiling array HS_52375


title: Human 36mer genome tiling array HS_52377


title: Human 36mer genome tiling array HS_12863


title: Human 36mer genome tiling array HS_12846


title: Human 36mer genome tiling array HS_12807


title: Human 36mer genome tiling array HS_12808


title: Human 36mer genome tiling array HS_30237


title: Human 36mer genome tiling array HS_12825


title: Human 36mer genome tiling array HS_12802


title: Human 36mer genome tiling array HS_12794


title: Human 36mer genome tiling array HS_30220


title: Human 36mer genome tiling array HS_30140


title: Human 36mer genome tiling array HS_11690


title: Human 36mer genome tiling array HS_11662


title: Human 36mer genome tiling array HS_11648


title: Human 36mer genome tiling array HS_52473


title: Human 36mer genome tiling array HS_52472


title: Human 36mer genome tiling array HS_30091


title: Human 36mer genome tiling array HS_52437


title: Human 36mer genome tiling array HS_52439


title: Human 36mer genome tiling array HS_29118


title: Human 36mer genome tiling array HS_29074


title: Human 36mer genome tiling array HS_29112


title: Human 36mer genome tiling array HS_52353


title: Human 36mer genome tiling array HS_52178


title: Human 36mer genome tiling array HS_52352


title: Human 36mer genome tiling array HS_29030


title: Human 36mer genome tiling array HS_25100


title: Human 36mer genome tiling array HS_25093


title: Human 36mer genome tiling array HS_30231


title: Human 36mer genome tiling array HS_30229


title: Human 36mer genome tiling array HS_30222


title: Human 36mer genome tiling array HS_25089


title: Human 36mer genome tiling array HS_30221


title: Human 36mer genome tiling array HS_25075


title: Human 36mer genome tiling array HS_24943


title: Human 36mer genome tiling array HS_30228


title: Human 36mer genome tiling array HS_24942


title: Human 36mer genome tiling array HS_30213


title: Human 36mer genome tiling array HS_24949


title: Human 36mer genome tiling array HS_30152


title: Human 36mer genome tiling array HS_30212


title: Human 36mer genome tiling array HS_24946


title: Human 36mer genome tiling array HS_24938


title: Human 36mer genome tiling array HS_30074


title: Human 36mer genome tiling array HS_30071


title: Human 36mer genome tiling array HS_29095


title: Human 36mer genome tiling array HS_30162


title: NMC_Rat_15k_cDNA_Ser6

status: Public on Oct 20 2004

first: Kristin

last: Nørsett

department: Dept of Cancer Research and Molecular Medicine

institute: Norwegian University of Science and Technology

organism: Rattus norvegicus

description: The 15k rat cDNA arrays were prepared from a collection of 14k cDNAs purchased from Research Genetics (Huntsville, AL) (http://www.mikromatrise.no). 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.

middle: G

first: Mette

last: Langaas

first: Astrid

last: Lægreid

last: Worlund

first: Helge

last: Waldum

first: Arne

last: Sandvik


title: Human 36mer genome tiling array HS_30146


title: Human 36mer genome tiling array HS_29035


title: TcBiochip 16k v. 3.1

status: Public on Oct 02 2004

city: Curitiba

first: Christian

middle: Macagnan

last: Probst

institute: IBMP - Instituto de Biologia Molecular do Paraná

description:
A Trypanosoma cruzi (Tc) microarray containing ~5200 probes spotted three times. The probes are dsDNA produced by genomic DNA PCR amplification (ESTs from Genbank) or EST library amplification (local EST library).
Keywords = Tc3.1

first: Marco Aurélio

last: Krieger


title: Human 36mer genome tiling array HS_25094


title: RNG-MRC_HU2k_v3

status: Public on Oct 05 2004

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

institute: IPMC/CNRS

first: Kévin

last: Le Brigand

first: Pascal

last: Barbry


title: Mice microarray for muscular dystrophy analysis (Layout 2).

status: Public on Aug 10 2004

city: Nantes

first: Nolwenn

last: Le Meur

address: 1 rue Gaston Veil

institute: INSERM

description: The microarray 1082 different cDNA clones (with 89 non-annotated), issued from four subtractive libraries, previously prepared by suppressive/subtractive hybridizations between control and mdx hindlimb muscles, and between control and mdx DIA muscles of 12 week-old mice.

first: Karl

last: Rouger

first: Martine

last: Le Cunff

first: Jean-Marie

last: Heslan

first: Jean

middle: J

last: Léger

first: Jacques

last: Noiraud


title: Human 36mer genome tiling array HS_29033

first: Paul

last: Bertone


title: Human 36mer genome tiling array HS_25070


title: Mice microarray for muscular dystrophy analysis (Layout 1).

description: The microarray 1082 different cDNA clones (with 93 non-annotated), issued from four subtractive libraries, previously prepared by suppressive/subtractive hybridizations between control and mdx hindlimb muscles, and between control and mdx DIA muscles of 12 week-old mice.


title: Human 36mer genome tiling array HS_25061


title: Human 36mer genome tiling array HS_24940