title: ISB Yeast Array

status: Public on Oct 01 2005

city: Bar Harbor

first: Gregory

last: Carter

state: ME

address: 600 Main Street

country: USA

institute: The Jackson Laboratory

organism: Saccharomyces cerevisiae

technology: in situ oligonucleotide

distribution: non-commercial

middle: W

first: Steffen

last: Rupp

first: Gerald

middle: R

last: Fink

first: Timothy

last: Galitski

manufacture_protocol: GeneChip


title: GBC_FOAR03_0001

status: Public on Nov 23 2004

city: Vancouver

first: Carl

middle: J

last: Douglas

state: BC

department: Department of Botany

country: Canada

institute: University of British Columbia

organism: Arabidopsis thaliana

technology: spotted oligonucleotide

description:
The Arabidopsis Genome Oligo Set Version 1.0 (Operon Biotechnologies, Huntsville, AL, USA) consists of 26090 70mer oligonucleotides (http://operon.com/arrays/oligosets_arabidopsis.php).  As positive controls, we included oligos for twelve housekeeping genes (Operon). As negative controls, we synthesized four oligonucleotides specific for human genes with no similarity to any Arabidopsis gene and included twelve oligonucleotides with no similarity to any Arabidopsis gene (Operon). We used a PCR amplified green fluorescent protein (GFP) cDNA (Invitrogen, Carlsbad, CA, USA) as an orientation marker. Oligonucleotides were resuspended in 384 well flat bottom plates (Nunc, Rochester, NY, USA) to a concentration of 100 mM in 3 x SSC. Oligos were printed on MicroGrid II robots using Microspot 10k pins (Biorobotics, Huntington, UK) depositing approximately 0.5 nl (0.0075 pmole) of each oligo onto EZ rays aminosilane slides (Apogent Discoveries, Hudson, NH, USA). The pitch of the grid used for this library was 0.2 mm. Oligos were UV cross linked at 3000 x 100 μJ using a UV Stratalinker 2400 (Stratagene, La Jolla, CA, USA).  We spotted single spots for 25,792 of the 26090 target oligonucleotides (due to software problems the print run was terminated shortly before completion); in addition, each subgrid contained six replicate spots of each of the four human negative controls, three spots of equally distributed Operon negative controls, a single spot of each of the twelve house keeping controls, and GFP marker on each corner of the s
Keywords = GenomeBC-Forestry
Keywords = 26k array v.1

first: Juergen

last: Ehlting

first: Jeff

last: Zeznik

first: Joerg

last: Bohlmann

first: Brian

middle: E

last: Ellis


title: CRUK 6.5K Genome-wide array

status: Public on Sep 30 2006

city: Birmingham

first: Nick

last: Underhill-Day

address: Edgbaston

department: Biosciences

country: United Kingdom

institute: University of Birmingham

organism: Homo sapiens

technology: spotted DNA/cDNA

first: Ian

last: Giddings

manufacture_protocol: Institute of Cancer Research in-house protocol


title: CodeLink™   UniSet Mouse 20K I Bioarray

status: Public on Sep 12 2006

city: Boston

first: Nathaniel

last: Treister

state: MA

address: 20 Staniford Street

institute: Schepens Eye Research Institute

organism: Mus musculus

description:
This platform submission represents a non-official version of the GE Healthcare/Amersham Biosciences CodeLink UniSet Mouse 20K I Bioarray.

This platform is not meant to serve as a data template for other submitters.

distribution: custom-commercial


title: CRUKDMF_22K_v1.0.0

status: Public on Sep 21 2006

city: Sutton

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

institute: Institute of Cancer Research

manufacturer: CANCER RESEARCH UK DNA Microarray Facility

manufacture_protocol: as described in Institute Labs manual


title: Marinebiotechnology laboratory Haematococcus pluvialis 1k cDNA microarray platform

status: Public on Sep 22 2006

city: InCheon

first: HyunSuk

last: Eom

state: Nam-gu

country: South Korea

institute: Inha University

organism: Haematococcus lacustris

first: Choul-Gyun

last: Lee

first: EonSeon

last: Jin

manufacture_protocol: We constructed the cDNA microarrays from the Haematococcus pluvialis cDNA library (Eom et al., 2005). One thousand selected expressed sequence tags (ESTs) from each clone, including housekeeping genes like ribosomal binding proteins, were amplified by PCR using T3/T7 primers or M13-20/M13 reverse primers and recovered by a MultiScreen PCR Filter Plate (Millipore, Billerica, MA, USA). Each cDNA chip was designed with 965 successfully amplified PCR products from the cDNA library. Additionally, several control clones from the Saccharomyces cerevisiae intergeneic sequence and the Haematococcus pluvialis housekeeping genes were included. Microarrays were produced using a fully automated system by robotic operation at Digital Genomics (Seoul, South Korea). The cDNA PCR products were spotted onto amine-coated GAPSII slides (Corning Inc., Corning, NY, USA) using MG II (Biorobotics Inc., Woburn, MA, USA) with a 240 um pitch between spots as a twin format. There were 18 x 18 spots per block, and the spot diameter was 100~140 um. To evaluate fabrication, a cDNA microarray was stained with Syto61 (Molecular Probes, Eugene, OR, USA).


title: 5808-spot_slide_version5

description: cDNA


title: CRUKDMF_11K-gw_v1.0.0

description: cDNA

manufacturer: Cancer Research UK DNA Microarray Facility at The Institute of Cancer Research


title: CRUKDMF_6.5K-gw_v1.1.0

description: cDNA


title: NCI Operon (second printing) Human MAQC

status: Public on Sep 08 2006

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

manufacture_protocol: NCI protocol


title: SBC Rat cDNA Microarray For GBE50 v1.0

status: Public on Sep 13 2006

first: Huasheng

last: Xiao

address: No.151,Libing Rd.,Zhangjiang Hi-Tech Park,Pudong

department: Department of Genechip

institute: Shanghai Biochip Co., Ltd.

organism: Rattus norvegicus

first: Jiajing

last: Zhou

first: Zhidong

last: Zhu

first: Junsong

last: Han

first: Xiaomei

last: Gu

first: Qi

last: Wang

first: Yuchen

last: Chen

first: Qinghua

last: Zhang

manufacture_protocol: The cDNA fragments of selected genes were amplified by PCR and the final concentration is ranged from 200 ng/µl to 250 ng/µl. The cDNA fragments were spotted on poly-lysine coated slides by using OmniGrid 100 spotter and cross linked in 400 mJ UV. Keep temperature(room temperature: around 20℃) and the humidity(50%-55%).


title: CRUKDMF_6K-gw_v1.0.0

description: cDNA


title: NGEL Mouse 22K Oligo Microarray

city: Bryan

first: Rajesh

middle: C

last: Miranda

state: TX

address: MREB, 8447 Riverside Parkway

department: Neuroscience

institute: Texas A&M HSC

description: Oligos designed by Compugen/Sigma-Genosys

first: Ron

last: Hart

first: Andy

last: Brooks

first: Arlene

last: Clarke

manufacture_protocol: contact NGEL


title: CIT M3 Mus musculus 1K BAC CGH array

status: Public on Sep 14 2006

city: Paris

first: Marc-Henri

last: Stern

address: 26 rue d'Ulm

department: Research Dept

country: France

institute: INSERM/Curie Institute

description: The construction of the mouse BAC-array was supported by grants from the Carte d Identite des Tumeurs (CIT) program of the Ligue Nationale Contre le Cancer.

first: Elodie

last: Manie

first: Carine

last: Ganem-Elbaz

first: Axel

last: Mazoyer

first: Alain

last: Aurias

first: Olivier

last: Delattre

manufacture_protocol: A home-made genome-wide mouse BAC array was built using 1081 BACs that were isolated, validated by end-sequencing and amplified by multiple displacement amplification (GE Healthcare). The 1017 validated clones, corresponding to 958 unique BACs, are considered for the analysis. The collection was spotted in quadruplicate (diameter 180 µm), in 75% formamide, on Corning Ultragaps aminosilane glass slides, using Telechem pins and a MicrogridII TAS printer (Biorobotics)


title: deLaat_4C_2005_06

status: Public on Sep 20 2006

city: Rotterdam

first: Wouter

last: de Laat

address: Dr. Molewaterplein 50

department: Cell Biology

country: Netherlands

institute: Erasmus MC

first: M

last: Simonis

first: W

manufacture_protocol: Details on the manufacture protocol can be found on http://www.nimblegen.com/technology/index.html


title: deLaat_4C_2005_11


title: TeleChem ArrayIt Human Microarrays for MAQC (H25K and H25K1 , two- and one-color)

first: Leming

last: Shi

distribution: commercial

manufacture_protocol: TeleChem ArrayIt Protocol


title: Qiagen-Operon Arabidopsis 28.8k Genome Array (AtOligo 1.16.2.Y)

city: Wageningen

first: Paul

last: Passarinho

address: Bornsesteeg 65

department: Business Unit Bioscience

institute: Plant Research International BV

description:
ArrayIt® brand SuperAmine 2 Microarray Substrates (25 x 76 mm).
48 pins=12 metarows and 4 metacolumns, and the subarrays comprise 24 columns and 25 rows (20 x 60 mm).

first: David

last: Galbraith

first: R.

last: Elumalai

last: Gong

last: Formosa

first: M.

last: Gchachu

first: H.

last: Ozkan

first: T.

last: Watson

first: L.

last: Cheam

manufacture_protocol:
(1) Microarray production and probe immobilization:
http://ag.arizona.edu/microarray/protocol1A.doc

(2) Oligo/gene list:
http://omad.operon.com/download/storage/arabidopsis_V1.0.2_genelist_s+.xls.zip

(3) Oligo data sheet:
http://omad.operon.com/download/storage/arabidopsis_V1.0.1_datasheet.pdf


title: Operon Human MAQC (OPN)

manufacture_protocol: Operon protocol


title: Human-mouse microRNA array v8.0

status: Public on Mar 31 2005

city: Chapel Hill

first: Scott

middle: M

last: Hammond

state: NC

department: Dept Cell and Developmental Biology

institute: University of North Carolina

organism:
Homo sapiens
Mus musculus

description:
Oligonucleotide probes to 191 human microRNA genes and 198 mouse microRNA genes were designed, antisense to the mature sequence as reported in the Sanger microRNA registry (4/1/04). Probes were spotted at 40 uM on Corning GAPS-II slides in 3X SSC, dried, and crosslinked by 600mJ UV. Slides were prehybridized in 3x SSC, 0.1% SDS, 0.2% BSA for 45 minutes, hybridized for 2h at 37C in 400mM Na2HPO4 pH 7.0, 0.8% BSA,
5% SDS, 12% formamide.

first: Michael

last: Thomson

first: Lin

last: He

first: Gregory

last: Hannon


title: CRUKDMF_Sanger-1Mb_v3.0.0

status: Public on Sep 26 2006

first: Ian

last: Giddings

description: BAC/PAC


title: CCRI/Munson Haemophilus influenzae (NTHI) 11k spotted array v1.00

status: Public on Sep 09 2006

city: Columbus

first: William

middle: Clarence

last: Ray

state: OH

address: 700 W. Children's Drive. Rm W531

department: Center for Microbial Pathogenesis

institute: Columbus Children's Research Institute

organism:
Haemophilus influenzae Rd KW20
Haemophilus influenzae 86-028NP

first: Robert

middle: S

last: Munson

first: Lauren

middle: O

last: Bakaletz

last: Armbruster

manufacture_protocol: The commercial oligo set for H. influenzae Rd KW20 was purchased from Operon.  548 additional custom 70-mers were designed and synthesized for ORFs unique to/with insufficient sequence similarity to H. influenzae strain 86-028NP.  Oligos were resuspended in 2.5xSSC to a final concentration of 25uM and arrayed in quadrupliate at 55% RH, using a Genetix QArray2 arrayer on Corning UltraGAPS slides.  Printed Arrays were re-hydrated and snap dried on a hot plate at 100C for 10s.  DNA was fixed to the surface using a UV cross-linker at 650mJ/cm^2


title: CIT M2 Mus musculus 1K BAC CGH array

first: Marc-Henri

last: Stern

first: Elodie

last: Manie

first: Carine

last: Ganem-Elbaz

first: Axel

last: Mazoyer

first: Alain

last: Aurias

first: Olivier

last: Delattre


title: Snyder - Nimblegen C.albicans WGT 50-60; 50-120

status: Public on Sep 19 2006

city: Urrbrae

first: Anthony

last: Borneman

state: South Australia

address: Paratoo Rd

country: Australia

institute: The Australian Wine Research Institute

organism: Candida albicans

description: Whole genome tiling array designed for C. albicans. 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

middle: D

last: Zhang

first: Joel

last: Rozowsky

last: Seringhaus

first: Mark

last: Gerstein

last: Snyder

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


title: IU/UNH/DU Daphnia pulex Generation2 3.1K

city: Bloomington

first: John

middle: Kenneth

last: Colbourne

state: IN

department: Biology

institute: Indiana University

organism: Daphnia pulex

description: The array was printed with duplicate spots side-by-side, and consisted of 24 blocks of 17 rows and 18 columns each.

manufacturer: Indiana University- Center for Genomics and Bioinformatics

first: Elizabeth

last: Bohuski

first: Joseph

last: Shaw

first: Darren

last: Bauer

first: Justen

last: Andrews

first: Brian

last: Eads

manufacture_protocol:
cDNA libraries were constructed as described in Colbourne et al. (submitted).  From each library, 384 samples were PCR amplified from plasmids purified using the PerfectPrep kit (Eppendorf) and sequenced using BigDye (ABI; v.2) on an ABI 3730 sequencer.  These samples served as a random sample for quality control in further analysis.  Remaining samples (3,168 in all) were PCR amplified from colony picks of transformed bacterial cells.  Template was generated by growing colonies in 1.2 ml of 2X YT and 0.005% chloramphenicol in 96-deepwell plates for 24 hours at 37 degrees C.  Reactions were run in 100 μl containing: 1X Taq buffer (Eppendorf), 0.2 mM dNTPs, 0.2 microM primers (Fwd. 5'-GTGTAAAACGACGGCCAGTAG 3’ and Rev. 5'-AAACAGCTATGACCATGTTCAC 3’), 5 U Taq (Eppendorf), and 5 microliters fresh bacterial growth or 2 microliters purified plasmid.  Quality of PCR amplifications was verified by gel electrophoresis, and number and size of bands was recorded using Kodak’s 1D imaging software (v.3.6).  Concentration of samples was determined by 96-well microplate spectrophotometer (Molecular Devices SpectraMax 190) and adjusted to 50-200 ng/microliter for printing.
A Genemachines Omnigrid 100 was used to print the D. pulex cDNA on GapsII aminosilane slides (Corning).  The cDNA was printed in 3X SSC and 1.5 M Betaine buffer and deposited with Stealth Micro-Spotting Pins (Telechem) at 20°C and 65% humidity.  The cDNA was fixed to the microarray slides by baking at 85oC for 3 hours.  Slides were processed by agitating in 0.2 % SDS for 5 min. and in HPLC-grade water, 5 min at 21°C., followed by 2 min. in 95oC water, rinsing briefly in ice-cold 100% isopropanol, and centrifuging at 500 x g for 5 min.  Five types of negative controls were printed, including printing buffer, failed PCR reaction with template DNA but no primers, ORFs from Arabidopsis and lambda phage, and bacterial PCR spikes (Ambion).  Positive controls of D. pulex genes were printed next to printing buffer to insure no carryover, and included cytochrome c (subunits I, II, and III), cytochrome b, actin, and ferritin.


title: NCI Operon Human MAQC

first: Leming

last: Shi


title: UBC/MSL C. neoformans serotype D 70K

first: Won Hee

last: Jung

state: British Columbia

address: 2185 East Mall

department: Michael Smith Laboratories

organism: Cryptococcus deneoformans

manufacturer: Washington University Genome Science Center

manufacture_protocol: Microarray contain long oligo 70 mers that are designed to uniquely represent each gene in C. neoformans serotype D. These oligomers are arrayed on treated glass slides using split pin technology together with control oligos.


title: 5808-spot_slide_version4

first: Ian

last: Giddings

description: cDNA


title: 20K Ovita Ovine Array print 73

status: Public on Sep 06 2006

city: Dunedin

first: Orla

middle: Mary

last: Keane

state: Otago

address: 710 Cumberland St

department: Animal Genomics

country: New Zealand

institute: AgResearch

organism: Ovis aries

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

first: Theresa

last: Wilson

first: Dianne

middle: L

last: Hyndman

first: Alan

middle: F

last: McCulloch

first: Allan

last: Crawford

manufacture_protocol: Ovine EST inserts were amplified in 96 well plates using the universal primers SP6 and T7 in 50 ul reactions (1.5 mM MgCl2, 2 mM each dNTP, 45 pmol primers and 2.5 units AB Red Hot Taq polymerase). The reactions were denatured at 94C for 3 minutes then cycled 36 times at 94C for 45 sec, 55C for 45 sec and 72C for 60 sec. Finally products were extended at 72C for 5 min. The PCR products were verified by agarose gel electrophoresis, precipitated and resuspended in printing solution. An ovine microarray consisting of 11,520 spots was printed onto poly-L-lysine coated glass slides using an ESI array robot with 32 split pinheads depositing 0.6 nl with a 100 um spot size. After printing the slides were UV irradiated to cross-link the DNA to the polylysine coating.


title: Small RNAs identified using 454 sequencing

city: Davis

first: Blake

middle: C.

last: Meyers

state: CA

address: 451 Health Sciences Dr.

department: UC Davis Genome Center

institute: University of California - Davis

technology: other

distribution: virtual

first: Cheng

last: Lu

first: Pamela

last: Green


title: SAGE:10:Sau3A:Sus scrofa

status: Public on Sep 05 2006

last: GEO

organism: Sus scrofa

technology: SAGE Sau3A

description: This is a virtual platform for SAGE libraries generated for Sus scrofa using Sau3A as an anchor enzyme.


title: Pseudomonas syringae pv. tomato str. DC3000 5.6K array

status: Public on Sep 01 2006

city: manhattan

first: Xiaoyan

last: Tang

email: xtang@ksu.edu, llan@ksu.edu

state: KS

address: 4702 Throckmorton

department: Plant Pathology

institute: Kansas State University

first: Lefu

last: Lan

manufacture_protocol: as described in Nimblegen Labs manual


title: Chicken mRNA MPSS signatures

city: Seoul

first: heebal

last: kim

address: San 56-1 Sillim-dong Gwanak-gu

institute: Seoul National University

organism: Gallus gallus

technology: MPSS

description:
The generation of MPSS datasets in the gonad and PGCs samples was performed by Takara Biotechnology Cooperation (Shiga, Japan).
Annotation Classe Table:
Virtual Signature Class mRNA Orientation Poly-Adenylation Features Position
Class   PASa    PATb    Strand                         Position
1     yes     yes     Forward                        The first one 5’ to the PAS and PAT
2     yes     no      Forward                        The first one 5’to the PAS
3     no      yes     Forward                        The first one 5’ to the PAT
4     no      no      Forward                        The most 3’ signature of the sequence
5     yes/no  yes/no  Forward                        Not the most 3’ signature of the sequence
11     yes     yes     Reverse complement             The first one 5’ to the PAS and PAT
12     yes     no      Reverse complement             The first one 5’to the PAS
13     no      yes     Reverse complement             The first one 5’ to the PAT
14     no      no      Reverse complement             The most 3’ signature of the reverse complement strand of the cDNA sequence
15     yes/no  yes/no  Reverse complement             Not the most 3’ signature of the reverse complement strand of the cDNA sequence
22     yes     no      unknown                        The first one 5’ to the polyA signal
23     no      yes     unknown                        The first one 5’ to the polyA tail
24     no      no      unknown                        The most 3’ signature of the sequence
25     yes/no  yes/no  unknown                        Not the most 3’ signature of the sequence
1000    NA      NA      Forward or reverse complement  The signature has only chromosome matches
0     NA      NA      Forward or reverse complement  The signature matches more than 100 chromosome loci

first: Heebal

last: Kim

first: Jae

middle: Y

last: Han

manufacture_protocol:
Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, Roth R, George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J, Fearon K, Mao J and Corcoran K. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18:630–634, 2000.
Brenner S, Williams SR, Vermaas EH, Storck T, Moon K, McCollum C, Mao JI, Luo S, Kirchner JJ, Eletr S, DuBridge RB, Burcham T and Albrecht G. In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc Natl Acad Sci U S A 97(4):1665-70, 2000.
Ruan Y, Le Ber P, Ng HH and Liu ET. Interrogating the transcriptome. Trends Biotechnol 22(1): 23-30, 2004.


title: Amersham Biosciences Codelink uniset rat 1 Bioarray

city: Lille

first: Jamal

last: Khalife

address: 1 rue du Prof. Calmette

institute: Inserm U547

description: ~10 000 rat genes — one specific, prescreened 30-mer probe per gene, functionally validated

first: James

last: George

first: Christine

last: Pierrot

first: David

last: Hot


title: 11K Ovita Ovine Array print 67

first: Orla

last: Keane

last: Wilson


title: 11K Ovita Ovine Array print 70

first: Theresa

last: Hyndman

last: McCulloch


title: Rosetta/Merck Mouse 25K v1.9 Array

status: Public on Sep 04 2006

city: Harlow

first: Ignacio

last: Munoz-Sanjuan

state: Essex

address: Terlings Park

department: Molecular & Cellular Neuroscience

institute: Merck Sharp & Dohme

manufacture_protocol: See Manufacturer's Web Site


title: Brandeis/Harvard Drosophila Melanogaster 3.7K

status: Public on Aug 17 2006

city: Boston

first: Meghana

last: Kulkarni

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

organism: Drosophila melanogaster

manufacturer: Biopolymers Facility, Harvard Medical School

first: Matthew

last: Booker

first: Serena

last: Silver

first: Adam

last: Friedman

first: Pengyu

last: Hong

first: Norbert

last: Perrimon

first: Bernard

last: Mathey-Prevot

manufacture_protocol: Custom cDNA-based Microarray: DNA probes to a set of approximately 3,000 strategically selected genes were generated by PCR. These probes were obtained from the PCR amplicons used to generate the dsRNA library 16. The 3,000 genes represented on the array include genes for all the Kinases (350) and Phosphatases (161) encoded in the Drosophila genome, known/canonical components and targets of the major signaling pathways such as Wg/Wnt, Hh, TGF-β, JAK/STAT, NFκB, Notch, RTK, JNK, and INR pathways 33,34; Life cycle website at Yale. Approximately 1,000 of the 3,000 genes were randomly selected to facilitate normalization of signal intensity across the array. Only PCR products showing a clear and strong bands were recovered using Montage PCR plates (Millipore). The DNA concentration was determined using PicoGreen reagent (Molecular Probes). The final concentration of DNA averaged 400 ng/µl. Samples were transferred to 384 well plates (Genetix: x6004) containing DMSO to give a final concentration of 200 ng/µl in 50% DMSO. The DNA probes were directly spotted onto Corning UltraGAPS coated glass slides using a Genetix QArray robot in the Biopolymer Facility at Harvard Medical School. Spots were arrayed in a 14 x 14 arrangement using 24 (4 x 6) Genetix 150µm diameter tip solid microarray pins with a center-to-center spacing of 315 µm. A number of controls were prepared and printed on the glass slides with the probe DNAs. These controls include Negative controls (water, 50% DMSO, sonicated salmon sperm DNA, human Cot1, mouse Cot1, GFP, CFP, YFP, LacZ, and Luciferase) to assess the degree of nonspecific hybridization, and Spiked controls (Lucidea Universal Scorecard, Amersham Biosciences).


title: University of Michigan/Bergman Bacillus anthracis

city: Atlanta

first: Nicholas

last: Bergman

state: GA

address: 310 Ferst Dr., Rm 231

institute: Georgia Institute of Technology

organism: Bacillus anthracis

middle: H

manufacture_protocol: Probe sets selected from Bacillus anthracis Ames ancestor sequence, including pXO1 and pXO2 sequences.  Array produced using standard Affymetrix protocols


title: NimbleGen Human Promoter Array

city: Singapore

first: Vinsensius

middle: B

last: Vega

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

manufacture_protocol: refer to Nimblegen Systems


title: IBMMPMC_Scerevisiae_12.8k_EGT_G250E

city: gosselies

first: Patrice

last: Godard

address: rue des professeurs Jeener et Brachet, 12

department: IBMM

country: Belgium

institute: Université Libre de Bruxelles

manufacture_protocol: See Talla et al. 2003 (PMID : 14499002)


title: RICE 22k oligo microarray

status: Public on Jun 13 2006

city: tsukuba

first: Chiharu

last: Akimoto-Tomiyama

address: 2-1-2 kannonndai

country: Japan

institute: NIAS

organism: Oryza sativa

description: Keywords = Rice, Plant, monocotyledons, full-length cDNA, 60mer oligonucleotide, NIAS

first: Kaku

last: Hanae

manufacture_protocol: On the basis of the collection, mapping and annotation of over 28,000 full-length cDNA clones from japonica rice(Science Jul 18 2003: 376-379), we have constructed a monitoring system that uses the sequence information of the full-length cDNA clones as a 60mer-single stranded oligonucleotide format. Probes on the array (ca 22,000) cover the whole transcription units corresponding to 28K full-length cDNA clones


title: IBMMPMC_Scerevisiae_12.8k_EGT_D290C

organism: Saccharomyces cerevisiae


title: Tufts Homo sapiens 21K V2.1.2

first: Ralph

last: Isberg

address: 150 Harrison Ave.

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

manufacturer: Operon and Tufts University Expression Analysis Core facility

first: Jim

last: Flynn

first: Lan

last: Wei

manufacture_protocol: see Tufts University Expression Analysis Core facility website for details


title: MBPL Human 30k P3

status: Public on Jul 26 2006

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

description: There are 32448 spots within a array.7334 human clone were printing 4 duplicate in a array. Additionally, we printing 10 spike genes (SpotReport?-10 Array Validation System , Stratagene)  and one house-keeping gene , 5 negative control gene as quality control indicator. total 16 quality control indicator were printing 2 duplicate in each block.

first: ChihYing

last: Hsu

first: YuLing

last: Hsieh

first: WeiChung

last: Cheng

first: KunYu

first: TsaiJiuan

last: Weng

first: MinLing

last: Tsai

first: HuaKuo

last: Lin

first: ChingLung

last: Huang

first: ChiuTing

manufacture_protocol: Arrayer obtained from Dr. Patrick O. Brown MGuide II and ArrayMarker program version 2.3.2 (Dr. Joseph DeRisi, university of California, San Francisco) with 48 spotting pins (TeleChem).We control printing condition in temperature 25~27°C and humidity about 41~43%, and printing in June 2003.cDNA clones were purchased from Incyte Genomics and 7334 sequence-verified clones were amplified by PCR.We purified these 7334 clones by isopropanol precipitation and used 3×saline-sodium citrate (SSC) as spotting solution. cDNA spotted on GAPS Ⅱ coated slides (Corning Incorporated)coating of pure gamma amino propylsilane.


title: MPIMG Homo sapiens 44K aCGH2_MPIMG_BERLIN

status: Public on Sep 12 2006

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

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: Rosetta/Merck Rat 50k v2.1 Array 1 microarray

status: Public on Apr 05 2006

city: Seattle

first: Amit

middle: V

last: Kulkarni

state: WA

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description:
Oligonucleotide array on glass.
Contains 60-mer probes (60-mer).

first: John

last: Castle

manufacture_protocol: see manufacturer's web site


title: Rosetta/Merck Rat 3.0 A1 microarray

status: Public on Mar 17 2006

manufacturer: Rosetta Inpharmatics / Merck Pharmaceuticals


title: MBPL human 30k P2

status: Public on Jun 27 2006

description: There are 32448 spots within a array.7334 human clone were printing 4 duplicate in a array. Additionally, we printing 10 doping control genes (SpotReport™-10 Array Validation System , Stratagene)  and one house-keeping gene , 5 negative control gene as quality control indicator. total 16 quality control indicator were printing 2 duplicate in each block.

first: ChinYing

manufacture_protocol:
 Arrayer obtained from Dr. Patrick O. Brown MGuide II and ArrayMarker program

version 2.3.2 (Dr. Joseph DeRisi, university of California, San Francisco) with 48

spotting pins (TeleChem).We control printing condition in temperature 25~27°C and Humidity about 41~43%, and printing on April 2003.

cDNA clones were purchased from Incyte Genomics and 7334 sequence-verified

clones were amplified by PCR.We purified these 7334 clones by isopropanol

precipitation and used 3×saline-sodium citrate (SSC) as spotting solution. cDNA spotted on GAPS Ⅱ coated slides (Corning Incorporated)coating of pure

gamma amino propylsilane.


title: Listeria monocytogenes (EGDe) macroarray, version 1

status: Public on Jul 03 2006

city: Ribeirao Preto

first: Ricardo

last: Vêncio

state: SP

address: Av. Bandeirantes, 3900

department: Computing and Mathematics Department

country: Brazil

institute: Universidade de São Paulo

organism: Listeria monocytogenes

first: Michel

last: Doumith

manufacture_protocol:
According to Doumith et al (2004, Infect Immun. 72:1072–1083):

MATERIALS AND METHODS - Probe selection, primer design, PCR amplification, and array construction.

The L. monocytogenes EGDe-specific probes spotted onto the Listeria array corresponded to the 270 genes defined previously as being specific for L. monocytogenes EGDe with respect to L. innocua CLIP 11262. As some genes were too small to allow amplification of a PCR product of optimal size, the final array contained 262 EGDe genes. The 94 probes that were specific for L. innocua CLIP 11262 relative to L. monocytogenes EGDe were also selected from the previously defined list of 149 genes specific for L. innocua CLIP 11262. For genomic regions containing several genes, only representatives were chosen for the array. In order to identify L. monocytogenes CLIP 80459-specific sequences, we used the program Cross-match (http:/bozeman.mbt.washington.edu/). With this approach, 141 sequence fragments, ranging from 33 to 3,025 bp, were identified as missing from both L. monocytogenes EGDe and L. innocua CLIP 11262. For probe design, only fragments longer than 1 kb were taken into account, allowing us finally to select 53 sequences that were specific for L. monocytogenes CLIP 80459. Primers were designed by use of a modified version of Primer 3 software (CAAT-box [18]) to amplify a specific fragment of 300 to 600 bp for each gene (melting temperatures were 55 to 65°C) (Eurogentec). Amplification reactions were performed in a 100-μl reaction volume containing 10 to 20 ng of chromosomal DNA. The concentration and size of each PCR product were verified on agarose gels. For array preparation, nylon membranes (Qfilter; Genetix) were soaked in TE solution (10 mM Tris [pH 7], 1 mM EDTA [pH 7.6]). Spot blots of PCR products and controls were performed by a Qpix robot (Genetix). Following spot deposition, membranes were fixed for 15 min in 0.5 M NaOH-1.5 M NaCl, washed briefly in distilled water, and stored wet at −20°C until use.


title: Novusgene type 4 Hematology/Oncology TMU667 array

status: Public on Jun 06 2006

city: Tokyo

first: Junko

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

institute: Tokyo Medical University

organism: Homo sapiens

first: Ryoko

last: Hamamura

manufacture_protocol: This 'condensed' DNA chip comprises 700 spots of highly specific 60-mer oligonucleotide probes that have been printed in triplicate.  The full array layout representing 2100 features is linked as a supplementary file.


title: Rosetta/Merck Human 44k 1.1 microarray

status: Public on Sep 28 2006


title: Upland Cotton Fiber-Specific cDNA Array

status: Public on Jan 01 2006

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

institute: College of life sciences, Peking University

organism: Gossypium hirsutum

description: To estabilish upland cotton fiber-specific cDNA array, we constructed cDNA library from 5-10 day post anthesis cotton fibers when fiber cells elongate most quickly. Secondly, we randomly sequenced over 35,000 ESTs from this library and acquired a gene pool of more than 11,000 UniESTs. The cotton UniESTs were then PCR-amplified and printed onto microarray. This array is comprised of 11,692 high-quality cotton cDNAs (each sequence length>300bp, average length = 586bp) representing over 8,000 cotton genes.

manufacturer: CapitalBio Corporation, National Engineering Research Center for Beijing Biochip Technology, 18 Life Science Parkway, Beijing 102206, China

first: Yong-Hui

last: Shi

first: Liang

last: Zhang

first: Jing

manufacture_protocol:
Individual bacterial clones were selected and distributed into 96-well plates. PCR amplification of DNA using primers specific to the plasmid vector sequences flanking the insert cDNA  (M13 forward and reverse primers) were performed in 96-well PCR plate in a Perkin-Elmer 9600 thermocycler in 50-µL reactions containing 1× PCR buffer (TaKaRa, Dalian, China), 2.0 mM MgCl2, 0.2mM dNTPs, 10 pmol of each primer, 5 units of Taq polymerase, and 10 ng plasmid template. The PCR cycle consisted of one round at 95℃ for 3 min, then 35 cycles including 95℃ for 1 min, 55℃ for 20 s and 72℃ for 90 s, with a final extension at 72℃ for 5 min. One µL of the PCR reactions was analyzed in a 1% agarose gel to verify the success of the amplification. The remaining PCR products were precipitated with addition of 100 µL of anhydrous ethanol and resuspended in 15 µL of 50% DMSO for arraying. As a result, 11,692 cDNA were amplified and printed on the cDNA microarrays.
Fluorescent dye (Cy5 and Cy3-dCTP) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. Double-stranded (ds) cDNA containing T7 RNA polymerase promoter sequence was synthesized from 10 µg of total RNA using a cDNA synthesis kit following the manufacturer’s instructions (TaKaRa). A T7-OligodT primer (5’-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTT TTTTTTTTTTTTTTTV -3’) was used to replace the poly T primer provided in the kit. Synthesized ds cDNA was purified using the PCR Purification kit (Qiagen) and purified products were eluted using 60-µL elution buffer. A half of the eluted ds cDNA was reduced to 8 µL before subjecting to in vitro transcription in 20 µL of reaction mixture using the T7 RiboMAX Express Large Scale RNA Production System (Promega) for 3 h at 37℃. Amplified RNA (aRNA) was purified using the RNeasy Mini kit (Qiagen). For labeling of the probes, 2 µg of aRNA was mixed with 2 µg of random hexamers, denatured at 70℃ for 5 min, cooled on ice before adding 4 µL of first strand synthesis buffer, 2 µL of 0.1M DTT, 1 µL 10 mM mixed dNTPs, and 1.5 µL SuperScript II (Invitrogen) to the system. The reaction mixture was first incubated at 25℃ for 10 min before transferring to 42℃ for 60 min. The labeled cDNA was purified using a PCR Purification kit (Qiagen), reduced to 10 µL volume and mixed with 2 µg of random nonamers, heated to 95°C for 3 min and cooled on ice immediately. 10×buffer, dNTP and Cy5- or Cy3-dCTP (Amersham Pharmacia Biotech) was added to a final concentration of 120 µM each for dATP, dGTP and dTTP, 60 µM for dCTP and 40 µM for Cy5 or Cy3 dyes respectively. One µL Klenow (Takara) was added to the mixture and the reaction progressed for 60 min at 37℃. The labeled cDNA was again purified with a PCR Purification kit (Qiagen), resuspended in elution buffer and quantitatively adjusted based on the efficiency of dye incorporation. Appropriate amount of the labeled cDNA was mixed in a final volume of 30 µL of hybridization solution that contains 50% formamide and 1×hybridization buffer (Amersham Bioscience), and was denatured at 95℃ for 3 min prior to loading onto a microarray. The array was hybridized at 42℃ overnight and was first washed for 5 min at 42°C with washing solutions that contain 0.2% SDS and 2×SSC followed by a second wash using washing solutions that contain 0.2% SSC for 5 min at room temperature.


title: OSU Upland cotton line Im216 SSH library array

city: Stillwater

first: Margaret

last: Essenberg

state: OK

address: 246 NRC, OSU

department: Biochemistry & Mol. Biol.

institute: Oklahoma State University

description: Production of spotted microarrays of PCR products from cotton cDNAs by OSU:  PCR products were from an SSH library enriched in transcripts up-regulated at 8, 14, 20, 30, 45, or 60 hpi in Im216 leaves following inoculation with Xanthomonas campestris pv. malvacearum relative to non-inoculated control tissue.  Using an OmniGrid 100 arrayer (GeneMachines) fitted with 2x2 Telechem SMP4 quill pins, 191 PCR products from the library (116 non-redundant) plus ones from 14 donated cotton cDNAs in 3xSSC at about 360 ng/µl were spotted onto GAPS II glass slides (Corning Life Sciences) at 23-26°C and 55% RH.  Spots were arranged 10x10 per block (48 total blocks), with spot centers 350 µm apart.  The collection was arrayed 12 times per slide, as two columns of six arrays.  Slides were left to dry overnight on the arrayer, rehydrated for 30sec, and snap-dried.  Probes were immobilized by baking at 85°C overnight, and the slides were stored in slide holders in a desiccator at room temperature.

first: Patricia

middle: J

last: Ayoubi

first: Mohini

middle: A

last: Patil

last: Pierce

first: Angela

last: Phillips

first: Bryan

last: Venters

manufacture_protocol: OminiGrid 100 fitted with Telechem SMP4 quill-style pins.  Printed at room temperature (23-26C) at 55% RH.


title: cDNA microarray Trymanosoma cruzi - v.2

status: Public on Jun 13 2005

organism: Trypanosoma cruzi

description: DNA microarrays were constructed with 755 ESTs obtained from non-normalised and normalised cDNA libraries of CL Brener epimastigotes and from amastigotas of Tulahuen (Ürmenyi et al., 1999; DaRocha et al., 2000). Polymerase chain reaction (PCR) amplification of the ESTs (average length 800 bp) was obtained with T3 and T7 primers using DNA polymerase (Biolase). The amplification products were purified with Multiscreen plates (Millipore). Inserts representing 32 cloned T. cruzi coding and non-coding genes, control sheared DNAs and oligonucleotides were also immobilised on the glass slides with Generation III Microarray System spotter (Molecular Dynamics) according to manufacturer's instructions.

first: Cassio

last: Baptista

first: Bianca

last: Zingales


title: yeast intergenic array

status: Public on Nov 10 2004

city: Geneva

first: Stephan

middle: B.

last: Schawalder

address: Quai Ansermet 30

department: Departement of Molecular biology

country: Switzerland

institute: University of Geneva

description:
-Platform: amino-silane coated glass slides (GAPS II, Corning)

-S. cerevisiae intergenic regions amplified from S288C genomic DNA (ResGen) using the intergenic region primer oligonucleotides (ResGen) (Harismendy et al. EMBO J. 22(18): 4738-4747, 2003). The primers allow the amplification of the sequence located on either side of elements such as open reading frames, tRNAs, small nuclear RNAs, Ty elements, solo δ, etc. A complete description of the primers can be obtained on the web site (ftp://ftp.resgen.com/pub/genepairs/yeast_intergenic).

-The PCR products were purified and spotted using an automated arrayer (MicroGrid II, BioRobotics)

first: Mehdi

last: Kabani

first: Urmilla

last: Choudhurry

first: Isabelle

last: Howald

last: Werner

first: David

last: Shore


title: Dexamethasone-regulated genes in M-1 CCD cells

status: Public on Aug 26 2005

city: Baltimore

first: Djikolngar

last: Maouyo

state: MD

institute: University of Maryland Baltimore

organism: Mus musculus

description: Experimental design. Cells were then treated with 100 nM hydrosoluble dexamethasone or steroid-free medium for 3 hours at 37˚C with 5% CO2. RNA samples from dexamethasone-treated and control cells were extracted with Trizol reagent, and DNA-decontaminated using DNA-free kit, commercially available (Ambion, Austin, TX). Yield and concentration was quantified by spectrophotometry. RNA quantity and integrity was confirmed by denaturing formaldehyde agarose gel electrophoresis and ethidium bromide staining. These samples were used for microarray labeling. Microarrays, RNA labeling, and hybridization. High quality spotted cDNA on glass slide microarrays were purchased from the Microarray Centre of the University Health Network (Toronto, Canada). These arrays contained PCR-generated cDNA inserts of all 15,264 sequence-verified mouse ESTs, from the National Institute of Aging collection. Duplicate 100-mm diameter cDNA spots are represented on GAPS II slides (Corning, Inc.). Spot cDNA identity is tracked by composed identifiers including clone identifier, description, and Unigene, and catalogued as “M15Kv1”. Briefly, 5 g total RNA was reverse-transcribed using oligo-dT flanked at 5’ end with capture sequences specific to fluorescent Cy3- or Cy5-coupled dendrimer complexes. The resulting cDNAs from the control and test samples were mixed and hybridized with the mouse cDNA arrays in humidified hybridization chambers at 60˚C for 18 hours. Following hybridization, microarrays were washed three times as described above. Quantitation. Slides were read using a laser confocal scanner, the GSI Lumonics ScanArray 5000 imaging system, at 10-µm resolution set up for excitation/emission at 543/570 and 649/670 nm, and for acquisition of Cy3 and Cy5-labeled spots respectively. Scanned image data were saved in 16-bit tiff files and quantitated with Imagene 4.0 (BioDiscovery, Marina del Rey, CA). The mean intensities of fluorescent spots were measured.

manufacturer: University Health Network Microarray Center: http://www.microarrays.ca

first: Paul

last: Welling


title: AECOM H1 series

status: Public on Jul 22 2003

city: Bronx

first: Weijia

last: Zhang

state: NY

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

description:
cDNA Spotted array; Research Genetics human EST clone set; 8,707 probe spots
Keywords = EMTs
Keywords = TGF-β

first: Jiri

last: Zavadil

first: Markus

last: Bitzer

first: Dan

last: Liang

first: Yaw-Ching

last: Yang

first: Aldo

last: Massimi

first: Susanne

last: Kneitz

first: Ester

last: Piek

first: Erwin

middle: P

last: Böttinger


title: AECOM 5H series

description:
cDNA spotted microarray; Research Genetics human EST library
Keywords = EMTs, TGF-β


title: Rosetta/Merck Mouse TOE 75k Array 1 microarray

first: Amit

last: Kulkarni

first: John

last: Castle


title: Rosetta/Merck Rat 25k v1.2 microarray

status: Public on May 17 2005

organism: Rattus norvegicus

description:
Oligonucleotide array on glass.
Contains 60-mer probes (60-mer).
Keywords = Rat 25k microarray Merck