title: SHCP

status: Public on Aug 27 2005

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

organism: Homo sapiens

technology: spotted DNA/cDNA

distribution: non-commercial

manufacturer: Stanford Functional Genomics Facility,  Stanford School of Medicine

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


title: UI-Robinson Apis mellifera brain 9k version 3.1

status: Public on Feb 28 2007

city: Alfenas

first: Angel

middle: Roberto

last: Barchuk

state: Minas Gerais

address: Rua Gabriel Monteiro Silva 700, Campus Unifal

department: Cell and Developmental Biology

country: Brazil

institute: Federal University of Alfenas

organism: Apis mellifera

description:
platform type: spotted cDNA
surface and coating specification: polished atomic flat glass surface treated with ultra-pure amine surface chemistry
physical dimensions of array support (slide): 25 x 76 x 0.94mm
number of features on the array: 19,200

manufacturer: Department of Entomology and Neuroscience Program, University of Illinois, Urbana, Illinois 61801, USA

middle: R

first: Alexandre

middle: S

last: Cristino

first: Robert

last: Kucharski

first: Luciano

middle: F

last: Costa

first: Zilá

middle: L

last: Paulino Simões

first: Ryszard

last: Maleszka

manufacture_protocol: See: Whitfield CW, Band MR, Bonaldo MF, Kumar CG, Liu L, Pardinas JR, Robertson HM, Soares MB, Robinson GE: Annotated Expressed Sequence Tags and cDNA Microarrays for Studies of Brain and Behavior in the Honey Bee. Genome Res 2002, 12:555-566


title: Penn/CHOP Homo sapiens 4.5K (BAC array for studying Neuroblastoma)

city: Philadelphia

first: Jayanti

last: Jagannathan

state: PA

address: 34th & Civic center blvd

department: Oncology

institute: Childrens Hospital of Philadelphia

manufacturer: non commercial: University of Pennsylvania / Childrens Hospital of Philadelphia

first: Yael

last: Mosse

first: Joel

last: Greshock

manufacture_protocol: BAC clone starter cultures were grown in 700ul 2X YT broth with 12.5 ug/mL chloramphenicol at 37 deg C for ~15h. Full cultures of 2.5 mL broth were inoculated from starter cultures and grown for 15 h in 48-well blocks. DNA was extracted using QAGEN real prep kits using high throuhput 96 well blocks. BAC DNA was then amplified using degenerate oligonucliotide primers (Cheung and Nelson 1996). Each BAC was amplified twice at different annealing temperatures (58 and 60 deg C). PCR products were pooled and purified with 96 well QiaQuick kits. Each clone DNA was lyphilized and resuspended in 50% DMSO/water. A minimum of two replicates per clone were printed on each slide using the aqueous DMSO buffer as spotting solution. Arrays were printed on Corning CMT Ultra GAP slides.


title: Tiling microarray OS18755 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 6

status: Public on Feb 21 2007

city: New Haven

first: Rajkumar

last: Sasidharan

state: CT

address: 266 Whitney Avenue

department: MB & B

institute: Yale University

organism: Oryza sativa

technology: in situ oligonucleotide

description: This experiment was designed to identify transcribed regions of japonica subspecies of the rice genome. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of all the 12 chromosomes were designed to measure genome-wide transcription. A total of 12253842 36mer oligonucleotide probes positioned every 46 nt on average were used for this purpose. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA population (seedling root, seedling shoot, panicle, and suspension cultured cells).

distribution: custom-commercial

first: Lei

last: Li

first: XiangFeng

last: Wang

first: Viktor

last: Stolc

first: Wei

last: Deng

first: Hang

last: He

first: Jan

last: Korbel

first: Xuewei

last: Chen

first: Waraporn

last: Tongprasit

first: Pamela

last: Ronald

first: Runsheng

first: Mark

last: Gerstein

first: XingWang

manufacture_protocol: Microarrays containing these oligos are synthesized on glass with Expedite DNA synthesizers (Applied Biosystems, Foster City, CA) in conjunction with Maskless Array Synthesis units (NimbleGen Systems, Madison, WI).


title: Tiling microarray OS16951 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 3


title: Tiling microarray OS18916 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 9


title: Tiling microarray OS18920 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 7


title: High-throughput sequenced small RNAs in Arabidopsis thaliana and its RISC complexes

city: Cold Spring Harbor

first: Gregory

middle: J.

last: Hannon

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

organism: Arabidopsis thaliana

technology: other

description: This dataset contains Arabidopsis thaliana endogenous small RNA sequences from total extraxts, AGO1 and AGO4 complexes. The sequences were obtained using high-throughput sequencing technology provided by 454. For technical details, see Qi, Y., He, X., Wang, X.J., Kohany, O., Jurka, J., and Hannon, G.J. 2006. Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 443(7114): 1008-1012.

distribution: virtual

manufacture_protocol: please see the 454 website


title: Tiling microarray OS18918 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 12


title: RPCI Human 19K

status: Public on Feb 27 2007

city: Buffalo

first: Devin

last: McQuaid

address: Elm and Carlton

institute: Roswell Park Cancer Institute

description: chromosome coordinates based on UCSC genome browser build hg18 which is based on the NCBI build 36.1

manufacture_protocol:
Isolation of BAC plasmid DNA: BAC clone plasmid DNAs, used as templates for PCR representations are prepared using a Qiagen BioRobot 3000. Each clone is retrieved from archival copies of the RPCI-11 BAC Resource, maintained at RPCI. The clones are streaked to single colony, grown overnight (16-18 hours) as 1.0ml pre-cultures in 96 deep-well plates at 37 C in a New Brunswick environmental shaker, and then re-inoculated as 2ml prep-cultures in 48 deep-well plates. After incubation, the cultures are RNase treated and prepped in the BioRobot 3000 using R.E.A.L. Prep 96 BioRobot kits (Qiagen). The BAC DNAs are resuspended in TE and serve as templates for restriction digestion and PCR amplification. We have found that Qiagen prepared DNA is of high quality and outperforms phenol:chloroform extraction methods for the highly sensitive restriction digestion and ligation steps.
Ligation of adapters: The adapters are ligated to the digested DNA by first annealing Mse-21 and Mse-12 primers. 1 ul of each digest (1 ng/ul), is added to 0.5 ul of 100 uM Mse-12 (TAACTAGCATGC), 0.5 ul of 100 uM Mse-21 (5’ aminolinker AGTGGGATTCCGCATGCTAGT) in a final volume of 7.5 ul using a thermalcycler (MJ Research). The mixture is incubated at 65 C for 1 min followed by ramping the temperature down to 15 C with a ramp-speed of 1.3 C per minute. When the temperature reaches 15 C, ligation proceeds with 1 ul of 10 mM ATP, 0.5 ul One-Phor-All-Buffer-Plus (10x) and 1 ul T4-DNA ligase (5 U/ul, Invitrogen) added to each tube and incubated at 15 C overnight.
PCR amplification: Two rounds of amplification are required to produce enough product for array generation as described in Cowell, J. K. and N. J. Nowak. 2003. High-resolution analysis of genetic events in cancer cells using bacterial artificial chromosome arrays and comparative genome hybridization. Adv Cancer Res 90:91-125. A single BAC PCR-representation produces enough printing solution for over 4,000 arrays. Preparation of DNA spotting solutions: PCR products (100 ul) are purified for printing by a series of ethanol precipitation steps, followed by resuspension of the pellets in 20 ul of 25% DMSO in H2O (final DNA concentration ~0.8 ug/ul) using a Qfill2 (Genetix). The DNA solutions are rearrayed into Genetix 384-well V-bottom plates using a Hydra 96-PP liquid handling system, and stored at 4 C until printing. We determined that DNA prepared using LM-PCR performed superiorly over other methods, including degenerate oligonucleotide primer PCR, inter Alu PCR and amplification of BAC subclones mixtures. 25% DMSO has several properties that make it an ideal solution for resuspending the amplicons. First, it acts as a denaturant, rendering the printing solution single-stranded for optimal slide binding and subsequent hybridization. Secondly, DMSO does not evaporate, so the printing solution volume is not affected by exposure to the environment during multiple print runs.
Array printing: Slides are printed using a MicroGrid ll TAS arrayer (Genomic Solutions) using 10K Microspot pins at 48% relative humidity, 22?C. We have a climate controlled, HEPA filtered room to minimize environmental changes that can affect printing. In addition, the arrayer is supplied with HEPA filtered air to further maintain a dust-free environment. We print each BAC clone in triplicate to create an array of on amino-silanated glass slides (Schott Nexterion, Type A+). The printed slides dry overnight, and are UV-crosslinked (350 mJ) in a Stratalinker 2400 (Stratagene). The slides are visually inspected and stored in a dessicated environment and are hybridized without additional treatment. Attempts at post-print processing or inclusion of pre-hybridization steps resulted in background issues that made the images difficult to analyze. We found no indication of DNA loss from the spots at any stage of the procedure when we performed hybridization in formamide buffers at 37°C (via DAPI staining).


title: Tiling microarray OS18913 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 10


title: USP/ANU-Barchuk Apis mellifera

first: Angel

last: Barchuk

description:
Array related information
array design name: 768Br (USP/ANU-Barchuk Apis mellifera)
platform type: spotted cDNA
surface and coating specification: see Adelaide Microarray Facility website
physical dimensions of array support (slide): 25 x 76 x 0.94mm
number of features on the array: 3,072

first: Alexandre

last: Cristino

first: Robert

last: Kucharski

first: Luciano

last: Costa

first: Zilá

last: Paulino Simões

first: Ryszard

last: Maleszka

manufacture_protocol:
ESTs cloning and sequencing, see in: Nunes F.M.F., et al. (2004).  The use of open reading frame ESTs (ORESTES) for analysis of the honey bee transcriptome. BMC Genomics, 5:84
cDNAs were PCR amplified (by using M13 primers), washed and precipitated.
For each reporter type:
•	the type of the reporter: double stranded, PCR products
For each reporter
•	sequence or PCR primer information: M13
•	approximate lengths if exact sequence not known: ~600bp
•	clone information: see Nunes F.M.F., et al. (2004)
For each feature type
dimensions: see Adelaide Microarray Facility
attachment (covalent/ionic/other): see Adelaide Microarray Facility
Control elements on the array
position of the feature (endogenous control): ribosomal protein S8


title: RIKEN Frontier Human 1K Glyco-gene Array ver1

status: Public on Feb 17 2007

city: Kyoto

first: Hiromu

last: Takematsu

state: Kyoto

address: Shogoin-Kawahara 53

department: Human Health Science

country: Japan

institute: Kyoto Univ. Sch. of Medicine

manufacturer: RIKEN Frontier Supra-Biomolecular System Research Group

first: Yasunori

last: Kozutsumi

first: Akemi

last: Suzuki

first: Reiko

last: Fujinawa

first: Harumi

last: Yamamoto

manufacture_protocol:
The RIKEN Frontier Human Glyco-gene Array  ver1 is  consisted of total 900 genes including genes for sugar  metabolism-, glycan modification-, glycan recognition-, and  glycosyltransferase genes and also lipid metabolism-related genes.
300 bp cDNA fragments selected for each gene were amplified by RT-PCR  from mixture of polyA+ RNA from human tissue, and then spotted on the  slide glass by TaKaRa(Japan). The array also contains various  positive and negative control spots.


title: Tiling microarray OS18910 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 12

first: Rajkumar

last: Sasidharan

first: Lei

last: Li

first: XiangFeng

last: Wang

first: Viktor

last: Stolc

first: Wei

last: Deng

first: Hang

last: He

first: Jan

last: Korbel

first: Xuewei

last: Chen

first: Waraporn

first: Pamela


title: EHD_FINAL

status: Public on Jul 22 2005

last: Stanford Microarray Database

organism: Entamoeba histolytica


title: Tiling microarray OS16946 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 11

last: Tongprasit

last: Ronald

first: Runsheng

first: Mark

last: Gerstein

first: XingWang


title: Tiling microarray OS16949 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 9


title: Tiling microarray OS18899 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 1


title: Tiling microarray OS18799 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 3


title: Tiling microarray OS16971 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 3


title: UHN Yeast 6.4kv6

city: Rehovot

first: sagi

last: levy

address: Hertzel

department: Molecular Genetics and Physics of Complex Systems

country: Israel

institute: Weizmann Institute of Science

organism: Saccharomyces cerevisiae

description: Grid rows-12; Grid columns-4; Rows-20; Columns-20; Grid to grid distance-4500um; Spot to spot distance-200um; Spot size-100um.

manufacturer: University Health Network Clinical Genomics Centre Microarray Centre

manufacture_protocol: 1. Acquisition of bacterial clone set — our Yeast 6.4k clone set is derived from Research Genetics Genepairs, Detailed information about the ORFs and sequences can be found at http://www.yeastgenome.org/  2. Clone set is PCR amplified and DNA purified in working 96 well plates. 3. The purified DNA is then transferred to 384 well source plates with DNA concentration ranging from .10ug/ul to 0.25ug/ul.  These are used for spotting. We use high precision robots that can use up to 48 pins or print heads.   The Y6.4kv6 slides are printed using 48 pins and we use UltraGAPS ™ slides (Corning Inc.).  We are able to print up to 120 slides in each batch and batches that result in greater than 95% printing fidelity are selected for post printing quality control tests.


title: Tiling microarray OS16969 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 10


title: Tiling microarray for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 12

description:
This experiment was designed to identify transcribed regions of japonica subspecies of the rice genome. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of all the 12 chromosomes were designed to measure genome-wide transcription. A total of 12253842 36mer oligonucleotide probes positioned every 46 nt on average were used for this purpose.
The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA populations (seedling root, seedling shoot, panicle, and suspension cultured cells).


title: NEFU Brasicca rapa 3k v1.0

status: Public on Feb 22 2007

city: Bunkyo-ku

first: Saneyuki

last: Kawabata

state: Tokyo

address: 1-1-1 Yayoi

institute: University of Tokyo

organism: Brassica rapa subsp. rapa

manufacturer: NEFU(North East Forestry University, China); Kaken Genecs (Matsudo, Japan); Lab.Horticultural Science,University of Tokyo

first: Yuhua

manufacture_protocol: A subtractive cDNAs libraries were constructed from Brassica rapa by conducting suppression subtractive hybridization (SSH) between sunlight exposed and shaded hypocotyls. Randamly selected 4.2k clones were sequenced and clutered by 'blastclust'. Basically, one clone for each cluster, 2.8k clones in total, was chosen as probes. The amplified inserts of these clones were printed in duplicate by Kaken Genecs (Chiba, Japan).


title: Tiling microarray OS18900 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 1


title: Tiling microarray OS18742 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 11


title: Sigma Genosys Panorama Bacillus subtilis Gene Array

status: Public on Dec 20 2002

city: The Woodlands

last: Sigma-Genosys

state: TX

address: 1442 Lake Front Circle

institute: Sigma-Genosys

organism: Bacillus subtilis

description: The Panorama Bacillus subtilis Gene Array contains 4,107 PCR-amplified ORFs, representing all of the protein-encoding genes, spotted in duplicate.

distribution: commercial

manufacture_protocol: see manufacturer's web site


title: Tiling microarray OS16618 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 12


title: Tiling microarray OS16974 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 8


title: SHBE

status: Public on Nov 03 2005


title: Tiling microarray OS16976 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 6


title: Tiling microarray OS16973 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 6


title: Tiling microarray OS16606 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 2


title: Tiling microarray OS18753 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 5


title: Tiling microarray OS16979 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 8


title: Tiling microarray OS18737 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 6


title: Tiling microarray OS16975 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 3


title: Tiling microarray OS16978 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 4


title: Tiling microarray OS16972 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 5


title: Tiling microarray OS18919 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 4


title: Tiling microarray OS18732 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 2


title: Maize cDNA Generation II Version A

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

organism: Zea mays

description: These cDNA clones were obtained from NSF Plant Genome EST projects led by Ginny Walbot and Pat Schnable.

manufacturer: Schnable Laboratory at Iowa State University(ISU)

first: Schnable

last: Patrick

manufacture_protocol: The ISU microarray facility have generated a maize gene chip that contains 13,056 spotted cDNA inserts. In this chip there are 12 x 4 subgrids, each grid contains 17x16=272 spots, totally the number of spots=14x4x272=13056, which includes 1056 empty spots, 22 unknown spots and 211 exogenous spots. After removing these uninformative spots, 11767 informative spots will be left for analysis.


title: Tiling microarray OS16945 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 7

first: Rajkumar

last: Sasidharan

first: Lei


title: PICME Poplar 28K 4_2_5

city: Champenoux

first: Sebastien

last: Duplessis

address: INRA Centre Grand Est - Nancy

department: UMR 1136 IAM

country: France

institute: INRA

organism:
Populus trichocarpa x Populus deltoides
Populus euphratica
Populus tremula x Populus alba

description:
Support: Corning GAPS II; Coating: Gamma Amino Propyl Silane
Number of spots: 2727648
Number of pins/blocks: 48
Spottdistance in µm: 180
Recurrances spots/slide: 1
Number of spots vertical: 24
Number of spots horinzontal: 24
Vertical offset of first block in µm: 1200
Horizontal offset of first block in µm: 3150
Lot number 13705000B

first: Francis

last: Martin

first: Jean-Charles

last: Leple

first: Jaakko

last: Kangasjarvi

first: Silvia

last: Fluch

first: Michael

last: Stierschneider

first: Dieter

last: Kopecky

manufacture_protocol:
Spottingbuffer: 3xSSC+ 1,5MBetain
Spottingplate setting: Biozym 10µl
Arrayer Hardware: GeneMachines Omnigrid II
Arrayer Software: OmniGrid Gridder 2.2.13
Humidity: 40%
Dipping time in sec: 1


title: Campylobacter NCTC 11168 ORF-based array printed at IFR (third type)

status: Public on Feb 15 2007

city: Norwich

first: Bruce

middle: MacKenzie

last: Pearson

state: Norfolk

address: Colney Lane

department: Food Safety

country: United Kingdom

institute: Institute of Food Research

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

description: Corning barcoded GAPSII slides used

middle: M

first: Claire

middle: E

last: Monk

last: Mulholland

first: Robert

middle: K

last: Poole

manufacture_protocol: PCR product array of ORF's from Campylobacter jejuni subsp. jejuni NCTC 11168. For description of PCR amplification see Pearson et al., FEBS Letters 554(2003) 224-230.


title: STv5B_MMCC_Locus_Tags

status: Public on Feb 14 2007

city: Durham

first: William

last: Ward

state: NC

address: 109 TW Alexander Dr

department: NHEERL

institute: United States EPA

organism: Salmonella enterica subsp. enterica serovar Typhimurium

first: Steffen

last: Porwollik

last: McClelland

first: Scott

last: Jackson

first: Felisa

last: Blackmer

first: Jonathan

middle: G

last: Frye

first: Colleen

last: Eckhardt

manufacture_protocol: Custom made spotted Salmonella array


title: SBTM Microarray Laboratory Operon Rat v3.0

city: Temple

first: Vincent

last: VanBuren

address: 702 SW HK Dodgen Loop

department: Systems Biology and Translational Medicine

institute: Texas A&M Health Science Center

organism: Rattus norvegicus

technology: spotted oligonucleotide

manufacturer: The SBTM Microarray Laboratory, Systems Biology, 702 SW HK Dodgen Loop, Temple, TX 76504

middle: C

last: Jamroz

first: Reza

last: Forough

manufacture_protocol: The Array-Ready Rattus norvegicus Genome Oligo Set Version 3.0 from Operon Biotechnologies, Inc. was spotted using a GeneMachines OmniGrid Arrayer (Arrayer manual/spotting protocol available at the Genomic Solutions website; complete genelists, annotations, and datasheets for oligos available at the Operon Biotechnologies website). Array descriptions may be found at the SBTM Microarray Laboratory website.


title: Rosetta/Merck Mouse 25k v1.4 microarray

status: Public on Feb 13 2007

city: Seattle

first: Amit

middle: V

last: Kulkarni

state: WA

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

organism: Mus musculus

description: Contains 60-mer probes (60-mer).

first: John

last: Castle

manufacture_protocol: See manufacturer's website


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

description: Contains 60-mer probes (60-mer).

manufacturer: Rosetta Inpharmatics / Merck Pharmaceuticals


title: Tiling microarray OS18752 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 2

first: Rajkumar

last: Sasidharan

first: Lei

last: Li

first: XiangFeng

last: Wang

first: Viktor

last: Stolc

first: Wei

last: Deng

first: Hang

last: He

first: Jan

last: Korbel

first: Xuewei

last: Chen

first: Waraporn

last: Tongprasit

first: Pamela

last: Ronald

first: Runsheng

first: Mark

last: Gerstein

first: XingWang


title: Tiling microarray OS16948 for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 2


title: Nimblegen Staphylococcus aureus 2.6K oligo array

city: Houston

first: Gabriela

last: Bowden

address: 2121 Holcombe Blvd

department: CEMB

institute: Texas A&M

organism: Staphylococcus aureus

description: Maskless Array Synthesizer (MAS) technology

first: Maria

last: Labandeira-Rey

first: Florence

last: Couzon

first: Sandrine

last: Boisset

first: Eric

last: Brown

first: Michele

last: Bes

first: Yvone

last: Benito

first: Elena

last: Barbu

first: Vanessa

last: Vazquez

first: Magnus

last: Hook

first: Jerome

last: Etienne

first: Francois

last: Vandenesch

manufacture_protocol: Available at manufacturer's website: www.nimblegen.com


title: Rice WRKY-custom oligo array

status: Public on Feb 10 2007

city: Milan

first: Stefano

last: Berri

address: via Celoria 26

department: biomolecular sciences and biotechnology

country: Italy

institute: University of Milan

organism: Oryza sativa Japonica Group

description: This set includes 144 oligonucleotides, 60-mers, generally designed on a gene-specific sequence in the 3'-UTR of WRKY genes.

first: Pietro

last: Piffanelli

first: Driss

last: Talibi

manufacture_protocol: Robotic Gridding onto glass slides. AR-GRID-GR


title: SBTM Microarray Laboratory Operon Pig v1.0

first: Vincent

last: VanBuren

organism: Sus scrofa

first: Robert

last: Jamroz

first: Reza

last: Forough

manufacture_protocol: The Array-Ready Pig Genome Oligo Set Version 1.0 from Operon Biotechnologies, Inc. was spotted using a GeneMachines OmniGrid Arrayer (Arrayer manual/spotting protocol available at the Genomic Solutions website; complete genelists, annotations, and datasheets for oligos available at the Operon Biotechnologies website). Array descriptions may be found at the SBTM Microarray Laboratory website.


title: Narusaka Lab. Arabidopsis 1.2K Full-length cDNA microarray ver.1

status: Public on Feb 08 2007

city: Kaga-gun, Okayama

first: Yoshihiro

last: Narusaka

address: 7549-1, Kibityuo-town Yoshikawa

institute: Research Institute for Biological Sciences

description: A total of 1.2K potential stress-related genes that encode known or putative protein were selected for this study from the genes covered by Arabidopsis 7K array (RIKEN, Japan) and Arabidopsis oligo microarray (Agilent technologies, USA), which these genes include biotic and abiotic stress-inducible genes (Seki M et al. Plant J 31: 279-292, 2002; Narusaka Y et al. Plant Cell Physiol 44: 1246-1252, 2003; Narusaka Y et al. Plant Cell Physiol 44: 377-387, 2003; Narusaka Y et al. Mol Plant-Microbe Interact 17: 749-762, 2004)

first: Mari

first: Hiroshi

last: Abe

first: Masatomo

last: Kobayashi

manufacture_protocol:
In the cDNA microarray analyses, we used ca.1.2K cDNA clones and the lambda control template DNA fragment (TX803; Takara) as an external control. The vectors used for cDNA library construction were modified lambda ZAP (Carninci et al. (1996) Genomics, 37, 327-336) and lambda FLC-1(Carninci et al. (2001) Genomics, 77, 79-90). Inserts of cDNA clones were amplified by PCR using primers complementary to vector sequences flanking both sides of the cDNA insert, as described previously (Seki et al. (2001) Plant Cell, 13, 61-72). PCR products were precipitated in isopropanol and the DNA was resuspended in 1 x Micro Spotting Solution (Arrayit; Telechem International Inc., Sunnyvale, CA). One aliquot of each finished reaction was electrophoresed on a 1 % agarose gel to confirm amplification quality and quantity. PCR products were arrayed from 384-well microtitre plates onto a micro slide glass (model Super Aldehyde substrates; Telechem International Inc., Sunnyvale, CA) using the microarray stamping machine (model SpotArray24; PerkinElmer, MA, USA).

Hybridization procedures and parameters (The protocol and conditions used during
hybridization, blocking and washing):
The slides were postprocessed according to the manufacturer's protocol (Telechem International Inc.). The printed slides were dried (RH < 30 %) and subjected to UV cross-linking. They were rocked in 0.2 % SDS for 2 min three times and then rocked in distilled water for 2 min twice vigorously. The slide racks were transferred into a chamber containing boiling water and left for 2 min. The blocking solution containing 1 g sodium borohydride, 300 ml PBS and 90 ml 100 % ethanol was poured into the glass chamber. The slide racks were shaken gently for 5 min, then transferred into a chamber containing 0.2 % SDS and shaken gently for 1 min three times. They were transferred into a chamber containing distilled water, shaken gently for 1 min, and dried by centrifugation for 20 min.The probe samples prepared as
described previously were denatured by placing them in a 100C heat block for 2
min, left at room temperature for 5 min, and then used for hybridization. The slides
were placed in a sealed hybridization cassette (Telechem International Inc.,
Sunnyvale, CA) and submerged in a 65C water bath for 16 to 20 h. After
hybridization, slides were washed in 2 X SSC, 0.03% SDS for 2 min, then in 1 X
SSC for 2 min, and finally in 0.06 X SSC for 2 min. Then, the slides were
immediately dried by centrifugation (2 min at 180 g). Slides were scanned with a
ScanArray (PerkinElmer, Wellesley, MA, USA) as described previously (Seki et al.
(2001) Plant Cell 13:61-72).


title: WCFS Lactobacillus plantarum 11K 60-mer array, Version 1, our ID LPAG1

city: Amsterdam

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

country: Netherlands

institute: Vrije Universiteit Amsterdam

organism: Lactiplantibacillus plantarum WCFS1

description: This array contains 60-mer probes that are designed for L. plantarum strain WCFS1. The sequence of this organism is present in public databases, Acc. Nr. AL935263.

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


title: NimbleGen_DesignID3426_UNC_LiebLab tiling array

status: Public on Feb 11 2007

city: Chapel Hill

first: Jason

middle: D

last: Lieb

address: 408 Fordham Hall, CB# 3280

department: Biology

institute: University of North Carolina at Chapel Hill

organism: Caenorhabditis elegans

first: Sevinc

last: Ercan

first: Paul

last: Giresi

first: Christina

last: Whittle

first: Xinmin

last: Zhang

first: Roland

last: Green

manufacture_protocol: see NimbleGen website


title: GMAT (Genome-wide MAppping Technique) [NlaIII: Homo Sapiens] tag list

status: Public on Feb 06 2007

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Rockville Pike

institute: NHLBI, NIH

organism: Homo sapiens

first: Tae-Young

last: Roh

first: S

last: Cuddapah

manufacture_protocol: The GMAT (Genome-wide MAppping Technique) was developed by the combination of ChIP (chromatin immunoprecipitation) and SAGE (serial analysis of gene expression) protocols. Briefly, the chromatin prepared by sonication is subject to immunoprecipitation using specific antibody. DNA from precipitated chromatin is ligated with biotinylated linker and digested with NlaIII restriction enzyme. The DNA fragments with biotinylated linker are isolated and ligated with NlaIII-site specific linker. The DNA is cut with MmeI restriction enzyme to generate 21-base seqeunce tags and ligated each other to form ditags. After removing linkers by NlaIII, isolated ditags are concatenated and determined the sequence. The genomic position of tags is identified by DNA sequences and the detected number of each tag sequence represents the degree of enrichment by means of specific antibody.


title: UMBI_Drosophila_1440_1

city: College Park

first: Subhamoy

last: Pal

address: 5126 Plant Sciences Building

department: Center for Biosystems Research

institute: University of Maryland

organism: Drosophila melanogaster

description: Spotted oligonucleotide microarray with a high representation of genes important for Drosophila immune responses.

first: Junlin

last: Wu

first: Louisa

middle: P

manufacture_protocol:
464 Genes important for Drosophila immune responses were selected from a literature survey and previous experiments. Primers were designed to be between 200 and 600 base pairs using manual techniques and Primer3.  These PCR primers were used to amplify the selected oligonucleotide regions from Genomic DNA, and run on agarose gels to confirm amplification success and specificity.  The reaction mixture to produce each amplicon contained 50 ng Drosophila genomic DNA, 1 uM forward primer, 1 uM reverse primer, 1xTitanium Taq (Invitrogen) and 0.5 mM dNTP. The following PCR protocol was used: an initial 95C denaturation step for 5 minutes followed by 20 cycles of 30 seconds of 95C denaturation, 30 seconds of 60C annealing, and 45 seconds of 75C extension. They were purified using QIAquick 96 PCR Purification Kit according to manufacturer's protocol and suspended in 3XSSC.
The purified DNA was spotted onto Corning GAPSII coated glass slides using a Affymetrix Arrayer 417, at the CBR/UMBI Core Microarray Facility.


title: RIKEN 16K tobacco cDNA microarray (Slide3A)

city: Yokohama

first: Ken

last: Matsuoka

state: Kanagawa

address: 1-7-22 Suehirocho, Tsurumi-ku,

department: Plant Science Center

institute: RIKEN

organism: Nicotiana tabacum

description: Mirror type slides were used.

first: Ivan

last: Galis

first: Mami

last: Sasaki

first: Tomoko

last: Narisawa

manufacture_protocol:
DNA for microarrays was prepared by amplification of cDNA cloned inserts using conventional PCR and the universal M13 forward (GTAAAACGACGGCCAGT) and reverse (CAGGAAACAGCTATGAC) vector primers (pGEM-Teasy), or M13 forward (GTAAAACGACG GCCAGT) and KS reverse (TCGAGGTCGACGGTATC) vector primers (pBII KS), with cDNA-containing plasmids as PCR templates. The microarray slides contained cDNA/EST clones described previously [1,2]. Control gene fragments cloned into the pBluescript vector (pBII KSt; Stratagene) were processed together with the cDNA/ESTs during microarray preparation. A complete set of 16 224 amplified cDNA inserts + control DNAs (672) was used to print a custom 16K BY-2 microarray (16,896). The complete microarray consisted of four microarray Bar Coded Slides, Type 7 star* or Lucidea (Amersham Biosciences UK Limited, Buckinghamshire, UK), with each PCRamplified cDNA sample spotted in duplicate on the slides. Standard slide arrangement consisted of 24 blocks with 12 rows and 32 columns each. The Array Spotter Generation III (Molecular Dynamics, Sunnyvale, CA, USA) was used for printing of slides.
Code and description of control spots that are repeatedly spotted on each sub-array slide. Controls are spotted as bottom row in each individual block. Control spots 18-23 hybridize to Kanamycin positive mRNA spike from Promega that was added to each sample before cDNA synthesis.
1-NPTII,neomycin phosphotransferase II [V00618.1]
2-HYG,hygromycin B phosphotransferase [K01193.1]
3-RFP,RFP - red fluorescent protein [AF168419.2]
4-GUS,GUS - beta-glucuronidase protein [U12639]
5-PolyA,poly A oligonucleotide hybridization control [synthetic]
6-STS1,Yeast STS1 gene negative control [Z37996.1]
7-PBKSII,(M13-KS) vector pBluescript KSII (+) sequence [commercial]
8-pGEMTe,(M13-M13) vector pGEM-Teasy sequence (Self-ligated) [commercial]
9-Act200,200 bp PCR amplified fragment of tobacco actin gene [X63603]
10-Tub200,200 bp PCR amplified fragment of tobacco tubulin gene [NTU91562]
11-RibS4,PCR amplified fragment of tobacco ribosomal protein S4 gene [BP129322]
12-RibS29,PCR amplified fragment of tobacco ribosomal protein S29 gene [BP129273]
13-Actin,PCR amplified fragment of tobacco actin gene [BP534187]
14-Tubulin,PCR amplified fragment of tobacco tubulin gene [BP534511]
15-18SRNA,tobacco 18S rRNA gene [AJ236016]
16-SsDNA,Salmon sperm DNA (high complexity non-specific hybridization control) [commercial]
17-lambda,HindIII digested lambda phage  DNA (low complexity non-specific hybridization control) [commercial]
18-Kan200,Promega kanamycin control RNA (Cat # C1381) corresponding DNA spot (spike control) [AY947641]
19-Kan200/2,Promega kanamycin control RNA corresponding DNA spot diluted 2x (spike control) [AY947641]
20-Kan200/5,Promega kanamycin control RNA corresponding DNA spot diluted 5x (spike control) [AY947641]
21-Kan200/10,Promega kanamycin control RNA corresponding DNA spot diluted 10x (spike control) [AY947641]
22-Kan200/50,Promega kanamycin control RNA corresponding DNA spot diluted 50x (spike control) [AY947641]
23-Kan200/100,Promega kanamycin control RNA corresponding DNA spot diluted 100x (spike control) [AY947641]
24-Water,deionized water control (negative control)
25-cDNA/2,PCR amplified cDNApool from BY-2 cells (diluted 5x) (positive control calibration) [custom]
26-cDNA/5,PCR amplified cDNApool from BY-2 cells (diluted 10x) (positive control calibration) [custom]
27-cDNA/10,PCR amplified cDNApool from BY-2 cells (diluted 20x) (positive control calibration) [custom]
28-cDNA/50,PCR amplified cDNApool from BY-2 cells (diluted 50x) (positive control calibration) [custom]
29-cDNA/100,PCR amplified cDNApool from BY-2 cells (diluted 100x) (positive control calibration) [custom]
30-cDNA/500,PCR amplified cDNApool from BY-2 cells (diluted 200x) (positive control calibration) [custom]
31-cDNA/1000,PCR amplified cDNApool from BY-2 cells (diluted 500x) (positive control calibration) [custom]
32-cDNA/5000,PCR amplified cDNApool from BY-2 cells (diluted 1000x) (positive control calibration) [custom]
[1] Matsuoka, K., Demura, T., Galis, I., Horiguchi, T., Sasaki, M., Tashiro, G. and Fukuda, H. (2004) A comprehensive gene expression analysis toward the understanding of growth and differentiation of tobacco BY-2 cells. Plant Cell Physiol. 45: 1280-1289.
[2] Galis, I., Simek, P., Narisawa, T., Sasaki, M., Horiguchi, T., Fukuda, H. and Matsuoka, K. (2006) A novel R2R3 MYB transcription factor NtMYBJS1 is a methyl jasmonate-dependent regulator of phenylpropanoid-conjugate biosynthesis in tobacco. Plant J. 46: 573-592.


title: RIKEN Mouse Neues microarray version 2

status: Public on Feb 09 2007

city: Hidaka

first: Itoshi

last: NIKAIDO

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical School

description: RIKEN Mouse Neues Microarray v2.0 contains 21,943 60-mer oligonucleotides representing over 20,000 known and predicted mouse genes. The sequence is based on the RIKEN cDNA clone sequences and public databases (RefSeq, Ensembl).

manufacturer: 4Genome Exploration Research Group, RIKEN Genomic Sciences Center

last: Nikaido

manufacture_protocol:
Validated probes are probes optimized using a novel experimental method for the selection and validation of highly specific oligonucleotide microarray probes. This probe optimization strategy is based on the assumption that, if multiple probes for a particular gene are specific for that gene, they will show similar differential expression behavior. Optimized 60-mer probes are selected from clusters of computationally determined candidate probes that perform similarly across a number of differential gene expression experiments. This method also enables verification of computationally predicted gene assemblies. These selected probes are then experimentally validated based on hybridization responses to all known genes for which they were designed.

Agilent uses its inkjet technology to print oligos and whole cDNAs onto glass slides. The non-contact inkjet technology produces microarrays with more uniform and consistent features. The inkjet technology is used as part of an industrial-scale manufacturing process that enables us to reliably produce uniform, high quality microarrays from lot to lot. Since the inkjet process is a non-contact process, it does not introduce defects as a result of surface tension interactions with the microarray surface.


title: RIKEN 16K tobacco cDNA microarray (Slide1B)

description: Mirror type slides were used.


title: GMAT (Genome-wide MApping Technique) [NlaIII: Saccharomyces cerevisiae] tag list

organism: Saccharomyces cerevisiae

first: W

last: Ngau

first: K

last: Cui

first: D

last: Landsman

manufacture_protocol: The GMAT (Genome-wide MApping Technique) was developed by the combination of ChIP (chromatin immunoprecipitation) and SAGE (serial analysis of gene expression) protocols. Briefly, the chromatin prepared by sonication is subject to immunoprecipitation using specific antibody. DNA from precipitated chromatin is ligated with biotinylated linker and digested with NlaIII restriction enzyme. The DNA fragments with biotinylated linker are isolated and ligated with NlaIII-site specific linker. The DNA is cut with MmeI restriction enzyme to generate 21-base seqeunce tags and ligated each other to form ditags. After removing linkers by NlaIII, isolated ditags are concatenated and determined the sequence. The genomic position of tags is identified by DNA sequences and the detected number of each tag sequence represents the degree of enrichment by means of specific antibody.


title: Lovett_WUSTL_TFarray_v2

status: Public on Feb 01 2007

city: Saint Louis

first: Kara

last: Powder

state: MO

address: 4566 Scott Ave

department: Genetics

institute: Washington University in St Louis

organism:
Gallus gallus
Homo sapiens
Mus musculus

description: The majority of probes interrogate transcription factors and are designed to coding regions.

first: Michael

last: Lovett

first: David

last: Alvarado

manufacture_protocol: Microarrays were printed on a GMS 417 Arrayer (Affymetrix, Santa Clara, CA) within the Washington University Division of Human Genetics.


title: Affymetrix custom made array SFORV2_2

city: Chicago

first: Omar

last: De la Cruz

state: IL

address: 5734 S University Ave

department: Department of Statistics

institute: University of Chicago

organism:
Pan troglodytes
Homo sapiens
Canis lupus familiaris
Rattus norvegicus

manufacture_protocol: see manufacturer's web site


title: UCSF HUMAN 1.14

status: Public on Feb 05 2007

city: Pamplona

first: Jose Angel

middle: Martinez

last: Climent

state: Navarra

address: PIO XII

country: Spain

institute: CIMA/Universidad De Navarra

description:
The arrays contain 2462 BAC clones printed as triplicated spots.
The array was used for genome wide measurement of DNA copy number.

manufacturer: University of California, San Francisco (UCSF)

manufacture_protocol: Production and validation of the array, hybridization methods and analytical procedures have been described elsewhere: Snijder AM, Nowak N, Segraves R, et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet. 2001;29:263-264.


title: Rice japonica 1Mb Tiling array by NimbleGen

city: New Haven

first: Xiangfeng

last: Wang

address: 352 OML, 165 Prospect st

department: MCDB

institute: Yale University

organism: Oryza sativa

description: TIGR build 3 of the rice genome, on chromosome 10

manufacture_protocol: rice japonica chromosome 10 (10Mb to 11Mb) region, tiling path microarray at 5bp resolution.


title: RIKEN 16K tobacco cDNA microarray (Slide4A)

description: Mirror type slides were used.


title: Rice japonica 400K NimbleGen Oligo Array

description: gene level expression array, contain 400k oligos, based on gene models from TIGR v3 build

manufacture_protocol:
1. Oligo length: 36.
2. Maximum distance accepted between the 5' end of the oligo and the 3' end of the input sequence: 2000
3. Minimum oligonucleotide Tm: 80.
4. Maximum oligonucleotide Tm: 95.
5. Temperature to use during secondary structure prediction (an oligo will be rejected if it can fold into a stable secondary structure at this temperature): 65,
6. Threshold to report putative cross-hybridizations (all targets hybridizing with a given oligo with a Tm exceeding this threshold are reported): 70,
7. Minimum oligonucleotide GC content: 40.
8. Maximum oligonucleotide GC content: 73 for gene models; 77 for TARs.
9. Minimum distance between the 5' end of two adjacent oligos: 1.


title: Interference of components of the PEP:phosphotransferase system (PTS) with PrfA of L. monocytogenes

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

country: Germany

institute: University of Wuerzburg

organism: Listeria monocytogenes

first: Sonja

last: Mertins

first: Biju

last: Joseph

first: Monika

last: Goetz

first: Regina

last: Ecke

first: Gerlad

last: Seidel

first: Mareen

last: Sprehe

first: Wolfgang

last: Hillen

first: Werner

last: Goebel

first: Stefanie

last: Müller-Altrock

manufacture_protocol:
ARRAY PRINTING
1. Dissolve oligonucleotide probe or PCR product in the appropriate spotting solution to obtain the
recommended final probe concentration:
DNA Probes Final Spotting Concentration
Oligonucleotides 10 - 20 ìM
PCR products 0.1 – 1 mg/ml
2. Transfer an appropriate volume of probes to a microtiter plate.
3. Set up the arrayer according to the manufacturer’s recommendations. If you were previously
using slides that were thicker than 1.0 mm, for optimal spotting you may need to re-calibrate
the distance between the slide surface and the spotting pins.
4. Print the substrates at 40-50% relative humidity at 20 to 25°C.
DNA IMMOBILIZATION
1. Incubate printed microarray slides in humidity chamber at room temperature for 30 min (see
appendix for details of how to prepare this chamber) to ensure quantitative immobilization.
2. Proceed to washing


title: Arabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology

first: James

last: Carrington

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

organism: Arabidopsis thaliana

description: The dataset contains unique, 20-25 nucleotide small RNA sequences identified using high-throughput 454 sequencing of samples prepared from Arabidopsis thaliana.  Each sequence has a minimum of one genomic locus.  Small RNAs were sequenced from inflorescence tissue (containing stage 1-12 flowers) of wildtype Col-0 plants, mutants with defects in each DCL gene (dcl1-7, dcl2-1, dcl3-1, dcl4-2), mutants with defects in each RDR gene for which a function has been established (rdr1-1, rdr2-1, rdr6-15), and whole seedling tissue (3 day post-germinations) of Col-0 and rdr6-15 plants.  Small RNA preparations from leaf samples of Col-O that were either uninoculated or inoculated by Pseudomonas syringae pv tomato (DC3000hrcC) for 1 hr and 3 hr were also sequenced.

first: Kristin

last: Kasschau

first: Noah

last: Fahlgren

first: Elisabeth

middle: J

last: Chapman

first: Christopher

last: Sullivan

first: Jason

last: Cumbie


title: RIKEN 16K tobacco cDNA microarray (Slide2B)

first: Ken

last: Matsuoka

description: Mirror type slides were used.

first: Ivan

last: Galis

first: Mami

last: Sasaki

first: Tomoko

last: Narisawa


title: RIKEN 16K tobacco cDNA microarray (Slide2A)

description: Mirror type slides were used.

manufacture_protocol:
DNA for microarrays was prepared by amplification of cDNA cloned inserts using conventional PCR and the universal M13 forward (GTAAAACGACGGCCAGT) and reverse (CAGGAAACAGCTATGAC) vector primers (pGEM-Teasy), or M13 forward (GTAAAACGACG GCCAGT) and KS reverse (TCGAGGTCGACGGTATC) vector primers (pBII KS), with cDNA-containing plasmids as PCR templates. The microarray slides contained cDNA/EST clones described previously [1,2]. Control gene fragments cloned into the pBluescript vector (pBII KSt; Stratagene) were processed together with the cDNA/ESTs during microarray preparation. A complete set of 16 224 amplified cDNA inserts + control DNAs (672) was used to print a custom 16K BY-2 microarray (16,896). The complete microarray consisted of four microarray Bar Coded Slides, Type 7 star* or Lucidea (Amersham Biosciences UK Limited, Buckinghamshire, UK), with each PCRamplified cDNA sample spotted in duplicate on the slides. Standard slide arrangement consisted of 24 blocks with 12 rows and 32 columns each. The Array Spotter Generation III (Molecular Dynamics, Sunnyvale, CA, USA) was used for printing of slides.
[1] Matsuoka, K., Demura, T., Galis, I., Horiguchi, T., Sasaki, M., Tashiro, G. and Fukuda, H. (2004) A comprehensive gene expression analysis toward the understanding of growth and differentiation of tobacco BY-2 cells. Plant Cell Physiol. 45: 1280-1289.
[2] Galis, I., Simek, P., Narisawa, T., Sasaki, M., Horiguchi, T., Fukuda, H. and Matsuoka, K. (2006) A novel R2R3 MYB transcription factor NtMYBJS1 is a methyl jasmonate-dependent regulator of phenylpropanoid-conjugate biosynthesis in tobacco. Plant J. 46: 573-592.


title: RIKEN 16K tobacco cDNA microarray (Slide1A)

description: Mirror type slides were used.


title: Maize SAM1.2 Array

status: Public on Nov 07 2006

city: Ames

first: Patrick

last: Schnable

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

organism: Zea mays

manufacture_protocol:
A 15,680 element microarray chip (SAM1.2 chip) was generated at Iowa State University’s Center for Plant Genomics.
Of the 15,680 elements printed on the UltraGAPs slide (Corning, Inc.), 5,753 cDNA clones from the Stanford UnigeneI developed by the National Science Foundation-funded Maize Gene Discovery Project (http://www.maizegdb.org) and re-sequenced at Dr. Schnable’s lab, 1,058 cDNA clones from the UnigeneIV-1091, 6,711 cDNA clones from the library 3529, 1,530 cDNA clones from the ISUM3, ISUM4, ISUM5, ISUM6, ISUM7, UGA-ZmSAM-XZ1 and UGA-ZmSAM-XZ2 libraries (http://schnablelab.plantgenomics.iastate.edu/research/genomics/htp_est/) prepared at Iowa State University as part of a National Science Foundation Plant Genome Project; In addition, 192 human gene spots are also included on the chip.
The full-length inserts from the library 3529 were PCR amplified from denatured O/N E. coli culture, then purified and quantified (Nakazono et al. 2003 Plant Cell, 583-596). The rest ESTs were PCR amplified using plasmid DNAs as template in 100 µl PCR reactions containing 1X PCR buffer (200 mM Tris-HCl, pH 8.4 and 500 mM KCl), 2.5 mM MgCl2, 0.2 mM dNTPs, 0.2 µM of each primer, and Taq polymerase. The PCR program cycle was: 94°C for 3 min followed by 35 cycles of 94°C for 45 sec, 60°C for 45 sec, 72°C for 2 min 30 sec, and a final elongation step of 2 min. Most PCR negative (no band, multiple bands or smears) wells were removed, and a few were spotted onto the slides with labeling badPCR in the GeneID file. PCR products were purified using Millipore 96-well multiscreen filter plates (LSKC09601) as recommended by the manufacturer and eluted in 50 µl of water. Five microliters of each purified PCR product were electrophoresed on a 1% agarose gel to examine quantity quality. The remaining 45 µl of purified PCR product were dried to completion in a vacuum oven and resuspended in 50% DMSO with a final DNA concentration 300 to 500 ng/µl.
The PCR amplified cDNA inserts were printed on UltraGAPS, which is uniform covalently bound of pure gamma amino propyl silane coating (Corning, NY, Cat. No. 40015).  The whole array consists of 48 subgrids printed in 18- x 54-mm array area.
PixSys 5500 arrayer (Cartesian Technologies, Irvine, CA) equipped with ChipMaker3 pins (TeleChem, Santa Clara, CA) is used for printing. Slides were UV cross-linking at 300 mJ with a Stratalinker (Stratagene) for immobilization, and stored in desiccator at ambient temperature.


title: UCSF HUMAN 1.14 v3

first: Jose Angel

last: Climent


title: C.elegans whole genome array Ecoworm I

status: Public on Oct 20 2006

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

first: Peter

last: Kille

first: Victoria

last: Workman

middle: R

manufacture_protocol: 19,873 amine modified 70 mer oligonucleotides (Array-Ready Oligo Set™ for the C. elegans genome, version 1.1; Qiagen) representing 20.445 transcripts of the C. elegans genome  were spotted on code link glass slides (Amersham) using a SpotArray 72 robot (Perkin Elmer) With 48 Telechem Smp3 pins


title: SHFK

status: Public on Jan 21 2006

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

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


title: Tsinghua University mammalian 2K microRNA microarray

status: Public on Feb 02 2007

city: Beijing

first: yong

last: guo

state: Beijing

address: Qinghuayuan

department: Medical Systems Biology Research Center

country: China

institute: Tsinghua University

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: Altogether 509 mature miRNA sequences were assembled and integrated into our miRNA microarray design, these comprised 435 human (including a further 122 predicted miRNA sequences from published references (Xie et al., Nature 2005,434:338-345 ), 196 rat and 261 mouse mature miRNAs from the miRNA Registry (Sanger, accessed Sept. 2005).  In addition, we designed 8 short oligonucleotides that possessed no homology to any known RNA sequence and we produced their corresponding synthetic miRNAs by in vitro transcription using Ambion's miRNA Probe Construction kit (Cat. No.1550, Austin, TX).  We added various amounts of these synthetic miRNAs into the human miRNA samples prior to analysis as internal controls.

first: Yong

last: Guo

manufacture_protocol: as described in CapitalBio lab manual


title: UCSF HUMAN 1.14 v2


title: UCSF HUMAN 1.14 v4

manufacturer: University of California, San Francisco (UCSF).


title: Medicago truncatula 16K Genome Oligo Set

city: St Paul

first: Kathryn

middle: A

last: VandenBosch

state: MN

address: Room 250 BioSci 6022 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

organism: Medicago truncatula

description:
The Medicago Genome Oligo Set Version 1.0 (Qiagen Operon, Alameda, CA) includes 70-mer oligonucleotides representing 16,086 M. truncatula tentative consensus sequences (TCs) from The Institute of Genome Research (TIGR) Gene Index Database (www.tigr.org/tdb/tgi/mtgi/) MtGI Release 5.0 as well as both positive and negative controls. Details of this oligo set are available at the Qiagen Operon website. The oligos were spotted in 3x SSC onto Superamine (Telechem) glass slides by the Galbraith lab at the University of Arizona (Tucson, AZ). A single array element was printed per oligo. After printing, slides were baked at 80°C for 1 hour and stored at RT.
Medicago
legume

first: David

middle: W

last: Galbraith


title: UMDNJ_Human_BCA1135

city: Shanghai

first: Guohong

last: Hu

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

first: Qifeng

last: Yang

first: Gang

last: Yue

first: Marco

last: Azaro

first: Hui-Yun

last: Wang

first: Xiangfeng

last: Cui

first: Honghua

last: Li

manufacture_protocol: The oligonucleotides were printed in duplicate spots with a center-to-center distance of 250 µm. Microarray preparation was performed according to a procedure established in our laboratory. Briefly, (1) preparation of microarray slides: Pre-cleaned Gold Seal Micro slides (Becton Dickson) without scratches were chosen, and were soaked in 30% bleach with shaking for 1-2 hrs followed by rinsing 5 times with deionized H2O and 3 times with MilliQ H2O. Slides were then sonicated in 15% Fisher brand Versa-Clean Liquid Concentrate with heat on for 1-2 hrs followed by rinsing with shaking in deionized H2O 10 times or until no bubbles occurring and 5 times with MilliQ H2O. Slides were dried by centrifugation at 1,000 rpm for 5 min in a GS-6 Beckman centrifuge with a slide holder and then were baked at 140oC vacuum oven for 4-5 hrs (Fisher Scientific Model 280A); (2) microarray preparation: oligonucleotides were mixed with microarray printing solution (GenScript, PiscatawayNJ) at a 1:5 ratio (v/v) to have a final concentration of 50 µM for each probe in the wells of 384-well plates. Probes were then spotted onto the washed glass slides under a humidity of 50% to 55% and temperature from 24.5oC to 26.5oC


title: Yale Caenorhabditis elegans 19K elegans_Dprint_YMD

first: Guoneng

last: Zhong

state: CT

address: 300 George St

institute: Yale Med

description: fourth print of sjj primer set 1st PCR

manufacture_protocol: proprietary


title: NCI-60 cell line Reverse Phase Protein Lysate Array_modified

first: Uma

middle: T

last: Shankavaram

address: 9000 Rockville Pike

department: NCI

institute: NIH

technology: spotted peptide or protein

description: 640 spots (plus eight spatial registration marks for use in image processing) on a 21 x 35 mm area of nitocellulose membrane.

first: Satoshi

last: Nishizuka

manufacture_protocol: Arrays were prepared on nitrocellulose-coated galss slides (FAST Slides, Schleicher & Schuell) by using a pin-in-ring format GMS 417 arrayer (Affymetrix, Santa Clara,CA) with four 500 um diameter pins. Because the cell lysates were viscous, we used pin-in-ring format to avoid clogging of quills. Ten two-fold serial dilutions were made from each lysate. Four 384-well microtiter plates (Genetix, New Milton, Hamphisire, UK) were used to array 640 spots (plus eight spatial registration marks for use in image processing) on a 21x 35 mm area of nitocellulose membrane. The first dilution (four-fold) was made with buffer containing 5M urea, 2% Pharmalyte, pH 8-10.5, and 65 mM DTT. Hence, only the lysate concentration changed along each dilution series. The urea concentration was kept at 6M and CHAPS concentration 2%, to keep proteins in their denatured form. We could remove lysates repeatedly from -80 degreeC storage for use without heating. To avoid evaporation in the microtiter plate during spotting, we kept the humidity in the array chamer at 70-90% with a Vicks ultrasonic humidifier. Arraying was completeed for each microtiter plate within 70 min. Arrays were produced in batches of 20, and the occassional low-quality array (e.g. with many spots dropouts) was discarded.


title: Forschungszentrum Karlsruhe Danio rerio microarray

city: Eggenstein-Leopoldshafen

first: Jessica

last: Legradi

state: Baden-Wuerttemberg

address: Hermann-von-Helmholtz-Platz 1

department: Institute of Toxicology and Genomics ITG

institute: Karlsruhe Institute of Technology

organism: Danio rerio

description: The oligos were spotted onto the chip in 4 by 12 blocks where each block is printed by one single pin. A block itself is divided into a subgrid of 27 x 27 spots and each sequence of 16 spots contains oligos from a different library plate. The spots are arranged densely on the array. An optimal spot has a diameter of 100 um and the distance between blocks is 150 um. The library provided by Sigma-Genosys/Compugen comprises 43 plates. A major drawback in the biosensor project is that only oligos from plate 1 to 28 yielded a proper signal. Oligos from the remaining plates 29 to 43 were extended with defect linkers. Hence, they were not able to bind permanently to the chip surface which made them useless for microarray analysis. Although the original library comprises of 16 228 oligonucleotides approximately one third had to be excluded completely from further statistical analysis. An additional plate with oligos from our lab was spotted onto the chip. Arrangement of spots impacts further ,statistical normalisation analysis. In order to increase precision of signals each oligo is spotted twice. In particular metacolumn 3 and 4 are an exact copy of metacolumn 1 and 2 which allows to calculate an average signal for each gene based on two spots. In order to minimize correlation caused by spatial background patterns, the two copies were not placed in adjacent blocks. To establish a thorough quality control of arrays, beta actin and so-called spikes were considered during microarray design. Beta actin is a housekeeping gene which is in constant use to maintain basic cell functions. Therefore, it is expected to express at the same level under different treatment conditions. The corresponding mRNA is present in large numbers so it yields signals of very high intensity. Beta actin is arranged multiple times on the last two metarows of the chip which can be observed as a chessboard-like pattern. Additionally, spikes were included to check the correct labelling of samples.

manufacturer: Forschungszentrum Karlsruhe Microarray Facility

first: Christian

last: Zinsmeister

first: Lixin

first: Matthias

last: Bauer

first: Joerg

last: Katzenberger

first: Nadine

last: Gretz

manufacture_protocol:
Printing is performed with the multi-axis Omnigridder 100 spotter1 from Genomic Solutions with a capacity of 100 chips.
For transferring the sample probes onto the array a printhead and 24 SMP3 pins from TeleChem are used.
The sample solution is spotted onto 'SurModics 3D-Link' slides which are available as 'CodeLink activated slides' from Amersham Biosciences3. To be more precise, those chips are covered by a 3-D gel matrix build up of a hydrophilic, long chain polymer that contains amine-reactive groups. The polymer is covalently cross-linked to itself and to the surface of the slide. It orients the immobilized oligos and thus holds them away from the surface of the slide. Accordingly, the sample probes have to be extended by an amino linker to stick permanently to the slide. As a consequence, the oligos are more readily available for hybridisation and spacers are not needed any more. In addition, the hydrophilic nature of the polymer provides a passivating effect after the DNA has been immobilized resulting in higher sensitivity and lower background.
We have used the oligo set from Sigma-Genosys/Compugen containing 16 228 oligos.
Prerequisites for microarray production include thorough cleaning of the equipment and calibration of the z-axis (vertical) movement of each pin. The latter is crucial as the pins are supposed to touch the slide surface only gently. Imprecise calibration of the pin movement possibly either fails to deliver the spot liquid or it hits and scratches the chip.
Before starting the actual print, test runs are conducted by spotting 2-3 test chips so that calibration and quality of pins can be refined. Optimal spotting results require a constant temperature of 18 C and humidity of 60%.
One of 43 sample library plates (384-well) is picked up by the server arm and placed in the nest.
The printhead with its 2 by 12 pins dips into the plate and takes up 24 different sample probes which are spotted simultaneously onto the array.
Afterwards the pins are sequentially dipped into water, dried with pressurised air, and cleaned in a sonicator.
This washing routine is performed three times before the next 24 samples are taken up by the pins.
After 16 cycles all samples of the 384-well have been spotted and the next plate is processed. The overall printing process of 100 chips runs for about one day.


title: Gene Express StaRT-PCR (GEX) Human MAQC

status: Public on Sep 08 2006

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

institute: Fudan University

technology: RT-PCR

manufacture_protocol: Gene Express protocol


title: Rice mRNA MPSS signatures

status: Public on May 26 2006

city: Davis

first: Blake

middle: C.

last: Meyers

address: 451 Health Sciences Dr.

department: UC Davis Genome Center

institute: University of California - Davis

technology: MPSS

description:
mRNA MPSS signatures capture the 17 bases from near the 3' end of poly(A)+ transcripts
All MPSS was performed as described by Brenner et al. (Nat Biotechnol. 2000 18:630).


title: Sigma Genosys Panorama Escherichia coli Gene Array

status: Public on Feb 01 2006

city: Plymouth

first: Michael

middle: James

last: Allen

address: Prospect Place

institute: Plymouth Marine Laboratory

organism: Escherichia coli

manufacture_protocol:
The Panorama Escherichia coli Gene Array was developed using E. coli ORFmers (PCR primers). The PCR primers were developed as part of a collaboration with the E. coli Genome Group, headed by Dr. Fred Blattner at the Department of Genetics, University of Wisconsin-Madison (http://www.genome.wisc.edu). The array contains 4,290 PCR-amplified ORFs, representing all of the protein-encoding genes.

Note: two spots per ORF


title: Avian Innate Immunity Microarray (AIIM)

status: Public on Sep 24 2004

city: Newark

first: Calvin

last: Keeler

state: DE

department: Animal and Food Sciences

institute: University of Delaware

organism: Gallus gallus

description:
This microarray was created using all of the unique elements in 4 individual EST libraries created using various sources of macrophages. It was further supplemented with RT-PCR amplified genes of interest and clones from Peter Kaiser. Three libraries were made from peripheral blood derived macrophages: Unstimulated (Control), LPS stimulated for 2-4 hours (LPS), and INF-gamma stimulated for 2-4 hours (IFN).  The fourth library was created from HD11 cell line macrophages stimulated for 0-72 hours (pmp1c).  134 additional clones were added from clones in the University of Delaware ChickEST library collections.  In addition, 13 full-length cDNA clones were kindly provided by Dr. Pete Kaiser. Finally, 40 elements were amplified directly by RT-PCR from targeted genes of interest identified on the avian genome.  Total, this array contains 4,959 unique elements.
Keywords = Avian
Keywords = innate immunity
Keywords = macrophage
Keywords = AIIM

middle: L

first: Travis

last: Bliss

first: Michele

middle: N

last: Maughan


title: General Electric/Amersham Biosciences Mouse CodeLink 10K and 20K arrays

status: Public on Feb 12 2006

city: Pittsburgh

first: Tamas

last: Dolinay

state: PA

department: Pulmonary, Allergy and Critical Care

institute: Univerisity of Pittsburgh Medical Center

organism: Mus musculus

first: Naftali

last: Kaminski

first: Augustine

middle: M

last: Choi

manufacture_protocol: CODELINK 10 and 20K mouse cRNA arrays