title: sea urchin tiling array urchin23 (BC447)

status: Public on Oct 23 2006

city: Los Altos

first: Manoj

last: Samanta

state: CA

address: 2240 Homestead Court #309

country: USA

institute: Systemix Institute

organism: Strongylocentrotus purpuratus

technology: in situ oligonucleotide

description:
50-mer probes tiling the entire S. purpuratus genome
Control probes were placed on all arrays for monitoring hybridization quality and data normalization.

distribution: non-commercial

middle: P

first: Waraporn

last: Tongprasit

first: Sorin

last: Istrail

first: R

middle: A

last: Cameron

first: Qiang

last: Tu

first: Eric

middle: H

last: Davidson

first: Viktor

last: Stolc

manufacture_protocol: Synthesized on glass-based slides using a maskless array synthesizer (Nimblegen technology).


title: sea urchin tiling array urchin26 (BC443)


title: sea urchin tiling array urchin24 (BC453)


title: Celltrans_5808_Osman_3xplt6

status: Public on Oct 31 2006

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

organism: Homo sapiens

technology: spotted DNA/cDNA

description: cDNA clones

manufacturer: Cell Transformation Team, Section of Molecular Carcinogenesis, Institute of Cancer Research

manufacture_protocol: as described in Institute Labs manual


title: sea urchin tiling array urchin14 (BC465)


title: sea urchin tiling array urchin22 (BC450)


title: Cryphonectria parasitica 4K spotted cDNA array

status: Public on Oct 28 2006

city: Rockville

first: Donald

middle: Lee

last: Nuss

state: MD

address: 9600 Gudelsky Drive

department: Center for Biosystems Research

organism: Cryphonectria parasitica

manufacturer: Center for Biosystems Research, University of Maryland Biotechnology Institute

first: Todd

middle: D

last: Allen

middle: L

first: Angus

last: Dawe

first: Fuyou

last: Deng

manufacture_protocol: The selected 3864 ESTs, representing approximately 2,200 unique genes, were ordered to form the array EST (AEST) library used for printing. Purified cDNAs were resuspended in 50 μm 3X SSC and arrayed using Affymetrix 417 Arrayer on poly-lysine-coated glass slides with an average spot diameter of 100 μm and a spot spacing of 300 μm. After printing, the spotted cDNA was cross-linked to the surface of the slides (at 65 mJ) by using a StrataLinker instrument and washed with a 1% SDS solution to minimize the background. Slides were subsequently placed in a blocking solution containing 0.2 M succinic anhydride and 0.05 M sodium borate prepared in 1-methyl-2-pyrrolidinone for 20 min. washed for 2 min in 95 C water, and rinsed five times in 95% ethanol. Slides were spin dried at 500 rpm for 5 min and stored for hybridizations.


title: sea urchin tiling array urchin20 (BC454)


title: sea urchin tiling array urchin25 (BC449)


title: FHCRC DMEL 4.2 Tiling 1 of 3

status: Public on Oct 24 2006

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

organism: Drosophila melanogaster

description: Fly tiling array using NimbleGen platform (DesignID=2347), chip 1 of 3. FlyBase release 4.2. All of Chr 3R with isothermal oligos averaging 50bp. Dense tiling of Chr 2L proximal, Chr X proximal and distal, first part of Chr 4, and Bithorax complex (BXC1).

distribution: custom-commercial

first: Steven

first: Yoshiko

last: Mito


title: sea urchin tiling array urchin27 (BC464)


title: SAGE:10:NlaIII:Gossypium hirsutum

last: GEO

organism: Gossypium hirsutum

technology: SAGE NlaIII

description: This is a virtual platform for SAGE libraries generated for Gossypium hirsutum using NlaIII as an anchor enzyme.

distribution: virtual


title: CRUKDMF_WGA_v1.0.0

description: cDNA

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


title: 3x19plt b 15 7 02

status: Public on Oct 27 2006

description: 3x19plt b 15 7 02


title: LNCaPsld1_MGII3x.Cmito v1

description: Microarray of clones randomly selected from a cDNA library prepared from the LNCaP prostate cancer cell line.  Only clones of interest were identified.

manufacturer: Cell Transformation Team, Section of Molecular Carcinogenesis


title: Identification of positional candidate genes for body weight and adiposity in subcongenic mice

status: Public on Oct 25 2006

city: Davis

first: Kyoungmi

last: Kim

address: One Shields Avenue

department: Rowe Program in Human Genetics

institute: University of California-Davis

organism: Mus musculus

description: We previously constructed a congenic mouse, B6.S-D2Mit194-D2Mit311 (B6.S-2) with SPRET/Ei donor DNA on distal chromosome 2 in a C57BL/6J background that captured an obesity quantitative trait locus (QTL). Mice homozygous for SPRET/Ei alleles at the donor region had decreased body weight and obesity related phenotypes. The B6.S-2 congenic donor region spanned a minimum of 26 Mb. In this study, we constructed five overlapping subcongenics with smaller SPRET/Ei donor regions to fine map the underlying gene(s). One of the five subcongenic lines derived from the B6.S-2 founding congenic, B6.S-2A, captures most of the body weight and adiposity phenotypes in a donor region with a maximum size of 7.4 Mb. Homozygous SPRET/Ei donor alleles in both the founding congenic and the derived B6.S-2A subcongenic exhibit significant decreases in body weight, multiple fat pad weights with the greatest decrease in mesenteric fat pad weight, and Adiposity Index (total fat pad weight divided by body weight). Interval specific microarray analysis in four tissues for donor region genes from the founding B6.S-2 congenic identified several differentially expressed genes mapping to the B6.S-2A subcongenic donor region, including prohormone convertase 2 (PC2). Quantitative real-time PCR confirmed a modest decrease of PC2 expression in whole brains of mice homozygous for SPRET/Ei donor alleles. Analysis of the relative levels of mRNA for B6 and SPRET/Ei in heterozygous congenic mice showed differentially higher expression of the C57BL/6J allele over the SPRET/Ei allele indicating a cis regulation of differential expression. Using subcongenic mapping, we have successfully narrowed a body weight and obesity QTL interval and identified PC2 as a positional candidate gene.

first: Sally

last: Chiu

first: Kari

last: Haus

first: Ricardo

last: Vedugo

first: Glenda

middle: M

last: Espinal

first: Carig

last: Warden

manufacture_protocol: cDNA was transcribed into cRNA using the MEGAscript T7 Kit (Ambion, Austin, TX) with biotin labeled CTP and UTP followed by purification with RNeasy (QIAGEN, Valencia, CA).


title: SAGE:17:NlaIII:Chlorocebus aethiops

status: Public on Oct 30 2006

organism: Chlorocebus aethiops

description: This is a virtual platform for SAGE libraries generated for Chlorocebus aethiops using NlaIII as an anchor enzyme.


title: FJL Human/Mouse miRNA Oligonucleotide Array

status: Public on Oct 26 2006

city: Cambridge

first: James

last: Smith

address: Tennis Court Road

department: Gurdon Institute

institute: Cambridge University

organism:
Homo sapiens
Mus musculus

technology: spotted oligonucleotide

first: Frederick

middle: J

last: Livesey

manufacture_protocol: Amine-linked oligonucleotides printed in house on Codelink slides in 150mM sodium phosphate pH 8.5 buffer.


title: Fox Chase Cancer Center Homo sapiens moNIA15k

city: Philadelphia

first: Xiangxi

last: Xu

state: PA

address: 333 Cottman Ave

department: Ovarian Cancer and Tumor Cell Biology

institute: Fox Chase Cancer Center

manufacturer: Fox Chase Cancer Center Microarray Facility

first: Callinice

last: Capo-chichi

first: Jennifer

last: Smedberg

first: Malgorzata

middle: E

last: Rula

first: Emmanuelle

last: Nicolas

first: Anthony

last: Yeung

first: Richard

middle: F

last: Adamo

first: Andrey

last: Frolov

first: Andrew

middle: K

last: Godwin

first: Xiang-Xi

manufacture_protocol:
Targets:
	cDNA (50-200ng/µl in 50% DMSO) 10µl
or
	Oligo (20-100 µM in 50% DMSO) 10 µl
	Targets are stored in a dessicator at –80 ºC after printing
Slides:
Home made Poly-L-Lysine coated slides should be aged for at least 3 weeks before printing. Coated slide can be stored at RT for at least 6 months.
Arrayer
OmniGrid (GeneMachines) with MicroSpotting pins (Telechem)
Printing Configuration
	Pin			4 x 4
	Spot-spot spacing	240 µm
	Spot size		150-200 µm
	Subgrid		18 x 18 spots
	Grid			12 x 4
	Humidity		45%
	Temperature		20-25 ºC
Post-Processing of Arrays
Following printing, the slides are allowed to dry and spotted DNA is bound to slide by baking slides at 80 ºC for 2 hours. Then printed slides are blocked with succinic anhydride (Brown protocol).
Arrays are used immediately or stored in dessicator at RT for at least 6 months.


title: FHCRC DMEL 4.2 Tiling 3 of 3

first: Jorja

last: Henikoff

description: Fly tiling array using NimbleGen platform (DesignID=2347), chip 3 of 3. FlyBase release 4.2. All of Chr 2L, Chr 3L and Chr 4 with isothermal oligos averaging 50bp. Dense tiling of second part of Chr 4 and Bithorax complex (BXC1).

first: Steven

first: Yoshiko

last: Mito


title: sea urchin tiling array urchin19 (BC466)

first: Manoj

last: Samanta

first: Waraporn

last: Tongprasit

first: Sorin

last: Istrail

first: R

last: Cameron

first: Qiang

last: Tu

first: Eric

last: Davidson

first: Viktor

last: Stolc


title: GE Healthcare/Amersham Biosciences CodeLink™ Rat Whole Genome Bioarray

city: College Station

first: Alan

middle: R.

last: Parrish

state: TX

address: 364 Reynolds

department: Systems Biology

institute: Texas A&M Health Science Center

organism: Rattus norvegicus

description:
CodeLink Rat Whole Genome Bioarray is designed to interrogate approximately 34,000 transcripts representing most of the known and predictive genes of the rat genome, as it is described today in the public domain. Each transcript is represented by a 30-mer probe which is designed to conserved exons across the transcripts of targeted genes. The probe sequences, representing well annotated, full length and partial rat gene sequences, were designed based on sequences selected from the NCBI UniGene build #129, RefSeq database (April 1, 2004 release) and dbEST database (March 20, 2004 release).
Well-annotated mRNA or coding sequences were chosen to ensure usefulness for a large range of applications in basic research, biotechnology, and drug development. Each sequence was carefully screened to ensure high-quality, specific probe design, and to reduce redundancy of gene targets. All of the probes designed to these sequences were functionally tested, and over 95% were functionally validated against 10 rat tissues to ensure best representation of the gene and biologically relevant results. For flexibility and data preservation, CodeLink Rat Whole Genome Bioarrays are compatible with lower density CodeLink rat bioarrays. This means that existing data from CodeLink UniSet™ Rat 10K Bioarrays can be continuously used in future studies along with newly generated data from CodeLink Rat Whole Genome Bioarrays.
This platform submission is identical to GPL2896, except that it utilizes the PROBE_NAME for the unique identifier (ID).  Additionally, duplicate PROBE_NAME values have been condensed so each probe is only represented once in the platform data table.   Finally, the annotations are derived from NCBI UniGene build #144, RefSeq database (August 8, 2005 release) and dbEST database (September 5, 2005 release).


title: sea urchin tiling array urchin17 (BC444)


title: sea urchin tiling array urchin13 (BC468)


title: sea urchin tiling array urchin21 (BC467)


title: FHCRC DMEL 4.2 Tiling 2 of 3

description: Fly tiling array using NimbleGen platform (DesignID=2347), chip 2 of 3. FlyBase release 4.2. All of Chr 2R and Chr X with isothermal oligos averaging 50bp. Dense tiling of Chr 2L distal, Bithorax complex (BXC1) and GenBank entries M21017, X51967 and X51968.


title: sea urchin tiling array urchin16 (BC462)


title: sea urchin tiling array urchin7 (BC460)


title: sea urchin tiling array urchin6 (BC458)


title: sea urchin tiling array urchin12 (BC451)


title: sea urchin tiling array urchin5 (BC455)


title: sea urchin tiling array urchin11 (BC452)


title: sea urchin tiling array urchin3 (BC457)


title: sea urchin tiling array urchin4 (BC459)


title: sea urchin tiling array urchin8 (BC461)


title: sea urchin tiling array urchin10 (BC448)


title: sea urchin tiling array urchin9 (BC446)


title: Mitchell Group Streptococcus pneumoniae TIGR V.2

city: Glasgow

first: Tim

last: Mitchell

address: 120 University Place

department: IBLS

institute: University of Glasgow

organism: Streptococcus pneumoniae

description: The full genome array of S. pneumoniae microarray v.2 consists of amplicons representing segments of 2,131 open reading frames from S. pneumoniae reference strain TIGR4 (Tettelin et al., 2001) spotted in quadruplicate on glass slides. Also, the array contains an additional 118 open reading frames from strains R6 (164) (Hoskins et al., 2001) and G54 (399).

manufacturer: The Institute for Genomic Research (TIGR)

first: Nuno

last: Silva

manufacture_protocol: see: Hendriksen et al. 2006


title: sea urchin tiling array urchin18 (BC445)


title: sea urchin tiling array urchin2 (BC442)


title: MPIMG Homo sapiens 43K aCGH2_MPIMG_BERLIN

status: Public on Oct 19 2006

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

institute: MPIMG

manufacture_protocol:
This BAC array consists of  the tiling path for chromosomes 4, 9, 10, 11, 16, 17, 21, 22  and X, derived from the human 32k BAC Re-Array Set (BAC PAC resources; DNA kindly provided by Pieter de Jong), the 1Mb Sanger set (clones kindly provided by Nigel Carter, Wellcome Trust Sanger Centre) and a set of subtelomeric clones (assembled by members of the COSTB19 Action: Molecular cytogenetics of solid tumours). Protocols for the isolation of DNA (1Mb Sanger set and subtelomeric set) and the amplification of insert DNA by linker adapter PCR are described in detail at Molecular Cytogenetics web site of MPG. Amplicons were ethanol precipitated, dissolved in 3xSSC/1,5M betaine and spotted on epoxy-coated slides (NUNC, Wiesbaden, FRG) by means of a modified Qarray (originally from Genetix, new Milton, U.K.) and Pointech (Gibbon, MN) Tungston PTL 2500 slit pins.
DNA is spotted in triplicates.


title: Hopkins S. Cerevisiae 44k Double Tiling Array v1.0

status: Public on Oct 22 2006

city: Baltimore

first: Sarah

last: Wheelan

address: 550 N. Broadway

department: Oncology

institute: Johns Hopkins University School of Medicine

organism: Saccharomyces cerevisiae

manufacture_protocol: in situ oligonucleotide synthesis of 60mer custom oligos


title: Human 19K Compugen Array spotted in GIS

status: Public on Oct 20 2006

city: Singapore

first: Martin

last: Hibberd

state: Singapore

address: 60, Biopolis Street

department: Population Genetics

country: Singapore

institute: Genome Institute of Singapore

first: Lance

last: Miller

manufacture_protocol: See GIS MADB Home page


title: Hopkins S. Cerevisiae 44k TIP-chip v1.0


title: Aedes aegypti hemocyte II

status: Public on Oct 17 2006

city: Madison

first: Bruce

last: Christensen

state: WI

address: 1656 Linden Drive

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

organism: Aedes aegypti

description: For the purpose of technical replication and to control for variation in hybridization across the slide, slides are designed such that each feature is desposited twice per grid, and that grid is duplicated on another part of the slide.  The result is that each feature is represented 4 times.

manufacturer: Bruce Christensen Laboratory, University of Wisconsin-Madison

first: Lyric

middle: C

last: Bartholomay

first: Jeremy

last: Fuchs

first: George

last: Mayhew

manufacture_protocol: 60-mer oligonucleotides were designed (for EST clusters generated for immune-response activated hemocytes from adult Ae. aegypti females (described in PMID: 15213157)) using OligoArray software version 1 (see PMID: 11934750).  Oligos were synthesized by Qiagen/Operon and resuspended to a final concentration of 40 uM in Pronto! Universal Spotting Solution (Corning Life Sciences).  The Biorobotics MicroGrid II microarrayer (Apogent Discoveries), fitted with 10K Tungsten pins was used with the following parameters: 0.275 pitch, -0.360 mm target height, 4mm/sec to 2mm/sec at 1mm above the slide deceleration, to acheive spots that are between 100 and 150 um in size.  The accompanying software TAS Application Suite version 2.2.2.6 was used to program the microarrayer.  Corning UltraGAPS slides (Cornign Life Sciences) were used as the array substrate.  After spotting, slides were subjected to 48 hours of vacuum desiccation at room temperature, then UV cross-linked at 600 mJ in a UV Stratalinker (Stratagene).


title: Yale Drosophila melanogaster 14K Whole Genome Embryogenesis Timecourse

status: Public on Oct 18 2006

city: New Haven

first: Christopher

last: Mason

state: CT

address: 1 Gilbert Street

department: Genetics

institute: Yale University

first: Kevin

last: White

manufacture_protocol: cDNA synthesis, spotted on poly-Lysine slides with a GeneMachines spotting system


title: UNIL_fireant_25K_vB1.0

status: Public on Oct 14 2006

city: Lausanne

first: John

last: Wang

address: Batiment Biophore

department: Department of Ecology and Evolution

country: Switzerland

institute: University of Lausanne

organism: Solenopsis invicta

manufacturer: UNIL: Laurent Keller Laboratory and DAFL

first: Stephanie

last: Jemielity

first: Paolo

last: Uva

first: Yannick

last: Wurm

first: Johannes

last: Gräff

first: Laurent

last: Keller

manufacture_protocol:
Bacteria clones were inoculated into PCR plates containing 5 µl modified LB-ampicillin broth (20% concentration LB and without NaCl) and grown overnight. Plasmid inserts were amplified by PCR after adding 95 µl of PCR mix. A single primer, SMART PCR primer 5’-AAGCAGTGGTATCAACGCAGAGT-3’, which matches both the 3’ and 5’ SMART adapter of the inserts was used. PCR mixes contained 0.4 µl 5U/µl TAQ (Qiagen), 10 µL 10x Qiagen buffer, 20 µl Q solution, 4 µl 25 mM MgCl2, 1.5 µl 25 mM dNTPs, and 1 µl 100 µM SMART PCR primer. An initial 9-min denaturation at 94 °C was followed by 40 cycles of 30 sec at 94°C, 30 sec at 59°C, and 3 min at 72°C. The reaction ended with an additional incubation of 7 min at 72°C. Two microliters of each PCR product were analyzed on a 1% agarose gel. Gel pictures were visually examined to classify all PCR products as follows: “strong single band” (78.4 %), “no band” (3.9 %), or “weak or multiple bands” (17.5 %). This data is in Supplemental Table F (http://fourmidable.unil.ch/).
PCR products were purified by a standard NaOAc/ethanol precipitation, resuspended in 30 µl water and transferred into duplicate 384-well plates using a Biomek FX liquid-handling robot (Beckman Coulter). Then PCR products were dried and resuspended in 20 µL 3x SSC, 1.5 M betaine. We also resuspended 48 times 10 commercial exogenous controls (SpotReport Alien cDNA Array Validation System, Stratagene) in 3x SSC, 1.5 M betaine, one set for each subgrid of the microarray. Microarrays were printed on aldehydesilane-coated slides (NexterionTM Slide AL, Schott Nexterion), using an OmniGrid 300 spotting robot (GeneMachines). Spot and printing quality were assessed visually under a dissecting microscope after printing. While a few slides had minor defects (e.g., a few spots missing or damaged by dust particles), the majority of slides exhibited no defects. DNA was crosslinked to slides by baking at 80°C for 1 h. Afterwards, the slides were post-processed with NaBH4 using the manufacturers recommended protocol.


title: sea urchin tiling array urchin1 (BC456)

first: Manoj

last: Samanta

first: Waraporn

last: Tongprasit

first: Sorin

last: Istrail

first: R

last: Cameron

first: Qiang

last: Tu

first: Eric

last: Davidson

first: Viktor

last: Stolc


title: Aedes aegypti hemocyte I

first: Bruce

last: Christensen

first: Lyric

last: Bartholomay

first: Jeremy

last: Fuchs


title: MBPL Human 30k P4

status: Public on Oct 12 2006

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

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

first: Ian

last: Hsu

first: MinLung

last: Tsai

first: ChihMing

last: Lin

first: WeiChung

last: Cheng

first: ChingLung

last: Huang

first: ChiuTing

first: YuLing

last: Hsieh

first: KunYu

first: TsaiJiuan

last: Weng

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


title: Escherichia coli MG1655 382K 50-mer tiling array

city: Boston

first: Nikos

last: Reppas

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard University

organism: Escherichia coli

manufacture_protocol: Custom NimbleGen maskless oligonucleotide E. coli tiling array that covers the entire genome with 382177 50-mers tiled every ~12 bp on alternate strands. A few regions are covered with 1 bp tiling.


title: UNIL_fireant_25K_vC1.0

first: John

last: Wang

first: Stephanie

last: Jemielity

first: Paolo

last: Uva

first: Yannick

last: Wurm

first: Johannes

last: Gräff

first: Laurent

last: Keller


title: Wistar Yeast YA04 array

status: Public on Oct 13 2006

first: Louise

last: Showe

address: 3601 Spruce St

institute: The Wistar Institute

first: Michael

first: Wenhwai

last: Horng

manufacture_protocol: cDNA spot array on nylon membrane.


title: UMRCNRS7637/EA3508_Human_HSA21_v1.0

status: Public on Oct 07 2006

city: PARIS

first: Emilie

last: Aït Yahya Graison

address: 2 place jussieu

department: UFR BIOCHIMIE

country: France

institute: UNIVERSITE PARIS 7

first: Marie-Claude

last: Potier

first: Jean

last: Delabar

last: Ait Yahya Graison

first: Luce

last: Dauphinot

first: Geoffroy

last: Golfier

manufacture_protocol:
50-mers oligonucleotide primers synthesized by EuroGentec.
spotting realized on CodeLink® activated glass slides (Amersham Biosciences) using a MicroGrid II spotter (Biorobotics) by the society Genescore.


title: UTHSCSA_Mm_17k_v1

status: Public on Oct 01 2006

city: San Antonio

first: Robert

middle: Brent

last: Calder

address: 15355 Lambda Dr.

department: Physiology

institute: University of Texas Health Science Center at San Antonio

manufacture_protocol: Operon Mouse Oligo Set version 2.0.  Lyophilized 70-mer oligonucleotides were resuspended in 20µl 2XSSC.  Printed using Gene Machines OmniGrid printer using Telechem Stealth pins in a 4X8 configuration on Corning Ultra-GAPS slides.


title: UCF BMS M. tuberculosis v1.0

status: Public on Sep 27 2006

city: Suwon

first: ChangMuk

last: Lee

address: 224, Suinro, Gwonseon-Gu

department: Microbial Genetics Division

country: South Korea

institute: National Institute of Agricultural Biotechnology

organism: Mycobacterium tuberculosis

description: The genome microarray consists of 4,750 70-mer oligonucleotides representing 4127 ORFs from Mycobacterium tuberculosis - reference strain H37Rv, and 623 unique ORFs from strain CDC1551 which are not present in the H37Rv strain's annotated gene complement. The full 70-mer complement is printed twice on the surface of the microarray. The microarray also contains 500 additional features which have been reserved for future use.

first: Chang-Muk

first: Pappachan

last: Kolattukudy

manufacture_protocol:
The slides are printed on 48 grids wiith each grid containing 15 columns and 15 rows with following pattern;
PinX metacol=4, PinY metarow=12, PinX spacing pixels=450, PinY spacing pixels=450, Spot spacing pixels=27, Spot size pixels =~15, Column number=15, Row number=15, 2QMT with arrayer LUCIDEA.


title: SAGE:17:NlaIII:Oncorhynchus tshawytscha

status: Public on Oct 10 2006

last: GEO

organism: Oncorhynchus tshawytscha

description: This is a virtual platform for SAGE libraries generated for Oncorhynchus tshawytscha using NlaIII as an anchor enzyme.


title: Mussel MytArray 1.0

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

organism: Mytilus galloprovincialis

description:
MytArray 1.0 is a cDNA platform, that consists of 1,712 different clones obtained from systematic sequencing of multiple Mytilus galloprovincialis tissues cDNA library and 46 unrelated controls (ESTs from Coffea and bacterial species) printed in duplicate and twice per slide. This library was produced using a strategy that allows the selection of a short 3’-end region of mRNAs and the tagging of each transcript with an unique probe. Moreover, since the 3’-end non coding region is the least conserved part of the genes, a microarray constructed in this way greatly reduces the cross hybridization of different mRNAs derived from genes with high homology in the coding region to the same probe. The strategy was also designed to obtain 3’-tags with very uniform size (400-800 bp). This feature ensures that all the cDNA clones of the collection can be PCR-amplified and spotted with comparable efficiency and that production of microarrays with uniform hybridization characteristics be obtained.
Keywords = cDNA microarray
Keywords = gene expression
Keywords = several mussel tissues

manufacturer: C.R.I.B.I.-Biotechnology Centre and Dept. Biology (University of Padova)

first: Paola

last: Venier

first: Cristiano

last: De Pittà

first: Francesco

last: Marsano

first: Alberto

last: Pallavicini

first: Laura

last: Varotto

first: Chiara

last: Romualdi

first: Aldo

last: Viarengo


title: UNC Saccharomyces cerevisiae 15K ORF_intergenic_P

status: Public on Sep 08 2006

city: Chapel Hill

first: Jason

last: Lieb

state: NC

address: CB# 3280, 202 Fordham Hall

department: Department of Biology

institute: University of North Carolina at Chapel Hill

description: 15230 spots

manufacture_protocol: as described in Iyer et al. 2001


title: UCF BMS M. tuberculosis ver 2.0

description: The genome microarray consists of 4,750 70-mer oligonucleotides representing 3,417 oligonucleotides from M. tuberculosis reference strain H37Rv, and 1,333 oligonucleotides from strain CDC1551. Oligos are designed to provide coverage across the above organisms used in the design. The full 70-mer complement is printed 4 times on the surface of the microarray. The microarray also contains 500 A. thaliana 70-mer oligonucleotides for internal controls.

manufacture_protocol:
The slides are printed on 96 grids with each grid containing 23 rows and 10 columns with following pattern;
MetaRow=12, MetaColumn=8, Pix X(pix)=225, Pix Y(pix)=450, Row number=23, Column number=10, X Spacing(pix)=17, Y Spacing(pix)=17. 2QMT with arrayer LUCIDEA.


title: SLVG E.coli_Shigella 6.5K array

city: Beijing

first: Junping

last: Peng

address: No 6, Rongjing Eastern Street, BDA

country: China

institute: Chinese center for disease control and prevention

organism:
Escherichia coli K-12
Shigella flexneri 2a str. 301
Shigella dysenteriae Sd197
Shigella boydii Sb227
Shigella sonnei Ss046

description:
A microarray with 6528 spot features.
Tip configuration: Standard 16-tip steel pin
Columns per Sector: 24
Rows per Sector: 17
Column spacing: 180 um
Row spacing: 180 um

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

first: Qi

last: Jin

manufacture_protocol: The PCR products were spotted onto glass slides to make DNA arrays as described in MGUIDE at http://cmgm.stanford.edu/pbrown/mguide/index.html and protocols on http://www.microarrays.org/


title: Wistar Human HA06 Array

status: Public on Jul 12 2006

city: Philadelphia

first: Louise

last: Showe

organism: Homo sapiens

description: cDNA spot array on nylon membrane.

first: Michael

first: Wenhwai

last: Horng


title: SAMF Mouse 7k

status: Public on Jul 06 2006

city: Calgary

first: Mayi

middle: Arcellana

last: Panlilio

state: Alberta

address: 3330 Hospital Drive, NW

department: Biochemistry&Molecular Biology

country: Canada

institute: University of Calgary

description: The array contains 32 subgrids arranged in 4 columns x 8 rows. Each subgrid has 19 rows and 24 columns. Grid to grid distance is 4500 um. Average spot diameter is 100um. Spot to spot distance is 180 um.

last: Arcellana-Panlilio

manufacture_protocol: Operon Mouse V1.0 70mer oligonucleotides were dissolved in 3xSSC at 40uM and spotted in duplicate on Corning GAPS II barcoded slide substrates using the Virtek ChipWriter SDDC 2.5 (now BioRad) equipped with 32 SMP3 Stealth 3 Micro spotting pins (Telechem).


title: UNC Saccharomyces cerevisiae 15K Yeast-CLK3

status: Public on Sep 12 2006

description: 15360 spots

first: Cheol-Koo

last: Lee


title: Human Phosphodiesterase Splice Variant Microarray

status: Public on Oct 06 2006

city: Berkeley

first: Jonathan

last: Bingham

address: 733 Allston Way

institute: Jivan Biologics, Inc

first: Subha

last: Srinivasan

manufacture_protocol: Exon and exon junction probes designed by Jivan Biologics, Inc. for splice variant detection and discovery. Average oligonucleotide length 38 bases. Synthesize by Sigma-Genosys with amine label. Spotted by Mergen Ltd on glass slides with covalent chemistry.


title: Candida Albicans Eurogentec 13440

city: Madrid

first: Concha

last: Gil

state: Madrid

address: Pza. Ramón y Cajal s/n

department: Departamento Microbiología II

country: Spain

institute: Universidad Complutense de Madrid

organism: Candida albicans

manufacture_protocol:
Construction of C. albicans MicroArray

The C. albicans MicroArray has been developed in collaboration with the European Galar Fungail Consortium (www.pasteur.fr/recherche/unites/Galar_Fungail/). The Stanford Genome Technology Center generated the nucleotide sequence data for C. albicans with fundings from the NIDCR, NIH and the Burroughs Wellcome Fund. Information about coding sequences and proteins were obtained from the CandidaDB database: www.pasteur.fr/recherche/unites/Galar_Fungail/CandidaDB/, which has been developed by the Galar Fungail European Consortium. Specific primers were designed to amplify all 6039 putative ORFs. The primers were selected carefully to amplify only a specific region of each ORF. Universal sequences of 15 bases were incorporated on the 5' of each specific forward and reverse primer. The two-step PCR method has been employed to generate 5' amino-modified PCR for covalent attachment to the aldehyde-coated support. All the amplicons have an average length of 300 bp and they were controlled systematically by electrophoresis on 2 % agarose gels. Two independent probes per gene were selected to represent 34 genes. The MicroArray covers nearly 98 % of the annotated C. albicans genes and includes twelve mitochondrial genes, five intergenic regions, five S. cerevisiae genes and five genes for hybridization quality control, human glycerol-3-phosphate dehydrogenase and actin gene. We include in the MicroArray probes to evaluate the dynamic range of signal intensities, reverse transcription efficiency and spatial hybridization.

Spotting design

C. albicans MicroArrays are manufactured by printing PCR amplicons suspended in optimized spotting buffer for high coupling efficiency of DNA to the most consistent aldehyde coated glass slides. This spotting chemistry provides us the highest hybridization intensities, which is a consequence of a better binding of the probe to the slides and their accessibility to the cDNA targets. We use ChipWriter™ Pro (Virtek) which is a high precision dispensing robot to spot the PCR products onto aldehyde glass slides. The robot is designed to collect 100 nl of DNA solution and to deposit 0.6 nl per spot. For C. albicans MicroArray, we use simultaneously 32 pins to place the spots in area of 3.6 x 1.8 cm. In order to generate high quality spots, the printing procedure is performed under a tight controlled humidity and temperature environment. This allows having the complete control on the spot morphology, the spot diameter and uniformity. This configuration of the robot generates 32 blocks, each containing 20 x 20 dots with 200 microns spacing center to center with a spot diameter of 100 microns.

MicroArray content

98 % of C. albicans genes were spotted twice in a single glass slide.

Tags (GFP, TAP, GST)
Marker genes Kan, Leu2, LacZ
Luciferase gene to spike mRNA samples
Negative controls (intergenic regions)
Cross hybridization S. cerevisiae genes having 70 %, 50 % and 30 % sequence identity with S. pombe genes
cDNA quality controls
Dynamic range controls
Spatial hybridization controls
Quality control

The C. albicans MicroArrays are certified to generate a high quality data.
All printed slides are previously selected for coating uniformity and low intrinsic background.
The MicroArrays are visually inspected for spotting quality (doughnuts), uniformity, integrity and for perfect alignment of spots and grids.
From each batch of printed MicroArray, three are randomly chosen for further quality control. We use the Terminal Transferase reaction to assess the amount of DNA covalently attached to the slides. Finally, we perform a real hybridization using labeled cDNA obtained from heat-choc cultured cells.


title: Mouse 23K oligo microarray_CD133-Prominin Study

city: Bryan

first: Rajesh

last: Miranda

address: MREB, 8447 Riverside Parkway

department: Neuroscience

institute: Texas A&M HSC

description: Custom-printed 23,000 feature mouse-oligonucleotide arrays, (provided by Dr. Brian Soriano, University of Colorado, Department of Pharmacology, Gene Expression Core Laboratory)

manufacturer: University of Colorado, Gene Expression Core Laboratory, Dr Brian Soriano

first: Brian

last: Soriano

manufacture_protocol: see manufacturer


title: UNC Saccharomyces cerevisiae 15K ORF_INT_UNC_CKL5

description: 15360 spots


title: UNC Saccharomyces cerevisiae 18K ORF_INT_UNC_B

description: 18432 spots


title: SAMF Human 14k Part1

description: The array contains 32 subgrids arranged in 4 columns x 8 rows.  Each subgrid has 18 rows and 24 columns.  Grid to grid distance is 4500 um. Average spot diameter is 100um. Spot to spot distance is 180 um.

manufacture_protocol: Operon Human V1.0 70mer oligonucleotides (Plates 1-72) were dissolved in 3xSSC at 40uM and spotted in duplicate on Corning GAPS II barcoded slide substrates using the Virtek ChipWriter SDDC 2.5 (now BioRad) equipped with 32 SMP3 Stealth 3 Micro spotting pins (Telechem).


title: Candida glabrata whole genome oligonucleotide array (70 mers)

status: Public on Jun 29 2006

city: Baltimore

first: Brendan

last: Cormack

address: Hunterian Building 617, 725 N. Wolfe St.

department: Molecular Biology & Genetics

institute: Johns Hopkins Univ. School of Medicine

organism: Nakaseomyces glabratus

description: UltraGAPs glass slides from Corning

manufacturer: Biotechnology Research Instit (Montreal)/NRC-Canada & Johns Hopkins Univ.

first: Biao

last: Ma

first: Tracey

last: Rigby

first: Andre

last: Nantel

manufacture_protocol: 5908 unique 69 or 70-mer oligonucleotides corresponding to all known and putative Candida glabrata coding sequences were synthesized on 384-well plates in Pasteur Institute, France. These oligoes were dissolved into 50% DMSO with a final concentration of 0.9 ug/ul and spoted on UltraGAPS glass slides (Corning) in duplicate using 48 pins at microarray facility in Biotechnology Research Instit (Montreal)/NRC-Canada.


title: SAMF Human 14k Part2

manufacture_protocol: Operon Human V1.0 70mer oligonucleotides (Plates 73-146) were dissolved in 3xSSC at 40uM and spotted in duplicate on Corning GAPS II barcoded slide substrates using the Virtek ChipWriter SDDC 2.5 (now BioRad) equipped with 32 SMP3 Stealth 3 Micro spotting pins (Telechem). This is part 2 of 2.  Also contains control oligos supplied by Operon as well as 3xSSC buffer spots.


title: GUELPH Bovine 180 immune-endocrine microarray

city: Guelph

first: Wenjing

last: Tao

state: ON

address: Gordon street

department: Department of Pathobiology

institute: University of Guelph

organism:
Arabidopsis thaliana
Bos taurus

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

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

first: Bonnie

last: Mallard

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


title: sea urchin tiling array urchin15 (BC463)

status: Public on Oct 23 2006

city: Los Altos

first: Manoj

last: Samanta

address: 2240 Homestead Court #309

institute: Systemix Institute

organism: Strongylocentrotus purpuratus

description:
50-mer probes tiling the entire S. purpuratus genome
Control probes were placed on all arrays for monitoring hybridization quality and data normalization.

first: Waraporn

last: Tongprasit

first: Sorin

last: Istrail

first: R

last: Cameron

first: Qiang

last: Tu

first: Eric

last: Davidson

first: Viktor

last: Stolc

manufacture_protocol: Synthesized on glass-based slides using a maskless array synthesizer (Nimblegen technology).