title: Illumina genome Analyzer II (Rattus norvegicus)

status: Public on Feb 28 2011

last: GEO

country: USA

organism: Rattus norvegicus

technology: high-throughput sequencing

distribution: virtual


title: HG18 RefSeq Promoter array (NimbleGen)

status: Public on Feb 22 2011

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

organism: Homo sapiens

technology: in situ oligonucleotide

description:
HG18
The array tiles 19000 RefSeq genes from -2200 to +500bp relative to the TSS, with a mean probe spacing of 100bp
native array description file: 2006-07-18_HG18_RefSeq_promoter.ndf
native array description file: 2006-07-18_HG18_RefSeq_promoter.pos
Platform Columns file: DesignNotes.txt

distribution: custom-commercial

manufacture_protocol: see the NimbleGen website


title: WU Streptococcus pyogenes 2K

status: Public on Feb 27 2011

city: St. Louis

first: Colin

middle: Christopher

last: Kietzman

state: MO

address: 660 S. Euclid Ave

department: Molecular Microbiology and Microbial Pathogenesis

institute: Washington University in St. Louis

organism: Streptococcus pyogenes

technology: spotted oligonucleotide

distribution: non-commercial

manufacturer: The microarray core facility in Washington University

manufacture_protocol: An antisense oligonucleotide array based on the published genome of S. pyogenes SF370 (Ferretti et al., 2001) was made at the Microarray Core Facility in the Genome-Sequencing Center at Washington University (GSC, http://genome.wustl.edu/groups/microarray/main_page/). A single 60–80 mer oligonucleotide was designed to hybridize to the putative transcripts from each annotated open reading frame using ‘TOP’ software that was created at the GSC. To reduce complexity, probes for rRNA, tRNA genes were not included. The oligonucleotides were synthesized by Illumina and were deposited onto a MWG epoxy microarray slide by custom Linear Servo Arrayer so that each slide included triplicates spots for each probe. Quality of the array was validated by hybridization with a Cyanine 5-labelled random nonamer (Hybchecker, Sigma) to ensure that the frequency of missed spots were less than 1.0% and by self-self hybridization using a single RNA sample to generate Cyanine 3- and Cyanine 5-labelled cDNAs, which were then co-hybridized on the slide. Slide batches were rejected if the average ratio of hybridization differed significantly from 1.0.


title: Agilent-019644 hg18-105k-v1.1_Rev_B

city: Spokane

first: Blake

middle: C.

last: Ballif

state: WA

address: 2820 North Astor Street

department: Research & Development

institute: Signature Genomic Laboratories

manufacture_protocol: Designed with one 50-60 bp probe every 10 kb in targeted regions (microdeletion/microduplication syndromes, pericentromeric regions, subtelomeres, and genes in important developmental pathways) for an average of 50 probes per clinical locus, and an average probe spacing of one probe every 35 kb throughout the rest of the genome.


title: CRG Human Splicing Array Custom 44K G2514F AMADID19952

status: Public on Mar 07 2011

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

description:
It was designed an alternative splicing-sensitive microarrays which focus on the analysis of two groups of genes: splicing regulatory factors and cancer-related genes, with the goal of establishing correlations between changes in splicing factor expression and pre mRNA alternative splicing under different biological situations. Databases of human SReg and other proteins involved in RNA metabolism (420 genes) and of genes implicated in tumor onset and progression (500 genes) were generated. Splicing events (about 1000 for each category) were identified computationally by alignment of genomic sequences to RefSeq, mRNA and ESTs. Probes complementary to alternative and constitutive exons as well as to splice junctions were selected and produced using AGILENT ink-jet technology.
Barcodes: from 251995210001 to 251995210099.

first: Minana

last: Belen

first: Valcarcel

last: Juan

first: Ben-Dov

last: Claudia

first: Lozano

last: Juanjo

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


title: LT Listeria monocytogenes F2365 4 × 72 k

status: Public on Feb 24 2011

city: Summit Argo

first: Zengxin

last: LI

address: 6502 S Archer Rd

institute: NCFST

organism: Listeria monocytogenes serotype 4b str. F2365

description: a gene expression microarray was designed to target 2821 protein-coding genes (including putative protein-coding genes). Each of the 2821 genes was targeted by 12 unique 60-mer oligonucleotide probes. Each unique probe was printed in duplicates on the microarray. The microarrays were in a format of 4 × 72 k (4 microarrays per slide, with each microarray containing 72,000 probes) and provided by Roche NimbleGen (Roche NimbleGen, WI).

manufacture_protocol: NimbleGen standard protocols (prepared and hybridized by NimbleGen)


title: GenoToul/Biopuces Yeast 22x22 (Oligo-Set_Contol-Toulouse-Yeast v1.1.2)

city: LOGROÑO

first: Vanessa

last: Penacho

state: LA RIOJA

address: c/ Madre de Dios, 51

department: Oenology & Viticulture

institute: ICVV/CSIC

organism: Saccharomyces cerevisiae

manufacture_protocol: DNA chips were manufactured at the Biochip platform of Toulouse-Genopole on dendrislides using 70-mer oligonucleotides representing c. 99% of the yeast genome purchased from Operon Inc. (Yeast v1.1.2). 4x8 pins each pin has spotted a block of 22x22 spots. Each well is spotted in duplicate.


title: UCM_Medina_Apalmata_13k_v1

status: Public on Mar 22 2011

city: San Francisco

first: Michael

last: DeSalvo

state: CA

department: Department of Anesthesia

institute: UC San Francisco

organism: Acropora palmata

technology: spotted DNA/cDNA

manufacture_protocol: This cDNA microarray platform is composed of PCR-amplified cDNAs generated from a Sanger EST library of the coral Acropora palmata. PCR clones were spotted on poly-lysine-coated slides using the DeRisi arrayer in the Genomics Core Facility at UC Merced.


title: [Mm35b_M12R_v01] Affymetrix Mouse Tiling 1.1R Array Set

status: Public on Feb 18 2011

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Mus musculus

distribution: commercial

manufacture_protocol: See manufacturer's web site


title: [Mm35b_M08R_v01] Affymetrix Mouse Tiling 1.1R Array Set


title: [Mm35b_M10R_v01] Affymetrix Mouse Tiling 1.1R Array Set


title: [Mm35b_M13R_v01] Affymetrix Mouse Tiling 1.1R Array Set


title: Nimblegen-hg18-135k-v2.0

description: hg18, NCBI 36

manufacture_protocol: Designed with one 60 bp probe every 10 kb in targeted regions and one probe every 35 kb in the genomic backbone. This array targets over 200 known genetic disorders and over 675 functionally significant genes in addition to all subtelomeric and pericentromeric regions of the genome.


title: [Mm35b_M09R_v01] Affymetrix Mouse Tiling 1.1R Array Set


title: UCSF Gladstone Mouse/Human miRNA 3.7k array

status: Public on Feb 23 2011

city: San FRANCISCO

first: David

last: Steiner

address: 513 Parnassus Ave UCSF Box 0414 HSE 201

department: Microbiology and Immunology

institute: UCSF

organism:
Homo sapiens
Mus musculus

description:
UCSF Gladstone-mouse and human mIRNA-3756 features-GenePix ArrayList V1.0
LNA array spotted oligo

manufacture_protocol: see Gladstone genomics core website


title: [Mm35b_M11R_v01] Affymetrix Mouse Tiling 1.1R Array Set


title: SignatureChip v3.0

manufacture_protocol: A total of 975 BAC clones were selected in contigs of three partially-overlapping clones to target clinically significant regions of interest across the genome. FISH analysis was used to confirm the chromosomal location of each clone and to eliminate clones which showed cross-hybridization to multiple locations. BAC insert DNA was isolated and 5ug of each insert was sonicated to a final size of 50 bp-20 kb and combined with 50% DMSO with nitrocellulose prior to printing. Each insert was printed in quadruplicate onto low-autofluorescence slides using an Omnigrid microarrayer. Printed slides were baked overnight at 80 degrees C, washed with water and 95% ethanol, and stored in a desiccator prior to use.


title: [Mm35b_M14R_v01] Affymetrix Mouse Tiling 1.1R Array Set


title: LBEG_Peach_1.5k_v1.0

city: Santiago

first: Leonardo

middle: Ignacio

last: Pavez

state: Santiago

address: Av Manuel Montt #948

country: Chile

institute: Universidad de Las Américas

organism: Prunus persica

manufacturer: Bioinformatics and gene expression laboratory

first: Christian

last: Hödar

first: Felipe

last: Olivares

first: Mauricio

last: González

first: Verónica

last: Cambiazo

manufacture_protocol: The source of the spotted cDNA was a cv. Loring and cv. O´henry ripe peach fruit (Prunus persica L. Batsch) cDNA library. A total of 1463 cDNAs were selected from this library based on the functional properties assigned to their encoded proteins using an in-house gene-ranking method.  Selected EST clones were picked from freezer stocks and grown overnight in 96 well plates in 200 µl LB plus 50 mµ/mL of ampicillin. Overnight cultures were used directly as templates in PCR reactions containing 10X buffer, 0.25 mM each of dATP, dCTP, dGTP, and dTTP, 2.5 units of Taq DNA polymerase and 0.2 µM of T3 and T7 forward/reverse primers. Aliquots (5 µl) of each reaction were loaded onto a 1.0% (w/v) agarose gel to determine product quality. 20 µL of PCR products were arrayed in 96-well plates and mixed with an equal volume of 50% of dimethyl sulfoxide. PCR products (70 ng) were single spotted onto nylon membranes (10 x 7 cm) Immobilon NY+ (Millipore) using an 8 pins print-head (Arraylt model SSP015) and the arraying robot Versarray Chip Writer Compact (BioRad). The membranes were treated and the cDNA was fixed to the membrane by UV-crosslinking using a Ultraviolet Crosslinker CL-1000 (UVP). In addition to the selected ESTs, the following controls were spotted onto membranes: (1) a fragment of the vector pBluescript II obtained by amplification with the T3 and T7 universal primers; (2) several aliquots of DMSO 50%; (3) cDNA from a B. subtilis gene dap (obtained from ATCC; number 87486) used as spike mRNA to normalize between membranes.


title: SignatureChip v4.0

manufacture_protocol: A total of 1900 BAC clones were selected in contigs of three partially-overlapping clones to target clinically significant regions of interest across the genome. FISH analysis was used to confirm the chromosomal location of each clone and to eliminate clones which showed cross-hybridization to multiple locations. BAC insert DNA was isolated and 5ug of each insert was sonicated to a final size of 50 bp-20 kb and combined with 50% DMSO with nitrocellulose prior to printing. Each insert was printed in quadruplicate onto low-autofluorescence slides using an Omnigrid microarrayer. Printed slides were baked overnight at 80 degrees C, washed with water and 95% ethanol, and stored in a desiccator prior to use.


title: cGRASP Salmonid array, 32K cDNA, version 2, 02/08

status: Public on Feb 26 2011

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

organism:
Oncorhynchus mykiss
Salmo salar


title: UCM_Medina_Mfaveolata_11k_v1

organism: Orbicella faveolata

manufacture_protocol: This cDNA microarray platform is composed of PCR-amplified cDNAs generated from a Sanger EST library of the coral Montastraea faveolata. PCR clones were spotted on poly-lysine coated slides using the DeRisi arrayer in the Genomics Core Facility at UC Merced.


title: Bacteroides fragilis YCH46 gene expression 4x72K array [2007-08-21_GFC235_Bfla_60mer_4plex]

city: tokushima

first: Haruyuki

last: Nakayama-Imaohji

address: 3-18-15 kuramoto-cho

country: Japan

institute: Tokushima University

organism: Bacteroides fragilis YCH46

description:
Array is included 4,527 target genes on the glass slide by fixing at least 8 unique probes consisting of 60-mer synthetic oligonucleotides for each gene. Each probe is replicated 2 times.
DESIGN_NAME: 2007-08-21_GFC235_Bfla_60mer_4plex
DESIGN_ID: 6296

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


title: MWG E. coli K12 Array

status: Public on Oct 07 2003

city: High Point

last: MWG Biotech

state: NC

address: 4170 Mendenhall Oaks Parkway, Suite 160

institute: MWG Biotech

organism: Escherichia coli K-12

description: 4239 E. coli K12 specific oligonucleotide probes represent the complete Escherichia coli (K12)genome.

manufacture_protocol: see manufacturer's web site


title: Medsaic Human DotScan antibody microarray v3

status: Public on Feb 20 2013

city: Boston

first: Joshua

middle: WK

last: Ho

state: MA

address: 41 Avenue Louis Pasteur

department: Department of Medicine

institute: Brigham and Women's Hospital

technology: spotted peptide or protein

manufacture_protocol: The use of CD antibody (DotScan) microarrays (Medsaic, veleigh, NSW, Australia) has been previously described. Briefly, they consist of grid pattern of antibody spots, each approximately 450 mm in diameter, robotically arrayed on a NC patch bound to a glass slide (FAST slides; supplied by Schleicher and Schuell, Keene, NH). The ability of an antibody spot to bind leukocytes depends on the number and availability of its corresponding antigens. Eighty-two mouse antihuman mAb spots were printed in duplicate on the slide, resulting in identical left and right panels of antibodies. Each spot contains a different CD antibody (the remaining spaces were reserved for testing new antibodies). Below the 82 spots is a smaller panel of monoclonal and polyclonal antimouse antibodies which serve as negative controls (not shown). Nonspecific binding to antibody spots was minimized by blocking slides with 5% w/v skim milk (Diploma; Bonlac Foods, Melbourne, Vic., Australia) in PBS overnight at 47C. After blocking, slides were washed twice in water, air-dried, and stored at 47C with desiccant. Processing of the microarrays and identification of spots has been described elsewhere.


title: SignatureChip WG v1.0.1

first: Blake

last: Ballif

manufacture_protocol: A total of 4697 BAC clones were selected in contigs of three partially-overlapping clones to target clinically significant regions of interest across the genome. FISH analysis was used to confirm the chromosomal location of each clone and to eliminate clones which showed cross-hybridization to multiple locations. BAC insert DNA was isolated and 5ug of each insert was sonicated to a final size of 50 bp-20 kb and combined with 50% DMSO with nitrocellulose prior to printing. Each insert was printed in quadruplicate onto low-autofluorescence slides using an Omnigrid microarrayer. Printed slides were baked overnight at 80 degrees C, washed with water and 95% ethanol, and stored in a desiccator prior to use.


title: [Mm35b_M07R_v01] Affymetrix Mouse Tiling 1.1R Array Set


title: Invitrogen NCode Mammalian miRNA Microarray 4K Probe Set Version 1.0  (Cat. # MIRMPS-01)

city: La Jolla

first: Nick

last: Webster

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

manufacture_protocol: see manufacturer's website


title: Arizona Gallus gallus 20.7K Oligo Array v1.5

status: Public on Feb 20 2011

city: Tucson

first: Parker

middle: B

last: Antin

state: AZ

address: 1656 E. Mabel Street

department: Cell Biology and Anatomy

institute: University of Arizona

organism: Gallus gallus

manufacturer: Genomics Research Laboratory, Steele Children's Research Center, University of Arizona

manufacture_protocol: 1. Oligo Design.  The chicken oligos were designed by Carre et al. (2007) using gene predictions from Ensembl, TIGR, full-length cDNAs from the BBSRC UMIST ChickEST database, and chicken bursal EST sequences from Jean-Marie Buerstedde's DT40 database. Sequences from these resources were aligned and 70mer oligos designed against regions common to more than one aligned sequence. Oligos were then designed using OligoArray2.0.  2. Oligo Array Manufacturer.  The chicken oligo set [Gallus gallus (chicken) Roslin/ARK CoRe Array V1.0] was manufactured by Operon Technologies, Inc.. The chicken oligo set (Catalog # 851102) contains 20,460 long oligo probes (300 pmol) arrayed in 54 384-well plates. Four wells in each of the 54 384-well plates contained the Operon Production Tracking Oligo opHsV04NC000001, which is a randomly-generated oligo sequence with a length of 30 bases.  3. Printing.  This 20.7K chicken oligo array contains 20,676 features that include 20,460 70mer oligos and 216 control spots of the Operon Production Tracking Oligo opHsV04NC000001. The oligos (300pmol) were dissolved in 8 microliters of 50% DMSO for printing. The chicken oligo array was printed on Corning® UltraGAPSTM aminosilane coated slides (Cat # 40018) using a Virtek ChipWriter Pro (Model # HCO1-M) robot fitted with 48 TeleChem (SMP2.5) pins. The slides were printed in a HEPA-filtered positive-pressure chamber maintained at 24 degrees C and 48% relative humidity (RH)(± 2 %RH). The printed slides were dried overnight at room temperature (22-25 degrees C with 20-40 %RH). The slides were then stored in a chemical (Drierite) desiccator at room temperature until use.


title: [Mm35b_M06R_v01] Affymetrix Mouse Tiling 1.1R Array Set


title: [Mm35b_M05R_v01] Affymetrix Mouse Tiling 1.1R Array Set


title: [Mm35b_M04R_v01] Affymetrix Mouse Tiling 1.1R Array Set


title: [Mm35b_M03R_v01] Affymetrix Mouse Tiling 1.1R Array Set


title: [Mm35b_M01R_v01] Affymetrix Mouse Tiling 1.1R Array Set


title: JCVI peanut oligonucleotide microarray (6,932 genes)

status: Public on Feb 19 2011

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

organism: Arachis hypogaea

first: Baozhu

last: Guo

first: Natalie

last: Fedorova

first: Xiaoping

last: Chen

first: William

middle: C

last: Nierman

first: Deepak

last: Bhatnagar

first: Jiujiang

last: Yu

manufacture_protocol: At the final stage of the microarray design, the total oligos spotted on the microarray were 6,932, which represent 6,932 expressed peanut genes.  The oligos were synthesized by Sigma-Aldrich (Saint Louis, MO). The oligos were spotted on to Corning ultraGAPs glass slides with 3 replications at different location.  With dye-flip, the total was equivalent 6 replications to accommodate bioinformatics statistic analysis. There are 4 meta columns and 12 meta rows.  Each meta square consists of 24 sub-columns and 24 sub-rows.  This provides a capacity to accommodate 27,648 spots on each glass slide.  The distance between samples is 180 microns. The microarray printing was done on a 48 pen IAS-2 machine.  The oligo DNA was attached to the glass slide using UV Stratalinker.


title: Illumina Genome Analyzer II (Rhodopseudomonas palustris)

status: Public on Feb 16 2011

last: GEO

organism: Rhodopseudomonas palustris


title: FilgenArray miRNA Caenorhabditis elegans V15

city: Sendai

first: Atsushi

last: Higashitani

address: Katahira

department: Graduate School of Life Sciences

institute: Tohoku University

organism: Caenorhabditis elegans

manufacture_protocol: According to the manufacture protocol


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array (CDF: HuGene10stv1_Hs_REFSEQ.cdf)

status: Public on Feb 15 2011

city: Vienna

first: Stefanie

last: Tauber

address: Dr. Bohr-Gasse 9

department: CIBIV

country: Austria

institute: MFPL

organism: Homo sapiens

relation: Alternative to: GPL6244 (Alternative CDF [official])


title: University of Cambridge, Dept of Pathology, Centre for Microarray Resources 1 Mb aCGH platform_3584 unique clones

city: Cambridge

first: Ian

last: Roberts

address: Hills Road

department: Cancer Cell Unit

country: United Kingdom

institute: Hutchison MRC Research Centre

description: This platform is almost identical to GPL7199, however annotation was taken from NCBI build 36, and a few more clones were included.


title: University of Pennsylvania/Nathanson Lab_HomoSapiens_5212 unique BACS_coleman_collaboration

manufacturer: Nathanson Laboratory/School of Medicine/University of Pennsylvania

manufacture_protocol: This BAC array platform consisted of 5217unique BACs spotted in-house on CorningCMT Ultra-Gap slides (Corning, USA) using two replicates printed on each slide. Details of array construction are described elsewhere (Greshock et al., 2004)  Greshock J, Naylor TL, Margolin A, Diskin S, Cleaver SH, Futreal PA, deJong PJ, Zhao S, Liebman M, Weber BL. 2004. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 14(1):179-87.


title: Illumina Genome Analyzer II (Thielavia terrestris)

organism: Thermothielavioides terrestris


title: Illumina Genome Analyzer II (Chaetomium globosum)

organism: Chaetomium globosum


title: [Mm35b_M02R_v01] Affymetrix Mouse Tiling 1.1R Array Set

last: Affymetrix


title: Human SMD Print_1372 (hor)

status: Public on Feb 12 2011

city: Stanford

first: Patrick

middle: O

last: Brown

address: Beckman Center b439

department: Department of biochemistry

institute: Stanford university school of medicine

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: Human SMD Print_1365 (cpbh)


title: NimbleGen Human CGH 2.1M Whole-Genome Tiling Array [080131_HG18_WG_CGH_v2D_HX1]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
Human CGH 2.1M Whole-Genome Tiling v2.0D Array
Annotation in this record based on hg18, NCBI human build 36.
Design name: 080131_HG18_WG_CGH_v2D_HX1
Design id: 6612

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


title: Homo sapiens microRNA profiling platform version 4

status: Public on Feb 17 2011

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description:
Capture oligonucleotides were crosslinked to uniquely-colored Luminex xMap beads, which serve as discriminators of probe identity
This set includes 358 oligonucleotides, designed based on rfam ver.7.0

manufacture_protocol: Luminex xMap beads were coupled with animo-labeled antisense oligonucleotides to microRNAs


title: Illumina Genome Analyzer II (Legionella pneumophila)

status: Public on Feb 11 2011

organism: Legionella pneumophila


title: Human SMD Print_1360 (hok)


title: MCD Agilent custom Mouse 4x44k X-linked genes

city: Tsukuba

first: Rieko

last: Ikeda

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Center

institute: RIKEN

description: This Platform contains X-linked genes (genes mapped on chromosome X) only.

first: Kuniya

last: Abe

manufacture_protocol: in situ oligo, positive strand, 60-mer


title: State Key Lab Homo sapien 2.6K

city: Guangzhou

first: Qingming

last: Zhou

state: Guangdong

address: 651 Dongfeng East Road

country: China

institute: Sun Yat-sen University

manufacturer: State Key Laboratory of Oncology in South China,Sun Yat-sen University

first: Meiyin

last: Zhang

first: Long

last: Huang

first: Rongrong

last: Wei

first: Huiyun

last: Wang

manufacture_protocol:
Probe:Designed by Array Designer 4.25 and synthesized by Invitrogen (Shanghai, China).
Microarray process: The microarray fabrication process in house was described in our previous study (Wang HY, Luo M, et.ct, Genome Res 2005;15:276-283) except for the printing by a SmartArrayTM -136 printer (CapitalBio Inc., Beijing, China).
Spotting protocol: Every probe was printed twice on the glass.
5280 spots were printed in 12 blocks. There were 440 spots (22 X 20) in every block.


title: Illumina human-6 v2.0 expression beadchip (using nuIDs as identifier)

city: Oslo

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

country: Norway

institute: Centre for Molecular Medicine Norway

technology: oligonucleotide beads


title: Applied Biosystems TaqMan MicroRNA Array (v 1.0, Early Access)

city: Rotterdam

first: Monique

last: Den Boer

address: POBox 2060

department: Pediatric Oncology

country: Netherlands

institute: Erasmus MC-Sophia Children's Hospital

technology: RT-PCR


title: Illumina Genome Analyzer Iix (Klebsiella pneumoniae)

status: Public on Feb 09 2011

last: GEO

organism: Klebsiella pneumoniae


title: Erasmus MC-Sophia Children's Hospital Custom TaqMan array


title: A-UMCU-H25k-1.0

city: Utrecht

first: Sander

last: van Hooff

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

institute: UMC Utrecht

manufacturer: Holstege Lab, UMC Utrecht, The Netherlands

first: Dik

last: van Leenen

first: Marian

last: Groot Koerkamp

first: Philip

last: Lijnzaad

first: Linda

last: Bakker

first: Erik

last: Sluiters

last: Kemmeren

first: Frank

last: Holstege

manufacture_protocol:
1. Oligos are resuspended and adjusted to 10µM in 150mM phosphatebuffer, pH8.5 in Genetix 384-wells plates
2. Array production is done using a Biorobotics MicroGridII spotter located in a low dust cleanroom (ISO7/ downflow ISO5) at 18C, at 48% humidity
3. Slide postprocessing is carried out according to CodeLink protocol: Printed slides are kept at 20C, 75% humidity for 24 hours
4. Residual reactive groups are blocked using pre-warmed blocking solution (50 mM ethanolamine, 0.1 M Tris (pH 9) at 50C for 30 min; slides are rinsed thoroughly with milliQ water; slides are washed with 4x SSC, 0.1% SDS (pre-warmed to 50C) for 30 min at 50C on a shaker
5. Slides are rinsed with milliQ water, centrifuged to dry and stored dessicated at room temperature.


title: NimbleGen E. faecalis v583 6.2K A7980-00-01

status: Public on Feb 14 2011

city: Rancagua

first: Mauricio

middle: Alejandro

last: Latorre

state: VI

address: Av. Libertador Bernardo OHiggins 611

department: ICI

institute: Universidad de OHiggins

organism: Enterococcus faecalis V583

description: Catalog design for Enterococcus faecalis V583 (Taxonomy Id: 226185) (genome plus 3 plasmids.  (NC_004668, NC_004669, NC_004670, NC_004671 - downloaded 6/5/2008).  Aimed to select 11 probes/target, N=33599 probes from 3114 targets, 125 targets have no probes, 26 targets are exemplars - probes are on the array 2 times. Deatails in www.nimblegen.com.

manufacture_protocol: For manufacture protocols visit website at http://www.nimblegen.com/. Catalog Number A7980-00-01, desing ID 7781


title: NimbleGen_GenAu MB BCELL v5.0

status: Public on Feb 10 2011

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

institute: Instutute of Molecular Pathology

organism: Mus musculus

description:
Custom array.
genomic regions of potential pax5 target genes from mm8
including IGH and surrounding genes
isothermal tiling oligos at 100bp
designname: 2007-06-28_imp_igh_2_ChIP
designid: 6006

first: Shane

last: McManus

first: Anja

last: Ebert

first: Maria

last: Novatchkova

manufacture_protocol: as described in www.nimblegen.com


title: Fusion gene microarray, human, 500k, v.2.0.

first: Gard

middle: Olav

last: Thomassen

address: Radiumhospitalet, Rikshospitalet HF

department: Institute for Cancer Research

institute: Rikshospitalet

manufacture_protocol: Custom designed fusion gene microarray, this is a version 2.0 of the array presented in PMID 19152679, data dervided from Biomart version 53, Homo sapiens


title: NimbleGen Leptosphaeria maculans whole genome 385K array v1

city: Thiverval-Grignon

first: Isabelle

last: Fudal

address: avenue Lucien Bretignieres

country: France

institute: INRA

organism: Plenodomus lingam

description:
The Leptosphaeria maculans custom-exon array (385K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) contains fourteen independent, non-identical, 60-mer probes per gene model, each being duplicated on the array. Included in the oligoarray are 12,396 predicted gene models, 63 genes encoding small secreted proteins not included in the predicted gene models, 1316 clustered EST that did not match with the gene models, 8651 random 60-mer control probes and labelling controls.

Native array description file: 090417_L_maculans_expr.ndf
Native array description file: 090417_L_maculans_expr.ngd

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


title: Agilent-020449 Mosquito Gene Expression Microarray (Probe name version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Anopheles gambiae

description:
A. gambiae (Mosquito) Oligo Microarray

Arrays of this design have barcodes that begin with 16020449 or 2520449.

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: Human SMD Print_1355 (hoq)

first: Patrick

last: Brown


title: Mycobacterium smegmatis version 4

status: Public on Feb 08 2011

city: Bronx

first: Michael

last: Berney

state: NY

address: 1301 Morris Park Avenue

department: Department of Microbiology and Immunology

institute: Albert Einstein College of Medicine

organism: Mycolicibacterium smegmatis MC2 155

description: 70mer Oligonucleotide, Aminosilane, 3x replicate oligo printings

manufacturer: Pathogen Functional Genomics Resource Center

manufacture_protocol: refer to Genomics Resource Center


title: Nimblegen Maize Whole-Genome Microarray 385K (VersionV1_4a.53)

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

organism: Zea mays

description: This platform version is based on gene-models (probe-sets) from Maize RefGen V1(4a.53) using the expression probes only.  The original design is a custom NimbleGen design which used 385k probes. The array design has 330803 expression probes and 58339 tiling probes.  Zea maize design from customer-provided regions with expression and tiling probes were placed into two different containers: 330803 expression probes (5 probes per gene, no additional replicates) and  58339 tiling probes (probe spacing of 45bp).

first: Rajandeep

last: Sekhon

first: Shawn

last: Kaeppler

first: John

last: VanHemert(PLEXdb Staff)

first: Sudhansu

last: Dash(PLEXdb Curator)


title: Bacillus cereus ATCC 14579 5.199k

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

organism: Bacillus cereus ATCC 14579

last: de Jong

manufacture_protocol: Standard spotting protocol for GenPak Arrayer 21


title: VUMC MACF Human 30K oligo (batch68.gal)

status: Public on Feb 01 2011

first: Nicholas

last: Shannon

address: Robinson Way

department: Oncology

institute: Cambridge Research Institute

manufacture_protocol: The Human Release 2.0 oligonucleotide library, containing 60-mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). The oligonucleotides were dissolved at 10 μM concentration in 50 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink™ slides (Amersham Biosciences), using an OmniGrid® 100 microarrayer (Genomic Solutions, Ann Arbor, MI, USA) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). After printing slides were processed and blocked prior to use according to the manufacturer’s protocol.


title: UGA Drosophila 20K Aug2001

city: Athens

first: Melissa

last: Davis

state: GA

address: 500 DW Brooks Dr S 270C

department: Genetics  and MCG/UGA Medical Partnership

institute: University of Georgia

organism: Drosophila melanogaster

manufacture_protocol: PCR fragment spotted array with 95% of the genes in D. melanogaster BDGP release 4.0. Array has 8 rows of 4 blocks each, numbered 1-32 starting in the upper left and ending in the lower right.  16 pins used to print.  Each KP is only spotted once.


title: Agilent custom-designed CpG island 60mer microarray 8x15k

city: London

first: Wei

last: Dai

address: Du Cane Road

department: Sugery and Cancer

institute: Imperial College London

manufacture_protocol: see www.agilent.com


title: UGA Drosophila 20K v.2


title: UGA Drosophila 20K


title: [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene10stv1_Mm_ENST]

city: Bar Harbor

first: Rachael

middle: S

last: Hageman

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

manufacture_protocol: This is identical to GPL6246 but a custom cdf environment was used to extract data.  The custom cdf file mogene10stvmmenstcdfV11.0.1 was obtained from Brainarray (http://brainarray.mbni.med.umich.edu/brainarray/default.asp). The custom cdf is linked below as a supplementary file.


title: 454 GS FLX (Olea europaea)

status: Public on Feb 05 2011

last: GEO

organism: Olea europaea


title: Thermoanaerobacter sp. X514 2.3K oligo array version 1.0

city: Qingdao

first: Lu

last: Lin

state: Shandong

address: 189 Songling RD

institute: QIBEBT

organism: Thermoanaerobacter sp. X514

manufacturer: Institute for Environmental Genomics, University of Oklahoma, USA

manufacture_protocol:
All designed oligonucleotides were commercially synthesized without modification by Invitrogen.
Oligonucleotide probes were prepared in 50% dimethyl sulfoxide (Sigma Chemical Co., MO).
(http://ieg.ou.edu/protocol/Protocols/DMSO_Printing_8.pdf)
The concentration of oligonucleotide probes was adjusted to 100pmol/L. were spotted onto SuperAmine glass slides (Telechem International, CA) using a PixSys 5500 robotic printer (CartesianTechnologies Inc., CA).
Each probe had two replicates on a single slide.
After printing, the oligonucleotide probes were fixed onto the slides by UV cross-linking (600 mJ of energy) according to the protocol of the manufacturer (Telechem International, CA). (http://aem.asm.org/cgi/reprint/71/7/3753)


title: Whole genome oligonucleotide microarray for Protochlamydia amoebophila

status: Public on Feb 04 2011

city: Vienna

first: Doris

last: Steger

state: Vienna

address: Althanstrasse 14

department: Department of Microbial Ecology

institute: University of Vienna

organism: Candidatus Protochlamydia amoebophila UWE25

manufacturer: University of Vienna, Department of Microbial Ecology

manufacture_protocol: 5´-amino modified oligonucleotide probes were printed onto silylated amine-aldehyde glass slides using a BioRobotics MicroGrid 610/TAS system and 16 MicroSpot 2500 split pins. The average spot diameter was about 150 μm and spot centres were 300 μm apart. The relative humidity during spotting was set to 50% within the spotting compartment. Spotted microarrays were stored one day at 100% humidity. Subsequently, slides were washed by soaking them twice in 0.2% SDS for 2 min and twice in double-distilled water for 2 min. After air drying for 5 min, the slides were incubated in freshly prepared sodium borohydride solution. Then, slides were rinsed in ice-cold absolute ethanol and subsequently washed two times in 0.2% SDS and two times in double-distilled water. Finally, slides were dried by centrifugation.


title: 090313_Zv7_PC_ChIP_HX1

status: Public on Feb 07 2011

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

institute: University of Oslo

organism: Danio rerio

description:
Sanger Zv7 assembly
Tiling of TSS (15kb upstream, 5kb downstream)
native array description file: 090313_Zv7_PC_ChIP_HX1.ndf
native array description file: 090313_Zv7_PC_ChIP_HX1.pos

manufacture_protocol: See manufacturer's web site (www.nimblegen.com)


title: Exiqon miRCURY LNA microRNA Array 5th generation

city: Houston

first: Mien-chie

last: Hung

state: Texas

address: 1515 Holcomb Blvd

department: Molecular and Cellular Oncology

institute: M.D. Anderson Cancer Center

organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

description:
ProductNumber = 208300-A, 208301-A, 208302-A
miRBase 15.0

manufacture_protocol: See manufacturer's website.


title: MVGE Trichophyton rubrum TRI_2007 10K array

status: Public on Sep 02 2008

city: Beijing

first: Qi

last: Jin

address: East Street 6, Yizhuang

institute: Institute of Pathogen Biology

organism: Trichophyton rubrum

description: In this chip there were two fields named A and B, they described the upper and lower part (location) of the chip. Each field contains 10,000 spots. The spots in field A are same with those in field B.

manufacturer: State Key Laboratory For Molecular Virology and Genetics Engineering，Beijing

manufacture_protocol: Materials are transferred from microtiter plate wells to the slide surface by automated print heads


title: IATA  Lactobacillus casei ATCC 334 2.7k array_v1

status: Public on Oct 22 2010

city: Paterna

first: Manuel

last: Zúñiga

state: Valencia

address: Avda. Profesor Agustín Escardino 7

department: Biotecnología

institute: Instituto de Agroquímica y Tecnología de Alimentos

organism: Lacticaseibacillus paracasei ATCC 334

description: Nylon membrane (11 x 9 cm) with spotted PCR products up to 2.5 Kb, representing the full-length genes or a 2.5 kb internal fragment for those genes exceeding 2.5 kb for 2390 L.casei genes.

manufacturer: Seccion de Chips de DNA-SCSIE (Universitat de Valencia)

manufacture_protocol:
Each selected ORF was amplified with specific primers from genomic DNA of Lactobacillus casei ATCC 334. As a general rule, the primers were selected to amplify the complete coding region excepting ORFs exceeding 2.5 kb for which a 2.5 kb internal fragment was amplified. PCR products were analyzed in agarose gels and their sizes estimated by comparison with standard markers. BioGrid (BioRobotics, UK) was used as the spotting robot. Macroarrays were made by printing the PCR products (without purification) onto a positively charged nylon membrane
(Amersham Hybond N+). Printing was done with a 384-pinhead printer, consisting of regular 3 × 3 spots per pin, yielding a total of 3456 available positions. Gene probes were printed in a single replicate. 2390 positions were used for probes, the remaining positions being empty. Membranes were kept humid by setting them onto three Hybond blotting-paper sheets soaked in denaturing solution (1.5M NaCl, 0.5M NaOH). Solid pins of 0.4-mm diameter were used. These pins spot 20 nl each time. PCR products were spotted five times so that each spot contained 20–30 ng DNA in a diameter of approximately 0.6 mm. After printing, the membrane was neutralized with 1.5 M NaCl, 0.5 M Tris/HCl (pH 7.2), 1 mM EDTA (pH 8.0) for 1 min and membranes were kept on filter paper until complete dryness.


title: RNG-MRC_HU25K_HsO4A

status: Public on Jan 29 2011

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

organism: Homo sapiens

relation:
Affiliated with: GPL13219
Affiliated with: GPL13218

manufacture_protocol: spotted DNA/cDNA


title: GRASP salmonid array, 16k v2.0 chip, updated data files 15 July 2005

status: Public on Sep 01 2006

city: Nanaimo

first: Shaorong

last: Li

state: British Columbia

address: 3190 Hammond Bay Road

department: Salmon and Freshwater Ecosystems Division

institute: Fisheries and Oceans Canada

organism:
Oncorhynchus mykiss
Salmo salar

description: 16k salmonid cDNA microarray from GRASP including features primarily from Atlantic salmon and rainbow trout

manufacturer: Genomic Research on Atlantic Salmon Project

manufacture_protocol: details on the manufacture and testing of the 16k v. 2.0 array may be found on the GRASP website: http://web.uvic.ca/cbr/grasp/


title: Viro5AGL-60k [Probe name version]

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

organism: Viruses

description:
This platform includes more than 60000 oligonucleotides for the detection and discovery of both known and novel viruses.  The sequences of ~36,000 of the viral
probes on this platform have been previously published in the GEO database as MegaViro  (GPL1834), Viro3 (GPL3429), and Viro4 (GPL6862).
For comparison purposes, both 70mer and 60mer representations of these viral oligos are present.
Some viral probes corresponding to phages and other less critical targets have been removed.
More than 20,000 additional probes have been added for (1) better subtyping of respiratory and diarrheal viral as well as nonviral pathogens,
(2) enhanced detection of specific viral families, and (3) subtyping of HIV/SIV strains.   Control oligonucleotides are also included in the design.

first: E

last: Chen

first: S

last: Arron

first: J

last: Hackett

first: G

last: Schochetman

middle: L

last: DeRisi

first: C

middle: Y


title: DGRC-D. melanogaster-DGRC1-15552-v5

status: Public on Jun 02 2006

city: Bloomington

last: Drosophila Genomics Resource Center (DGRC)

state: IN

department: Indiana University

description: DGRC-1 amplicon transcriptome microarrays are spotted with DNA fragments amplified from genomic DNA of the Oregon R strain of Drosophila melanogaster using gene-specific oligonucleotide primer pairs made by Incyte Genomics.  The primers were designed against release 1 of the annotated genome sequence and were selected to amplify fragments which have minimal sequence similarity to other genes, size range between 100-600 bp, and location biased towards the 3'-end of transcripts. The array also contains the following controls: a ubiquitously expressed gene (actin 5C), a spotting buffer-only control (3XSSC plus 1.5M Betaine), exogenous(non-Drosophila) probes (7 from Arabidopsis and 8 Ambion array control PCR spots from bacteria that can be used with spiking RNAs), and three exogenous markers: GAL4, lacZ, and FLP.  The DGRC arrays are printed using an Omnigrid 300 contact-printing instrument and 48 silicon split-pins on Corning GAPS II slides.

first: Justen

last: Andrews

first: Peter

last: Cherbas

first: Kevin

last: Bogart

first: Monica

last: Sentmanat

first: Jim

last: Costello

first: Angela

last: Burr


title: NimbleGen Human 2.1M array [080131_HG18_WG_CGH_v2DCR_HX1]

status: Public on Nov 15 2010

city: Cold Spring Harbor

first: Yoon-Ha

last: Lee

address: One Bungtown Road

institute: Cold Spring Harbor Lab

description:
Annotation in this record based on NCBI human build 36.
designname: 080131_HG18_WG_CGH_v2DCR_HX1
designid: 7058

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