title: Illumina Genome Analyzer (Citrullus lanatus)

status: Public on Oct 25 2011

last: GEO

country: USA

organism: Citrullus lanatus

technology: high-throughput sequencing

distribution: virtual


title: Anopheles gambiae GAMV1

status: Public on Oct 31 2011

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

technology: in situ oligonucleotide

distribution: custom-commercial

manufacture_protocol: In situ


title: UHN Yeast 6.4Kv7

status: Public on Oct 26 2011

city: Burjassot

first: Agustin

last: Aranda

state: Valencia

address: Moliner 50

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Valencia

organism: Saccharomyces cerevisiae

technology: spotted DNA/cDNA

distribution: non-commercial

manufacture_protocol: cDNA double-spotted in 48 grids on UltraGAPS slides (Corning, Inc.)


title: UCSF Operon Yeast oligos 2007 [YeastOligo_2007TM.gal]

status: Public on Oct 29 2011

city: Davis

first: Ted

last: Powers

state: CA

address: One Shields Ave

department: Molecular and Cellular Biology

institute: UC Davis

technology: spotted oligonucleotide

description: Operon Yeast oligos

manufacture_protocol: Spotted Arrays as described according to references available at www.microarrays.org


title: Anopheles gambiae GAMV2


title: Illumina HiSeq 2000 (Bacillus halodurans)

status: Public on Oct 27 2011

organism: Halalkalibacterium halodurans


title: ZINF/Krappmann_14k_v1

status: Public on Oct 30 2011

city: Wuerzburg

first: Patrick

last: Olbermann

address: Josef-Schneider-Strasse 2

department: Research Center for Infectious diseases research

country: Germany

institute: University of Wuerzburg

organism: Aspergillus fumigatus Af293

first: Thomas

last: Hartmann

first: Sven

last: Krappmann

manufacture_protocol:
Febit´s Geniom RT Analyzer was used for automated processing of biochips,
hybridization, washing and detection of signals.
One probe for each gene of Afs 293 was synthesized on array. Furthermore, for a selected set of genes, 8 additional copys of a probe had been used as technical replicates.
Whole processing including sample labelling, washing and detection was done by febit GmbH.
febit used MessageAmpTMII-Biotin Enhanced RNA kit (Ambion) for labelling of RNA for mRNA expression analysis.


title: Anopheles gambiae GAMBER1


title: GeneScan_SigB_350

status: Public on Mar 13 2012

city: Greifswald

first: Leif

last: Steil

address: Friedrich-Ludwig-Jahn Str. 15A

department: Genetics and Functional Genomics

institute: University of Greifswald

organism: Bacillus subtilis

manufacture_protocol: ORF sequences of 350 selected genes from Bacillus subtilis were exported from Genbank. 50 nt long isothermal probes were derived from the ORF sequences and spotted in triplicate (GeneScan, Freiburg, Germany). Probes were covalently attached to a hydrophobic substrate on the surface of glass slides(Waldmüller et al., 2002).


title: Illumina HiSeq 2000 (Bos grunniens)

organism: Bos grunniens


title: Candida albicans 385K tiled array

status: Public on Oct 20 2011

city: Carlisle

first: Dana

middle: Jasmine

last: Wohlbach

state: PA

department: Biology

institute: Dickinson College

organism: Candida albicans WO-1

description: NimbleGen design name: 091217_Calb_KR_EXP; NimbleGen design ID: 26563.  A tiled genome array from Candida albicans WO-1 with 373,067 probes (average probe length 55.2 +/- 4.0 nt, median spacing distance 31 nt).  The design includes random GC and other control probes.

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


title: JHUHIT Human 17K v2010

first: Mary Katherine

last: Tarrant

address: 725 N. Wolfe Street, 317 Hunterian Bldg.

department: Pharmacology and Molecular Sciences

institute: Johns Hopkins University School of Medicine

organism: Homo sapiens

technology: spotted peptide or protein

description:
Human proteins expressed and purified from yeast
Homo sapiens

manufacturer: Johns Hopkins University Hit Throughput Biology Center, Heng Zhu laboratory

manufacture_protocol: DNA corresponding to the human proteins (ORFs from the Invitrogen collection) was cloned into the pEGH-A vector (a derivative of the yeast glutathione S-transferase, GST, vector) using the Gateway system.  The plasmid DNAs corresponding to the GST-fusion proteins were transformed into yeast (WT Y258A) for protein expression and purification.  Cultures were grown at 30° to an optical density at 600 nm of 0.7 to 0.9 and induced with 2% galactose for 4 to 6 h.  Harvested cells were lysed with zirconia beads in lysis buffer (50 mM Tris pH 7.5, 100 mM NaCl, 1 mM EDTA, 10% glycerol, 0.1% Triton X-100, 0.1% 2-mercaptoethanol, 1 mM phenylmethylsulfonyl fluoride plus Roche protease inhibitor cocktail).  GST fusion proteins were bound to glutathione beads for 1 h at 4°C and washed three times with wash I buffer (50 mM Tris pH 7.5, 500 mM NaCl, 1 mM EDTA, 10% glycerol, 0.1% Triton X-100, 0.1% 2-mercaptoethanol, 1 mM phenylmethylsulfonyl fluoride) and washed three times with wash II buffer (50 mM HEPES pH 7.5, 100 mM NaCl, 1 mM EDTA, 10% glycerol, 0.1% Triton X-100, 0.1% 2-mercaptoethanol, 1 mM phenylmethylsulfonyl fluoride) and eluted in elutions buffer (50 mM HEPES pH 7.5, 100 mM NaCl, 30% glycerol, 0.03% Triton X-100, 0.1% 2-mercaptoethanol, 40 mM glutathione).  The eluate was collected through a filter unit and stored in plates in a -80°C freezer.  The protein products were printed in duplicate on modified glass slides (Full Moon, Biosystems) using a NanoPrint Microarrayer (ArrayIt).  To reduce the merged features, printing is done at lower humidity (~30%) using SMP3 pins from ArrayIt with column and row spacing 135 microns and 170 microns, respectively.


title: [HT_Rat230_PM] Affymetrix GeneChip® HT RG-230 PM Array Plate [cdf: HTRat230PM_Rn_ENTREZG_13.0.0]

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

organism: Rattus norvegicus

description: Custom CDF (Brainarray ENTREZG 13.0.0)

manufacture_protocol: Affymetrix's protocol (see web site)


title: Agilent-027061/Klug lab Rhodobacter sphaeroides - 15k array v2 (144 sRNA)

city: Giessen

first: Sebastian

middle: Harald Michael

last: Metz

address: Heinrich-Buff-Ring 26-32

department: Institut für Mikro- und Molekularbiologie

institute: Justus-Liebig-Universität Giessen

organism: Cereibacter sphaeroides 2.4.1

description: spotted 60 nt oligonucleotide

manufacture_protocol: The microarray contains probes against 4,304 protein-coding genes, 79 rRNA and tRNA genes, and 144 intergenic regions. Three antisense probes with a length of 60 nt were designed for each gene or intergenic region, when possible. Microarray construction was performed following the instructions of Agilent (www.chem.agilent.com).


title: [TB-All-Antisense] Affymetrix M. tuberculosis Antisense Array

status: Public on Nov 03 2006

city: Santa Clara

last: Affymetrix

institute: Affymetrix, Inc.

organism: Mycobacterium tuberculosis H37Rv

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

Array name:      TB-All-Antisense
Part Number:     510285
Organism:        Mycobacterium tuberculosis strain H37Rv
Genome assembly: NC_000962.2
NetAffx version: Oct 2006
CSV version:     1.0

This annotation table was derived Affymetrix CSV file TB-All-Antisense_annot.csv [Version 1.0, 2006-10-31].
Appended README provides a guide to the contents of the CSV file containing annotations for the probe sets on the Affymetrix M. tuberculosis antisense array.

distribution: commercial

manufacture_protocol:
The TB-All-Antisense GeneChip(R) array was manufactured by Affymetrix in 1998 for gene expression analysis of the M. tuberculosis H37Rv strain. This was a PM/MM design which covers all ORFs and intergenic regions described by GenBank as of Oct 1998.  3924 ORFs and 738 intergenic regions and their reverse complements are interrogated with 20 probe pairs each (25mers). There is a total of 118,180 probe pairs on the chip.

Note that this array is not the same as the M. tuberculosis array available through the Affymetrix NimbleExpress(TM) Made-To-Order program (array name: M_tubercul530104):

http://www.affymetrix.com/products/arrays/specific/nimble_prokaryotic.affx

The newer NimbleExpress array was designed using a more recent version of the M. tuberculosis genome, though most of the probe sets should detect largely the same set of expressed genes as the older TB-All-Antisense array.


title: Illumina Genome Analyzer IIx (Pyrococcus furiosus)

organism: Pyrococcus furiosus


title: Illumina Genome Analyzer (Sorghum bicolor)

organism: Sorghum bicolor


title: NuGO array (human) NuGO_Hs1a520180 [CDF: Hs_ENTREZG_10]

status: Public on Aug 07 2008

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description:
CDF file was created by Microarray Lab at the Molecular and Behavioral Neuroscience Institute at the University of Michigan.
Oligonucleotide probes on GeneChips were reorganized based on the latest genome and transcriptome information. In this particular case the Entrez Gene database (build: Sept 11, 2006) was used as source.
For the CDF file based on Entrez Gene:
A probe must hit only one genomic location;
Probes that can be mapped to the same target sequence in the correct direction are grouped together in the same probe set;
Each probe set must contain at least three oligonucleotide probes and probes in a set are ordered according to their location in the corresponding exon.
For detailed description please see the paper and website.

relation: Alternative to: GPL7020 (Alternative CDF [official])

manufacture_protocol: This array is identical to GPL7020 but a custom, remapped CDF environment is used to extract data. This is version 10 of the remapped CDF (see supplementary file linked below). The CDF for various platforms can be found at the Web link below.


title: Agilent-024600/Klug lab Rhodobacter sphaeroides 2.4.1 - 15k array v1 (122 sRNAs)

description: spotted 60 nt oligonucleotides

manufacture_protocol: High-density oligonucleotide R. sphaeroides microarrays (Agilent gene chips corresponding to the whole 4.6-Mb genome, Peuser et al., 2011) were used for transcriptome profiling. The microarray contains probes against 4,304 protein coding genes and, 122 intergenic regions and 79 rRNA and tRNA genes; its construction and performance analysis was performed according to the instructions of Agilent (www.chem.agilent.com). Three antisense probes with a length of 60 nt were designed for hybridization to each gene.


title: Illumina HiSeq 2000 (Physcomitrella patens)

organism: Physcomitrium patens


title: Yersinia pestis cDNA microarray

status: Public on Oct 24 2011

city: Beijing

first: Dongsheng

last: Zhou

address: NO.20 Dongdajie, Fengtai

country: China

institute: Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China

organism: Yersinia pestis

manufacturer: Beijing Institute of Microbiology and Epidemiology, Beijing, China

manufacture_protocol:
Based on the whole-genome sequences of Y. pestis CO92, KIM and 91001, a total number of 4015 annotated open reading frames (ORFs) were selected after the exclusion of ORFs encoding IS protein, integrase, and transposase (The word “gene” will be used in the following part of this paper in reference to the ORF). Those highly homologous to each other at nucleotide level were also excluded. Gene specific primer pairs (16bp to 18bp in length) were designed to amplify nearly the full length of each gene. All primers were synthesized by Illumina Co. (San Diego, CA, U. S. A).
300µl of PCR product was obtained for each gene. PCR amplifications were performed in 96-well plates by using a DNA thermocycler (Biometra UNOII). 100 µl of PCR reaction mixture, containing 50 mM KCl, 10 mM Tris-HCl (pH8.0), 2.5 mM MgCl2, 0.001% gelatin, 0.1% BSA, 150 µM of each dATP, dCTP, dGTP and dTTP, 0.6 µM of each primer, 5 units of Taq DNA polymerase (MBI Fermentas), and 20 ng of template DNA, was predenatured at 95°C for 5 min. Then 30 cycles of 94°C for 1 min, 60°C for 1 min 30 sec and 72°C for 2 min were performed with a final extension at 72°C for 10 min. Each PCR product was verified by agarose gel electrophoresis and was scored as successful if a single band of the expected mobility was detected. DNA smear, multiple bands, or single band of unexpected size were characterized as unsuccessful reactions. Primer pairs from unsuccessful PCR reactions were re-amplified with altered annealing temperatures to get the desired single band of products. A few primers had to be redesigned to ensure successful amplification. In the end, 4005 genes were amplified successfully without any byproduct from strain 91001 or 82009 (Y. pestis 82009, a biovar Orientalis strain isolated from a natural focus in China, was used as an alterative of CO92 in this study).
PCR products were purified by using 96-well Multiscreen PCR plates (Millipore) following the user manual’s instruction. The purified DNAs were air dried at 65°C, and were resuspended in 30 µl of 50% DMSO solution. 10 µl of the purified PCR product was transferred into Genetix 7020 384-well Polystyrene Plates for microarray printing. Each of the PCR products was spotted in duplicate on CSS-1000 silylated glass slides (CEL) by using a SpotArray72 Microarray Printing System (Perkin Elmer Life Sciences) with 32 Telechem SMP3 Stealth Pins (4×8 Layout). Genomic DNA of strain 91001, salmon sperm DNA and 50% DMSO solution were included in the microarray design as internal control elements. The spotted slides were stored in dry environment at room temperature for at least 12 hr, and then were crosslinked twice by using a UV Stratalinker (Hoefer) each at a total energy of 60 microjoules. The spotted CSS-1000 silylated slides need not any blocking procedure, such as the blocking of unreacted aldehyde groups and the prehybridization. The microarray slide to be hybridized was simply washed in water for 2 min to remove the unbounded DNA and then was blown to dry with hot air.


title: NimbleGen Human DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Array

status: Public on Apr 18 2012

city: London

first: Muy-Teck

last: Teh

state: England

address: Blizard Building, 4, Newark Street,

department: Centre for Clinical & Diagnostic Oral Sciences

country: United Kingdom

institute: Queen Mary University of London

description: Build: HG18, NCBI 36

manufacture_protocol: see NimbleGen


title: UAB human 32K BAC tiling array

city: Birmingham

first: Theresa

middle: V

last: Strong

state: AL

address: 1530 3rd Avenue South

department: Medicine

institute: University of Alabama at Birmingham

description:
The 32K BAC Re-Array library is available from the BACPAC Resource Center at Children's Hospital Oakland Research Institute in Oakland, CA.

NCBI genome Build 36 (UCSC hg18).

manufacturer: Howell and Elizabeth Heflin Center for Human Genetics, University of Alabama at Birmingham (UAB)

manufacture_protocol: The 32,450 BAC clones were amplified using three independent DOP PCR amplifications, followed by pooling of the DOP PCR products and re-amplification using a universal amino-modified primer. The amino-PCR-products were then purified using Millipore filter plates, eluted with printing buffer. Quality control agarose gel electrophoresis was performed for all clones after the universal amino PCR, and the gel images were stored in an image database. All DNA transfers were performed using a Hydra 96 channel micro-dispenser (Matrix Technologies, Hudson, NH) and a Biomek FX robot (Beckman-Coulter, Fullerton, CA). The aminogroup attached at the 5’ end of the universal primer allows for covalent attachment of DNA fragments to the CodeLink HD slide surface (GE Healthcare, Piscataway, NJ). We used the spotting solution recommended for these slides (GE Healthcare). Printing of the clones was carried out using a high-throughput printing robot (http://www.heflingenetics.uab.edu/CORE/array_printing.shtml). The center-to-center distance between the spots was 160 micrometers using a hexagonal printing pattern.


title: Affymetrix Zea mays A1ZMa520113

status: Public on Oct 22 2011

city: Saint Louis

first: Jim

last: Morrell

state: Missouri

address: 800 North Lindbergh Blvd

department: Biotechnology

institute: Monsanto Co.

organism: Zea mays

description: Affymetrix chip designed from EST sequences by Monsanto and Affymetrix. PM only

manufacture_protocol: See manufacturer's web site


title: IBMT Campylobacter jejuni Halolink fusion-protein array

city: Potsdam

last: Hoppe

address: Am Mühlenberg 13

department: Bioanalytics and Biosensorics

institute: Fraunhofer Institute for Cell Therapy and Immunology

organism: Campylobacter jejuni

description:
Spotted fusion protein.
HaloTag-fusion proteins derived from Campylobacter jejuni and expressed in KRX E.coli overexpression strains.
We incorporated a fusion tag prior to our genes of interest and attached the expressed fusion proteins covalently on microarrays. This enhances the specific binding of the proteins compared to nitrocellulose.
Platform Halolink Arrays (Promega), spotting performed at IBMT.

manufacture_protocol: Spotting was performed with a Qarray2


title: LC Sciences miRPlants miRBase_10.0

city: Shanghai

first: Zaochang

last: Liu

address: 2901 Beidi Rd., Minhang District

department: Lab

institute: SAAS

organism: Oryza sativa

manufacture_protocol:
1. 623 miRNAs based on Sanger miRBase Release 10.0 and 100 custom miRNA sequences are arrayed on the chip. Each probe is repeated 5 times.
2. Multiple redundant regions are included.  Each region further comprises a miRNA probe region, which detects miRNA transcripts listed in Sanger miRBase Release 10.0.
3. Multiple control probes are included in each chip.  The control probes are used for quality controls of chip production, sample labeling and assay conditions.
4. Among the control probes, PUC2PM-20B and PUC2MM-20B are the perfect match and single-based match detection probes, respectively, of a 20-mer RNA positive control sequence that is spiked into the RNA samples before labeling.
5. One may assess assay stringency from the intensity ratio of PUC2PM-20B and PUC2MM-20B, which is normally larger than 30.


title: JHUHIT Human 17K v2009

description: Human proteins expressed and purified from yeast


title: HMGU/BIOP_European beech_1802_2009

status: Public on Oct 21 2011

city: Neuherberg

first: Maren

last: Olbrich

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

organism: Fagus sylvatica

description: Slides were coated with aldehydes.

manufacturer: Helmholtz Zentrum München, Biochemical plant pathology, Molecular diagnostic

first: Dieter

last: Ernst

manufacture_protocol:
Spotting buffer: 3xSSC+ 1,5MBetain
Spotting plate setting: 384-well Mikrotiterplatte, Greiner bio-one, Frickenhausen
Arrayer Hardware: Micro Grid II, BioRobotic, Cambridge, GB


title: [Eh_Eia520620F_Ei] Affymetrix Entamoeba invadens Array

city: Shnjuku

first: Ghulam

last: Jeelani

state: Tokyo

department: Parasitology

country: Japan

institute: National Institute of Infectious Diseases

organism: Entamoeba invadens

description: EIN_nnnn identifiers represent TIGR locus_tag

manufacture_protocol: see manufacturer's web site


title: NCI NimbleGen Homo sapiens HG19 Whole Genome 385K Tiling Set version 1

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

description: 385K element tiling array based on NCBI Build 35 of the human genome (HG17) and re-mapped to NCBI Build 35 (HG19); 50-mer tiling with a median probe spacing of 6,000 bp. Positional information for re-mapped probes available in included file 2005_03_16_HG19_WG_CGH.pos

manufacture_protocol: Tiling-path CGH arrays were designed for whole-genome analysis with a single array minimum probe spacing of 5 Kb, and a median probe spacing of 6 Kb.  HG17 (NCBI 35) sequence was repeat-masked using Repeat-Masker (20).  Unique probes were selected as described by Selzer et al. (Pubmed ID: 16075461). Instead of being of fixed length, oligonucleotides were of variable length, adjusted to match a melting temperature of 76°C and constrained to a minimum of 45 bp and maximum of 85 bp in length.  The arrays were constructed by maskless array synthesis technology, with ~385,000 oligonucleotides being synthesized by photolithography on an array.


title: Spathaspora passalidarum 385K tiled array

organism: Spathaspora passalidarum NRRL Y-27907

description: NimbleGen design name: 090803_SP_DW_EXP; NimbleGen design ID: 23872.  A tiled genome array from Spathaspora passalidarum NRRL Y-27907 with 362,487 probes (average probe length 54.5 +/- 4.0 nt, median spacing distance 29 nt).  The design includes random GC and other control probes.


title: Picha stipitis 385K tiled array

organism: Scheffersomyces stipitis CBS 6054

description: NimbleGen design name: 090803 PS DW EXP; NimbleGen design ID: 23871.  A tiled genome array from Pichia stipitis CBS 6054 with 374,100 probes (average probe length 53.6 +/- 4.1 nt, median spacing distance 33 nt).  The design includes random GC and other control probes.


title: Candida tenuis 385K tiled array

organism: Yamadazyma tenuis ATCC 10573

description: NimbleGen design name: 090803_CT_DW_EXP; NimbleGen design ID: 23870  A tiled genome array from Candida tenuis NRRL Y-1498 with 363,196 probes (average probe length 53.1 +/- 3.8 nt, median spacing distance 24 nt).  The design includes random GC and other control probes.


title: Lodderomyces elongisporus 385K tiled array

organism: Lodderomyces elongisporus NRRL YB-4239

description: NimbleGen design name: 091217_Lelo_KR_EXP; NimbleGen design ID: 26564.  A tiled genome array from Lodderomyces elongisporus NRRL YB-4239 with 371,451 probes (average probe length 54.1 +/- 4.1 nt, median spacing distance 33 nt).  The design includes random GC and other control probes.


title: Agilent-024664 chlamydomonas full genome

status: Public on Oct 19 2011

city: Bielefeld

first: Jörg

last: Toepel

address: Universitätsstrasse 27

institute: University of Bielefeld

organism: Chlamydomonas reinhardtii

description:
Arrays of this design have barcodes that begin with 16024664 or 2524664.

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 Genome Analyzer IIx (Leishmania tarentolae)

status: Public on Oct 14 2011

last: GEO

organism: Leishmania tarentolae


title: Helicos HeliScope (Mus musculus)

status: Public on Oct 18 2011

organism: Mus musculus


title: AB SOLiD System 2.0 (Saccharomyces mikatae IFO 1815)

status: Public on Oct 06 2011

organism: Saccharomyces mikatae IFO 1815


title: Illumina Genome Analyzer IIx (Leishmania major)

organism: Leishmania major


title: Agilent_028085 Ketogulonigenium vulgare custom microarray [Feature Number version]

city: Rockville

first: Panos

last: Pan

address: 9430 Key West Avenue

institute: Arraystar Inc.

organism: Ketogulonicigenium vulgare WSH-001

description:
The Ketogulonigenium vulgarum WSH-001 custom Microarray is a broad view that represents well-known and predicted Ketogulonigenium vulgarum WSH-001 genes and transcripts. Coupled with NCBI’s gene prediction processes and Agilent's probe selection, this design delivers increased data quality and less gene coverage redundancy.

Design ID : 028085
***A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL14693.

relation: Alternative to: GPL14693 (Probe Name version)


title: CSHL-Human-MOMA3, 368K CpG tiling array

status: Public on Oct 17 2011

city: Cold Spring Harbor

first: Kazimierz

middle: O.

last: Wrzeszczynski

state: NY

address: One Bungtown Rd.

institute: Cold Spring Harbor Laboratory

organism: Homo sapiens

description: Human Genome Build 36 (hg18)

manufacture_protocol: Our approach to map genome-wide methylation involves tiling all the predicted CpG islands. All annotated CpG islands were obtained from the UCSC genome browser. These islands were predicted using the published Gardiner-Garden and Frommer (1) definition and involves the following criteria: length >= 200bp, %GC >= 50%, observed/expected CpG >= 0.6. There are ~26219 CpG islands in the range of 200bp to 2000bp in the genome. These islands are well covered by Msp I restriction fragmentation. Arrays were manufactured by Nimblegen Systems Inc using the 390K format to the following specifications. The CpG island annotation from human genome build 33 (hg17) was used to design a 50 mer tiling array. The 50 mers were shifted on either side of the island sequence coordinates to evenly distribute the island. The 390K format has 367,658 available features which would not fit all islands with a 50 mer tiling. Therefore we made a cutoff on the islands to be represented based on size, with only CpG islands of size 200b-2000b being assayed. The array represents classical CpG islands and does not include imprint control regions or other non-island promoters known to be methylated. Background hybridization signal could be high with probes of high GC content since by definition these probes will be. Therefore, control probes which are not in a MspI representation were designed to represent background signal, and these probes were used to calculate signal to noise.


title: Illumina Genome Analyzer II (Candida parapsilosis)

status: Public on Oct 11 2011

organism: Candida parapsilosis


title: Genome Institute of Singapore Burkholderia pseudomallei 390K tiling array [2007-02-26_BpK96243_Yiting_FT]

status: Public on Oct 07 2011

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

organism: Burkholderia pseudomallei K96243

description: aCGH experiments were performed using oligonucleotide microarrays comprising > 390,000 50-mer probes providing tiling coverage of the Bp K96243 reference genome (15 bp overlap) (NimbleGen, Reykjavik, Iceland)

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


title: Agilent_028085 Ketogulonigenium vulgare custom microarray [Probe Name version]

description:
DesignID : 028085
*** 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 GPL14692

relation: Alternative to: GPL14692 (Feature Number version)


title: AB SOLiD System 2.0 (Saccharomyces bayanus MCYC 623)

organism: Saccharomyces uvarum CLIB 533


title: AB SOLiD System 2.0 (Saccharomyces paradoxus NRRL Y-17217)

organism: Saccharomyces paradoxus NRRL Y-17217


title: SABiosciences Mouse Apoptosis PCR Array PAMM-012

city: Cincinnati

first: George

middle: Samuel

last: Deepe

state: Ohio

address: 231 Albert Sabin Way

department: Dept. of Medicine/Division of Infectious Diseases

institute: University of Cincinnati College of Medicine

technology: RT-PCR


title: AB SOLiD System (Drosophila melanogaster)

organism: Drosophila melanogaster


title: microRNA array

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

first: Huiyun

last: Wang

manufacture_protocol: 873 microRNA probes were printed onto slides using the SmartArrayer™ 136 printer (CapitalBio, Inc., Beijing, China)


title: Mm-FDA-OperonV4-35K

city: Bethesda

first: Amy

middle: Xiaoyun

last: Yang

address: 8800 Rockville Pike

department: Division of Celular and Gene Therapies

institute: CBER, FDA

manufacture_protocol: The mouse genome oligonucleotide probe set version 4.0 contains 35,852 optimized 70mers (plus controls) obtained from Operon (no more existing). The oligonucleotide probes were purchased in 384-well polypropylene plates (Genetix, 384 micro array) and dissolved in a print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate) at a concentration of 15 uM. The microarray is composed of 48 blocks and one spot is printed per probe per slide. The spot size is 70 micron and spot distance is 155 microns (center-to-center). The microarrays were printed on epoxide coated slides (Corning).


title: AB SOLiD System 2.0 (Saccharomyces cerevisiae S288c)

organism: Saccharomyces cerevisiae S288C


title: Agilent-025088 Pichia pastoris Gene Expression 8x15k array

status: Public on Oct 13 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: Komagataella pastoris

description: Pichia pastoris Gene Expression 8x15k array designed by Genotypic Technology Pvt. Ltd (Agilent AMADID ID 025088 )

first: Mugasimangalam

middle: C

last: Raja


title: Ciona intestinalis Oligoarray ver.2 4X44k

city: Onna

first: Nori

last: Satoh

state: Okinawa

institute: OIST

organism: Ciona intestinalis

description:
A publicly-accessible accession ID or clone ID is not available.
The microarray probes were designed by combination of some gene models and EST/cDNA information.
Users can search the corresponding genemodel/EST/cDNA using the probe sequence.

first: Yutaka

last: Satou

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


title: LBEG Prunus persica 4.8K

city: Santiago

first: Leonardo

middle: Ignacio

last: Pavez

state: Santiago

address: Av Manuel Montt #948

country: Chile

institute: Universidad de Las Américas

organism: Prunus persica

first: Talía

last: Del pozo

first: Felipe

last: Olivares

first: Mauricio

last: González

manufacture_protocol:
1.Oligos are arrayed in Genetix 384 Well Microarray Plates (Cat# X7020). Each well contains 600 pmol of 70-mer oligo.
2. Resuspend oligos in 17 µL of Telechem Microspotting solution 1X.
3. Seal plates with Corning seals and after oligos resuspenction print probe with the MicroGrid II Biorobotics spotter.
4. Print is performed with 48 Stealth pins.
5. After printing run plates are stored at -20 C degree.
6. Every 4 months plates are lyophilized and resuspended in adjusted water volume according to the number of spotting runs. This, to maintain the same volume and concentration in all plate well.


title: Illumina Genome Analyzer (Beauveria bassiana)

organism: Beauveria bassiana


title: AB SOLiD 4 System (Caenorhabditis elegans)

organism: Caenorhabditis elegans


title: NimbleGen Mus musculus MM8 Expression Array (4x72k) [gene-level version]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
This is a mouse whole-genome expression array in 4-plex format provided by nimblegen. See manufacturer's website at http://www.nimblegen.com/.
Format: 4x72K
Source: NCBI
Build: MM8
Probe Length: 60mer
Design Name: MM8 60mer expr X4
Genes: 18,869
Probes/ Target: 3
Replicates: 1


title: Agilent-4x44k-POCI-015425

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

organism: Solanum tuberosum


title: A-UMCU-M35K-1.0

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

organism: Mus musculus

manufacturer: Holstege Lab, UMC Utrecht, The Netherlands

first: dik

last: van Leenen

first: Philip

last: Lijnzaad

first: Linda

last: Bakker

first: Erik

last: Sluiters

first: Sander

last: van Hooff

first: Patrick

last: Kemmeren

first: Frank

last: Holstege

manufacture_protocol:
1. 70-mers from 384-well plates are printed with a BioRobotics MicroGridII spotter in an environment controlled room
2. Humidity is 50% ± 3%
3. Temperature is 18C in the spotter
4. Quill Pins type MicroSpot2500 (BioRobotics) are used for spotting
5. The printed slides are treated with UV-light after spotting by using a Stratalinker2400 from Stratagene: Energy 2400 mJ, Time 10 minutes (settings 23744 x 100 uJoule)
6. The Stratalinker works with 254 nm UV-light and irradiates the slides with circa 4000 uWatt/cm2
7. After UV-crosslinking, slides are stored in a desiccator-cabinet


title: UoL-LMF Zebrafish 17K v2.0

city: Liverpool

first: Catherine

last: Turner

state: Merseyside

address: Crown Street

department: Institute of Integrative Biology

institute: University of Liverpool

organism: Danio rerio

manufacturer: Liverpool Microarray Facility, University of Liverpool, UK

manufacture_protocol: The oligonucleotide arrays were printed in-house by the Liverpool Microarray Facility. The probes included on the array were 65 base pair oligonucleotides from the Zebrafish OligoLibrary™ designed by Compugen (Jamesburg) and an additional 400 customs probes designed at the labs of Professor Charles Tyler, University of Exeter, and Dr. Peter Kille, Cardiff University. The oligos were synthesised by Sigma-Genosys. These together with control and blank spots were printed onto Nexterion® E Slides (Schott) with a BioRobotics MG2 contact-printing robot (Genomic Solutions) giving a total of 16578 features.


title: [HuGene10stv1_Hs_ENSG] Affymetrix GeneChip Human Gene 1.0 ST Array [Brainarray Version 11.0.1]

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: Probe set data extracted from custom CDF [Brainarray Version 11.0.1, HuGene10stv1_Hs_ENTREZG]

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


title: Agilent Human Promoter CpG Oligo Array 44K

status: Public on Oct 05 2011

city: Indianapolis

first: Jaesik

last: Jeong

address: 410 West 10th Street, Suite 3000

institute: IUPUI

description: 60-mer oligonucleotides

manufacture_protocol:
1. Customized probes by picking probes that brack CpG dinucleotides from the Agilent probe database.
2. Array chip manufactured by Agilent following standard protocols.


title: Streptococcus pyogenes (Group A Strep) amplicon array

status: Public on Oct 03 2011

city: Baltimore

first: NIKHIL

last: KUMAR

address: 801 W. Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

organism: Streptococcus sp. 'group A'

manufacture_protocol:
Pan-genome microarray was constructed using Alab49 as the reference.
PCR primers were designed for predicted genes in Alab49 using Primer3, followed by 11 subsequent strains not already represented by Alab49 and were tested for uniqueness using in-house scripts.
The resulting 3388 amplicons ranged in size from 51 to 1170 bp; all of these were amplified using 10X PCR Buffer, MgCl2, 100mM dNTP mix, Taq Polymerase, and water (all Applied Biosystems).
30uL of amplicon are in 384-well Genetix plates in 50% DMSO, which is used as printing buffer.
Amplicons are spotted in triplicate on Corning Ultra-GAPS aminosilane slides, using a Lucidea (GE Healthcare) or Aushon Biosystems (www.aushon.com) microarray-printing robot.
After print run, slides cross-linked at 750E.


title: NimbleGen_mouse(MM8)_60mer_expr array [Design_ID: 5045]

city: Paris

first: Daniel

last: Vaiman

address: 24 rue du Faubourg St Jacques

department: Genetics and Development

country: France

institute: INSERM

description:
native array description file: Vaiman_MM8_60mer_expr.ndf
native array description file: Vaiman_MM8_60mer_expr.ngd
Design ID: 5045

first: Ludivine

last: Doridot

manufacture_protocol: Classical hybridization protocol performe at the genomic platform of the Cochin Institut


title: Agilent-023387 Rhagoletis pomonella custom cDNA array

status: Public on Oct 01 2011

city: Gainesville

first: Greg

last: Ragland

state: FL

department: Entomology and Nematology

institute: University of Florida

organism: Rhagoletis pomonella

description:
Probesets:
CUST_1_PI414333030 to CUST_23040_PI414333030: two forward probes for each annotated R. pomonella EST.
CUST_1_PI414333074 to CUST_11521_PI414333074: one reverse (minus strand) probe for each annotated R. pomonella EST.
CUST_1_PI414333083 to CUST_3770_PI414333083: two forward probes for each unannotated R. pomonella EST.
CUST_1_PI414333086 to CUST_1886_PI414333086: one reverese probe for each unannotated R. pomonella EST.
CUST_1_PI415094689 to CUST_20_PI415094689: forward probe for each of 20 R. pomonella house keeping genes (for QC, replicated 10 times each on array).
CUST_1_PI414333099 to CUST_356_PI414333099: two forward probes from diapaue candidate genes in Drosophila melanogaster (note: poor hybridization).
CUST_1_PI414333102 to CUST_178_PI414333102: reverse probes from diapause candidate genes in Drosophila melanogaster.
CUST_1_PI414333089 to CUST_2340_PI414333089: two forward probes from diapaue candidate genes in Sarcophaga crassipalpis (note: poor hybridization).
CUST_1_PI414333095 to CUST_1171_PI414333095: reverse probes from diapause candidate genes in Sarcophaga crassipalpis.
NOTE: all reverse probes for annotated genes included to establish distribution-based presence/absence calls if desired.

manufacture_protocol: 60-mer oligo probes designed from R. pomonella EST contigs and singletons using Agilent eArray v2.0 and synthesized in situ by an ink-jet printing (Agilent) method on glass slides.


title: MYcroarray CAT-3x20K-Corynebacterium_glutamicum_ATCC_13032

status: Public on Oct 04 2011

city: Seoul

first: Jeong Eun

last: Hyeon

address: Anamdong

country: South Korea

institute: Korea University

organism: Corynebacterium glutamicum

manufacture_protocol: See manufacturer's web site  (http://www.mycroarray.com/technology/synthesis.html)


title: Auburn University Ichthyophthirius multifiliis 40K v1.0

city: Auburn

first: Eric

last: Peatman

address: 203 Swingle Hall

department: Fisheries and Allied Aquacultures

institute: Auburn University

organism: Ichthyophthirius multifiliis

description:
NimbleGen design name 2007-08-29_ICHTTPF_JA_EXPR, NimbleGen design ID 6612.  The probe design strategy was to create 60 base pair (60-mer) oligonucleotide probes, including 12 60-mer oligos per I. multifiliis sequence, and 10 60-mer oligos for both T. thermophila and P. falciparum sequences (PM/MM) per gene. The design includes control probes.
native array description file: 2007-08-29_ICHTTPF_JA_EXPR.ndf
native array description file: 2007-08-29_ICHTTPF_JA_EXPR.ngd

manufacture_protocol: in situ cDNA array prepared with Maskless Array Synthesizer (MAS) technology. See www.nimblegen.com for further details.


title: NCSU_Thermotoga species

city: Raleigh

first: Andrew

last: Frock

state: NC

address: 840 Main Campus Drive, Partners II, Room 3304

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

organism:
Thermotoga maritima
Thermotoga neapolitana
Thermotoga petrophila
Thermotoga sp. RQ2

description: Because some probes were designed based on SSH results, some probes duplicate the same ORF or cover intergenic DNA. Here is a key for the notation used for probe names: TRQ2_0171a means there is more than one probe for this ORF, TRQ2_1842-1843 means this probe covers part of 1842 as well as part of 1843 and any intergenic DNA in between, TRQ2_1803-1820739-1820933 means that this probe covers the genome coordinates listed. The probe may cover part of the indicated ORF or it may only cover intergenic DNA in the vicinity of that ORF.

manufacture_protocol: Probes were initially designed based on open reading frames from the published genome sequence for T. maritima. Additional probes were designed based on T. sp. RQ2/T. maritima suppressive subtractive hybridization results (Nesbo et al, 2002), a TIGR draft sequence of T. neapolitana, and the published genome sequence for T. petrophila. All probes were generated by PCR amplification of genomic DNA, purified using QIAquick kits (Qiagen), and resuspended in 50% dimethyl sulfoxide to 100 ng/ul. DNA was printed onto UltraGAPS slides (Corning) with five replicates for each probe using a Genetix QArray Mini.


title: Nimblegen/Affymetrix Bifidobacterium longum 2.7K Oligo Array

city: Tsuruoka

first: Shinji

last: Fukuda

state: Yamagata

address: 246-2 Mizukami, Kakuganji

department: Institute for Advanced Biosciences

institute: Keio University

organism: Bifidobacterium longum

first: Yumiko

last: Nakanishi

first: Hiroshi

last: Ohno

first: Jun

last: Kikuchi

manufacture_protocol:
Probes: 192,000
Probes/Target: 20


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [cdf: HGU133Plus2_Hs_ENTREZG.cdf]

city: Toronto

first: Maud

middle: HW

last: Starmans

state: Ontario

address: 661 University Avenue

department: Informatics and Biocomputing Program

country: Canada

institute: Ontario Institute for Cancer Research (OICR)

organism: Homo sapiens

manufacture_protocol: Affymetrix's protocol (see web site)


title: At35b_MR_v04-2 TIGRv5 Arabidopsis Tiling Array

status: Public on Feb 27 2011

city: Oxford

first: Quinn

last: Li

state: OH

address: 316, Person Hall, High Str.

department: Botany

institute: Miami University

organism: Arabidopsis thaliana

manufacture_protocol: see manufacturer's web site


title: Agilent SMD Print_1600 Saccharomyces bayanus and Saccharomyces cerevisiae

city: Stanford

first: Barbara

last: Dunn

state: CA

department: Genetics

institute: Stanford University

organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

manufacture_protocol: Agilent


title: Streptococcus suis serotype 2 05ZYH33 strain

status: Public on Jun 20 2010

city: Nanjing

first: Feng

last: Zheng

address: 293 East Zhongshan Road

institute: Research Institute for Medicine of Nanjing Command

organism: Streptococcus suis 05ZYH33

manufacture_protocol: According to the whole genome sequence of 05ZYH33 (NC_009442), specific oligo-nucleotide probes with an average length of 35 nt were designed to cover every putative ORF (2194 in total) in SS2 genome using Array Designer 2.0 and then synthesized onto complementary metal oxide semiconductor (CMOS) matrix utilizing in situ electrochemical synthesis technique.


title: OSU-CCC Human and Mouse MicroRNA Microarray Version 4.0

city: Bethesda

first: Robert

middle: Scott

last: Hudson

address: National Cancer Institute Room Blgd.37/3044

department: NCI

institute: NIH

organism:
Homo sapiens
Mus musculus

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.   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.   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: AECOM Operon 3.0 34K Mouse Array

city: Scarsdale

first: Joseph

last: Locker

address: Pathology

institute: Albert Einstein College of Medicine

manufacturer: Microarray Facility, Albert Einstein College of Medicine of Yeshiva University

first: Aldo

last: Massimi

manufacture_protocol:
The arrays were printed with 31,769 70mer probes Qiagen V3.0 oligo set plus controls.
Each array was composed of 48 blocks, arranged in 4 columns and 12 rows, each block containing 700 spots in a staggered pattern of 28 columns and 25 rows.
The arrays were printed under rigorous clean-room conditions and with quality control at multiple stages.


title: University of of Jyvaskyla FIN D. montana and D. virilis microarray 219

city: Jyväskylä

first: Laura

last: Vesala

address: Survontie 9

department: Department of Biological and Environmental Science

country: Finland

institute: University of Jyväskylä

organism:
Drosophila virilis
Drosophila montana

description: The array contains multiple probes per a particular gene, designed separately for the two study species, using species-specific sequences (either D.montana or D. virilis).

manufacture_protocol: Since there is no genome sequence available for D. montana (and only partial annotations for D. virilis genome), we selected genes on the array from the D. melanogaster genome using FlyBase gene ontology searches on biological response of interest (http://flybase.org/). The most conserved regions of the candidate genes were then identified by aligning the exon regions of the D. melanogaster gene sequence to their orthologs in D. virilis with Blat search in UCSC Genome Bioinformatics database (http://genome.ucsc.edu). The primers for the candidate genes of D. montana and D. virilis were designed for one to four unique 200-500 bp regions with Primer3 program (http://www-genome.wi.mit.edu/genome software/other/ primer3.html) or manually, using information on the gene alignments. Next, an online program e-Array 5.3 (Agilent) was used to design one to four 60 bp oligonucleotide probes per gene (based on species-specific sequences) using exon regions. Finally, the probes were synthesized in situ with liquid chemistry and arrayed on an “Agilent 60-mer Multi-Pack Gene Expression Microarray” platform with one-color system.


title: NimbleGen Mus musculus MM8 Expression Array (4x72k)

status: Public on Oct 16 2010

city: Madison

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

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


title: 080616_Melogen_60mer_x4

city: Espinardo

first: Daniel

last: Gonzalez-Ibeas

state: Murcia

address: Campus de Espinardo s/n

department: Biologia Estres y Patologia Vegetal

institute: CEBAS-CSIC

organism: Cucumis melo

description:
NimbleGen design name 080616_Melogen_60mer_x4.  Expression design for 17,444 melon unigenes freely available from Melogen database (http://www.melogen.upv.es/).  Four 60-mer probes for every unigen. Microarray 4-plex format (4 x 75K probes). The design includes random GC and other control probes.
native array description file: 080616_Melogen_60mer.ndf
native array description file: 2006-08-08_Melogen_60mer.ngd


title: MPIMarburg_Piriformospora_indica_105k_v1.0

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

institute: Fraunhofer ITEM

organism: Serendipita indica

manufacture_protocol: Both catalog and custom microarrays are manufactured using a proprietary non-contact industrial inkjet printing process, in which oligo monomers are deposited uniformly onto specially-prepared glass slides. This in situ synthesis process prints 60-mer length oligonucleotide probes, base-by-base, from digital sequence files. The precise inkjet process enables the delivery of extremely small, accurate volumes (picoliters) of the chemicals to be spotted. Standard phosphoramidite chemistry used in the reactions allows for very high coupling efficiencies to be maintained at each step in the synthesis of the full-length oligonucleotide. Precise quantities are reproducibly deposited “on the fly.” This engineering feat is achieved without stopping, to make contact with the slide surface and without introducing surface-contact feature anomalies, resulting in consistent spot uniformity and traceability. In addition, multiple microarrays can be printed simultaneously in a single manufacturing run.


title: Agilent-021626 Danio rerio LU/IBL_D.rerio_44k (Feature Number version)

city: Amsterdam

first: Oliver

last: Stockhammer

state: NH

address: Meibergdreef 15

department: Medical Microbiology

institute: AMC

manufacture_protocol: Agilent Ink Jet manufactured


title: Agilent custom Kluyveromyces lactis 11K Array [G2509F]

city: Thiverval-Grignon

first: Jean-Marie

last: Beckerich

address: Campus Agroparistech

institute: INRA

organism: Kluyveromyces lactis

description:
catalog number G2509F (november 2007), Custom Microarray GE 8X15K Custom Microarray GE 8x15K 60mer, sold in multiples of 1-1'x3' slides, 8 microarrays per slide
oligoset design: /K. lactis /NRRL Y-1140 genome version 3 (S. Casaregola, personal  communication) was used as a reference for microarray design. Probe  design was performed using ROSO software completed with in-house  scripts. ROSO takes a number of parameters into account to design  effective oligonucleotide probes: (i) uniqueness among the genomes and  lack of cross-hybridization against exclusion genomes; (ii) melting  temperature (Tm); (iii) lack of secondary structures; and (iv) distance  from the 3' end of the gene. ROSO was run on the 5,270 candidate target  genes. Our objective was to obtain one probe with a length of between 40  and 60 nucleotides per target gene. Probes have to be in exons and are  preferably located at the 3' end of the gene. The genomes of  /Arthrobacter aurescens /TC1/, Arthrobacter sp./ (strain FB24),  /Corynebacterium glutamicum,/ /Lactococcus lactis/ IL1403, /Debaryomyces  hansenii/ CBS767, /Brevibacterium aurantiacum/ATCC9174 (formerly /B.  linens/) and /Yarrowia lipolytica/ CLIB99 were used as exclusion  genomes, creating prospects for transcriptomic ecosystem studies.

manufacture_protocol: See manufacturer's website


title: NimbleGen Pfalciparum 720K 1.0

status: Public on Apr 01 2011

city: Notre Dame

first: Michael

last: Ferdig

state: IN

address: 280 Galvin Life Science

department: Biological Sciences

institute: University of Notre Dame

organism: Plasmodium falciparum

description: PlasmoDB v5.5 P.falciparum genome

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


title: JCVI Aspergillus fumigatus AF293 29.9K amplicon array

status: Public on Apr 20 2010

city: Atlanta

first: John

last: Varga

state: GA

address: 1510 Clifton Road

department: Pediatrics

institute: Emory University

organism: Aspergillus fumigatus Af293

first: Stanley

last: Kim

middle: J

first: Dan

last: Chen

first: Yan

last: Yu

first: William

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: Agilent-015425 PSUMAC-Solanum tuberosum-44K (Probe Name version)

city: Erie

middle: A

last: Campbell

state: PA

address: 4205 College Drive

department: School of Science

institute: Penn State Erie

organism: Solanum tuberosum

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


title: Illumina mouseRef-8 v1.0 expression beadchip

status: Public on Dec 31 2009

city: München-Neuherberg

first: Dietrich

last: Trümbach

address: Ingolstädter Landstraße 1

department: Institute of Developmental Genetics

institute: Helmholtz Zentrum München, German Research Center for Environmental Health

organism: Mus musculus

technology: oligonucleotide beads

description: The Mouse-8 BeadChip can be used to study expression of over 24,000 mouse transcripts based on MEEBO, RefSeq and RIKEN FANTOM2 content. researchers can generate whole-genome expression profiles for 8 samples in parallel on a single BeadChip.

manufacture_protocol: see manufacturer's website


title: Yale University Nimblegen 2005-05-12_Yeast_PM_MM

status: Public on Feb 18 2009

city: New Haven, BASS 437

middle: R

last: Seringhaus

state: CT

address: 266 Whitney Ave

department: Molecular Biophysics & Biochemistry

institute: Yale University

organism: Saccharomyces cerevisiae

manufacture_protocol: maskless-photolithography. Maximum of 396,000 spots per array.


title: Alternative Human Exon 1.0 ST Array [custom CDF (version 9) mapping of probes to Ensembl genes]

status: Public on Sep 13 2009

city: Cambridge

first: Xinshu

last: Xiao

state: MA

address: 77 Mass Ave. MIT, 68-211

department: Biology

institute: MIT

description:
Probe set data extracted from custom CDF version 9 'hsex10stv2hsensecdf_9.0.1.tar.gz' and mapped to Ensembl genes.
http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download_v9.asp

manufacture_protocol: See manufacturer's web site


title: UPR-DevNeuro H.glaberrima_regenearation 8x15K v1.1 (Agilent custom)

status: Public on May 21 2009

city: Amherts

first: Pablo

middle: Andres

last: Ortiz-Pineda

address: 661 N Pleasant st

department: Veterinary & Animal Sciences

institute: University of Massachusetts

organism: Holothuria glaberrima

first: Jose

middle: E

last: Garcia-Arraras

first: Francisco

last: Ramirez-Gomez

manufacture_protocol: Two-Color Microarray-Based Gene Expression Analysis. Agilent  (manual part #: G4140-90050)


title: Alternative Human Exon 1.0 ST Array [custom CDF (version 9) mapping of probes to Ensembl exons]

description:
Probe set data extracted from custom CDF version 9 'hsex10stv2hsensecdf_9.0.1.tar.gz' and mapped to Ensembl exons.
http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download_v9.asp


title: Oligo GEArray Human Inflammatory Cytokines & Receptors Microarray

status: Public on Sep 17 2009

city: Ithaca

first: Chia-Hsin

last: Ju

state: NY

address: VMC C5 151 Cornell University

institute: Cornell University

manufacture_protocol:
The Oligo GEArray microarray contains oligonucleotide probes
representing genes associated with a specific biological pathway. The proprietary probes are printed on a 2.5 x 3.8 cm nylon membrane with an advanced non-contact printing technology in rows of 8, 12, or 16 columns.
Reference:  http://sabiosciences.com/gene_array_product/HTML/OHS-011.html


title: TNO/Mic-B.subtilis-8.2k-v3

status: Public on Dec 08 2008

city: Zeist

first: Remco

last: Kort

address: Utrechtseweg 48

department: Microbiology

institute: TNO

organism: Bacillus subtilis

description:
This is a condensed platform of the full 9.2K array. The full layout is described in a supplementary file.
Previous versions of this platform have been described by Bart Keijser (GPL4415) and Anna Magdalena Zakrzewska (GPL6257)

manufacturer: Micro Array Department (MAD), University of Amsterdam, The Netherlands

manufacture_protocol: An oligonucleotide library of 65-mers (Cat#BACLIB384 Sigma-Compugen Inc.), which covered 4100 open reading frames of the B. subtilis 168 genome, was spotted in duplicate on glass slides with a Generation III microarray spotter (Molecular Dynamics, Sunnyvale, California, USA) using Lucidea Spotting Pins (GE Healthcare).


title: Yale University Nimblegen 2005-05-12_Human_ENCODE_PM_MM


title: LC_MRA-1001_miRHuman_12.0_080901

status: Public on Apr 01 2009

city: Houston

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

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

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: BTI oligonucleotide microarray using Ambion miRNA probesets (#1564v1)

status: Public on Dec 01 2008

city: Singapore

first: Peter

last: Nissom

address: 20 Biopolis Way

institute: Bioprocessing Technology Institute

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

manufacturer: Bioprocessing Technology Institute, Singapore

first: Angie

last: Chang

first: Eugene

last: Koh

middle: M

manufacture_protocol:
1.Ambion probes ( #1564v1) were dissolved in 25 ul of printing buffer to 25um.
2. Rearray 10 µL into 384-well, Abgene 384-well microarray plates (AB-1056/w).
3. Print arrays using Biorad chipwriter pro, after print run is completed, let slides dry through passive evaporation in the arrayer.


title: Human Promoter ChIP-on-chip Microarray - custom annotation

status: Public on Aug 26 2008

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

organism: Homo sapiens

first: Roberto

last: Ferrari

first: Matteo

last: Pellegrini

first: Greg

last: Horwitz

first: Wei

last: Xie

first: Arnold

last: Berk

manufacture_protocol:
The Human Promoter ChIP-on-chip Microarray Set is specifically designed for location analysis of human DNA-binding proteins by pairing chromatin immunoprecipitation (ChIP) with Agilent DNA microarrays. Each microarray contains optimized and validated probes specifically designed for ChIP-on-chip. Coupled with Agilent's probe selection and stringent design processes, the set delivers robust hybridization and reliable binding data with greater true binding events and fewer false positives.
~17,000 of the best-defined human transcripts represented as defined by RefSeq
Enriched content sourced from UCSC hg18, NCBI build 36.1 (March 2006)
Set covers -5.5kb upstream to +2.5kb downstream of the transcriptional start sites
Individual slide contents defined by Array Design ID
1 x 244K slide format printed using Agilent's 60-mer SurePrint technology
2 slides per set. Each slide contains one 244K microarray.


title: Ambion Human Mouse Rat miRNA microarray (probes_1564V1_Oct05)

status: Public on Aug 12 2008

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

description:
http://www.ambion.com/techlib/resources/miRNA_array/
Ambion_probes_1564V1_Oct05


title: HUCMC Ruthia magnifica v1.0

status: Public on Nov 28 2008

first: Irene

last: Newton

address: 16 Divinity Ave

department: OEB

institute: Harvard University

organism: Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)

manufacture_protocol: arrayer hardware/software


title: OUHSC_Neisseria gonorrhoeae_MPAUT1a520274F

status: Public on Dec 26 2008

city: Oklahoma City

first: Lydgia

last: Jackson

state: OK

address: 975 NE 10th Street

department: Microbiology and Immunology

institute: University of Oklahoma Health Sciences Center

organism: Neisseria gonorrhoeae

first: David

middle: W

last: Dyer

first: Jason

middle: P

last: Folster

first: William

last: Shafer

first: Paul

middle: T

last: Johnson

first: Vijaya

last: Dhulipali

first: Alexandra

last: Mercante

first: Virginia

last: Stringer

manufacture_protocol: Affymetrix;Custom multipathogen array


title: ENCODE NimbleGen HG17 50mer 390K tiling array (catalog number C1980001)

status: Public on Aug 15 2008

city: Århus

first: Pascal

last: Preker

address: C. F. Møllers Alle, Bldg 1130

country: Denmark

institute: Århus University

description: Differential expression array of siRNA mediated exosome (hRrp40/EXOSC3) knock-down versus control (eGFP) knock-down.

first: Jesper

last: Nielsen

first: Susanne

last: Kammler

first: Søren

last: Lykke-Andersen

first: Marianne

middle: S

last: Christensen

first: Mikkel

middle: H

last: Schierup

first: Torben

last: Jensen

manufacture_protocol: see NimbleGen website (http://www.nimblegen.com/products/chip/)


title: BTI DNA microarray for Actinosynema pretiosum

first: Peter

last: Nissom

organism: Actinosynnema pretiosum

first: Angie

last: Chang

manufacture_protocol:
1.PCR products were obtained from PCR reactions on genomic DNA of A. pretiosum. The primers were designed based on DNA sequences, AF453501 and U33059 as discussed in Yu et. al., 2002, PNAS, 99:7968. The DNA were arrayed in Abgene 384-well plates. Each well contains 100-150 ng/ul of DNA.
2. Rearray 10 µL into 384-well, Abgene 384-well microarray plates (AB-1056/w).
3. Print arrays using Biorad chipwriter pro, after print run is completed, let slides dry through passive evaporation in the arrayer.


title: S. cerevisiae Tiling1.0R Array SNPScanner compatible

status: Public on Jul 23 2008

city: London

first: Tamar Tom

last: Rolef Ben-Shahar

address: 44 Lincoln's Inn Fields

institute: Cancer Research UK London Research Institute

description:
GEO platform for S.cerevisiae Tiling1.0R Sc03b_MR_v04 containing per base pair features compatible with SNPScanner output.
Gresham, D. et al. Genome-wide detection of polymorphisms at nucleotide
resolution with a single DNA microarray. Science 311, 1932-1936 (2006).

first: Tom

last: Ben-Shahar

first: Philip

last: East

manufacture_protocol: Affymetrix tiling array for S.cerevisiae whole genome, 2micron plasmid, and mitochondrial DNA. 5bp resolution chip. Covers Crick strand.


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array based on a custom CDF (REFSEQ_7)

status: Public on Nov 21 2008

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description: This identical to GPL570 but a custom cdf environmnet was used to extract data. The cdf can be found at the link below. We used the REFSEQ7 version for HGU-133_plus2

manufacture_protocol: see the Affymetrix website


title: Rosetta/Merck DT_Phase2_7_of_17 microarray

status: Public on Jul 15 2008

city: Seattle

first: Amit

middle: V

last: Kulkarni

state: WA

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description:
Oligonucleotide array on glass.
Microarray pattern generation.  We downloaded genome and transcript sequences from the National Center for Biotechnology Information on January 8, 2003.  We aligned RefSeq, mRNA, EST57 and patent transcripts to the genome using sim458 and identified all exons and exon-exon junctions.  We also aligned mouse transcripts to the human genome to identify possible splice forms not yet present in human transcript databases59.  An optimized 60 nt probe was designed to monitor each exon and a 36 nt probe was centered across each exon-exon junction60.  Exons less than 60 nt were monitored using shorter probes attached to T-stilts.  Probes predicted to perform poorly, such as those associated with repeat sequences or containing unacceptable GC-content, were discarded.  In total, 383,014 oligonucleotide probes to monitor 203,672 exons and 178,351 exon-exon junctions in 17,939 genes were synthesized to a 17 array set, with each array containing 23,107 non-control probes. Arrays were ordered from Agilent (California).  Probes have been mapped to the hg18 genome and can be viewed with the UCSC genome browser using a supplemental probe alignment file (see Probes.GenomeAlignments.psl linked at the foot of the record) in BED format.

first: John

last: Castle

manufacture_protocol: See manufacturer's website


title: Rosetta/Merck DT_Phase2_14_of_17 microarray

manufacturer: Rosetta Inpharmatics / Merck Pharmaceuticals


title: Rosetta/Merck DT_Phase2_8_of_17 microarray


title: Rosetta/Merck DT_Phase2_16_of_17 microarray


title: Rosetta/Merck DT_Phase2_12_of_17 microarray


title: Rosetta/Merck DT_Phase2_5_of_17 microarray


title: Rosetta/Merck DT_Phase2_10_of_17 microarray


title: Rosetta/Merck DT_Phase2_6_of_17 microarray


title: Rosetta/Merck DT_Phase2_15_of_17 microarray


title: Rosetta/Merck DT_Phase2_9_of_17 microarray


title: Rosetta/Merck DT_Phase2_11_of_17 microarray


title: Rosetta/Merck DT_Phase2_17_of_17 microarray


title: Rosetta/Merck DT_Phase2_13_of_17 microarray


title: Rosetta/Merck DT_Phase2_4_of_17 microarray


title: Rosetta/Merck DT_Phase2_3_of_17 microarray


title: Rosetta/Merck DT_Phase2_2_of_17 microarray


title: Rosetta/Merck DT_Phase2_1_of_17 microarray


title: Illumina HumanHap550v3 Genotyping BeadChip (HumanHap550v3_B)

status: Public on Jun 23 2008

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

description: over 555,000 tag SNP markers derived from the International HapMap Project

relation:
Alternative to: GPL6434
Alternative to: GPL6433


title: Illumina HumanExon510-Sv1 DNA Analysis BeadChip (HumanExon510Sv1_D)

description: over 510,000 markers to interrogate human genetic variation using SNP and copy number variation (CNV) probes


title: Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array (Sc03b_MR_v04)

status: Public on Feb 08 2008

first: Toshio

last: Tsukiyama

address: 1100 Fairview Ave N

institute: FHCRC

manufacture_protocol: Affymetrix


title: Illumina HumanHap300v1 Genotyping BeadChip (HumanHap300_(v1.0.0))

description: over 317,000 tagSNP markers derived from the International HapMap Project


title: LaSalle/UCDavis-Human custom tiling 26.3mb

status: Public on Dec 01 2007

city: Davis

first: Dag

last: Yasui

address: 1 Shields Avenue

department: Medical Microbiology and Immunology

institute: University of California at Davis

first: Sailaja

last: Peddada

first: Mark

middle: C

last: Bieda

first: Roxanne

middle: O

last: Vallero

first: Amber

last: Hogart

first: Raman

last: Nagarajan

first: Karen

middle: N

last: Thatcher

first: Peggy

last: Farnham

first: Janine

last: LaSalle

manufacture_protocol: As described on NimbleGen website


title: NimbleGen 1500b Promoter Array

status: Public on Dec 06 2007

manufacture_protocol: NimbleGen


title: FHCRC-Francisella tularensis subsp. novicida-2K OligoArray Version 1

status: Public on Jun 02 2008

first: Allison

last: Mitchell

department: Human Biology

institute: Fred Hutchinson CRC

organism: Francisella tularensis subsp. novicida

manufacturer: Fred Hutchinson Cancer Research Center, Genomics Shared Resources

manufacture_protocol: The array was constructed by mechanically spotting Oligos onto Corning UltraGAP slides using an Omnigrid 300. The Platform table represents a condensed version of the full array which is provided as a supplementary file.


title: Affymetrix Helicobacter pylori Hp-AG78a520172F

status: Public on Feb 22 2008

city: Saint Louis

first: Marios

last: Giannakis

state: MO

address: 4444 Forest Park Blvd.

department: Developmental Biology

institute: Washington University in Saint Louis

organism: Helicobacter pylori


title: NimbleGen Pseudomonas putida KT2440 custom array (2006-10-10_TI160488_60mer)

status: Public on Oct 11 2007

first: Enid

last: Gonzalez

address: One Shields Drive

department: Crops Pathology and Genetics Research Unit

institute: USDA-Agricultural Research Service

organism: Pseudomonas putida KT2440

description: Custom design for Pseudomonas putida KT2440 (Taxonomy Id: 160488) covering NC_002947. Organism is > 60% GC.  Probes selected for 5350/5350 sequences. Median number of probes/sequence is 18 with an average of 18.00. Each probe will be replicated 4 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. Design_ID: 4764.

manufacture_protocol: Nimblegen Systems


title: Illumina HumanHap300-Duov2 Genotyping BeadChip (HumanHap300v2_A)

description: over 318,000 tag SNPs derived from Phase I HapMap data


title: DJF Pig oligo 27K1 ver1

status: Public on Feb 20 2008

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

institute: Aarhus University, Faculty of Agricultural Sciences

organism: Sus scrofa

manufacturer: University of Aarhus, Faculty of Agricultural Sciences, Department of Genetics and Biotechnology, Group for Molecular Genetics and System Biology

first: Henrik

last: Hornshøj

first: Lene

last: Conley

first: Christian

last: Bendixen

manufacture_protocol: DJF_PIG_OLIGO_27K1_ver1 consists of 27.648 features - 25.210 unique oligonucleotides representing porcine transcripts and 2.438 control features - all printed as single spots in a 4 x 12 array with sub-arrays each consisting of 24 x 24 spots. The primary sequence source used for designing the oligonucleotides representing porcine transcripts was generated in the Sino-Danish Pig Genome Sequencing Project including more than 0.8 million EST sequences (Gorodkin et al.: Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 ESTs. Genome Biology 2007, 8:R45) and 3.8 million whole-genome shotgun sequences (Wernersson et al.: Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC.Genomics 2005, 6 (1)). An additional 1.6 million porcine sequences were retrieved from the public domains ENSEMBL (www.ensembl.org), NCBI (www.ncbi.nlm.nih.gov) and TIGR (www.tigr.org) yielding a total of approximately 6.2 million porcine sequences. A pipeline was set up to generate both candidate input sequences and final input sequences for oligonucleotide design. For human gene transcript, 15.700 sequences were generated and used as input for oligonucleotide design with SEPON (Hornshoj et al.: SEPON, a Selection and Evaluation Pipeline for OligoNucleotides based on ESTs with a non-target T-m algorithm for reducing cross-hybridization in microarray gene expression experiments. Bioinformatics 2004, 20 (3)). In addition, 5.500 transcript sequences for other mammalians and 5.100 sequences for uncharacterized genes were generated and used as input to OligoArray (Rouillard et al.: OligoArray: genome-scale oligonucleotide design for microarrays. Bioinformatics 2002, 18 (3)). The oligonucleotide design programs produced a total of 25.210 oligonucleotides representing approximately 19.000 genes. The oligonucleotides were synthesised by Isogen Life Science (www.isogen-lifescience.com) and delivered in 96 well plates. The oligonucleotides were resuspended in 0.01x SSC. Using a Sciclone ALH 3000 workstation (Caliper Life Sciences, www.caliperls.com), complete plates were rearrayed from 96 to 384 well library plates and incomplete plates were hitpicked into 384 well library plates. In average 200 pmol of each oligonucleotide were transferred to a 384 well spotting plate, dried by speed vac and resuspended in spotting solution (1 X Micro Spotting Solution Plus, Telechem International, www.arrayit.com). The 2.438 control features consist of 48 unique features printed in all 48 sub-arrays and 134 presumed blank features, which origin from presumed empty positions in the oligonucleotide plates supplied by Isogen Life Science. The 48 unique control features consists of a positive spot (also known as “landing lights”), a blank spot (spotting buffer), 10 oligonucleotides designed for Arabidopsis genes (Wang et al.: Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays. Genome Biology 2003, 4 (1) R5), 18 random 70 mer sequences selected to have no homology to known transcripts and 18 oligonucleotides representing the Lucidea Universal ScoreCard (GE Healthcare, www.gelifesciences.com). The positive spot was prepared by PCR amplification of a bovine EST fragment using a aa-dUTP containing dNTP mix followed by coupling of Alexa-555 or Alexa-647 using ARES DNA Labelling kits (Molecular Probes/Invitrogen, www.probes.invitrogen.com). The Arabidopsis and random oligonucleotides were synthesised by DNA Technology (www.dna-technology.dk). The 18 oligonucleotides representing the Lucidea Universal ScoreCard contains 10 oligonucleotides resulting in an intensity dilution series and 8 oligonucleotides resulting in different ratios when the labelling reactions are spiked in with the supplied RNA. The Lucidea Universal ScoreCard oligonucleotides were designed and synthesised by TIB MOLBIOL (www.tib-molbiol.com). The 46 unique control oligonucleotides were resuspended in 0.01x SSC and 200 pmol of each oligonucleotide was transferred to a 384 well spotting plate, dried by speed vac and resuspended in spotting solution (1 X Micro Spotting Solution Plus, Telechem International). The arrays were spotted on UltraGAPS slides (Corning Incorporated, www.corning.com) at 20 C/55 % RH using a ChipWriter Pro MicroArrayer (Bio-Rad Laboratories, www.bio-rad.com) with 48 x 946 MP2.5 pins (Telechem International, www.arrayit.com). Slides were dried and UV cross-linked (600 mJ) and stored in a vacuum desiccator until use.


title: Thalassiosira pseudonana NimbleGen 36mer oligo tiling array

status: Public on Jan 05 2008

first: E.

middle: Virginia

last: Armbrust

address: Ben Hall IRB, 616 NE Northlake Pl, Room 306

department: Oceanography

institute: University of Washington

organism: Thalassiosira pseudonana CCMP1335

description: The layout files for the individual chips that make up the 8-array set are linked below as supplementary files.

manufacturer: University Wisconsin, Madison; Biotechnology Center

first: Matthew

last: Rodesch

last: Robison

first: Sandra

last: Splinter BonDurant

first: Kathryn

last: Richmond

first: Manoj

last: Samanta

manufacture_protocol:
1.  Tiling array design: A total of 1,308,958 36-mer probes were chosen uniformly from both strands of the 34 Mb T. pseudonana genome (Version 2, http://www.jgi.doe.goc) with gaps of 10 nucleotides between consecutive probes. No probes were chosen from the ambiguous or repetitive regions of the chromosome (Todd Richmond; personal communication) or the unassembled scaffolds. The selected probes were synthesized on eight glass-based microarrays, with 178,600 probes on the first 7 microarrays and 58,758 probes on the eighth microarray. Each array also included ca. 500 random duplicated probes for normalization and noise estimation purposes. The location of the probes on each array was randomized in order to eliminate any positional bias in the synthesis and hybridization.
2. Synthesis: Two complete sets of the tiling microarrays were synthesized for hybridization with labeled cDNA from the control and the low silicon growth conditions. Microarrays were fabricated using a modified Maskless Array Synthesizer (MAS) as described previously (Sing-Gasson et al. 1999, Nuwaysir et al. 2002) on SuperClean (ArrayIT) glass substrates functionalized with N-(3-Triethoxysylylpropyl)-4-hydroxy-butryamide (Gelest Inc). Delivery of standard DNA synthesis reagents (Proligo) and NPPOC phosphoramidite (Nimblegen) was performed via an Expedite DNA synthesizer.
3. Array Processing: After synthesis, microarrays were deprotected by immersion in EDA/EtOH (1:1 vol) for two hours at room temperature.  Arrays were then washed in water, dried with argon, and stored desiccated prior to hybridization.  Hybridization was performed with 10ug of fragmented cRNA in 300ul in the presence of 100mM MES, 1M Na, 20mM EDTA and 0.01% tween20 for 17 hours at 45C.  After hybridization, arrays were washed with a non stringent wash buffer (NSWB) (6X SSPE and 0.01% Tween 20) followed by incubation with a stringent wash buffer (100mM MES, 0.1M Na+, 0.01% Tween 20) for 30 minutes at 45C.  Arrays were stained with streptavidin-cy3 (Amersham) for 25 minutes at room temperature, washed with NSWB, rinsed with Final Wash Buffer (Nimblegen) and dried under argon. Arrays were scanned using an Arrayworx scanner (Applied Precision).  Array feature intensity was extracted from images using in-house software.


title: UW_Homo_sapiens_condensed_array_36848_v1

status: Public on Sep 14 2007

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

description: Standard 60-mer hg17 gene expression array

first: Guangjin

last: Pan

first: Shulan

last: Tian

first: Jeff

last: Nie

first: Chuhu

last: Yang

first: Hairong

last: Wei

first: Gudrun

last: Jonsdottir

first: Ron

last: Stewart

first: James

last: Thomson

manufacture_protocol: Standard NimbleGen maskless array synthesis for standard 60-mer hg17 gene expression array


title: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array based on a custom CDF

status: Public on Oct 18 2006

first: Ola

last: Larsson

description: This identical to GPL570 but a custom cdf environmnet was used to extract data. The cdf can be found at the link below. We used the REFSEQ6 version for HGU-133_plus2

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


title: Lieb Lab at UNC-CH_Yeast Whole-genome Array (PCR-based)

status: Public on Aug 11 2006

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 203 Fordham Hall

department: Department of Biology

institute: University of North Carolina at Chapel Hill

description: Whole-genome microarrays with PCR-amplified products represent ORFs, intergenic regions, and other noncoding regions (rDNA, tRNA, transposons, transposon long terminal repeats, telomeres, centromeres, and introns). Generally, each ORF was represented from start codon to stop codon. The intergenic regions consisted of the DNA between annotated ORFs divided such that PCR products were not longer than 1.5 kb, with a few exceptions. The noncoding regions conform to boundaries as annotated by the Saccharomyces Genome Database (SGD) as of the year 2000. Mitochondrial segments did not necessarily conform to annotated functional boundaries. This platform covers several print runs, in which print plates were arranged in different orders.

first: Gregory

middle: J

last: Hogan

manufacture_protocol: see Iyer et al. 2001, Nature 409: 533-538


title: Anopheles gambiae GAMBER_AG Array

status: Public on Aug 15 2007

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

manufacture_protocol: AGILENT


title: IGG_Mouse_178_AP1

status: Public on Jan 05 2007

city: Genoa

first: Paolo

last: Fardin

address: Largo G. Gaslini 5

department: Molecular Biology

country: Italy

institute: Istiuto Giannina Gaslini

manufacturer: Microarray Core Facility, Gaslini Institute, Genoa, Italy

first: Annamaria

last: Ricciardi

first: Luigi

last: Varesio

manufacture_protocol: C6-amino-linker oligonucleotides (50 nucleotides in length) were obtained from MWG oligoset (MWG-Biotech AG, Ebersberg, Germany), and spike-in controls oligonucleotides were purchased from Ambion ArrayControl Spot (Ambion Inc., Austin TX). Oligonucleotides were printed on e-Surf Activated Slides (Life Line Lab S.r.l., Italy) with a SpottingArray 24 (PerkinElmer, Wellesley, MA) using 4 Stealth Micro Spotting Pins (Telechem International, Inc. Sunnyvale, CA) in 150 mM phosphate buffer pH 8,5 at 40% humidity. E-surf activated slides are obtained by adsorption on glass of a hydrophilic polymer containing N,Nacryloyloxysuccinimide (NAS). Oligonucleotides were printed at a final concentration of 10 pmol/ml. The coupling reaction was performed o/n in a saturated NaCl solution chamber with a 75% relative humidity. All oligonucleotides were printed in quadruplicates over 4 subarrays with a 2x2 print head. Spike-in controls oligonucleotides, negative control and buffer were printed in quadruplicates onto each subarray. The scheme is repeated 3 times on the entire slide surface resulting in 12 replicates for each gene element and 48 replicates for each control element.


title: Lieb Lab at UNC-CH_Yeast Whole-genome Array (PCR-based)_for Lee CK et al.

status: Public on Apr 28 2006

country: USA


title: Lieb Lab at UNC-CH_Yeast Oligo Tiling Array from (RandoLab_Harvard)

description: The sequence from S. cerevisiae chromosome III was fragmented into 50-mers overlapping every 20 base pairs. Potentially cross-hybridizing probes were filtered by BLASTing these sequences against the entire genome and eliminating sequences from chromosome III that included 5 or more contiguous probes with perfect BLAST matches, leaving 30 contigs covering 278,960 base pairs. Oligonucleotides were also tiled over one kilobase of 230 promoters on other chromosomes, starting at -900 from the start codon and extending to +100.

manufacturer: Center for Genomics Research, Harvard University

first: OJ

last: Rando

manufacture_protocol: MGuide, www.microarrays.org


title: NIAID - Hsbb

status: Public on Mar 03 2004

city: Bethesda

first: Michael

last: Wilson

address: 50 South Drive, Room 5509

department: Division of Intramural Research

description:
Printing by NIAID / Microarray Research Facility
Surface type: non-adsorptive, epoxy-coated glass
Attachment: covalent
Array description: The custom microarrays are manufactured by the Microarray Research Facility of the National Institute of Allergy and Infectious Diseases (NIH/NIAID). Microarrays are printed with an Omnigrid robotic arrayer by Genomic Solutions (http://www.genomicsolutions.com ) that is fitted with a printhead and 48 SMP3 print tips from Telechem (http://www.arrayit.com ). The human microarray (Hsbb) probe set is based on 70mer oligonucleotides from Qiagen's Human Genome Oligo Set V2.0 ( http://oligos.qiagen.com/arrays/omad.php ).  A comprehensive gene list is also available at http://madb.niaid.nih.gov/
Oligonucleotide probes are distributed into 384-well polypropylene plates (Genetix, 384 micro array) and dissolved to a normalized 25 micromolar concentration in print buffer (150mM sodium phosphate, pH 8.5, 4% sodium sulfate, 0.0001% N-lauryl sarcosyl).  The Hsbb microarray spot densities are 190 microns (center-to-center).  The microarrays are printed on MWG Epoxy Slides (MWG Biotech Inc., # 1150-000000) and treated by a method that is an adaptation of the manufacturer's instructions to allow higher throughput processing.


title: Oligo array for Plasmodium berghei

status: Public on Sep 22 2006

organism: Plasmodium berghei

description: This microarray is a high-resolution, high performance 60-mer oligonucleotide array that represents the Plasmodium berghei transcriptome.

manufacture_protocol: Agilent Technologies in situ oligonucleotide method


title: NIH-DUKE ZEBRAFINCH 18K v1.0

status: Public on Apr 06 2006

city: Durham

first: Osceola

last: Whitney

address: Research Drive, Bryan Research Building, Room 401E

department: Neurobiology

institute: Duke University Medical Center

organism: Taeniopygia guttata

manufacturer: NIH Neuroscience Microarray Consortium, DUKE-Erich Jarvis Lab

manufacture_protocol: All of the details of the manufacture protocol can be found in Wada et al. 2006.


title: Netherlands Cancer Institute human 3.5k BAC array

status: Public on Nov 16 2006

city: Hamburg

first: Simon

middle: A

last: Joosse

address: Martinistrasse 52

department: Institute of Tumor Biology

institute: University Medical Center Hamburg-Eppendorf

description: Slides: Code Link Activated Slides (Amersham Biosciences, Prod. No. 300011 00)

manufacturer: the Netherlands Cancer Institute - Central Microarray Facility

manufacture_protocol: Degenerate oligonucleotide PCR-products from all BAC clones were prepared for spotting according to detailed protocols (Pinkel et al, 1998) with some modifications (Alers et al, 1999). All clones (three replicates for each probe) were spotted in randomised fashion across 48 subarrays, each containing 270 spots.


title: UWVJLAB RT 150 v.1.0

status: Public on Jul 01 2006

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

organism: Oncorhynchus mykiss

manufacturer: Genomics and Microarray Laboratory, University of Guelph

first: Mathilakath

last: Vijayan

first: Thomas

last: Mommsen

first: Graham

last: VanAggelen

manufacture_protocol:
PCR products were cloned into the Invitrogen pCR-Topo II vector (Invitrogen, Burlington, ON, Canada) according to the manufacturer’s protocol.  Ligation of the PCR products into the vector was verified by PCR with the vector specific M-13 forward and reverse primers.  Plasmids containing the desired PCR fragments were isolated using a Qiaprep Spin miniprep plasmid isolation kit (QIAgen).  All plasmids were sequenced, for correct insert confirmation, at the Center for Environmental Health, at the University of Victoria (Victoria, B.C. Canada).

Each gene fragment was amplified in ten PCR reactions (100 µl each or 1 ml total) in a thermal cycler (MJ Research, Watertown, MA, USA) using gene specific primers in the following PCR reaction: 1X Taq Polymerase buffer containing magnesium chloride, each dNTP at a concentration of 300 µM, 3.75 U of Taq (Promega, Madison, WI, USA), 3 ng of plasmid, and 0.6 µM of each specific primer.  The following conditions applied: 35 cycles of 94°C for 30 s, appropriate annealing temperature (45 to 55 oC depending on gene specific primers) for 60 s, and 72 °C for 2 min followed by a final 12 min extension at 72°C.  PCR products were visualized on a 1.2% agarose gel stained with 1 µg of ethidium bromide/ml to confirm correct size of amplicon as well as minimal primer dimer.  The ten PCR reactions for each gene fragment were pooled and purified using the Qiagen QIAquick PCR Purification kit.  Concentration of each gene fragment was determined via spectrophotometry, the samples were speed vacuum dried, resuspended in 3X SSC to a final concentration of 0.5 µg/ml for each gene fragment.  The gene fragment was confirmed with a 1.2% agarose gel.

Prior to printing, cDNA clones were diluted to 50 ng/µL in 3x SSC and placed in a 384 well plate.  The cDNA fragments were printed on ArrayIt Superamine glass slides (Telechem, Sunnyvale, CA, USA) using a BioRad ChipWriter Pro robotic System (BioRad, Mississauga, ON, Canada) equipped with 4 pins for printing one array (Telechem).  Each cDNA fragment was printed side by side in triplicate.  In addition, a 500 bp fragment from the Lambda Q bacterial gene was printed onto each slide as a control for hybridization inefficiencies.