title: AB SOLiD System 3.0 (Aspergillus niger)

status: Public on Nov 21 2011

last: GEO

country: USA

organism: Aspergillus niger

technology: high-throughput sequencing

distribution: virtual


title: Illumina HiSeq 2000 (Saccharina japonica)

organism: Saccharina japonica


title: 454 GS FLX (Hordeum vulgare)

status: Public on Nov 22 2011

organism: Hordeum vulgare


title: NimbleGen IGH Mus musculus array [100718_MM9_EXP]

city: MARSEILLE CEDEX 09

first: Christelle

last: Cayrou

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

organism: Mus musculus

technology: spotted oligonucleotide

distribution: custom-commercial

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


title: Ecogenomis Medaka EG21000 CustomArray

status: Public on Jun 16 2012

city: Itakura-machi

first: Shosaku

last: Kashiwada

state: Ora-gun, Gunma

address: 1-1-1 Izumino

department: Department of Life Sciences

country: Japan

institute: Toyo University

organism: Oryzias latipes

description:
Japanese medaka
oligo DNA (35 to 40-mer)
20,960 spots were designated to Oryzias latipes (medaka fish) gene probes on this microarray.  In addition, 351 negative control probes (derived from bacteria, plants, and bacteriophages) were spotted, and 66 factory QC probes were also spotted on the microarray.  Therefore, signal data from total of 417 control spots were included in 21,377-spot data on the custom-designed Oryzias latipes 21K oligo DNA microarray.


title: Illumina Genome Analyzer II (Streptomyces griseus)

status: Public on Nov 30 2011

organism: Streptomyces griseus


title: UCSF_MouseArray_1.0_972 [BAC array]

city: San Francisco

first: David

last: Quigley

state: CA

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

technology: spotted DNA/cDNA

distribution: non-commercial

manufacture_protocol: Isolation of BAC/P1 DNA. We inoculated 0.1ul of a glycerol stock of BAC or P1 containing bacteria into 5 ml LB media containing chloramphenicol (10 ug/ml) or kanamycin (50 ug/ml) for BACs or P1s, respectively and incubated the cultures overnight (~16 h) at 37 degrees C with agitation at 225 rpm. We prepared larger cultures for DNA isolation, by inoculating 25 ml LB media, containing the appropriate antibiotic with 200 ul of the previously grown overnight culture and incubating in a shaking incubator at 37 degrees C at 225 rpm overnight (~16 h). We monitored bacterial growth by measuring the OD of a 1:10 dilution, which preferably ranged between 0.25 and 0.35 at a wavelength of 600 nm. We used the Qiagen Plasmid Mini kit to isolate DNA, following a modified version of the Qiagen Plasmid Mini Purification protocol. We transferred the 25 ml cultures into 50 ml tubes and centrifuged them for 15 min at 4000 rcf at 4 degrees C to pellet the bacteria. We re-suspended the pellet in Qiagen buffer P1 (1.5 ml), containing RNase A at the manufacturer’s recommended concentration and then added buffer P2 (1.5 ml). We mixed the tubes extremely gently by inversion and incubated at room temperature for 5 min. Then, we added buffer P3 (1.5 ml), again mixed very gently by inversion and incubated on ice for 10 min. We inverted each tube once and centrifuged at 4000 rpm at 4 degrees C until the supernatant became clear (45 to 60 min). We filtered the supernatant through a 35-micron nylon mesh prior to loading onto Qiagen-tip 20 columns, which had been equilibrated following the manufacturer’s protocol. We followed the manufacturer’s protocol for the DNA isolation steps with the exception that the elution buffer QF was heated to 65 degrees C before it was added to the column. After elution, we added 0.56 ml isopropanol to the DNA and incubated overnight at 4 degrees C. We collected the DNA pellet by centrifugation for 45 min at 14000 rpm at 4 degrees C. After aspirating the supernatant, we allowed the pellet to dry in air for at most 30 min before re-suspending the DNA in 50 ul of H2O. We determined the DNA concentration using a fluorometer. The yield typically ranged between 60-100 ng/ul (i.e. 3-5 ug per isolation). To ascertain DNA purity, we digested each BAC (200 ng) with HindIII and electrophoresed the digest through a 0.75% agarose gel. We discarded DNA preparations that showed a significant contamination with host bacterial DNA, seen as a background smear of degraded DNA in the gel. Preparation of BAC/P1 DNA representations by ligation-mediated PCR. We digested the DNA with MseI by incubating overnight at 37 degrees C in a 5 ul reaction containing 1.5 ul DNA (20 to 600 ng), 0.4 U/ul MseI (New England Biolabs), and 0.4x One-Phor-All-Buffer-Plus (Amersham). For ligation of adapters, we diluted 1 ul of each digest to a final concentration of 1 ng/ul with H2O and then mixed 1 ng of the digested DNA with 0.5 ul One-Phor-All-Buffer-Plus (10x, Amersham), 0.5 ul of 100 uM Primer 1 (TAACTAGCATGC), 0.5 ul of 100 uM Primer 2 (5’ aminolinker AGTGGGATTCCGCATGCTAGT) and 5.5 ul H2O. We incubated the mixture at 65 degrees C for 1 min after which we ramped the temperature down to 15 degrees C with a ramp-speed of 1.3 degrees C per minute. When the temperature reached 15 degrees C, we added 1 ul of 10 mM ATP and 1 ul T4-DNA ligase (5 U/ul, Gibco BRL) and continued incubation at 15 degrees C overnight. To initiate the first round of PCR amplification, we added a 40 ul mixture, consisting of 3 ul PCR Buffer 1 (Expand Long Template PCR System, Roche), 2 ul of a mixture of each nucleotide (10 mM) and 35 ul H2O to the ligation reaction. Before we started the PCR program, we incubated the reaction at 68 degrees C for 4 min and then added 1 ul DNA polymerase (3.5 U/ul, Expand Long Template PCR System, Roche). We carried out thermal cycling in a Perkin-Elmer Gene Amp PCR System 9700 block as follows: 94 degrees C for 40 s, 57 degrees C for 30 s, 68 degrees C for 1.25 min for 14 cycles, followed by, 94 degrees C for 40 s, 57 degrees C for 30 s, 68 degrees C for 1.75 min for 34 cycles and 94 degrees C for 40 s, 57 degrees C for 30 s and 68 degrees C for 5 min for the final cycle. We electrophoresed 3.5 ul of the PCR product through a 1% agarose gel to determine the size range of the amplified DNA, which ideally ranged from 100 to 2000 bp. To make the DNA for spotting on the arrays, we carried out a second round of amplification in a 100 ul reaction containing 1 ul of the primary PCR product, 4 uM Primer 2, TAQ-buffer II (1x; Perkin Elmer), 0.2 mM dNTP mix, 5.5 mM MgCl2 (Perkin Elmer), 2.5 U Amplitaq Gold (Perkin Elmer) and H2O. We carried out an initial incubation at 95 degrees C for 10 min in a MJ Research Peltier Thermal Cycler 225, followed by 95 degrees C for 30 s, 50 degrees C for 30 s and 72 degrees C for 2 min for 45 cycles and finally 7 min at 72 degrees C. This reaction yields ~10 ug of DNA, with each fragment containing a 5’ amino linker. Preparation of DNA spotting solutions. We evaporated the amplification reaction (100 ul) to a final volume of 50 ul by incubation at 45 degrees C in a hybridization oven (Techne, Hybridizer HB-1D) for approximately 75 min and then added 2.5 volumes of ice-cold ethanol and 0.1 volumes of 3 M NaOAc to precipitate the DNA. (The use of ethanol precipitation proved superior to isopropanol precipitation.) We inverted the tubes and chilled them at –20 degrees C for 15 min before collecting the precipitate by centrifugation at 1699 rcf for 90 min. We washed the pellets with 70% ethanol (150 ul) and collected them by centrifugation at 1699 rcf for 45 min. We air-dried the pellets for approximately 60 to 90 min and then re-suspended them in 12 ul of 20% DMSO in H2O (~0.8 ug/ul). We transferred the DNA solutions into 864 well microtitre plates for robotic arraying. Previously, we prepared DNA for spotting in 80% DMSO and 0.3 ug/ul nitrocellulose. However, we subsequently evaluated spotting solutions containing various concentrations of dimethyl formamide, formamide or DMSO, with or without nitrocellulose. We determined that nitrocellulose was not required for spotting DNA prepared by PCR using primers with 5’amino linkers and that spotting solutions made with 20% DMSO performed well. We have also generated representations of large insert clones for arraying by using degenerate oligonucleotide primed PCR and by amplification of mixtures of subclones from BACs, but found the ligation-mediated PCR procedure to be superior. Array printing. We used a custom built printer, employing a 4 x 4 array of quartz capillary tubes spaced on 3 mm centers to print ~70-100 μm diameter spots on 130 μm centers. We printed each DNA solution in triplicate to create an array of ~7500 elements in a 12 mm square area. We printed the arrays on chromium coated microscope slides (PTI or Nanofilm) for these studies, but also routinely print the arrays on glass slides (Corning GAPs). We allowed the printed slides to dry overnight, then exposed the slides to UV light (65 mJ) in a UV Stratalinker 2400 (Stratagene). We hybridized to these slides without additional treatment, except for the pre-hybridization slide blocking described below. We found no indication of DNA loss from the spots at any stage of the procedure when we performed hybridization in formamide buffers at 37 °C.


title: Nimblegen S. pombe 10K

city: Tokyo

first: Akira

last: Yamashita

address: Hong

department: Department of Biophysics and Biochemistry

institute: University of Tokyo

organism: Schizosaccharomyces pombe

technology: in situ oligonucleotide

description:
TI4896_60mer_expr.ndf
TI4896_60mer_expr.ngd

manufacture_protocol: See manufacturer's website


title: NimbleGen Human 2.1M array [100428_HG19_CHARM_HX1]

status: Public on Nov 29 2011

city: Baltimore

first: Akiko

last: Doi

state: MD

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

organism: Homo sapiens

description:
Custom design.
Annotation based on UCSC human genome assembly Feb 2009 (HG19)

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


title: Agilent-031120 TLL S. cerevisiae 60K v1.0 (Probe Name version)

status: Public on Nov 23 2011

city: Singapore

first: Guillaume

last: Thibault

address: 1 Research Link, National University of Singapore

department: Cell Stress and Homeostasis

country: Singapore

institute: Temasek Life Sciences Laboratory

organism: Saccharomyces cerevisiae

description: The ID column represents the Agilent Probe Names.

manufacture_protocol:
see manufacturer's web site at http://www.agilent.com/
http://www.genomics.agilent.com/CollectionSubpage.aspx?PageType=Product&SubPageType=ProductData&PageID=1512


title: NIAID Mmeb - Mouse 44k - mAdb [OligID version]

city: Bethesda

first: Natalia

last: Shulzhenko

address: 9000 Rockville Pike

department: Laboratory of Cellular and Molecular Immunology

institute: NIAID, USA

description: NIAID Mmeb 44k (37.5k reporters) derived from Operon Mouse V4 oligo set. Length 60 bp probe sequences were generated by extracting base 10 through base 69 from the original 70 bp Operon probe. Agilent design number is 017138. For direct access, please contact tmyers@nih.gov.

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


title: Mus musculus HoxD cluster tiling PRNFGMm2b520462F

status: Public on Nov 28 2011

city: Lausanne

first: Thomas

last: Montavon

address: SV 2843, Station 19

country: Switzerland

institute: EPFL

manufacture_protocol: Oligonucleotide tiling arrays manufactured using photolithography contain probes mapping to a 2 Mb region around the HoxD cluster. Probes corresponding to repetitive or low complexity sequences located within the region were excluded from the array. The arrays are based on NCBI build 36 of the mouse genome (mm8) and contained a total of 75,097 25-mer oligonucleotides (PM and MM) positioned every 15 bp mapping to the reverse strand of chr2: 73,709,305-75,470,233 and 6,323 probes (PM and MM) mapping to the forward strand of chr2: 74,453,853-74, 565,969.


title: LC Sciences Human miRNA v9.0

city: Philadelphia

first: Ke

last: Yuan

state: PA

address: 1900 N 12th Broad St

department: Biology

institute: Temple University

manufacture_protocol: see manufactuer's web site


title: Scheffersomyces_stipitis_CBS 6054_385k_array

city: Espoo

first: Mikko

middle: Ilari

last: Arvas

address: Tietotie 2

department: Cell Factory

country: Finland

institute: VTT Technical Research Centre of Finland

organism: Scheffersomyces stipitis CBS 6054

description:
NimbleGen design name 2007-01-31_TJ_Picst3 Nimblegen design id 5183.  Array contains 13 60-mer probes for each open reading frame. Each probe was replicated five times on the chip.  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.
native array description file: 2007-01-31_TJ_Picst3.ndf
native array description file: 2007-01-31_TJ_Picst3.ngd

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


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [hugene10stv1hsentrezg]

city: Goettingen

first: Frank

last: Kramer

address: Humboldtallee 32

department: Department of Medical Statistics

country: Germany

institute: University Medical Center Göttingen

description: Probe set data extracted from custom CDF (hugene10stv1hsentrezg.cdf)

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

manufacture_protocol: See manufacturer's web site


title: AGP Porcine 44K oligo array v2 AGPOA2

status: Public on Nov 27 2011

city: Tsukuba

first: Hirohide

last: Uenishi

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

organism: Sus scrofa

manufacture_protocol: see manufacturer's website


title: TaqMan qRT-PCR Homo sapiens Low-Density Array 380 v 2

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

country: Belgium

institute: University of Namur

technology: RT-PCR

description: TaqMan-based qRT-PCR assay similar to GPL13728


title: NimbleGen D. melanogaster Gene Expression 4x72K Array [081202_DM_TW_exp]

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

organism: Drosophila melanogaster

description:
Annotation in this record based on DM4.3 genome release
Probe Length: 60mer
4x72K per dot
designname=081202_DM_TW_exp
designid=8572


title: SA Biosciences Human Genome V2.0 miRNA PCR Arrays: MAH-3200 (MAH-3100 & MAH-3101)

city: Pittsburgh

first: Pruthvi S. R.

last: Nagilla

address: 416 Parran Hall, 130 DeSoto Street

department: Infectious Diseases and Microbiology

institute: University of Pittsburgh


title: Agilent-021623 Barley Gene Expression Microarray [Probe name version]

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

description:
Feature number version: GPL14904

H. vulgare (Barley) Oligo Microarray

Arrays of this design have barcodes that begin with 16021623 or 2521623.

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.

distribution: commercial

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


title: Agilent-024903 Common Primate Array 1x1M (Probe Name version)

status: Public on Jul 31 2012

city: Boston

first: Charles

last: Lee

state: MA

address: 221 Longwood Ave., EBRC-422

department: Pathology

institute: Brigham and Women's Hospital/Harvard Medical School

description:
Agilent catalog probes for human (hg18) were downloaded from eArray and aligned against the chimpanzee (panTro2) and rhesus macaque(rheMac2) reference genomes using BLAT. Those probes that had at least 100% match to both reference genomes were similarity filtered based on the human reference genome (i.e. probes with only 1 perfect hit to hg18 were considered for the array).

This array should not be considered as a genome-wide, unbiased copy number difference copy number discovery array. Since the probes were required to have 100% identity across human, chimpanzee, and rhesus macaque, the probes cluster together in regions of high conservation.

Probe sequences and alignment locations are based on human (hg18),however, great apes and some old world monkeys can also be applied to this array.

manufacture_protocol:
see manufacturer's web site at http://www.agilent.com/
Agilent's website at: http://www.chem-agilent.com/pdf/G4410-90020v3_1_CGH_ULS_Protocol.pdf


title: NimbleGen_Tufts University Pseudomonas fluorescens Pf0-1 373K array

first: Matthew

last: Mastropaolo

address: 136 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts Universicty School of Medicine

organism: Pseudomonas fluorescens Pf0-1

description:
NimbleGen design name 2006-07-27_TI205922_60mer, NimbleGen design ID 4328.
Catalog design for Pseudomonas fluorescens PfO-1 (Taxonomy Id: 205922) covering NC_007492. Probes selected for 5736/5736 sequences. Median number of probes/sequence is 13 with an average of 13.00. Each probe will be replicated 5 times on the chip. Probes are  randomly distributed over the surface of the array. Unused features have been filled with randomly generated probes of comparable GC content.
The .ndf and .ngd files are linked below as supplementary files.

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


title: 3D-Gene Human miRNA V16_1.0.0

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


title: JCVI Aspergillus fumigatus AF293 29.9K amplicon array [ORF version]

city: Tel-Aviv

first: Nir

last: Osherov

address: Ramat Aviv Campus

department: Medical Microbiology and Immunology

country: Israel

institute: Tel-Aviv University

organism: Aspergillus fumigatus Af293

description: This platform represents the ORF-centere version of GPL10341.

first: Stanley

last: Kim

first: John

middle: J

last: Varga

first: Dan

last: Chen

first: Yan

last: Yu

first: William

middle: C

last: Nierman

manufacture_protocol: The PCR amplicon microarray was designed based on CDS annotated from the A. fumigatus AF293 whole genome sequence.  The array consists of 29,952 spots.  The spots represent 9796 A. fumigatus AF293 genes spotted in triplicate with the remaining spots being empty.   The PCR products were printed on Corning glass UltraGAPs amino-silane coated slides at JCVI using a high density automated arrayer (Intelligent Automation, Cambridge, MA 02139).  The array consists of spots arranged 26 x 24 grids.  There are 48 grids in 4 columns (meta-columns) and 12 rows (meta-rows).


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

city: Bar Harbor

first: Ricardo

middle: Alejandro

last: Verdugo

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

manufacture_protocol: This Platform is identical to GPL6246 but a custom cdf environment was used to extract data. The custom cdf file MoGene10stv1_Mm_ENST cdf V11.0.1 was obtained from Brainarray (http://brainarray.mbni.med.umich.edu) and is linked below as a supplementary file.


title: US Army Northern bobwhite (Colinus virginianus) custom brain tissue cDNA microarray

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

organism: Colinus virginianus

description: Northern bobwhite

manufacturer: US Army, Engineer Research and Development Center (ERDC)

manufacture_protocol: Microarrays were constructed by spotting the Northern bobwhite cDNA library, ArrayControl™ Spot cDNAs (Ambion), and printing buffer blanks onto Ultra GAPS-coated microarray slides (Corning Inc., Corning, NY).  Spotted cDNAs were immobilized on the chip surface by applying 300 mJ of UV radiation in a Stratagene™ UV Stratalinker 2400 (Agilent Technologies, Waldbronn, Germany).  Each microarray included 2 technical replicates for each microarray target.


title: Affymetrix Human Genome U133 Plus 2.0 Array [CDF: XLab gahgu133plus2_2.1.0]

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

description: NCBI36/hg18 assembly

relation: Alternative to: GPL570 (Alternative CDF [official])

manufacture_protocol: See GPL570 platform for the complete description of HG-U133 Plus 2.0 manufacture protocol


title: Thermococcus gammatolerans microarray

city: Orsay

first: Arnaud

last: Lagorce

address: Université Paris-Sud 11

department: Institut de Génétique et de Microbiologie

institute: University Paris Sud

organism: Thermococcus gammatolerans

manufacture_protocol:
Array design and printing
Microarray DNA probes were designed using Primer3 Software available at the website http://primer3.sourceforge.net/ (Rozen, 2000). This program designs optimal microarray oligonucleotides of all genomic ORFs. The parameters set in the program included a probe length range between 49 and 51-mers (optimal 50mers), primer melting temperature range of 70 to 90°C (optimal: 80°C), and a BLAST identity score of 100. Oligonucleotides defined by Primer3 were synthesized by Sigma-Proligo and printed with the MicroGrid II arraying robot (Biorobotics) on commercial HydroGel slides (Schott, Germany). Quality of each microarray batch was checked using sybr green.


title: UCSF/Sil lab-Histoplasma capsulatum-G217Borfs2

city: San Francisco

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

organism: Histoplasma capsulatum

description: This is a revision of UCSF/Sil lab-Histoplasma capsulatum-G217Bprint2 (GEO accession GPL6125) adding 15 oligos relative to the original design.  The new oligo IDs are prefixed with G217Borfs2.  G217Borfs2.38n17 targets MS8 (GenBank AF292398) which is incorrectly merged with HISTO_ZT.Contig181-snap.97 in the predicted gene set, and the remaining 14 target novel transcripts identified during preliminary analysis of whole genome tiling array data (published with a revised and expanded set of novel transcripts in BMC Microbiol. 11:216).

first: Catherine

middle: K

last: Foo

first: Anita

last: Sil

first: Diane

middle: O

last: Inglis

manufacture_protocol: Spotted using DeRisi arrayer in Center for Advanced Technology, Genentech Hall, Mission Bay.  70-mer oligonucleotides representing each predicted gene are resuspended in 3XSSC and spotted on poly-lysine slides purchased from Erie Scientific.


title: Illumina HiSeq 2000 (Physarum polycephalum)

status: Public on Nov 17 2011

last: GEO

organism: Badhamia polycephala


title: Chicken Oligo 20.6K 70-mer microarray v3

status: Public on Nov 18 2011

city: Jouy-en-Josas

first: Sylvain

last: Marthey

address: Domaine de Vilvert Bat 320

department: Animal Genetics

institute: INRA

organism: Gallus gallus

description:
Roslin/ARK Cooperative Research Chicken Array set.
The oligo set (20,673) were designed by ArK using ENSEMBL genes transcripts, the BBSRC fully sequenced set and the DT40 full length sequencing set.
This oligo set was synthesized by Operon (2007).

manufacture_protocol:
Oligo resuspension
1-1. Oligos from 20K set are arrayed by Operon in 384-well V-bottom plates (Genetix). Each well contains 1 nmol of oligo
1-2. Resuspend oligos in water (20µM) on Staccato Sciclone (Caliper LS)
1-3. Incubate at room temperature overnight shaking plates to resuspend DNA
1-4. Freeze the plates and subsequently thaw them by centrifuging at 1000 rpm for 16 minutes. Centrifuge again at 2000 rpm for 3 minutes
1-5. Take 10 µl oligos and put it into new polypropylene v-bottom plates (cat# X7022, Genetix)
1-6. Add 10 µL of 1X Pronto! Universal Spotting Solution (Corning) to each well and mix
Spotting
2-1. Centrifuge plates at 2000 rpm for 3 minutes
2-2. Oligos are ready for spotting
2-3. Spot onto glass slides (Corning, Ultragaps), with 48 Microspotting pins 946 MP3 on Q-array2 (Genetix). Humidity must be 45-50% and temperature 20-22 °C
2-4. Fix the oligos slides using UV rays (600 mJoules)
2-5. Store the slides under vacuum
2-6. After the print run is completed, cover oligos plates with seals and freeze them at -20°C in a protected environment


title: Illumina HiSeq 2000 (Culex quinquefasciatus)

status: Public on Nov 16 2011

organism: Culex quinquefasciatus


title: TaqMan qRT-PCR Homo sapiens Low-Density Array 380

first: jean-pierre

last: gillet

description: TaqMan-based qRT-PCR assay.

manufacture_protocol: See manufacturer's website.


title: Human DNA Methylation 4x72K ENCODE HG17 Targeted Tiling Array

city: Edinburgh

first: Colm

middle: E

last: Nestor

address: Western General Hospital, Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: Univeristy of Edinburgh

description:
Human genome build hg17
Tiles all biologically significant ENCODE regions
2007-04-30_HG17_encode_4plex.ndf
2007-04-30_HG17_encode_4plex.pos

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


title: SMD Print_1670 CAT07L3 (Saccharomyces cerevisiae and Methanococcus jannaschii)

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

organism:
Methanocaldococcus jannaschii
Saccharomyces cerevisiae

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: SMD Print_1530 YPROT1 Saccharomyces cerevisiae


title: LC_MRA-1001_miRHuman_12,0 (miRNA ID version)

status: Public on Nov 14 2011

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

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


title: Agilent-021623 Barley Gene Expression Microarray

last: Agilent Technologies

organism: Hordeum vulgare

description:
H. vulgare (Barley) Oligo Microarray

Arrays of this design have barcodes that begin with 16021623 or 2521623.

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: Illumina Genome Analyzer II (Colletotrichum higginsianum)

organism: Colletotrichum higginsianum


title: Illumina Genome Analyzer II (Sordaria macrospora)

organism: Sordaria macrospora


title: Illumina HiSeq 2000 (Sordaria macrospora)


title: Affymetrix Human Exon 1.0 ST Array, Ensembl transcript probe sets [custom CDF: huex10stv2_58_37c_0112.cdf]

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

organism: Homo sapiens

description:
Probe set data extracted from custom CDF:
huex10stv2_58_37c_0112.cdf
CDF contains probe set definitions for Ensembl transcripts (i.e. one probe set per transcript, probe sets with identical probe content were merged; annotation based on Ensembl version 58). Probe sequences were re-aligned to the human genomic DNA sequence (GRCh37) and subsequently annotated to Ensembl genes/transcripts/exons. Probes with multiple alignments, additional alignments allowing one missmatch or a C-G content higher 18 were discarded.

first: Julien

last: Lelong

first: Daniel

last: Bindreither

relation: Alternative to: GPL5175 (Alternative CDF [official])

manufacture_protocol: see manufacturer's web site


title: Agilent 023389 GRL_V7_Staphylococcus_aureus

status: Public on Nov 11 2011

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

organism: Staphylococcus aureus

description: 60-mers oligonucleotide probes, in-situ synthesis

first: Patrice

last: Francois

first: Adrien

last: Fischer

first: Antoine

last: Huyghe

first: Jacques

last: Schrenzel

manufacture_protocol: SurePrint Technology (in situ synthesis)


title: CombiMatrix Bovine 90K Array TM 1.0

status: Public on Nov 13 2011

city: Lodi

first: Marcello

last: Del Corvo

address: via Einstein - Loc. Cascina Codazza

department: Bioinformatics

institute: CNR-Ibba

organism: Bos taurus

description: The Bovine array includes 43,822 probes designed using the program OligoArray 2.1 (Rouillard et al. 2003): 20,859 specific oligos (35-40mer) were designed on Ensembl release 50, 19,230 were designed on Bovine Unigene and 3,550 on Bovine EST database (Jul 2008), while 183 oligonucleotides sequences, provided by the manufacturer, were used as quality and negative controls. The 90K BovineArrayTM 1.0 was designed with two replicates of each probe randomly distributed across the array to allow measurement of the variability within the array. All the procedures provided were performed as indicated by CombiMatrix protocols available at the CombiMatrix website (www.combimatrix.com)

manufacturer: University of Verona - Biotechnology Department - Functional Genomics Centre

manufacture_protocol: Probes are directly synthesized on a 90k Combimatrix array by an in situ oligo synthesis system developed by CombiMatrix Corporation (Mukilteo, USA) using the CombiMatrix CustomArray synthesizer. Standard synthesis protocol provided by CombiMatrix was used


title: Panomics_Protein/DNA array 1_MA1210

status: Public on Nov 12 2011

city: Doylestown

first: Saifur

last: Rahman

address: 3805 Old Easton Rd

institute: Drexel University

description: catalog number : MA1210


title: Duke_HspNRC1_ORF_Array_v1.0

city: Durham

first: Nicholas

last: Gillum

state: North Carolina

institute: Duke University

organism: Halobacterium salinarum NRC-1

description: Platform for gene expression microarrays in Halobacterium sp. NRC1

first: Amy

last: Schmid

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


title: Applied Biosystems Human Wnt gene set (customised) PCR array v1

status: Public on Nov 10 2011

city: Dublin

first: Antoinette

last: Perry

address: Room 2.15, Institute of Molecular Medicine, Trinity Centre, St. James's Hospital

department: Clinical Medicine

country: Ireland

institute: Trinity College Dublin

description:
PCR assay
TaqMan Low Density Custom Arrays

manufacture_protocol: see manufacturer's website


title: OMRF Human Oligonucleotide Microarray 2

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

description: gamma amino propyl silane coated slides (Corning UltraGAPS)

first: M

middle: B

manufacture_protocol: Qiagen Operon Human Genome Oligo Set version 2 70-mer oligonucleotide library was resuspended in 3x SSC as a printing buffer and spotted on Corning UltraGAPS slides using a GeneMachines OmniGrid 100 arrayer with a 48 pin configuration.


title: Agilent-013809 Custom Gene Expression Array for Lotus japonicus 1x22k (Kazusa-001)

city: Kisarazu

first: Nozomu

last: Sakurai

state: Chiba

address: 2-6-7 Kazusa-kamatari

department: Biotechnology Research

institute: Kazusa DNA Research Institute

organism: Lotus japonicus

description:
Gene specific probes were designed by the comparison of the genome sequence and the 3'-terminal sequences of the transcripts (ESTs, full-length cDNAs, and tentative contigs).
Design Format: 1 X 22K
Probe Group Name: 013809_Kazusa-001_1.  Only the arrangement (printing position) of the probes and the combination of the control probes (designed by Agilent) differ between Platforms GPL14826 and GPL14827.

first: Hideyuki

last: Suzuki

first: Mitsuyo

last: Kohara

first: Shinobu

last: Nakayama

first: Yasukazu

last: Nakamura

first: Shusei

last: Sato

first: Daisuke

last: Shibata

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


title: Agilent-015205 Custom Gene Expression Array for Lotus japonicus 4x44k (4x44K_Kazusa-001)

description:
Gene specific probes were designed by the comparison of the genome sequence and the 3'-terminal sequences of the transcripts (ESTs, full-length cDNAs, and tentative contigs).
Design Format: 4 X 44K
Probe Group Name: 013809_Kazusa-001_1.  Only the arrangement (printing position) of the probes and the combination of the control probes (designed by Agilent) differ between Platforms GPL14826 and GPL14827.


title: Agilent-029842 60K_CpG2

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

manufacture_protocol: The same as the manufacture protocol of Agilent Human CpG Island Microaray Kit, 1x244K (Catalog:G4492A).See manufacturer's web site at http://www.agilent.com/


title: NimbleGen A. thaliana Gene Expression 12x135K Array TAIR 9.0

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

institute: Huazhong Agricultural University

organism: Arabidopsis thaliana

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


title: Giardia lamblia 20K v2 array

status: Public on Nov 09 2011

city: North Grafton

first: Giovanni

last: Widmer

address: 200 Westboro Rd

institute: Tufts University

organism: Giardia duodenalis

manufacture_protocol: 2QGL, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000


title: Salmonella enterica serovar Typhimurium, LT2 (SGSC1412), version 8

city: Vancouver

first: L. Caetano

middle: M.

last: Antunes

state: BC

department: Michael Smith Laboratories

country: Canada

institute: The University of British Columbia

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

manufacturer: NIAID’s Pathogen Functional Genomics Resource Center, managed and funded by Division of Microbiology and Infectious Diseases, NIAID, NIH, DHHS and operated by the J. Craig Venter Institute

manufacture_protocol: Number of grids: 48; element type: 70-mer oligonucleotides; surface coating: aminosilane; oligonucleotides designed: 5967; replicate oligo printings: 2; controls: 500 Arabidopsis thaliana 70-mers and 10 A. thaliana amplicons.


title: Affymetrix Human Genome U133 Plus 2.0 Array [Brainarray Version 13, HGU133Plus2_Hs_ENTREZG]

first: GEO

last: admin

description: This array is identical to GPL570 but the data were analyzed with a custom CDF Brainarray Version 13, hgu133plus2hsentrezg.

relation: Alternative to: GPL570 ([Alternative CDF])

manufacture_protocol: see the Affymetrix website (www.affymetrix.com).


title: NimbleGen Homo sapiens HG18 expression array (12x135k) [2007-09-12_HG18_opt_expr]

city: Novato

first: Simon

last: Melov

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description:
This is a whole human genome array in 12-plex format provided by NimbleGen. See manufacturer's website at http://www.nimblegen.com/.
designname: 2007-09-12_HG18_opt_expr
designid: 6364


title: Illumina Genome Analyzer IIx (Aedes aegypti)

last: GEO

organism: Aedes aegypti


title: NimbleGen_mouse(MM8)_Hoxa9 and Meis1 Binding Sequence Custom Tiling Array [Design_ID: 537603]

city: Ann Arbor

first: Yongsheng

last: Huang

state: MI

address: 100 Washtenaw Ave

institute: University of Michigan

organism: Mus musculus

description:
Annotation in this record based on UCSC Mus musculus 8, Feb 2006
Genomic regions bound by Hoxa9/Meis1 in hematopoietic cells, isothermal tiling oligos at 100bp

DESIGN_ID : 537603
native array description file: 100702_YH_MM8_regions_ChIP.ndf
native array description file: 100702_YH_MM8_regions_ChIP.pos


title: Applied Biosystems Human Taqman Array MicroRNA Card A v2.0

status: Public on Nov 08 2011

city: Parma

first: Claudio

last: Casoli

address: Vicolo delle Asse 1

institute: GEMIB Laboratory

description: PCR assay

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


title: MRA-1002_miRMouse_13 [miRNA_ID version]

status: Public on Nov 05 2011

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

description:
Mouse miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 13.0.
miRNA_ID alternative to GPL8530

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


title: 454 GS FLX Titanium (Solanum lycopersicum)

status: Public on Nov 07 2011

organism: Solanum lycopersicum


title: Illumina Genome Analyzer IIx (Xenopus laevis)

status: Public on Nov 03 2011

organism: Xenopus laevis


title: 454 GS FLX Titanium (Solanum pimpinellifolium)

organism: Solanum pimpinellifolium


title: NimbleGen_mouse(MM8)_Hoxa9 and Meis1 Binding Sequence Custom Tiling Array [Design_ID: 10451]

description:
Annotation in this record based on UCSC Mus musculus 8, Feb 2006
Genomic regions bound by Hoxa9/Meis1 in hematopoietic cells, isothermal tiling oligos at 100bp

DESIGN_ID : 10451
native array description file:090807_UM_MM8_regions_ChIP.ndf
native array description file:090807_UM_MM8_regions_ChIP.pos

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


title: Applied Biosystems Human Toll-like Receptors Pathway Array

status: Public on Nov 04 2011

city: San Francisco

first: Kevin

last: Wilhelmsen

address: 513 Parnassus Ave.

department: Anesthesia

institute: University of California, San Francisco

description:
catalog number : 4418838
PCR assay
TaqMan fast 96-well PCR array plate


title: Agilent-014810 UMCU-Y44K-3.0

city: Utrecht

first: Sander

last: van Hooff

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

organism: Saccharomyces cerevisiae

description:
A-UMCU-Y44K-3.0
Agilent design ID: 014810

manufacturer: Holstege Lab, UMC Utrecht, The Netherlands

first: Dik

last: van Leenen

first: Marian

last: Groot Koerkamp

first: Philip

last: Lijnzaad

first: Linda

last: Bakker

first: Erik

last: Sluiters

first: Patrick

last: Kemmeren

first: Frank

last: Holstege

manufacture_protocol: 1. Slides are obtained from a commercial provider (Agilent) and reannotated using blat to obtain the latest gene annotations from ensembl.


title: Exiqon miRCURY LNA microRNA array v.11.0 Gene ID Version - hsa, mmu & rno

city: Philadelphia

first: Joshua

last: Friedman

address: ARC 1007B, 3615 Civic Center Blvd.

department: Pediatrics

institute: University of Pennsylvania School of Medicine

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description:
Array represents miRBase version 11.0 with additional features.
ArrayContents_CurrentNameColumnCoverage: Homo sapiens and related vira:93.31%, Mus musculus and related vira: 88.6%, Rattus norvegicus:98.85%

manufacture_protocol: See manufacturer's website (www.exiqon.com)


title: Agilent-031189 Unrestricted_Rat_miRNA_v16.0_Microarray (Feature Number version)

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Rattus norvegicus

description:
rat miRNAs miRbase 16.0

Arrays of this design have barcodes that begin with 16031189 or 2531189.

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: 454 GS FLX Titanium (Caenorhabditis elegans)

organism: Caenorhabditis elegans


title: Illumina MouseWG-6 v2.0 expression beadchip (Gene version based on mouseWG-6_V2_0_R3_11278593_A)

city: new york

first: hui

last: zhao

state: NY

address: 430 east 67th street

institute: MSKCC

technology: oligonucleotide beads


title: Applied Biosystems Human MicroRNA Array (A) plates

city: Leicester

middle: David

last: Wagner

address: Lancaster Road

department: CSMM

institute: University of Leicester

organism: Homo sapiens

description: Human MicroRNA Array (A) plates (containing assays for 377 miRNA) were used (Applied Biosystems, #4398965).


title: Exiqon custom Homo sapiens miRNA array [DesignedForVersion: miRBase ver.9.2, CurrentVersion: miRBase ver.10.0]

status: Public on Nov 02 2011

city: Shanghai

first: Weiwen

last: Jiang

address: Room305,building1,No.639 Zhizaoju Road

institute: Shanghai Ninth People’s Hospital

manufacture_protocol: See manufacturer's website: http://www.exiqon.com/array miRBase_Designed For Version=miRBase ver. 9.2 miRBase_CurrentVersion=miRBase ver. 10.0


title: LC Sciences_Vertebrate_microRNA_Version17 (MRA-1033)

city: Jefferson

first: Fanxue

last: Meng

state: AR

address: 3900 NCTR Road, HFT-130

institute: National Center for Toxicological Research

organism:
Petromyzon marinus
Danio rerio
Oryzias latipes
Xenopus laevis
Xenopus tropicalis
Gallus gallus
Ornithorhynchus anatinus
Ateles geoffroyi
Macaca mulatta
Macaca nemestrina
Symphalangus syndactylus
Pan paniscus
Pan troglodytes
Pongo pygmaeus
Homo sapiens
Canis lupus familiaris
Equus caballus
Sus scrofa
Bos taurus
Ovis aries
Mus musculus
Rattus norvegicus
Takifugu rubripes
Taeniopygia guttata
Rhinopithecus bieti
Saguinus labiatus
Tetraodon nigroviridis

description:
Platform table annotations based on miRBase release version 17
catalog number : MRA-1033
http://www.lcsciences.com/applications/transcriptomics/mirna-profiling/mirna/mirna-available-arrays/vertebrates-array-content/

manufacture_protocol: Arrays are made based µParaflo microfluidic technology.


title: Jiang lab Clostridium acetobutylicum ATCC 824 agilent 8×15K one-color v1

first: Cong

last: Ren

address: 300 Feng Lin Road

institute: Institute of Plant Physiology and Ecology, SIBS, CAS.

organism: Clostridium acetobutylicum

first: Yang

last: Gu

first: Shiyuan

last: Hu

first: Yan

last: Wu

first: Sheng

last: Yang

first: Weihong

manufacture_protocol: see Agilent Technologies's website for details (www.genomics.agilent.com)


title: JCVI PFGRC Staphylococcus aureus array v6

city: Fayetteville

first: Arunachalam

last: Muthaiyan

address: 2435 N Hatch Ave

department: Food Science

institute: University of Arkansas

organism: Staphylococcus aureus

description:
This is a condensed template of quadruplicated features of PFGRC/TIGR Staphylococcus aureus version 6 array.
For full template information please refer to: http://pfgrc.jcvi.org/index.php/microarray/array_description/staphylococcus_aureus/version6.html
The GAL Annotation File is linked as a Supplementary file at the foot of the record.


title: JCVI PFGRC Campylobacter jejuni 23K array [full array version]

city: Ames

first: Qijing

last: Zhang

state: Iowa

address: 1600 Christensen Drive

department: Veterinary Microbiology and Preventive Medicine

institute: Iowa State University

organism: Campylobacter jejuni

manufacturer: Pathogen Functional Genomics Resource Center

first: Taradon

last: Luangtongkum

first: Zhangqi

last: Shen


title: [Barley1] Affymetrix Barley Genome Array

status: Public on Jul 09 2004

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Hordeum vulgare

description:
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The GeneChip Barley Genome Array was designed and funded by the USDA-IFAFS Triticeae Improvement group (R. Wise, T. Close, G. Muehlbauer, R. Wing, and A. Kleinhofs) in collaboration with Affymetrix and the international barley community. A community effort resulted in a significant improvement to sequence quality through better clustering and derived annotations.

Sequences used for the Barley Genome Array design were collected from consortia labs submitting EST sequences and by collecting sequences from the NCBI/GenBank non-redundant database. Approximately 400,000 raw barley ESTs were submitted from 84 libraries, and about 350,000 survived quality pruning.

Stringent CAP3 clustering (-p95 -d60 -f100 -h50) was performed and resulted in 53,030 "unigenes" (26,634 contigs and 26,396 singletons). 25,500 contigs and singletons had complete 3' ends suitable for array design (see HarvEST Triticeae v0.95 and higher). This included all 1,145 known barley genes (including alleles) from the NCBI non-redundant database. The nonredundant cloned gene set was integrated with the EST clusters to aid in scaffolding the ESTs and also to retrieve any rare interesting genes (e.g., Mla, Rar1, Sgt1, Rpg1) for inclusion on the GeneChip microarray. After pruning against an enhanced Triticeae repeat element database (TREP), the exemplar set of 25,500 contigs and singletons was submitted to Affymetrix for initial computation.

Potential applications for the barley array include analysis of malting properties, pest and disease control, abiotic stress tolerance, nutritional characteristics, and reproductive development. The GeneChip Barley Genome Array was released in June, 2003.

Annotations derived from Affymetrix CSV file dated 6/23/2004

manufacture_protocol: see manufacturer's web site


title: LC_MRA-1001_miRHuman_12.0_080901 (miRNA ID version)

status: Public on Nov 01 2011

first: Christoph

last: Eicken

description:
Human miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 12.0
Alternative to GPL8365

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


title: Agilent-027004 Human Whole Genome 8x15k Oligo Microarray [mismatch]

city: Koto

first: Jun

last: Sese

state: Tokyo

institute: National Institute of Advanced Industrial Science and Technology


title: Agilent-027003 Human Whole Genome 8x15k Oligo Microarray [exactmatch]


title: Methanococcus maripaludis 1.7K

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

organism: Methanococcus maripaludis S2

first: Arkin

middle: P

last: Adam

first: Jason

last: Baumohl

manufacture_protocol: Thompson, D., Beliaev, A., Giometti, C., Tollaksen, S.,Khare, T., Lies, D., Nealson, K., Lim, H., Yates, J., Brandt, C. Tiedje, J., and Zhou, J. 2002. Transcriptional and Proteomic Analysis of a Ferric Uptake Regulator (Fur) Mutant of Shewanella oneidensis: Possible Involvement of Fur in Energy Metabolism, Transcriptional Regulation, and Oxidative Stress. Appl. Environ. Microbiol. 68:881-892.


title: DrexelMed-Plasmodium yoelii-7K-Version 2.0 [condensed version]

first: James

last: Burns

state: PA

address: 2900 Queen Lane

department: Microbiology and Immunology

institute: Drexel University College of Medicine

organism: Plasmodium yoelii

manufacturer: Center for Molecular Parasitology, Drexel University College of Medicine

manufacture_protocol:
1. Oligonucleotides with a concentration of 80 uM in dH20, from Illumina, Inc., were originally arrayed from 96-well plates into MJ Research 384-well flat-bottom plates.  Each well received an equal volume of 6X SSC so that each 65-mer oligo was a final concentration of 40 uM in 3X SSC.  Plates were then dried by SpeedVac, sealed and stored at 4C.
2. One day prior to printing, oligos were rehydrated to 40uM with sterile de-ionized water, sealed with ABGene adhesive films and incubated overnight in a humid environment with continuous agitation on a flat-bed shaker.
3. The next day, plates were centrifuged at 2K rpm for 1 min. and then stored at 4C.
4. Each plate, as needed, was unsealed and placed onto the plate holder of a Brown Lab (Stanford) style 32-pin array printer and the oligos spotted.
5. Following printing, each plate was re-sealed and stored at 4°C until re-dried and re-sealed as above.
6. For subsequent printings, oligos were resuspended in 0.5ul less sterile de-ionized water to compensate for the 0.5ul removed during the previous printing.


title: DualChip human SBCL

status: Public on Mar 25 2009

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

institute: University of Namur

manufacture_protocol:
The genes on the low density microarray (termed DualChip human SBCL) are presented in Table I in Gillet JP et al. J. Pathol. in submission. This microarray contains two arrays per slide with a range of 107 genes whose role in classification or lymphomagenesis of small B-cell lymphomas is known. The microarray is based on the Xmer technology developed by Eppendorf (Hamburg, Germany). It is composed of single strand DNA probes attached to a glass support by a covalent link. Each DNA probe is present in triplicate on the array and designed for the detection of gene expression (Figure 1).
To minimize the effect of variation sources, the microarray contains several controls which are also intended for normalization of signal intensities. This set of controls includes positive and negative hybridization controls, a positive detection concentration curve, negative detection controls, internal standards (mix of spiking RNAs), and a set of housekeeping genes. The specificity of the capture-probes has been checked in vitro and in silico. The reproducibility and the sensitivity of low density arrays (termed DualChip) were demonstrated previously:
Gillet JP, Efferth T, Steinbach D, Hamels J, de Longueville F, Bertholet V et al. Microarray-based detection of multidrug resistance in human tumor cells by expression profiling of ATP-binding cassette transporter genes. Cancer Res 2004; 64:8987-8993.
de Longueville F, Lacroix M, Barbuto AM, Bertholet V, Gallo D, Larsimont D et al. Molecular characterization of breast cancer cell lines by a low-density microarray. Int J Oncol 2005; 27:881-892.
Meneses-Lorente G, de Longueville F, Dos Santos-Mendes S, Bonnert TP, Jack A, Evrard S et al. An evaluation of a low-density DNA microarray using cytochrome P450 inducers. Chem Res Toxicol 2003; 16:1070-1077.


title: Illumina HiSeq 2000 (Pyrus x bretschneideri)

last: GEO

organism: Pyrus x bretschneideri


title: Affymetrix GeneChip Mouse Genome 430 2.0 Array [CDF: Mouse4302_Mm_REFSEQ_v11]

city: Stockholm

first: Rickard

last: Sandberg

address: Berzelius vag 35

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

organism: Mus musculus

description: This is identical to GPL1261 but a custom CDF environment was used to extract data [Brainarray Version 11.0.1, Mouse4302_Mm_REFSEQ].

relation: Alternative to: GPL1261 (Alternative CDF [official])


title: AGRF Human 8K cDNA Microarray (muscle study)

city: Melbourne

first: Christopher

last: Bye

state: Victoria

address: University of Melbourne

country: Australia

institute: The Florey Institute of Neuroscience and Mental Health

manufacture_protocol: H8K020304  Spotted  Corning GAPS-II Amino silane Slides  25x75mm Slides  Corning GAPS-II Amino silane Slides  16128 dots  Reporter Type:  PCR products of cDNA clones  Double stranded  Primer sequence used to amplify human 8K clone set plates 1-75  Reverse 5'gtgagcggataacaatttcacacaggaaacagc3'  Forward 5'ctgcaaggcgattaagttgggtaac 3'  Primer sequence used to amplify human 8K clone set plates 76-78  Reverse 5'cacaggaaacagctatgacca3'  Forward 5'acggccagtgccagcttat3'  cDNA Clone set from Research Genetics, Alabama, USA  Human 8K clone set obtained Nov 2001, Housed at AGRF, Melbourne Australia  Amplification Protocol: (Human 8K only)  0.2mM dNTP, 25 pmols each primer, 2.5 units HotStar Qiagen TAQ, 1X HotStar buffer, and 1ul straight clone culture in 100ul reactions.  95C for 15min; 7 cycles of 94C for 30s; 72C for 1min (-1C every cycle); 72C for 2min; 23 cycles of 94C for 30s; 65C for 1min; 72C for 2min; final elongation 72C for 5min; 4C 2min.  Millipore PCR plate purification, gel analysis, aliquot into 384 well plates by robot (A1,A2,B1,B2).  Resuspended in water for 4 days in fridge, then added an equal amount of DMSO.  Printing concentration was ~250 ng/ul in 50% DMSO, 6ul total.  Please see GAL file for sequence information and accession numbers for individual clones.  Post Processing: UV crosslinked 70mj; baked 2hrs at 80C; stored dessicated.  Feature Information:  ~150um diameter  Covalent and ionic attachment.  All other information, please see GAL file.  Control Elements on the array (see location on GAL file):  Amersham Lucinda Universal Scorecard version 2 spots. Spike mix available from the AGRF


title: E. coli K-12 O157 version 2.0

city: Albany

first: Craig

middle: T

last: Parker

address: 800 Buchanan St

department: PSM

country: USA

institute: USDA ARS

organism: Escherichia coli

manufacturer: Produce Safety and Microbiology, USDA-ARS, Albany, CA

manufacture_protocol:
PCR products of ORF's from E. coli K-12 str. MG1655 and E. coli O157 str. EDL933.   Spotted on Corning barcoded UltraGAPS slides using a GeneMachine Accent printer with ChipMaker pins.
PCR products resuspended to an average concentration of 0.1-0.2 µg µl-1 in 20 µl of 50% dimethyl sulfoxide (DMSO) containing 0.3× Saline-Sodium Citrate (SSC).
Spotted on Corning barcoded UltraGAPS slides using a GeneMachine Accent printer with ChipMaker pins.
The DNA was UV cross-linked to the microarray slides with a Stratalinker at 300 mJ.


title: Human MyoChip 17K oligonucleotide array

city: Nantes

first: Daniel

last: BARON

state: Loire-Atlantique (44)

address: 30 Bd Jean Monnet

department: UMR1064 - Centre de Recherche en Transplantation & Immunologie

country: France

institute: Institut national de la santé et de la recherche médicale-INSERM

description: oligonucleotide probe sequences are confidential

manufacturer: Plateforme Puces à ADN - OUEST Genopole (Nantes)

manufacture_protocol: Microarrays were prepared in-house using 50-mer oligonucleotides probes (MWG Biotech). The probes were spotted onto epoxy-silane coated glass slides using the Lucidea Array Spotter (AMERSHAM, Uppsala, Sweden). Each gene was spotted in quadruplicate and therefore spatially distributed on the slide.


title: Anopheles gambiae GAN_V2_2010

city: Baltimore

first: George

last: Dimopoulos

state: MD

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

organism: Anopheles gambiae

description: Custom-made 60-mer oligonucleotide microarray representing the full A. gambiae transcriptome.

manufacture_protocol: Agilent


title: EcoArrayBass-4x44K-001

status: Public on Dec 17 2008

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

organism:
Micropterus salmoides
Micropterus dolomieu

description: Our bass microarray contains genes for both largemouth (Micropterus salmoides) and smallmouth (Micropterus dolomieu) bass.  It was constructed by assembling over 40,000+ sequences to identify non-overlapping, unique sequences (singlets and contigs) in both species.  These data include our own proprietary sequences obtained from suppressive subtraction hybridizations and library construction plus sequence information licensed from the University of Florida.  Homology searches (Blast) were performed on these sequences in order to provide annotation (gene name) and ontology (gene function) information where present.  A total of 19,308 contigs were assembled.  Probes, 60-bases in length, were designed using Agilent’s web-based E-Array program.  The content of our bass microarray is located on our web site and contains 19,308 sequences.

manufacturer: Applied Food Technologies/EcoArray, Agilent

manufacture_protocol: EcoArray selected Agilent Technologies as the manufacturer of our microarrays for environmental toxicology.   Probes are synthesized in situ using Agilent’s inkjet based “SurePrint” technology.  These arrays are manufactured on superior quality 1” x 3” (24.2 mm x 76.2 mm) treated glass slides for overall excellent performance.  This process minimizes variability across each production lot (batch to batch) and provides the highest consistency in slide-to-slide comparisons.  These glass slide microarrays are designed for either a one- or two-color  (cyanine-3 and cyanine-5) labeling reaction, the most reliable and sensitive methods for detecting differentially expressed genes.  Agilent's Feature Extraction software, when used with a high resolution (5 micron) scanner, provides QA metrics for each indivdual microarray, ensuring quality results.  Each slide contains four individual 44K arrays.


title: Agilent-030829 Human, Rat and Mouse 8x60k Oligo Microarray [multiple species]

country: Japan

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


title: hMitChip3 cDNA Microarray

status: Public on Jan 28 2009

city: Washington

first: Yan

middle: A.

last: Su

state: DC

address: 2300 I Street NW, Ross Hall Rm555

department: Biochemistry and Molecular Biology

institute: George Washington University

first: Salvatore

last: Alesci

last: Chrousos

last: Wu

first: Irini

last: Manoli

manufacture_protocol: Bai XY, Wu J, Zhang Q, Alesci A, Manoli I, Blackman MR, Chrousos GP,  Goldstein AL, Rennert OM, Su YA.  The Third Generation of Human Mitochondria-Focused cDNA Microarray (hMitChip3) and its Bioinformatics Tools for Analysis of Gene Expression.  BioTechniques.  2007 March, 42:365-375.


title: LC_MRA-1002_miRMouse_13.0_090309

status: Public on May 19 2009

city: Houston

last: Eicken

address: 2575 W. Bellfort

institute: LC Sciences, LLC

description: Mouse miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 13.0

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


title: Culex quinquefasciatus genome array annotation 1

organism: Culex quinquefasciatus

description: Array Designer 4.2 software (Premier Biosoft International) was used to design a core set of 57- to 60-mer oligonucleotides for all predicted C. quinquefasciatus transcripts according to the software developer's instructions.  Oligonucleotides were complementary to regions within 1 kb of the 3' UTR of transcripts and had a minimal sequence identity overlap with non-target transcript sequences. Glass slide oligonucleotide microarrays were constructed by Agilent Technologies (www.agilent.com).

manufacture_protocol: Agilent Technologies


title: Atlantic Bluefin Tuna 4 X 44K Array

status: Public on Apr 10 2011

city: Pacific Grove

first: Luke

last: Gardner

state: California

address: 120 Ocean View Blvd, Hopkins Marine Station

institute: Stanford University

organism: Thunnus thynnus

description: The array is a 4 X 44K design with each sub-array representing approximately 7000 ESTs. An average of 3 different oligos are included for each EST. All EST derived oligos are duplicated on each sub-array totaling 45220 features including Agilent added features. After combining the duplicated oligos present on the array a total of 21006 unique EST oligos remain.

first: Nishad

last: Jayasundara

middle: D

last: Block

manufacture_protocol: Please refer to manufacture's website - https://earray.chem.agilent.com


title: [mjay] Custom Affymetrix Mouse Exon Junction Array

status: Public on Mar 03 2011

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

relation: Alternative to: GPL14865 (Alternative [MJAY_r2.pgf])

manufacture_protocol: see website