title: CapitalBio Silkworm microRNA _microarray Release 1

status: Public on Feb 21 2010

city: Beibei

first: Qingyou

last: Xia

state: Chongqing

address: Tiansheng Road

department: College of Biotechnology

country: China

institute: Southwest University

organism: Bombyx mori

technology: spotted oligonucleotide

distribution: custom-commercial

manufacture_protocol:
1.Specification of microarray test over silkworm microRNA. Antisense probes of 40 nt corresponding to 106 miRNAs were synthesized and were then printed with the Biochip Microarrayer, SmartArrayTM (CapitalBio Corp., Beijing, China ), on the chemically modified slides of 75×25 mm. Probes of U6 and 5srRNA were also printed on the slides as the internal controls; probes of 8 artificial sequences with 30 nt each were printed on the slides as the exogenous control (Zip5,Zip13,Zip15,Zip21,Zip23,Zip25,Y2,and Y3). Hex was used as the immobilized positive control,  50% DMSO was used for hybridizing negative control. Each block has 20 rows and 18 columns, with space 2,255 µm between any two dots. The diameter of each printed dot is 130µm. Every probe has three duplicates on each block.a
2.Quality control of microarray test on silkworm miRNAs a
The quality control is mainly based on series of negative and positive controls.a
2.1 Three types of positive controlsa
(1) Positive control for immobilizationa
The artificial sequence, 5'-GTCACATGCGATGGATCGAGCTCCTTTATCATC-3', will emit very strong fluorescent signal under excitation wavelength of cy3. A scanning signal over 8,000 of this sequence means the successful immobilization of probes on the array blocks. The name of this positive control is Hex, which is presented as follows.a
Namea
HEXa
(2) Positive controls for hybridizationa
We used small RNAs, U6 and 5srRNA of the silkworm itself as internal positive controls. The probes of U6 and 5srRNA are 5?-ATTTGCGTGTCATCCTTGCG-3? and 5?-GTACTGACCACGCCCGATGTTGCTTGACTT-3?, respectively; generally, they will produce high hybridization signals over 5,000. a
(3) Microarray-systematic positive controlsa
To avoid the interference from biomaterial RNAs, the probes unrelated to samples were also printed on the blocks to ensure microarray-systematic validity. These probes are called exogenous controls, which comprise 8 artificial sequences presented in the table below. These 8 sequences are actually not homologous to or unrelated to the silkworm genome. We synthesized the corresponding RNAs with 20?30nt to the 8 probes using Ambion?s miRNA Probe Construction kit (Cat#. 1550)?and incorporated these synthesized RNAs into the sample RNAs for microarray hybridization. In general, these exogenous controls will emit signals higher than 5,000, whereas diverse signals might be detected depending on the actual amount dosed in the sample RNAs.a
ID sequence(5'-3')a
Zip23 CAGCATCGGACCGGTAATCGGACCa
Zip5 GACCACCTTGCGATCGGGTACAGCa
Zip15 GACCGGTATGCGACCTGGTATGCGa
Zip13 CAGCGGTAGACCACCTATCGTGCGa
Zip21 TGCGATCGCAGCGGTAACCTGACCa
Zip25 GACCATAGTGCGGGTAGGTAGACCa
Y2 AGGTACGAAACGCTAAGAATa
Y3 CATTCCTAAACGGGCTGATa
a
2.2 Negative controlsa
We used two types of negative controls. One is the blank control printed with the gap-like liquid, the other is Y2 in the table above. Y2 is the best negative control due to no corresponding RNAs dosed in the sample RNAs. The hybridization signals from negative controls are so low that they cannot be filtered out to be valid signals for the subsequent analysis.a
a
The oligo name of a probe was denoted 'SW' followed by a serial number on the microarray. 106 probes for 92 unique miRNAs were used to establish the existence and profiling of miRNAs in the silkworm. These comprised 45 probes for the homology-found miRNAs, 2 for special silkworm miRNAs, 4 for the antisense strands of miRNAs, 42 for miRNAs of other organisms, and 13 as replicate probes (with unique ID) for several miRNAs.


title: NimbleGen Plasmodium yoelii + Mus musculus 189K array v1.0

status: Public on Feb 24 2010

city: Seattle

last: Phan

state: WA

address: 307 Westlake Av N

country: USA

institute: SBRI

organism:
Plasmodium yoelii
Mus musculus

technology: in situ oligonucleotide

description: NimbleGen design name 2006-05-15_Tarun_Plasmodium, NimbleGen design ID 3624.  Expression design for P. berghei and P. yoelli with 12 probes/gene. Additional control probes were included in separate containers.  100 copies of GFP probes (12/species) were included in the eGFP container. Design also contains 188,608 60mer probes representing 32,650 transcripts from mouse.

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


title: Illumina Genome Analyzer II (Drosophila melanogaster; Drosophila sechellia)

status: Public on Feb 19 2010

last: GEO

organism:
Drosophila melanogaster
Drosophila sechellia

technology: high-throughput sequencing

distribution: virtual


title: Multispecies miRNA 1K

status: Public on Feb 28 2010

city: Minneapolis

first: Xiaoxiao

last: Zhang

address: 312 Church St. SE

institute: University of Minnesota

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

distribution: non-commercial

manufacturer: Biomedical Genomics Center Microarray Facility at the University of Minnesota

manufacture_protocol: A miRNA probe set was purchased from Invitrogen, which was designed based on the Sanger miRBase Sequence Database, Release 9.0.  The set contains approximately 1,140 oligonucleotides of 34 to 44 nt long as probes.  They are complementary to C. elegans, Drosophila, zebrafish, mouse, rat, and human miRNAs, and also include a number of internal and negative control probes.  The oligonucleotides were dissolved in 3 x SSC and quadruply printed on Corning® GAPSTM II coated slides  using a BioRobotics Microgrid II spotter


title: Affymetrix Yeast Genome 2.0 Array [custom CDF: Sp-EMA.cdf]

status: Public on Feb 23 2010

city: Salamanca

first: Luis

last: Quintales

address: Calle Zacarías González, 2

department: Universidad de Salamanca / CSIC

country: Spain

institute: Instituto de Biología Funcional y Genómica (IBFG)

organism: Schizosaccharomyces pombe

description:
Affymetrix GeneChip Yeast Genome 2.0 (GPL2529)  Array based on a custom CDF (Sp-EMA.cdf) for Schizosaccharomyces pombe.
Identical to GPL2529 but a custom cdf environment was used to extract data. To obtain the custom CDF we filter probes present in Affymetrix Genechip Yeast Genome 2.0 Array mapping against the Sanger Centre Schizosaccharomyces pombe genome annotation release of July 17, 2009.

first: Mar

last: Sánchez

first: Francisco

last: Antequera

relation: Alternative to: GPL2529 (Alternative CDF [official])

manufacture_protocol: see the Affymetrix website


title: AB SOLiD System 3.0 (Arabidopsis lyrata)

status: Public on Feb 22 2010

organism: Arabidopsis lyrata


title: Affymetrix S. pombe Tiling 1.0FR Array [custom CDF: Sp-TMA.cdf]

description:
Affymetrix S. pombe Tiling 1.0FR(GPL7715) Array based on a custom CDF (Sp-TMA.cdf) for Schizosaccharomyces pombe.
Identical to GPL7715 but a custom cdf environment was used to extract data. To obtain the custom CDF we filter probes present in Affymetrix S. pombe Tiling 1.0FR Array mapping against the Sanger Centre Schizosaccharomyces pombe genome annotation release of July 17, 2009.

relation: Alternative to: GPL7715 (Alternative CDF [official])


title: Culex quinquefasciatus 11k by NIID Japan

city: Shinjyuku-ku, Tokyo

first: Osamu

last: Komagata

address: Toyama 1-23-1

country: Japan

institute: National Institute of Infectious Diseases, Japan

organism: Culex quinquefasciatus

last: KOMAGATA

first: Shinji

last: KASAI

first: Takashi

last: TOMITA

manufacture_protocol: Agilent's flexible SurePrint in situ synthesis


title: GIS Zebrafish 22K oligonucleotide array

city: Singapore

first: Jan

last: Brocher

address: 14 Science Drive 4, Block S1A, Level 6

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

organism: Danio rerio

description: 16.4K designed by Compugen (USA). The rest of the probes were designed inhouse by the bioinformatics department of GIS (Singapore). The array was spotted at GIS Singapore

manufacture_protocol: Oligos were resuspended in 3× SSC at 20 µM concentration and spotted onto poly-L-lysine-coated microscope slides using a custom-built DNA microarrayer in GIS (Singapore)


title: Eichler-NimbleGen Human 135K Custom CNV array

status: Public on Feb 18 2010

first: Jeffrey

middle: M

last: Kidd

address: 1705 NE Pacific St

department: Department of Genome Sciences

institute: University of Washington

organism: Homo sapiens

first: Can

last: Alkan

first: Evan

middle: E

last: Eichler

manufacture_protocol: Custom design targeting regions of predicted segmental duplication and copy-number variation.  Design is for a NimbleGen 12-plex array


title: Molecular Immunogenetics Group FMRP-USP Human cDNA 4.6K

city: Rio de Janeiro

first: Marcelo

last: Ribeiro-Alves

state: RJ

address: Avenida Brasil 4365. Manguinhos.

department: Centro de Desenvolvimento Tecnológico em Saúde

country: Brazil

institute: Fundação Oswaldo Cruz

technology: spotted DNA/cDNA

manufacturer: Molecular Immunogenetics Group, Department of Genetics, University of São Paulo School of Medicine, Ribeirão Preto, Brazil.

manufacture_protocol:
1. The Molecular Immunogenectis Group keep a human cDNA library (MTB IMAGE) with 4,500 clones from IMAGE Consortion. The clones are  0.75–1.0 kb from expressed sequence tags (ESTs) sequenced and identified with Clone ID. Each clone is preserved in plasmids in 384 wells microplates at -80°C.
2. The clones were transferred for 384 well microplates with 2x LB medium and ampicilin and incubated during 16 hours.
3. After incubation 8mL of culture were transferred to new 384 microplate with 72mL of water and incubated 10 minutes in 95°C.
4. The plates were centrifugate 4000g during 5 minutes and 10mL of supernant was used for PCR  with consensus primers for the library: primer LBP 1S (5´TGTGGATTGTGAGCGGATAA3´) e primer 1AS (5´GGGTTGAATTAGCGGAACG3´).
5. The PCR program was 5 min a 94°C, followed by 30 cycles (94°C-30 seg.; 55°C-30 seg., 72°C-2 min.), and a final step of 7 min. at 72°C and 5 min. at 4°C.
6. The quality of PCR product was verified by eletrophoresis in 1% agarose gel.
7. The PCR products were purified with sodium acetate 3M pH4.8 and absolut ethanol for 16 hours at -20°C.
8. Purified PCR products and D reagent (GE Healthcare) in same volume were transferred for 384 microplates using Array Spotter III (Amersham Molecular Dynamics).
9. The microarray were constructed on silane-coated UltraGAPS slides (Corning ® UltraGAps 40015) using a Generation III array spotter (Amersham Biosciences).
10. PCR products were deposited by a set of 12 pens that deposit 0,9nL of each sample by capillarity.
11. After print each sample group the 12 pens were washed in purified water, absolut ethanol, 0.2M KOH solution and water again. And dried with liquid nitrogen before print other samples.
12. After the print run is completed, allowed slides to dry and fixed the DNA by cross-linking by ultraviolet radiation to 500mJ of energy (Hoefer UV Crosslinker).


title: Deinococcus Radiodurans R1_Microarray V1.0

status: Public on Feb 27 2010

city: chongup

first: sun

middle: wook

last: Jeong

state: Chonbuk

address: Sinjeongdong 1266

department: Radiation biotechnology

country: South Korea

institute: Korea atomic energy research institute

organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

first: Jung

last: Sunwook

first: Joe

last: Minho

manufacture_protocol:
1. PCR produts are arrayed in 96-well round-bottom plates. Each well contains 500ng/ul of PCR products in DW
2. Mix with 5μL of PCR products in DW and 5μL of DMSO into 384-well, Genetix polystyrene V-bottom plates (cat# X6004)
3. Seal plates with Corning seals.
4. Incubate at 37℃ for 30 minutes to aid resuspension of DNA
5. Shake plates near maximum rotational speed on flat-bed shaker for 1 minute.
6. Centrifuge plates at 2000 rpm for 3minutes.
7. Remove seals and cover with plate lids. Place  plates and slides(Corning GAPSII) in microarrayer
8. Start printing slides according to microarrayer manual
9. After the print run, put out 2 microarray slides from microarrayer and prescan them with microarray scanner for spot QC
10. All microarray slide is preformed UV-cross linking to immobilize spotted DNA at 200mJ of UV energy
11. Spotted cDNA microarrays are packed in slide case and deposited in dessicator


title: Myzus persicae gene expression microarray 1.0 - Jander Lab Design ID 017179

city: Ithaca

first: John

middle: Sawyer

last: Ramsey

state: NY

address: Comstock Hall

institute: Cornell University

organism: Myzus persicae

manufacture_protocol: Agilent in situ oligonucleotide synthesis


title: SuperArray Oligo GEArray® Mouse Angiogenesis Microarray OMM-024

city: Pittsburgh

first: Jill

last: Siegfried

state: PA

address: The Hillman Cancer Center, UPCI Research Pavilion Suite 2.18, 5117 Centre Avenue

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

organism: Mus musculus

description: The Oligo GEArray® Mouse Angiogenesis Microarray profiles the expression of 113 key genes involved in modulating the biological processes of angiogenesis. This array includes the growth factors and receptors that play a role in angiogenesis. Also included are the adhesion molecules and matrix proteins involved as well as proteases and their inhibitors. Cytokines and chemokines related to angiogenesis are contained in the array along with transcription factors and other related genes.

manufacture_protocol: See manufacturer's website (http://www.superarray.com/)


title: Illumina Genome Analyzer (Arabidopsis thaliana; Turnip mosaic virus)

last: GEO

organism:
Arabidopsis thaliana
Turnip mosaic virus


title: Nimblegen T.atroviride&virens Trichochip-1 393K v1.0

status: Public on Feb 25 2010

first: Enrique

last: Monte

state: Salamanca

address: Rio Duero

department: Spanish-Portuguese Centre for Agricultural Research

institute: University of Salamanca

organism:
Trichoderma virens
Trichoderma atroviride

description: Design exception: Probe ID names including virens were incorrectly labelled in the design process as atroviride and viceversa. SEQ ID names are correctly labelled and belong to the referred genomes.

manufacture_protocol: 090209_Tricho_EM_exp: The  microarray was composed of 392,779 60-mer probes designed against 13,443  EST-derived transcripts and the genomes of T. atroviride (11,100 genes) and T.  virens (11,643 genes). Selected 5 probes per gene and have two copies of each probe set on the final array.


title: Custom Febit Shewanella oneidensis MR-1 13.5K biochip

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

organism: Shewanella oneidensis MR-1

first: Juergen

last: Lassak

manufacture_protocol: DNA-Synthesis takes place in the Geniom® One Instrument, a compact benchtop device that utilizes microfluidics for light-activated oligonucleotide synthesis and QC. This enables dynamic, effective and flexible handling of all reagents and processes required for multiplex DNA synthesis.


title: 090122_Orange_MY_exp

status: Public on Feb 20 2010

city: Cordeirópolis

first: Leonardo

middle: Pires

last: Boava

state: São Paulo

address: Via Anhanguera, km158

institute: Centro de citricultura 'Sylvio Moreira' /IAC

organism:
Citrus sinensis
Citrus trifoliata
Citrus reticulata

description:
NimbleGen design name 2005-08-12_B_fragilis_24mer, NimbleGen design ID 2451.  A expression design for 62,876 unigenes (18,712 unigenes of C. sinensis; 31,583 unigenes of C. reticulata and 12,581 unigenes of P. trifoliate) selected from CitEST database assembled from the EST submitted to NCBI (Genebank accession number EY649559 to EY842485).  Each probe is replicated 2 times.  The design includes random GC and other control probes.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.


title: AB SOLiD System 3.0 (Arabidopsis thaliana)

organism: Arabidopsis thaliana


title: Illumina Genome Analyzer (Saccharomyces bayanus x Saccharomyces cerevisiae)


title: Illumina Genome Analyzer II (Drosophila sechellia)

organism: Drosophila sechellia


title: Ocimum Biosolutions Zebrafish 14K OciChip

city: Hyderabad

first: Ocimum

last: Biosolutions

email: govind.a@ocimumbio.com, sandhya.p@ocimumbio.com, hazira.b@ocimumbio.com, anwaruddin.m@ocimumbio.com

state: Andhra Pradesh

address: Banjara Hills Road No., 1 VI Floor Reliance Classic

department: Bioinformatics

country: India

institute: Ocimum Biosolutions

distribution: commercial

first: Govind

middle: A

last: Roa

first: Rashmi

last: Sharma

first: Sandhya

middle: P

last: Kiran

first: Hazira

last: Begum

first: Deepak

last: Manohar

manufacture_protocol:
Array Design and Printing
Zebrafish 14K Ocichip consists of 14240 spots printed on Corning® epoxy coated  glass slides using Omnigrid (Gene Machines). Chip has been printed using 4x8 SMP3 pins on 75.5x 25.5x1.3 mm microarray glass slides. The origin offset values were 0 for X direction and 10000 for Y direction. The dot to dot distance is 190 mm; distance between subarrays is 150 mm and no of dots per array is 21x22=462. Oligos were printed using spotting buffer A from Ocimum Biosolution at 50% humidity and temperature at 22°C. The time taken by the robotic gridder to print Zebrafish14K altogether was 28 hrs. Each probe was checked for its performance by standard QC process followed at Ocimum Biosolutions. Printed slides were stored in a light-tight box in a bench-top dessicator, with desiccant and were kept at 4°C until they were used for hybridization


title: UKU_trout_1.8K_v1 (condensed)

city: Barcelona

first: Diego

last: Crespo

state: Barcelona

address: Avenida Diagonal 645

department: Physiology

institute: University of Barcelona

organism: Oncorhynchus mykiss

manufacture_protocol: Inserts were PCR amplified in a 96-well format with universal primers in detergent-free buffer and products were purified. Materials were consolidated to 384-well plates and spotting buffer was added. Spotting was conduced using R-ray microarray printer, a home-made spotter at Finninsh DNA Microarray Centre.


title: MIT M. Musculus Promoter array 44K

status: Public on Feb 26 2010

city: Cambridge

first: Charles

last: Lin

state: MA

address: 9 Cambridge Center

department: Biology

institute: Massachusetts Institute of Technology

manufacture_protocol: Agilent mouse 4x44k custom array


title: ABI Human Genome Survey Microarray Version 1

status: Public on Feb 21 2008

first: MONTSERRAT

last: FITO COLOMER

address: DR.AIGUADER 88

institute: IMIM


title: Illumina Genome Analyzer II (Drosophila melanogaster x Drosophila sechellia)


title: Rhesus cytomegalovirus 68-1 platform

city: Beaverton

first: Rebecca

last: Richards

state: OR

address: 505 NW 185th Ave

department: Microbiology and Immunology

institute: Vaccine and Gene Therapy Institute

organism: macacine betaherpesvirus 3

first: Scott

last: Hansen

first: Colin

last: Powers

first: Abigail

last: Ventura

first: Julia

last: Ford

first: Don

last: Seiss

first: Michael

last: Axthelm

first: Jay

last: Nelson

last: Jarvis

first: Louis

last: Picker

first: Klaus

last: Fruh

manufacture_protocol: A RhCMV comparative genomic hybridization array was created using the published sequence for RhCMV 68.1.  Oligonucleotides that comprised this array were designed to be between 29 and 32 bp, with overlapping sequences of at least 7 bp, with coverage of both strands of the RhCMV 68.1 genome.


title: NIA_Human_Achannels 9k splice array

city: Baltimore

first: Nikolai

last: Soldatov

state: MD

address: 5600 Nathan Shock Drive

institute: National Institute on Aging, NIH

manufacturer: ExonHit Therapeutics, Gaithersburg, MD, USA

first: Naomi

last: Gronich

first: Azad

last: Kumar

first: Yuwei

last: Zhang

first: William

middle: H

last: Wood

first: Kevin

last: Becker

first: Igor

middle: R

last: Efimov

manufacture_protocol: ExonHit Ion Channel SpliceArrays are manufactured by Agilent Technologies. Splice events are profiled with a combination of six exon and junction probes, that allow robust, specific detection of the two possible molecular species resulting from each splice event. The probes are synthesized in duplicate and distributed randomly on the array. Custom-built Human Ion Channel Splice Array was manufactured on the Ion Channel Splice Array sv1.1 platform containing known and potential splice events derived from 287 human sequence identities, including 248 alternatively spliced ones in total 1655 splicing events and supplemented with capabilities to recognize connexins and ryanodine receptors.


title: Ocimum Biosolutions Arabidopsis 25K OciChip

first: Ocimum

last: Biosolutions

first: Govind

last: Roa

first: Rashmi

last: Sharma

first: Sandhya

last: Kiran

first: Hazira

last: Begum

first: Deepak

last: Manohar

manufacture_protocol:
Array Design and Printing
Arabidopsis 25K Ocichip consisting of 24960 spots printed on Corning® epoxy coated  glass slides using Omnigrid (Gene Machines). Chip has been printed using 4x12 SMP3 pins on 75.5x 25.5x1.3 mm microarray glass slides. The origin offset values were 0 for X direction and 0 for Y direction. The dot to dot distance is 180 mm; distance between subarrays is 150 mm and no of dots per array is 23x23=529. Oligos were printed using spotting buffer A from Ocimum Biosolution at 50% humidity and temperature at 22°C. The time taken by the robotic gridder to print Arabidopsis 25K altogether was 30 hrs. Each probe was checked for its performance by standard QC process followed at Ocimum Biosolutions. Printed slides were stored in a light-tight box in a bench-top dessicator, with desiccant and were kept at 4°C until they were used for hybridization.


title: SuperArray Oligo GEArray® Mouse Cancer PathwayFinder Microarray OMM-033

first: Jill

last: Siegfried

description: The Oligo GEArray® Mouse Cancer PathwayFinder™ Microarray profiles the expression of 113 genes representative of the six biological pathways involved in transformation and tumorigenesis listed below. Through a simple side-by-side hybridization experiment you can simultaneously determine which of the 6 pathways is involved in your experimental treatment.

manufacture_protocol: See manufacturer's website (http://www.sabiosciences.com/)


title: BCBC Mouse PancChip 4.0 Array

city: Philadelphia

first: Chiao-Feng

last: Lin

address: 1413 Blockley Hall, 423 Guardian Dr.

institute: Penn Center for Bioinformatics

description: array containing probes representing mostly genes expressed in the pancreas

last: Kaestner

manufacture_protocol: Bacterial clones were grown to confluence overnight in flat-bottom 96-well square block plates with a volume of 1 ml LB-Amp medium per well. Plasmid DNA was prepared for each clone using a Qiagen 3000 robot, and the purified DNA was used as a template to amplify the inserts with PCR. The clones were assigned a PCR score of pass indicating a single strong band and fail if there were no bands or multiple bands. All the PCR products were purified, eluted with deioinzed sterile water, diluted with an equal volume of DMSO (Sigma) and printed on poly-L-lysine-coated slides with a Biorobotics Microgrid II. The PancCHip 4.0 contains the 3,840 elements of PancChip 2.0 plus 7226 clones derived from the mouse Consorium libraries plus various control spots.


title: Agilent-017048 Human Whole Genome ChIP Tiling Array Set 10 of 10

status: Public on Feb 11 2010

city: Palo Alto

last: Agilent Technologies

state: CA

institute: Agilent Technologies

description:
Human Whole Genome ChIP Tiling Array Set 10 of 10

Arrays of this design have barcodes that begin with 16017048 or 2517048.

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: [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array - custom CDF (AtH1_At_TAIR)

status: Public on Feb 17 2010

city: Austin

first: Thomas

middle: E.

last: Juenger

state: TX

address: 1 University Station, C0930

department: Section of Integrative Biology

institute: University of Texas at Austin

relation: Alternative to: GPL198 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: Yeast_16p_DNA_Feb_2010

city: Cerdanyola

first: Antonio

last: Casamayor

address: Edifici IBB, Campus UAB

institute: Universitat Autonoma de Barcelona

organism: Saccharomyces cerevisiae

manufacturer: DNA microarray facility. Dept. Biochemistry, Universitat Autonoma de Barcelona

first: Joaquin

last: Arino

first: Anna

last: Barcelo

first: Laia

last: Viladevall

manufacture_protocol: Constructed in our laboratory by arraying 6127 different PCR-amplified ORF from S. cerevisiae on UltraGAPS slides (Corning) using a MicroGrid TM II (BioRobotics) machine. Details on the generation of the PRC fragments and chip construction are provided in Alberola et al. Int Microbiol. 2004 7(3):199-206


title: Agilent-017036 Human Whole Genome ChIP Tiling Array Set 3 of 10

description:
Human Whole Genome ChIP Tiling Array Set 3 of 10

Arrays of this design have barcodes that begin with 16017036 or 2517036.

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-017042 Human Whole Genome ChIP Tiling Array Set 5 of 10

description:
Human Whole Genome ChIP Tiling Array Set 5 of 10

Arrays of this design have barcodes that begin with 16017042 or 2517042.

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-017025 Human Whole Genome ChIP Tiling Array Set 1 of 10

description:
Human Whole Genome ChIP Tiling Array Set 1 of 10

Arrays of this design have barcodes that begin with 16017025 or 2517025.

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: Oligo GEArray, Mouse Inflammatory Cytokines & Receptors Microarray.

city: Chicago

first: Lester

middle: F

last: Lau

state: IL

address: 900 S. Ashland Avenue

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description: An oligonucleotide array representing 113 murine inflammation-related genes (from SA Biosciences at www.sabiosciences.com, Cat. Number OMM-011.) The array is a nylon membrane based DNA microarray on which 60-mer oligonucleotides probes were printed.

manufacturer: SABiosciences Corporation, 6951 Executive Way, Frederick, MD 21703, USA.


title: DKFZ human 8k BAC chip

status: Public on Feb 10 2010

city: Heidelberg

first: Aurelie

last: Ernst

address: Im Neuenheimer Feld 280

institute: DKFZ

description: Spotted genomic DNA fragments from BACs

manufacturer: Division of molecular genetics, German Cancer Research Center, Heidelberg, Germany

manufacture_protocol: DOP-PCR products were spotted in triplicate onto NexterionTM Slide E epoxysilane-coated slides (PEQLAB, Erlangen, Germany) using a spotting robot (VersArray ChipWriterTM Pro system,BioRad, Munich, Germany) at 20C and 40% humidity. After spotting, slides were cross-linked,baked for 1 hr at 80C, and cross-linked again.


title: Agilent-017047 Human Whole Genome ChIP Tiling Array Set 9 of 10

description:
Human Whole Genome ChIP Tiling Array Set 9 of 10

Arrays of this design have barcodes that begin with 16017047 or 2517047.

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-017046 Human Whole Genome ChIP Tiling Array Set 8 of 10

description:
Human Whole Genome ChIP Tiling Array Set 8 of 10

Arrays of this design have barcodes that begin with 16017046 or 2517046.

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-017034 Human Whole Genome ChIP Tiling Array Set 2 of 10

description:
Human Whole Genome ChIP Tiling Array Set 2 of 10

Arrays of this design have barcodes that begin with 16017034 or 2517034.

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: SMD Print_1214 Homo sapiens

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

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: Wyeomyia smithii cDNA microarray (U of Oregon)

status: Public on Feb 13 2010

city: Eugene

first: Kevin

middle: James

last: Emerson

address: 5289 University of Oregon

department: Center for Ecology and Evolutionary Biology

institute: University of Oregon

organism: Wyeomyia smithii

description:
This is a spotted cDNA microarray.
ONLY CLONES OF INTEREST (30) HAVE BEEN SEQUENCED AND IDENTIFIED.

middle: J

first: William

last: Bradshaw

first: Christina

last: Holzapfel

manufacture_protocol:
Construction of the cDNA Library.
Generation of the Hybrid Line
In order to maximize the coverage in our cDNA library of the among-population variation that exists within Wyeomyia smithii, we generated a hybrid line that includes both the nuclear and cytoplasmic genomic components of eight populations representing the latitudinal and altitudinal range of the species (Table 2).  The hybrid line was created with a four-generation crossing design (Figure 4), that, in the first three generations, created eight lines that each had a single population’s cytoplasmic component combined with all eight nuclear genomes.  These eight lines were combined in the fourth generation that then contained the cytoplasmic and nuclear genetic variation present within all eight parental populations.
To begin each generation of crosses, larvae were synchronized into diapause by rearing individuals from the day of oviposition under short-day (Light:Dark = 8:16) conditions for at least 30 days.  At least 100 animals from each parental cross were then allowed to develop and mate under long-day (Light:Dark = 18:6), field-based conditions with a smooth, sine-wave thermoperiod that ranged from 13 to 29°C each day.
Creation of the cDNA library
To allow for the greatest representation of variation in the cDNA library, RNA was collected from the eight-population hybrid line.  Total RNA was extracted (TRIzol Reagent, Invitrogen) from three replicate samples of 30 III and 30 IV instar larval heads sampled at four times of day (1, 7, 13, 19 h after lights on) under both short-day (L:D = 10:14) and long-day (L:D = 18:06) conditions.  These samples (all with a 260/280 ratio of 2.0 ± 0.1) were all pooled into a total RNA pool.  One µg from this pooled RNA preparation was used to create a cDNA library using the Clontech SMART cDNA Library Construction Kit (BD Biosciences; Protocol #PT3000-1), following the manufacturer’s instructions.  Briefly, Sfi-I digested and purified cDNAs were directionally ligated and packaged into the Lamda TrplEx2 vector using Gigapack III Gold Packaging Extract (Stratagene).   The library was amplified according the Kit’s Instructions (BD Biosciences; Protocol #PT3000-1).
The phage library was converted to a plasmid library and transformed into competent Escherichia coli (BM25.8) (Clontech protocol PT3003-1).  Individual colonies were isolated, and after overnight incubation, were used as templates for Polymerase Chain Reaction (PCR) amplification using the LD-amplimer primer pair from Clontech (forward: 5’ TCCGAGATCTGGACGAGC 3’; reverse: 5’TAATACGACTCACTATAGGG 3’) with a 5’ amine modification (IDT; /5AmMC12/).  Sixteen reactions from each 96-well PCR plate were examined using 1.0% agarose gel electrophoresis to check product sizes.  Insert sizes were between 0.25 kb and 3 kb, and a vast majority of these were single products.
PCR reactions were precipitated (2.5 volumes 95% EtOH, 1/10 volume 3M NaOAc) and re-suspended in nanopure water.  Reactions were then dried under vacuum and each reaction was re-suspended in 10 µl 3X SSC.  The cDNA library was assessed for redundancy by sequencing 1000 random clones.  Of the 1000 sequences, 43.2% were unique suggesting that the library has a redundancy of ~60%.  As the redundancy was low for a cDNA library, no normalization was performed.
Printing of Microarrays.
The W. smithii microarrays were printed on silylated aldehyde (CEL-1) glass slides at the Genomics Facility of the University of Oregon.  The slides were printed, allowed to dry overnight, and then UV cross-linked at 6000J.  On the day of hybridization, slides were post-processed by immersing slides in a wash buffer (5X SSC, 0.1% SDS, 0.1 mg/mL BSA) at 42ºC for 60 minutes, and then washing the slides three times in 0.1X SSC.  The slides were then immersed in the blocking solution (2X SSC, 0.05% SDS, 2.5 mg/mL NaBH4).  After 3 washes in 0.1X SSC, slides were dried by centrifugation at 800 rpm for 5 minutes.


title: Agilent-017038 Human Whole Genome ChIP Tiling Array Set 4 of 10

description:
Human Whole Genome ChIP Tiling Array Set 4 of 10

Arrays of this design have barcodes that begin with 16017038 or 2517038.

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 Burkholderia cenocepacia 11K

status: Public on Feb 06 2010

city: Boston

first: Deborah

middle: R.

last: Yoder-Himes

address: 77 Louis Pasteur Ave, 1038 NRB

department: Microbiology and Molecular Genetics

institute: Harvard Medical School

organism: Burkholderia cenocepacia

manufacture_protocol: see the manufacturer's website


title: Agilent-017045 Human Whole Genome ChIP Tiling Array Set 7 of 10

description:
Human Whole Genome ChIP Tiling Array Set 7 of 10

Arrays of this design have barcodes that begin with 16017045 or 2517045.

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: RT2 miRNA Mouse Genome PCR Array

status: Public on Feb 05 2010

city: Jefferson

first: Zhiguang Li

state: AR

address: HFT130, 3900 NCTR Road

department: Division of Genetic an Reproductive Toxicology

institute: National Center for Toxicological Research

first: Zhiguang

last: Li

first: Tao

last: Chen

manufacture_protocol:
MicroRNA (miRNA), first discovered in C. elegans in early 1990s, are a class of naturally occurring small RNA molecules, generally 17 to 30 nucleotides long, processed from much larger stem-loop structures (pri-miRNA and pre-miRNA). Mature miRNA is recognized by and guides the RNA-Induced Silencing Complex (RISC) to specific messenger RNA transcript sequences, causing either translation repression or mRNA degradation. This phenomenon adds even more complexity to the regulation of gene expression. Each miRNA can regulate multiple mRNA targets, and a single target mRNA may be regulated by multiple miRNA sequences. Researchers are currently correlating miRNA expression profiles to biological phenotypes in attempts to better understand miRNA-based regulation of gene or mRNA expression.
The RT2 miRNA PCR Array, a patent-pending technology from SABiosciences, is the latest innovation designed to analyze miRNA expression using real-time, reverse transcription PCR, or qRT-PCR, the most sensitive and reliable method for nucleic acid expression analysis. The arrays take advantage of a SYBR Green real-time PCR detection system optimized for high performance to analyze the expression of many mature miRNA sequences simultaneously. Each 96- or 384-well array plate contains a panel of primer sets for a thoroughly researched set of 88 or 376 relevant, pathway- or disease-focused miRNA, plus four housekeeping assays and two RNA and PCR quality controls. The RT2 Genome miRNA PCR Arrays reflect miRNA sequences annotated by the Sanger miRBase Release 14, and are available for the human (704/752:96/384), mouse (528/579:96/384), and rat (352/370:96/384). (See Figure 2 for the layout of a typical PCR Array.) The specificity and single mismatch discrimination, sensitivity and dynamic range, and reproducibility of the miRNA expression analysis is guaranteed when using the complete miRNA PCR Array System.
To complete the miRNA PCR Array procedure, reverse transcribe your experimental small RNA samples into first strand cDNA, the template for the PCR, using our RT2 miRNA First Strand Kit. (See Figure 1 for an overview of the miRNA PCR Array procedure.) Then, mix the template with one of our instrument-specific and ready-to-use RT2 SYBR Green qPCR Master Mixes. Aliquot the mixture into each well of the same plate containing the predispensed miRNA-specific assays. Perform PCR, and finally determine relative expression with your real-time instrument and the Ct method. The simplicity of the miRNA PCR Arrays makes them accessible for routine use in every research laboratory.
Platform instruction link: http://www.sabiosciences.com/Manual/mirnapcrarray.pdf


title: Illumina Genome Analyzer (Brachypodium distachyon)

status: Public on Feb 04 2010

last: GEO

organism: Brachypodium distachyon


title: TIFR-Rat-8X15K v1.0

city: Mumbai

first: Madhurima

last: Benekareddy

state: Maharashtra

address: 1, Homibhabha Road, Colaba

institute: Tata Institute of Fundamental Research

organism: Rattus norvegicus

first: Vidita

last: Vaidya

manufacture_protocol: Refer www.opengenomics.com


title: Pinctada maxima 5K

city: Pacific Grove

first: Luke

last: Gardner

state: California

address: 120 Ocean View Blvd, Hopkins Marine Station

institute: Stanford University

organism: Pinctada maxima

description: ONLY CLONES OF INTEREST HAVE BEEN SEQUENCED AND IDENTIFIED

middle: D

first: Abigail

last: Elizur

manufacture_protocol: cDNA clones, generated using the SMART cDNA library construction kit (Clonetech, Mountain View, CA, USA), were amplified using kit supplied primers and spotted (split pin spotter) onto glass, aminosilane slides. The slides were baked and UV cross linked to bind the DNA.


title: Potato bacteria 19586 pathogenicity island array

status: Public on Feb 01 2010

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

organism:
Streptomyces scabiei
Streptomyces turgidiscabies

description: 40mer oligos

manufacture_protocol: See manufacturer's website


title: MHP Human 1Mb_Chr18 CGH array

first: George

last: Poulogiannis

address: Tennis Court Road

department: Pathology

country: United Kingdom

institute: University of Cambridge

organism: Homo sapiens

description: The 1Mb and Chromosome 18 clone set has been assembled by the Mapping Core, Map Finishing and Microarray Facility groups of the Wellcome Trust Sanger Institute, Hinxton, UK. Additional clones were also kindly supplied by the Wellcome Trust Sanger Institute. The array has 312 subarrays (13 rows by 24 columns), each subarray consists of 18 rows by 18 columns.

manufacturer: Department of Pathology, Univeristy of Cambridge

first: Koichi

last: Ichimura

first: Danita

last: Pearson

first: David

last: Carter

first: Anthony

last: Brown

first: Ming

middle: Q

last: Du

first: V

last: Collins

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


title: National Engineering Research Center mammalian microRNA microarray

city: beijing

first: wu

last: jp

address: 18 Life Science Parkway

institute: National Engineering Research Center

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: Altogether 924 mature miRNA sequences were assembled and integrated into our miRNA microarray design, these comprised 677 human (including a further 122 predicted miRNA sequences from published references (Xie et al., Nature 2005,434:338-345 ), 292 rat and 461 mouse mature miRNAs from the miRNA Registry (Sanger, accessed Aug. 2007). In addition, we designed 8 short oligonucleotides that possessed no homology to any known RNA sequence and we produced their corresponding synthetic miRNAs by in vitro transcription using Ambion's miRNA Probe Construction kit (Cat. No.1550, Austin, TX). We added various amounts of these synthetic miRNAs into the human miRNA samples prior to analysis as internal controls.

manufacture_protocol: as described in CapitalBio lab manual


title: AB SOLiD System (Mus musculus)

organism: Mus musculus


title: JCOLL Zebrafish 189 qRT-PCR v1.0

city: Madrid

first: Julio

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

institute: INIA

organism: Danio rerio

technology: RT-PCR


title: Streptomyces scabiei (potato bacteria) 19585 oligo array

description:
Agilent 60mer
Array probes (those which are of interest in this study) are from two bacteria genomes: S.turgidiscabies and S.scabies.


title: Neisseria meningitidis MC58 hfq- mutant examination array

first: Ryan

middle: S

last: McClure

address: 650 Albany St.

department: Microbiology

institute: Boston University

organism: Neisseria meningitidis MC58

description:
DNA microarrays were designed by Nimblegen Inc. (Nimblegen, Madison, WI) using the N. meningitidis MC58 genome as a reference (Genbank, accession # NC_003112) (Tettelin et al., 2000).  Arrays were designed using the Nimblegen 4-plexTM format consisting of four arrays on each individual chip.  Each array contained 72,000 probes, for a total of 385,000 probes per chip.   For interrogation of each target open reading frame, ten unique corresponding 60-mer synthetic DNA oligonucleotide probes were synthesized directly onto Nimblegen 4-plexTM arrays, and each probe was printed in duplicate.  100% of identified open reading frames were represented on the arrays.  Intergenic probes were also printed on each array in duplicate.  An additional set of 859 random sequence oligonucleotide probes were designed and included on the arrays to estimate non-specific binding.
The design (.ndf) file and description (.ngd) file are available as Supplementary files (at the foot of this record).
The .ndf file contains oligo probe sequence information.
NCBI Reference Sequence: NC_003112.2

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


title: Chromosome 3 dedicated BAC/PAC array with 3q26.3 tiling coverage for arrayCGH

status: Public on Feb 08 2010

city: ILLKIRCH

first: Thomas

last: Hussenet

address: 1 rue Laurent Fries

department: Cancer Biology Department

country: France

institute: IGBMC

first: Bernard

last: Jost

first: Stanislas

last: du Manoir

manufacture_protocol: Two-level polymerase chain reaction (PCR) amplifications were used to prepare DNA for spotting. BAC DNAs were extracted using Millipore (Billerica, MA) Montage BAC96 miniprep kit following supplier instructions after culture in 96-well plates with 1.5 mL 2× LB medium. Each BAC was then amplified by two independent degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) procedures using two different primers: 6MW and DOP2. About 75 ng of DNA of the primary DOP-PCR products was then amplified through a secondary PCR. Finally, PCR products corresponding to a single BAC were pooled, ethanol-precipitated, dried, and resuspended in 75% formamide and 25% water for spotting using a Microgrid II automated microarrayer (Biorobotics; Genomic Solutions, Ann Arbor, MI) on GAPS II slides (Corning Life Sciences, Acton, MA).


title: 2006-07-18_MM8_RefSeq_promoter

status: Public on Feb 09 2010

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description:
UCSC MM8; NCBI Build 36
Promoter design based only on normal RefSeq genes (NM_) for mouse (MM8; NCBI Build 36). Includes 2000 bp upstream of transcriptional start and 500 bp downstream. Isothermal probes using dual tm/cycle restriction:, 50-75 bp, tm 76, 148 cycles, 15-mer frequency of 100. Interval spacing of 100 bp

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


title: Agilent Human miRNA Microarray Rel12.0

city: Nashville

first: Kimryn

last: Rathmell

state: TN

address: 2220 Pierce Ave

department: Medicine

institute: Vanderbilt

manufacture_protocol: see manufacturer's website


title: Streptomyces scabiei (potato bacteria) 15758 oligo array


title: Chromosome 3 dedicated BAC/PAC array for arrayCGH


title: IU/UNC Coprinopsis cinerea

city: Bloomington

first: Claire

last: Burns

state: IN

address: 1001 E 3rd St

institute: Indiana University

organism: Coprinopsis cinerea

manufacturer: Indiana University Center for Genomics and Bioinformatics

manufacture_protocol: Synthesised 70mer oligonucleotides (Illumina) designed using ArrayOligoSelector, resuspended at 20uM in 3xSSC.  Printed on amine slides (Cel) using an Omnigrid 300 microarrayer.


title: Illumina Genome Analyzer (Corallus hortulanus)

status: Public on Jan 15 2010

last: GEO

organism: Corallus hortulana


title: Agilent Clostridium perfringens 15K array

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

organism: Clostridium perfringens

description:
Clostridium Perfringens S13 expression array (Genome + plasmide)
The ID column represents the Agilent Feature Extraction feature number.

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


title: Oxford Gene Technology Chip2 Salmonella typhimurium microarray SL1344 strain product code: 010021

status: Public on Feb 07 2010

city: Hamilton

first: Brian

last: Coombes

state: Ontario

address: 1200 Main St. West

department: Biochemistry & Biomedical Sciences

country: Canada

institute: McMaster University

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

manufacture_protocol: 60bp oligonucleotide probes spaced approximately 60bp apart throughout the genome (42,021 for the genome, additional probes for the three plasmids).  Probes were evenly distributed between strands.  Probes were synthesised on the glass surface by ink jet printer which deposits phosphoramidites onto the glass (ink-jet in-situ synthesis) followed by coupling and repeat of the cycle.  Probes are spotted onto standard 1 by 3 microscope slides with four arrays per slide.


title: Agilent-017044 Human Whole Genome ChIP Tiling Array Set 6 of 10

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Human Whole Genome ChIP Tiling Array Set 6 of 10

Arrays of this design have barcodes that begin with 16017044 or 2517044.

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: C. coli design 1_slide ID #4649

status: Public on Feb 02 2010

city: Ithaca

first: Michael

last: Stanhope

state: NY

address: Schurman Hall

department: Population Medicine and Diagnostic Sciences

institute: Cornell University

organism: Campylobacter coli


title: C. coli design 2_slide ID #5543


title: Salmonella whole-genome custom Agilent array

city: College Station

first: Huaijun

last: Zhou

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

organism: Salmonella enterica

first: Scot

last: Dowd

first: Hsin-I

last: Chiang

manufacture_protocol:
Two-Color Microarray-Based Gene Expression Analysis
Protocol
For use with Agilent Gene Expression oligo microarrays
(Version 5.0.1) August 2006


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array [HGU133Plus2_Hs_ENSG (v11.0.1) CDF]

status: Public on Dec 01 2008

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

description: This is identical to GPL570 but a custom CDF environment was used to extract data. The custom chip definition files (CDF) was based on Ensembl gene annotation from build 42 rather than Affymetrix annotation (Dai et al., PMID: 16284200).

manufacture_protocol: see manufacturer's web site


title: 3D-Gene Mouse miRNA Oligo chip v13.0

status: Public on Jan 26 2010

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

manufacture_protocol: See manufacture's web site