title: Mycoplasma hyopneumoniae spotted PCR array

status: Public on Oct 31 2007

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

country: USA

institute: Iowa State University

organism: Mesomycoplasma hyopneumoniae

technology: spotted DNA/cDNA

description: Corning UltraGAPS substrates (catalog #40016)

distribution: non-commercial

manufacturer: Chris Minion Laboratory at Iowa State University

first: Melissa

middle: L

last: Madsen

manufacture_protocol: The M. hyopneumoniae microarray consists of PCR products (125-450 bp) spotted to Corning UltraGAPS™ substrates. Each probe was printed in triplicate, in non-adjacent spots to reduce non-uniform substrate errors in replicated probes. The array consisted of 16 subarrays, with a 12-column x 12-row configuration.


title: Drosophila Chromosome 2L microarray (based on Dmel release 3.0)

status: Public on Oct 27 2007

city: Basel

first: Oliver

last: Bell

address: Maulbeerstr. 66

department: Epigenetics

country: Switzerland

institute: Friedrich Miescher Institute

organism: Drosophila melanogaster

description:
The genomic array used in this study, dros_chrom_array_MIT_120803, was designed in the laboratory of Stephen P. Bell at the Massachusetts Institute of Technology. The array contains 13440 features spotted on glass Gaps II slides (Corning) in 32 meta grids. There are 11816 1.5 kb pcr products that tile the non-repetitive sequences of chromosome 2L. In addition there are 287 1.5 kb features from chromosome 4, 90 features from chromosome 3L, 177 features from chromosome 3R and finally 48 features corresponding to telomeric sequences. The features were all amplified from BACs and visually verified. The oligos for amplification were designed from the final release candidate for release 3.0 of the Drosophila genome using custom perl scripts and primer3. The primers were synthesized by Operon.
The file, dros_chrom_array_MIT_120803.csv, describes and provides coordinates for all the features on the array.

first: David

middle: M

last: Macalpine

first: Stephen

middle: P

manufacture_protocol: For details see http://chromosome2l.mit.edu/array/


title: UCD/LLNL_PM1_Array

status: Public on Oct 20 2007

city: Livermore

first: Anu

last: Chakicherla

state: CA

address: 7000 East Avenue, Mail Stop: L-446

institute: Lawrence Livermore National Lab

organism: Methylibium petroleiphilum PM1

technology: in situ oligonucleotide

distribution: custom-commercial


title: DTU/CMB_Aspergillusnidulans_9371_v1.0

status: Public on May 30 2006

city: Kgs. Lyngby

first: Ana Paula

last: Oliveira

address: Building 223

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

organism: Aspergillus nidulans

description: Custom CDF file linked at foot of record as a supplementary file.

manufacture_protocol: Arrays manufactured by a Maskless Array Synthesizer systems, which makes use of a Digital Micromirror Device


title: Irradiated Mouse liver array_Gamma-ray

city: sendai-city

first: Taisuke

last: Baba

state: Miyagi

address: seiryo-machi 4-1

country: Japan

institute: Tohoku Univ. IDAC

organism: Mus musculus

technology: spotted oligonucleotide

manufacture_protocol:
1.  Oligos are arrayed in Genetix 384-well V-bottom plates. Each well contains 300 pmol of 60-mer oligo.
2. Resuspend oligos in 30-percent DMSO to 30 uM and rearray 10 uL into 384-well, Genetix polystyrene V-bottom plates (cat# X6004).
3. After printing, rehydrate arrays by holding slides ( array side down) over a bath of hot double distilled H2O (95-C) for approximately 5 sec until a light bapor film is observed across the slide.
4. Plate to dry on a 100-C hot plate for approximately 5 to 10 sec.
5. Crosslinked DNA to the array slide using a UV crosslinker (150mJoules).
6. Incubate at 42-C for 30 minutes by 5XSSC, 0.1-percent SDS, 0.1mg/mL BSA 25-percent formamide.
7. Washing to remove the SDS completely.
8. Centrifuge plates at 2000 rpm for 3 minutes.


title: A genome proxy array for profiling marine micobial communities

city: Tucson

first: Virginia

middle: Isabel

last: Rich

state: AZ

address: 1041 E. Lowell St.

institute: University of Arizona

organism:
uncultured crenarchaeote 4B7
Prochlorococcus marinus subsp. pastoris str. CCMP1986
uncultured marine alpha proteobacterium
uncultured marine gamma proteobacterium EBAC31A08
uncultured marine group II euryarchaeote 37F11
uncultured Pseudomonadota bacterium
uncultured crenarchaeote 74A4
uncultured marine bacterium 440
uncultured marine bacterium 577
uncultured marine bacterium 583
uncultured gamma proteobacterium eBACHOT4E07
uncultured marine bacterium EB0_41B09
uncultured proteobacterium 60D04
uncultured proteobacterium 65D09
uncultured marine group II euryarchaeote EF100_57A08
uncultured marine bacterium EB000_55B11

description: ***Design Overview***  The prototype microarray targeted thirteen BAC or fosmid genome fragments (20-160kb) from both bacteria and archaea (Table 1), recovered from a variety of marine habitats (Table 2), as well as the cyanobacterium Prochlorococcus MED4. These clones were originally sequenced because of the presence of taxonomic marker or specific functional genes. This array consisted of sets of 70-bp oligonucleotides targeting each genome or genome fragment (Fig. 1), dispersed along the target sequences with no more than one probe per gene, and excluding rRNA genes as targets. The probes were selected solely based on theoretical thermodynamic properties and GC content (~40%); that is, probe selection did not focus on specific genes or regions, but simply produced the “optimal” probes for each genome proxy based on the probes’ predicted hybridization properties. rRNA genes were excluded, because this probe design approach, which avoids sequence alignments and considerations of RNA secondary structure, would be unlikely to result in useful rRNA probes. Furthermore, rRNA probes of traditional design could not be included on the array because their appropriate hybridization conditions would be very different from those of this array’s probes.

middle: I

first: Edward

middle: F

last: DeLong

manufacture_protocol: ***Microarray construction***  Oligonucleotides were synthesized (Illumina, San Diego, California), suspended in 3XSSC to a concentration of 40pmol/μl, and spotted on homemade poly-L-lysine-coated glass slides using a QArray 2 microarraying robot (Genetix, Hampshire, England). Six replicates of each probe were spotted.


title: ROMA-mouse-85K-v1.0

status: Public on Oct 28 2007

city: Cold Spring Harbor

first: Ira

last: Hall

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

manufacture_protocol: NimbleGen manufactures custom, high-density D arrays based on its proprietary Maskless Array Synthesizer (MAS) technology. The MAS system is a bench top, solid-state, high-density D array fabrication instrument comprised of a maskless light projector, a reaction chamber, a personal computer, and a D synthesizer. NimbleGen builds its arrays using photo-mediated synthesis chemistry with its MAS system. See http://www.nimblegen.com/technology/manufacture.html for more details.


status: Public on Oct 30 2007

city: Tsukuba

first: Emiko

last: Kitagawa

state: Ibaraki

address: Onogawa 16-1

institute: National Institute of Advanced Industrial Science and Technology

organism: Saccharomyces cerevisiae

description:
Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 73,74,75,77,80)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.

manufacture_protocol: see manufacturer's web site


title: Vibrio parahaemolyticus RIMD2210633 5k microarray

city: Suita

first: Kaori

last: Izutsu

state: Osaka

address: 1-1 Yamadaoka

department: Research Institute for Microbial Diseases

institute: Osaka University

organism: Vibrio parahaemolyticus RIMD 2210633

manufacturer: Molecular Gene Technics, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.

first: Kosuke

last: Tashiro

first: Satoru

last: Kuhara

first: Tetsuya

last: Iida

manufacture_protocol: PCR products were prepared for all the protein-coding genes on the V. parahaemolyticus RIMD2210633 genome (4,832 genes in total).Principles for the probe design were average 500bp in length and 1 probe for each gene. 4,866 probes were amplified and each probe was spotted onto poly-L-Lysine coated glass slides (SD10011; Matsunami Glass Ind., Osaka Japan) using SPBIO (Hitachi Software Engineering, Tokyo, Japan).


title: CapitalBio Saccharomyces cerevisiae 23K oligo array

status: Public on Oct 24 2007

city: Changchun

first: Xuming

last: Deng

address: Xi'an Street 5333#

country: China

institute: College of Animal Science and Veterinary Medicine, Jilin University

manufacture_protocol: A Yeast Genome Oligo Set consisting of 5’ amino acid-modified 70-mer probes was purchased from Operon. Then Oligonucleotides were dissolved in EasyArrayTM spotting solution (CapitalBio Corp) at 40 uM concentration, and printed on PolymerSlide (75×25 mm), in which the surface was covered by a thin layer of aldehyde group modified three-dimensional polymer chain (CapitalBio Corp.). A set of microarray containing a total of 23184spots, including 6400 clones in the form of PCR products and controls: Hex was used as mobilized positive control; DMSO was used as spot solution and negative control; Five housekeeping genes of yeast genome, ACT1, RPL32, SSA4, TUB4, UB14 were used as positive controls, and Eight sequences derived from intergenic regions of the yeast genome were used as external controls. These sequences were PCR amplified and cloned into plasmid pSP64Poly (A) (Promega) to produce poly (A)-RNA after in vitro transcription. All of the PCR products and controls were spotted in triplicate on slide. On the slide, there are 48 blocks and every block has 21 columns and 22 rows.


description:
Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 71,72)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


title: Nimblegen Catfish 28K Oligo Microarray

status: Public on Oct 23 2007

city: Auburn

first: Eric

last: Peatman

state: AL

address: 203 Swingle Hall

department: Fisheries and Allied Aquacultures

institute: Auburn University

organism:
Ictalurus punctatus
Ictalurus furcatus

description: This platform builds upon a previous 19K channel catfish microarray design (GPL2814). Newly sequenced immune and miscellaneous transcripts from channel catfish were added bringing the number of sequences from that species to 21,359.  Additionally, 7,159 unique ESTs from the closely-related species blue catfish (Ictalurus furcatus) were added.

first: Puttharat

last: Baoprasertkul

first: Jefferey

last: Terhune

first: Rex

last: Dunham

first: Zhanjiang

last: Liu

manufacture_protocol: Nimblegen utilized an in situ maskless array synthesis technology to synthesize 24 base pair (24mer) oligos on the surface of the microarray slides.  At least 6 perfect match and 6 mismatch oligos were designed for each provided sequence using Nimblegen proprietary software.


title: TwinChip_EColi_6k

status: Public on Oct 26 2007

city: Daejeon

first: Sang Yup

last: Lee

address: Dept. of Chemical & Biomolecular Engineering, KAIST, 373-1 Guseong-dong, Yuseong-gu

country: South Korea

institute: KAIST

organism: Escherichia coli

distribution: commercial

manufacture_protocol: The arrays are of 3- by 3-mm size and have an active surface area of 2.4 by 2.4 mm mounted onto the bottom of standard 1.5-ml microreaction tubes.


title: Nimblegen Caenorhabditis elegans 385K array_WS120

city: Vancouver

first: Martin

middle: Richard

last: Jones

state: BC

address: Room 419 NCE Building 2125 East Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

organism: Caenorhabditis elegans

manufacture_protocol: see NimbleGen website at http://www.nimblegen.com


title: Colorado State University Mycobacterium Tuberculosis V2

status: Public on Oct 22 2007

city: Baltimore

first: Petros

last: Karakousis

state: MD

address: 1550 Orleans St

department: Medicine

institute: Johns Hopkins University School of Medicine

organism: Mycobacterium tuberculosis H37Rv

description: The oligo set represents 4505 70mer probes representing 3926 Open Reading Frames (ORFs) from the mycobacterium tuberculosis H37Rv strain and also representing 3811 ORFs from the CDC-1551 strain.  3932 probes were obtained from the sanger institute (http://www.sanger.ac.uk) representing H37Rv while 573 probes are designed from ORFs from the Institute for Genomic Research (http://www.tigr.org).  H37Rv has 3926 ORFs represented while CDC1551 has 3811 ORFs represented. Each oligo is designed to be within 5oC of 79oC using Tm=81.5+16.6*log[Na+]+41*(#G+#C)/Length-500/length with [Na]=0.1M and length equaling the total bases.  Oligo's are then screened for hairpin and cross-reactivity.

manufacturer: Colorado State University TB Vaccine Testing and Research NIH, NIAID Contract No. HHSN266200400091C

middle: C

first: Ernest

last: Williams

manufacture_protocol: Oligonucleotide 70mers were generated from whole genome sequence within coding regions.  Features were designed to have similar hybridization temperatures.  Samples were spotted and pre-processed using standard procedures from the Brown lab at Stanford University School of Medicine


title: NimbleGen Streptococcus agalactiae A909 2K array

status: Public on Oct 18 2007

city: Seattle

first: Lakshmi

last: Rajagopal

state: WA

address: 1900 9th Ave

department: Pediatric Infectious Disease

institute: Seattle Children's Hospital Research Institute

organism: Streptococcus agalactiae A909


title: Streptococcus gordonii Challis whole genome array SG-1

city: Buffalo

first: M

last: Vickerman

address: 3435 Main St.

department: Oral Biology

institute: University at Buffalo

organism: Streptococcus gordonii str. Challis

manufacturer: Gill, Steven, R.; SUNY-Buffalo, Center of Excellence in Bioinformatics and Life Sciences, Infectious Disease and Genomics, Buffalo. NY, United States; (716) 881-8956; srgill@buffalo.edu

first: A

last: Jesionowski

first: S

last: Iobst

middle: R

last: Gill

manufacture_protocol:
Unique 70-mer oligonucleotides were identified for each of the 2,186 open reading
frames (ORFs) identified in the initial annotation of the Streptococcus gordonii genome.  Oligonucleotides were resuspended at 25 uM final concentration in Pronto universal spotting solution (Corning #40027) and printed onto bar-coded UltraGAPs Coated Slides (Corning #40015) using an Automated Microarraying System from Brooks Automation, Inc. (Chelmsford, MA) equipped with a 48 pin printhead containing Stealth 3 MicroSpotting Pins Telechem International, Inc.).  Print configuration is 48 blocks in a 4 X 12 arrangement.  Spot diameters are approximately 90-100 microns.  Control reporters included 10 Arabidopsis gene fragments.   After printing, oligonucleotides were cross-linked to the slides by UV irradiation at 250 mJ/cm2 (Stratalinker UV Crosslinker, Stratagene) and subsequently stored at room temperature in a desiccated chamber until use.


title: Bovine Total Leukocyte cDNA microarray: Fifth generation microarray

status: Public on Oct 16 2007

city: Dublin

first: David

middle: E

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

organism: Bos taurus

manufacturer: Center for Animal Functional Genomics, Michigan State University

first: Paul

last: Coussens

first: Steve

last: Suchyta

first: Sue

middle: S

last: Sipkovsky

first: Robert

middle: G

last: Halgren

first: Stephen

middle: D

last: Park

manufacture_protocol:
Clone inserts from the BOTL library were amplified by inoculating bacteria directly into PCR master mix (20 μM each dNTP, 0.2 μM M13-forward primer, 0.2 μM M13-Reverse primer, 200mM Tris-HCl (pH 8.4), 500mM KCl, and 2.0 units of Taq DNA polymerase) in 96-well plates. Following a pre-heat step of 95°C for 10 min to disrupt the bacteria, PCR was performed in a PE 9700 Thermocycler (Perkin Elmer Corp., Palo Alto, CA) using the following conditions: 95°C for 30 sec; 55°C for 30 sec and 72°C for 1 min. Based on agarose gel electrophoresis of purified amplicons, our success rate of clone insert amplification with this protocol has typically been >90%. Insert amplicons were purified in 96-well format using Millipore filter plates (Millipore Corp., Bedford, MA) filled with Sephadex G-50 (Amersham Pharmacia Biotech.). Final insert amplicons were resuspended in 17 μl of 50% DMSO for low-density (3000 to 4000 amplicons per slide) spotting on microarrays. Approximately 1 μl of each purified insert amplicon was separated on a high-volume 1.2% agarose gel to ensure that each clone was represented on the final microarrays. This check also allowed final adjustment for differences in amplicon concentration just prior to microarray source plate set up. Finally, a total of 5 μl of each purified amplicon was transferred to 384-well microarray source plates.
Microarrays were spotted using a GeneTAC G3 arraying robot (Genomic Solutions, Inc., Ann Arbor, MI) equipped with a 48-pin head, with each pin having a nominal end diameter of 200 microns. In 50% DMSO (low-density arrays), this arrangement yields spots of approximately 250-350 microns. The pin configuration of the G3 yields microarrays consisting of 48 “patchs” of spots. (81 spots per patch).


title: EMBL30807 (GE Healthcare/Amersham Mouse Whole Genome Bioarray)

city: Heidelberg

first: Bibhuti

middle: Bhusan

last: Mishra

state: Heidelberg

department: Cell Biology and Biophysics

country: Germany

institute: EMBL-Heidelberg

manufacturer: GE Healthcare/Amersham Biosciences CodeLink™ Mouse Whole Genome Bioarray


title: Hitachisoft Hypergene Yeast Chip Ver. 1-1 (Lot01-05)

first: Emiko

last: Kitagawa

description: Hitachisoft Hypergene Yeast Chip Ver. 1-1 (48 block Lot01-05)


title: tiling-mouse-385K-v1.0

first: Ira

last: Hall

manufacture_protocol: NimbleGen manufactures custom, high-density DNA arrays based on its proprietary Maskless Array Synthesizer (MAS) technology. The MAS system is a bench top, solid-state, high-density DNA array fabrication instrument comprised of a maskless light projector, a reaction chamber, a personal computer, and a DNA synthesizer. NimbleGen builds its arrays using photo-mediated synthesis chemistry with its MAS system. See http://www.nimblegen.com/technology/manufacture.html for more details.


title: AGRF Human 8K cDNA Microarray (muscle study)

city: Clayton

first: Nigel

middle: Keith

last: Stepto

state: VIC

address: Wellington Road

department: Physiology

country: Australia

institute: Monash University

organism: Homo sapiens

middle: K

first: Andrew

last: Carey

first: Vernon

last: Coffey

first: Anna

last: Ponnampalam

first: Benedict

middle: J

last: Canny

last: Powell

first: John

middle: A

last: Hawley

manufacture_protocol:
Array information:
H8K020304
Spotted
Corning GAPS-II Amino silane Slides
25x75mm Slides
Corning GAPS-II Amino silane Slides
16128 dots
Reporter Type:
PCR products of cDNA clones
Double  stranded
Primer  sequence used to amplify human 8K clone set plates 1-75
Reverse 5'gtgagcggataacaatttcacacaggaaacagc3'
Forward 5'ctgcaaggcgattaagttgggtaac 3'
Primer  sequence used to amplify human 8K clone set plates 76-78
Reverse 5'cacaggaaacagctatgacca3'
Forward 5'acggccagtgccagcttat3'
cDNA Clone set from Research Genetics, Alabama, USA
Human 8K clone set obtained Nov 2001, Housed at AGRF, Melbourne Australia
Amplification Protocol: (Human 8K only)
0.2mM dNTP, 25 pmols each primer, 2.5 units HotStar Qiagen TAQ, 1X HotStar buffer, and 1ul straight clone culture in 100ul reactions.
95C for 15min; 7 cycles of 94C for 30s; 72C for 1min (-1C every cycle); 72C for 2min; 23 cycles of 94C for 30s; 65C for 1min; 72C for 2min; final elongation 72C for 5min; 4C 2min.
Millipore PCR plate purification, gel analysis, aliquot into 384 well plates by robot (A1,A2,B1,B2).
Resuspended in water for 4 days in fridge, then added an equal amount of DMSO.
Printing concentration was ~250 ng/ul in 50% DMSO, 6ul total.
Please see GAL file for sequence information and accession numbers for individual clones.
Post Processing: UV crosslinked 70mj; baked 2hrs at 80C; stored dessicated.
Feature Information:
~150um diameter
Covalent and ionic attachment.
All other information, please see GAL file.
Control Elements on the array (see location on GAL file):
Amersham "Lucinda Universal Scorecard version 2" spots. Spike mix available from the AGRF


title: Hitachisoft Hypergene Yeast Chip Ver. 0 (lot 83,85,87)

description:
Hitachisoft Hypergene Yeast Chip Ver. 1 (lot 83,85,87)
ID is made by connecting BlockX, BlockY, SpotX and SpotY.


title: nhgri_qiagenv3_cgh

city: Bethesda

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

description:
36288 spots
nt coordinates correspond to hg16 (UCSC) or build 34 (NCBI)

manufacture_protocol: Qiagen/operon version 3, robotically spotted onto glass


title: Dictyostelium discoideum small RNA sequences

status: Public on Oct 17 2007

city: Uppsala

first: Johan

last: Reimegård

address: Biomedical Center

department: Department of cell and molecular biology

country: Sweden

institute: Uppsala University

organism: Dictyostelium discoideum

technology: other

distribution: virtual

first: Andrea

last: Hinas

first: Gerhart

last: Wagner

first: Wolfgang

last: Nellen

first: Victor

last: Ambros

first: Fredrik

last: Söderbom


title: Irradiated Mouse liver array

city: sendai-city

first: Taisuke

last: Baba

institute: Tohoku Univ. IDAC


title: PIWI-associated piRNA in Drosophila melanogaster ovary

status: Public on Oct 25 2007

city: New Haven

first: Hang

last: Yin

state: CT

address: 10 Amistead Street, Room 220

department: Department of Cell Biology

institute: Yale University Stem Cell Center

first: Haifan

last: Lin


title: Maize 12K cDNA Generation II Version B.1

city: Ames

first: Patrick

middle: S.

last: Schnable

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

organism: Zea mays

manufacturer: Schnable Laboratory at Iowa State University(ISU)

manufacture_protocol: The ISU microarray facility have generated a maize gene chip that contains 12,160 spotted cDNA inserts. These cDNA clones were obtained from NSF Plant Genome EST projects led by Ginny Walbot and Pat Schnable.


title: Earthworm 4K cDNA array version 1.0

status: Public on Oct 15 2007

city: Vicksburg

first: Ping

last: Gong

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: US Army ERDC

organism: Eisenia fetida

manufacturer: USACE-ERDC-EL Environmental Genomics and Genetics team

first: Xin

last: Guan

first: Mehdi

last: Pirooznia

first: Karl

last: Indest

first: Edward

last: Perkins

manufacture_protocol:
1. A total of 4032 purified cDNA clones were loaded on 384-well plates and completely dried down in a Vacufuge Concentrator 5301 (Eppendorf, Westbury, NY).
2. The dried cDNA was re-suspended in 15 ?̬ of 1??printing buffer (ArrayIt, Sunnyvale, CA).
3. Each clone was spotted twice (i.e., in two super grids) on Ultra GAPS amino silane coated glass slides (Corning, Acton, MA) using 16 pins on a VersArray ChipWriter (Bio-Rad, Hercules, CA).
4. Five alien cDNAs, i.e., PCR product 1 to 5 selected from SpotReport Alien cDNA Array Validation System (Stratagene, La Jolla, CA) prepared at 15, 30, 60, 125 and 250 ng/?̬, were also spotted twice along with printing buffer and water as control spots.
5. A total of 4032 purified cDNA clones were loaded on 384-well plates and completely dried down in a Vacufuge Concentrator 5301 (Eppendorf, Westbury, NY).
6. The total number of spots on each array was 8704 including 60 alien cDNA spots, 84 water spots, 256 blank spots and 240 printing buffer spots.
7. After printing, arrays were incubated in a dessicator 2-3 days and were then snap-dried on a hot plate after being rehydrated over a boiling water bath.
8. The arrays were further immobilized using a UV Cross-linker (Stratagene) by applying 300 mJ per 10 arrays.


title: HatfullPitt Mycobacterium smegmatis 30K v2

status: Public on Oct 04 2007

city: Pittsburgh

first: Graham

last: Hatfull

state: PA

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

organism: Mycolicibacterium smegmatis

manufacturer: PFGRC, The Institute for Genomic Research

first: Anil

last: Ojha

manufacture_protocol:
Slide Information
Array Name : 	Mycobacterium smegmatis microarray version 2
Elements on Array : 	29184
Elements on Array (minus empties): 	28904
Grids: 	48
Array Type : 	ss_oligo (70-mer)
Surface Coating: 	Epoxy
Printing Buffer(s): 	Nexterion with .01 CTAB, Schott buffer LEB E2
Arraying Machine(s): 	Genetix
Oligo Replicates : 	4x
Oligos Designed : 	6746
ORFs w/o oligo*: 	1
Controls: 	480 A. thaliana (70-mers)
Strain Information
Design Strain : 	ORFs in Design: 	Oligos Designed **:
MC2 155
	6898
	6746
TIGR Spotfinder Printing Pattern
MetaRow
12
	MetaColumn
4
Pix X (pix)
450
	Pin Y (pix)
450
Row Number
25
	Column Number
25
X Spacing (pix)
17
	Y Spacing (pix)
17
The user should remove slides from their packaging as soon as possible and store them at room temperature in a desiccator or a Rubbermaid®   or Tupperware® container containing a bottom layer of anhydrous calcium sulfate such as Drierite®. Handle slides with extreme care as any scratching or rubbing of the slide surface may damage the printed DNA. Additionally, slides must be kept away from dust. Printed material is on the same side of the glass as the barcode. Slides should never be placed DNA side down.


title: Treenomix spruce 21.8K cDNA microarray

status: Public on Oct 12 2007

first: Joerg

last: Bohlmann

department: Michael Smith Laboratories

organism: Picea

description: Corning UltraGaps

manufacturer: Treenomix consortium at the University of British Columbia, Vancouver, Canada; BC Cancer Agency Genome Sciences Centre, Vancouver, Canada; National Research Council Biotechnology Research Institute, Montreal, Canada

first: Steven

last: Ralph

manufacture_protocol:
Microarray Fabrication and Quality Control
Clones were selected from 12 spruce cDNA libraries based on a CAP3 assembly (Huang and Madan, 1999; 95% identity and 40 bp overlap) of 50,770 high-quality 3’ ESTs processed for quality as described in Ralph et al. (2006).  This assembly yielded 22,154 contigs and 13,423 singletons.  For each contig, the EST member having the longest quality- and vector-trimmed (QVT) sequence was chosen as the representative. Only those singleton sequences or contig representatives with a QVT of more than 300 bp were considered further.  To further reduce sequence redundancy, all candidate clones were compared against each other using BLASTN and any clones sharing 95% or greater identity over a length of at least 150 bp were considered redundant.  In these cases, the clone with the longest QVT sequence was chosen as the representative on the array.  Following these procedures a set of 21,843 clones were selected.
Following in silico selection of candidates, clones were robotically rearrayed from daughter glycerol stock 384-well plates into 96-well plates prefilled with 7% glycerol in LB + ampicillin, incubated overnight at 37°C, and checked for uniform optical density.  Prior to PCR, 5 µL of overnight culture was lysed in 100 µL nuclease-free H2O (Invitrogen) for 10 min at 95°C.  Plasmid inserts were PCR amplified in a GeneAmp PCR System 9700 (Applied Biosystems) by using 2.5 µL of lysed culture, 0.2 µM M13 reverse, 0.2 µM -21M13 forward, 15 mM MgCl2, 100 mM Tris-HCL, 500 mM KCl, 250 µM dNTPs, 9U AmpliTaq (Applied Biosystems), and nuclease-free H2O (Invitrogen) to 100 µL.  PCR conditions were as follows: 5 min at 94°C denaturation; 31 cycles of 30 sec at 94°C, 30 sec at 50°C, and 2 min at 72°C; and 7 min at 72°C.  Three microliters of each PCR product were run on a 1.2% agarose gel (E-Gel® Pre-cast Agarose Electrophoresis System, Invitrogen) to assess quality and yield was determined at 260 nm with a SpectraMax plus (Molecular Device).  Out of 21,843 clones, more than 93% of amplicons consisted of a single product of sufficient intensity and of the expected size.  PCR products were robotically cleaned (Millipore) and consolidated into 384-well plates, lyophilized by speed-Vac, and resuspended in 20 µL 50% DMSO.
cDNAs were printed on Corning UltraGaps slides with the Chipwriter Pro microarray printer (Bio-Rad).  SMP3 Microspot quill pins (TeleChem) in a 48-pin tool were used to deposit ~7 nL (~0.2 ng cDNA) per spot onto the slide.  The resulting microarrays have a 4 x 12 subgrid layout with 528 spots per subgrid, each spot having approximate diameter and pitch of 100 µM and 200 µM, respectively.   A 280 bp green fluorescent protein (GFP) cDNA was amplified from a GFP-containing plasmid (BD Biosciences) using the primers (5’-AGACAAGTTGGTAATGGTAGCGA-3’) and (5’-ACAGGAAACAGCTATGACCA-3”), and printed five spots per subgrid as orientation markers.  A set of five E. coli cDNAs (fus-A, ilv, inf-C, met-E and rps-A) were amplified from genomic DNA using the E. coli ORFmer PCR primer set (Sigma-Genosys) and spotted 24 times each throughout the array.  A set of five human cDNAs (I.M.A.G.E IDs 5320247, 5785983, 7260066, 7483277 and 8683) were amplified from plasmid DNA using –21M13 forward and M13 reverse primers and spotted 24 times each throughout the array.  Other negative controls included pBluescript II SK(+) vector DNA spotted 24 times (Stratagene), polydeoxyadenylic acid DNA spotted 24 times (Amersham Pharmacia Biotech), 50% DMSO spotted 1,149 times and 1,104 empty spots.  An additional set of three human cDNAs (GenBank IDs BC001473, BC001146 and BC007231) were also amplified from plasmid DNA as described above and spotted five times per subgrid.  Using these templates, in vitro transcribed products (MEGAscript SP6 kit, Ambion) were generated according to manufacturer’s instructions and spiked into our hybridization reactions to serve as positive controls for 1st strand synthesis and slide hybridization.  The slides were crosslinked in a UV Stratalinker 2400 (Stratagene) at 120 mJ.  Spot morphology was assessed on all slides by visual inspection, and a representative slide from each print batch was also evaluated using the Paragon DNA Microarray QC Stain Kit (Invitrogen) according to manufacturer’s instructions.  To check clone tracking, high-quality sequences were obtained from randomly selected re-arrayed glycerol stocks, and more than 91% (165 of 180) of these templates had BLAST identifiers matching gene identifications predicted from the rearray spreadsheet, indicating highly accurate clone tracking throughout the process of microarray fabrication.
Huang X, Madan A (1999) CAP3: a DNA sequence assembly program.  Genome Res 9: 868-877.
Ralph SG, Yueh H, Friedmann M, Aeschliman D, Zeznik JA, Nelson CC, Butterfield YSN, Kirkpatrick R, Liu J, Jones SJM, Marra MA, Douglas CJ, Ritland K, Bohlmann J (2006) Conifer defense against insects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils (Pissodes strobi) reveals large-scale changes of the host transcriptome.  Plant Cell & Environ 29: 1545-1570.


title: UCSF HumArray 2.0

city: San Francisco

first: Donna

last: Albertson

department: Comprihensive Cancer Center

institute: University of California San Francisco

description: The arrays contain 2464 BAC clones printed as triplicate spots and are described in: Snijders AM, Nowak N, Segraves R, et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nature Genetics 2001; 29:263-264.

manufacturer: UCSF Comprehensive Cancer Center Array Core


title: Nimblegen Human Expression array

status: Public on Oct 09 2007

city: Davis

first: Kimberly

middle: Rose

last: Blahnik

address: GBSF 1 Shields Ave

department: Genome and Biomedical Sciences

institute: University of California Davis

manufacture_protocol: as described on Nimblegen website


title: OSU RIGUA (Ruminant Immuno-inflammatory Gene Universal Array) 4K

city: Stillwater

first: Patricia

last: Ayoubi

state: OK

address: 246 NRC

department: Biochemistry and Molecular Biology

institute: Oklahoma State University

organism:
Sus scrofa
Bos taurus
Ovis aries

description: For additional information please contact Prof. John Hopkins or S. Rhind at The University of Edinburgh

manufacturer: Edinburgh Research and Innovation, The University of Edinburgh

manufacture_protocol:
Researchers at the University of Edinburgh have constructed a microarray to allow investigation into a large set of immuno-inflammatory genes regulated in response to disease, vaccination and therapeutic interventions in ruminants. Specifically designed to investigate the host response to infection by Mycobacterium avium subsp. paratuberculosis (Johne's disease), the microarray can also be applied to other disease states in ruminants. The array will also provide information on selectable traits that may confer resistance to Johne's disease and responses to vaccination. The gene array consists of approximately 600 ruminant immuno-modulatory genes backed up by a database and management system to allow full interrogation of experimental data.
The full array, or RIGUA (Ruminant Immuno-inflammatory Gene Universal Array), consists of some 600 ruminant genes each represented by two non-overlapping 75-mer oligonucleotides. These have been selected to enable investigations into the immune response to infection and other challenges, including vaccination, in ruminants. It will therefore be useful in defining those genes involved in the development of disease, which have an immuno-inflammatory component thus contributing to animal improvement and breeding. It will also be useful in vaccine and adjuvant response studies in the development of vaccines to ruminant disease.
Validation experiments have confirmed the array's applicability to the study of host responses to infection by M. avium subsp. paratuberculosis. Validation has been performed by detailed analysis of sheep with confirmed diagnosis of mycobacterial infection. This analysis has demonstrated the array's power in detecting changes in the regulation of immuno-inflammatory genes in response to infection by Mycobacterium avium subsp. paratuberculosis


title: Neisseria meningitidis 053442 2.5K

status: Public on Oct 10 2007

city: Beijing

first: Junping

last: Peng

address: No 6, Rongjing Eastern Street, BDA

institute: Chinese center for disease control and prevention

organism: Neisseria meningitidis

manufacturer: State key laboratory for molecular virology and genetic engineering,China CDC

first: Xiaobing

last: Zhang

first: Li

last: Yang

first: E

first: Jing

last: Wang

first: Qi

last: Jin

manufacture_protocol: The PCR products were spotted onto glass slides as described in the MGUIDE (Brown Lab website at Stanford) and on the microarrays.org website (DeRisi Lab at UCSF).


title: UCSF Hum32k Array

status: Public on Oct 08 2007

description:
The tilling path array with continuous, overlapping coverage of the genome contains 32,144 mapped BAC clones described in Krzywinski et al.  DNA was amplified by ligation mediated PCR and each BAC is represented by a single spot on the array.
Krzywinski M, Bosdet I, Smailus D, Chiu R, Mathewson C, Wye N, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Girn N, Lee D, Masson A, Mayo M, Olson T, Pandoh P, Prabhu AL, Schoenmakers E, Tsai M, Albertson D, Lam W, Choy CO, Osoegawa K, Zhao S, de Jong PJ, Schein J, Jones S, Marra MA: A set of BAC clones spanning the human genome. Nucleic Acids Res 2004, 32:3651-3660.


title: Chromosome 4 tiling array (genome release 4)

status: Public on Oct 03 2007

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

institute: Umea University

organism: Drosophila melanogaster

first: Per

last: Stenberg

first: Anna-Mia

last: Johansson

manufacture_protocol: as described at www.nimblegen.com


title: UCSF HumArray 3.1


title: Genomessage Homo sapiens 0.7k

city: Kawagoe-shi, Saitama

first: Tsutomu

last: Takeuchi

address: 1981 Tsujido-machi, Kamoda

department: Department of Internal Medicine

institute: Saitama Medical University

manufacture_protocol: For most of the genes, each cDNA was designed approximately 500-600 bp and within approximately 1 kb region from the 3’-poly(A) tail and all cDNAs for microarray probe were cloned into the pGEM vector (Promega, Madison, WI).  We also selected and cloned external control genes (approximately 0.5-1 kb) into the pGEM vector to establish the dynamic range of the microarray.  Renilla luciferase (RL), baculovirus envelope gp64 (GP), and lambda phage DNA (LD).  All clones for capture probe on microarray were sequenced and validated by comparison with the GenBank sequence.   The aminosilane surfaces of SuperAmine glass slides (TeleChem International, Sunnyvale, CA) were stamped with quadruply spots of cDNA probe corresponding to each of the capture probe genes with a Geneqs 2000 arrayer (KakenGenex, Matsudo, Japan).  The average spot size was 150 mm and separated each other with a distance (500 mm).


title: CRG Human Breast Cancer Array v4.0-0.8K

status: Public on Oct 05 2007

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

manufacturer: Center for Genomic Regulation (CRG)/Microarray Core Facility

first: Belen

last: Miñana

first: Lauro

last: Sumoy

first: Miguel

last: Beato

first: Albert

last: Jordan

first: Cecilia

last: Ballare

first: Maria

last: Melia

manufacture_protocol:
826 cDNA clones corresponding to genes possibly involved in breast cancer were selected to constitute our Breast Cancer Array (BCA) cDNA platform. In this platform there are different interlinked biological pathways represented: cell cycle, DNA repair, DNA damage, apoptosis, DNA remodeling, PR related pathways, endometrial and ovarian cancer related genes, and prognosis genes. Clones were selected from the German Human Genome Resource Center (http://www.rzpd.de/) from different cDNA of endometrial, ovary or breast cDNA libraries, and a clone information database was constructed using several web resources such as SOURCE (http://source.stanford.edu/cgi-bin/source/ sourceSearch, Diehn et al. 2003). The selection criterion was to choose the most 3’ end clone, which contained a polyadenylation signal with a maximum length of 2 kb. We visualized these features and confirmed the position of the clone within its cluster using GeneNest graphical database (http://genenest.molgen.mpg.de). All cDNA clones were confirmed by sequencing from the 5’-end, and their position within the gene was determined by BLAST (http://www.ncbi.nlm.nih.gov/BLAST/).
DNA plasmid preparations were generated using Plasmid miniprep 96 kit (Millipore; cat.no.LSKP09604). Inserts were PCR amplified using a homemade thermostable Thermus aquaticus (Taq) DNA polymerase clone (Desai and Pfaffle, 1995), with vector specific primers. PCR products were purified with PCR 96 Cleanup kit (Millpore; cat.no.LSKC09604). PCR products were normalized to 100 ng/uL and allocated on 384-well plates. PCR products were printed in 2 x Corning Pronto! ® spotting solution on CORNING UltraGAPS® II amino-modified glass slides, using a Robotic arrayer ChipWriter (Bio-Rad) and a pin-head of 16 SMP3 printing needles (Telechem®). cDNA spots were immobilized by UV crosslinking at 2500 mJ/s with an UV oven and stored under vacuum at desiccators until they were used for hybridization.
Each gene product was printed in quadruplicates on each microarray, two of them side-by-side on the same row, and the other two in different subgrids, by inverting the spotting plates, on the top or bottom halve of the array.


title: UCSF Johnson Candida albicans tiling 185K v1.0 (assembly 20)

status: Public on Oct 01 2007

first: David

last: Galgoczy

state: CA

address: 600 16th Street

department: Biochemistry and Biophysics

institute: UCSF

organism: Candida albicans

first: Brian

middle: B

last: Tuch

first: Alexander

last: Johnson

manufacture_protocol: Custom Agilent 185,000 spot 60-mer DNA oligonucleotide array.  Manufactured by Agilent in situ oligonucleotide synthesis.


title: Treenomix poplar 15.5K cDNA microarray

status: Public on Oct 02 2007

city: Vancouver

first: Joerg

last: Bohlmann

institute: University of British Columbia

organism: Populus

description: Corning UltraGaps

first: Steven

last: Ralph

first: Claire

last: Oddy

first: Dawn

last: Cooper

first: Hesther

last: Yueh

first: Sharon

last: Jancsik

first: Natalia

last: Kolosova

first: Ryan

middle: N

last: Philippe

first: Dana

last: Aeschliman

first: Rick

last: White

first: Dezene

last: Huber

first: Carol

last: Ritland

first: Francois

last: Benoit

first: Tracy

last: Rigby

first: Andre

last: Nantel

first: Yaron

last: Butterfield

first: Robert

last: Kirkpatrick

first: Elizabeth

last: Chun

first: Jerry

last: Liu

first: Diana

last: Palmquist

last: Wynhoven

first: Jeff

last: Stott

first: George

last: Yang

first: Sarah

last: Barber

last: Holt

first: Asim

last: Siddiqui

last: Jones

first: Marco

last: Marra

last: Ellis

first: Carl

last: Douglas

first: Kermit

manufacture_protocol:
The 15,496 clones from 14 poplar cDNA libraries (Ralph et al., 2006) were selected based on a CAP3 assembly (Huang and Madan, 1999; 95% identity and 40 bp overlap) of ca. 37,000 high-quality 3’ ESTs (i.e. longest available EST sequence from each putative unique transcript).  Following in silico selection of candidates, clones were robotically rearrayed from daughter glycerol stock 384-well plates into 96-well plates prefilled with 7% glycerol in LB + ampicillin, incubated overnight at 37°C, and checked for uniform optical density.  Prior to PCR, 5 µL of overnight culture was lysed in 100 µL nuclease-free H2O (Invitrogen) for 10 min at 95°C .Plasmid inserts were PCR amplified in a GeneAmp PCR System 9700 (Applied Biosystems) by using 2.5 µL of lysed culture, 0.2 µM M13 reverse, 0.2 µM -21M13 forward, 15 mM MgCl2, 100 mM Tris-HCL, 500 mM KCl, 250 µM dNTPs, 9U AmpliTaq (Applied Biosystems), and nuclease-free H2O (Invitrogen) to 100 µL.  PCR conditions were as follows: 5 min at 94°C denaturation; 31 cycles of 30 sec at 94°C, 30 sec at 50°C, and 2 min at 72°C; and 7 min at 72°C.  Three microliters of each PCR product were run on a 1.2% agarose gel (E-Gel® Pre-cast Agarose Electrophoresis System, Invitrogen) to assess quality and yield was determined at 260 nm with a SpectraMax plus (Molecular Device).  Out of 15,496 clones, more than 92% of amplicons consisted of a single product of sufficient intensity and of the expected size.  PCR products were robotically cleaned (Millipore) and consolidated into 384-well plates, lyophilized by speed-Vac, and resuspended in 20 µL 50% DMSO.

     cDNAs were printed on Corning UltraGaps slides with the Chipwriter Pro microarray printer (Bio-Rad).  SMP3 Microspot quill pins (TeleChem) in a 48-pin tool were used to deposit ~7 nL (~0.2 ng cDNA) per spot onto the slide.  The resulting microarrays have a 4 x 12 subgrid layout with 360 spots per subgrid, each spot having approximate diameter and pitch of 100 µM and 200 µM, respectively.   A 280 bp green fluorescent protein (GFP) cDNA was amplified from a GFP-containing plasmid (BD Biosciences) using the primers (5’-AGACAAGTTGGTAATGGTAGCGA-3’) and (5’-ACAGGAAACAGCTATGACCA-3”), and printed in subgrid corners (five spots per subgrid) as an orientation marker.  A set of five E. coli cDNAs (fus-A, ilv, inf-C, met-E and rps-A) were amplified from genomic DNA using the E. coli ORFmer PCR primer set (Sigma-Genosys) and spotted 24 times each throughout the array.  A set of five human cDNAs (I.M.A.G.E IDs 5320247, 5785983, 7260066, 7483277 and 8683) were amplified from plasmid DNA using –21M13 forward and M13 reverse primers and spotted 24 times each throughout the array.  Other negative controls included pBluescript II SK(+) vector DNA spotted 24 times (Stratagene), polydeoxyadenylic acid DNA spotted 24 times (Amersham Pharmacia Biotech), 50% DMSO spotted 296 times and 240 empty spots.  An additional set of three human cDNAs (GenBank IDs BC001473, BC001146 and BC007231) were also amplified from plasmid DNA as described above and spotted five times per subgrid.  Using these templates, in vitro transcribed products (MEGAscript SP6 kit, Ambion) were generated according to manufacturer’s instructions and spiked into our hybridization reactions to serve as positive controls for 1st strand synthesis and slide hybridization.  The slides were crosslinked in a UV Stratalinker 2400 (Stratagene) at 120 mJ.  Spot morphology was assessed on all slides by visual inspection,  and a representative slide from each print batch was also evaluated using the Paragon DNA Microarray QC Stain Kit (Invitrogen) according to manufacturer’s instructions.  To check clone tracking, high-quality sequences were obtained from 50 randomly selected wells of each purified, consolidated 384-well plate used for microarray printing, as well as 164 randomly selected re-arrayed glycerol stocks, and more than 96% of these templates had BLAST identifiers matching gene identifications predicted from the rearray spreadsheet, indicating highly accurate clone tracking throughout the process of microarray fabrication.
Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Research 9: 868-877.
Ralph S, Oddy C, Cooper D, Yueh H, Jancsik S, Kolosova N, Philippe RN, Aeschliman D, White R, Huber D, Ritland CE, Benoit F, Rigby T, Nantel A, Butterfield YSN, Kirkpatrick R, Chun E, Liu J, Palmquist D, Wynhoven B, Stott J, Yang G, Barber S, Holt RA, Siddiqui A, Jones SJM, Marra MA, Ellis BE, Douglas CJ, Ritland K and Bohlmann J (2006) Genomics of hybrid poplar (Populus trichocarpa x deltoides) interacting with forest tent caterpillars (Malacosoma disstria): Normalized and full-length cDNA libraries, expressed sequence tags (ESTs), and a cDNA microarray for the study of insect-induced defenses in poplar. Molecular Ecology 15: 1275-1297.


title: Gillichthys mirabilis cDNA microarray

city: Portland

first: Brad

last: Buckley

state: OR

address: 1719 SW 10th Ave

department: Biology

institute: Portland State University

organism: Gillichthys mirabilis

manufacturer: Hopkins Marine Station, Stanford University

first: Andrew

middle: Y

last: Gracey

first: Bradley

last: Somero

manufacture_protocol: This microarray consists of spotted cDNAs, generated by reverse transcribing mRNA collected from several tissues of the goby Gillichthys mirabilis. RNA was collected from liver, gill, brain and muscle tissue, extracted from individuals that had been exposed to heat, hypoxia or osmotic stress. cDNAs were directionally cloned into pTriplEx2 vector (Clontech; Mountain View, CA, USA). Plasmid libraries were transformed into E. coli and bacterial colonies were picked at random into 384-well microtiter plates and grown overnight at 37˚C. cDNA inserts were amplified by PCR using 1 μl of bacterial suspension in 50 μl standard PCR reactions with vector specific primers. After ethanol precipitation, and one round of washing in 70% ethanol, PCR products were prepared in 3X sodium citrate (SSC) and 1.5 mol-1 betaine, for spotting onto Fisher Scientific (Hampton, NH, USA) Gold Seal glass microscope slides. Slides were coated with poly-L-lysine.


title: Applied Biosystems TaqMan mouse B cell_low density array

city: Birmingham

first: Kai-Michael

last: Toellner

address: Medical School

department: Immunity and Infection

country: United Kingdom

institute: University of Birmingham

organism: Mus musculus

technology: RT-PCR

description: A custom designed low density TaqMan array.

first: Lalit

last: Pallan


title: wheat 22k

city: Yokohama

first: Kanako

last: Kawaura

address: Maioka-cho 641-12

institute: Kihara Institute for Biological Research, Yokohama City University

organism: Triticum aestivum

first: Yasunari

last: Ogihara

first: Keiichi

last: Mochida

first: Yukiko

last: Yamazaki

manufacture_protocol: see manufacture's web site


title: Transcriptome of Lilium longiflorum generative cells

status: Public on Oct 24 2007

city: Parkville

first: Takashi

last: Okada

address: Cnr of Royal pde and Tin alley

department: Faculty of Land and Food Resources

institute: The University of Melbourne

organism: Lilium longiflorum

first: Prem

middle: L

last: Bhalla

first: Mohan

last: Singh

manufacture_protocol: Insert of 1234 cDNA clones and 3 marker genes were amplified with an M13 universal primer set.  PCR products were purified and resuspended in 50% DMSO solution.  Array was printed on Corning Gaps II slides (Corning Incorporated Life Sciences, MA, U.S.A.) using a 4 x 4 array of 16 telecam pins 21 dots x 21 dots per grid each dot approximately 100 microns apart.  Each cDNA was spotted in triplicate.  A set of universal control including human and mouse genes was also spiked.  Post printing cross-linking consisted of UV and slide baking for 2 hours at 80oC.


title: IFTC Saccharomyces cerevisiae 154 v1.0

city: Leipzig

first: Jeannette

last: Achilles

address: Permoserstraße 15

department: Environmental Microbiology

institute: Helmholtz-Centre for Environmental Research - UFZ

organism: Saccharomyces cerevisiae

description: The microarray presents 154 oligonucleotides (70mer) in triplicate encoding for selected proteins of the G1- and S-phase from the cell cycle of S. cerevisiae as well as selected oligonucleotides encoding for proteins belonging to the various metabolic pathways, glucose transporters and flocculins of S. cerevisiae.

manufacturer: Working group "Chiptechnology" at the Institute of Technical Chemistry of the University of Hanover, Germany

first: Frank

last: Stahl

first: Cornelia

last: Repenning

first: Klockow

last: Christine

manufacture_protocol:
Oligonucleotide design and synthesis: Oligonucleotides were designed and synthesised by the manufacture Operon excepting oligonucleotides representing lgFLO1. These oligonucleotides were designed using DNA-Star, blasted at NCBI (National Center for Biotechnology Information) and afterwards synthesised by Operon.
Spotting protocol: To produce microarrays silylated slides were purchased from TeleChemTM International Inc. (Sunnyvale, CA, USA) and the printing of the oligonucleotides was performed by using an AffymetrixTM 417 arrayer. Oligonucleotide solutions were prepared in 96-well-plates containing each 30 µl. The concentration of the printed oligonucleotides was 50 µM in 1x ArrayItTM Microarray Spotting Solution Plus. After spotting, the slides were incubated at 80 °C for 2 h. Slides were blocked in SSC containing 1% BSA (Sigma) for 45 min and rinsed with water for 5 min.


title: Geobacter sulfurreducens sense-detecting 12K oligo array

city: Amherst

first: Derek

last: Lovley

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

organism: Geobacter sulfurreducens

description: each oligonucleotide is synthesized on an array of gold electrodes embedded in a silicon chip

last: Postier

first: Raymond

last: DiDonato jr.

manufacture_protocol: in-situ electrochemically synthesized oligonucleotide array.  For reference see: Mauer et al.  Electrochemically generated acid and its containment to 100 micron reaction areas for the production of DNA microarrays.  PLoS ONE.  2006 Dec 20;1:e34.


title: CGH X 1K-2

status: Public on Sep 25 2007

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

organism: Homo sapiens

description:
In total the array design contains 8096 features printed in a layout of 4 meta rows, 4 meta columns,  18 rows per block and 16 columns per block.  The distinct BAC and PAC sequences were printed in 2 replicates. This grid is printed twice on the glass slides allowing for two microarray arrays per slide.
The Platform data table reflects a condensed representation of the array's replicate features.  The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.

first: Guy

last: Froyen

first: Paul

last: Van Hummelen

first: Joris

last: Vermeesch

manufacture_protocol:
MicroGrid Printing ProtocolEquipment:
1. Microgrid (Genomics Solutions, UK).
2. 384 microtiter plates (X7022, Genetix)
3.  4x4 MicroSpot quill pins - 10K (cat# BR001489, Genomics Solutions, UK)
4. Codelink slides (cat#: 30001100, GE Healthcare).
Printing 2 arrays of 4x4 blocks on 1 microscope slide:
1. Dissolve PCR products in 250mM Phosphate buffer, 0.00025% sarcosyl at concentrations of 300 ng/ul.
2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 200 um, row pitch = 200 um; Humidity 55%; 101 spots per source visit.
3. Make sure room temperature is between 20-24 degrees Celsius.
4. Place microtiter plates in the plate hotel with A1 in front left corner.
5. Place 50 slides on the slide-deck.
6. Start spotting early in the morning and stop spotting procedure at end of the day and remove pin set. Leave spotter overnight with vacuum and humidity settings on.
7. Incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
8. Block 1%NH4OH.
9. Slides can be stored for at least 6 months in a dry-cabinet.


title: UMGC-IRCNA 9k A

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

first: Stéphane

last: Minvielle

first: Florence

last: Magrangeas

first: Pascal

last: Jézéquel

manufacture_protocol:
One channel DNA microarrays were constructed from EST cDNA clones (based on Homo sapiens).
End-sequence-verified I.M.A.G.E. clones were purchased from RZPD German Resource Center for Genome Research (Berlin, Germany) or provided by the Human Genome Mapping Project Resource Centre (Hinxton, UK) and sequenced by MilleGen (Labege France).
The cDNA clones were amplified in 96-well microtiter plates with universal primers.
PCR products were spotted onto nylon using a robot-based high-speed contact spotting facility which ensures high precision positioning and constant droplet volumes of cDNA samples to provide an reproducible spot morphology and DNA content over the whole array.
The process is performed under dust free, temperature-and humidity controlled conditions.
The spotted cDNA is covalently bound by U.V. rays to the nylon surface.
The feasibility, reproducibility and sensitivity of spotting procedures onto nylon membrane currently used in our laboratory to produce cDNA arrays have been previously described (Nguyen et al., Genomics. 1995;29:207-216; Bernard et al., Nucleic Acids Res. 1996;24:1435-1442; Bertucci et al. Hum Mol Genet. 1999;8:1715-1722; Magrangeas F et al. Blood. 2003;101:4998-5006.).


title: wheat 11k

first: Kanako

last: Kawaura

first: Yasunari

last: Ogihara

first: Keiichi

last: Mochida


title: DASL Human Cancer Panel by Gene

status: Public on Sep 16 2007

city: Rochester

first: Robert

middle: B.

last: Jenkins

state: MN

address: 200 First Street SW

department: Laboratory Medicine and Pathology

institute: Mayo Clinic

technology: oligonucleotide beads

description: DASL Human Cancer Panel by Probe may be viewed at GPL5826.

first: Thomas

middle: M

last: Kollmeyer


title: JCVI PFGRC Mycobacterium tuberculosis 32K v3 array designed primarily based on strain H37Rv

status: Public on Sep 12 2006

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Mycobacterium tuberculosis

description: This set includes 4742 oligonucleotides, has 32448 spots distributed in 48 blocks.

manufacture_protocol: 3QMT, with arrayer LUCIDEA, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: DASL Human Cancer Panel by Probe

description:
DASL Human Cancer Panel by Gene may be viewed at GPL5858.

The GPL5826.dap file (linked as a Supplementary file at the foot of the record) is required by BeadStudio for processing Illumina image files.


title: Affymetrix GeneChip Early Access Mapping 500K Set Array (250K_Nsp_SNP)

status: Public on May 25 2006

city: Santa Clara

first: Fan

last: Shen

address: 3420 Central Expressway

institute: Affymetrix, Inc

description:
Early Access Array
The GeneChip® Human Mapping 500K Array Set is comprised of two arrays (Nsp/Sty arrays).

manufacture_protocol: see manufacturer's web site


title: JCVI PFGRC Mycobacterium tuberculosis 22K v2.1 array designed primarily based on strain H37Rv

description: This set includes 4742 oligonucleotides, has 22080 spots distributed in 96 blocks.

manufacture_protocol: 2QMT, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 1783814, pen id 0, pen cycles -1, operator Jon, humidity control On, humidity set point65


title: Affymetrix GeneChip Mapping 500K Early Access Array (250K_Sty_SNP)


title: Streptococcus pyogenes SF370 strain 3.2K

city: Kansas City

first: Alexander

middle: V

last: Dmitriev

state: KS

address: 3901 Rainbow Boulevard

institute: Kansas University Medical Center

organism: Streptococcus pyogenes

description: Nimblegen Streptococcus pyogenes SF370 strain based platform including 660 phage ORFs of the strains MGAS5005, MGAS315, MGAS8232

manufacture_protocol: The platform was done according to Maskless Array Synthesizer (MAS) technology