title: Saur2a custom-made Affymetrix array

status: Public on Aug 01 2006

city: Pearl River

first: Ellen

last: Murphy

state: NY

address: 401 N. Middletown Road

department: Vaccines

country: USA

institute: Wyeth Research

organism: Staphylococcus aureus

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol:
Affymetrix standard 25-mers, match/mismatch 18 micron array
Nominally 34 probepairs/ORF, 15 probepairs/intergenic region
alpha1=0.0575, alpha2=0.0971


title: Affymetrix GeneChip Mapping Pre-Release 10K Array (ax13339)

status: Public on Aug 29 2006

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

organism: Homo sapiens

description:
This is the pre-release version of the Affymetrix 10K array (GPL1266).
This platform appears to be referring to the same Affymetrix chip as the 'early access' array in GPL1855. However, GPL1855 did not appear to have all necessary IDs, and therefore, necessitated the submission of this platform.

manufacture_protocol: see web site of Affymetrix


title: VUMC MACF human 5K BAC v21

status: Public on Aug 30 2006

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

technology: spotted DNA/cDNA

description:
- clones were mapped to the UCSC July 2003 Freeze of the Human Golden Path (NCBI build 34)
- oncobacs were mapped using their overgo-primers and are available via www.ensembl.org

distribution: non-commercial

first: Paul

last: van den IJssel

first: Bauke

last: Ylstra

manufacture_protocol: as described in: Carvalho et al (J. Clin. Path.,2004, vol. 57, 644-646). DNA from the 1 Mb resolution Sanger BAC clone set (see Ensembl), the Caltech OncoBac set, and in house clones of interest, supplemented with clones from the Children’s Hospital Oakland Research Institute (CHORI), amounting to a total of 4678 clones with known chromosomal positions, was isolated according to the CHORI protocol. Amplification of the DNA was done by ligation mediated polymerase chain reaction (PCR) according to Snijders et al. (Nat. Genet.,2001, vol.29, 263-264) and PCR clones were purified using Montage PCR µ96 filter plates (Millipore BV, Amsterdam, the Netherlands). Clones were spotted in triplicate at a concentration of 1 µg/µl, in 150 mM sodium phosphate (pH 8.5), on CodeLink™ slides (Amersham BioSciences, Roosendaal, the Netherlands), using a SpotArray 72 robot (Perkin Elmer Life Sciences, Zaventum, Belgium) 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: Bovine muscle and adipose cDNA array2

status: Public on Aug 25 2006

city: St Lucia

first: Yonghong

last: Wang

state: Queensland

address: 306 Carmody Road

department: Livestock Industries

country: Australia

institute: CSIRO

organism: Bos taurus

first: Sigrid

middle: A

last: Lehnert

first: Keren

last: Byrne

manufacture_protocol: Development and application of a bovine cDNA microarray for expression profiling of muscle and adipose tissue. Lehnert, S. A. Wang, Y. H. Byrne, K. A. Australian Journal of Experimental Agriculture  Vol: 44, Issue: 11, 2004 pp. 1127 - 1133


title: VUMC MACF human 5K BAC v16


title: Sentrix Mouse-6 Expression BeadChip

city: San Diego

last: Illumina Inc.

state: CA

address: 9885 Towne Centre Drive

institute: Illumina Inc.

organism: Mus musculus

technology: oligonucleotide beads

description: The Sentrix Mouse-6 BeadChip can be used to study expression of over 47,000 mouse transcripts based on MEEBO, RefSeq and RIKEN FANTOM2 content. researchers can generate whole-genome expression profiles for 6 samples in parallel on a single BeadChip. Each array is composed of 3 micron features with average feature redundancy of 30-fold . All features are QCed by a sequential hybridization process called array decoding. The probes are fully screened all-full-length 50-mers and the assay requires 50-100ng of total RNA input.

distribution: commercial


title: Spotting_muscle_21OCT03

city: Castanet tolosan

first: Laurence

last: Liaubet

address: chemin de borde rouge

department: Animal Genetic

country: France

institute: INRA

organism: Sus scrofa

manufacturer: RGS platform of Genopole Toulouse Midi Pyrénées (http://genopole-toulouse.prd.fr/) and UR 444 Cellular Genetics INRA, chemin de Borde Rouge  Auzeville, BP 52627, 31326 Castanet-Tolosan cedex, France

manufacture_protocol: Gene expression was analyzed by hybridization of nylon cDNA arrays (18x72 mm, Immobilon-NY+, Millipore, Bedford, MA)with radioactive probes. The arrays contained PCR products from 3456 pig cDNA clones, spotted in duplicate on two separate fields of the same membrane with aMicrogrid II fitted with a 32 pins microarray tool (BioRobotics MicroGrid, Genomic Solutions Ltd., 8 Blackstone Road, Huntingdon, Cambridgeshire PE29 6EF, United Kingdom). The cDNA clones came mainly from a pig normalized multi-tissue cDNA library (scag, Tosser-Klopp G, unpublished 1056 clones) and from a muscle library (Bendixen C, Department for Livestock Breeding and Genetics, Danish Institute of Agricultural Sciences, DK-8830 Tjele; 2208 clones). Other clones came from libraries from USDA MARC (MARC 1 and 2 pig) and SENAH INRA laboratory (INRA - UMR SENAH, Domaine de la Prise, F 35590 Saint Gilles, France).


title: OSUGW_MG_21K_vA.7.1.1

status: Public on Aug 18 2006

city: Columbus

first: Mohan

middle: B

last: Raghupathy

email: mohanbabu_r@yahoo.com, wang.620@osu.edu

state: OH

address: 201 Kottman Hall, 2021 Coffey Rd

department: Department of Plant Pathology

institute: The Ohio State University

organism: Pyricularia grisea

first: Guo-Liang

first: Sean

last: Couglan


title: BCM-Shaulsky-7744-v1

city: Houston

first: Ezgi

last: Booth

state: TX

address: S430, One Baylor Plaza

institute: Baylor College of Medicine

organism: Dictyostelium discoideum

first: Michelle

middle: C

last: Mendoza

middle: O

first: Gad

last: Shaulsky

first: Richard

last: Firtel

manufacture_protocol:
•	General array design:  Glass slides were coated with 3-Glycidoxypropyltrimethoxysilane (Aldrich).  Target DNA was printed on the activated glass slides on 200 µm centers with a Cartesian Pixsys5500 robot and with a GeneMachines OmniGrid Accent robot with Chipmaker II pins (Tele-chem Intl.).  The full ‘Cartesian’ array has 8x4 sub-arrays, each containing 22x22 targets (total 7,744 targets) as indicated in supplemental table 4 (see supplemental file ‘5_arrayMap1(table4).xls’).  The full ‘Accent” array has 22x24 targets (total 8,488 targets) targets.
•	The source of the reporter molecules: 5,655 cDNA clones were from the Dictyostelium cDNA project; 987 extra cDNA clones were selected from a low redundancy screen of a lambda library and a plasmid library of late developmental stage, vegetative and early developmental stage of AX4 cells, respectively; 647 genomic DNA clones were selected as long open reading frames that matched published protein sequences; and 96 clones were from miscellaneous sources.  Sequences were compared to public databases and annotated 4.  The degree of redundancy is less than 15%.  The control targets that were made from the Dictyostelium ribosomal 17S RNA gene, histone H1, actin8 and mhcK as well some yeast genes and ‘no DNA’ controls.
•	The method of reporter preparation:  DNA targets were amplified from plasmids by PCR with common oligonucleotides and their size verified by gel electrophoresis.  PCR products were purified by precipitation with 50% isopropyl alcohol 0.3 M sodium acetate pH5.2, washed once with 70% ethanol, dissolved in water and adjusted to 800 mM sodium chloride 200 mM sodium phosphate pH10.5.
•	The spotting protocols used, including the array substrate, the spotting buffer, and any post-printing processing, including cross-linking:  Glass slides (Gold Seal Products, VWR) were washed by sonication in acetone for 10 minutes, rinsed twice in distilled water, immersed in 1 N NaOH for 10 minutes, washed in distilled water, and immersed for 3 minutes in 3% (v/v) 3-Glycidoxypropyltrimethoxysilane (Aldrich) made in 95% ethanol/acetic acid pH 5.0.  The slides were washed in 100% ethanol, dried with nitrogen gas and baked for at least 2 hrs at 100°C.  Target DNA in 800 mM sodium chloride 200 mM sodium phosphate pH10.5 solution was printed on the activated glass slides. Arrays were stored desiccated in the dark.
•	Any additional treatment performed prior to hybridization: The arrays were treated with hot water for 1 min at 100°C for target denaturation prior to hybridization.
For reference see Van Driessche, N., C. Shaw, et al. (2002). "A transcriptional profile of multicellular development in Dictyostelium discoideum" Development 129(7):1543-52.


title: Agilent-014794 C. elegans Whole Genome ChIP-on-Chip Set 244K, Microarray 2 of 2 (G4495A)

status: Public on Aug 17 2006

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Caenorhabditis elegans

description:
C. elegans Whole Genome ChIP-on-Chip Set 244K, Microarray 2 of 2

Arrays of this design have barcodes that begin with 16014794 or 2514794.

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: UCSF Gladstone Genomics Core Human 21k Oligo array (2003)

status: Public on Aug 31 2006

city: San Francisco

first: Sergio

last: Baranzini

address: 513 Parnassus Ave

department: Neurology

institute: University of California San Francisco

technology: spotted oligonucleotide

description: This set includes 21486 oligonucleotides, mostly 70-mers based on the Operon set

manufacture_protocol: Please Contact UCSF Gladstone Genomics Core


title: Agilent-013870 Human Promoter ChIP-on-Chip Set, Microarray 8 of 10 (G4483A)

description:
The Human Expanded Promoter ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to promoter regions spanning    -8.0KB upstream to +2.0KB downstream of the transcriptional start sites. The ten slide set provides coverage for ~17,000 of the best defined human transcripts.

Arrays of this design have barcodes that begin with 16013870 or 2513870.

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: Trichoderma array (1.5 K) 'est_unig1'

status: Public on Aug 22 2006

city: Irapuato

first: Enrique

middle: Ibarra

last: Laclette

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León, A.P. 629

country: Mexico

institute: Laboratorio Nacional de Genomíca (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV)

organism: Trichoderma atroviride

manufacturer: The design and printing of microarrays took place at the University of Texas A&M, College Station

first: T.

last: Rosales-Saavedra

first: U.

last: Esquivel-Naranjo

first: S.

last: Casas-Flores

first: P.

last: Martínez-Hernández

first: E.

last: Ibarra-Laclette

first: C.

last: Cortes-Penagos

first: A.

last: Herrera-Estrella

manufacture_protocol: Custom cDNA-based Microarray: DNA probes to a set of 1,655 strategically selected genes were generated by PCR. The DNA concentration was determined using Nanodrop equipment. Samples were transferred to 96 well plates containing DMSO to give a final concentration of 200 ng/ul in 50% DMSO. The DNA probes were directly spotted onto Corning UltraGAPS coated glass slides. Each of the genes selected was printed in two contiguous replicates laid out in 8 grids of 22 rows by 22 columns.


title: FUGE Hs-OperonV3

city: Oslo

first: Bjorn

last: Grinde

state: Oslo

address: Geitmyrsveien 75

department: Infectious Disease Control

country: Norway

institute: Norwegian Institute of Public Health

manufacturer: FUGE microarray facility (Radiumhospital, Norway)

manufacture_protocol:
Array Production Details:
•Spotting Instrumentation: MicroGrid II arrayer (model# 600),
MicroSpot pin tool (Cat# BR001482),
MicroSpot 10 K Split pins (Cat# BR001489),
BioRobotics (Genomic Solutions, http://www.genomicsolutions.com//files/MicroGrid.pdf )
•Slide substrates: CMT UltraGAPS slides (25x75 mm) , Aminosilane coating (Corning Cat# 40016)
•Oligonucleotide consentration: 40 μM (600 pmol oligonucleotide dissolved in 15 μL 50% DMSO)
•Spotting buffer: 50% Dimethyl Sulphoxide (DMSO), (Sigma Cat# D-8418)
•Printing plates: 384 well low profile plates from Genetix (Cat# X60004)
•Spotting conditions: 20–22°C and at 45–55% RH.
•Slide post-processing: Slides are stored in a desicator cabinet to dry for 24-48 hours after spotting, and UV-crosslinked at 800 mJ/cm2
(active side up) using a UV-Stratalinker 2400 from Stratagene Inc. The arrays are stored in Corning slide boxes before use.


title: ORF_intergenic_E

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 203 Fordham Hall

department: Biology

institute: University of North Carolina at Chapel Hill

organism: Saccharomyces cerevisiae

manufacture_protocol:
Tip Configuration: Standard 32-tip
Columns per Sector: 24


title: Agilent-013872 Human Promoter ChIP-on-Chip Set, Microarray 10 of 10 (G4483A)

description:
The Human Expanded Promoter ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to promoter regions spanning    -8.0KB upstream to +2.0KB downstream of the transcriptional start sites. The ten slide set provides coverage for ~17,000 of the best defined human transcripts.

Arrays of this design have barcodes that begin with 16013872 or 2513872.

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: Bovine muscle and adipose cDNA array1

first: Yonghong

last: Wang

first: Sigrid

last: Lehnert

first: Keren

last: Byrne


title: Agilent-013869 Human Promoter ChIP-on-Chip Set, Microarray 7 of 10 (G4483A)

description:
The Human Expanded Promoter ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to promoter regions spanning    -8.0KB upstream to +2.0KB downstream of the transcriptional start sites. The ten slide set provides coverage for ~17,000 of the best defined human transcripts.

Arrays of this design have barcodes that begin with 16013869 or 2513869.

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: Agilent-014799 Arabidopsis Whole Genome ChIP-on-Chip Set 244K, Microarray 2 of 2 (G4495A)

organism: Arabidopsis thaliana

description:
Arabidopsis Whole Genome ChIP-on-Chip Set 244K, Microarray 2 of 2

Arrays of this design have barcodes that begin with 16014799 or 2514799.

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: TaqMan Human MAQC (TAQ)

status: Public on Aug 19 2006

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

technology: RT-PCR

distribution: virtual


title: Panomics Human MAQC (QGN)

technology: other

description: technology type: Branched DNA (bDNA)


title: Agilent-014798 Arabidopsis Whole Genome ChIP-on-Chip Set 244K, Microarray 1 of 2 (G4495A)

description:
Arabidopsis Whole Genome ChIP-on-Chip Set 244K, Microarray 1 of 2

Arrays of this design have barcodes that begin with 16014798 or 2514798.

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: Eppendorf DualChip Human MAQC (EPP)

manufacture_protocol: Eppendorf protocol


title: Agilent-013880 Human ENCODE ChIP-onChip Set V2, Microarray 2 of 2 (G4485A)

description:
The Human ENCODE ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to specific ENCODE regions covering 30MB. The 2-slide set contains over 80,000 probes that cover human chromosomes 1-22 within specific ENCODE regions.

Arrays of this design have barcodes that begin with 16013880 or 2513880.

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: Agilent-014793 C. elegans Whole Genome ChIP-on-Chip Set 244K, Microarray 1 of 2 (G4495A)

description:
C. elegans Whole Genome ChIP-on-Chip Set 244K, Microarray 1 of 2

Arrays of this design have barcodes that begin with 16014793 or 2514793.

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: Agilent-013866 Human Promoter ChIP-on-Chip Set, Microarray 4 of 10 (G4483A)

description:
The Human Expanded Promoter ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to promoter regions spanning    -8.0KB upstream to +2.0KB downstream of the transcriptional start sites. The ten slide set provides coverage for ~17,000 of the best defined human transcripts.

Arrays of this design have barcodes that begin with 16013866 or 2513866.

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: Agilent-014792 Human ENCODE ChIP-on-Chip Microarray 244K (G4495A)

description:
Human ENCODE ChIP-on-Chip array 1x244K Unrestricted

Arrays of this design have barcodes that begin with 16014792 or 2514792.

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: Eurogentec S. pombe IGR+ORF array (F060D)

status: Public on Aug 15 2006

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

organism: Schizosaccharomyces pombe

description: 22176 IGRs and ORFs were spotted in duplicate on a glass slide

first: Fredrik

last: Fagerstrom-Billai

middle: P

manufacture_protocol:
Primary PCR: The PCR reactions are performed using tagged genome specific primers in the presence of genomic DNA (provided by your laboratory). We normally achieve a success rate of 93 % of PCR reactions. For the failed PCR reactions we perform three different protocols of PCR conditions, which include different MgCl2 concentrations and different Taq polymerase. We should normally get an additional 2 % working and reach a success rate of 95 % in total. We check 5 % of the total oligos by Mass Spectrometry and will re-synthesize maximum 2 % of the oligos based on a newly designed primer. We will perform the PCR reactions with the new designed oligonucleotides with the standard PCR protocol. Following this process we reach usually 97 % success rate.
Secondary PCR: amplifications will be performed using a single pair of primers annealing to tag sequences introduced on primary PCR primers. These PCR amplifications will also be controlled by agarose gel electrophoresis and repeated if required reaching a minimum of 95 % success rate. The final PCR products will contain an amino group at their 5' end to promote the attachment of the predicted gene coding DNA strand to the treated glass slides.


title: Agilent-013871 Human Promoter ChIP-on-Chip Set, Microarray 9 of 10 (G4483A)

last: Agilent Technologies

description:
The Human Expanded Promoter ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to promoter regions spanning    -8.0KB upstream to +2.0KB downstream of the transcriptional start sites. The ten slide set provides coverage for ~17,000 of the best defined human transcripts.

Arrays of this design have barcodes that begin with 16013871 or 2513871.

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: Agilent-013879 Human ENCODE ChIP-onChip Set V2, Microarray 1 of 2 (G4485A)

description:
The Human ENCODE ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to specific ENCODE regions covering 30MB. The 2-slide set contains over 80,000 probes that cover human chromosomes 1-22 within specific ENCODE regions.

Arrays of this design have barcodes that begin with 16013879 or 2513879.

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: SAGE:17:NlaIII:Sus scrofa

status: Public on Aug 06 2006

last: GEO

technology: SAGE NlaIII

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


title: SAGE:21:NlaIII:Magnaporthe grisea

status: Public on Aug 11 2006

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


title: PHRI-UMNDJ Mycobacterium tuberculosis 4.8K CAG_Mtb

status: Public on Aug 04 2006

city: Newark

first: Virginie

middle: Marie

last: Aris

state: NJ

address: W420M, 225 Warren St

department: Center For Applied Genomics

institute: PHRI-UMNDJ

organism: Mycobacterium tuberculosis

first: Patricia

last: Soteropoulos

first: Saleena

middle: S

last: Ghanny

middle: M

manufacture_protocol: Oligonucleotide 70mer long from the OPERON TB set version 1.0 are spotted using an omnigrid arrayer at a concentration of 25uM in 3x SSC onto glass slides coated with Poly-L-Lysine.


title: ORF_intergenic_J


title: VUMC MACF human 5K BAC v12

first: Daoud

last: Sie

description:
- clones were mapped to the UCSC July 2003 Freeze of the Human Golden Path (NCBI build 34)
- oncobacs were mapped using their overgo-primers and are available via www.ensembl.org

first: Paul

last: van den IJssel

first: Bauke

last: Ylstra


title: Agilent-013868 Human Promoter ChIP-on-Chip Set, Microarray 6 of 10 (G4483A)

description:
The Human Expanded Promoter ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to promoter regions spanning    -8.0KB upstream to +2.0KB downstream of the transcriptional start sites. The ten slide set provides coverage for ~17,000 of the best defined human transcripts.

Arrays of this design have barcodes that begin with 16013868 or 2513868.

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: NKI-CMF Mus musculus 32k oligo array with DamID annotations

status: Public on Jul 28 2006

address: Plesmanlaan 161

institute: Dutch Cancer Institute

description: This platform is identical to GPL3675. Due to application in DamID experiments custom annotations are provided. The annotations are derived from blast analysis of the oligo sequence to the genomic sequence. The EnsEMBL release used for retrieving gene, transcript and exon annotations is v33.34. The assembly build that is used as genomic sequence is NCBIM34.

manufacturer: Central Microarray Facility, NKI Amsterdam

first: W

last: Brugman

first: M

last: Heimerikx

first: D

first: A

last: Velds

last: Nieuwland

first: R

last: Kerkhoven

first: E

last: de Wit

last: Vogel

manufacture_protocol: The Mouse Genome Oligo Set Version 3.0 arrays contain 31,769 probes representing 24,878 genes and 32,829 gene transcripts. All oligos are 70-mer sequences. The arrays consist of 37632 features (oligos and controls) and are printed in a 28x28 subarray layout using 48 Biorobotic 10K-microspot pins. We use 14 different Bacillus subtilus sequences as spike-controls printed in triplo in every subarray.


title: Agilent-013867 Human Promoter ChIP-on-Chip Set, Microarray 5 of 10 (G4483A)

description:
The Human Expanded Promoter ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to promoter regions spanning    -8.0KB upstream to +2.0KB downstream of the transcriptional start sites. The ten slide set provides coverage for ~17,000 of the best defined human transcripts.

Arrays of this design have barcodes that begin with 16013867 or 2513867.

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: Agilent-013864 Human Promoter ChIP-on-Chip Set, Microarray 2 of 10 (G4483A)

description:
The Human Expanded Promoter ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to promoter regions spanning    -8.0KB upstream to +2.0KB downstream of the transcriptional start sites. The ten slide set provides coverage for ~17,000 of the best defined human transcripts.

Arrays of this design have barcodes that begin with 16013864 or 2513864.

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: Agilent-012713 Yeast Whole Genome ChIP-on-chip Microarray (G4486A)

status: Public on May 09 2006

description:
The Yeast Whole Genome ChIP-on-chip microarray is a high-resolution, high performance 60-mer oligonucleotide that allows the location analysis of DNA binding proteins over 85% (the non-repetitive portion) of 12MB of the yeast genome on a single chip. This chip offers genome-wide coverage and  consists of 41,441 oligos (60mer); 14,256 from intergenic pathway, 27,175 from ORF pathway with an average prob spacing of approximately every 266 bp.  Arrays with this part number have a design ID 12713.

Arrays of this design have barcodes that begin with 16012713 or 2512713.

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: Agilent-013865 Human Promoter ChIP-on-Chip Set, Microarray 3 of 10 (G4483A)

description:
The Human Expanded Promoter ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to promoter regions spanning    -8.0KB upstream to +2.0KB downstream of the transcriptional start sites. The ten slide set provides coverage for ~17,000 of the best defined human transcripts.

Arrays of this design have barcodes that begin with 16013865 or 2513865.

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: Agilent-013863 Human Promoter ChIP-on-Chip Set, Microarray 1 of 10 (G4483A)

description:
The Human Expanded Promoter ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to promoter regions spanning    -8.0KB upstream to +2.0KB downstream of the transcriptional start sites. The ten slide set provides coverage for ~17,000 of the best defined human transcripts.

Arrays of this design have barcodes that begin with 16013863 or 2513863.

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: NSF Rice Oligonucleotide Array 45K (23K B)

city: Rockville

first: Jia

last: Liu

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

organism: Oryza sativa

manufacture_protocol: Visit http://www.ricearray.org


title: S. cerevisiae ORF_INT_UNC_A array

status: Public on Oct 01 2005

first: Jason

last: Lieb

address: 203 Fordham Hall CB# 3280

institute: UNC-Chapel Hill

description: This set includes 16916 spots

first: Rao

last: Bhargavi

manufacture_protocol: as described in Iyer et al


title: Eurogentec S. pombe ORF array (L040B)

first: Anthony

last: Wright

description: 11520 ORFs were spotted in duplicate on glass slide

last: Fagerstrom-Billai


title: Eurogentec S. pombe ORF array (J290D)

first: Fredrik


title: Eurogentec S. pombe IGR+ORF array (E120D)


title: S. cerevisiae ORF_INT_UNC_G array

description: This set includes 16916 spots


title: Osmotic stress in Siokra L23 roots

status: Public on Aug 14 2006

city: Fayetteville

first: James

middle: Mac

last: Stewart

state: AR

address: 115 Plant Science Bldg

department: Crop, Soils, and Environmental Science

institute: University of Arkansas

organism: Gossypium hirsutum

manufacturer: Wilkins Lab, University of California Davis

first: Thea

last: Wilkins

first: Aladdin

last: Arpat


title: cDNA microarray Van Andel Institute for Day1 samples

status: Public on Aug 03 2006

city: East Lansing

first: Zheng

last: Li

state: MI

address: 2527 Engineering Building

department: Chemical Engineering and Materials Science

institute: Michigan State University

first: Christina

last: Chan

first: Shireesh

last: Srivastava

last: Norton

last: Resau

first: Brian

last: Haab

manufacture_protocol:
MicroArray Protocol For Total RNA
Ramsi Haddad
3/14/02
This protocol requires 50 µg of each type of RNA to be compared for each microarray. The word probe will be used to describe the labeled cDNA that binds to the DNA on the microarray.
Materials
The following is a list of supplies required to perform cDNA microarray hybridizations. Most items are available in the Invitrogen Freezer Program.
Company Cat. Number Description Amersham Pharmacia Biotech 27-7836-01 poly d(A) sodium salt or use Sigma poly d(A) Perkin Elmer NEL576 Cy3-dCTP NEL577 Cy5-dCTP Ambion 9915G DepC treated water 9480 7.5 M LiCl solution Brinkmann/Eppendorf 0032 005.330 Phase Lock Gel-Heavy, 50 mL tubes Qiagen 28104 QIAquick PCR purification Kit (50 columns) Roche 799-017 Rnasin (2000 U) 1467140 ss Salmon Sperm DNA PGC Scientifics 62-6504-04 22 X 40 mm hybrislip, pack of 100 Fisher 42416 Microcon-50 microconcentrators (Amicon no. 42416) 2551 CMT Hybridization Chamber (Corning no. 2551), 5 chambers 08-812 Histology staining dish (horizontal) 08-953-E Jewelers Microforceps, 10.8 cm (straight) 13-812-14 Kelly Forceps, curved, 140 mm 12-548-5J 24 X 40 mm glass coverslips, 1 oz pack 05-669-39 1.5 mL microfuge tubes with screw cap O-ring seal, 500 tubes Gibco/BRL Invitrogen 15279-011 Human Cot-1 DNA, 500 ug 18064-014 SuperScript II RT. 18440-016 Mouse Cot-1 DNA (if required) 10297-018 100 mM dNTP Set 15596-026 TRIzol Reagent, 100 mL (200 mL bottle is also available) 15634-017 Herring Sperm DNA, 5 X 1 mL or below 15632-011 Salmon Sperm DNA, 5 X 1 mL or above Promega PRM-4261 Rnase One Sigma D-2532 Denhardt's Solution 50X concentrate, 5 mL S-2015 20X SSPE, 1 L S-6639 20X SSC, 1 L F-9037 Formamide, 100 mL P-9403 Poly d(A) or use Pharmacia Amersham. R-7876 2500 U tRNA (type V wheat germ) Ambion 9906 10 X 50mL DepC treated water 9480 100 mL 7.5 M LiCl solution for RNA purification, 100 mL
Reverse transcription of probes.
1. Start with 50 µg RNA of each type in 9 µL water.
2. Have the following temperatures available:
a) 37°C, 50°C water baths
b) 42°C, 68°C and 95°C heating blocks
c) Thaw 5X 1st strand buffer, 0.1M DTT, oligo d(T)20VN, Cy3-dCTP,
Cy5-dCTP, 10X Low dC/dNTP, microarray pre-hybridization and
hybridization solution.
3. Anneal oligo dT primers to RNA.
a) Add 1 µL dTVN primer (0.5 µg/µL) and incubate 5 minutes at 68°C
b) Give a quick spin to collect condensation. Keep at room temperature or
solution will get too viscous.
4. Prepare 2 separate tubes of each fluorescent mix.
(X4.5) (X 5.5 reactions)
a) 4 µL 5X 1st strand buffer 18 (22 µL)
b) 2 µL 0.1 M DTT 9 (11 µL)
c) 2 µL 10X low dC dNTP 9 (11 µL)
d) 2 µL Cy3 or Cy5 dCTP 9 (11 µL)
e) 0.5 µL RNAsin 2.2 (2.7 µL)
f) This should give a total of 10.5 µL.
5. Mix annealed RNA with appropriate fluorescent mix.
6. Add 1 µL SuperScript II RT per RNA reaction and incubate at 42°C for 45 minutes.
Using another pipettor at ~15 µL, pipette up and down to mix. This mixing step is VERY important. Since Cy5 and Cy3 are light sensitive, cover tops of tubes with foil during reaction. Do not let the temperature exceed 44°C.
7. Add another 1 mL SuperScript II RT per RNA reaction, mix with 15 mL pipette, and
incubate at 42°C for another 45 minutes. Subsequently place at 94°C for 2 minutes,
quench on ice and then combine reactions in one tube.
GO TO STEP 10 FOR MICROARRAY PREHYBRIDIZATION, THEN
COMPLETE STEPS 8 AND 9.
8. Clean up cDNA.
a) Get rid of RNA
i) Add 50 µL water
ii) 10 µL 10X RNAse One buffer
iii) 2 µL RNAse One
iv) Incubate at 37°C for 30 minutes.
v) This should give a total of 99 µL
b) Remove unincorporated label and small cDNA fragments using the QIAquick PCR
Purification Kit.
i) Add 500 µL Qiagen Buffer PB to probe and mix.
ii) Apply the sample to QIAquick spin column and centrifuge at Room
Temperature 45 seconds, 10 000 g.
iii) Discard flow through, add 750 µL Buffer PE (wash buffer) to spin column
and centrifuge for 45 seconds, 10 000 g.
iv) Discard flow through and spin again for an additional minute to remove
residual Buffer PE.
v) Elute probe by adding 50 µL Buffer EB (elution buffer) to the center of the QIAquick membrane, let sit one minute and then centrifuge for one minute.
vi) Place probe eluted from QIAquick column on a MICRON YM 50 column and centrifuge at Room Temperature for 1.5 minutes, 12400g. This should concentrate the probe to less than 15 µL.
vii) To collect purified probe, invert column into new tube. Set centrifuge to 3000 RPM and spin for 15 seconds.
viii) Check the volume and bring up to 15 µL.
9. Probe pre-hybridization.
a) To purified probe, add 28.8 µL probe hybridization and 2.3_µL 20X Blocking solution to probe. This gives a total of 46 µL (extra is due to evaporation during prehybridizaiton ).
b) Place in 94°C heating block for 2 minutes.
c) To remove any particulate matter, centrifuge at 14K g for 5 minutes and transfer to a clean tube with a rubber o-ring cap to prevent excessive evaporation.
d) Place probe at 50°C for one hour (minimum 45 minutes ) to pre-hybridize. Do not exceed 1.5 hours due to evaporation.
e) Once probe has pre-hybridized, centrifuge 5 minutes at14K g and use 32-36 µL per microarray for hybridization in step 11.
10. Prehybridize microarrays.
a) Add 34 µL of microarray prehybridization buffer solution (frozen aliquots at -20°) over microarray. This is accomplished by slowly ejecting the solution to form a drop on the pipettor tip and gently touching the drop (NOT the tip) to the middle of the microarray.
b) Place coverslip over the prehybe. Use Plastic Coverslips or you’ll have a difficult time removing it later! Coverslips are sandwiched between two plastic films. Break one film by bending coverslip to one side and remove coverslip with forceps. This gives a coverslip with the plastic film on one side. Using 90° forceps, lay so that tips are on line defining arrray. Coverslips will use this as a fulcrum to prevent sliding. While holding the corner of the coverslip, place the edge of the coverslip at the border of the micro array at ~45° angle, against the forcep. A line of prehybridization solution will form at the contact. Gently lower the slide until its almost down and then let go with the forceps. Do not drop the slide from too high a height or it will move. Once the coverslip is positioned, do NOT move it.
c) Place the microarray with coverslip into hybridization chamber. Add
10 µL of 50% formamide/50% water to each dimple at the end of the CMT hybridization chamber.
d) Place cover on chamber and place in 50°C water bath. Allow prehybridization of microarray to proceed for at least two hours.
11. Remove prehybridization and add hybridization solution.
a) Rinse hybridization chamber and dry the outside of the chamber well. Make sure to keep chamber level at all times. Remove microarray from chamber and place on paper towel.
b) Remove coverslip and microarray prehybridization solution. Using the left hand, tilt the slide so that its long edge remains in contact with paper towel and an acute angle forms between the coverslip side of the slide and the paper towel. Grasp the top corner of the coverslip with forceps and while holding coverslip in place, gently tilt the slide away. The prehybe solution will be seen to separate from the coverslip just like a acrlyamide gel pulling away from a glass plate. Make sure the slide and coverslip maintain contact at the bottom edge where all the solution will gather. Once the coverslip touches the paper towel, the prehybe will blot all over.
c) Add 32-36 µL hybridization solution to each microarray and hybridize overnight. Add 10 µL of 50% formamide/50% water to each dimple at the end of the CMT hybridization chamber.
The next day, wash and scan the microarrays and scan them.
12. Prepare 500 mL of the following wash solutions:
a) 1X SSC/0.1% SDS (25 mL 20X SSC/2.5 mL 20% SDS)
b) 0.2X SSC/0.1% SDS (5 mL 20X SSC/2.5 mL 20% SDS)
c) 0.2X SSC (5 mL 20X SSC)
d) 0.1X SSC (2.5 mL 20X SSC)
13. Rinse hybri


title: Eppendorf DualChip MAQC

status: Public on Aug 09 2006

city: Namur

first: Vincent

middle: L.

last: Bertholet

state: Namur

address: Rue du seminaire 20 A

department: EAT

country: Belgium

institute: Eppendorf


title: Salmonella virulence, membrane protein, and Regulatory array

city: Lubbock

first: Scot

last: Dowd

address: 4321 Marsha Sharp Fwy

department: MBRI

institute: MBRI

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

middle: E

manufacture_protocol:
Oligo design based upon the following publication.
Charbonnier Y, Gettler B, Francois P, Bento M, Renzoni A, Vaudaux P, Schlegel W, Schrenzel J: A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus. BMC Genomics 2005, 6: 95.
Using the transcriptome of Salmonella Typhimurium LT2, an oligonucleotide microarray, made up of 43-45 mers, was designed.  Based upon available funding we were able to choose 1152 genes, that were selected based upon their being associated with virulence or with regulation of virulence genes.  Specifications of oligos were based upon various design characteristics such as temperature of melting, 3’ location, specificity, lack of repeat nucleotides, and other consideration as previously described [121].  Oligos were synthesized and normalized in concentration by Integrated DNA Technologies Inc. (Coralville, IA).  Oligos were resuspended in Epoxide Slide Spotting Solution and printed onto Epoxide Coated Slides (Corning Inc., Corning, NY) using a GeneMachine’s Omnigrid Accent microarray printer (Genomic Solutions Ann Arbor, MI).  Each array also contains duplicate elements for each gene.


title: cDNA microarray Van Andel Institute

status: Public on Aug 02 2006

first: Paul


title: UCB Methanocaldococcus jannaschii 7K v1.0

status: Public on Aug 01 2006

city: Berkeley

first: Boonchai

last: Boonyaratanakornkit

address: 201 Gilman Hall #1462

department: Chemical Engineering

institute: UC Berkeley

organism: Methanocaldococcus jannaschii

description: Each sub-array contains blocks arranged 4 by 4 with each block running 22 rows by 20 columns.

first: Vivian

last: Peng

first: Douglas

last: Clark

first: Anjana

middle: J

last: Simpson

first: Najib

last: El-Sayed

manufacture_protocol:
Primers (Invitrogen) were designed for all 1738 open reading frames (ORFs) using Primer 3 software. Polymerase chain reaction was performed with 50 ng of genomic DNA, 0.8 uM of each forward and reverse primer, and 10 U of Taq DNA polymerase (New England Biolabs). Products were precipitated on 96 well plates with isopropanol and 3M sodium acetate at 4C and analyzed on a 0.8% agarose gel.
Poly-L-lysine SuperChip slides (Erie Scientific) were printed using a homemade linear servo arrayer.  For more details, please see the documentation provided by the Derisi Lab on their homepage at UCSF.  Dried PCR products were resuspended in 3X SSC and rearrayed in 384 well plates. Three copies of each ORF were printed in two sub-arrays on the slides for a density of 6018 PCR spots (total of 7040 spots) on each sub-array.


title: CSIRO cotton whole plant cDNA array

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

description: 48 blocks consisting of 22 columns and 23 rows each. Blocks are numbered left to right and top to bottom on the array.

first: Danny

last: Llewellyn

manufacture_protocol: cDNAs spotted in DMSO using a Cartesian robot?


title: CNCR Mus musculus 7K array

city: Amsterdam

first: Jildau

last: Bouwman

address: de Boelelaan 1085

department: Functional genomics

institute: CNCR, Vrije Universiteit

first: Sabine

last: Spijker

first: Desirée

last: Schut

first: Betty

last: Wächtler

first: Bauke

last: Ylstra

first: August

last: Smit

first: Matthijs

last: Verhage

manufacture_protocol: Compugen 7K mouse oligonucleotide library, 5' C6-amino modifier printed on CodeLink Activated Slides


title: NKI-CMF Homo sapiens 35k oligo array with DamID annotations

first: Daoud

last: Sie

description: This platform is identical to GPL3676. Due to application in DamID experiments custom annotations are provided. The annotations are derived from blast analysis of the oligo to the genomic sequence. The EnsEMBL release used to for retrieving gene, transcript and exon annotations are v31.35. The assembly build that is used as genomic sequence is NCBI35.

first: W

last: Brugman

first: M

last: Heimerikx

first: D

first: A

last: Velds

last: Nieuwland

first: R

last: Kerkhove

first: E

last: de Wit

last: Vogel

manufacture_protocol: The Human Genome Oligo Set Version 3.0 arrays contain 34,580 probes representing 24,650 genes and 37,123 gene transcripts. All oligos are 70-mer sequences. The arrays consist of 37632 features (oligos and controls) and are printed in a 28x28 subarray layout using 48 Biorobotic 10K-microspot pins. We use 14 different Bacillus subtilus sequences as spike-controls printed in triplo in every subarray.


title: Eichler Segmental Duplication BAC array

status: Public on Jul 22 2006

city: Seattle

first: Andrew

last: Sharp

state: WA

address: 1705 NE Pacific St

department: Genome Sciences

institute: University of Washington

description: Standard glass microscope slides coated with chromium

manufacturer: Spotting solutions made in Eichler laboratory, UW; arrays printed in Pinkel laboratory, UCSF, USA

first: Evan

last: Eichler

first: Dan

last: Pinkel

manufacture_protocol:
Snijders AM, Segraves R, Blackwood S, Pinkel D, Albertson
DG (2004) BAC microarray-based comparative genomic hybridization.
Methods Mol Biol 256:39–56


title: Sentrix® Linkage IV Panel BeadChip

status: Public on Jun 27 2006

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

department: Pathology

institute: Leiden University Medical Center

description: Illumina's SNP-based Linkage IV Panel is a marker map for genetic disease studies. The panel contains over 6000 highly informative SNP markers distributed evenly  across the human genome and delivering high information optimized for linkage mapping studies.


title: PIQOR Immunology Microarray Human Antisense

status: Public on May 26 2006

city: Vienna

first: Thomas

last: Weichhart

address: Waehringerstraße 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

manufacture_protocol:
- The region is selected to contain no
repetitive elements.
- The region selected has minimal homology (<85%) to other members of the same gene family.
- PIQOR cDNA fragments are 200-400 bp in length.


title: NKI-CMF Mus musculus 32k oligo array

status: Public on Apr 20 2006

last: Kerkhoven


title: FHCRC Mouse 22K v1.0

status: Public on Oct 14 2005

first: Ryan

last: Basom

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

manufacture_protocol:
The FHCRC Mouse 22K array was manufactured by combining the
15,341 PCR amplified clones from the NIA 15K Mouse cDNA Clone Set and 7409 PCR amplified clones from the NIA 7.4K Mouse cDNA Clone Set along with 240 'control' spots and printing them on glass microscope slides with a Genomic Solutions Omnigrid arrayer.


title: S. cerevisiae ORF_intergenic_Q array

first: Jason

last: Lieb

description: This set includes 16128 spots

first: Rao

last: Bhargavi


title: S. cerevisiae ORF_YINT_BRMB1 array

description: This set includes 16916 spots


title: CJ1

status: Public on Aug 27 2005

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism: Campylobacter jejuni

manufacturer: Gavin,,Sherlock; School of Medicine, Department of Genetics, Stanford, CA, United States, 94305; 650-498-6012; sherlock@genome.stanford.edu

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


title: CJ4

status: Public on Aug 26 2005


title: FHCRC Chicken 13K v2.0

status: Public on Feb 05 2005

organism: Gallus gallus

description:
The 13,000-feature chicken spotted cDNA microarray ("Chicken 13k") manufactured at the Fred Hutchinson Cancer Research Center (FHCRC) is the result of the combined efforts of the University of Delaware (Dr. Joan Burnside), FHCRC (Drs. Paul Neiman and Jeff Delrow), and the RoslinInstitute (Dr. Dave Burt).
The array was constructed by mechanically spotting PCR products onto standard glass microscope slides. Each PCR product is represented once on the array. In addition, each array sub-grid (i.e., "block") contains spots representing 4 different Arabidopsis genes (negative control) and 1
spot consisting of sheared chicken genomic DNA.  The clones represented in the platform description file total 15,769; however, after identifying poor quality PCR products (e.g., no detectable product, detection of multiple products), the number of useable features actually totals 13,007, including control features.

first: Jeff

last: Delrow