title: E.coliOKchip.ver1.0

status: Public on Dec 25 2006

city: Ikoma

first: Naotake

last: Ogasawara

state: Nara

country: Japan

organism: Escherichia coli

technology: spotted oligonucleotide

distribution: non-commercial

manufacturer: Laboratory of Functional Genomics, Nara Institute of Science and Technology

manufacture_protocol: E.coli Oligo Library (Sigma-Genosys. The Woodland, Texas) was printed by Lucidea microarray spotter (Amersham Biosciences) on Corning UltraGAPS slides (Corning) and treated 1/2 diluted DNA cross linking reagent (Amersham Biosciences).


title: University Health Services (Toronto) Yeast ORF, Version 6.4k

status: Public on Dec 13 2006

city: Boston

first: Michael

middle: J

last: Moore

state: MA

address: 200 Longwood Ave

department: Systems Biology

country: USA

institute: Harvard Medical School

organism: Saccharomyces cerevisiae

technology: spotted DNA/cDNA

distribution: commercial

middle: C

last: Yu

first: Pamela

middle: A

last: Silver

manufacture_protocol: Full length cDNAs from roughly 6000  S. cerevisiae ORFs are printed in duplicate on each array, along with controls.


title: SIBS rice microRNA microarray v2.0

status: Public on Dec 31 2006

city: Shanghai

first: Youxin

last: Jin

address: 320 Yueyang Road

country: China

institute: Institute of Biochemistry and Cell Biology,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

organism: Oryza sativa

description: epoxide coated slide made in our lab

first: Botao

last: Zhao

first: Ruqiang

last: Liang

first: Kangcheng

last: Ruan

manufacture_protocol: Antisense probes of microRNAs and small RNAs were spotted at 20 uM on epoxide slides. Labeled PCR products from small RNA libraries were hybridized for 16h at 48°C in 4XSSC,0.1% SDS.


title: SHAT

status: Public on Jul 23 2005

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism: Homo sapiens

manufacturer: Stanford Functional Genomics Facility,  Stanford School of Medicine

manufacture_protocol: Material is transferred from microtiter plate wells to the slide surface by an automated print head


title: Human KUGI14K

status: Public on Apr 06 2004

city: Seoul

first: Inchul

last: Lee

address: 388-1 Poongnap-Dong, Songpa-Gu

department: Pathology

country: South Korea

institute: University of Ulsan College of Medicine

description: 14K Human cDNA chip


title: Galbraith Laboratory Operon Long Oligonucleotide Microarray Version 1.0 (AtOligo 2.9.2.Y)

city: Tucson

first: David

middle: William

last: Galbraith

state: AZ

address: 303 Forbes Building

department: Plant Sciences and Bio5 Institute

institute: University of Arizona

organism: Arabidopsis thaliana

description: This oligonucleotide array is produced from the Operon Version 1.0 Array-Ready Oligo set (AROS). The Arabidopsis V1.0 AROS is designed from UniGene Build At. #4 (www.operon.com). This set comprises 26,000 oligonucleotides. Additional elements are printed as controls.  This platform represents slides AtOligo 2.9.2.1-AtOligo 2.9.2.100 (http://www.ag.arizona.edu/microarray).

manufacturer: The Galbraith Laboratory, University of Arizona

middle: W

manufacture_protocol: GeneMachines, Omnigrid


title: Dichelobacter nodosus oligonucleotide microarray-altered spot pattern,power outage

status: Public on Dec 27 2006

city: Melbourne

first: Julian

middle: I

last: Rood

state: Victoria

address: Wellington Road

department: Microbiology

country: Australia

institute: Monash University

organism: Dichelobacter nodosus

description: Microarrays consisted of 2,317 custom 70-mer oligonucleotides (designed to reduce cross-hybridisation) spotted in triplicate on Ultra-GAPS slides (Corning) using a QArray Mini (Genetix) arrayer, representing 1,343 ORFs as determined from the unpublished D. nodosus genome sequence (http://www.tigr.org) and where possible two gene probes per ORF were synthesised. Oligonucleotides were spotted on a 2X6 metagrid, which was composed of 24X26 subgrids.

first: Dane

last: Parker

first: Garry

middle: S

last: Myers

first: Ruth

middle: M

last: Kennan

first: Ian

middle: T

last: Paulsen

manufacture_protocol: Microarrays were constructed in house and consisted of 2,317 custom 70-mer oligonucleotides (designed to reduce cross-hybridisation; Gary Myers and Ian Paulsen, TIGR) spotted in triplicate with 50% DMSO on Ultra-GAPS slides (Corning) using a QArray Mini (Genetix) arrayer, representing 1,343 ORFs, as determined from the unpublished D. nodosus genome sequence (http://www.tigr.org).


title: SIBS rice microRNA microarray v1.0

description: epoxide coated slide made in our lab

first: kangcheng


title: Galbraith Laboratory Operon Long Oligonucleotide Microarray Version 1.0 (AtOligo 3.1.2.Y and AtOligio 3.2.2.Y)

description: This oligonucleotide array is produced from the Operon Version 1.0 Array-Ready Oligo set (AROS). The Arabidopsis V1.0 AROS is designed from UniGene Build At. #4 (www.operon.com). This set comprises 26,000 oligonucleotides. Additional elements are printed as controls.  This platform represents slides AtOligo 3.1.2.1-AtOligo 3.1.2.100 and AtOligo 3.2.2.1-AtOligo 3.2.2.100 (http://www.ag.arizona.edu/microarray).


title: GSF/IEG mouse 20K array version2

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

organism: Mus musculus

manufacturer: IEG, Gene regulation and Expression Profiling Group

first: Marion

last: Horsch

first: Johannes

last: Beckers

manufacture_protocol: PCR amplification of cDNA clones, purification of PCR product using 96-well filter plates, 3x SSC as spotting buffer. spotting robot: Microgrid II


title: Pinus taeda 5K cDNA microarray Platform 2

city: Uppsala

first: Johan

last: Wadenbäck

department: Plant Biology and Forest Genetics

country: Sweden

institute: Swedish University of Agricultural Sciences (SLU)

organism: Pinus taeda

manufacturer: North Carolina State University, Forestry, Forest Biotechnology, 840 Main Campus Drive, Raleigh, NC, 27695, USA

first: Sara

last: von Arnold

first: Ulrika

last: Egertsdotter

first: Hanna

last: Göransson

first: Adam

last: Ameur

last: Clapham

manufacture_protocol: 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.


title: UWCEA_HumanHD1

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description:
Attachment = UV cross-linked
Strandedness = double

manufacturer: Jiangning,,Li; 960 Republican St. Rosen 204, Seattle, WA, 98195, USA; 206-732-6141; ljn68@u.washington.edu

manufacture_protocol: This is a human array created by spotting PRC products from IMAGE clones.


title: MPIMG Homo sapiens 44K aCGH3_MPIMG_BERLIN

status: Public on Dec 22 2006

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 Pieter de Jong), the 1Mb Sanger set (clones kindly provided by Nigel Carter, Wellcome Trust Sanger Centre) and a set of subtelomeric clones (assembled by members of the COSTB19 Action: Molecular cytogenetics of solid tumours). Protocols for the isolation of DNA (1Mb 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: TumorTest

first: Thomas

last: Engleitner

address: Ihnestr. 73

institute: Max-Planck-Institute

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: Codelink Uniset Mouse-1 Array Platform

status: Public on May 11 2005

city: Pittsburgh

first: Tamas

last: Dolinay

state: PA

department: Pulmonary, Allergy and Critical Care

institute: Univerisity of Pittsburgh Medical Center

description: GE (formerly Amersham Biosciences)  CODELINK UNISET MOUSE-1 (10K) array expression data

distribution: custom-commercial

first: Naftali

last: Kaminski

first: Hong

middle: P

last: Kim

first: Paul

last: Reynolds

first: Doerte

last: Karp

first: Stefan

last: Uhlig

first: Augustine

last: Choi


title: Streptococcus pneumoniae TIGR4/R6 v4

status: Public on Dec 21 2006

city: Rotterdam

first: Wouter

last: Hendriksen

address: Dr. Molewaterplein 50

department: Pediatrics

country: Netherlands

institute: Erasmus MC

organism: Streptococcus pneumoniae

manufacturer: Department of Molecular Genetics, university of Groningen, the Netherlands

first: Anne

last: de Jong

first: Sacha

last: van Hijum

manufacture_protocol: See Van Hijum et al, 2005, PMID: 15907200 and Hendriksen et al, 2006, PMID: 17085554


title: OHU28K-OI-072404-YMD.gal

city: New Haven

first: E. Janet

last: Hager

state: CT

address: 300 George Street, Suite 2110

department: W.M. Keck Foundation Biotechnology Resource Laboratory

institute: Yale University School of Medicine

description: A set of 28K Operon Version 2.1 and Version 2.1 upgrade -70 mer oligos. It has 48 pins with 24 columns and 25 rows in each subarrays. ID is Operon ID#.

manufacture_protocol: academic core lab


title: Nimblegen-S.cerevisiae-expression-24mer

city: Aarhus

first: Francisco

last: Malagon

address: C.F. Mollers Alle, Bldg. 130

department: Department of Molecular Biology

country: Denmark

institute: Aarhus University

technology: in situ oligonucleotide

description:
The grid of features is 768x1024 (X, Y). Each ORF represented by 16 probes. The locations of the probes correspond to the position of the 5' end base of the probe in the ORF (with introns removed). Each probe is duplicated and present in different locations (BLOCK1 and BLOCK2). Each probe has two associated values, PM (Perfect
Match) and MM (MissMatch). PM and MM match for each block are located in close proximity (coordinates (Xn, Yn) and (Xn+1, Yn+1)).

first: Mike

last: Hogan

manufacture_protocol: High-density microarrays based on Maskless Array Synthesizer (MAS) technology. At the heart of the MAS technology is the Digital Micromirror Device (DMD), an array of 786,000 tiny aluminum mirrors, arranged on a computer chip, where each mirror is individually addressable. Using these tiny aluminum mirrors to shine light in specific patterns, coupled with the photo deposition chemistry, produces arrays of oligonucleotide probes.


title: High density Euphorbia esula and Manihot esculenta array

status: Public on Dec 12 2006

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

description: ~19000 unigene set from leafy spurge EST database supplemented with ~4000 cassava clones that had no obvious homology with any leafy spurge clone.

first: James

middle: V

last: Anderson

first: Mark

last: Band

manufacture_protocol: standard


title: Dow Chemical Company Pseudomonas fluorescens oligo spotted array

status: Public on Dec 11 2006

city: San Diego

first: Hongfan

last: Jin

address: 5501 Oberlin Drive

department: Biotechnology

institute: The Dow Chemical Company

organism: Pseudomonas fluorescens

manufacture_protocol: Follwoing MWG's instruction on oligo arrays


title: Daphnia magna DGC cDNA array ver.1

first: Helen

last: Poynton

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

organism: Daphnia magna

manufacturer: UC Berkeley Dept. of Nutr. Sci. and Toxicology Genomics Facility

first: Patricia

last: Holman

first: Darren

last: Bauer

first: John

middle: K

last: Colbourne

manufacture_protocol:
The 5000 randomly selected cDNA clones from the Daphnia Genome Consortium (DGC) library (generous gift from D. Bauer at University of New Hampshire, NH and J. Colbourne at Indiana University, IN) were PCR amplified from the pDNR-LIB vector using the following primers: forward: AGTCGACGGTACCGGACATA and reverse: GCCAAACGAATGGTCTAGAAA.  PCR products were purified by ethanol precipitation and resuspended in distilled water. cDNA clones were printed onto lysine-coated glass slides (Cheung et al. 1999).
Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G.  1999.  Making and reading microarrays. Nat Genet 21:15-9.


title: UW-Madison Saccharomyces cerevisiae tiling array_24mer oligos

city: Madison

first: Christopher

middle: Lawrence

last: Warren

state: WI

address: 1400 University Ave

institute: University of Wisconsin - Madison

description: ChIP-chip whole-genome tiling design.  24mer oligonucleotides.

first: Eric

last: Steinmetz

first: Christopehr

middle: L

first: Jason

middle: N

last: Kuehner

first: Bahmen

last: Panbehi

first: Aseem

middle: Z

last: Ansari

last: Brow

manufacture_protocol: NimbleGen maskless array synthesis.  Refer to Nimblegen Systems.


title: Agilent Escherichia coli 2.7K aCGH custom-array

status: Public on Dec 19 2006

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description:
Microarray designed on E. coli K12 genome sequence containing 2700 probes covering 60% of the 4488 ORFs
Used for comparative genomic hybridization of environmental isolates of E.coli

Platform GPL4618 is derived from two distinct microarray designs containing 8.4K features for the 1st version and 22K features for the last version; both the 8.4K and 22K arrays contain oligos representing S.aureus AND E.coli).  The E.coli probes are EXACTLY THE SAME on both the 8.4K and 22K arrays, ie, the same number of probes, the same sequences, and the same ORFs.  The only difference concerns S.aureus probes (more probes, different sequences, and matching ORFs from newly sequenced S.aureus strains) which don't have any relevance to the GPL4618-related study and, thus, have not been included in GPL4618.

first: Julian

last: Ihssen

first: Elena

last: Grasselli

first: Claudio

last: Bassin

first: Patrice

last: Francois

first: Jean-Claude

last: Piffaretti

first: Wolfgang

last: Köster

first: Jacques

last: Schrenzel

first: Thomas

last: Egli

manufacture_protocol: Sure Print technology (Proprietary, Agilent)


title: GeneFilter Human Microarray Release I (GF200)

status: Public on Dec 24 2006

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center


title: University of London Bacterial Microarray Group at St George's S. pneumoniae 2.3K

city: Adelaide

first: Alistair

last: Standish

address: North Terrace

department: School of Molecular and Biomedical Sciences

institute: University of Adelaide

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

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

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


title: HMS_Vibrio_cholerae1206

status: Public on Dec 28 2006

city: Boston

first: David

last: Raskin

address: 200 Longwood Avenue

department: Microbiology & Molecular Genetics

institute: Harvard Medical School

organism: Vibrio cholerae

first: John

last: Mekalanos

manufacture_protocol: N16961 spotted PCR array.  Two sets of every ORF spotted.  8192 spotted products and controls, including buffer and GFP.


title: AntrHuman20kv03

status: Public on Dec 23 2006

city: Nijmegen

first: Gys

middle: de

last: Jongh

state: Gelderland

address: Rene Descartesdreef 1

department: Dermatology

institute: Nijmegen Centre for Molecular Life Sciences

description: Oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions

manufacturer: Radboud University Nijmegen Medical Centre,Department:Antropogenetics,Lab:Microarray Facility Nijmegen , E-mail: Microarrayfacility@antrg.umcn.nl ,Website: http://www.microarraynijmegen.nl/index.htm

first: Rolph

last: Pfundt

first: Walter

last: Vliet

manufacture_protocol:
A 19 K oligonucleotide set consisting of 18,861 oligonucleotides representing 18,664 unique sequences (synthezised and sold by Sigma-Genosys,Cambridge,UK . Designed by Compugen,San Jose, CA,USA ,http://www.cgen.com/ , http://www.labonweb.com/ , Catl# HUMLIB384 )was printed (spotting solution:3 x SSC, pH7.0 , 1.5 M betaine ,12 fmol/spot)onto UltraGAPS glass slides (Corning , Schiphol-rijk ,The Netherlands),using an Omnigrid 100 arrayer (Genomic Solutions,Michigan,Ann Harbor USA) equipped with 32 SMP3 pins (ArrayIt , California , Sunnyvale , USA).The program CloneTracker (Biodiscovery , http://www.biodiscovery.com/index/clonetracker )was used to control the printing robot.Printed slides were dried overnight and cross-linked with UV light at 600 mJ using a Strata-linker 2400 Stratagene (Virginia, Glenville, USA).
For quality control of the chip itself the grid for finding the spots was defined outside the printing area of the robot.Description is “Nothing printed,undisturbed background”.For quality control of the printing robot and the printing process the pins were cleaned and dried in the usual way,dipped in an empty well of the 384-well high throughput plate and a spot was printed.Description is “empty”.
Cy5 and Cy3 labelled random nona-mers were printed to assist in the visual alignment of the grid for finding the spots on the raw *.tiff image. (Amersham , http://www.amersham.com/ , custom made).
The SpotReport Alien Oligo Array Validation System( http://www.stratagene.com/manuals/252270.pdf , Stratagene Europe , Gebouw California , Hogehilweg 15 , 1101 CB Amsterdam Zuidoost,The Netherlands )was printed to allow normalisation and calibration of the microarray.This system consists of : Human β-actin oligo , GB_ACC = X63432 , Poly(dA)40–60 oligo , Human COT-1 , Spotreport oligo 1 till 10.
The Raw image files were collected with a GenPix 4100A laser scanner.
For a visual interpretation of the *.Tiff files with the raw data the array should be viewed from above,the side where the oligo’s were printed,with a small side of the rectangular array at the top.This is the picture that was produced by the GenePix software.The GenePix software uses the variables “Block” , “Row” and “Column” to indentify the spots.The Genepix software sorts the output data on 1) “Block” , 2) “Row” and 3) “Column” , ascending.We added the variable “KeySpot” .The variable "KeySpot" is an unique address for the spots on the array. It was computed from the GenePix variables "Block" , "Row" and "Column" as : KeySpot = Column + Row x 100 + Block x 10,000 The variable "KeySpot" can be used as a Primary Key to link data base tables.The variable "KeySpot" was also used as the mandatory variable "ID" for the GEO data base at the NCBI.

The array consists of 48 subgrids.
Subgrids are organised in 12 rows of 4 columns.
The subgrids are numbered in the normal "reading direction" in the variable "Block" from upperleft =1 to lower right = 48
The features in the subgrids are organised in 21 rows , numbered in the variable "Row" , of 20 columns , numbered in the variable "Column".
The rows are numbered from top=1 to bottom= 21.The columns are numbered from left=1 to right=20.
This pattern was printed in two printing sessions. In the first printing session the print head , equipped with the first 4 x 8 =32 pins , was used to print all the features in Block 1 - 32. In the second printing session the print head , now with the first 4 x 4 =16 pins , was used to print all the features in Block 33 - 48.
The print head of  the arrayer should be viewed from behind , the position in which it printed the oligo’s on the array.It was equipped with the the first 32 (16) pins arranged as 8 x 4 (4 x 4) pins numbered the normal "reading direction" in the variable PinNum from upperleft =1 to lower right =  32 (16 ).
The number of the pin that printed a particular spot can be determined from the Block Number with the VB Excel formula  : MOD((Block-1),32)+1 or an equivalent modular function in an other language.
The variable ID , together with this description , makes all other spot reference variables on the array redundant.We did not include them in the GEO data base. If you would still like to have them , please feel free to email us directly.


title: GeneFilter Human Microarray Release II (GF201)


title: Galbraith Laboratory Operon Long Oligonucleotide Microarray Version 1.0 (AtOligo 2.6.2.Y)

city: Tucson

last: Galbraith

address: 303 Forbes Building

institute: University of Arizona

description: This oligonucleotide array is produced from the Operon Version 1.0 Array-Ready Oligo set (AROS). The Arabidopsis V1.0 AROS is designed from UniGene Build At. #4 (www.operon.com). This set comprises 26,000 oligonucleotides. Additional elements are printed as controls.  This platform represents slides AtOligo 2.6.2.1-AtOligo 2.6.2.100 (http://www.ag.arizona.edu/microarray).

manufacture_protocol: GeneMachines, Omnigrid


title: Snyder - Nimblegen S.cerevisiae WGT 50-60; 50-120

status: Public on Dec 10 2006

city: Urrbrae

first: Anthony

middle: R

last: Borneman

state: South Australia

address: Paratoo Rd

institute: The Australian Wine Research Institute

description: Whole genome tiling array designed for S. cerevisiae. 50mer oligos tiled every 60 bp on the Watson Strand, 50mer oligos tiled every 120bp on the Crick strand with a 30bp offset.

first: Zhengdong

last: Zhang

first: Joel

last: Rozowsky

first: Michael

last: Seringhaus

first: Mark

last: Gerstein

last: Snyder

manufacture_protocol: maskless-photolithography. Maximum of 396,000 spots per array.


title: mamLab_Silicibacter pomeroyi DSS-3_12k_v1.0

status: Public on Dec 07 2006

city: Athens

first: Shulei

last: Sun

state: GA

address: Department of Marine Science

department: Marine Science

institute: UGA

organism: Ruegeria pomeroyi DSS-3

first: Helmut

last: Buergmann

first: Erinn

last: Howard

first: Wenying

last: Ye

first: Feng

first: Sarah

last: Napierala

first: MaryAnn

last: Moran

manufacture_protocol: Hybridization protocol for customarray 12k microarrays by COMBIMATRIX


title: BCCRC Lam NG_OID3949_389027 oligo array

status: Public on Dec 06 2006

city: Vancouver

first: Kendy

last: Wong

state: British Columbia

address: 675 West 10th Avenue

department: Cancer Genetics

country: Canada

institute: BC Cancer Research Center

first: K

first: R

middle: J

last: deLeeuw

first: N

last: Dosanjh

first: L

last: Kimm

first: Z

last: Cheng

first: D

middle: E

last: Horsman

first: C

last: MacAulay

last: Ng

last: Brown

first: E

last: Eichler

first: W

last: Lam

manufacture_protocol: NimbleGen's photo deprotection chemistry with its proprietary Maskless Array Synthesizer system


title: Dartmouth V. cholerae Taylor 10 array

city: Lebanon

first: Francisca

middle: A

last: Cerda-Maira

state: NH

address: 16 Cavendish Court

department: Microbiology and Immunology

institute: Dartmouth College

first: Fransisca

last: Cerda

manufacture_protocol: 50mers and 70mers designed synthesized by Illumina.  3956 probes for 3929 genes, 51 probes for 25 controls, 10 positive and 15 negative, 25 blanks.  Total of 4032 spots.  Printed on Corning Ultra GAPS slides in 50%DMSO.


title: GUELPH Bovine immune-endocrine microarray

city: Guelph

first: Wenjing

last: Tao

state: ON

address: Gordon street

department: Department of Pathobiology

institute: University of Guelph

organism: Bos taurus

description: The in-house microarray consists of 167 RT-PCR derived DNA fragments representing 167 ORFs from bovine. The DNA fragments are printed 4 times on the surface of the microarray (four-replicate blocks). The 167 immune and endocrine genes grouped into the following categories: cytokine genes, chemoattractants or chemokines and their respective receptor genes, immune regulatory genes, T-cell associated genes, pattern recognition or innate host defense genes, immunglobin (Ig) or Ig-related genes, complement genes, antigen processing or presenting genes, and genes encoding endocrine hormones or their receptors. As positive controls, the array includes 5 “housekeeping” genes (GAPDH, HPRT, PRL19, β-actin, β2-microglobulin), negative controls consisted of a Rhodococcus equi 17kD virulence protein gene, plasmid pACYC177 DNA, and a thaliana photosystem I chlorophyll a/b-binding protein gene, and the FcRgII gene intron. The printing controls included serially diluted bovine genomic DNA, and printing buffer only.

manufacturer: Immunogenetics lab, Department of Pathobiology, Universitu of Guelph

first: Bonnie

last: Mallard

manufacture_protocol: The slides are printed on 4-replicate grids, each grid containing 18 rows and 10 columns


title: Matsumoto (Agilent Rat cDNA Microarray G4105A)

city: Machida-shi

first: Mineo

last: Matsumoto

state: Tokyo

address: 11 Minamiooya

institute: Mitsubishi Kagaku Institute of Life Sciences

organism: Rattus norvegicus

description:
This is a custom representation of Agilent's Rat Microarray G4105A
This platform is formatted specifically for this user's normalized data and should not be referenced by other users.

manufacture_protocol: see manufacturer's web site


title: Lactobacillus paracasei 7.8 K

city: Lincoln

first: Yong Jun

last: Goh

state: NE

address: 332 Food Industry Complex

department: Food Science and Technology

institute: University of Nebraska

organism: Lacticaseibacillus paracasei

manufacturer: University of Nebraska-Lincoln, Department of Food Science and Technology

first: Yong-Jun

first: Chaomei

last: Zhang

first: Andrew

last: Benson

first: Robert

middle: W

last: Hutkins

manufacture_protocol: A shotgun genomic library of L. paracasei was constructed using Zero Blunt TOPO Cloning Kit (Life Technologies, Carlsbad, CA) based on the manufacturer’s instructions.  Briefly, genomic DNA was mechanically sheared and size fractionated on 0.8% (w/v) agarose gel.  Fragments of 1 to 4 kb were purified from gels, ligated into pCR-Blunt II-TOPO vector, and electroporated into One Shot TOP10 Electrocomp E. coli (Invitrogen).  A total of 7,680 independent clones were selected and grown in individual wells of 96-well round-bottom microtiter plates containing 120 microliter of LB supplemented with 50 microgram/ml of kanamycin.  For amplification of the cloned genomic fragments, 2 microliter of each cell suspension was used as amplification template in 50 microliter PCR reactions containing 200 microM of each dNTP (Takara Mirus Bio Inc., Madison, WI), 2.4 mM MgCl2, 50 pmol of each M13-forward and M13-reverse primers, and 2.5 U of Taq DNA polymerase in 1X PCR buffer (Sigma).  PCR amplifications were performed in 96-well PCR plates, and aliquots of the PCR products were analyzed on agarose gels (with an average size of 1.5 kb).  The remaining amplified mixtures were transferred into 96-well microtiter plates, precipitated by addition of 0.1 volume of 3 M sodium acetate (pH 5.2) and 2 volumes of ice-cold ethanol, washed, and resuspended in 30 microliter of 3X SSC (450 mM NaCl, 45 mM sodium citrate, pH 7.0).  The purified amplicons were spotted onto silanated glass slides (CEL Associates, Inc., Pearland, TX) in 4 subarrays (2 x 2 format), each subarray consisted of 44 x 44 clones using an OmniGrid robotic arrayer (GeneMachine, San Carlos, CA).


title: Chr8 BACs 5.7K DNA array

status: Public on Dec 02 2006

city: bethesda

first: abdel

last: elkahloun

state: MD

address: 50 south dr

institute: nih

first: Abdel

middle: G

last: Elkahloun

manufacture_protocol: Pure BAC DNA was extracted from BAC clones, amplified with Phi29 overhight at 37 degree, digested with enzymes to generate 200-400 bp fragments, purified by ethanol precipitation, dried and resuspended in 3X SSC.


title: UHN_yeast_6.4kv6

city: Haifa

first: Shay

last: Stern

address: Haifa

department: Chemical Engineering, Physics

country: Israel

institute: Technion- Israel Institute of Technology

manufacture_protocol:
Refer to the manufacturer website:
www.microarray.ca


title: Qiagen Mouse V3 31K Oligo array (MV3)

manufacture_protocol: please see the NHGRI Microarray Core Facility website


title: Chicken Immune Sytem-Specific Microarray Version 2

status: Public on Dec 01 2006

first: Shayan

last: Sharif

state: Ontario

address: Ontario Veterinary College

organism: Gallus gallus

first: Aimie

last: Sarson

first: Leah

last: Read

first: Hamid

last: Haghighi

first: Melissa

middle: D

last: Lamburne

first: Jennifer

last: Brisbin

first: Huaijun

last: Zhou

manufacture_protocol: Array spotted with three identical grids each containing 16 columns and 17 rows.


title: National Yang-Ming University Homo sapiens 8K

city: Taipei

first: Ann-Ping

last: Tsou

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

department: Inst. Biotechnology in Medicine

country: Taiwan

institute: National Yang-Ming University

description: Human hepatocellular carcinoma cells, namely, HuH7 were seeded. Samples were cultured in 0.1 μM sodium selenite-containing medium for 15 passages (SeLT) or in serum-free medium for 30 h (SF30) or in the regular complete medium containing 10 % fetal calf serum (HuH7) for 30 h. All the samples were collected at the time indicated above. The total RNA were reverse transcried and hybridized to Human 8K-1 (Egenomix Technology Corp., Taiwan). The hybridization time and temperature was 16 h and 62℃, respectively. SF30 sample was labeled with Cy3. SeLT and HuH7 samples were labeled with Cy5.

first: Yi-Hsien

last: Chen

first: Yu-Chun

last: Lin

first: Cha-Ming

last: Chang

first: Yu-Chi

last: Lee

manufacture_protocol: Custom Array


title: Illumina Mouse 38K Oligo array(MEEBO)


title: CUFSL Listeria interalins 384 v1

city: Ithaca

first: Patrick

last: Mc Gann

state: NY

address: 412 Stocking Hall

department: Food Science

institute: Cornell University

organism: Listeria monocytogenes

manufacturer: Big Red Spots, T2 002B Vet Research Tower, Cornell university, Ithaca NY 14853 USA

last: McGann

first: Martin

last: Wiedmann

first: Kathryn

last: Boor

manufacture_protocol: Oligonucleotides were resuspended in 1× SSC, 0.0025% Sarcosyl to a final molarity of 30uM. All oligonucleotides and controls were spotted in duplicate on Amino-silane coated Corning UltraGAPS slides (Corning, NY USA) using a custom built XYZ microarrayer. Oligonucleotides were UV-crosslinked at 300mJ for 1 minute. Printing quality was checked using Cy3-labeled random sequence nonamers


title: Human whole genome tiling array, chip 14 of 14

first: Kevin

last: Struhl

state: MA

address: 240 Longwood Ave.

department: Dept. Of Biological Chemistry & Molecular Pharmacology

first: Annie

last: Yang

first: Zhou

last: Zhu

first: Philipp

last: Kapranov

first: Frank

last: McKeon

first: George

last: Church

first: Thomas

last: Gingeras

manufacture_protocol: See manufacturer's web site


title: Human whole genome tiling array, chip 10 of 14


title: Human whole genome tiling array, chip 03 of 14


title: Human whole genome tiling array, chip 07 of 14


title: Human whole genome tiling array, chip 08 of 14


title: Human whole genome tiling array, chip 04 of 14


title: Incyte Genomics Mouse Life Array v1.16 and v1.26

city: Bryan

first: Rajesh

middle: C

last: Miranda

state: TX

address: MREB, 8447 Riverside Parkway

department: Neuroscience

institute: Texas A&M HSC

description: 9000 cDNA clones including controls

manufacture_protocol: cDNA clones spotted on a glass slide


title: Human whole genome tiling array, chip 09 of 14


title: Human whole genome tiling array, chip 11 of 14


title: Human whole genome tiling array, chip 02 of 14


title: Human whole genome tiling array, chip 06 of 14


title: Zebrafish 34K Oligo array

first: abdel

last: elkahloun

organism: Danio rerio

first: Abdel

last: Elkahloun


title: Human whole genome tiling array, chip 05 of 14

organism: Homo sapiens


title: Human whole genome tiling array, chip 12 of 14


title: CodeLink Uniset Mouse I Bioarray

status: Public on Dec 30 2005

city: Houston

first: Bogdan

last: Wlodarczyk

address: 2121 W Holcombe Blv.

department: CEGM

institute: IBT


title: Populus 1.0

status: Public on Sep 01 2005

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: Stephen

last: DiFazio

first: Amy

middle: M

last: Brunner

first: Palitha

last: Dharmawardhana

first: Kyle

last: Munn

manufacture_protocol: Propriety in situ oligonucleotide synthesis.


title: GSF mouse array

status: Public on Sep 28 2004

city: Munich - Neuherberg

first: Johannes

last: Beckers

state: Bavaria

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: GSF - National Research Center

description: cDNA array of commercially available set of 20.400 clones (Mus musculus) and specific mouse genes spotted on aldehyde coated slides.

first: Marion

last: Horsch

first: Tomek

last: Mijalski

first: Matthias

last: Seltmann


title: GSF ArrayTAG

status: Public on May 08 2004

description: cDNA array of commercially available set of 20k clones (Mus musculus) spotted on aldehyde coated slides.

first: Alexei

last: Drobyshev

first: Yali

last: Chen


title: Spotted RIKEN cDNA array 40-60K

status: Public on Dec 20 2005

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

institute: Institute for Molecular Bioscience, Uni of Qld

manufacture_protocol: spotted cDNA


title: DGRC-D. melanogaster-DGRC2-17328-v1

status: Public on Jun 20 2006

city: Bloomington

state: IN

department: Indiana University

organism: Drosophila melanogaster

description: DGRC-2 transcriptome microarrays are spotted with gene-specific Drosophila melanogaster 70 N long oligonucleotides.  The oligos were designed against release 4.1 of the genome annotation using a custom implementation of OligoArray2. Oligos selected have minimal sequence similarity to other genes, size range between 65-69 nucleotides with a minimal Tm window, and locations biased towards the 3'-ends of transcripts.  Oligo Synthesis was completed by Illumina. The array also contains the following controls: a ubiquitously expressed gene (actin 5C), a spotting buffer-only control (150 mM NaPO4, pH 8.5), exogenous (non-Drosophila) probes: 9 from Arabidopsis, 2 from soybean, 1 from apple and Ambion’s  Array Control Sense Oligo Spots bacterial sequences that can be utilized with spiking RNAs, four exogenous markers - GAL4, lacZ, modified GFP, and FLPase, and a 70mer probe degradation long oligonucleotide set.  DGRC-2 arrays are printed using an Omnigrid 300 contact-printing instrument and 48 silicon split-pins on Corning UltraGAPS slides.

first: Justen

last: Andrews

first: Peter

last: Cherbas

first: Kevin

last: Bogart

first: Monica

last: Sentmanat

first: Jim

last: Costello

first: INDAC

manufacture_protocol:
Fabrication of DGRC-2 oligonucleotide microarrays
Bogart, K., Cherbas, L., and Andrews, J.
INTRODUCTION
The Drosophila Genomics Resource Center (DGRC) provides the research community with access to genomics resources including microarrays. The first generation transcriptome microarrays fabricated by the DGRC (DGRC-1 arrays) are spotted with amplified DNA fragments. The DNA fragments are amplified from genomic DNA template by polymerase chain reaction using gene-specific primers. The primers were designed against release 1 of the D. melanogaster genome annotation, and the amplified DNAs were validated to perform well as microarray targets (Johnston et al. 2004). In recent annotations the coverage of the amplicons fell to 88% of the predicted genes (Costello and Andrews, 2006).
Several recent studies have demonstrated the favorable performance of spotted oligonucleotide microarray platforms (Kane et al. 2000; Bozdech et al. 2003; Wang et al. 2003). Long oligonucleotides perform as well as cDNAs in detecting differential gene expression. Additionally, since oligonucleotides are shorter, they can be selected against unique sequences that distinguish between members of a gene family or alternative transcripts from a single gene. Motivated by the advantages of oligonucleotide microarrays and the need to update the existing Drosophila transcriptome platforms, the International Drosophila Array Consortium (INDAC) developed a set of oligonucleotides for microarray fabrication. This set of oligonucleotides is now being used by several Drosophila genomics facilities to fabricate transcriptome microarrays (FlyChip, CDMC, DGRC).
Oligonucleotide design and synthesis
The International Drosophila Array Consortium (INDAC) was formed to produce a widely available and uniform set of array reagents, so that microarray data collected from different studies may be more easily compared. On behalf of INDAC, the FlyChip group (Gos Micklem, Steve Russell, and their collaborators at the University of Cambridge) designed a set of long oligonucleotides to release 4.1 of the D. melanogaster genome, using a custom implementation of OligoArray2. Oligos were chosen to have minimal sequence similarity to other genes, size range between 69-65 nucleotides with a minimal Tm window, and location biased towards the 3'-end of transcripts. The final set of 15,158 oligonucleotides has the size distribution give in Table 1. The sequences of the oligonucleotides can be downloaded from DGRC platforms, and Flymine.

Table 1. Distribution of oligonucleotide lengths
Length (nt)	Total #	%
69	9791	64.6
68	749	4.9
67	730	4.8
66	713	4.7
65	3175	20.9
Annotation
We have updated the annotation of the oligonucleotides to release v4.3 of the Drosophila genome (Rupali Patwardhan, James Costello, Justen Andrews, Peter Cherbas, unpublished). Full details can be found in the gene list master file which is posted for each DGRC-2 print run on the DGRC web-site; these files will be updated as new annotations of the Drosophila genome are released. Briefly, of the 15,158 oligonucleotides, 14,543 are designed against Drosophila sequences (the remainder being controls of various sorts); after correction for sequences that are repeated in the collection, there are 14,447 unique Drosophila oligo sequences. Of these, 14,047 are predicted to hybridize to transcripts defined in the v4.3 annotation of the Drosophila genome; 142 of them hybridize to transcripts from more than one gene. Altogether, of the 14486 genes in the v4.3 annotation of the Drosophila genome, 13548 (93.5%) are represented unambiguously in the INDAC collection of oligonucleotides. 72 of these
genes express non-coding RNAs, some of which are not polyadenylated and therefore will not be detected with oligo-d(T)-primed fluorescent targets. In the INDAC set of oligonucleotides, no attempt was made to include probes specific for different transcripts  from individual genes; specific transcripts predicted to hybridize to each oligonucleotide probe are listed in the gene list master file on the DGRC web-site.
The probe sequences were designed to be as close as possible to the 3’ end of transcripts. Probes generally hybridize within a few hundred nucleotides of the polyadenylation site of the transcripts against which they were designed, but some probes also hybridize to longer alternative transcripts. For each probe, we have calculated the distance from the 3’ end of the probe to the polyadenylation site of each predicted transcript to which it can hybridize; for all probe/transcript combinations, the mean distance is 723 N (S.D. = 576).
Internal controls and array layout
The set of INDAC oligonucleotides includes the following internal controls:
1. Exogenous targets: 9 from Arabidopsis, 2 from soybean, 1 from apple. These serve as negative controls or targets for mRNA spike-in controls.
2. Exogenous genes: GAL4, lacZ, modified GFP, and FLPase.
3. A series of oligos designed to test for the intactness of RNA targets. The array contains multiple copies of a set of oligos made from different parts of the eukaryotic initiation factor (eIF-4a) transcript. Since most labeled targets are made as oligo(dT)-primed cDNAs, mRNA degradation and/or incomplete reverse transcription will result in overrepresentation of sequences from the 3’ portion of an mRNA. Therefore, a degraded RNA sample may be detected by a relative decrease in hybridization to the more 5’ eIF-4a probes. We have not yet experimentally validated this test.
We have supplemented these controls with the following:
1. The ubiquitously expressed genes actin 5c (act5c) and eiF-4a printed at a characteristic location in each of the 48 sub-arrays. These positive control spots serve as an easily recognized registration mark and as a check on the uniformity of hybridization across the slide.
2. A spotting-buffer-only control printed in each of the 48 sub-arrays. This serves as a negative control for background and check for carry-over between samples.
3. Array Control Sense Oligo Spots (Ambion Inc.). These serve as additional negative controls and can also be utilized with spiking RNAs for normalization to verify the equivalence of labeling between channels.  Oligo Spots are PAGE-purified C6 amino-modified 70-mers single-stranded ("sense" orientation). Oligo Spot sequences have been designed for optimal annealing and minimal self-hybridization and are also checked for lack of cross hybridization to all sequences catalogued in public databases.
The spotting buffer negative control, act5c and eiF-4a positive controls, and Array Control
Sense spiking controls (Ambion) are printed by each of the 48 pins at the start of each block.
This report gives an overview of the DGRC-2 oligonucleotide transcriptome microarrays
printed by the DGRC using the INDAC set of oligos. It is intended to inform DGRC users
about the platform and provide information on the production of the arrays.  The key issues in oligonucleotide microarray construction are 1)  the resuspension of lyophilized oligonucleotide in spotting buffer and 2) the deposition and immobilization of those DNAs onto glass slides. Below we describe the high throughput resuspension, printing and immobilization of oligonucleotides to create the DGRC-2 arrays.

Part A. Resuspension
Below, we will describe the Biomek FX methods for preparation of DNA for printing (deposition) by resuspending a 625 pmol plate of lyophilized oligonucleotides in 21 uL spotting buffer (i.e. giving a 30uM concentration) and aliquoting to 2 final 10 uL source print plates.  This method is repeated for each of the 41 384-well plates used for the DGRC-2 arrays.
As a general cautionary note, it is important to avoid the use of latex gloves in all matters associated with the fabrication and use of microarrays. Latex contains a fluorescent component which will leach from the gloves and cause significant artifacts. Nitrile gloves are a readily available substitute and sh


title: Entamoeba histolytica E_his-1a520285F array (coding regions)

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

address: Grant S-143, 300 Pasteur Dr.

institute: Stanford Uninversity

organism: Entamoeba histolytica

first: Carol

last: Gilchrist

first: William

last: Petri

first: Upinder

last: Singh

manufacture_protocol: A custom generated Affymetrix platform full genome microarray (E_his-1a520285F). This array has 7,712 unique probe sets representing 9,435 open reading frames (ORFs). Due to the highly repetitive nature of the E. histolytica genome, some of the probe sets are predicted to cross-hybridize with other sequences. Probe sets that represent a single gene are labeled as (_at). Probe sets in which at least one probe may cross-hybridize with another gene(s) are labeled as (_x_at). In situations where all the probe sets for a given gene cross-hybridize with another gene(s), the probe sets are labeled as (_s_at) and additional genes that cross-hybridize with these probe sets are listed in Supplementary Table 2. This array also contains probes for intergenic non-coding regions, however, these are not included in this submission.


title: Human whole genome tiling array, chip 13 of 14

city: Boston

last: Struhl

institute: Harvard Medical School

first: Annie

last: Yang

first: Zhou

last: Zhu

first: Philipp

last: Kapranov

first: Frank

last: McKeon

first: George

last: Church

first: Thomas

last: Gingeras


title: Arabidopsis 15k AFGC Shauna 58

status: Public on Aug 31 2004

first: Shauna

last: Somerville

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institution of Washington

organism: Arabidopsis thaliana

description: cDNA array from the Arabidopsis Functional Genomic Consortium (Stanford), 15,000 elements.


title: Human whole genome tiling array, chip 01 of 14


title: UWCEA_HumanHD2

status: Public on Dec 31 2006

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description:
Attachment = UV cross-linked
Strandedness = double

manufacture_protocol: This is a human array created by spotting PRC products from IMAGE clones.