title: Meyerowitz Lab Arabidopsis Operon Array Version 1

status: Public on May 02 2004

city: Pasadena

first: Frank

last: Wellmer

state: CA

address: 1200 E. California Blvd.

department: Biology 156-29

country: USA

institute: California Institute of Technology

organism: Arabidopsis thaliana

technology: spotted oligonucleotide

description: This oligonucleotide array is based on the Arabidopsis Genome Oligo Set Version 1.0 (Operon). This set consists of 26,090 oligonucleotides that correspond to 23,542 annotated genes in Release 4.0 of The Institute for Genomic Research Arabidopsis thaliana Genome Annotation Database. In addition, several elements of a flower-specific cDNA array were printed (this array is deposited at GEO under the name 'Meyerowitz lab flower-specific cDNA array'; accession number GPL1069). The ID of these elements starts with GP.

distribution: non-commercial

first: Jose Luis

last: Riechmann

first: Marcio

last: Alves-Ferreira

first: Elliot

middle: M

last: Meyerowitz


title: Meyerowitz Lab Arabidopsis Flower-specific cDNA Array

technology: spotted DNA/cDNA

description:
Elements for the flower-specific cDNA microarray were obtained from three different sources. First, for those genes that are known or suspected to be involved in flower development, we either amplified fragments of their transcribed regions from cDNA or, if available, obtained cDNA clones from EST clone collections. Second, we generated cDNA libraries using RNA extracted from different floral tissues. For all libraries, the RNA preparations were subtracted with leaf RNA to reduce the abundance of clones representing ubiquitously expressed genes and thus, to enrich for flower-specific transcripts. The identity of most of the library clones was not determined prior to their use for preparing the array. Lastly, we added a set of 2632 non-redundant clones from a non-subtracted flower-derived library.
The array is comprised of 10,816 elements representing approximately 5000-6000 genes.
Keywords = Flower
Keywords = cDNA array


title: pan-Neisseria microarray

status: Public on Jul 11 2005

city: Oklahoma City

first: Thomas

middle: Francis

last: Ducey

state: OK

address: 975 NE 10th Street, BRC 366

department: Microbiology and Immunology

institute: University of Oklahoma Health Sciences Center

organism: Neisseria gonorrhoeae

description: pan-Neisseria microarray.  cDNA array containing single cDNA elements that are common between Ng FA1090, Nm Z2491 and Nm MC58.  Also contains cDNA elements unique to each strain.

first: John

middle: K

last: Davies

first: Lori

middle: A

last: Snyder

first: Charlene

last: Kahler

first: Elizabeth

last: Stohl

first: Ishara

middle: C

last: Gunesekere

first: Michael

last: Apicella

first: Joseph

middle: P

last: Dillard

middle: F

first: David

middle: W

last: Dyer

last: Entz

first: Jason

last: Foster

last: Powell

first: Hank

middle: S

last: Seifert

first: William

last: Shafer

first: Daniel

last: Williams

first: Nigel

middle: J

last: Saunders


title: Lactococcus lactis IL1403 (v1)

status: Public on Jul 25 2005

city: Haren

first: Sacha

last: van Hijum

address: Kerklaan 30

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

organism: Lactococcus lactis subsp. lactis Il1403

description: Aldehyde slides

first: S

manufacture_protocol: Amplicons were designed using GenomePrimer in combination with UniFrag, amplified by Eurogentec (Belgium), purified using Qiagen 96-wells purifying plates. Amplicons (about 10 microL) diluted 2x with ArrayIT 2x spotting buffer, in Genetix 384 wells spot plates, spotted on aldehyde slides (ArrayIt) with a GenPak spotter at about 55 % humidity. Blocking of reactive aldehyde groups by boric anhydride treatment.


title: Galbraith Laboratory Operon Long Oligonucleotide Microarray version 3.0 (ATv301.01.Z)

status: Public on Jan 09 2005

city: Tucson

middle: William

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 ATv301.01.001-ATv301.01.308 (http://www.ag.arizona.edu/microarray).


title: JAKE

status: Public on Jul 01 2005

city: San Francisco

first: Ekaterini

last: Blaveri

address: 2340 Sutter street

department: Laboratory Medicine

institute: UCSF Comprehensive Cancer Center

organism: Homo sapiens

description: cDNA arrays


title: Yale 9.2K arabidopsis array

status: Public on Jun 15 2005

city: Brookings

first: Anne

middle: Y

last: Fennell

state: SD

address: 201 N. Campus Dr

department: Plant Science

institute: South Dakota State University

organism: Vitis riparia

distribution: commercial

manufacturer: W.M Keck Foundation Biotechnology Resource Lab, Yale university

last: Horvath


title: Hopkins Tag Array

status: Public on Nov 05 2004

city: Baltimore

first: Xuewen

last: Pan

state: MD

address: 733 N. Broadway, Room 331

department: Department of Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

organism: Saccharomyces cerevisiae

description:
Comprehensive array of all 6018 UpTag/DnTag pairs designed for incorporation into yeast deletion strains by the Yeast Deletion Project (June 2002).
Custom-designed negative and positive controls comprise almost half of the 215x105 array.
Keywords = yeast, deletion, knockout, tag, barcode, synthetic, control, oligonucleotide

last: Yuan

first: Jef

middle: D

last: Boeke


title: Affymetrix GeneChip Human Mapping 50K Xba - prerelease

status: Public on Jul 02 2005

city: Boston

middle: R.

last: Sellers

state: MA

address: 44 Binney Street

department: Medical Oncology

institute: Dana-Farber Cancer Institute

technology: in situ oligonucleotide


title: yeast_nucleosome_positioning_microarray

status: Public on Jul 14 2005

city: Worcester

first: Oliver

last: Rando

address: 364 Plantation St.

institute: UMass Medical School

description:
The sequence from S. cerevisiae chromosome III was fragmented into 50-mers overlapping every 20 base pairs. Potentially cross-hybridizing probes were filtered by BLASTing these sequences against the entire genome and eliminating sequences from chromosome III that included 5 or more contiguous probes with perfect BLAST matches, leaving 30 contigs covering 278,960 base pairs. Oligonucleotides were also tiled over one kilobase of 223 promoters on other chromosomes, starting at -900 from the start codon and extending to +100.
Keywords = nucleosome
Keywords = yeast
Keywords = tiling microarray


title: Mouse CDNA P11

status: Public on Jul 22 2005

city: Dallas

first: Wendy

state: TX

address: 5323 HarryHines Blvd

institute: UT Southwestern

organism: Mus musculus

description: mouse heart CDNA array

manufacture_protocol: spotted CDNA Array


title: M. tuberculosis oligo

city: New York

last: Glickman

state: NY

institute: Sloan Kettering Institute for Cancer Research

organism: Mycobacterium tuberculosis

description:
This M. tuberculosis whole genome microarray was constructed from the Operon Tuberculosis whole genome oligo set, version 1.0 (http://www.operon.com/arrays/oligosets_tb.php).
The complete array was spotted in duplicate on each slide using a Biorobotics Microgrid II with oligonucleotides resuspended at 20 micromolar in 50%DMSO on Corning UltraGaps Coated slides. Arrays were crosslinked immediately after printing in a Stratalinker with 300mJ.

first: Hideki

last: Makinoshima


title: Codelink Uniset 1

status: Public on Jul 06 2005

city: Galveston

first: Aaron

middle: M.

last: Domina

address: 301 University Blvd

department: HBCG

institute: University of Texas Medical Branch

distribution: custom-commercial

first: Stanley

last: Watowich


title: 24K AgR Bovine Array

status: Public on Feb 08 2005

city: Dunedin

first: Theresa

last: Wilson

address: 710 Cumberland Street

country: New Zealand

institute: AgResearch

organism: Bos taurus

description: This array contains spotted PCR products from our bovine EST collection. Included are housekeeping genes, water blanks (negative PCR) and no DNA blanks (to estimate carryover).

first: Adrian

last: Molenaar

first: Alan

last: McCulloch

first: Murray

last: Grigor

first: Steve

last: Davis

first: M

last: Glenn

first: I

last: Havukkala

first: J

last: Watson

first: Allan

last: Crawford

first: Tom

last: Wheeler

first: Lora

last: Hagemann

first: Rita

last: Lee

first: Wayne

last: Hein

first: Peter

last: Johnstone

first: Nauman

last: Maqbool

first: Chris

last: McMahon

first: Judy

last: McCracken

first: Kerst

last: Stelwagen

first: V

last: Farr

first: Kuljeet

last: Singh

first: Jane

last: Whitley

first: Kevin

last: Nicholas

first: Keith

last: Savin

first: A

last: Mather

first: Helen

last: McPartlan

first: Michelle

last: Wells

first: P

last: Bowman

first: Mike

last: Goddard

last: Langford

first: John

last: McEwan

first: Paul

last: Atkinson


title: CRUKDMF_22Kminus6K_v1.1.0

status: Public on Jul 07 2005

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

description: cDNA

manufacturer: CANCER RESEARCH UK DNA Microarray Facility

manufacture_protocol: as described in Institute Labs manual


title: CRUKDMF_15K_v1.1.0

description: cDNA


title: Incyte Mouse Unigem 1.37

status: Public on Jul 16 2005

city: Rockville

first: Alexandra

middle: Geraldine

last: Dace

address: 9600 Gudelsky Drive

department: University of Maryland Biotechnology Institute

institute: University of Maryland

description: Array contains 9641 spots in total: 9300 cDNAs + 341 control spots (ratio controls, complex target control, RNA quality control, sensitivity control, or buffer only).

first: Shoshana

last: Segal

first: Cathryn

last: Stevens

first: Nilton

last: Medina

first: James

middle: B

last: Ames

first: David

last: York

middle: G


title: Drosophila Incyte arrays, Klebes/Kornberg v1

status: Public on Jul 08 2005

city: Berlin

first: Ansgar

last: Klebes

address: Chausseestr. 117

department: Biology

country: Germany

institute: Humboldt University Berlin

organism: Drosophila melanogaster

description:
The array was assembled using amplicons representing approximately 93% of the genes predicted in version 1.0 of the Drosophila genome from sequences released by the Berkeley Drosophila Genome Project and Celera Genomics in March 2000. The amplicons represent approximately 75% of the genes predicted in the January 2003 release 3.1 Drosophila genome annotation update.
Incyte in-house algorithms were used to develop gene-specific primers averaging 20 nucleotides in length that were used to PCR amplify one exon or exon fragment from every predicted gene in the fly genome. The regions amplified to build the array ranged in size from 150 to 600 bp with an average size of 410 bp.

Additionally, non-Drosophila sequences (Adenovirus, GFP) were spotted for spiking controls, background control, and orientation purposes.

Hybridized slides were read with a GenePix 4000A scanner (Axon Instruments, Foster City, CA).

first: Thomas

last: Kornberg

manufacture_protocol:
The arrays were produced essentially as Brian Oliver's 'Incyte Drosophila LifeArray v1.0', GEO platform GPL20.

These arrays were described in Xu et al., Human Molecular Genetics, 2003, Vol. 12, No. 2 169-175; and Klebes et al., Development, 2005, in press.

In brief: The Easy-to-Spot Drosophila ORF PCR Primer Set (Incyte Genomics Inc.) with 14 151 primer pairs to unique open reading frames and additional control sequences was used for PCR amplification. The amplicons represent non-intronic sequences. All PCR products were analyzed on agarose gels and a success rate of >94% was estimated. Reactions were arrayed into 384-well plates and printed on poly-L-lysine-coated glass slides using a linear servo arrayer and ArrayMaker version 2 control software.


title: Codelink Uniset 2

first: Aaron

last: Domina

middle: M

first: Stanley

last: Watowich


title: microRNA microarray MAS7

status: Public on Jul 04 2005

city: Cambridge

first: Eric

middle: A.

last: Miska

address: Tennis Court Rd

department: Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry We

institute: University of Cambridge

description:
A oligonucelotide base microarray platform for expression profiling of vertebrate microarrays
Keywords = miRNA
Keywords = microRNA

first: Ezequiel

last: Alvarez-Saavedra

first: H

middle: R

last: Horvitz


title: NimbleGen/GeneFrontier Medaka array 2.0

status: Public on May 20 2005

city: Chuo

last: GeneFrontier Corporation

state: Tokyo

address: 3-2-10, Nihonbashi-Kayabacho

country: Japan

institute: GeneFrontier Corporation

organism: Oryzias latipes

description:
Target sequences come from TIGR Medaka Gene Index Release 5.0 (May 17, 2004).
Number of targets: 26,689
Number of probes per target: 7
Length of probes: 60mer
Keywords = medaka
Keywords = Oryzia latipes
Keywords = high density
Keywords = custom array

first: Mikihiko

last: Nimura

manufacture_protocol: see manufacturer's web site


title: Incyte Human UniGEMV Ver2.0

city: Kyoto

first: Motoko

last: Naitoh

state: Kyoto

address: Shyogoin-Kawahara cho 53

department: Molecular and Cellular Biology

institute: Institute for Frontier Medical Science, Kyoto University

first: Naitoh

last: Motoko

first: Kubota

last: Hiroshi

first: Nagata

last: Kazuhiro

manufacture_protocol: 9,128 human cDNA and EST clones are spotted on the glass plates. These clones are derived from Incyte's GEM Library which contains cDNA colnes representing unique human genes identified in NCBI's UniGene database.


title: SRC mouse 16K

city: St Lucia

first: Sean

last: Grimmond

state: QLD

address: IMB, Uni of Qld

country: Australia

institute: Institute of Molecular Bioscience

manufacturer: ARC SRC for functional and Applied Genomics

manufacture_protocol: ESI Chip writer pro array spotting protocol.


title: Affymetrix GeneChip Human Mapping 50K Hind - prerelease

first: William

last: Sellers


title: Yale 12K Arabidopsis array

first: Anne

last: Fennell

last: Horvath


title: UIUC Porcine muscle plus

status: Public on Nov 15 2003

city: Urbana

first: Yewon

last: Cheon

state: IL

institute: University of Illinois at Urbana Champaign

organism: Sus scrofa

description: cDNA microarray from porcine muscle cDNA library

first: Mark

last: Band

first: Jonathan

middle: E

last: Beever

first: Manabu

middle: T

last: Nakamura


title: MAS7.5

status: Public on Jul 05 2005

last: Miska

description:
A oligonucleotide based microRNA microarray.
Keywords = microRNA
Keywords = miRNA
Keywords = Danio rerio
Keywords = development

middle: A