title: MG400 custom Nanostring codesets

status: Public on Nov 24 2014

city: Boston

first: Oleg

last: Butovsky

state: MA

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

country: USA

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

organism: Mus musculus

technology: other

distribution: custom-commercial

manufacture_protocol: according to the manufacturer’s protocol


title: Nanostring mouse Inflammation kit


title: MG447 custom Nanostring codesets

organism: Homo sapiens


title: Nanostring Mouse miRNA Assay Kit (mirBase 15)


title: Nanostring mouse MG400 chip


title: Nanostring Human Immunology Kit


title: Nanostring Human miRNA Assay Kit (mirBase 17)


title: Apis mellifera LC_miRBee

status: Public on Dec 31 2013

city: Stanford

first: Xiangqian

last: Guo

state: CA

address: 300 Pasteur Dr.

department: Department of Pathology

institute: Stanford University

organism: Apis mellifera

technology: in situ oligonucleotide

manufacture_protocol: uParaflo Microfluidics Chip X. Gao, E. Gulari, X. Zhou, Biopolymers 73, 579 (Apr 5, 2004).


title: Agilent-034167 Streptococcus mutans SmUA159_110513

city: Kagoshima

first: Kawada-matsuo

last: Miki

department: oral microbiology

country: Japan

institute: Kagoshima University

organism: Streptococcus mutans UA159

description:
14,028 probes (60-mers) were designed for the 2,012 protein-coding genes of S. mutans UA159 (up to seven probes per gene).

Arrays of this design have barcodes that begin with 16034167 or 2534167.

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: NanoString nCounter rat mRNA Custom CodeSet

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

organism: Rattus norvegicus

manufacture_protocol: see manufacturer's website


title: Agilent-026648 Landry_NIH_Nucleosome_400K_Array

status: Public on Nov 06 2014

city: Richmond

first: Joseph

middle: William

last: Landry

state: Virginia

address: 401 College Street

department: Human and Molecular Genetics

institute: Virginia Commonwealth University

description:
ES Cell  Thymocytes  Nucleosome
Arrays of this design have barcodes that begin with 16026648 or 2526648.
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.
Agilent Custom High Density Oligonucleotide 400K Array [MM9 Build]

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


title: Homarus americanus 15K array v2.1 (oligo ID version)

city: Charlottetown

first: Dan

last: Hines

state: PE

address: 550 University Ave

institute: AVCLSC

organism: Homarus americanus

technology: spotted oligonucleotide

description:
The ID column represents oligo ID

A different version of this platform with the feature numbers (UID) in the ID column is assigned accession number GPL16521

distribution: non-commercial

manufacturer: Vancouver Prostate Centre DNA Microarray Facility


title: Agilent-024768 TAL_calbicans

city: Zuerich

first: Lennart

last: Opitz

address: Winterthurerstr. 190

country: Switzerland

institute: FGCZ Zuerich

organism: Candida albicans

description:
C. albicans, Assembly21

Arrays of this design have barcodes that begin with 16024768 or 2524768.

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: 330K random-sequence peptide microarrays

city: Tempe

first: Phillip

last: Stafford

state: Arizona

address: 727 E. Tyler St.

department: Biodesign Institute

institute: Arizona State University

organism: synthetic construct

technology: spotted peptide or protein

manufacture_protocol: In-situ synthesis on silicon wafers (www.healthtell.com)


title: Agilent-027618 Mycobacterium tuberculosis H37Rv 8X15K Microarray (Probe Name version)

city: shanghai

first: qian

last: jin

address: libing road

country: China

institute: MSP

organism: Mycobacterium tuberculosis H37Rv

description: Arrays of this design have barcodes that begin with 16027618 or 2527618.


title: MRA-1038B_miRPlants_16

city: hangzhou

first: miao

last: dong

address: No.2 street

institute: Zhejiang Sci-Tech University

organism:
Pinellia pedatisecta
Pinellia ternata

manufacture_protocol:
1. Arrays are made based µParaflo microfluidic technology (Atactic Technologies).
2. 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).
3. A spacer segment of polyethylene glycol to extend the coding segment away from the substrate.
4. The detection probes are made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: Streptococcus pneumoniae JCorbeil-Spneumoniae-39-v1

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

institute: Université Laval

organism: Streptococcus pneumoniae

description: Spotted-oligonucleotide. Hybridization of primer-extension products to tag sequences

manufacture_protocol: Primer extension solution is custom-prepared in our institution.


title: LC Sciences Pig miRNA array miRPig_15_BST_100720 [miRNA ID version]

city: xian

first: Ang

last: Li

address: Xi wu Road98#

institute: Stomatological Hospital of Xi’an Jiao-Tong University

organism: Sus scrofa

description: Catalog number: MRA-2001

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: TUG/IGB-hsa/mmu/rno-2383-v16.0

status: Public on Jan 12 2014

city: Vienna

first: Michael

last: Karbiener

address: Benatzkygasse 2-6 / G

department: Global Pathogen Safety

country: Austria

institute: Takeda

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacturer: Exiqon (probe set) / Graz University of Technology (array production)

manufacture_protocol: Lyophilized oligonucleotides (Exiqon miRCURY LNA microRNA Array, ready-to-spot probe set, 6th gen, Catalog number 208410, lot number 9000, plate 1-9) were obtained in 384-well plates, dissolved in 3x SSC / 1.5 M betaine (20 µl / well), and spotted in a 4 x 4 print tip group pattern on epoxy-coated glass slides (Schott Nexterion).  For fixation, slides were baked at 120°C for 1 h.


title: NimbleGen Streptomyces coelicolor 12 × 135k array

city: Beijing

first: Keqian

last: Yang

address: NO.1 Beichen West  Road, Chaoyang District

institute: IMCAS

organism: Streptomyces coelicolor

description:
For the total 7,768 genes from Streptomyces coelicolor M145,  6 probes were designed for each sequence. 39 sequences share the same probes with the rest genes owing to the high homogeneous. The design includes random GC and other control probes.
120305_Scoel_YR_til_exp.ndf
120305_Scoel_YR_til_exp.ngd

manufacture_protocol: NimbleGen Expression user’s guide. http://www.nimblegen.com/support/dna-microarray-support.html


title: RMIT University Echinacea-specific array

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

country: Australia

institute: RMIT University

organism: Echinacea

technology: spotted DNA/cDNA

description: Specific for all species belonging to the Echinacea genus.

manufacturer: Alexandra Olarte/Nitin Mantri/Edwin Pang, RMIT University

manufacture_protocol:
In order to develop a gDNA representation for the subtraction, DNA from a total of 143 species including angiosperms and non-angiosperms were soured. Non-angiosperms were collected from Toolangi State Park, Victoria (Australia) and identified (Duncan and Isaac, 1994). Angiosperms were obtained only from verified nursery species; a total of 118 species were sourced to represent all angiosperm clades. Additionally, a total of 24 lines were used to represent the Echinacea genus. Five Echinacea species, as mentioned by McGregor (E. angustifolia, E. paradoxa, E. pallida, E. purpurea and E. tennesseensis), were obtained from three different sources. The other four species (E. atrorubens, E. laevigata, E. sanguinea, E. simulata) could not be obtained as quarantine restrictions prevented importation into Australia. Nineteen of the 24 lines were selected from the germplasm collection of the U.S. National Plant Germplasm System maintained by the USDA-ARS North Central Regional Plant Introduction Station (NCRPIS). The other remaining lines were obtained from Botanical Resources Australia (Tasmania) and from verified specimens from a specialized plant nursery (The Diggers Club, Dromana Victoria). Total DNA was extracted from fresh leaves using a modification of the standard CTAB procedure (Doyle and Doyle, 1987) and subsequent cleanup was performed by using the DNeasy® column of the DNeasy® Plant Mini Kit (Qiagen) following the protocol in the user manual.The quantity of DNA was measured using Eppendorf spectrophotometer whilst the quality/integrity was assessed by 1.5% agarose gel electrophoresis.

Genomic DNA subtraction and library construction: All DNA samples were pooled based on the Angiosperm Phylogeny Group (2009) classification (Bremer et al., 2009) in order to obtain representations of the following seven groups: all Echinacea species (subtraction pool), Asterids (excluding Asteraceae), non-angiosperms, Monocots, Magnoliids, Rosids, and Eudicots not belonging to the Rosids or Asterids (Eudicots and Core Eudicots). Subtraction was performed using the PCR-Select™ Bacterial Genome Subtraction Kit (Clontech), following the manufacturer's protocol. The Echinacea pool (tester) was prepared by mixing equal amounts of DNA extracted from the 24 genotypes mentioned above. The driver pool was formed by bulking 700 ng of each non-Echinacea representation [Asterids (excluding Asteraceae), non-angiosperms, Monocots, Magnoliids, Rosids, and Eudicots not belonging to the Rosids or Asterids]. Subsequently, 4 μg of pooled gDNA from each group was restriction digested in a 50 μL reaction using 5U of HaeIII and AluI (New England Biolabs). As previously described (Mantri et al., 2012), the digested diver gDNA pool was subtracted from digested tester gDNA pool to isolate Echinacea-specific DNA. The Echinacea-specific DNA fragments were cloned into pGEM-T® Easy Vector (Promega, Madison, WI) and transformed into Escherichia coli JM109 competent cells (Promega, Madison, WI).

Microarray construction and printing: The 283 Echinacea-specific DNA clones were amplified in 100 µl PCR reactions using nested primers 1 and 2R (Clontech). The template used for the amplification was obtained by mixing 10 µl of bacterial cell culture with 10 µl of MilliQ water and then heated at 100°C for 10 min to disrupt the cells and release the plasmid DNA. Then, 1.5 µl of this sample was used as template. After that, PCR products were precipitated in 96% ethanol and 3 M sodium acetate (pH 5.2). The precipitation was carried out at -20 °C overnight. The pellets obtained were washed with 70% ethanol, air dried and resuspended in 10 µl of 50% DMSO. Finally, a total of 283 clones with inserts ranging from 250 bp to 1000 bp were transferred individually into a 384-well plate (Genetix, Hampshire, UK), together with positive and negative controls. Among the positive controls were three housekeeping genes (ribulose-1,5-bisphosphate carboxylase/oxygenase, ribosomal RNA, and chlorophyll a/b binding protein) sourced from Cicer arietinum (Coram and Pang, 2005). The 283 clones, together with the controls, were printed on aminosilane-coated slides using a BioRobotics® MicroGrid II Compact arrayer (Genomic Solutions) at RMIT University, Australia. Ten subarrays were gridded on a Corning® GAPS II-coated slide (Corning Incorporated Life Sciences, Acton, MA). Each subarray was composed of 283 samples and 17 controls.


title: Affymetrix Rat Genome 230 2.0 Array (CDF: Rat2302_Rn_ENTREZG.cdf)

city: Leiden

first: Regina

last: Bokenkamp

address: Albinusdreef 2

department: Dept of Pediatric Cardiology

country: Netherlands

institute: LUMC

relation: Alternative to: GPL1355 (Alternative CDF [official])

manufacture_protocol: See manufacturer's web site.


title: Agilent Custom Zinkchip2 4x44K (Design ID 020962)

city: Umeå

first: Joscha

last: Muck

address: Analysvägen 1

department: UCMM

country: Sweden

institute: Umeå University


title: [Sorgh-WTa520972F] Affymetrix Whole-transcriptome Sorghum Array

city: Chicago

first: Nadia

last: Shakoor

state: Illinois

address: 10 South LaSalle Street, Suite 2100

institute: Chromatin, Inc.

organism:
Sorghum bicolor
Saccharum hybrid cultivar
Zea mays subsp. mays

description:
The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast and mitochondrial genomes.  Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e.g., microRNAs), and confirmed functional small RNAs in related species (corn and sugarcane) were also included in our array design.
The Sb01gnnnnn.n ids represent the Ensembl Transcript ids. The FRnnnn, M-sbi-miR, zma-MIRnnn, etc. are probes for small RNAs from Sorghum bicolor as well as non-Sorghum bicolor organisms (sbi=sorghum bicolor, zma=maize, ssp=sugarcane).  These were included in our microarray design as add-on probes, in case there are researchers that are interested in the expression of small RNAs.
Briefly, the PMRD sequences (zma-MIR437f, M-sbi-miR)  were obtained at the plant microRNA database http://bioinformatics.cau.edu.cn/PMRD/.  fRNAdb (FRnnnn) sequences were obtained at the functional noncoding RNA sequence database http://www.ncrna.org/frnadb/.

manufacture_protocol: see manufacturer's web site


title: CIMAP Papaver somniferum

status: Public on Dec 30 2013

city: Lucknow

first: Ashutosh

middle: K

last: Shukla

state: Uttar Pradesh

address: P.O. CIMAP

department: Biotechnology Division

country: India

institute: CSIR-Central Institute of Medicinal and Aromatic Plants

organism: Papaver somniferum

first: Nidarshana

last: Chaturvedi

first: Mridula

last: Singh

first: Ajit

last: Shasany

first: Suman

last: Khanuja

manufacture_protocol: Five microgram of total RNA was used for amplification using Amino Allyl MessageAmp™ II aRNA Amplification Kit from Ambion by linear transcription based RNA amplification system to produce cRNA. Briefly, mRNA is reverse transcribed with a oligo (dT) primer bearing T7 promoter at 42°C for 2 hrs and second strand cDNA synthesis at 16°C for 2 hrs. The resulting cDNA was then purified and was then transcribed with T7 RNA polymerase to generate multiple copies of aminoallyl antisense RNA (aRNA) at 37°C for 16 hrs. aRNA is then labelled with Cy3TM/Cy5TM post-labelling reactive dye pack (GE Healthcare, UK) at room temperature and unincorporated Cy3/Cy5  molecules were removed by purification process.


title: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZ, Brainarray v12.1.0]

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

country: Germany

institute: Universitaetsmedizin Goettingen

manufacture_protocol: See manufacturer's web site


title: Agilent-020586 Daphnia3_1_Of_1 4x44k custom array (Probename version)

city: Okazaki

first: Kenji

last: Toyota

address: 5-1 Higashiyama

institute: National Institute for Basic Biology

organism: Daphnia magna

description:
Arrays of this design have barcodes that begin with 16020586 or 2520586.

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 Probe names.

distribution: commercial


title: 3D-Gene human cytokines

city: Kamakura

first: Satoko

last: Takizawa

state: Kanagawa

address: 6-10-1 Tebiro

department: New Frontiers Research Laboratories

institute: TORAY Industries, Inc.

organism: Homo sapiens


title: Exiqon A/S miRCURY LNA microRNA Array, 6th generation - hsa, mmu & rno - miRBase 16.0

status: Public on Dec 27 2013

city: Qingdao

first: Ye

last: Wang

address: No. 5 Yan'erdao Road

institute: Shandong Eye Institute

organism:
Mus musculus
Murid betaherpesvirus 1
Murid gammaherpesvirus 4

description:
Array Contents Designed For=miRBase 16.0
ProductNumber=208400,208401,208402
LotNumberRange=34101-34101

manufacture_protocol: see Exiqon site


title: Illumina HiSeq 2000 (Rhinopithecus roxellana)

status: Public on Dec 23 2013

last: GEO

organism: Rhinopithecus roxellana

technology: high-throughput sequencing

distribution: virtual


title: NimbleGen Mus musculus 2006-08-03_MM8_60mer_expr array

city: Montreal

first: Brian

last: Wilhelm

address: 2950 Chemin Polytechnique

institute: University of Montreal

organism: Mus musculus

description: NimbleGen design name: 2006-08-03_MM8_60mer_expr, NimbleGen design ID 4543

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


title: Rhizobium etli CFN 42 385K 071203_ReCFN42JM_Tiling (probeset version)

status: Public on Dec 20 2013

city: Leuven

first: Kristof

last: Engelen

address: Kasteelpark Arenberg 20

country: Belgium

institute: KULeuven

organism: Rhizobium etli CFN 42


title: Agilent-046692 Streptomyces coelicolorA 3(2) 8X15K Microarray (Feature Number version)

status: Public on Dec 25 2013

city: shanghai

first: qian

last: jin

address: libing road

institute: MSP

organism: Streptomyces coelicolor A3(2)


title: Agilent-046692 Streptomyces coelicolorA 3(2) 8X15K Microarray (Probe Name version)


title: Agilent-026033 HORSE-GENOPOLE

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

country: France

institute: INRAE

organism: Equus caballus

description:
Horse Agilent + 384 equine oligo

Arrays of this design have barcodes that begin with 16026033 or 2526033.


city: Madison

first: Adam

last: Book

state: WI

address: 1550 Linden Drive

department: GLBRC

institute: University of Wisconsin Madison

organism: Streptomyces sp. SirexAA-E

description: UW-Madison_GLBRC_Fox_Currie Streptomyces sp. SirexAA-E (ActE) 72k v 1.0 Carbon Source Induced Gene Expression

first: Taichi

middle: E

last: Takasuka

middle: J

first: Cameron

middle: R

last: Currie

middle: G

last: Fox

manufacture_protocol:
Roche NimbleGen manufactures custom, high-density DNA arrays based on its proprietary Maskless Array Synthesizer (MAS) technology. The MAS system is a bench top, solid-state, high-density DNA array fabrication instrument comprised of a maskless light projector, a reaction chamber, a personal computer, and a DNA synthesizer. Roche NimbleGen builds its arrays using photo-mediated synthesis chemistry with its MAS system.
At the heart of the system is a Digital Micromirror Device (DMD), similar to Texas Instruments' Digital Light Processor (DLP), employing a solid-state array of miniature aluminum mirrors to pattern 786,000 to 4.2 million individual pixels of light. The DMD creates "virtual masks" that replace the physical chromium masks used in traditional arrays.
These "virtual masks" reflect the desired pattern of UV light with individually addressable aluminum mirrors controlled by the computer. The DMD controls the pattern of UV light projected on the microscope slide in the reaction chamber, which is coupled to the DNA synthesizer. The UV light selectively cleaves a UV-labile protecting group at the precise location where the next nucleotide will be coupled. The patterns are coordinated with the DNA synthesis chemistry in a parallel, combinatorial manner such that 385,000 to 4.2 million unique probe features are synthesized in a single array.


title: NimbleGen Pseudomonas putida  KT2440 12x135k

status: Public on Dec 22 2013

city: Kgs Lyngby

first: Gamze

last: Gulez

address: Miljoevej 113

department: Environmental Engineering

country: Denmark

institute: Technical University of Denmark

organism: Pseudomonas putida KT2440

description:
Custom 12x135k expression and tiling design for Pseudomonas putida KT2440 genome (AE015451) and plasmid pWW0 (AJ344068)
The expression probes were selected as follows:   Sequence and annotation for both accession numbers were downloaded from NCBI on January 18th, 2012. 5350 CDS features were extracted from AE015451 and 140 CDS features were extracted from AJ344068. The sequence IDs (SEQ_ID) for the AJ344068 include PWW0.   45-60mer probes were selected from the entire length of the 5490 CDS sequences. 6 probes were selected for 5440 sequences. 50 sequences share all 6 probes with another sequence and are represented on the array by exemplars. All 32640 expression probes were added to container EXPRESSION.      The tiling probes were selected as follows:   Probes were selected for AE015451 and AJ344068 using a median probe spacing of 1 probe starting every 58 base pairs (interval=43, window=15). Unique probes were used (mm=1). Every other probe was reverse complemented to generate reverse strand probes. 52434 forward strand probes were added to container FORWARD. 52434 reverse strand probes were added to container REVERSE.       The remainder of the array was filled with randomly generated probes of comparable length and composition.
120123_Pput_LG_til_exp_HX12.ncd
120123_Pput_LG_til_exp.ndf
120123_Pput_LG_til_exp_HX12

manufacture_protocol: Array prepared using Maskless Array Synthesizer (MAS). For more information  www.nimblegen.com


title: Agilent-031113 Streptomyces sp. C 8X15K Microarray (Probe Name version)

status: Public on Dec 24 2013

organism: Streptomyces sp. C

description:
Arrays of this design have barcodes that begin with 16031113 or 2531113.

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 Probe Name.

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: Ct 5k cDNA array  v1.0

city: Guangzhou

first: SH

last: Shi

address: 135 Xin Gang Xi

institute: Sun Yat-Sen University

organism: Ceriops tagal

manufacture_protocol: Mono-clones were collected from a root cDNA library and a leaf SSH library, and the cDNA insertion was amplified by hot-start PCR using the following program: hot-start at 94℃ and a 4 minute hold for pre-denaturation of the template; 32 cycles of 1 minute at 94℃, 30 seconds at 56℃ and 1.5 minutes at 72℃. The M13F/M13R primer pair (5’- GTA AAA CGA CGG CCA GT -3’/ 5’- AAA CAG CTA TGA CCA TGT TCA -3’) was used to prime the reactions. The PCR products were purified using the Multiscreen-PCR 96-well purification system (Millipore, Bedford, MA), dried down, resuspended in 50% DMSO before loaded onto 384-well plates. A total of 3909 cDNA from the root cDNA library and 1330 cDNA from the leaf SSH library were printed onto the poly-L-lysine modified slide (Full Moon Biosystems, Inc.) in duplicate using the GeneMachines Omingrid 100 Arrayer (GeneMachine, San Carlos). Each cDNA chip composes of 48 blocks. Within each block, additional cDNA fragments from six C. tagal housekeeping genes (actin 11, actin 2, ubiquitin 3, ubiquitin 4, 18s rRNA and β-tubulin used as positive controls) and one animal gene (serving as negative control), and the pDNR-LIB vector and 50% DMSO (for background signal monitoring) were also included.


title: Bos taurus 13.2 K 70-mer array

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

organism: Bos taurus

manufacturer: W.M. Keck Center, University of Illinois Urbana

manufacture_protocol: 70-mer oligos were printed in 150 mM Phosphate buffer at 20 uM concentration


title: State Key Laboratory Human microRNA array 1104

status: Public on Dec 28 2013

first: Mei-Yin

last: Zhang

state: Guangdong

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

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

manufacture_protocol: 1104 microRNA probes were printed onto slides using the SmartArrayerTM 136 printer (CapitalBio,Inc.,Beijing,China)


title: Agilent-031115 Streptomyces coelicolor A3(2) 8X15K Microarray (Probe Name version)

description:
Arrays of this design have barcodes that begin with 16031115 or 2531115.

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 Probe Name.

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: LC Sciences A. thaliana miRNA LC_MRA-1010_miRArabidopsisT_17

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism: Arabidopsis thaliana

manufacture_protocol: Arabidopsis thaliana miRNA microarray with 100% coverage of mature Arabidopsis thaliana miRNAs listed in miRBase version 17.0. 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://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: Illumina Genome Analyzer IIx (Vibrio parahaemolyticus)

organism: Vibrio parahaemolyticus


title: Low-density 16S rDNA array for NOMA

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: Bacteria

description: Bacterial flora; Oligonucleotides 25-mer, CloneDiag

first: Antoine

last: Huyghe

first: Patrice

last: Francois

first: Jacques

last: Schrenzel

first: Didier

last: Pittet

manufacture_protocol: CloneDiag


title: 384 TaqMan Low Density Gene Expression Array, Human Apoptosis Panel

city: Lodz

first: Ida

last: Franiak-Pietryga

address: Pabianicka 62

country: Poland

institute: Copernicus Memorial Hospital in Lodz

technology: RT-PCR

description: Human Apoptosis PCR assay panel

manufacture_protocol: see manufacturer's website


title: Agilent-035154 HFM87_33500_exp_v2 (Probe Name version)

status: Public on Dec 18 2013

city: Beijing

first: Lei

last: Cai

address: No.1 Beichen West Road, Chaoyang District,

institute: Institute of Microbiology, Chinese Academy of Sciences

organism: Haloferax mediterranei

description:
Arrays of this design have barcodes that begin with 16035154 or 2535154.

The ID column represents the Agilent Probe name.

*** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL15465


title: NanoString nCounter Human miRNA assay (v1)

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

country: Italy

institute: Consiglio Nazionale delle Ricerche (CNR)

manufacture_protocol: see manufacturer's website: http://www.nanostring.com/


title: Agilent-019078 Custom Burkholderia pseudomallei 8X15K microarray (Probe Name Version)

city: Minden

first: Hokchai

last: Yam

state: Pulau Pinang

address: Jalan Batu Uban

department: School of Biological Sciences

country: Malaysia

institute: University Sains Malaysia

organism: Burkholderia pseudomallei K96243

first: Sylvia

last: Chieng

first: Sheila

last: Nathan


title: Agilent-030273 Jatropha curcas 4X44k micrarray (probe name version)

status: Public on Dec 19 2013

first: qian

last: jin

organism: Jatropha curcas

description: Arrays of this design have barcodes that begin with 16030273 or 2530273.


title: Plant Viroid Detection Microarray

first: Yongjiang

institute: Chinese Academy of Inspection and Quarantine

organism:
Hostuviroid
Pospiviroid
Cocadviroid
Apscaviroid
Coleviroid
Avsunviroid
Pelamoviroid
Elaviroid

description: This microarray platform is designed to detect plant viroids infection at the genus level. It is able to detect a wide spectrum of all the 8 reported viroid genera, including 37 known plant viroid species.

manufacture_protocol: Microarrays were synthesized using 40-mer probes on 75-mm×25-mm glass slides using the SmartArrayer system. All probes were spotted in triplicate on the microarray. Several control probes were used to monitor the performance of the microarray. (i) The 5' amino-linker oligonucleotide (5'-TTTTTTTTTTTTTTTCTCATGCCCATGCCGATGC-3') was a random sequence which did not hybridize with any viroid sequences. The targeting sequence of this probe was mixed with the samples before hybridization. This probe was used as a positive control (PC) monitoring the probe hybridization efficiency. (ii) The internal control (HEX) was spotted on the microarray to monitor the probes linking to the chips. It was a 5' Hex-linker oligonucleotide (5'-GTCACATGCGATGGATCGAGCTCCTTTATCATCGTTCCCACCTTAATGCA-3').(iii) The spotting buffer was used as the negative control (NC). Spotted slides were air dried for 10 min and then fixed by UV exposure at 240mJ/cm2. After being incubated in a 0.5% sodium dodecyl sulfate solution at 60oC for an hour, slides were rinsed in 100 mM Tris (pH 8.0) for 5 min, and kept moist at 4oC for use.


title: Agilent-038619 Yeast ORF + regions A, B and C + KHR1 + MPR1 (Probe Name version)

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

institute: INRA

organism: Saccharomyces cerevisiae


title: [DroGene-1_0-st] Drosophila Gene 1.0 ST Array [transcript (gene) version]

city: London

first: Ariana

middle: Pia

last: Gatt

address: London

country: United Kingdom

institute: King's College London

organism: Drosophila melanogaster


title: Illumina mouse-6 v1.1 expression beadchip [Array_Address_Id version]

city: Dallas

first: yun

last: lian

address: 5323 Harry Hines Blvd.

country: USA

institute: UT Southwestern Medical Center

organism: Mus musculus

technology: oligonucleotide beads

manufacture_protocol: See manufacturers website. http://www.illumina.com


title: Agilent-032722 Halobacterium sp. NRC-1 Tiling V2 030521

status: Public on Dec 21 2013

city: Seattle

first: Nicolas

last: Pinel

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

organism: Halobacterium salinarum NRC-1

description:
Arrays of this design have barcodes that begin with 16032722 or 2532722.
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.
Halobacterium sp. NRC-1 Whole genome tiling Array. 60 bp tiles with 24 bp spacing. Includes 227 probes for ncRNAs selected from Next-Gen sequencing plus 10 probes for non-Halo random sequences that can be used for spike-in controls
Orientation:
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
The ID column represents the Agilent Feature Extraction feature number.
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: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [AltAnalyz probeset-to-Ensembl mapping]

city: Iowa City

first: S. Scott

last: Whitmore

state: IA

address: 375 Newton Road

department: The University of Iowa Institute for Vision Research

institute: The University of Iowa

organism: Homo sapiens

description: Ensembl 65 database, genome build Hg19, using only probesets mapping to consitutive exons [shared by all Ensembl transcripts for a given gene; see AltAnalyze (ver. 2.0.7 beta) documentation]

manufacture_protocol: see manufacturer's web site


title: Illumina Genome Analyzer IIx (Caenorhabditis briggsae)

status: Public on Dec 16 2013

last: GEO

organism: Caenorhabditis briggsae


title: SA Biosciences Rat Skeletal Muscle Development and Disease RT2 Profiler PCR Array

city: Gainesville

first: Heather

last: Ross

state: FL

institute: University of Florida

organism: Rattus norvegicus

description:
PCR assay
SABiosciences RT² Profiler panel of PCR assays.


title: Illumina Genome Analyzer II (Citrus reticulata)

status: Public on Dec 17 2013

organism: Citrus reticulata


title: Illumina HiSeq 2000 (Drosophila miranda)

organism: Drosophila miranda


title: Applied Biosystems Taqman Array Rodent MicroRNA Cards v3.0

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

institute: Ludwig-Maximilians-University


title: AB 5500xl Genetic Analyzer (Synechococcus sp. PCC 7002)

organism: Picosynechococcus sp. PCC 7002


title: Affymetrix GeneChip Mouse Genome 430 2.0 Array [AffyProbeMiner cdf (Mouse430_2_transcript_refseq) version 1.0.0]

city: Hamburg

first: Florian

last: Wegwitz

state: Hamburg

address: Martinistraße 52

department: Department of Tumor Biology

institute: University Medical Center Hamburg-Eppendorf

description:
An alternative probe set mapping published by the AffyProbeMiner project (remapped transcript consistent cdf-file, using validated complete coding sequences in GenBank, version 1.0.0)
Mouse430_2_transcript_refseq.cdf

manufacture_protocol: This identical to GPL1261 but an alternative cdf environment was used to extract data.


title: NimbleGen Edwardsiella ictaluri 4x72K array

status: Public on Dec 15 2013

city: Mississippi State

first: Attila

last: Karsi

state: MS

address: 240 Wise Center Drive

department: Department of Basic Sciences, College of Veterinary Medicine

institute: Mississippi State University

organism: Edwardsiella ictaluri 93-146

description:
Expression desgin for Edwardsiella ictaluri strain 93-146 (customer supplied gbk file) plus native plasmid sequences (NC_002497 and NC_002498).
native array description file: 090422_Edwardi_MS_State_AK_expr.ndf
native array description file: 090422_Edwardi_MS_State_AK_expr.ngd


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [hjay.r1 version]

city: San Sebastian

first: Ravi

middle: Datta

last: Sharma

state: Gipuzkoa

address: Parque Tecnológico de San Sebastián, Paseo Mikeletegi, Nº 48,

department: Biomedical Engineering

country: Spain

institute: CEIT

description:
probe group file: hjay.r1.pgf
meta-probeset file: hjay.r1.mps

manufacture_protocol: See manufacturers website


title: Illumina MiSeq (Brassica oleracea var. italica)

status: Public on Dec 13 2013

organism: Brassica oleracea var. italica


title: [EquGene-1_0-st] Equus caballus Gene 1.0 ST Array [transcript (gene) version]

city: Santa Clara

last: Affymetrix

state: CA

institute: Affymetrix, Inc.

organism: Equus caballus

description:
#%create_date=Wed Sep 25 10:46:24 2013 PDT
#%chip_type=EquGene-1_0-st-v1
#%lib_set_name=EquGene-1_0-st
#%lib_set_version=v1
#%genome-species=Equus caballus
#%genome-version=equcab2
#%genome-version-ucsc=equcab2
#%genome-lifted-method=NONE
#%genome-lifted_from-species=Equus caballus
#%genome-lifted_from-version-ucsc=equcab2
#%netaffx-annotation-date=2012-09-05
#%netaffx-annotation-netaffx-build=33

manufacture_protocol: See manufacturer's web site


title: NimbleGen Haemophilus influenzae R2866 4x72K Custom Expression Array [110421_HB_Hin_R2866_expr]

city: Nijmegen

first: Jeroen

middle: Daniel

last: Langereis

address: PO Box 9101

department: Department of Pediatrics

institute: Radboud University Medical Centre

organism: Haemophilus influenzae

description: Genbank accession number CP002277 was used for the array design. 4 replicate probes are present on the array.

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


title: Arraystar Human LncRNA microarray V2.0 (Probe Name version)

city: Staten Island

first: Nanbert

last: Zhong

state: NY

address: 1050 Forest Hill Road

department: Human Genetics

institute: New York State Institute fro Basic Research in Developmental Disabilities


title: Illumina HiSeq 2000 (Saccharum sp.)

organism: Saccharum sp.


title: Illumina Genome Analyzer IIx (Saccharum sp.)


title: Agilent-023529 Danio rerio 44K

status: Public on Dec 09 2013

city: Worcester

first: Steven

last: Weicksel

state: Massachusetts

address: 55 Lake Ave

department: BMP

institute: UMass Medical School

organism: Danio rerio

description:
Arrays of this design have barcodes that begin with 16023529 or 2523529.

The ID column represents the Agilent Probe names.

This is a tiled array across large stretches of genomic sequence, with the oligo sequences as unique identifiers.


title: NimbleGen Human CGH array [091130_HG18_DL_CGH; condensed PROBE_ID version]

first: Matt

last: Walter

address: 4940 parkview

department: oncology

institute: washington university in st.louis school of medicine

description:
Build: Hg18, NCBI 36
HX1 HG18 whole genome CGH design, using empirically optimized probes distributed across the genome.

Design ID: 11006
091130_HG18_DL_CGH.ndf
091130_HG18_DL_CGH.pos

Please note that there are 1,867 duplicated PROBE_IDs (with different SEQ_ID) in the .pos design file. This platform represents the condensed PROBE_ID view.

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


title: miRCURY LNA microRNA Array, v.11.0 - hsa, mmu & rno [miRNA ID version]

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

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

description:
Homo sapiens and related vira:96.97%, Mus musculus and related vira: 97.3%, Rattus norvegicus:99.71%"

ArrayContents_DesignedFor=miRBase 11.0
ArrayContents_CurrentNameColumn=miRBase 12.0

Names, accession numbers and sequences are listed for mature miRNAs in miRBase 12.0. Some probes may target multiple miRNAs, in which case multiple miRNA names, accession numbers and sequences are listed separated by '/'

manufacture_protocol: See manufacturers website (www.exiqon.com),


title: Agilent-042818 Human lncRNA Micorarray 8_24_v2 [Probe Name version]

status: Public on Dec 31 2013

city: Shanghai

first: Rui

last: Dong

address: 399 Wan Yuan Roa

department: Department of Pediatric Surgery

country: China

institute: Children’s Hospital of Fudan University

description:
Arrays of this design have barcodes that begin with 16042818 or 2542818.

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 Probe Names.

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-034169  Propionibacterium freudenreichii Custom Microarray (Probe Name version)

status: Public on Dec 10 2013

city: Rennes

first: Hélène

last: Falentin

address: 65 rue de St Brieuc

department: Microbiologie

institute: INRA

organism: Propionibacterium freudenreichii


title: Illumina HiSeq 2000 (Phlebiopsis gigantea)

status: Public on Dec 08 2013

organism: Phlebiopsis gigantea


title: AB 5500xl Genetic Analyzer (Shewanella sp. W3-18-1)

organism: Shewanella sp. W3-18-1


title: Illumina HiSeq 1000 (Clio pyramidata)

organism: Clio pyramidata


title: Agilent-027346 human hg18 promoters 180K

status: Public on Dec 11 2013

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

organism: Homo sapiens

description:
Arrays of this design have barcodes that begin with 16027346 or 2527346.

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: [MoGene-1_1-st] Affymetrix Mouse Gene 1.1 ST Array [probe set (exon) version]

status: Public on Dec 12 2013

organism: Mus musculus

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


title: [DogSty06m520431P] Affymetrix version 2 canine SNP array

status: Public on Dec 20 2013

city: Cambridge

first: Hyun Ji

last: Noh

state: MA

address: 7 Cambridge Center

department: Genome Sequencing and Analysis

institute: Broad Institute

organism: Canis lupus familiaris

description: Affymetrix version 2 custom canine SNP array (part number 520431)


title: Affymetrix Gene Human Arrays 1.0 ST

status: Public on Dec 07 2013

city: Goettingen

first: Raphael

last: Koch

address: Robert Koch Str

department: Hematology

institute: University Medicine of Goettingen

manufacture_protocol: Affymetrix


title: Fermlab 12K Aspergillus oryzae oligonucleotide microarray

city: Tsukuba

first: Myco

last: Umemura

state: Ibaraki

address: Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

organism: Aspergillus oryzae

manufacture_protocol: The DNA microarray harbors the 60-mer oligonucleotide probes covering 12,168 genes predicted from 38 Mb of the Aspergillus oryzae genome.  The probes are designed to exclude non-specific hybridization and are highly specific to their target mRNAs.  See manufacturer's web page (http://www.fermlab.com/motechinfo.html)


title: NimbleGen Cryptomeria japonica 4x72k

status: Public on Dec 06 2013

city: Hitachi

first: Kentaro

last: Mishima

address: 3809-1 Juochoishi

department: Breeding Department

institute: Forest Tree Breeding Center

organism: Cryptomeria japonica

description: NimbleGen design name 2012-02, NimbleGen design 110720_RDKK311_Cjap_expr_X4. The custom microarray platform containing 60-mer oligonucleotide probes designed based on a contig assembly consensus sequences in proprietary cDNA library and sequences from “sapwood” and “inner bark” (including a full-length cDNA library) in the ForestGen database.  Each probe is replicated 3 times at least .

manufacture_protocol: see manufacturer's web site www.nimblegen.com. The custom microarray platform containing 60-mer oligonucleotide probes designed based on a contig assembly consensus sequences in proprietary cDNA library and sequences from “sapwood” and “inner bark” (including a full-length cDNA library) in the ForestGen database.


title: Agilent-028999 Boea hygrometrica Array [Feature Number version]

city: Beijing

first: Xin

last: Deng

address: No.20 Nanxincun, Xiangshan

institute: Institute of Botany, the Chinese Academy of Science

organism: Dorcoceras hygrometricum

description:
Arrays of this design have barcodes that begin with 16028999 or 2528999.

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: Illumina HiSeq 2000 (Chlamydia trachomatis; Homo sapiens)

status: Public on Dec 05 2013

last: GEO

organism:
Chlamydia trachomatis
Homo sapiens


title: Agilent-027505 Promoter-CpG-1Mb

status: Public on Dec 03 2013

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

institute: CABIMER

description:
Arrays of this design have barcodes that begin with 16027505 or 2527505.

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: Medsaic Human DotScan antibody microarray v1

city: Boston

first: Joshua

middle: WK

last: Ho

address: 41 Avenue Louis Pasteur

department: Department of Medicine

institute: Brigham and Women's Hospital

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


title: AB 5500xl-W Genetic Analysis System (Mus musculus)


title: [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array [HGU133A2_Hs_ENTREZG_17.0.0]

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: Brainarray: HGU133A2_Hs_ENTREZG_17.0.0


title: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [CDF: huex10stv2_67_020]

status: Public on Dec 02 2013

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

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
This Platform is identical to GPL5175 but a custom CDF environment was used to extract data. Annotation is based on Ensembl version 67.

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


title: Agilent-024656 ATCC17978_ec (Probe Name version)

city: North Ryde

first: Karl

middle: Adam

last: Hassan

state: NSW

address: Eastern Rd, Macquarie University

department: Dept. Chemistry and Biomolecular Sciences

country: Australia

institute: Macquarie University

organism: Acinetobacter baumannii

description: *** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL11113

manufacture_protocol: see Agilent


title: [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array [HGU133A2_Hs_ENTREZG_17.1.0]

description: Brainarray: HGU133A2_Hs_ENTREZG_17.1.0


title: Agilent-037369 Staphylococcus aureus 3K

status: Public on Sep 30 2013

city: He Fei

first: Haipeng

last: Sun

state: An Hui

address: Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

organism: Staphylococcus aureus

description:
Arrays of this design have barcodes that begin with 16037369 or 2537369.

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: OspC Protein Microarray v2

status: Public on Aug 22 2013

city: Irvine

first: Elisabeth

last: Baum

address: Med Surge II

institute: University of California Irvine

organism: Borreliella burgdorferi

manufacture_protocol: Primers used for amplifying full-length ospC alleles had sequences corresponding to positions 16903 through 16925 (Forward) and 17529 through 17558 (Reverse) of cp26 of the B31 strain. For amplification of subcloning targets for protein expression the Forward primer eliminated the signal peptide and 4 different Reverse primers  (to accommodate 3’ end nucleotide polymorphisms amongst ospC alleles), corresponding to nucleotide positions 614 through 633 were used. Sequence-verified clones of full-length ospC alleles were subcloned into a pXT7 expression vector containing an amino-terminal 10X-Histidine (His) fusion tag. Plasmids were transformed into E. coli BL21(DE3)pLysS (Promega, Madison, WI) for protein expression in Terrific Broth (MP Biomedicals, Solon, OH) induced with IPTG (RPI, Mt. Prospect, IL), lysed and  centrifuged. Cleared bacterial lysate was incubated with Ni-coupled magnetic beads (MagneHis kit, Promega, Madison, WI). Purified recombinant proteins were eluted from beads and sample purity was estimated by densitometry of coomassie-blue stained protein bands on sodium dodecyl sulfate-polyacrylamide (SDS-PAGE) gels; protein concentration was determined by BCA Protein Assay kit (Pierce, Rockford, IL). Purified recombinant-OspC proteins were printed on nitrocellulose-coated glass FAST slides (Whatman, Piscataway, NJ) using an Omnigrid 100 apparatus (Digilab, Holliston, MA), in duplicate spots and 2 different amounts of approximately 10 pg and 30 pg of protein per spot. Protein storage buffer alone was printed on the array to serve as a background signal control.


title: Illumina HiSeq 2000 (Loxodonta africana)

organism: Loxodonta africana


title: Illumina HiSeq 2000 (Citrus maxima)

status: Public on Dec 04 2013

organism: Citrus maxima


title: Illumina HiSeq 2000 (Macropus eugenii)

organism: Notamacropus eugenii


title: [RaGene-1_0-st] Affymetrix Rat Gene 1.0 ST Array [transcript (gene) version] [CDF: Brainarray ENTREZG Version 15]

status: Public on Dec 01 2013

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

organism: Rattus norvegicus

description: [RaGene10stv1_Rn_ENTREZG_V15] Affymetrix GeneChip  RaGene10stv1 Array [Brainarray Entrez Version 15]

relation: Alternative to: GPL6247 (Alternative CDF [official])

manufacture_protocol: This is identical to GPL6247 but a custom CDF environment was used to extract data [Brainarray Version 15, RaGene10stv1_Rn_ENTREZG]. CDF and other files can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp#v15


title: Medsaic Human DotScan antibody microarray v2


title: Illumina HiSeq 2000 (Plasmodium falciparum NF54)

organism: Plasmodium falciparum NF54


title: Illumina HiSeq 2500 (Sinorhizobium fredii)

organism: Sinorhizobium fredii


title: Agilent-020856 DTU Lactococcus_lactis_MG1363 8x15k v1.0

city: Hørsholm

first: Christian

middle: Bille

last: Jendresen

address: Kogle Allé 6

institute: Technical University of Denmark

organism: Lactococcus cremoris subsp. cremoris MG1363

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


title: Agilent-023616 Custom Gallus gallus Array

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

institute: University of Birmingham

organism: Gallus gallus

description: design similar to 015068


title: OSU-CCC Human and Mouse MicroRNA Microarray Version 4.0 [condensed human miRNA version]

city: Columbus

first: Ramiro

last: Garzon

address: 460 12th street

institute: Ohio State University

organism: Homo sapiens

manufacturer: Microarray Shared Resource, Comprehensive Cancer Center, The Ohio State University (OSU-CCC)

manufacture_protocol: Manufacured using GE Healthcare's CodeLink (TM) 3-D Gel Matrix Technology. CodeLink(tm) Activated Slides are designed to covalently immoblize amine-modified DNA for microarrays. The slides are coated with a 3-D surface chemistry comprised of a long-chain, hydrophilic polymer containing amine-reactive groups. This polymer is covalently crosslinked to itself and to the surface of the slide. The crosslinked polymer, combined with end-point attachment, orients the immobilized DNA, and holds it away from the surface of the slide. The 1x printing buffer consists of 50 mM sodium phosphate at pH 8.5. Codelink slides are manufactured by SurModics and were formally sold as 3D-Link(tm) Activated Slides. Â  Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions (http://www.genomicsolutions.com ) that is fitted with a printhead and 16 SMP3 print tips from Telechem (http://www.arrayit.com). The microRNA microarray probe set is based on 40mer oligonucleotides from Sigma-Genosys. Â  Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl) to a normalized 25 micromolar concentration. The miRNA microarray spot densities are 200 microns (center-to-center). The microarrays are printed on Codelink Activated Slide (PN300011)) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: UnivMinnesota/Dunny Efaecalis v1.0

city: Minneapolis

first: Kristi

middle: L

last: Frank

state: MN

address: 420 Delaware St SE, MMC196

department: Dept. of Microbiology

institute: University of Minnesota

organism: Enterococcus faecalis V583

description: GAPS II coated slides, Corning Incorporated (Corning, NY)

first: Suzanne

middle: M

last: Grindle

first: Gary

last: Dunny

manufacture_protocol:
The oligonucleotides used in this array have been described previously: Solheim M, Aakra A, Snipen LG, Brede DA, Nes IF (2009) Comparative genomics of Enterococcus faecalis from healthy Norwegian infants. BMC Genomics 10: 194.
Oligonucleotides were synthesized by Invitrogen Corporation (Carlsbad, CA).  Oligos were spotted in quadruplicate on GAPS II coated slides (Corning Incorporated, Corning, New York) with a Biorobotics Microgrid II spotter (Digilab, Inc., Holliston, MA) at the University of Minnesota Biomedical Genomics Center Microarray Facility.  Slides were prehybridized at 42°C in prehybridization buffer according to the instructions in the Corning GAPS II manual immediately before use.


title: Agilent-024503 Rickettsia rickettsii str. Taiacu 15k v1.0

city: São Paulo

first: Maria

middle: Fernanda

last: Galletti

state: São Paulo

address: Av. Prof. Lineu Prestes, 1374 sala 39

department: Department of Parasitology

country: Brazil

institute: Universidade de São Paulo - Instituto de Ciências Biomédicas - Departamento de Parasitologia

organism: Rickettsia rickettsii

description:
Rickettsia microarray (15k chip, agilent)
The complete genome sequence of the strain Sheila Smith of R. rickettsii (GenBank CP000848.1) was submitted to Agilent eArray web tool for gene expression probe (60mer) design (https://earray.chem.agilent.com/earray/)
The total of 13,049 60-mer probes representing 99.5% of the bacterium genome (at least six probes per coding sequence) were spotted on an 8 x 15k chip

first: Andrea

middle: C

last: Fogaca

middle: F

manufacture_protocol:
We labeled, hybridized, and washed the arrays according to Agilent's Gene Expression FFPE adapted protocol.
Two-color Microarray-Based Procaryote (version 1.2) FairPlay Labeling


title: Exiqon miRCURY LNA microRNA array v.11.0 (condensed Version)

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

description: Array represents miRBase version 11.0 with additional features.

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


title: Exiqon miRCURY LNA microRNA array, 7th generation [miRBase v18]

status: Public on Sep 01 2013

city: Fontenay-aux-Roses

first: Guillaume

last: Vares

institute: IRSN

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: A different version of this platform with the Probe_ID and human_miRNA in the ID column is assigned accession number GPL18058 and GPL18066, respectively.


title: Illumina HiSeq 2500 (Caulobacter vibrioides)

last: GEO

organism: Caulobacter vibrioides


title: Agilent-032976 Plasmodium berghei_Mar2010_transcriptome

city: Cambridge

first: Katarzyna

middle: Kinga

last: Modrzynska

address: Genome Campus

department: Malaria program

institute: Wellcome Trust Sanger Institute

organism: Plasmodium berghei

description:
Arrays of this design have barcodes that begin with 16032976 or 2532976.

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: [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_68_020]

last: Rainer

description:
custom CDF: hugene10stv1_68_020.cdf
Alternative to GPL6244

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

manufacture_protocol: See manufacturer's web site


title: Illumina HiSeq 2500 (Atriplex lentiformis)

organism: Atriplex lentiformis


title: Agilent-020181 Genotypic Technology designed Custom Mycobacterium tuberculosis h37Rv Whole Genome 8x15k GE Microarray

status: Public on Mar 05 2011

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

organism: Mycobacterium tuberculosis H37Rv

description:
Total number of features on array: 15744
Total number of available features: 15208
Agilent control grid: IS-15744-8-V1_8x15K_Gx_EQC_V20060608
Agilent controls: 536
Total number of probes designed: 15208
No. of Genes with unique sequence: 3988
Probe Length: 60 mer
Check for Cross hybridization: Yes
Repeat/Vector Masked: Yes
Source: Tuberculist (Web site: http://genolist.pasteur.fr/TubercuList/)
Negative controls added to the array: 34 (human, yeast and mouse)

first: Raja

last: Mugasimangalam


title: Illumina MiSeq (Callithrix jacchus)

organism: Callithrix jacchus


title: Agilent-019078 Custom Burkholderia pseudomallei 8X15K microarray

status: Public on Dec 31 2011

city: Bangi

first: Sheila

last: Nathan

state: Selangor

address: Jalan Universiti

department: Faculty of Science & Technology

institute: Universiti Kebangsaan Malaysia

organism: Burkholderia pseudomallei K96243

first: Sylvia

last: Chieng


title: Borrelia burgdorferi Partial Genome Array

last: Baum

organism: Borreliella burgdorferi

manufacture_protocol: see manufacturer


title: Agilent-023299 Fucus_454

status: Public on Jun 19 2013

city: Bremerhaven

first: Carla

last: Flöthe

address: Am Handelshafen 12

country: Germany

institute: Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung

organism: Fucus vesiculosus

description:
Project Kiel

Arrays of this design have barcodes that begin with 16023299 or 2523299.

The ID column represents the Agilent Probe Name.


title: Agilent-029152 Unrestricted Mouse miRNA v15.0 Microarray 028772 (miRNA_ID version)

status: Public on Jan 28 2012

city: Palo Alto

last: Agilent Technologies

institute: Agilent Technologies

organism: Mus musculus

description:
Mouse miRBase 15.0

Arrays of this design have barcodes that begin with 16029152 or 2529152.

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 miRNA_ID and controls

relation: Alternative to: GPL14971 (Feature Number version)


title: UHN Yeast 6.4k v6

status: Public on Aug 30 2013

city: Marburg

first: Florian

last: Finkernagel

address: Emil-Mannkopff-Str 2

institute: Institute for molecular biology and tumor research

organism: Saccharomyces cerevisiae

manufacturer: University Health Network Clinical Genomics Centre Microarray Centre

manufacture_protocol: Yeast 6.4K clone set is derived from Research Genetics Genepair. Detailed information about the ORFs can be found at the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/).


title: [pCAR1_8b520435F] Affymetrix CustomExpress IncP-7 plasmid pCAR1 Tiling Array

status: Public on Apr 18 2008

city: Sendai

first: Masatoshi

last: Miyakoshi

state: Miyagi

address: Aoba-ku, Katahira, 2-1-1

department: Department of Environmental Life Sciences

institute: Tohoku University

organism: Pseudomonas

description:
This is an Affymetrix custom-commercial tiling array that covers the IncP-7 plasmid pCAR1 (RefSeq: NC_004444) at 9-bp density.
BPMAP files are provided as supplementary files.  pCAR1_8b520435FF-3.bpmap represents the forward strand of pCAR1, and pCAR1_8b520435FR-3.bpmap represents the reverse strand of pCAR1.

first: Hiromi

last: Nishida

first: Masaki

last: Shintani

first: Hideaki

last: Nojiri

manufacture_protocol: See manufacturer's web site.


title: Rhizobium etli CFN 42 385K 071203_ReCFN42JM_Tiling

status: Public on Oct 14 2009

city: Leuven

first: Kristof

last: Engelen

address: Kasteelpark Arenberg 20

country: Belgium

institute: KULeuven

organism: Rhizobium etli CFN 42

description: Whole genome expression tiling array for Rhizobium etli CFN42, representing the forward strand of the chromosome and all 6 plasmids (NC_007761, NC007762, NC_007763, NC_007764, NC_004041, NC_007765, NC_007766), included repeat regions, 60mers, Ctrl (RNA) probes replicated 50 times, ERCC probes replicated 6 times, probe interval 13bp

first: Maarten

last: Vercruysse

last: Fauvart

first: Jan

last: Michiels

first: Lore

last: Cloots

manufacture_protocol: Design ID 6790


title: DIAS_PIG_55K2_v1

status: Public on May 23 2006

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

organism: Sus scrofa

manufacturer: Danish Institute of Agricultural Sciences

first: Christian

last: Bendixen

first: Per

last: Horn

first: Lene

middle: N

last: Conley

first: Henrik

last: Hornshøj

first: Frank

last: Panitz

manufacture_protocol:
DIAS_PIG_55K2_v1 consists of 55.548 features: 26.877 PCR products amplified from cDNA clones and 867 control features spotted as neighbor duplicates in a 4 x 12 array with sub-arrays each consisting of 34 x 34 spots.
The DNA fragments were amplified from cDNA clones selected from the cDNA libraries generated in the Sino-Danish Pig Genome Sequencing Consortium (Gorodkin et al.: Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 ESTs. Genome Biol 2007, 8:R45). The cDNA clones were selected to represent the largest possible number of human gene transcripts. EST clusters for human gene transcripts in NCBI’s RefSeq database release 17 were created using BLASTN sequence similarity program implemented to run on a DeCypher computer [http://www.timelogic.com] with P-value at or below 10-8. Within each cluster one cDNA with the minimum predicted distance to the 3’ end of the human gene transcript was selected. Microarray cDNAs were mapped to GO terms and KEGG pathways based on the human accession id, obtained from BLASTN, using the AnnBuilder package from Bioconductor. To represent uncharacterized genes on the microarray, a set of EST sequence clusters without BLASTN sequence similarity to any known human gene transcript was created and clustered using the “all-vs-all” TERACLU algorithm on a DeCypher computer from TimeLogic [http://www.timelogic.com]. We added one cDNA to the selection list for each of EST clusters with a minimum depth of 3 ESTs and minimum predicted distance to the 3’ end of the assembled EST contig. Of the 26.877 cDNAs, 21.417 map to 15.831 human gene transcript IDs corresponding to roughly 1.35 cDNAs per gene transcript. The remaining 5.460 cDNAs were thus estimated to cover around 4.036 gene transcripts yielding approximately 19.867 gene transcripts in total. The selected clones were rearrayed from the libraries using a QPixII (Genetix), amplified by PCR and purified using the 384 well Microarray PCR Purification Kit (Telechem International). The PCR products were evaluated by agarose gels and dried by speed vac and resuspended in spotting solution. The control features consists of positive spots (also known as “landing lights”), blanks (spotting buffer) and selected spots from the Lucidea Universal ScoreCard (GE Healthcare) which contains both intensity dilution series and different ratios. The positive spot was prepared by PCR amplification of a bovine EST fragment with a primer pair where one of the primers was labeled with Alexa-488 or Alexa-594. The arrays were spotted on UltraGAPS slides (Corning Incorporated) at 20 C/55 % RH using an SDDC-2 MicroArrayer (BioRad) with 48 x 946 MP2.5 pins (Telechem International) with DNA resuspended in Micro Spotting Solution Plus (Telechem International). Slides were dried and UV cross-linked (300 mJ) and stored in a vacuum desiccator until use.

The sequences of the cDNA clones can be found in the attached file "GPL3585_array_cDNA_28k_2005-07-13.cDNA.scr.zip". The attached .gal file contains the original annotation, but an updated version of the annotations have been obtained by blast against mammalian refseq (version 34, file: "GPL3585_p55k-vs-mam-refseq34-2009-04-17.txt") and against Human refseq (release 2009-03-09, file: "GPL3585_p55k-vs-hsa-refseq-2009-04-17.txt") (Rank = 1, Minimum alignment length = 50, Minimum percent alignment = 85 %). An annotation package (file: "GPL3585_p55k3Ver2HsRs20090309AL50PA85_1.0.zip") has furthermore been built in R (version 2.8.0) using AnnBuilder (version 1.20.0).


title: [KT2440b520511F] Pseudomonas putida KT2440 chromosome Array

status: Public on Dec 25 2009

city: Tokyo

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

organism: Pseudomonas putida KT2440

description: This is an Affymetrix custom-commercial tiling array that covers thePseudomonas putida KT2440 chromosome (RefSeq: NC_002947) at 11-bp density. BPMAP files are provided as supplementary files. KT2440b520511FF-3.bpmap represents the forward strand of KT2440 chromosome, and KT2440b520511FR-3.bpmap represents the reverse strand of KT2440 chromosome.


title: FL003 - INDAC Drosophila melanogaster 14.5K long oligo array (FlyBase r.5.39)

status: Public on Aug 09 2011

first: Bettina

last: Fischer

address: Tennis Court Road

department: Systems Biology Centre

institute: Unversity of Cambridge

organism: Drosophila melanogaster

description:
Array mapping available at the FlyChip_long_oligonucleotide_003 (FL003) - INDAC page at the Flychip website.

Sequences aligned to FlyBase release r.5.39.

first: Steven

last: Russell

first: Lisa

middle: A

last: Meadows

first: Richard

middle: P

last: Auburn

first: Gos

last: Micklem

first: Roslin

middle: R

first: Debashis

last: Rana

first: Santiago

middle: S

last: Matila

first: Peter

last: Sykacek

first: David

last: Kreil

manufacture_protocol: FL003 microarrays were printed using the Genetix Qarray2 contact-printing instrument and 48 Genetix aQu75 split-pins on FMB PowerMatrix slides. Probe DNA was dissolved in 150 mM NaPO4. Full details on Flychip website (http://www.flychip.org.uk/)


title: CDMC_Drosophila_Oligo14kv1/Oligo14kv2

status: Public on Mar 31 2006

city: Mississauga

first: Zak

last: Razak

state: ON

address: 3359 Mississauga Road

department: Zoology Department

institute: University of Toronto

description: The CDMC_Drosophila_Oligo14k1 and The CDMC_Drosophila_Oligo14k2 platforms are oligonucleotide-based glass microarrays. Transcript-specific probes were designed by the International Drosophila Array Consortium (INDAC, www.indac.net) based on release 4.1 of the D. melanogaster genome and synthesized by Illumina (www.Illumina.com). This array is produced by the Canadian Drosophila Microarray Centre located at the University of Toronto. It is available for distribution to academic labs.

first: J

middle: T

last: Westwood

first: M

last: Lam

first: D

last: Kasimer

first: K

last: Mo

first: Z

first: S

middle: J

last: Neal

manufacture_protocol: The CDMC_Drosophila_Oligo14kv1 and Oligo14kv2 arrays are printed on CMT-UltraGAPS slides (Corning Inc, Acton, MA) with an aminosilane coating using a SpotArray 72 microarrayer (Perkin Elmer, Boston, MA). There are 32448 spots on each array in a 12 row by 4 column arrangement of blocks (sub-grids). Each block contains 672 spots arrayed in a 26 row by 26 column grid. Spots designated as 'EMPTY' contain only NaPO4 spotting buffer for the 14kv1 arrays or 3x SSC for the 14kv2 arrays and occupy positions 23 through 26 of the 26th row. The blocks are spaced at 4500 micron intervals and the spot-to-spot distance is 166 microns. The nominal spot diameter is 125 microns. Further information including information regarding printing conditions and post-print treatments can be found at http://www.flyarrays.com/index.php?option=com_content&task=view&id=15&Itemid=38


title: NimbleGen Mus musculus MM9 Expression Array (12x135k)

status: Public on Mar 17 2010

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description: NimbleGen design name 090901_MM9_EXP_HX12. This is a whole mus musculus genome array in 12-plex format provided by nimblegen. See manufacturer's website at http://www.nimblegen.com/.

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


title: Illumina HiSeq 2000 (synthetic construct)

status: Public on Feb 14 2012

last: GEO

organism: synthetic construct