title: SCRI Pectobacterium atrosepticum 11K (SCRI_012663_Eca_11k)

status: Public on Aug 26 2008

city: Dundee

first: Pete

last: Hedley

address: Invergowrie

department: Genetics

country: United Kingdom

institute: SCRI

organism: Pectobacterium atrosepticum

technology: in situ oligonucleotide

distribution: custom-commercial

first: Ian

last: Toth

first: Paul

last: Birch

first: Leighton

last: Pritchard

first: Hui

last: Liu

manufacture_protocol: Probes designed to Pectobacterium atrosepticum (strain SCRI1043) genome sequence. Microarray manufactured using Ink Jet In Situ Synthesis (IJISS) technology using standard proprietry Agilent methodology (SurePrint) in 2x 11k format.


title: CSIRO-PI Oryza Sativa small RNA sequences 2007 (Solexa sequenced)

status: Public on Aug 21 2008

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

organism: Oryza sativa

technology: other

description: Small RNAs from Oryza Sativa were sequenced from 1-5 days-after-fertilisation grains and 6-10 days-after-fertilisation grains, using the Solexa sequencing technology.  This is the unique list of trimmed sequences obtained from these experiments

distribution: virtual

first: Chris

last: Helliwell

first: Frank

last: Gubler

first: Longjiang

last: Fan

first: Louisa

last: Matthew

first: Gavin

last: Kennedy


title: University of Utah Schmidtea mediterranea cDNA array generation I

city: Salt Lake City

first: Alejandro

last: Sánchez Alvarado

state: UT

department: Neurobiology and Anatomy

country: USA

institute: University of Utah School of Medicine

organism: Schmidtea mediterranea

technology: spotted DNA/cDNA

distribution: non-commercial

manufacturer: Microarray Core Facility at the University of Utah

first: George

middle: T

last: Eisenhoffer

first: Hara

last: Kang

manufacture_protocol: 3,435 cDNAs from two asexual cDNA libraries, a neoblast-enriched cell population (NB) and animal heads (H) (Sánchez Alvarado et al., Development. 129:5659-5665), were printed in triplicate on Corning UltraGAPS glass microscope slides using an Amersham BioSciences Lucidea Array Spotter.  The PCR products were prepared for spotting by diluting the samples in a solution of 50% DMSO to an average final concentration of 100 ng/ul.  Following the print session, the DNA targets were cross-linked to the slide surface at 250mJ using a Stratagene Stratalinker.


title: Agilent Saccharomyces cerevisiae array

status: Public on Aug 19 2008

city: Stanford

last: Sherlock

state: CA

address: 300 Pasteur Drive

institute: Stanford University

organism: Saccharomyces cerevisiae

manufacture_protocol: Agilent


title: Print_627

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

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: Agilent Whole Human Genome Oligo Microarray - custom annotation

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

organism: Homo sapiens

first: Roberto

last: Ferrari

first: Matteo

last: Pellegrini

first: Greg

last: Horwitz

first: Wei

last: Xie

first: Arnold

last: Berk

manufacture_protocol: The Whole Human Genome Oligo Microarray Kit is a broad view that represents all known genes and transcripts in the human genome. Sequence was compiled from a broad source survey, and then verified and optimized by alignment to the assembled human genome. Coupled with Agilent's probe selection and robust validation processes, this design delivers increased data quality and less gene coverage redundancy. 41,000+ unique human genes and transcripts represented, all with public domain annotations. Content sourced from RefSeq, Goldenpath Ensembl Unigene Human Genome (Build 33) and GenBank databases. Over 70% of the represented probes are validated by Agilent's laboratory validation process4 X 44K slide formats printed using Agilent's 60-mer SurePrint technology 5 slides per kit. Each slide contains four 44K microarrays.


title: CSIRO-PI Oryza Sativa small RNA sequences 2007 (454 sequenced)

last: Spriggs

description: Small RNAs from Oryza Sativa were sequenced from 1-5 days-after-fertilisation grains, 6-10 days-after-fertilisation grains, and from roots and shoots, using the 454 sequencing technology.  This is the unique list of trimmed sequences obtained from these experiments.


title: Nimblegen 2007 Danio rerio Gene Expression Array

status: Public on Aug 22 2008

city: Bronx

first: Lisa

middle: J.

last: McReynolds

state: NY

address: 1300 Morris Park Ave. Chanin 501

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

organism: Danio rerio

description: Expression design for Danio rerio from ZGI release 16. Selected 9 probes per target for 43422 targets (33752 EST entries, with some represented on both strands). Several hundred targets have less than 9 probes with many as low as one probe per target. There are 1,347 targets for which we cannot select any probes.

middle: J

first: Sunny

last: Gupta

first: Maria

middle: E

last: Figueroa

first: Mary

middle: C

last: Mullins

first: Todd

last: Evans

manufacture_protocol:
Organism: Danio rerio
Source: Ensembl and UCSC
Build: Zv6
Probe Length: 60mer
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
Recommended Storage: Store arrays desiccated at room temperature.
Catalog Number A6183-00-01
Design Name 2007-03-01 Zv6 60mer EXP
Description Danio rerio 1-Plex Array
Genes 32,292
Probes/ Target 12
Features 385,000
Replicates 1
from www.nimblegen.com
Array Synthesis
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. At the heart of the system is a Digital Micromirror Device (DMD), similar to Texas Instruments' Digital Light Processor (DLP), employing a solid-state array of miniature aluminum mirrors to pattern 786,000 to 4.2 million individual pixels of light. The DMD creates "virtual masks" that replace the physical chromium masks used in traditional arrays. These "virtual masks" reflect the desired pattern of UV light with individually addressable aluminum mirrors controlled by the computer. The DMD controls the pattern of UV light projected on the microscope slide in the reaction chamber, which is coupled to the DNA synthesizer. The UV light selectively cleaves a UV-labile protecting group at the precise location where the next nucleotide will be coupled. The patterns are coordinated with the DNA synthesis chemistry in a parallel, combinatorial manner such that 385,000 to 2.1 million unique probe features are synthesized in a single array.
Hybridization
NimbleGen Systems has developed a proprietary hybridization system, including protocols, buffers, hybridization cassettes, hardware, and temperature control instrumentation that generate highly reproducible and sensitive hybridizations. These protocols have been optimized to require minimum amounts of sample, while providing a hybridization volume that can be continually mixed over the time-course of the incubation. This method generates arrays with extremely high inter-array reproducibility (up to r2>0.99) and very low intra-array coefficient of variation (cv < 12%) across the array surface. In a typical gene expression experiment, each gene is represented by a minimum of 10 and as many as 25 probe-pairs complementary to different portions of the mRNA transcript. This guarantees that at least 10 independent measurements of mRNA concentration are included in the final value for the expression level for the gene, resulting in more reliable and reproducible gene expression calculations. In addition, these 10 to 25 probe-pairs are distributed evenly across the surface of the array. This distribution effectively eliminates problems associated with any local variation in the spatial uniformity or noise in the hybridization, because expression values are derived from a minimum of ten different locations on the array.


title: University of Illinois at Chicago Human 19K proximal promoter (HuIG19K_v5) array

status: Public on Aug 29 2008

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

manufacture_protocol: refer to Whitehead Institute Center for Microarray Technology website


title: Print_626


title: UMDNJ/Lukac Human herpesvirus 8/107+GAPDH

status: Public on Aug 30 2008

city: Newark

first: David

middle: M.

last: Lukac

state: NJ

address: 225 Warren St.; ICPH E350C; PO Box 1709

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers Univ./NJ Medical School

organism: Human gammaherpesvirus 8

technology: spotted oligonucleotide

manufacturer: Lukac laboratory and Center for Applied Genomics/UMDNJ/NJ Medical School

last: Bu

first: Diana

last: Palmeri

first: Virginie

last: Aris

first: Patricia

last: Soteropoulos

middle: M

manufacture_protocol: The KSHV microarray consists of 60-70-mer oligonucleotides (oligos) designed to detect 96 predicted KSHV ORFs and splice variants, identical to those published by Lu, et al (Journal of Virology, December 2004, p. 13637-13652, Vol. 78, No. 24), updated to include newer annotated transcripts.  A detector oligo for the Human housekeeping genes glyceraldehyde-3-phosphate dehydrogenase was also synthesized. Operon Biotechnologies synthesized all oligos with 5' amino-C6 modifications. Oligos were spotted in triplicate onto poly-L-lysine-coated glass microscope slides using a GeneMachines Omnigrid 100 Arrayer (Genomic Solutions) and SMP3 pins (Telechem).


title: Rosetta/Merck Dog 44k 1.0 microarray

city: Seattle

first: Amit

last: Kulkarni

state: WA

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

organism: Canis lupus familiaris

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

distribution: commercial

first: John

last: Castle

manufacture_protocol: Dog 44k 1.0 microarray Merck


title: University of Illinois at Chicago Human 19K proximal promoter (HuIG19K_v4) array

manufacturer: Whitehead Institute Center for Microarray Technology


title: Print_835

first: Andre

last: Gerber


title: OHSU_macaque_RRV_252_v1

city: Beaverton

first: Scott

middle: William

last: Wong

state: OR

address: 505 NW 185th Avenue

department: Vaccine and Gene Therapy Institute

institute: Oregon Health & Science University

organism: Macaca mulatta rhadinovirus 17577

manufacturer: Oregon Health & Science University/Spotted Microarray Core

middle: W

first: Robert

middle: P

last: Searles

manufacture_protocol: Arrays were printed onto UltraGAPS slides (Corning) using a PixSys 5500XL microarray printer (Cartesian) and CMP3 pins (Telechem).  Spots were made from 1-2 nl of solution with a center-to-center distance of 183 microns.  Arrays were printed in duplicate on each slide.  After printing arrays were baked for 3.5 hours at 80 C, then stored in a dark dessicator until use.  Prior to use arrays were blocked with 2% BSA in 5x SSC / 0.1% SDS.


title: Fred Hutchinson Cancer Research Center human 4.3K BAC array

status: Public on Aug 17 2008

first: Ilona

middle: N

last: Holcomb

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

first: Douglas

middle: I

last: Grove

first: Martin

last: Kinnunen

first: Cynthia

last: Friedman

first: Ian

last: Gallaher

last: Morgan

first: Cassandra

middle: L

last: Sather

first: Jeffery

last: Delrow

first: Peter

middle: S

last: Nelson

first: Paul

middle: H

last: Lange

first: William

last: Ellis

first: Lawrence

middle: D

last: True

first: Janet

last: Young

first: Li

last: Hsu

first: Barbara

last: Trask

last: Vessella

manufacture_protocol:
This array consists of 4342 clones that are placed at a single location on the May 2004 draft assembly. 99% of map locations have been FISH verified. The clones have a median spacing of 402 kb across the chromosomes, excluding the repetitive regions around the centromeres, the short arms of the acrocentric chromosomes, and the long arm of the Y chromosome.
To construct the array, BAC DNA was extracted from 1.5-mL cultures with a modified Qiagen R.E.A.L. Prep96 plasmid kit (Qiagen). Purified BAC DNA was then amplified with ligation-mediated PCR (as indicated in Klein C, Schmidt-Kittler O, Schardt J, Pantel K, Speicher M, Riethmuller G Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells. Proc Natl Acad Sci USA 1999;96:4494-9.) and cleaned with the Multiscreen-PCR filtration system (Millipore) on a Biomek FX automated liquid handling system (Beckman Coulter, Fullerton, CA). Purified products were transferred to 384-well plates, air-dried, and then resuspended in 3x SSC. Each amplified/purified BAC was then mechanically spotted in triplicate onto poly-L-lysine-coated slides using an Omnigrid arrayer (GeneMachines, San Carlos, CA).


title: University of Illinois at Chicago Human Expression 35K - Operon version 3.0

first: Elizaveta

last: Benevolenskaya

manufacture_protocol: Arrays are printed on Corning UltraGAPS slides. The protocol is available at www.wi.mit.edu/CMT/protocols.html


title: OSU-CCC MicroRNA Microarray Version 3.0 (Merged replicated probes)

city: Madrid

first: Almudena

middle: R.

last: Ramiro

state: Madrid

address: Calle Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

organism:
Homo sapiens
Mus musculus

manufacturer: Microarray Shared Resource, Comprehensive Cancer Center, The Ohio State University (OSU-CCC)

manufacture_protocol: Manufactured using GE Healthcare's CodeLink (TM) 3-D Gel Matrix Technology. CodeLink(tm) Activated Slides are designed to covalently immoblize amine-modified DNA for microarrays. The slides are coated with a 3-D surface chemistry comprised of a long-chain, hydrophilic polymer containing amine-reactive groups. This polymer is covalently crosslinked to itself and to the surface of the slide. The crosslinked polymer, combined with end-point attachment, orients the immobilized DNA, and holds it away from the surface of the slide. The 1x printing buffer consists of 50 mM sodium phosphate at pH 8.5. Codelink slides are manufactured by SurModics and were formally sold as 3D-Link(tm) Activated Slides. ¹ Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions that is fitted with a printhead and 16 SMP3 print tips from Telechem. The microRNA microarray probe set is based on 40mer oligonucleotides from Sigma-Genosys. ¹ Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normalized 25 micromolar concentration. The miRNA microarray spot densities are 200 microns (center-to-center). The microarrays are printed on Codelink Activated Slide (PN300011)) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: Global proteomic characterization of photosystem II complexes from Synechocystis sp. PCC 6803

status: Public on Aug 18 2008

city: Saint Louis

first: Eric

middle: Agnew

last: Welsh

state: MO

address: One Brookings Drive; Campus Box 1137

department: Biology

institute: Washington University in Saint Louis

organism: Synechocystis sp. PCC 6803

technology: MS

description: Proteins identified in photosystem II complexes from Synechocystis sp. PCC 6803


title: Burkholderia thailandensis 70mer triplicate array

status: Public on Aug 13 2008

city: Atlanta

first: John

last: Varga

state: GA

address: 1510 Clifton Road

department: Pediatrics

institute: Emory University

organism: Burkholderia thailandensis

last: Nierman

first: Stanley

last: Kim

middle: J

first: Yan

last: Yu

first: Dan

last: Chen

manufacture_protocol: Commercially synthesized oligonucleotides were diluted in pronto buffer (corning) and printed on corning UltraGAPS slides.  The array consists of 19,200 spots arranged in 48 grids (4 columns and 12 rows).  Each grid consists of a 20x20 set of spots.  The 5210 ORFs represented on the array were spotted in triplicate and the remaining 3570 spots are blank.


title: PDP Mouse 16K BMAP-MSV

status: Public on Aug 27 2008

city: Winnipeg

first: Debra

last: Parchaliuk

state: Manitoba

address: 1015 Arlington Street

department: Prion Diseases Program

country: Canada

institute: Public Health Agency of Canada

organism: Mus musculus

manufacture_protocol: Libraries and clones derived from brain regions of adult mouse (C57BL/6) were obtained from Research Genetics. The 11 136 clones represent expressed sequence tags (ESTs) from some 5471 unique known genes and 5665 as yet uncharacterized mRNAs and form part of a library that was created as part of the Brain Molecular Anatomy Project (BMAP). In addition, a Mouse Sequence Verified (MSV) Unigene library, containing 5179  ESTs was added to the array. Each insert from these 3' EST libraries was amplified by PCR. cDNA was purified using Millipore multiwell purification plates and lyophilized PCR products were resuspended in 1x Micro-Spotting Solution Plus (TeleChem) at a concentration of 0.25-0.75 ug ul -1. DNA was spotted onto CMT-GAPS-coated glass slides (Corning) by using Stealth micro-spotting pins (TeleChem).


title: MWG Zebrafish 14K-1 Array

city: Milwaukee

first: Ramani

last: Ramchandran

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

manufacture_protocol: see manufacturer's website


title: US EPA Ecoarray FHM Pimephales promelas 10K 2000 gene (pilot) array

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

organism: Pimephales promelas

first: Iris

last: Knoebl

first: Patrick

last: Larkin

first: Ann

last: Miracle

last: Carter

first: Nancy

last: Denslow

first: Gerald

middle: T

last: Ankley

manufacture_protocol: Briefly, probes for each gene were designed using Agilent’s probe design software.  Each of the 60-mer probes was synthesized in situ on 1” x 3” (24.2 mm x 76.2 mm) treated glass slides using SurePrint inkjet deposition technology (http://www.chem.agilent.com).  All probes were synthesized in duplicate at random locations on the slide surface.  Since we could not confirm the direction of genes with an E-value greater than 1E-5, probes were designed and synthesized from both strands (forward and reverse complement) for the sequences.  To facilitate evaluations of the microarray (described below), multiple probes that spanned the vitellogenin (vtg) 1 genes were also synthesized on the chips.  Probe sequences for each of the genes are available (under license agreement) from EcoArray.  Probes for specific genes on the microarrays were assigned a unique Probe Identification number, similar in concept to Accession numbers that are assigned to sequences in National Center for Biotechnology Information databases.  This number (EA_Pp_###) allows for the cross-referencing of sequences from one experiment.


title: Nimblegen 2006 Danio rerio Gene Expression Array

first: Lisa

middle: J.

last: McReynolds

first: Sunny

last: Gupta

first: Maria

middle: E

last: Figueroa

first: Mary

middle: C

last: Mullins

first: Todd

last: Evans

manufacture_protocol:
Organism: Danio rerio
Source: Ensembl and UCSC
Build: Zv6
Probe Length: 60mer
Probes per Array: 385,000
Feature Size: 16μm x 16μm
Array Dimensions: 17.4mm x 13mm
Overall Slide Dimensions: 1" x 3" (25 x 75mm)
Recommended Storage: Store arrays desiccated at room temperature.
Catalog Number A6183-00-01
Design Name 2006-05-16 Zv6 60mer EXP
Description Danio rerio 1-Plex Array
Genes 32,292
Probes/ Target 12
Features 385,000
Replicates 1
from www.nimblegen.com
Array Synthesis
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. At the heart of the system is a Digital Micromirror Device (DMD), similar to Texas Instruments' Digital Light Processor (DLP), employing a solid-state array of miniature aluminum mirrors to pattern 786,000 to 4.2 million individual pixels of light. The DMD creates "virtual masks" that replace the physical chromium masks used in traditional arrays. These "virtual masks" reflect the desired pattern of UV light with individually addressable aluminum mirrors controlled by the computer. The DMD controls the pattern of UV light projected on the microscope slide in the reaction chamber, which is coupled to the DNA synthesizer. The UV light selectively cleaves a UV-labile protecting group at the precise location where the next nucleotide will be coupled. The patterns are coordinated with the DNA synthesis chemistry in a parallel, combinatorial manner such that 385,000 to 2.1 million unique probe features are synthesized in a single array.
Hybridization
NimbleGen Systems has developed a proprietary hybridization system, including protocols, buffers, hybridization cassettes, hardware, and temperature control instrumentation that generate highly reproducible and sensitive hybridizations. These protocols have been optimized to require minimum amounts of sample, while providing a hybridization volume that can be continually mixed over the time-course of the incubation. This method generates arrays with extremely high inter-array reproducibility (up to r2>0.99) and very low intra-array coefficient of variation (cv < 12%) across the array surface. In a typical gene expression experiment, each gene is represented by a minimum of 10 and as many as 25 probe-pairs complementary to different portions of the mRNA transcript. This guarantees that at least 10 independent measurements of mRNA concentration are included in the final value for the expression level for the gene, resulting in more reliable and reproducible gene expression calculations. In addition, these 10 to 25 probe-pairs are distributed evenly across the surface of the array. This distribution effectively eliminates problems associated with any local variation in the spatial uniformity or noise in the hybridization, because expression values are derived from a minimum of ten different locations on the array.


title: TIGR_Mouse_25K cDNA array

city: Cleveleand

first: Joseph

last: Nadeau

state: OH

address: 10900 Euclid Avenue

institute: Case Western Reserve University

manufacturer: John Quackenbush, The Institute for Genomic Research

manufacture_protocol:
Detailed protocol referred to
Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N, Quackenbush J. A concise guide to cDNA microarray analysis. Biotechniques. 2000 Sep;29(3):548-50, 552-4, 556 passim.


title: JCVI PFGRC Staphylococcus aureus version 4 array

status: Public on Aug 25 2008

city: Las Cruces

first: John

last: Gustafson

email: jgustafs@nmsu.edu, amuthai@gmail.com

state: NM

address: PO Box 30001 Dept. 3AF

department: Department of Biology and Molecular Biology Program

institute: New Mexico State University

organism: Staphylococcus aureus

description:
This set includes 20224 elements on array in 96 grids.
This is the condensed template of replicated (4x) features of PFGRC/JCVI Staphylococcus aureus version 4 array.
For full template information please refer to: http://pfgrc.jcvi.org/index.php/microarray/array_description/staphylococcus_aureus/version4.html

manufacture_protocol: Number of Grids - 96; Element Type - 70mer Oligonucleotide; Surface Coating - Epoxy; Oligonucleotides Designed - 4546; Replicate Oligo Printings - 4x; Controls - 500 Arabidopsis thaliana 70mers; 10 Arabidopsis thaliana amplicons.


title: EBT Cyprinus carpio cDNA 1.6K array version 1

status: Public on Aug 15 2008

city: Wilrijk

first: An

last: Hagenaars

state: Antwerp

address: Groenenborgerlaan 171

country: Belgium

institute: University of Antwerp

organism: Cyprinus carpio

description: Aminosilane coated GenoramaTM microarray slides (Asper Biotech, Tartu, Estonia)

first: Lotte

last: Moens

manufacture_protocol: A Qarray Mini Robot (Genetix, Hampshire, UK) with 16-solid pin-head was used to spot 1632 clones from two different cDNA libraries. Each cDNA clone was spotted in triplicate on the microarray.


title: Carrington-Arabidopsis-Illumina-miRNA-AGO-high-throughput sequencing

status: Public on Aug 16 2008

first: James

last: Carrington

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

organism: Arabidopsis thaliana

description:
Sequencing-by-synthesis technology was used to sequence small RNA from input and co-immunoprecipitation fractions from cell lysates of inflorescence  tissue from Arabidopsis plants transformed with HA epitope-tagged AGO2 or AGO7 constructs. Meaningful intepretation requires comparison between the input and co-immunoprecipitation datasets.
Small RNA sequences were parsed from Illumina sequencing data files through identification of adaptor boundaries. Only sequences that mapped to the Arabidopsis thaliana Col-0 genome were included in the analysis.

manufacturer: Center for Genome Research and Biocomputing, Oregon State University


title: Dmel_chrX_XHet

status: Public on Aug 08 2008

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

organism: Drosophila melanogaster

description: The array is a custom designed, high density, 4x44k Agilent microarray. The probe sequences and locations are based on the complete D. melanogaster genome sequence, release 5, downloaded from ftp.fruitfly.org at March 7, 2007. The median probe spacing is 136 bp. Probe sequences do not contain the sequence motif GATC, the recognition sequence of Dam. The array was designed to accommodate both DamID and Chip-on-chip experiments.

first: Maartje

last: Vogel

first: Ludo

last: Pagie

first: Marja

last: Nieuwland

first: Ron

middle: M

last: Kerkhoven

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


title: NIMBLE_MMCCSAL01_380k

status: Public on Aug 07 2008

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

description: This set includes 386350 46~50mer oligonucleotides, mostly 50-mers. The probes were designed based on Salmonella typhimurium LT2 (NC_003197.1) genome, with a moving window of about 12 bases. ONLY the SalmP probes are represented in this file.

first: Fred

last: Long

first: YiPeng

last: Wang

first: Steffen

last: Porwollik

manufacture_protocol: in situ oligonucleotide, designs 2005-04-06_Wang_OID1618_ChIP & 2007-03-13_Wang_ChIP


title: OHSU Vibrio vulnificus Nimblegen 4K

city: Portland

first: Jorge

last: Crosa

address: 3181 SW Sam Jackson Park Road

department: Molecular Microbiology and Immunology

institute: Oregon Health and Science University

organism: Vibrio vulnificus CMCP6

first: Alejandro

middle: F

last: Alice

first: Hiroaki

last: Naka

manufacture_protocol: 1:2 catalog design of  Vibrio vulnificus CMCP6 from GenBank with 14 pp/gene.  Each probe replicated 3x.  Design includes random GC probes.


title: Jones Lab Human PC3/PrEC selected promoter arrays, 20bp resolution, 389K

city: Rehovot

first: Amos

last: Tanay

address: The Weizmann Insititute

department: Computer Science and Applied Math

country: Israel

institute: The Weizmann Institute

description: The .ndf and .pos files have been linked below as supplementary files.

first: Einav

last: Gal-Yam

first: Gerda

last: Egger

first: Peter

last: Jones

manufacture_protocol: See manufacturer's website


title: Human H1299 cells p73 ChIP-seq

status: Public on Aug 06 2008

city: Nashville

first: Jennifer

last: Pietenpol

state: TN

address: 23rd Ave South at Pierce

department: Biochemistry

institute: Vanderbilt University Medical Center

description: Genpathway FactorPath Discovery Assay - H1299 cells

manufacture_protocol: not applicable


title: CiC Homo sapiens Bac array version 1

status: Public on Aug 01 2008

city: Salamanca

first: Olga

last: Lopez

address: P/ San Vicente 58-182

department: Hematology

institute: Hospital Universitario de Salamanca

last: Lopez-Villar

first: Juan

last: Garcia-Hernandez

first: Fermin

last: Sanchez-Guijo

first: Cristina

last: Robledo

first: Eva

last: Villaron

first: Natalia

last: Lopez-Holgado

first: Maria

last: Diez-Campelo

first: Victoria

last: Barbado

first: Jose

middle: A

last: Perez-Simon

first: Jesus

last: Hernandez-Rivas

last: San Miguel

first: Consuelo

last: Del Cañizo

manufacture_protocol: Slides containing 3032 BACs were produced in “Centro de Investigación del Cáncer” (Salamanca, Spain). The particular BAC and P-1 derived artificial chromosome set used to produce this array is distributed to academic institutions by the Welcome Trust Sanger Institute (Cambridge, United Kingdom) and contains targets spaced at 1 Mb density over full genome, a set of subtelomeric sequences for each chromosome arm, and a few hundred probes selected for their involvement in oncogenesis. The clone content is available in the “Cytoview” windows of the Sanger Institute mapping database site, Ensembl (http://www.ensembl.org/). According to this database, clones were ordered along the chromosomes. These clones were isolated from their bacterial cultures with the relevant antibiotics and the DNA was extracted with standard protocol Welcome Trust Sanger Institute (Cambridge, UK). 10 ng of DNA (BAC/PAC) was used as a template for three DOP-PC. 22;23 These products were ethanol precipitated and dissolved in distilled water. A minimum of three replicates per clone were printed by Microgrid II (Biorobotics) on each slide (Ultragaps Coated Slides, Corning) using the aqueous dimethylsulfoxide buffer as spotting solution. Briefly, for labelling reactions, 1 μg of nonamplified genomic DNA, test and reference were digested separately with DpnII restriction enzyme (New England Biolabs, Beverly, MA). For microarray hybridization, the digested DNAs were separately labelled using random primers (Bioprimer labelling kit, Invitrogen) and cyanine dye-3-dCTP and cyanine dye-5-dCTP fluorescent dye to paired hybridisation samples (Amersham Biosciences). The incorporated of the label nucleotide was quantified using the Nanodrop spectrophotometer. Labelled test and reference DNAs were mixed equitably, co-precipitated in presence of Cot-1 human DNA (Roche, Indianapolis, IN) with ethanol, washed, and resuspended in hybridization solution (50% Formamide, 10% Dextran sulfate, 2X standard saline citrate, 10 mM Tris pH 7.6, 2.7% sodium dodecyl sulfate and 10 μg/ μl of yeast tRNA). DNA mixtures were hybridized to the arrays in the TECAN HS4800 Pro according to the manufacturer’s recommended protocol. Images and signal intensities were acquired using GenePix4000B (Axon Instruments, Burlingame, CA) dual laser scanner in combination with GenePixPro4.0 (Axon Instruments) imaging software.


title: ORNL-ESD Desulfovibrio vulgaris 70mer oligo-array

status: Public on Aug 10 2006

city: Knoxville

first: Qiang

last: He

address: 57A Perkins Hall

department: Civil and Environmental Engineering

institute: The University of Tennessee

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

description: This DNA microarray covers 3,482 of the 3,531 protein-coding sequences of the D. vulgaris genome with 3,439 specific, and 43 non-specific 70-mer oligonucleotide probes.

manufacturer: Microbial Ecology and Functional Genomics Laboratory, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN

first: Zhili

first: Jizhong

last: Zhou

first: Matthew

last: Fields

manufacture_protocol: All 70mer oligonucleotides were commercially synthesized without modification by MWG Biotech Inc. (High Point, NC). The concentration of oligonucleotides was adjusted to 100 pmol/µl. Oligonucleotide probes were prepared in 50% vol/vol DMSO (Sigma-Aldrich, St. Louis, MO) and spotted onto UltraGAPS glass slides (Corning Life Sciences, Corning, NY) using a BioRobotics Microgrid II microarrayer (Genomic Solutions, Ann Arbor, MI). Each oligonucleotide probe had two replicates on a single slide. After printing, the oligonucleotide probes were fixed onto the slides by UV cross-linking (600 mJ of energy) according to the protocol of the manufacturer of the UltraGAPS glass slides (Corning Life Science, Corning. NY).


title: ASG Porcine jejunum spleen cDNA array

city: Lelystad

first: Gabriele

last: Gross

address: P.O. Box 65

institute: Animal Sciences Group of Wageningen UR

organism: Sus scrofa

manufacture_protocol: according to Niewold, T.A., Kerstens, H.H., van der Meulen, J., Smits, M.A., Hulst, M.M., 2005: Development of a porcine small intestinal cDNA micro-array: characterization and functional analysis of the response to enterotoxigenic E. coli. Vet Immunol Immunopathol 105, 317-329, and: Gross, G., van der Meulen, J., Snel, J., van der Meer, R., Niewold, T.A., Hulst, M.M., Smits, M.A., manuscript submitted: Mannose-specific interaction of Lactobacillus plantarum with porcine jejunal epithelium induces expression of host pancreatitis-induced protein in situ.


title: Affymetrix GeneChip Porcine Genome Array probe-level

status: Public on Feb 09 2008

city: Raleigh

first: Nicholas

middle: Eldon

last: Hardison

state: NC

address: 4700 Hillsborough St., Room 318A

institute: North Carolina State University

manufacture_protocol: see manufacturer's web site


title: OSU-CCC hsa-miRNA-chip version 3

status: Public on Aug 05 2008

city: Bethesda

first: Robert

middle: Scott

last: Hudson

state: MD

address: National Cancer Institute Room Blgd.37/3044

department: NCI

institute: NIH

manufacture_protocol: Manufacured using GE Healthcare's CodeLink (TM) 3-D Gel Matrix Technology. CodeLink(tm) Activated Slides are designed to covalently immoblize amine-modified DNA for microarrays. The slides are coated with a 3-D surface chemistry comprised of a long-chain, hydrophilic polymer containing amine-reactive groups. This polymer is covalently crosslinked to itself and to the surface of the slide. The crosslinked polymer, combined with end-point attachment, orients the immobilized DNA, and holds it away from the surface of the slide. The 1x printing buffer consists of 50 mM sodium phosphate at pH 8.5. Codelink slides are manufactured by SurModics and were formally sold as 3D-Link(tm) Activated Slides.   Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions (http://www.genomicsolutions.com ) that is fitted with a printhead and 16 SMP3 print tips from Telechem (http://www.arrayit.com). The microRNA microarray probe set is based on 40mer oligonucleotides from Sigma-Genosys.   Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normalized 25 micromolar concentration. The miRNA microarray spot densities are 200 microns (center-to-center). The microarrays are printed on Codelink Activated Slide (PN300011)) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: ICAT Humulus lupulus 3.5K array version 1

status: Public on Jul 10 2008

city: Lisboa

first: Ana

middle: Margarida

last: Fortes

address: Campus da FCUL

department: Plant Biology

country: Portugal

organism: Humulus lupulus

description:
Technical Details of Array Design and Spotting
Platform type: spotted glass array coated with Poly-L-lysine
Microarrayer: ChipWriter Compact System (Biorad)
Pins: 12 printing pins (Telechem International, Sunnyvale, CA, USA)
Pin configuration: 2 x 6
Number of repeats: spots are repeated once on the same subgrid in the same order. Last plate contains only printing solution.
Printing plates: 36 x 2 (96 wells, one plate contains only printing solution)
Printing scheme: 12 subgrids, each subgrid with 24 columns and 24 rows
Distance between spots: 320μm
Humidity: 40%
Temperature: 22ºC
This is a condensed version of the physical array, 7K. The full array linked as a supplementary file.

manufacturer: Unit of Molecular Biology and Plant Biotechnology, ICAT, FCUL, Lisbon, Portugal

first: Filipa

last: Santos

first: Marta

last: Silva

first: Bartolomeu

last: Acioli-Santos

last: Pais

manufacture_protocol:
Amplified cDNA inserts were purified with MultiScreen-PCR plate (Millipore), transferred to printing plates (Microtiter V plates, Sigma), resuspended in 50% dimethylsulphoxide, 0,2 % SSC and spotted in duplicate onto Poly-L lysine treated glass slides using VersArray ChipWriter Compact® (Bio-Rad Lab., Hercules, CA, USA). After printing, cross-linking was performed with heat and UV according to the protocol from Vodkin laboratory (http://soybeangenomics.cropsci.uiuc.edu/).
Pins: 12 printing pins (Telechem International, Sunnyvale, CA, USA)
Pin configuration: 2 x 6
Number of repeats: spots are repeated once on the same subgrid in the same order.
Printing plates: 36 x 2 (96 wells, one plate contains only printing solution) Printing scheme: 12 subgrids, each subgrid with 24 columns and 24 rows


title: NimbleGen Watermelon 12-plex NimbleScreen array

city: Charleston

first: Patrick

last: Wechter

state: SC

address: 2700 Savannah Highway

department: U.S. Vegetable Laboratory

institute: USDA-ARS

organism: Citrullus lanatus

description:
Custom NimbleGen 12-plex NimbleScreen design. 24-mer oligos. 1:2 12plex design of 832 Watermelon EST sequences with 16pp/gene.  Each well includes random GC probes. Design_ID: 2381
Design and gene description files (.ndf, .ngd) appended below as supplementary files.

manufacture_protocol: NimbleGen Systems


title: AMMS_PBS_Y. pestis 201

city: Beijing

first: Ruifu

last: Yang

address: No.20, DOngdajie, Fengtai

country: China

organism: Yersinia pestis

manufacturer: State Key laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences

manufacture_protocol:
Based on the whole-genome sequences of Y. pestis CO92, KIM and 91001, a total number of 4015 annotated open reading frames (ORFs) were selected after the exclusion of ORFs encoding IS protein, integrase, and transposase (The word “gene” will be used in the following part of this paper in reference to the ORF). Those highly homologous to each other at nucleotide level were also excluded. Gene specific primer pairs (16bp to 18bp in length) were designed to amplify nearly the full length of each gene. All primers were synthesized by Illumina Co. (San Diego, CA, U. S. A).
300µl of PCR product was obtained for each gene. PCR amplifications were performed in 96-well plates by using a DNA thermocycler (Biometra UNOII). 100 µl of PCR reaction mixture, containing 50 mM KCl, 10 mM Tris-HCl (pH8.0), 2.5 mM MgCl2, 0.001% gelatin, 0.1% BSA, 150 µM of each dATP, dCTP, dGTP and dTTP, 0.6 µM of each primer, 5 units of Taq DNA polymerase (MBI Fermentas), and 20 ng of template DNA, was predenatured at 95°C for 5 min. Then 30 cycles of 94°C for 1 min, 60°C for 1 min 30 sec and 72°C for 2 min were performed with a final extension at 72°C for 10 min. Each PCR product was verified by agarose gel electrophoresis and was scored as successful if a single band of the expected mobility was detected. DNA smear, multiple bands, or single band of unexpected size were characterized as unsuccessful reactions. Primer pairs from unsuccessful PCR reactions were re-amplified with altered annealing temperatures to get the desired single band of products. A few primers had to be redesigned to ensure successful amplification. In the end, 4005 genes were amplified successfully without any byproduct from strain 91001 or 82009.
PCR products were purified by using 96-well Multiscreen PCR plates (Millipore) following the user manual’s instruction. The purified DNAs were air dried at 65°C, and were resuspended in 30 µl of 50% DMSO solution. 10 µl of the purified PCR product was transferred into Genetix 7020 384-well Polystyrene Plates for microarray printing. Each of the PCR products was spotted in duplicate on CSS-1000 silylated glass slides (CEL) by using a SpotArray72 Microarray Printing System (Perkin Elmer Life Sciences) with 32 Telechem SMP3 Stealth Pins (4×8 Layout). Genomic DNA of strain 91001, salmon sperm DNA and 50% DMSO solution were included in the microarray design as internal control elements. The spotted slides were stored in dry environment at room temperature for at least 12 hr, and then were crosslinked twice by using a UV Stratalinker (Hoefer) each at a total energy of 60 microjoules. The spotted CSS-1000 silylated slides need not any blocking procedure, such as the blocking of unreacted aldehyde groups and the prehybridization. The microarray slide to be hybridized was simply washed in water for 2 min to remove the unbounded DNA and then was blown to dry with hot air.


title: UMNENT Anaplasma phagocytophilum Hz whole genome tiling array 256K

status: Public on Aug 04 2008

city: St. Paull

first: Michael

last: Herron

address: 1980 Folwell Avenue, Room 219 Hodson Hall

department: Entomology

institute: Michael Herron

organism: Anaplasma phagocytophilum str. HZ

description: BPMAP files are provided as supplementary files.  030806HZb530241N+.bpmap describes the + DNA strand of  A. phagocytophilum Hz, 030806HZb530241N-.bpmap describes the - DNA strand.

manufacture_protocol: 25-mer oligonucleotides representing the entire Ap Hz genome (1.47 Mb; accession CP000235.1), each overlapping its neighbor by 11 bases, were tiled by photolithography onto chips using maskless DLP process. For additional details, see the manufacturer's website.


title: JCVI Aspergillus flavus NRRL3357 27.6k oligo array

city: Rockville

first: Natalie

last: Fedorova

address: 9704 Medical Center Dr

department: Infectious Disease

institute: JCVI

organism:
Aspergillus flavus NRRL3357
Aspergillus oryzae RIB40

description: At least one oligo was designed from each gene model larger then 100 amino acids.  For genes with more than one exon, oligos were designed based on the second exon sequence.  For genes bigger than 4 kb, two oligos were designed from 5’ and 3’ ends.

first: Chunhua

last: Wan

first: Charlie

last: Sun

first: Jiujiang

last: Yu

first: William

last: Niermann

first: John

last: Varga

manufacture_protocol: The 70-mer oligo microarray was designed based on CDS annotated from the A. flavus NRRL 3357 whole genome sequence.  A total of 12,160 oligos were synthesized by Invitrogen.  They represent 12,125 sequences, including 11,837 A. flavus genes, 278 A. oryzae–specific genes (not present in A. flavus), and 10 corn genes that show resistance to A. flavus.  The oligos were printed in duplicate on Corning glassUltraGAPs amino-silane coated slides at JCVI using a high density automated arrayer (Intelligent Automation, Cambridge, MA 02139).


title: Sugden Lab Epstein-Barr virus (EBV) miRNA microarray

city: Madison

first: Zachary

last: Pratt

state: WI

address: 1400 University Avenue

department: Oncology

institute: University of Wisconsin-Madison

organism:
Arabidopsis thaliana
Homo sapiens
human gammaherpesvirus 4

description: 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.

manufacturer: Sugden Lab, University of Wisconsin-Madison

first: Bill

last: Sugden

middle: L

first: Srikumar

last: Sengupta

first: Malika

last: Kuzembayeva

manufacture_protocol: Oligonucleotides are tandem complements of mature miRNA sequences and snoRNA sequences.  they contain 5' C6 amino linkers to allow binding the the aldehyde microarray slide upon drying.  Oligonucleotides were spotted at a 40 micromolar concentration in 2.4x SSC.  After spotting, slides remained in a high-humidity chamber for 4 hours, and were then allowed to dry overnight.  Dried slides were washed twice 0.2% SDS solution for 2 minutes each time, twice in H2O for 2 minutes each time, for 5 minutes in sodium borohydride solution (375 ml 1x PBS, 1.3 g sodium borohydride, 125 ml 100% ethanol after sodium borohydride has dissolved).  After sodium borohydride wash, the SDS and H2O washes were repeated.  Slides were spun dried and stored at 4 degrees celcius in a dry environment.


title: SuperArray GEArray Q Series Human Chemokines & Receptors cat. #HS-005.2

status: Public on Jun 13 2006

city: Frederick

first: SuperArray

last: Bioscience Corporation

address: Suite 101, 7320 Executive Way

institute: Technical Support

organism: Homo sapiens

description: The GEArray Q Series Human Chemokines & Receptors Gene Array contains 96 genes that encode chemokines or their receptors as well as other related genes. The array focuses all of the subfamilies of small inducible cytokines. The regulation of chemokine and chemokine receptor gene expression plays fundamental roles in the development, homeostasis, and function of immune system. Chemokines are secreted by activated immune cells and target not only other immune cells but also endothelial cells and cells of the nervous system. This array can help you determine which chemokines your activated immune cell of choice expresses or determine to which chemokine a given cell type responds.

manufacture_protocol: see http://www.superarray.com/


title: USouthAL_Rickettsia prowazekii Madrid E 1.5K array version 1

city: Mobile

first: Jonathon

last: Audia

state: AL

address: 307 University Blvd N

department: Microbiology and Immunology

institute: University of South Alabama

organism: Rickettsia prowazekii str. Madrid E

manufacturer: Washington University Microarray Core Genome Sequencing Center

middle: P

first: Herbert

middle: H

last: Winkler

first: Mary

last: Patton

first: Seth

last: Crosby

manufacture_protocol: Glass slides were spotted with (where possible) two unique 70-mer oligonucleotides corresponding to all 835 annotated ORFs from the R. prowazekii genome sequence.  70-mer oligonucleotides were designed from these sequences by using ArrayOligoSelector.  All 70-mer oligonucleotides were verified as specific for R. prowazekii and not Mus musculus (the host cell used for rickettsial infections) under the conditions of hybridization used in this study using the BLAST algorithm.  The arrays consisted of two unique 70-mer oligonucleotides for 666 ORFs and a single unique oligonucleotide for 169 ORFs.  The oligos were synthesized by using standard methods by illumina (San Diego). The oligonucleotides were dissolved at a concentration of 50 mM in 3 × SSC with 0.75 M betaine and were printed in duplicate on MWG Epoxy slides (MWG Biotech, Ebersburg, Germany) by a locally constructed linear servo arrayer (after the DeRisi model).  The oligonucleotides were spotted in triplicate.  In addition, oligonucleotide probes corresponding to 32 mouse genes were included as negative controls and oligonucleotide probes corresponding to 10 Arabidopsis genes (SpotReport® Oligo Array Validation System, Stratagene) were included as cDNA synthesis validation controls.


title: OSU Tick salivary gland v.1

status: Public on May 13 2006

city: Stillwater

first: Richard

middle: C.

last: Essenberg

state: OK

address: 246 NRC

department: Department of Biochemistry and Molecular Biology

institute: Oklahoma State University

organism: Amblyomma americanum

first: Majd

middle: N

last: Aljamali

first: Patricia

last: Ayoubi

middle: R

last: Sauer

manufacture_protocol: Plasmid DNA templates were chosen from three EST libraries. About 10 ng each of 1152 purified plasmid DNAs chosen from the three libraries were PCR amplified in 100 μl total volume using Hot Start Platinum® Taq DNA polymerase (Invitrogen, CA) and the 5` and 3` sequencing primers appropriate to the vector. The amplification was done according to the PCR program; 94°C for 2 min, 26 cycles of (94°C for 30 sec, 55°C for 30 sec and 72°C for 1 min), followed by a final extension step at 72°C for 20 min.  The PCR samples were purified using Multiscreen™ filter plates (Millipore, MA) according to the manufacturer and random purified PCR products were run on 1% agarose gel to estimate the yield. The purified PCR products were transferred to 384 well microarray printing plates (Genetix, UK), dried at 42°C for 6 hours and reconstituted with 3X SSC printing solution to a final concentration of ~150 ng/μl. Eight ArrayControl™ control PCR spots (Ambion, TX) were reconstituted with printing solution to the final concentration of 160 ng/μl. The printing was performed on ArrayIt™ SuperAmine substrates (TeleChem, CA) using the Cartesian pix 5500 (Genomic Solutions, MI) microarrayer in 56% relative humidity. Four pins were used for spotting, arranged in a row.  Each PCR product was printed four times on each slide. After drying, the slides were baked at 85°C for two hours and stored at room temperature in a desiccator. Prior to hybridizations, slides were washed with 1% SDS then boiled for two minutes in sterile water, snap-cooled in ice-cold 95% ethanol and then dried by 10 sec centrifugation in ArrayIt™ slide centrifuge (TeleChem, CA). The quality of the printed slides was investigated by Syto61 staining.


title: Earthworm 4K cDNA array version 1.1

status: Public on Aug 26 2008

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

middle: J

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 15ul of 1¡Á 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/ul were also spotted twice along with printing buffer and water as control spots.
5. 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.
6. 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.
7. The arrays were further immobilized using a UV Cross-linker (Stratagene) by applying 300 mJ per 10 arrays.
8. Printing time: May 12, 2006