| 1 |
GPL5441 |
UCSF Johnson Candida albicans tiling 185K v1.0 (assembly 20) |
184,672 |
UCSF |
2007-06-27 |
Agilent |
Candida albicans
 |
Tiling Array |
spotted oligonucleotide, UCSF Johnson Candida albicans tiling 185K v1.0 (assembly 20), |
| 2 |
GPL5365 |
SAGE:10:NlaIII:Oryza sativa |
68,462 |
|
2007-06-07 |
|
Oryza sativa
 |
SAGE NlaIII |
SAGE NlaIII, SAGE:10:NlaIII:Oryza sativa, This is a virtual platform for SAGE libraries generated for Oryza sativa using NlaIII as an anchor enzyme. |
| 3 |
GPL5189 |
NSF_Pinus_taeda_49K |
49,152 |
Plant Genomics |
2007-05-21 |
NSF |
Pinus taeda
 |
cDNA Array |
spotted DNA/cDNA, NSF_Pinus_taeda_49K, The below table is based on the GAL file. This platform may not be suitable for submission of data in which replicate features have been averaged during normalization. In such cases users should submit their own platform representing merged features. |
| 4 |
GPL5389 |
AtMap1.0 |
45,014 |
Kyoto University |
2007-06-14 |
Agilent Technologies |
Arabidopsis thaliana
 |
Tiling Array |
in situ oligonucleotide, AtMap1.0, The AtMap1 array was designed on 4 x 44k format custom oligonucleotide microarray with the eArray system ver. 4.5 (Agilent Technologies, Palo Alto, CA). Data probes were selected from high-density tiling probes designed by Agilent. A control grid (IS-45220-4-V1_4x44K_LA_At_V20060828) for tiling array was used as control probes. The ID column represents the Agilent Feature Extraction feature number. Supplementary file is ExternalFullGEML2 file. |
| 5 |
GPL5101 |
Rice 44K |
40,901 |
National Institute of Agrobiological Sciences |
2007-04-18 |
Agillent |
Oryza sativa
|
Oligo Array |
in situ oligonucleotide, Rice 44K, |
| 6 |
GPL5439 |
Maize oligo array version 1.9 array A |
32,448 |
Plant Genomics |
2007-06-27 |
University of Arizona |
Zea mays
 |
Oligo Array |
spotted oligonucleotide, Maize oligo array version 1.9 array A, Spotted oligo array on glass. The whole maize array set 1.9 version contains 56310 unique probes from maize and array A contains 29270 of them. The number of total spots including empty and controls is 32448. |
| 7 |
GPL5440 |
Maize oligo array version 1.9 array B |
32,448 |
Plant Genomics |
2007-06-27 |
University of Arizona |
Zea mays
|
Oligo Array |
spotted oligonucleotide, Maize oligo array version 1.9 array B, Spotted oligo array on glass. The whole maize array set 1.9 version contains 56310 unique probes from maize and array B contains 28470 of them. The number of total spots including empty and controls is 32448. |
| 8 |
GPL5397 |
TIGR PFGRC Aspergillus nidulans version 1 array designed primarily based on strain FGSC A4 |
25,392 |
Faculty of Pharmaceutical Sciences of Ribeirão Preto |
2007-06-18 |
TIGR PFGRC (The Pathogen Functional Genomics Resource Center) |
Emericella nidulans
 |
Oligo Array |
spotted oligonucleotide, TIGR PFGRC Aspergillus nidulans version 1 array designed primarily based on strain FGSC A4, This set includes 11481 oligonucleotides (ss oligo 70 mer), has 23962 spots (2x oligo replicates) distributed in 48 blocks. The condensed array layout file (ie, 1x representation of oligos) is linked below as a supplementary file. |
| 9 |
GPL5423 |
Treenomix spruce 21.8K cDNA microarray |
25,344 |
University of British Columbia |
2007-06-22 |
Treenomix consortium at the University of British Columbia, Vancouver, Canada; BC Cancer Agency Genome Sciences Centre, Vancouver, Canada; National Research Council Biotechnology Research Institute, Montreal, Canada |
Picea
 |
cDNA Array |
spotted DNA/cDNA, Treenomix spruce 21.8K cDNA microarray, Corning UltraGaps |
| 10 |
GPL5337 |
URGV Arabidopsis thaliana 25K CATMA_v2.1 |
25,228 |
INRA |
2007-05-29 |
INRA-URGV (Plant Genomic Research Unit) |
Arabidopsis thaliana
|
cDNA Array |
spotted DNA/cDNA, URGV Arabidopsis thaliana 25K CATMA_v2.1, Corning Ultra-GAPS (TM) slides are spotted with 64 pins (8x8) therefore the spotted area is divided into 3 metablocks, each containning 64 blocks of 144 spots (12x12). The arrray contains 24576 Gene Specific Tags (GST) and 615 Chloroplastic and Mitochondrial Tilling array probes. |
| 11 |
GPL5336 |
URGV Arabidopsis thaliana 25K CATMA_v2 |
24,595 |
INRA |
2007-05-29 |
INRA-URGV (Plant Genomic Research Unit) |
Arabidopsis thaliana
|
cDNA Array |
spotted DNA/cDNA, URGV Arabidopsis thaliana 25K CATMA_v2, Corning Ultra-GAPS (TM) slides are spotted with 64 pins (8x8) therefore the spotted area is divided into 3 metablocks, each containning 64 blocks of 144 spots (12x12). The array contains 24576 Gene Specific Tags (GST) |
| 12 |
GPL5343 |
wheat 22k |
22,575 |
Kihara Institute for Biological Research, Yokohama City University |
2007-05-31 |
Agilent Technologies |
Triticum aestivum
 |
Oligo Array |
in situ oligonucleotide, wheat 22k , |
| 13 |
GPL5116 |
CSHL Arabidopsis thaliana (ecotype Columbia) Chromosome 4 Genomic Tiling Array |
21,761 |
University of Texas at Austin |
2007-04-23 |
Cold Spring Harbor Laboratory |
Arabidopsis thaliana
|
Tiling Array |
spotted DNA/cDNA, CSHL Arabidopsis thaliana (ecotype Columbia) Chromosome 4 Genomic Tiling Array, The entire TIGR4 Arabidopsis thaliana ec. Col chromosome 4 assembly was used to design a genomic tiling microarray. This ~18.6 Mb sequence represented on the microarray starts downstream of the nucleolar organizing region (NOR) comprising the 5’ terminus of the chromosome. Notably, it contains several megabases of pericentromeric heterochromatin. In the microarray design, annotation was intentionally ignored, thus ensuring that repeated and unique sequences were equally represented. PCR primer pairs were selected using the Primer3 software. Probe selection was first accomplished by BLASTN analysis of sequential 100-bp windows of sequence along chromosome 4 against the whole genome to discriminate between unique and repeated DNA. Whenever a window gave at least one hit with 85% identity elsewhere in the genome, that window was marked as repeated, or unique otherwise. This information was then used to define "repeated" and "unique" segments of at least 300bp along the chromosome, as follows. Repeat segments were composed of successive repeat windows, possibly interrupted by series of contiguous unique windows spanning less than 300bp in each case. Conversely, unique segments were composed of successive unique windows, never interrupted by more than 300bp of contiguous repeat windows. Series of alternate unique and repeated windows were treated as repeat segments. Within each repeated or unique segment, PCR primer pairs were then selected using the Primer3 software and a routine that ensured maximum coverage of the segment and limited overlap between successive probes. Briefly, primer pairs were designed from both ends of the segment, considering sequential 1.2 kb windows, amplicon sizes ranging from 850 bp to 1.2 kb (optimum 1 kb) and primers (19-23 nt each, optimum 21 nt, 40-60% GC) with similar melting temperatures in the 57°CÂÂ63°C range (optimum 60°C). Each new 1.2 kb window was positioned 50 bp within the end of the preceding amplicon. Successive amplicons could therefore overlap by up to 50 bp or be separated by up to 250 bp. When no primer pair was found in a given window, window size was increased to 1.4 kb, and if still unsuccessful, amplicons were finally designed using the forward and reverse primers of the upstream and downstream amplicons, respectively. When the last (central) window of a segment was less than 1.2kb but more than 300bp, primer pair selection was carried out by considering the actual size of that window plus 50bp on either side. Using this approach, 21,405 amplicons were designed with an average size of ~950bp. An additional 356 amplicons were designed that cover 36 genes of interest and neighboring sequences located on the other 4 chromosomes. Most amplicons were produced using BAC clones as templates, and all amplicons were verified by gel electropheresis. |
| 14 |
GPL5125 |
Lieb Lab at UNC-CH_Yeast Whole-genome and Chr III Tiling Array (PCR-based) |
15,355 |
UNC-Chapel Hill |
2007-04-25 |
Lieb Lab at UNC-CH |
Saccharomyces cerevisiae
 |
Tiling Array |
spotted DNA/cDNA, Lieb Lab at UNC-CH_Yeast Whole-genome and Chr III Tiling Array (PCR-based), Microarrays consisted of two types of probes. The first type represents the whole genome based on annotated functional boundaries. These PCR-amplified products represent ORFs, intergenic regions, and other non-coding 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 non-coding 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. The second type of probes are higher resolution PCR-amplified products that span almost all of chromosome III at 200 base pair resolution with additional overlapping products covering on third of the chromosome at 100 base pair resolution (coordinates the 10,000 to 83,000). This platform covers several print runs, in which print plates were arranged in different orders. |
| 15 |
GPL5147 |
LLHoyer_Calbicans_6k_v1.0 |
14,112 |
University of Illinois |
2007-05-06 |
LLHoyer Laboratory, University of Illinois, Urbana, IL and Microarrays Inc., Nashville, TN |
Candida albicans
|
cDNA Array |
spotted DNA/cDNA, LLHoyer_Calbicans_6k_v1.0, |
| 16 |
GPL5076 |
UT Austin Iyer yeast whole genome platform |
13,051 |
University of Texas at Austin |
2007-04-10 |
Iyer Lab UT Austin |
Saccharomyces cerevisiae
|
cDNA Array |
spotted DNA/cDNA, UT Austin Iyer yeast whole genome platform, |
| 17 |
GPL5138 |
TIGR PFGRC Aspergillus nidulans v1 array based on strain FGSC A4 (condensed - does not contain replicate spots) |
11,982 |
University of Georgia Athens |
2007-05-01 |
TIGR PFGRC |
Emericella nidulans
|
Oligo Array |
spotted oligonucleotide, TIGR PFGRC Aspergillus nidulans v1 array based on strain FGSC A4 (condensed - does not contain replicate spots), This set includes 11481 oligonucleotides distributed in 48 blocks |
| 18 |
GPL5099 |
Eurogentec S. pombe ORF array (A170F) |
11,520 |
Karolinska Inst |
2007-04-18 |
Eurogentec AG |
Schizosaccharomyces pombe
 |
Oligo Array |
spotted oligonucleotide, Eurogentec S. pombe ORF array (A170F), |
| 19 |
GPL5333 |
Trichophyton rubrum cDNA microarray 3 |
11,232 |
National Institute for Viral Disease Control and Prevention |
2007-05-28 |
State Key Laboratory for Molecular Virology and Genetic Engineering |
Trichophyton rubrum
 |
cDNA Array |
spotted DNA/cDNA, Trichophyton rubrum cDNA microarray 3, |
| 20 |
GPL5344 |
wheat 11k |
10,807 |
Kihara Institute for Biological Research, Yokohama City University |
2007-05-31 |
Agilent Technologies |
Triticum aestivum
|
Oligo Array |
in situ oligonucleotide, wheat 11k, |