title: de los Reyes Lab Rice cDNA array

status: Public on May 31 2007

city: Orono

first: Benildo

middle: G

last: de los Reyes

state: ME

address: 5735 Hitchner Hall

department: School of Biology and Ecology

country: USA

institute: University of Maine

organism: Oryza sativa

technology: spotted DNA/cDNA

description:
The microarray consists of a total of 12,160 spots. These spots represent to duplicate panels for each unique feature (including blanks), thus each panel of duplicate feature consists of 6,080 spots.

The Platform data table reflects a condensed representation of the duplicate features. The complete array layout file is linked as a supplementary file at the foot of this record.

distribution: non-commercial

manufacturer: Genomics Technology Support Facility, Michigan State University, East Lansing, MI

first: Chen

last: Cheng

first: Kil-Young

last: Yun

first: Habtom

middle: W

last: Ressom

first: Bijayalaxmi

last: Mohanty

first: Vladimir

middle: B

last: Bajic

first: Yulin

last: Jia

first: Song-Joong

manufacture_protocol: The cDNAs on the microarray were amplified from the pBluescript EST library of cold stress rice seedlings (De los Reyes et al., 2003, Theor Appl Genet 107:1071-1082) by T3 and T7 primers. Single bands were gel-purified and samples were spotted on ArrayIt brand superamine slides (Cat. # SMM) by the Michigan State University Genomics Technology Support Facility (www.genomics.msu.edu).


title: NCI_UniGEM2_HCC

status: Public on Apr 02 2003

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

organism: Homo sapiens

description:
The array consists of 9128 wells. The gene set was based on the Incyte Human UniGem 2.0 version (Hs UniGene, Build #131, released on Feb 28, 2001) provided by Incyte Genomics, Inc. The set includes 122 Incyte EST clones; 8998 identifed with a public GenBank Accession; 8905 Unique GenBank Accessions; 8882 mapped into Hs UniGene Build #131; 8281 Unique UniGene Clusters; 1179 EST clusters; 7102 "Named" clusters.
Keywords = hepatocellular carcinoma
Keywords = metastasis
Keywords =

manufacturer: Advanced Technology Center Microarray Facility (NIH/NCI/CCR/ATC)


title: UofG_Mallard_Bovine_Immune-endocrine_v2.0

status: Public on May 19 2007

city: Guelph

first: Maria

middle: Isabel

last: Nino-Soto

state: Ontario

address: College Ave. West

department: Pathobiology

country: Canada

institute: University of Guelph

organism: Bos taurus

description: The cDNA microarray is defined as 4 replicate blocks were each block consists of 20 columns and 21 rows, with features (PCR products, positive and negative controls) printed in duplicate. The microarray is printed twice on the slide surface.

manufacturer: University of Guelph and CRBR - Université Laval

middle: I

first: Jennifer

last: Huffman

first: Wenjing

last: Tao

first: Catherine

last: Gravel

first: Bonnie

last: Mallard

manufacture_protocol: This platform is based on a previously developed cDNA microarray (Tao et al, 2004, Vet Immunol Immunopathol. 101(1-2):1-17). The present version consists of 183 RT-PCR derived DNA fragments, of which 20 represent new sequences with respect to the previous version (GPL4473). The microarray includes 5 housekeeping genes and bovine genomic DNA as positive controls as well as Rhodococcus equi 17kD virulence protein gene, plasmid pACYC177 DNA and printing buffer as negative controls. Total RNA was extracted from several sources including bovine blood mononuclear cells, spleen, ovaries and placenta. Total RNA was reverse transcribed with Superscript III (Invitrogen Canada Inc., Ontario, Canada) and sequences were amplified from cDNA with gene-specific primers. PCR products were cloned using the TOPO TA Cloning® kit for Sequencing (Invitrogen Canada Inc., Ontario, Canada). PCR products amplified from cell lysates using M13 primers were purified using the 384 Well DNA Binding UNIFILTER® (Whatman Inc., New Jersey, USA) according to the manufacturer’s instructions. Purified PCR products were dehydrated by lyophilization and resuspended in H2O/DMSO [1:1] for printing. Printing was performed on Corning® UltraGAPS™ Coated Slides (Corning Inc., New York, USA) using a VersArray ChipWriter Pro robot (Bio-Rad Laboratories (Canada) Ltd., Ontario, Canada). Slides were incubated in a dessiccator for 48 hours before UV cross-linking with 300 mJ. Slides were heat-sealed back into their original storage pouch to protect them from light and humidity changes. Quality control was performed with The PARAGON™ DNA Microarray QC Stain Kit (Invitrogen Canada Inc., Ontario, Canada).


title: Technical Microbiology-Viable beer spoilage bacteria microarray V2

status: Public on May 23 2007

city: Bochum

first: Daniel

middle: Gilbert

last: Weber

address: Bürkle-de-la-Camp Platz 1

department: Molekulare Medizin

country: Germany

institute: IPA

organism:
Pectinatus frisingensis
Levilactobacillus brevis
Lacticaseibacillus casei
Loigolactobacillus coryniformis
Megasphaera cerevisiae
Pediococcus damnosus
Pectinatus cerevisiiphilus
Schleiferilactobacillus perolens
Pediococcus inopinatus

technology: spotted oligonucleotide

description: Each oligonucleotide species-specific probe was spotted in 70 replicate spots on the microarray. Nine single beer spoilage bacteria species were detected with the developed prototype oligonucleotide microarray and also three mixes of two different beer spoilage bacteria species.

first: Kerstin

last: Sahm

first: Tino

last: Polen

first: Volker

middle: F

last: Wendisch

first: Garabed

last: Antranikian

manufacture_protocol: Standard glass microscope slides were coated with a poly-L-lysine solution and stored for several weeks to allow the surface to become sufficiently hydrophobic. Species-specific probes were spotted in 3x SSC onto the glass surface using a robotic printing system. For routine experiments 50 μM was used as probe concentrations. The diameter of the spots was 150 μm and the space between the centres of two spots was 205 μm allowing the preparation of seven grids each containing 70 spot replicates. To distribute the oligonucleotides more evenly, the spots were rehydrated using a 1x SSC bath at 40°C until the spots were glistening, followed by snapped-drying at 120°C using a heat block. To increase the amount of hybridisable oligonucleotides, stably attached to each spot, the nucleic acids were cross-linked by UV irradiation.


title: SWEGENE H_v3.0.1 35K

status: Public on May 24 2007

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

first: Ake

last: Borg

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


title: CAG Mouse 22k array v1.0 with Stratagene Spot Report Alien Oligo

city: Newark

first: Virginie

middle: Marie

last: Aris

state: NJ

address: W420M, 225 Warren St

department: Center For Applied Genomics

institute: PHRI-UMNDJ

organism: Mus musculus

first: Patricia

last: Soteropoulos

first: Tongsheng

first: Saleena

middle: S

last: Ghanny

manufacture_protocol:
Compugen Mouse OligoLibraryTM, 2002, Cat# MOULIB96.
60-mer oligonucleotides in a 3x SSC solution are printed on Poly-L-Lysine coated glass slides with 48 TeleChem SMP3 pins on a GeneMachines OmniGrid 100 Microarrayer. Slides are post processed by rehydrating, snap drying, UV crosslinking (600x100 microjoules of energy), and blocking with Succinic Anhydride.


title: NimbleGen/GeneFrontier Pseudomonas putida KT2440(pCAR1) array

status: Public on May 01 2007

city: Sendai

first: Masatoshi

last: Miyakoshi

state: Miyagi

address: Aoba-ku, Katahira, 2-1-1

department: Department of Environmental Life Sciences

country: Japan

institute: Tohoku University

organism: Pseudomonas putida

technology: in situ oligonucleotide

description:
Target sequences come from NCBI accession number NC_002947 and NC_004444 (2004/11/30)
Number of targets: 5,350 CDS and 21 rRNA from NC_002947 and 190 CDS from NC_004444
Number of probes per target: 15 for NC_002947 and 45 for NC_004444
Length of probes: 24mer
Keywords = Pseudomonas putida KT2440
Keywords = pCAR1
Keywords = high density
Keywords = custom array

distribution: custom-commercial

first: Masaki

last: Shintani

first: Mikihiko

last: Nimura

first: Hideaki

last: Nojiri

manufacture_protocol: see manufacturer's web site (http://www.genefrontier.com)


title: OSU-CCC MicroRNA Microarray Version 2.0

status: Public on May 14 2007

first: Xin

last: Wang

organism:
Homo sapiens
Mus musculus

manufacturer: Microarray Shared Resource, Comprehensive Cancer Center, The Ohio State University (OSU-CCC)

manufacture_protocol: Manufacured using GE Healthcare's CodeLink (TM) 3-D Gel Matrix Technology. CodeLink(tm) Activated Slides are designed to covalently immoblize amine-modified DNA for microarrays. The slides are coated with a 3-D surface chemistry comprised of a long-chain, hydrophilic polymer containing amine-reactive groups. This polymer is covalently crosslinked to itself and to the surface of the slide. The crosslinked polymer, combined with end-point attachment, orients the immobilized DNA, and holds it away from the surface of the slide. The 1x printing buffer consists of 50 mM sodium phosphate at pH 8.5. Codelink slides are manufactured by SurModics and were formally sold as 3D-Link(tm) Activated Slides. ¹ Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions that is fitted with a printhead and 16 SMP3 print tips from Telechem. The microRNA microarray probe set is based on 40mer oligonucleotides from Sigma-Genosys. ¹ Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normalized 25 micromolar concentration. The miRNA microarray spot densities are 200 microns (center-to-center). The microarrays are printed on Codelink Activated Slide (PN300011)) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: AGRS Human 19.2k Array

city: Melbourne

first: Maria

last: Schache

country: Australia

institute: St Vincents Institute

manufacture_protocol: DNA on these slides has been printed in a 50% DMSO solution with a DNA concentration range of 100-250ng/ul on Corning CMT-GAPS aminosilane slides. Microarray slides are fixed by UV cross-linking at 70mj and baked for 2-4 hours prior to use for hybridisations


title: SUCAST Sugarcane 2208 v1.0

status: Public on May 20 2007

city: São Paulo

first: Milton

middle: Yutaka

last: Nishiyama Jr

state: São Paulo

address: Av. Professor Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: Universidade de São Paulo - USP

organism: Saccharum officinarum

description: Six 384-well plates representing 1830 unique SUCAST SAS were rearrayed for spotting

manufacture_protocol: Sugarcane cDNA plasmid clones obtained from the SUCEST collection were re-arranged and amplified in 100ul PCR reactions (40 cycles, annealing at 51°C), directly from bacterial clones in culture, using T7 and SP6 primers. PCR products were purified by filtration using 96 well filter plates (Millipore Multiscreen MAFBN0B50). Samples were visualized on 1% agarose gels to inspect PCR-amplification quality and quantity. Purified PCR products (in 10mM Tris-HCl solution at pH 8.0) were mixed with an equal volume of DMSO in 384 well V-bottom plates. Microarrays were constructed by arraying cDNA fragments on DMSO optimized, metal coated glass slides (type 7, Amersham Biosciences) using the Generation III Microarray Spotter (Molecular Dynamics/Amersham Pharmacia Biotech). Each cDNA fragment was spotted on the slides at least twice (i.e., technical replicates). Following printing, the slides were allowed to dry and the spotted DNA was bound to the slides by UV-cross linking (50mJ).


title: LeBeau Human 91k v1.0

city: Chicago

first: Isabelle

middle: A

last: Lucas

state: IL

address: 5841 S Maryland

institute: University of Chicago

first: Aparna

last: Palakodeti

first: Yanwen

last: Jiang

first: Kyle

last: Munn

manufacture_protocol: Repeat masked sequence data for the seven regions was obtained from UCSC. All regions were tiled with 50mer probes avoiding ambiguous bases and repeat masked regions. The minimum and median tiling intervals were 30bp for the five regions. The sense and anti-sense probes were then randomly placed on the array in duplicate using ArrayScribe array design software (NimbleGen Systems Inc.,Madison, WI). The arrays were constructed by NimbleGen using maskless array synthesis technology, with ~385,000 oligonucleotides being synthesized by photolithography on an array by previously described methods (Singh-Gasson et al., (1999) Nat Biotechnol 17: 974-978).


title: NimbleGen pathogenic virus whole-genome tiling array_Patharray2

status: Public on May 29 2007

city: Singapore

first: Christopher

last: Wong

address: 60 Biopolis St #02-01

country: Singapore

institute: Genome Institute of Singapore

organism: Viruses

description:
Pathogen detection chip Patharray2 is a tiling array covering the full genomes of 35 viruses (sequence downloaded from NCBI taxonomy webpage).  Pathogen recognition signatures, comprising all probes which will hybridize to a given pathogen (including all similar probes from other pathogens which are predicted to cross-hybridize) were created.  There are 7 replicates of each 40-mer probe, together with hybridization controls.

The Platform data table reflects a condensed representation of the array. The complete array layout file (including the 7 replicates of each 40-mer probe) is linked as a supplementary file.

manufacture_protocol: According to standard NimbleGen protocols.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 37 of 37

status: Public on Mar 20 2007

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 37.

first: Zirong

last: Li

first: Leah

last: Barrera

first: Andrew

last: Smith

first: Michael

middle: Q

last: Zhang

first: Roland

middle: D

last: Green

manufacture_protocol: Whole mouse genome tiling arrays and the design principle of this array has been described previously (Kim et al., 2005).


title: Agilent-014329 Prototype Human CpG Island ChIP-on-Chip Microarray 185K

status: Public on May 07 2007

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Prototype Human CpG Island Chip-on-Chip Set 244K

Arrays of this design have barcodes that begin with 16014329 or 2514329.

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

The ID column represents the Agilent Feature Extraction feature number.

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

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

distribution: commercial

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


title: CSHL Arabidopsis thaliana (ecotype Columbia) Chromosome 4 Genomic Tiling Array

status: Public on May 09 2007

city: Austin

first: Matthew

middle: Wayne

last: Vaughn

state: TX

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

institute: University of Texas at Austin

organism: Arabidopsis thaliana

description: The entire TIGR4 Arabidopsis thaliana ec. Col chromosome 4 assembly was used to design a genomic tiling microarray. This ~18.6 Mb sequence represented on the microarray starts downstream of the nucleolar organizing region (NOR) comprising the 5’ terminus of the chromosome. Notably, it contains several megabases of pericentromeric heterochromatin. In the microarray design, annotation was intentionally ignored, thus ensuring that repeated and unique sequences were equally represented. PCR primer pairs were selected using the Primer3 software. Probe selection was first accomplished by BLASTN analysis of sequential 100-bp windows of sequence along chromosome 4 against the whole genome to discriminate between unique and repeated DNA. Whenever a window gave at least one hit with 85% identity elsewhere in the genome, that window was marked as repeated, or unique otherwise. This information was then used to define "repeated" and "unique" segments of at least 300bp along the chromosome, as follows. Repeat segments were composed of successive repeat windows, possibly interrupted by series of contiguous unique windows spanning less than 300bp in each case. Conversely, unique segments were composed of successive unique windows, never interrupted by more than 300bp of contiguous repeat windows. Series of alternate unique and repeated windows were treated as repeat segments. Within each repeated or unique segment, PCR primer pairs were then selected using the Primer3 software and a routine that ensured maximum coverage of the segment and limited overlap between successive probes. Briefly, primer pairs were designed from both ends of the segment, considering sequential 1.2 kb windows, amplicon sizes ranging from 850 bp to 1.2 kb (optimum 1 kb) and primers (19-23 nt each, optimum 21 nt, 40-60% GC) with similar melting temperatures in the 57°C63°C range (optimum 60°C). Each new 1.2 kb window was positioned 50 bp within the end of the preceding amplicon. Successive amplicons could therefore overlap by up to 50 bp or be separated by up to 250 bp. When no primer pair was found in a given window, window size was increased to 1.4 kb, and if still unsuccessful, amplicons were finally designed using the forward and reverse primers of the upstream and downstream amplicons, respectively. When the last (central) window of a segment was less than 1.2kb but more than 300bp, primer pair selection was carried out by considering the actual size of that window plus 50bp on either side. Using this approach, 21,405 amplicons were designed with an average size of ~950bp. An additional 356 amplicons were designed that cover 36 genes of interest and neighboring sequences located on the other 4 chromosomes. Most amplicons were produced using BAC clones as templates, and all amplicons were verified by gel electropheresis.

first: Milos

last: Tanurdzic

first: Zachary

last: Lippman

first: Pablo

last: Rabinowicz

first: Neilay

last: Dedhia

first: W

middle: R

last: McCombie

first: Nicholas

last: Agier

first: Agnes

last: Bulski

first: Vincent

last: Colot

first: Robert

last: Martienssen

manufacture_protocol: PCR was performed in 100 ul volume using 100 pmole of each primer, and either BAC (20-40 pg) or genomic (100ng) DNA. Reactions were systematically analyzed by agarose gel electrophoresis. Approximately 5% of PCRs failed to give any product or gave multiple products or products of the wrong size. PCR products (2-8ug) were purified using Millipore Multiscreen FB Plates (MAFBN0B50), eluted in 60ul of 50% DMSO, and dispensed in 1536-well plates. Microarray slides (UltraGAPS, Corning) were printed using a MicroGrid arrayer (Genomic Solutions).


title: Chick Pineal 2006

status: Public on May 05 2007

city: College Station

first: Phillip

middle: D.

last: Beremand

department: Biology

institute: Texas A&M University

organism: Gallus gallus

manufacturer: Laboratory for Functional Genomics, Department of Biology, Texas A&M University, College Station, TX 77843

first: S

middle: P

last: Karaganis

first: M

middle: J

last: Bailey

first: P

first: R

middle: L

last: Hammer

first: T

last: Thomas

first: V

middle: M

last: Cassone

manufacture_protocol:
The cDNA microarrays were prepared based upon approximately 4,000 PCR products from each of the two chicken pineal cDNA libraries constructed, for a total of ~8,000 ESTs. Briefly, the cDNA in plasmids from each library were PCR amplified using flanking primers (SK and T7), purified by ethanol precipitation using ammonium acetate, and placed in the wells of 96 well plates at a concentration of 50 ug/ml in 3X SSC. A GeneMachines OmniGrid microarrayer equipped with 8 Telechem SMP3 pins was used to spot the samples onto poly-L-lysine coated slides (CEL Associates). Duplicate 100 micron diameter spots were placed at intervals of 190 microns (center to center). Slides were printed in batches of 50–100. Printing was accomplished at 21.1 C and 60% humidity. The OmniGrid’s operating software used information on the position of the individual clones within the 96-well sample plates and the order in which the plates were used to create a file describing the position of each cDNA clone on the array for later analysis.

Slides were stored desiccated at room temperature until their subsequent use. Prior to hybridization, the dried spots were hydrated gently over a steaming water bath, snap dried, and the DNA was UV cross-linked using a Stratalinker (Stratagene).

Keywords = chick pineal gland
Keywords = circadian oscillator


title: Mouse NIA 15K Custom Duplicate Spots

city: Tucson

first: Kevin

last: Greer

state: AZ

department: Biomedical Engineering

institute: University of Arizona

description: Custom array including the NIA Mouse 15K Cloneset plus addition unidentified clones printed in duplicate

first: Heddwen

last: Brooks

manufacture_protocol: The mouse NIA 15K cDNA library was amplified using M13 primers, resuspended in 50% DMSO, and printed in duplicate on in-house aminosilane microscope slides.


title: CAG Human 20k array v1.0 with Alien Controls

first: Virginie

last: Aris

first: Patricia

last: Soteropoulos

first: Tongsheng

last: Wang

first: Saleena

last: Ghanny

manufacture_protocol: Compugen Human OligoLibraryTM, 2001. 60-mer oligonucleotides in a 3x SSC solution are printed on Poly-L-Lysine coated glass slides with 48 TeleChem SMP3 pins on a GeneMachines OmniGrid 100 Microarrayer. Slides are post processed by rehydrating, snap drying, UV crosslinking (600x100 microjoules of energy), and blocking with Succinic Anhydride.


title: PIQOR (TM) Stem Cell, human AS (688)

city: Cologne

first: Sebastian

last: Knoebel

address: Nattermannallee 1

institute: MiltenyiBiotec GmbH

description:
The PIQOR Immunology Microarray is composed of 942 human specific cDNAs. These cDNAs include for each array six house-keeping genes as positive controls. In addition four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer, respectively. All features are spotted in quadruplicate.
The Platform data table reflects a condensed representation of the quadruplicate features.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

manufacture_protocol: Defined 200-400 bp fragments of selected cDNAs were generated by RT-PCR, cloned and sequence-verified. Amplified and purified cDNA inserts were spotted in quadruplicate on PIQOR slides using a proprietary piezoelectric spotter. The PIQOR slides were coated in a 2 step process generating a surface which covalently binds DNA molecules.


title: S. mutans UA159 v2

city: Jerusalem

first: Moshe

last: Shemesh

address: Hebrew University-Hadassah POB 12272

department: Institute of Dental Sciences

country: Israel

institute: Hebrew University-Hadassah

organism: Streptococcus mutans

description:
Grids: 96  Array Type : ss_oligo (70-mer) Surface Coating: Epoxy
Printing Buffer(s): Schott Nexterion
Arraying Machine(s): Lucidea
Controls: 500 A. thaliana (70-mers)

manufacture_protocol: 2QSM, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 6075497, pen id 10185, pen cycles -1, operator cs, humidity control On, humidity set point65


title: JCL_Ecoli_2

city: Logan

first: Daniel

last: Hyduke

state: UT

address: 4105 Old Main Hill ENGR 402S

department: Biological Engineering

institute: Utah State University

organism: Escherichia coli

manufacturer: James C. Liao's Metabolic Engineering Laboratory, UCLA

first: Laura

last: Jarboe

first: James

middle: C

last: Liao

manufacture_protocol: Oligonucleotides from Operon AROS E. coli set, were printed on Corning UltraGAPS slides.


title: INDAC_CAM_FL002

status: Public on May 04 2007

city: Cambridge

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

organism: Drosophila melanogaster

description: Full Moon BioSystems PowerMatrix.  3-D matrix polymer coated porous glass   surface.

first: Richard

middle: E

last: Auburn

first: Bettina

last: Fischer

first: David

last: Kreil

first: Lisa

last: Meadows

first: Gos

last: Micklem

first: Roslin

first: Steven

manufacture_protocol: microarrays were printed using the Genetix Qarray2 contact-printing instrument and 48 Genetix aQu75 split-pins on FMB PowerMatrix slides. Probe DNA was dissolved in 150 mM NaPO4. See http://www.flychip.org.uk/ for full details


title: UPMC_PACCM_MOUSE_20K_14

status: Public on May 08 2007

city: Philadelphia

first: Tamas

last: Dolinay

state: PA

address: 220 S. 33rd St., Towne building, Room 390

department: Bioengineering

institute: University of Pennsylvania

first: Naftali

last: Kaminski

first: Wei

last: Wu

first: Augustine

last: Choi

manufacture_protocol:
CodeLink UniSet Mouse Bioarrays
CodeLink UniSet Mouse Bioarrays deliver superior results through:
quality probe design and selection that includes functional validation for accurate and reproducible biological results
manufacturing process control checkpoints to ensure probe and deposition quality for reproducible experimental results
unique three-dimensional aqueous gel matrix for higher assay sensitivity and specificity
optimized reagents, protocols, processing tools, and software for ease of use and reliable performance
CodeLink UniSet Mouse Bioarrays provide reliable results for comprehensive mouse gene expression profiling.
Specificity: 90% probe to target sequence identity for better discrimination of highly homologous genes
Sensitivity: < 1 transcript per cell for better detection of rare messages
Dynamic range: signal response > 3 orders of magnitude; linear signal response > 2.5 orders of magnitude for more usable data
Signal reproducibility (total CV): typically < 16% CV for reproducible results in every experiment
Minimum detectable fold change: > 98% within two-fold change for same-same target hybridization which means reduced noise for better detection of small changes in gene expression and more usable data per bioarray
High-quality, high-density bioarray for expression profiling
CodeLink UniSet Mouse Bioarrays are powerful tools for gene expression using the widely adopted mouse model system. Each CodeLink UniSet Mouse Bioarray covers a wide range of the most well-annotated mouse genes published in public databases. These transcripts are useful for performing differential expression studies of many important biological processes in a single experiment. For instance, CodeLink UniSet Mouse Bioarrays can be used to study unique gene expression profiles at different stages of oncogenesis. These studies help to characterize and understand tumor types and tumor progression for use in drug target identification and personalized medicine. In addition, this bioarray enables the investigation of cell and tissue reactions to their environment from stimulus reception to signal transduction processing and response. This bioarray comprehensively covers cell differentiation, development, apoptosis, and metabolism for drugs and other cellular biomolecules.
Expression profiling information from this bioarray can also provide accurate and reproducible transcriptional expression data that can be used to better understand developmental and morphological differences in cells and tissues. Expression profiling of the genes involved in these types of biological processes can be directly applied to target identification, pathway characterization, and drug effect prediction in basic research and drug development.
CodeLink UniSet Mouse 20K I Bioarray
CodeLink UniSet Mouse 20K I Bioarray targets ~20 000 unique, well-annotated mouse genes. This high-density bioarray is part of the CodeLink System solution for higher quality, reproducible gene expression profiling.
CodeLink UniSet Mouse 20K I gene classification
Major biological process Number of genes present
Oncogenesis ~500
Cell cycle ~500
Cell-cell signaling ~250
Signal transduction ~750
Metabolism ~400
Developmental process ~250
Transcription and translation ~400
Immune and inflammation response ~300
Protein phosphorylation ~250
Apoptosis ~100
RNA processing ~100
Ion transport ~700
Table. The biological processes listed are approximate and conservative estimates of the minimum number of genes covered in each CodeLink UniSet Mouse 20K I Biorarray for study. The above classification is based on the “BIOLOGICAL PROCESS” organizing principle from Gene Ontology™ Consortium.
Specifications
CodeLink UniSet Mouse 20K I Bioarray content is based on the public NCBI, UniGene, and RefSeq databases. Well-annotated mRNA or coding sequences were chosen to ensure usefulness for a large range of applications in basic research, biotechnology, and drug development. Each sequence was carefully screened to ensure high-quality, specific probe design, and to reduce redundancy of gene targets. Every probe was functionally validated against multiple tissues to ensure best representation of the gene so that the results will be biologically relevant. Every bioarray is also functionally validated during production to further ensure quality performance.
Number of arrays in set: 1
Number of probes: 20 209
Total number of transcripts targeted: 19 932
Number of discovery genes: 19 801
Positive controls: 108
Negative controls: 300
Housekeeping genes: 100
Fiducials: 8
Number of probes per gene: one specific and functionally validated probe
Oligonucleotide probe length: 30-mer
RNA sample input: 0.2-2.0 µg total RNA
Type of assay: one-color
Storage and handling temperature: room temperature


title: NSF_Pinus_taeda_49K

city: Rockville

first: Jia

last: Liu

address: 9712 Medical Center Drive

institute: Plant Genomics

organism: Pinus taeda

description: The below table is based on the GAL file. This platform may not be suitable for submission of data in which replicate features have been averaged during normalization. In such cases users should submit their own platform representing merged features.

first: John

last: Cairney

first: Robin

last: Buell

manufacture_protocol:
The elements on the microarray were selected from the pine embryo-derived cDNA libraries sequenced at TIGR in collaboration with Dr. John Cairney as part of the NSF Genomics of Loblolly Pine Embryogenesis Project. Details on the sequencing and the origins of the cDNA libraries of these clones can be found at: http://www.tigr.org/tdb/e2k1/pine/pine_status.shtml.
A total of 16,992 cDNAs were selected for the microarray. The pine cDNA clones were rearrayed, resequenced, and the inserts were amplified using universal primers that flank the insertion site. All PCR products were run on agarose gels to check for amplification of single bands. Only 12,536 clones could be verified by both resequencing and agarose gel inspection. However, all 16,992 cDNAs were spotted in duplicate on the slides.
Methods used successfully at TIGR with pine microarrays can be found at http://www.tigr.org/tdb/e2k1/pine/pine_protocols.shtml.


title: TIGR PFGRC Listeria version 1

status: Public on May 17 2007

city: Normal

first: Arunachalam Muthaiyan

email: amuthai@gmail.com, bjwilkin@ilstu.edu

address: Julian Hall

department: Biological Sciences

institute: Illinois State University

organism: Listeria monocytogenes

description:
This set includes 6228 oligonucleotides, has 13872 spots distributed in 48 blocks.

This is condensed template of replicated features of PFGRC/TIGR Listeria monocytogenes version 1 array. For full template information please refer: http://pfgrc.tigr.org/descriptionPages.shtml
http://pfgrc.tigr.org/slide_html/annotation_index/L_Monocytogenes_index.shtml

manufacture_protocol: QLM, with arrayer LUCIDEA, mode Normal, replicates 2, repeats 1, slide_dips 38, machine cycles 3617783, pen id 10175, pen cycles -1, operator MICROARRAY, humidity control On, humidity set point65


title: OMRF zebrafish 15K

status: Public on May 02 2007

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

organism: Danio rerio

description: gamma amino propyl silane (Corning UltraGAPS slides)

first: Mark

middle: B

last: Cadwell

manufacture_protocol: MWG 50-mer oligonucleotide library resuspended in 3XSSC; printed on Cornings UltraGAPS slides with GeneMachines OmniGrid 100 arrayer, 32 pin configuration.


title: MPIMG Homo sapiens 36k_arrayCGH8

status: Public on May 22 2007

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

manufacture_protocol: The submegabase resolution whole genome tiling path BAC array consists of the human 32k BAC Re-Array Set* (BACPAC Resources Center, DNA kindly provided by Nigel Carter, Wellcome Trust Sanger Centre) and a set if subtelomeric clones (assembled by members of the COSTB19 Action: Molecular cytogenetics of solid tumours). Protocols for the isolation of DNA (1 Mb Sanger set and subtelomeric set) and the amplification of insert DNA by linker adapter PCR are described in detail at the Molecular Cytogenetics website of MPG. Amplicons were ethanol precipitated, dissolved in 3XSSC/1,5M betaine and spotted on epoxy-coated slides (NUNC, Wiesbaden, FRG) by means of a modified Qarray (originally from Genetix, new Milton, U.K.) and Pointech (Gibbon,MN) Tungston PTL 2500 slit pins. Each BAC is represented by a single spot on the array. * due to recurrent abnormal ratios in a series of control hybridisation encompassing 30 tumors, clones from plate HGP DNA RP C 12_2 were excluded from further analysis.


title: MPIIB_Mtb_V2

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

organism: Mycobacterium tuberculosis

manufacture_protocol: Microarray capture probes were obtained as a collection of  “Array-Ready” 70mer DNA oligonucleotides at 600 pmol each comprising 4,325 M. tuberculosis-specific sequences and 25 controls (Operon Biotechnologies). The major portion of M. tuberculosis-specific oligonucleotides was designed from 3,924 predicted protein coding sequences of M. tuberculosis H37Rv (Sanger Center). A smaller portion was designed from the strain CDC-1551, sequenced and predicted by The Institute for Genomic Research (TIGR). At least 371 predicted genes from CDC-1551 were found to have less than 97% homology to M. tuberculosis H37Rv predicted genes, and therefore these sequences were included in the M. tuberculosis probe set. The oligonucleotides were suspended at a final concentration of 100 µM in Nexterion spot2 buffer (Schott) and printed by a BioRobotics MicroGrid II robot (Genomic Solutions) onto glass slides coated with poly-L-lysine at 50–55% humidity and room temperature using MicroSpot 2500 quill pins (Genomic Solutions). Oligonucleotides were cross-linked to the support by UV irradiation with a total energy of 240 mJ UV and blocked with succinic anhydride and 1-methyl-2-pyrrolidone in borate buffer (Fluka).


title: Nimblegen Homo sapiens promoter array hg17

city: Copenhagen

first: Jesper

middle: T

last: Troelsen

address: Blegdamsvej 3b

country: Denmark

institute: Univ. of Copenhagen

organism: Homo sapiens

manufacture_protocol: see the Nimblegen Promoter Tiling Arrays web page


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 35 of 37

first: Bing

last: Ren

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 35.

first: Zirong

last: Li

first: Leah

last: Barrera

first: Andrew

last: Smith

first: Michael

last: Zhang

first: Roland

last: Green

manufacture_protocol: Whole mouse genome tiling arrays and the design principle of this array has been described previously (Kim et al., 2005).


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 33 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 33.


title: Lieb Lab at UNC-CH_Yeast Whole-genome and Chr III Tiling Array (PCR-based)

city: Chapel Hill

first: Jason

last: Lieb

state: NC

address: 203 Fordham Hall

department: Department of Biology

institute: University of North Carolina at Chapel Hill

organism: Saccharomyces cerevisiae

description: Microarrays consisted of two types of probes. The first type represents the whole genome based on annotated functional boundaries. These PCR-amplified products represent ORFs, intergenic regions, and other non-coding regions (rDNA, tRNA, transposons, transposon long terminal repeats, telomeres, centromeres, and introns). Generally, each ORF was represented from start codon to stop codon. The intergenic regions consisted of the DNA between annotated ORFs divided such that PCR products were not longer than 1.5 kb, with a few exceptions. The non-coding regions conform to boundaries as annotated by the Saccharomyces Genome Database (SGD) as of the year 2000. Mitochondrial segments did not necessarily conform to annotated functional boundaries. The second type of probes are higher resolution PCR-amplified products that span almost all of chromosome III at 200 base pair resolution with additional overlapping products covering on third of the chromosome at 100 base pair resolution (coordinates the 10,000 to 83,000). This platform covers several print runs, in which print plates were arranged in different orders.

first: Gregory

last: Hogan

manufacture_protocol: see Iyer et al. 2001, Nature 409: 533-538


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 30 of 37

institute: Ludwig Institute for Cancer Research

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 30.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 36 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 36.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 32 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 32.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 34 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 34.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 31 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 31.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 25 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 25.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 28 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 28.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 29 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 29.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 27 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 27.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 24 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 24.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 26 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 26.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 22 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 22.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 23 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 23.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 20 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 20.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 15 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 15.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 21 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 21.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 11 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 11.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 12 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 12.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 09 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 09.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 19 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 19.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 18 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 18.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 17 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 17.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 14 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 14.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 04 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 04.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 05 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 05.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 13 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 13.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 03 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 03.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 16 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 16.


title: Nimblegen 1.5M Mouse Condensed Tiling array of mm5 at 100bp resolution v1.0 set 2 of 4

status: Public on Mar 18 2007

description: The 4 condensed scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 1,495,582 50-mer oligonucleotides. The tiled probes are within the regions bound by Pol2 in brain, heart, kidney, liver or mES from the genomewide scan. There are a total of 4 arrays. This is set 2.

manufacture_protocol: Condensed mouse genome tiling arrays and the design principle of this array has been described previously (Kim et al., 2005).


title: Nimblegen 1.5M Mouse Condensed Tiling array of mm5 at 100bp resolution v1.0 set 4 of 4

description: The 4 condensed scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 1,495,582 50-mer oligonucleotides. The tiled probes are within the regions bound by Pol2 in brain, heart, kidney, liver or mES from the genomewide scan. There are a total of 4 arrays. This is set 4.


title: NimbleGen Lactobacillus helveticus CNRZ32 169/tiling

status: Public on Feb 10 2007

city: Madison

first: James

last: Steele

email: jlsteele@wisc.edu, vvsmeianov@wisc.edu

state: WI

address: 1605 Linden Dr.

department: Food Science

institute: UW-Madison

organism: Lactobacillus helveticus CNRZ32

first: Vladimir

middle: V

last: Smeianov

first: Patrick

last: Wetcher

first: Jeffery

last: Broadbent

first: Joanne

last: Hughes

first: Beatriz

last: Rodriguez

first: Tove

middle: K

last: Christensen

first: Ylva

last: Ardo

manufacture_protocol: High-density microarrays based on Maskless Array Synthesizer technology.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 10 of 37

city: La Jolla

organism: Mus musculus

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 10.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 07 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 07.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 08 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 08.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 01 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 01.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 06 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 06.


title: Nimblegen 1.5M Mouse Condensed Tiling array of mm5 at 100bp resolution v1.0 set 1 of 4

description: The 4 condensed scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 1,495,582 50-mer oligonucleotides. The tiled probes are within the regions bound by Pol2 in brain, heart, kidney, liver or mES from the genomewide scan. There are a total of 4 arrays. This is set 1.


title: Nimblegen 1.5M Mouse Condensed Tiling array of mm5 at 100bp resolution v1.0 set 3 of 4

description: The 4 condensed scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 1,495,582 50-mer oligonucleotides. The tiled probes are within the regions bound by Pol2 in brain, heart, kidney, liver or mES from the genomewide scan. There are a total of 4 arrays. This is set 3.


title: Nimblegen 14.4M Mouse Tiling array of mm5 at 100bp resolution v1.0 set 02 of 37

description: The 37 genome scan arrays were based on NCBI33 build of the mouse genome (mm5) and contained a total of 14,375,432 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 37 arrays. This is set 02.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 34 of 38

status: Public on Jan 01 2007

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 34.

first: Tae

middle: H

last: Kim

first: Ziyedulla

last: Abdullayev

first: Keith

last: Ching

first: Dmitri

last: Loukinov

first: Victor

last: Lobanenkov

manufacture_protocol: Whole human genome tiling arrays and the design principle of this array has been described previously (Kim et al., 2005b).


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 35 of 38

first: Bing

last: Ren

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 35.

middle: A

first: Andrew

last: Smith

first: Michael

last: Zhang


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 33 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 33.

first: Roland

last: Green

middle: Q


title: Nimblegen Condensed array of hg17 v1.0

description: A condensed array was used to verify the results from the whole genome scan arrays.  It contained a total of 742,156 oligonucleotides to represent the 15,221 putative CTCF binding sequences plus 44 ENCODE regions, each ranging in size from 500 Kbp to 1.9 Mbp at 100 bp resolution.  Each of the 15,221 binding sites were extended at both ends by 2.5 Kbp upstream and downstream of the site.

middle: D


title: SWEGENE_BAC_32K_Full

status: Public on Jan 11 2007

city: Lund

first: Johan

last: Staaf

address: Medicon Village

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

description: The 32k BAC Re-Array set Ver. 1.0 (32,433 BAC clones) was obtained from the BACPAC Resource Center at Children's Hospital Oakland Research Institute, Oakland (CA, US). The average resolution of the whole genome tiling clone set is 46kb. Clones were mapped to human genome build 17 (UCSC Human Genome Browser)

first: Ake

last: Borg

manufacture_protocol: Arrays were produced using amplified genomic DNA from BAC clones. Amplification was performed using degenerate oligonucleotide primed PCR and products were purified by size-exclusion filtration and verified by agarose gel electrophoresis. After purification, products were dried down, recovered in 50% DMSO to a concentration of 500-1000ng/µl, and printed on amino-silane-coated glass slides (UltraGAPS from Corning) using a MicroGrid2 robot (BioRobotics) equipped with MicroSpot2500 pins (BioRobotics).


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 25 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 25.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 32 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 32.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 38 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 38.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 37 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 37.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 26 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 26.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 20 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 20.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 36 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 36.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 19 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 19.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 29 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 29.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 30 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 30.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 28 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 28.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 23 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 23.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 31 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 31.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 27 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 27.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 15 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 15.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 16 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 16.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 13 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 13.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 12 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 12.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 22 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 22.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 21 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 21.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 17 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 17.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 18 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 18.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 24 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 24.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 06 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 06.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 10 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 10.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 14 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 14.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 07 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 07.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 04 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 04.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 11 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 11.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 01 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 01.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 09 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 09.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 08 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 08.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 03 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 03.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 02 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 02.


title: Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 05 of 38

description: The 38 genome scan arrays were based on NCBI35 build of the human genome (hg17) and contained a total of 14,628,366 50-mer oligonucleotides, positioned at every 100 basepairs (bp) throughout the human genome as described in the oligonucleotide array description files. There are a total of 38 arrays. This is set 05.