title: Custom NimbleGen Xenopus tropicalis Oligo Expression Array

status: Public on Aug 31 2009

city: Davis

first: Matt

middle: L

last: Settles

state: CA

address: 451 Health Sciences Sr

department: Genome Center

country: USA

institute: University of California, Davis

organism: Xenopus tropicalis

technology: in situ oligonucleotide

description: 2006-09-29_X_tropicalis_60mer_expr; NimbleGen microarray for S. tropicalis based on full length coding sequence (CDS) and expressed sequence tags (ESTs) from the JGI (available at http://genome.jgi-psf.org/Xentr4) and Gurdon Institute (available at http://informatics.gurdon.cam.ac.uk/online/xt-fl-db.html)

distribution: custom-commercial

manufacture_protocol: See manufacturer's website


title: SMD Print_1319 Mus musculus

status: Public on Aug 30 2009

city: Stanford

first: Elizabeth Ann

last: Joyce

email: ejoyce@stanford.edu, ea.joyce@gmail.com

address: Mail Code: 5124

department: Microbiology and Immunology

institute: Stanford University School of Medicine

organism: Mus musculus

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: 2D-LC MS/MS Analyses of HLA Class I Peptides Isolated from B-cells Infected with Vaccinia Virus

city: Rochester

first: Kenneth

middle: L.

last: Johnson

state: MN

address: 200 First Street S.W.

institute: Mayo Clinic

organism:
Homo sapiens
Bos taurus
Orthopoxvirus vaccinia

technology: MS

description: B-cell cultures were infected with live vaccinia virus (NYBOH strain).  Cells were lysed, HLA/peptide complexes were enriched by immunoaffinity (W6/32 mAb), peptides were released with acid and separated from HLA proteins by 10 kDa ultrafilitration.  HLA class I peptides were separated and identified by 2-dimensional liquid chromatography and tandem mass spectrometry to identify class I peptides derived from vaccinia proteins, that were being presented to the immune system.

distribution: virtual

first: Inna

middle: G

last: Ovsyannikova


title: C. briggsae 42K expression microarray

city: Haifa

first: Itai

last: Yanai

address: Technion City

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

organism: Caenorhabditis briggsae

first: Craig

middle: P

last: Hunter

manufacture_protocol: Agilent SurePrint


title: Prove-it Bacteria v 0.1

city: Helsinki

first: Anna-Kaarina

last: Jarvinen

address: Biomedicum Helsinki 2U, Tukholmankatu 8

country: Finland

institute: Mobidiag

organism:
Acinetobacter baumannii
Neisseria meningitidis
Klebsiella pneumoniae
Haemophilus influenzae
Staphylococcus aureus
Staphylococcus epidermidis
Streptococcus agalactiae
Streptococcus pneumoniae
Streptococcus pyogenes
Enterococcus faecalis
Enterococcus faecium
Listeria monocytogenes

technology: spotted oligonucleotide

description: Diagnostic array for the simultaneous detection and identification of 12 bacterial pathogens at the species level.

distribution: commercial

manufacture_protocol: see manufacturer website (http://www.clondiag.com/)


title: 454 GS FLX (Caenorhabditis elegans)

status: Public on Aug 24 2009

last: GEO

organism: Caenorhabditis elegans

technology: high-throughput sequencing


title: Illumina Genome Analyzer II (Chlamydomonas reinhardtii)

status: Public on Aug 26 2009

organism: Chlamydomonas reinhardtii


title: NimbleGen Escherichia coli K12 TI83333 (385K)

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Escherichia coli str. K-12 substr. MG1655

description: NimbleGen cat # A4516-00-01. Design name TI8333 60mer.  4,237 genes, with average of 18 probes per gene.  385,000 probes, 5 replicates.

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.


title: Montastraea faveolata 1.3 K

city: Thuwal

first: Christian

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

organism: Orbicella faveolata

first: Julia

last: Schnetzer

middle: R

first: Leonid

last: Peshkin

first: Carly

middle: J

last: Randall

first: Alina

middle: M

last: Szmant

first: Monica

last: Medina

manufacture_protocol: Microarrays consist of PCR-amplified cDNAs from M. faveolata. 1,314 PCR-amplified cDNAs were spotted in duplicate on poly-lysine-coated slides yielding a microarray with 2,628 total features. cDNAs were chosen from EST libraries described in (Schwarz et al., 2008). To annotate the cDNAs, we performed a BLASTx analysis (E-value cut-off 1e-5) against the GenBank non-redundant DNA and protein database (nr).


title: IMCAS Streptococcus suis 385K array (MAP02)

status: Public on Aug 29 2009

city: Ames

first: Zuo-Wei

last: Wu

state: IA

address: 1113 Veterinary Medicine Bldg

institute: Iowa state university

organism: Streptococcus suis

description: Annotation in this record based on NCBI Streptococcus suis 05ZYH33 NC_009442.

manufacture_protocol: see manufacturer's web site www.nimblegen.com


title: LC_Sanger miRBase 9.0 oligo array_miRNA ID version

status: Public on Aug 25 2009

city: Lexington

first: Esther

middle: E.

last: Dupont-Versteegden

state: KY

address: 900 S. Limestone

department: Rehabilitation Sciences

institute: University of Kentucky

organism:
Rattus norvegicus
synthetic construct

description:
Rat miRNA microarray based on miRBase version 9.0, additional custom sequences

This is the miRNA ID version of GPL8195 (Feature Number version).

manufacture_protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes are made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: SRI Human 27K version 2 slide 2

status: Public on Aug 27 2009

city: Toronto

first: Azza

last: Al-Mahrouki

address: 2075 Bayview Avenue

department: Radiation Oncology & Imaging Research

country: Canada

institute: Radiation Oncology, Sunnybrook Health Sciences Centre

organism: Homo sapiens

manufacturer: SRI Genomics Core Facility, Sunnybrook Health Science Centre.

manufacture_protocol: Using epoxy coated slides under 50% humidity and Perkin Elmer SpotArray 72 in 4 x 12 pin configuration and 18 x 17 spot configuration of each subarray.


title: Custom Agilent Pseudomonas aeruginosa PAO1 Microarray

status: Public on Aug 21 2009

city: Lubbock

first: Scot

last: Dowd

state: TX

address: 4321 Marsha Sharp Fwy

department: MBRI

institute: MBRI

organism: Pseudomonas aeruginosa PAO1

middle: E

manufacture_protocol: SurePrint technology


title: SWEGENE_BAC_38K

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

first: Ake

last: Borg

manufacture_protocol: Arrays were produced by SCIBLU - Swegene Centre for Integrative Biology at Lund University - at Lund University by using amplified genomic DNA targets from BAC clones. Target amplification was performed using degenerate oligonucleotide primed PCR and products were purified by size-exclusion filtration and verified by agarose gel electrophoresis. After purification, products were dried down, recovered in 50% DMSO to a concentration of 500-1000ng/µl, and printed on amino-silane-coated glass slides (UltraGAPS from Corning) using a MicroGrid2 robot (BioRobotics) equipped with MicroSpot2500 pins (BioRobotics).


title: UniHH/Scholten_zea mays_heterosis 3k-array

status: Public on Aug 28 2009

city: Hamburg

first: Stefan

last: Scholten

address: Ohnhorststrasse 18

department: Biocenter Klein Flottbek

country: Germany

institute: University of Hamburg

organism: Zea mays

manufacture_protocol: Individual cDNA inserts of diverse cDNA libraries were amplified with insert flanking primers. The PCR products were visualized on 1% agarose gels to test the quality and quantity of amplification, followed by purification with Multiscreen PCR plates (Millipore). The clean PCR products were reformatted in 384 well plates, dried and resuspended in 15 µl spotting buffer (3 x SSC, 1,5 M betain). Each PCR product was printed twice onto poly-L-lysine (Sigma) coated glass slides with a Microgrid II robot (BioRobotics). Slides were blocked with succinic anhydride and denatured in boiling water.


title: Operon Homo sapiens 25.4k v2

city: Maastricht

first: Florence

last: van Tienen

address: Universiteitssingel 50

department: Genetics and Cell biology

country: Netherlands

institute: Maastricht University

manufacturer: Microarray Facility University Medical Center Utrecht

manufacture_protocol: The Operon V2 set consists of 21,329 70mer oligonucleotides designed on Human Unigene clusters, mainly in the 3 end terminal region. The microarrays are printed onto Corning UltraGAPS slides by our robotic station Biorobotics Microgrid II. The deposition is qualitatively assessed by a scan of the spotted slide at 10 micron resolution, and  microarray slides that meet the quality standards, are washed as recommended by the supplier and the glass slides are stored, ready for use, in the dark under deep vacuum.


title: MHP Human 1Mb CGH array

city: Cambridge

first: George

last: Poulogiannis

address: Tennis Court Road

department: Pathology

country: United Kingdom

institute: University of Cambridge

description: The 1Mb clone set has been assembled by the Mapping Core, Map Finishing and Microarray Facility groups of the Wellcome Trust Sanger Institute, Hinxton, UK. Additional clones were also kindly supplied by the Wellcome Trust Sanger Institute. The array has 24 subarrays (6 rows by 4 columns), each subarray consists of 18 rows by 18 columns.

manufacturer: Department of Pathology, Univeristy of Cambridge

first: Koichi

last: Ichimura

first: Danita

last: Pearson

first: David

last: Carter

first: Anthony

last: Brown

first: V

last: Collins

manufacture_protocol:
1.BAC/PAC clones were grown in 2xTY medium in a deep-well titre plate at 37°C overnight with chloramphenicol 25µg/ml (BAC) or kanamycin 20µg/ml (PAC).
2. DNA was extracted from BAC or PAC clone using modified alkali-lysis method (microprepping).
3. Approximately 5ng of BAC/PAC DNA was PCR-amplified using three DOP-primers (Fiegler H, Genes Chromosomes Cancer 36:361-374, 2003).
4. Two microlitre of the DOP-PCR products was further amplified using 5'-Aminolink universal primer (Fiegler H, Genes Chromosomes Cancer 36:361-374, 2003).
5. Three volumes of the Amino-PCR products were mixed with one volume of 4xSpotting buffer (1M Sodium phosphate buffer, pH8.5, 0.001% Sarkosyl) to make a spotting mix.
6. The spotting mix was filtered through Corning 96 well white polystyrene filter plate with modified styrene insert (0.2µm PVDF) by centrifugation.
7. The filtered spotting mix was transferred to a 384-well plate.
8. The spotting mix was printed printed in duplicate onto a CodeLink slide (GE Healthcare) using a MicroGrid II robot (Genomic Solutions, Huntingdon, UK) in 4x4 subarrays.
9. The printed slides were incubated at room temperature for 24-72 hours in a humidified chamber.
10. The slides were treated with 1% ammonium hydroxide at room temperature for 5 min, then with 0.1% SDS at room temperature for 5min.
11. The slides were heat-denatured in a boiling water for 2 min, cooled, rinsed with water and dried.


title: IFR_Salmonella_5.3k_v1.1

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

institute: Institute of Food Research

organism: Salmonella enterica

first: Arthur

last: Thompson

first: Jay

middle: C

last: Hinton

manufacture_protocol: PCR product array of whole ORF's from S. Typhimurium LT2. For description of PCR amplification and printing procedures see Eriksson et al., Molecular Microbiology(2003) 47(1): 103-118.


title: C. elegans 33.8K expression microarray

first: Itai

last: Yanai

first: Craig

last: Hunter


title: Rubin M. tuberculosis 2.3K PCR-based genomic array v1.0

status: Public on Aug 20 2009

city: La Jolla

first: Jeffrey

middle: P.

last: Murry

address: 10010 N. Torrey Pines Road

department: IMPL-Y

institute: Salk Institute

organism: Mycobacterium tuberculosis

manufacturer: Tufts University microarray printing facility

manufacture_protocol:
PCR was used to amplify a fragment corresponding to each predicted ORF of the genome.
BLAST was used to design primer pairs that generate products that do not crosshybridize to other genes in the M. tuberculosis H37Rv genome. Primer pairs were found for 3,855 predicted ORFs.  PCR products varied in length from 70 bp to 499 bp, with a median length of ~350 bp.  Forward and reverse primers contained 5' extensions: GGCATCTAGAG and CCGCACTAGTCCTC, respectively.
PCRs with these gene-specific primers were performed by using 1.25 units of Taq and 0.15 units of Pfu polymerase (Stratagene) in 50 ml reactions containing 2.5 mM MgCl2, 10% (vol/vol) DMSO and H37Rv genomic DNA as template. PCR conditions were 94°C for 2 min; 30 cycles of 94°C for 30 sec, 60°C for 30 sec, 72°C for 1 min; and 72°C for 5 min.
First round PCR products were diluted 1:100, and 2.5 microliters were used as a template for PCR with the following universal primers (both contain 5' amino modifications including a three-carbon linker; Genosys, The Woodlands, TX): GAACCGATAGGCATCTAGAG and GAAATCCACCGCACTAGTCCTC. PCR was performed as follows: 94°C for 2 min; 3 cycles of 94°C for 30 sec, 40°C for 30 sec, 72°C for 1 min; 20 cycles of 94°C for 30 sec, 60°C for 30 sec, 72°C for 1 min; and 72°C for 5 min.
Second round PCR products were analyzed by gel electorphoresis on 2% agarose gels.  PCR of all but 11 ORFs produced single products.  Those reactions that did not produce products of appropriate size or produced multiple products were not included in further analysis.
PCR products were purified by using multiscreen PCR plates (Millipore).
PCR products were arrayed onto 3D-Link slides (Surmodics, Eden Prairie, MN) in duplicate, as recommended by the manufacturer.


title: Agilent-022589 Clostridium_botulinum_species_cgh_array 022588

city: Rockville

first: PFGRC

last: JCVI

state: MD

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

organism: Clostridium botulinum

description: clostridium botulinum species array for CGH study. Arrays of this design have barcodes that begin with 16022589 or 2522589.. Orientation:. Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.. The ID column represents the Agilent Feature Extraction feature number.. Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).. To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions..

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


title: Dendroctonus ponderosae midgut array

city: Reno

first: Claus

last: Tittiger

state: NV

address: Mail Stop 330

department: Biochemistry and Molecular Biology

institute: University of Nevada, Reno

organism: Dendroctonus ponderosae

description: NimbleGen design name 080407_D_ponderosae_expr, NimbleGen design ID 7440.  4x expression for Dendroctonus ponderosae (4034 initial contig seqs + 4 controls; 3738 exemplars for 3745 seqs; two long controls re-selected to distribute probes along whole length), 3 copies of each probe on array pairs (PM/MM) per gene.  Each probe is replicated 3 times.  The design includes random GC and other control probes.


title: GE Healthcare/Amersham Biosciences CodeLink™ Mouse Whole Genome Bioarray (EMBL180809)

city: Rostock

first: Eik

last: Hoffmann

address: Albert-Einstein-Str. 3

department: Institute of Biological Sciences

institute: University of Rostock

organism: Mus musculus


title: NimbleGen_HG18_WG_385k_v2

status: Public on Aug 23 2009

city: Durham

first: Michael

last: Kelley

state: NC

address: 508 Fulton St. (111G)

institute: Duke University

manufacture_protocol: 385K element tiling array based on NCBI Build 36 of the human genome (HG18); 60-mer tiling with a median probe spacing of 7,073 bp. The NimbleGen design files (080101_HG18_WG_CGH_v2_X1.pos and 080101_HG18_WG_CGH_v2_X1.ndf) are included as supplementary files.


title: Silkworm Microarray 22k v1

city: BeiBei

first: Qingyou

last: Xia

state: Chongqing

address: No.2 Tiansheng Road

country: China

institute: Southwest University

organism: Bombyx mori

first: Daojun

last: Cheng

first: Jun

last: Duan

first: Genhong

last: Wang

first: Tingcai

first: Xingfu

last: Zha

first: Chun

last: Liu

first: Ping

last: Zhao

first: Fangyin

last: Dai

first: Ze

last: Zhang

first: Ningjia

last: He

first: Liang

first: Zhonghuai

last: Xiang

manufacture_protocol:
All sequences that were regarded as probe designing models were derived from the draft silkworm genome sequence in SilkDB (http://silkworm.genomics.org.cn/; xia et al. 2004) and other resources available in GenBank. These data set contained 21,302 predicted genes (including 13,093 complete and 8,209 partial) from WGS, 212 full-length cDNA sequences from GenBank, and 16 425 Unigens based on ~150000 ESTs from different silkworm tissues. We also integrated 554 GenBank genes of other Lepidoptera and 521 silkworm genes homologous to other lepidopteran insect genes.
A 70-mer oligonucleotide modified at 5' ends with a 6-carbon linker and a primary amine corresponding to each sequence was designed by CapitalBio Corporation (Beijing, China) and synthesized by MWG Biotech (Ebersberg, Germany). Then Oligonucleotides were dissolved in EasyArrayTM spotting solution (CapitalBio Corp.) at 40μM concentration. Probe was printed on amine silaned slides using a SmartArrayTM microarrayer (CapitalBio Corp.). On the slide, there are 48 blocks and every block has 23 columns and 22 rows. Probes for four house keeping genes and eight yeast intergenic sequences were printed on every block used as internal and external controls respectively.


title: Agilent-022729 Vibrio_species_20090128

first: PFGRC

organism: Vibrio cholerae

description: Vibrio cholerae species cgh. Arrays of this design have barcodes that begin with 16022729 or 2522729.. Orientation:. Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.. The ID column represents the Agilent Feature Extraction feature number.. Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).. To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: IMCAS Streptococcus suis 385K array (MAP01)

first: Zuo-Wei

last: Wu


title: miRNA profile from LPS-treated Akt1-/- macrophages

city: Heraklion

first: Christos

last: Tsatsanis

state: Crete

address: Voutes

department: School of Medicine

country: Greece

institute: University of Crete

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

technology: RT-PCR

manufacture_protocol: TaqMan arrays


title: Affymetrix Human Genome U133A Array [CDF: XLab gahgu133a_2.0.1]

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Custom definition files for Affymetrix HG-U133A arrays

first: Francesco

last: Ferrari

first: Stefania

last: Bortoluzzi

first: Alessandro

last: Coppe

first: Alexandra

last: Sirota

first: Marilyn

last: Safran

first: Michael

last: Shmoish

first: Sergio

first: Doron

last: Lancet

first: GianAntonio

last: Danieli

first: Silvio

last: Bicciato

relation: Alternative to: GPL96 (Alternative CDF [official])

manufacture_protocol: Refer to GPL96 platform for the complete description of HG-U133A manufacture protocol


title: Stowers Institute Uber Array Whole Yeast genome PCR Product version 1

city: Kansas City

first: Raymond

last: Camahort

state: MO

institute: Stowers Institute

organism: Saccharomyces cerevisiae

first: Jennifer

last: Gerton

manufacture_protocol: PCR was used to amplify all known ORFs and Intergenic regions of the S.cerevisiae genome.  PCR products were spoted by a custom-made spotting robot onto poly-lysine coated glass slides and allowed to dry.


title: SuperArray Mouse Dendritic and Antigen Presenting Cell

status: Public on Aug 19 2009

city: Dallas

first: Kiyoshi

last: Ariizumi

address: 5323 Harry Hines Blvd

department: Dermatology

institute: UT Southwestern Medical Center

manufacture_protocol: see manufacturer's web site at www.superarray.com


title: UCSB/Hofmann_Spurp_44K_v1.0

status: Public on Aug 14 2009

city: San Francisco

first: Anne

last: Todgham

address: 1600 Holloway Ave

institute: San Francisco State University

organism: Strongylocentrotus purpuratus

first: Gretchen

last: Hofmann

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


title: Centre de Recherche en Infectiologie du CHUL_Leishmania 9K array v1.0

status: Public on Aug 15 2009

city: Québec

first: Philippe

last: Leprohon

state: Québec

address: 2705 boulevard Laurier

department: Centre hospitalier de l'Université Laval

institute: Université Laval

organism: Leishmania infantum

description: The Platform data table reflects a condensed representation of the array's replicate features.

manufacturer: BIOGEM (BioMedical Genomics Microarray Facility), University of california

first: Eric

last: Madore

manufacture_protocol:
70-mer oligonucleotides probes were designed for each open reading frame of L. infantum and L. major
The microarrays were printed on SuperChip (Erie Scientific) using a  BioRobotics Microgrid (Genomic solutions Inc). Pin type: Micro-Spot 10K split pins. We used 48 matched pins.
Each probe was printed in duplicate.  The fill volume was 55 nl of oligos at 50uM in 50%DMSO.


title: VMSR Compugen Human Oligo by OligoID_29k array

city: Nashville

first: Braden

last: Boone

state: TN

address: 465 21st Ave South

department: Vanderbilt Microarray Shared Resource

institute: Vanderbilt University

manufacture_protocol: Microarrays containing all oligonucleotides from the Compugen Human Release 2.0 OligoLibrary were resuspended in 150mMol phosphate buffer and arrayed according to the manufacturers recommendations. Microarrays were produced by Microarrays Incorporated (www.microarrays.com) utilizing custom, high precision robotics and amine-coated glass slides from Genexprex. The microarrays were then crosslinked using 80mjoules of ultraviolet energy (Stratagene Stratalinker, LaJolla, CA). Following crosslinking, the arrays were baked for two hours at 70C in a standard oven and stored under low humidity conditions until use.


title: SuperArray Mouse Autoimmune and Inflammatory response


title: Illumina Genome Analyzer II (Bacteroides thetaiotaomicron)

status: Public on Aug 18 2009

last: GEO

organism: Bacteroides thetaiotaomicron

technology: other


title: JCVI PFGRC Salmonella typhimurium 13K v7 array designed primarily based on strain Ty2

status: Public on Aug 13 2009

first: PFGRC

last: JCVI

organism: Salmonella enterica subsp. enterica serovar Typhi str. Ty2

description: This set includes 5936 oligonucleotides, has 13872 spots distributed in 48 blocks.

manufacture_protocol: 7QST, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Salmonella typhimurium 13K v7 array designed primarily based on strain LT2(SGSC1412)

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


title: Illumina Genome Analyzer (Bacteroides thetaiotaomicron)


title: JCVI PFGRC Salmonella typhimurium 31K v4 [full array layout]

city: Boston

first: Richelle

middle: C.

last: Charles

state: MA

address: 55 Fruit Street, Gray 504

department: Infectious Diseases

institute: Massachussetts General Hospital

organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Salmonella enterica subsp. enterica serovar Typhi str. CT18

manufacture_protocol: 4QST, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Dstl Mouse 1.5K SA52

city: Salisbury

first: Jonathan

last: David

address: Porton Down

department: Biomedical Sciences

institute: Dstl

manufacture_protocol: 50mer olgionucleotides selected from commercial arrays spotted onto glass slides


title: Custom made Escherichia coli K12 MG1655 tiling array

city: Oslo

first: Gard

last: Thomassen

state: Oslo

address: Rikshospitalet University Hospital

department: Molecular microbiology

country: Norway

institute: Centre for Molecular Biology and Neuroscience (CMBN) and Institute of Medical Microbiology

organism: Escherichia coli str. K-12 substr. MG1655

description:
This is a custom made tiling array, with probes for almost all genes and all intergenic regions. Intergenic regions have much denser coverage than coding regions, and a uniform probe affinity has been strived after. The array design is described in Thomassen et al. (submitted)
The genome used is:NC_000913

middle: O

first: Jessica

last: Lindvall

first: Karin

last: Lagesen

first: Torbjørn

last: Rognes

manufacture_protocol: Photolitography


title: JCVI PFGRC Yersinia pseudotuberculosis 18K v5 array designed primarily based on strain PB1/+

organism: Yersinia pseudotuberculosis PB1/+

description: This set includes 7359 oligonucleotides, has 18240 spots distributed in 48 blocks.

manufacture_protocol: 5QYP, with arrayer AUSHON, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Yersinia pestis 18K v5 array designed primarily based on strain KIM

organism: Yersinia pestis KIM10+


title: JCVI PFGRC Yersinia pestis 18K v5 array designed primarily based on strain Antiqua

organism: Yersinia pestis Antiqua


title: JCVI PFGRC Yersinia pestis 18K v5 array designed primarily based on strain CO92

organism: Yersinia pestis CO92


title: Duke-GE/Amersham CodeLink UniSet Mouse 20K I

first: Barry

last: Stripp

address: 106 Research Drive, DUMC Box 103000

department: Medicine


title: SMD Print_1651 Mycobacterium tuberculosis

first: Helena

middle: I

last: Boshoff

address: 12441 Parklawn Drive

department: LIG

institute: NIAID/ NIH

organism: Mycobacterium tuberculosis

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


title: MPI oyster gigas 9K v1.0

city: Plouzane

first: Arnaud

last: Huvet

address: Ifremer centre de Brest BP 70

department: Physiologie Fonctionnelle des Organismes Marins

country: France

institute: IFREMER

organism: Magallana gigas

manufacturer: MPI Molecular Genetics Berlin-Dahlem Germnay

first: Elodie

last: Fleury

first: JeanYves

last: Daniel

first: Richard

last: Reinhardt

first: Patrick

last: Prunet

first: Jeanne

last: Moal

first: Pierre

last: Boudry

first: Pascal

last: Favrel

manufacture_protocol: Microarray slides were printed by the Max Planck Institute (Berlin, Germany) with a GMS417 Arrayer (Genetic Microsystems) on poly-L-lysine-coated slides prepared locally according to a standard protocol. Each slide contained a total of 11,088 features spotted in duplicate to reduce positional bias of the fluorescence readout, and divided into 48 blocks of 22 rows and 21 columns each. Replicate spots were located within the same block (i.e. spotted with the same pin) but were never side-by-side. Printed slides were exposed to UV light for cross-linking and blocked in a succinic anhydride/sodium borate solution. Excess DNA probe material was then washed off in a water bath at 95°C. Blocked slides were dehydrated in a bath of 100% ethanol, centrifuged, and stored in a dark, cool, dry location until use.


title: chromosome 9 INK locus tiling array

city: Bethesda

first: Thomas

middle: A

last: Paul

address: 37 Convent Dr.

department: Laboratory of Cellular Oncology

institute: NCI-CCR

organism: Homo sapiens

manufacture_protocol: The oligonucleotide microarray were 4x44k or 8x15k custom designs using probes from the Agilent HD ChIP library and user defined probes.Probes are on average 60 nt in length


title: Murine custom chip-on-chip 244k oligo array (AMADID: 018915)

status: Public on Aug 10 2009

city: Regensburg

first: Elmar

last: Schilling

address: Franz-Josef-Strauss Allee 11

institute: University Hospital Regensburg

organism: Mus musculus

first: Michael

last: Rehli

manufacture_protocol: Agilent SurePrint technology, see manufacturer's website at http://www.agilent.com/


title: JCVI PFGRC Salmonella typhimurium 13K v7 array designed primarily based on strain 14028

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

institute: J. Craig Venter Institute

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S


title: JCVI PFGRC Yersinia pestis 19K v4 array designed primarily based on strain KIM

status: Public on Aug 04 2009

organism: Yersinia pestis

description: This set includes 7359 oligonucleotides, has 19200 spots distributed in 48 blocks.

manufacture_protocol: 4QYP, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: JCVI PFGRC Yersinia pestis 19K v4 array designed primarily based on strain 91001


title: Whitefly (Bemisia tabaci) unique EST array Bemisia tabaci (Gennadius)

city: Bet Dagan

first: Murad

last: Ghanim

address: Derech Hamakabim

department: Entomology

institute: Volcani Center

organism: Bemisia tabaci

description: Bemisia tabaci (Gennadius)

first: Assaf

last: Mahadav

first: Henryk

last: Czosnek

first: Svetlana

last: Kontsedalov

manufacture_protocol: standard PCR of ESTs from a cDNA library, amplified, cleaned and spotted on glass slides


title: JCVI PFGRC Salmonella typhimurium 13K v7 array designed primarily based on strain CT18

organism: Salmonella enterica subsp. enterica serovar Typhi str. CT18


title: NRC-BRI_16S rRNA PsychroChip_528

status: Public on Aug 06 2009

city: Montreal

first: Etienne

last: Yergeau

state: Qc

address: 6100 Royalmount Ave

department: Environmental Microbiology

institute: NRC-BRI

organism:
Bacteria
Archaea

first: Charles

middle: W

last: Greer

first: Roland

last: Brousseau

first: Luke

last: Masson

first: Melanie

last: Arbour

first: John

last: Lawrence

manufacture_protocol: The 16S rRNA gene probe design for the microarray was as follows: 1) database searches in Greengenes (http://greengenes.lbl.gov) for 16S rRNA gene sequences with keywords "Arctic," "Antarctic," "Polar," "Cold," "Psychro" (2891 sequences retrieved, performed on April 15th, 2008); 2) clustering of the database sequences together with 16S rRNA gene sequences from strains isolated in our lab in previous studies of polar environments using Blastclust (NCBI, Bethesda, MD); 3) design of five 25-mer probes for each of the 99%-similarity clusters having 3 or more representatives using OligoPicker (32); 4) elimination of probes having a ΔG >-3 kJ; 5) BLAST comparison of the central 17 nucleotides of each probe against all the original sequences; 6) selection, for each cluster, of the probe that showed less significant hits to sequences outside the cluster and most significant hits within the cluster. Oligonucleotides (synthesized by IDT, Coralville) were printed in triplicate on amino-silane coated glass slides (Corning, Acton, MA) using a VersArray Chip Writer Pro printer (Bio-Rad, Hercules, CA). Including control spots, the microarray consisted of 528 spots. Each slide contained three identical sub-arrays.


title: febit Homo Sapiens miRBase 13.0

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

description: Based on Sanger miRBase Release 13.0.

manufacture_protocol:
MicroRNAs (miRNAs) are endogenous, non-coding RNAs that play a fundamental role in gene regulation and have critical functions across various biological processes. Pairing to mRNAs of protein-coding genes, they direct posttranscriptional repression by altering the stability or translational efficiency of their target mRNAs.
Recent studies indicate that miRNAs are involved in the development of human malignancies, suggesting that they represent a promising new class of cancer biomarkers. Identifying miRNAs involved in specific cancers could provide useful diagnostic information, allow disease classification and reveal potential treatment targets.
MPEA: On-Chip Labeling for Highest Sensitivity
Enzymatic labeling assay requires minimal sample amount
In addition to the standard hybridization of pre-labeled RNA, the microfluidic Geniom Biochip enables a highly sensitive enzymatic labeling protocol.
MPEA benefits
* Higher sensitivity and specificity
* miRNA hybridization without preceding treatment like enrichment, PCR -based amplification or labeling eliminates potential bias
* High discriminatory power
* Minimal amount of sample RNA needed (more than or equal 20 ng total RNA)
* Easy to use protocol for Geniom RT Analyzer

The unique Microfluidic Primer Extension Assay (MPEA) uses unlabeled miRNAs for hybridization. In a second step, Klenow fragment of DNA polymerase I is added directly into the channels of the microfluidic chip, where the specific elongation of the bound miRNAs takes place.
The method combines the specificity of a hybridization assay with the discriminatory power of an enzymatic extension and reduces the required sample amount to a minimum.
Details provided at www.febit.com


title: JCVI PFGRC Yersinia pestis 18K v5 array designed primarily based on strain Pestoides_F

department: PFGRC

organism: Yersinia pestis Pestoides F


title: JCVI PFGRC Yersinia pestis 18K v5 array designed primarily based on strain Nepal516

organism: Yersinia pestis Nepal516


title: Bifidobacterium breve UCC2003 Agilent 2x11K format

status: Public on Aug 11 2009

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

institute: Utrecht University

organism: Bifidobacterium breve UCC2003

middle: L

first: Douwe

last: van Sinderen

manufacture_protocol: Chemical In-situ oligonucleotide synthesis.


title: Agilent Aedes aegypti 16K transcripts (VectorBase build 1.0)

status: Public on Aug 03 2009

city: Oxford

first: Steven

last: Sinkins

address: South Parks Rd

department: Department of Zoology

institute: University of Oxford

organism: Aedes aegypti

description:
Agilent-019493

There are multiple oligonucleotide sequences for probes from the same transcript. The supplementary file 'GPL8972_oligo_sequences.txt' contains the sequences for all probes on the array with the corresponding ID.

manufacture_protocol: See manufacturer's website at http://www.agilent.com/ .


title: JCVI PFGRC Yersinia pestis 18K v5 array designed primarily based on strain 91001

organism: Yersinia pestis biovar Microtus str. 91001


title: Reference Epigenome, UCSF-UBC Illumina Genome Analyzer II

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

institute: UCSF-UBC

description: Illumina Genome Analyzer II


title: HML/MUSC-Eubalaena_glacialis-8X15K

city: Charleston

first: Marine

last: Genomics

state: SC

address: 331 Ft. Johnson Road

institute: Medical University South Carolina

organism:
Tursiops truncatus
Eubalaena glacialis

description:
An 8X15k oligonucleotide microarray was developed consisting of 2334 E. glacialis probes and 2166 Tursiops truncatus probes.
There are 3 spot replicates/probe on the array, along with Agilent control grid specific for 8X15K arrays.
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.

manufacture_protocol: See manufacturer's website


title: Agilent Custom Mouse 244K Alternative Splicing Oligo Microarray

status: Public on Aug 01 2009

city: Toronto

first: Qun

last: Pan

address: 160 College St.

institute: University of Toronto

description: A microarray platform to profile alternative splicing levels for 8714 cassette-type alternative exons across a diverse spectrum of mouse tissues.

last: Calarco

first: Simone

last: Superin

first: Dave

last: O’Hanlon

first: Ursula

last: Skalska

first: Mathieu

last: Gabut

first: Bushra

last: Raj

first: Laura

last: Clarke

first: Danielle

last: Gelinas

first: Derek

last: van der Kooy

first: Mei

last: Zhen

first: Brian

last: Ciruna

first: Benjamin

last: Blencowe

manufacture_protocol: 60-mer ink-jet Agilent microarray


title: RASTA Rattus norvegicus 0.3 k ver. 1

city: Berlin

first: Oleg

last: Tchernitsa

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite

organism: Rattus norvegicus

first: Anita

last: Geflitter

manufacture_protocol:
The Ras signaling target array was designed and produced as described
(Tchernitsa et al., 2005). Briefly, we selected 121 genes recovered from subtracted cDNA libraries representing sequences differentially expressed in parental and KRAStransformed ROSE 199 cells (Tchernitsa et al., 2004). In addition, we selected genes from subtracted libraries representing sequences differentially expressed in normal 208F
fibroblasts and the HRAS-transformed derivative FE-8 (Zuber et al., 2000). Previously described Ras pathway targets and 13 different genes described as housekeeping 20 genes in many different tissues and cell lines were included to permit normalization of hybridization intensities on microarrays. The total number of gene probes is 324 on the
array.
Unmodified 70-mer DNA oligonucleotides were chosen as probe sets for the array. The oligonucleotide design was performed with software available on the web (http://oligo.lnatools.com/expression/) using the following parameters: option for LNA frequency=0, melting temperature between 74캜 and 76캜, GC content between 45-55%, absence of strong secondary structures and proximity to 3’ end of coding sequence. Oligonucleotides were synthesized at Illumina, Inc (San-Diego, USA) at the 50 nmol scale. Super Frost glass slides (Menzel GmbH, Braunschweig, Germany) were soaked in 200 ml of washing solution containing 80 ml of 5M NaOH and 120 ml of 95%
ethanol and agitated by a magnet stirrer for 5-6 h. Slides were washed 10-times with 200ml of ddH2O, incubated for 30 min on a shaker with poly-L-lysine solution (20ml of poly-L-lysine, Sigma-Aldrich, St. Louis, USA, mixed with 160 ml of ddH2O and filtered) and again washed 10-times with 200 ml of ddH2O. Afterwards, the remaining washing
solution was removed by centrifugation of slides in a microarray centrifuge (Telechem, Sunnyvale, USA) and the slides were dried in an incubator for 2 h at 45oC. The oligonucleotides were adjusted to a concentration of 20킡 in 3xSSC/0.01% SDS buffer and spotted using a MicroGrid compact microarrayer (Genomic Solutions, Ann Arbor, USA) equipped with MicroSpot 2500 quill pins. The pins have a diameter of
100 탆 and typically deliver spot diameters of 180 탆. Microarrays were printed at a relative humidity of 50 - 60%. Pins were rinsed twice in distilled water between each probe aspiration/dispense cycle. Each of the 325 oligonucleotides was spotted four times at a different location on the slides. Thus, the array contains 1,300 features. After printing, microarrays were re-hydrated twice by placing them over boiling water for five sec each. Then each array was snap-dried on a hot plate (90캜) for 10 sec (DNA side 21facing upwards). Slides were cross-linked with an intensity of 60mJ (UVC-500 crosslinker, Hoefer, Inc, USA). Afterwards, slides were incubated in blocking solution (3.2 g of succinic anhydride mixed with 200ml of N-methyl-pyrolidone and 4.45 ml of 1M sodium borate) for 20 min on an orbital shaker, rinsed three-times with ddH2O and dried by centrifugation.


title: OvHV-2 Agilent custom 10K microarray

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

organism:
Bos taurus
Ovine gammaherpesvirus 2

manufacture_protocol: See manufacturer's web site.


title: NRC-BRI_Hydrocarbon degrading genes v6.1_141

first: Etienne

last: Yergeau

first: Charles

last: Greer

first: David

last: Juck

first: Sylvie

last: Sanschagrin

first: Diane

last: Labbé

first: John

last: Lawrence

first: Lyle

last: Whyte

manufacture_protocol: All PCR amplified target fragments were produced using the rTaq DNA polymerase (Amersham Bioscience, Baie d’Urfé, QC, Canada) with the appropriate DNA template (either genomic DNA or plasmid) and primers.  The amplification program was as follows: hot start at 96°C for 5 min; 30 PCR cycles consisting of denaturation at 94°C for 1 min, annealing at the appropriate temperature (variable for each PCR amplified fragment) for 1 min and elongation at 72°C for 1 min; final elongation at 72°C for 3 min.  Each PCR amplified fragment was purified using the Qiaquick PCR Purification kit (Qiagen Inc, Mississauga, ON, Canada) according to the manufacturer’s protocol with the exception that the DNA fragment was eluted from the column with H2O freshly brought to pH 8.0 with 2N NaOH. Each fragment was dried and re-dissolved to a final concentration of 200 ng/µL in 50% DMSO (Sigma, St. Louis, Mo) for printing.  In order to monitor for printing problems, a 500 base pair fragment amplified from lambda DNA was added as a printing control (PC) to each target fragment at a concentration of 20 ng/µL.  The targets were arrayed with four Stealth Micro Spotting SMP3 pins (TeleChem Intenational Inc., Sunnyvale, CA) at a spacing of 250 µm on GAPS II microarray slides (Corning Inc, Acton, MA) using a VersArray ChipWriter Pro system (Bio-Rad, Hercules, CA).  The DNA target fragments were immobilized by UV cross-linking at 300 mJ in a UV Stratalinker 1800 (Stratagene,  La Jolla, CA) and then baked overnight at 80°C.


title: JCVI PFGRC Yersinia pestis 19K v4 array designed primarily based on strain Pestoides_F

first: PFGRC

last: JCVI


title: Agilent whole-genome Cryptococcus gattii tiling array

status: Public on Aug 07 2009

city: Birmingham

first: Robin

last: May

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

organism: Cryptococcus bacillisporus

description:
Agilent-017863
The array was designed to two C. gattii genomes, WM276 and R265, before assembly was fully complete.  Therefore, probes do not have Genbank accession references.  During array construction, probes were placed approximately 400bp apart along all of the available contigs, without regard to open reading frames or other features.  Please note that, although both genomes were relatively complete at the point of array design, subsequent changes may have been introduced during assembly/annotation which renders specific probes on the array invalid.  For more information on the array and probe design, please contact Oxford Gene Technology (OGT) or Robin May (r.c.may@bham.ac.uk).

manufacture_protocol: Agilent custom synthesis


title: NIAID Mmca -- Mouse 38K - mAdb

status: Public on Mar 12 2009

first: Timothy

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

manufacturer: NIAID, Genomic Technologies Section (NIH)

first: Guojian

last: Jiang

manufacture_protocol: Microarrays were printed with an Omnigrid robotic arrayer by Genomic Solutions ( http://www.genomicsolutions.com ) that is fitted with a printhead and 32 SMP3 print tips from Telechem ( http://www.arrayit.com ). Oligonuclotide probes (70-mer) were purchased from Operon, mouse AROS version 4. An additional 384 well plate containing control oligos was also included. Oligonucleotide probes in 384-well polypropylene plates (Genetix, 384 micro array) were dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normalized 25 micromolar concentration. Spot density was 240 microns (center-to-center). The microarrays were printed on Epoxy Slides from Corning (Catalog # 40042) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: JCVI PFGRC Yersinia pestis 19K v4 array designed primarily based on strain CO92


title: JCVI PFGRC Yersinia pestis 19K v4 array designed primarily based on strain Antiqua


title: JCVI PFGRC Yersinia pestis 19K v4 array designed primarily based on strain Nepal516


title: TMHRI_GAS

status: Public on Dec 04 2007

city: Reno

first: Paul

last: Sumby

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

organism: Streptococcus pyogenes

relation:
Affiliated with: GPL9080
Affiliated with: GPL9953

manufacture_protocol: Standard Affymetrix procedures.


title: Bhabha Atomic Research Centre Deinococcus radiodurans 3166 array [condensed version]

status: Public on Jul 30 2009

city: Mumbai

first: Hari

middle: S

last: Misra

state: MS

address: 2-46 S, Moldular Laboratories, Central Avenue, Bhabha Atomic Research Centre

department: Molecular Biology Division

country: India

institute: Bhabha Atomic Research Centre

organism: Deinococcus radiodurans

description: Oligonucleotides microarray corresponding to all the ORFs of Deinococcus  radiodurans (NC_001263, NC_001264, NC_000958, NC_000959)

manufacturer: The Bioinformatics and Molecular Regulation Laboratory, Zhejiang University

first: Y

last: Rajpurohit

first: L

last: Wang

last: Yin

last: Hua

manufacture_protocol: The oligonucleotides designed to represent the respective predicted ORFs of Deinococcus radiodurans ((NC_001263, NC_001264, NC_000958, NC_000959) are synthesized and purified by hydrophobic column on HPLC. The oligonucleotides are deposited on to poly-L-Lysine slide in duplicate. There are 32 blocks on the array. In each blocks there were 18 columns and 17 rows. Details can also be found in (Huan Chen, Guangzhi Xu, Ye Zhao, Bing Tian, Huiming Lu, Xiaoming Yu, Songnian Hu, Yuejin Hua*, A Novel OxyR Sensor and Regulator of Hydrogen Peroxide Stress with One Cysteine Residue in Deinococcus radiodurans, PLoS One, 2008, 3 (2): e1602.)


title: Eppendorf DualChip Mouse inflammation

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

organism: Mus musculus

description:
No. of genes: 233 (including 10 housekeeping genes)
No. of housekeeping genes: 10
No. of spots per gene: 3
Average spot size: 200 µm
Controls: housekeeping genes, positive/negative hybridization controls, positive/negative detection controls and internal controls for normalization

first: Benjamin

last: Otto

first: Kristin

last: Reeck

manufacture_protocol:
Each slide features two identical microarrays, printed side-by-side.
Unique Xmer® probe technology features 200-400 nucleotides long sense DNA.
Each Xmer® is in silico designed and tested in real hybridization experiments.


title: Codelink_Rat_ADME_Bioarray

city: Davis

first: eskouhie

middle: Hagop

last: Tchaparian

address: UC Davis, One Shields Ave

department: Nutrition

institute: University of Ca, Davis

manufacturer: Amersham Biosciences (Now, Applied Microarrays)


title: NimbleGene-P.tetrauerlia-variousSETs-50mer-v1

city: Villerubanne

first: Jean-François

last: Gout

address: 43 Bld du 11 Novembre 1918

institute: Laboratoire Biométrie et Biologie Evolutive

organism: Paramecium tetraurelia

description:
The grid of features is 768x1024 (X, Y). It consists of 11 different SETs as described below.
SET01 : Probes that match annotated transcripts. Each transcript has 6 probes (3 on the forward strand and 3 on the reverse strand).
SET02 : Probes for complete tilling of 4 scaffolds : SCAFFOLD_106, SCAFFOLD_142, SCAFFOLD_164, SCAFFOLD_96. The probes cover both strands of the 4 scaffolds with a 25 nucleotides overlap.
SET03 : Probes designed specifically to distinguish spliced and unspliced transcripts from the 4 scaffolds described in SET02. For each annotated intron, one probe covers the genomic sequence, centered on the middle of the intron (since introns in P. tetraurelia are between 20 and 30 nt length these probes contain the full sequence of the intron and a few bases from the surronding exons) while an other probe covers the spliced version of the transcript, centered on the exon-exon junction site.
SET04 : Probes that match 219 annotated tRNAs. Each tRNAs has 4 probes (2 on the forward and 2 on the reverse strand).
SET05 : Probes that match 3 non-codgin RNAs of particular interrest : AB059619, MS2B and PTU45433. Each ncRNA is fully tilled by the probes on both strands.
SET06 : Probes that match the rDNA.
SET07 : Probes designed specifically to study retention and expression of known IESs in paramecium (see Duret & al. Genome Res. 2008; 18(4):585-96 for more informations about IESs).
SET08 : Probes that match 74 known transposons. Each transposons is fully coverd by tilling on both strands.
SET09 : Tilling of both strands for 51Gmic gene.
SET10 : Probes that match the mitochondrial genome (both strands)
SET11 : Probes designed to distinguish spliced and unspliced transcripts from 6137 annotated genes confirmed by EST alignment. The protocol is the same than described for SET03.
RANDOM : random probes.

first: Linda

last: Sperling

last: Manak

manufacture_protocol: In situ oligonucleotide synthesis as described in www.nimblegen.com


title: Glyco-gene Mus musculus 1.2K Chip GLYCOv3

status: Public on Aug 05 2009

city: Clemson

first: Sarah

last: Harcum

address: 105 Collings Street

department: Bioengineering

institute: Clemson University

description: A custom-designed Glyco-gene Chip array that contains probe sets to monitor the expression of approximately 2000 human and mouse transcripts relevant to the Consortium for Functional Glycomics has been developed using Affymetrix technology. The array is updated periodically, incorporating the latest glycobiology annotation and up-to-date microarray technology.

manufacture_protocol: Affymetrix custom array standard protocol.  Please see http://www.affymetrix.com for more information.


title: Lund Strategic Center Mouse Illumina Expression Chip V6.1.1

city: Lund

first: Stefan

last: Jovinge

address: Klinikgatan 26

institute: Lund Strategic Center for Stem Cell Biology and Cell Therapy

technology: oligonucleotide beads

manufacture_protocol: see Illumina website


title: LC_miRRat 9.0_UK_061204-MRA-1003

status: Public on Feb 21 2009

city: Houston

first: Christoph

last: Eicken

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism:
Rattus norvegicus
synthetic construct

description:
Rat miRNA microarray based on miRBase version 9.0, additional custom sequences

This platform contains 9 probes for each of 238 miRNAs.

This is the Feature Number version (miRNA ID version is GPL9082).

manufacture_protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes are made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: JCVI PFGRC Yersinia pestis 19K v4 array designed primarily based on strain PB1/+

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

institute: J. Craig Venter Institute

organism: Yersinia pestis

manufacture_protocol: 4QYP, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Bacillus subtilis bso8 spotted oligo platform

status: Public on Jul 22 2009

city: Cambridge

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

address: 31 Ames Street, 68-530

department: Biology

institute: MIT

organism: Bacillus subtilis

manufacture_protocol:
As previously described in:
Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis.
Britton RA, Eichenberger P, Gonzalez-Pastor JE, Fawcett P, Monson R, Losick R, Grossman AD.
J Bacteriol. 2002 Sep;184(17):4881-90.
PMID: 12169614


title: Acropora millepora_18KcDNA_v1.0

city: Lafayette

first: Mauricio

last: Rodriguez-Lanetty

state: LA

address: 300 E St Mary blvd

institute: University of Louisiana at Lafayette

organism: Acropora millepora

manufacturer: Adelaide Microarray Facility, University of Adelaide, Adelaide, Australia

first: David

last: Miller

first: Eldon

last: Ball

manufacture_protocol: Microarrays were generated by spotting amplified cDNA onto GAPSII slides using a Biorad Chipwriter Pro, and then fixed by a combination of UV light exposure (150 mJ) followed by baking at 80°C for 3 hours.


title: SMD Print_853

status: Public on Aug 12 2009

city: Stanford

first: Stephen

last: Popper

department: Division of Infectious Diseases, Dept. of Medicine

institute: Stanford University

organism: Homo sapiens

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