| 1 |
GPL3923 |
Affymetrix Drosophila Melanogaster Antisense Tiling Array |
3,214,785 |
Affymetrix, Inc. |
2006-06-26 |
Affymetrix |
Drosophila melanogaster
 |
Tiling Array |
in situ oligonucleotide, Affymetrix Drosophila Melanogaster Antisense Tiling Array, 35bp Resolution Oligonucleotide Tiling Array Annotation in this record is based on BDGP Release 4, Apr 2004 version Keywords: synthetic, oligonucleotide, tiling array |
| 2 |
GPL3955 |
Anopheles gambiae high density oligonucleotide microarray |
195,213 |
Yale University |
2006-06-29 |
NASA Ames Center |
Anopheles gambiae
 |
Oligo Array |
in situ oligonucleotide, Anopheles gambiae high density oligonucleotide microarray, |
| 3 |
GPL3636 |
Aplysia Discovery (un-annotated) Array DAA |
44,290 |
University of Florida |
2006-04-06 |
Agilent Technologies |
Aplysia californica
 |
Oligo Array |
in situ oligonucleotide, Aplysia Discovery (un-annotated) Array DAA, Microarray Probe Design and Aplysia Oligo-array Fabrication. We constructed two custom 44,000 oligonucleotide arrays in collaboration with Agilent TechnologiesTM. The 60-mer oligonucleotide sequences were designed from a set of 56,071 non-redundant Aplysia sequences from the current assembly, based on bioinformatics criteria such as melting temperature and secondary structure. Based on the content of the arrays we distinguish between an annotated and discovery array. While the annotated array primarily contains probes originating from assembled sequences or full length clones with known identity, the majority of probes on the discovery array are unknown. Briefly, the first 44,000 features array called the Aplysia Annotated Array (AAA) had all annotated sequences consisting of: full length clones from the table 4S (labeled as f), 32 sequences which were truncated sequence from these same clones that were over 1.5 Kb in length (labeled as d); 67 NCBI Aplysia californica specific sequences (labeled as n); and 90 truncated sequences from NCBI (labeled as b). All these sequences have their ‘1st best’ selected probes spotted 3 times, 2nd best probe spotted once, and 3rd best probe spotted once giving (76+67+32+90)*5 = 1325 features which are also spotted on all 2 custom arrays. In addition, AAA represents Aplysia sequences from our EST assembly that have any of the following terms in their blast hit definition: “receptorâ€Â, “hormoneâ€Â, “channelâ€Â, “transcriptionâ€Â, “factorâ€Â, “RNAâ€Â, “Hoxâ€Â, “Homeoboxâ€Â, “neuro*â€Â, “synap*â€Â, “calciumâ€Â, “cyclicâ€Â, “CREBâ€Â. These terms are matched as either complete word or part of the word in the transcriptome annotation and account for 6188 sequences. These sequences have their “1st best†probes spotted 3 times, and “2nd best probes†spotted once, occupying 6188*4 = 24,744 features (labeled as m). For all the remaining sequences with nr blastx e-value < 4e-6, their “1st best probes were spotted twice giving 7961 such sequences. They occupy 7961*2 = 15,922 features and are labeled as a. Thus, on AAA we have 1325 + 24,744 + 15,922 = 41,991 features. All the rest of the Aplysia sequences are regarded as un-annotated sequences and their best probe was spotted once on the 2nd Aplysia array that we named as DAA. There were 72,280 (including both plus and minus directions because direction is unknown) un-annotated Aplysia sequences and if they were contigs, they were spotted on DAA. There were 29,572 un-annotated contigs (labeled as c) leaving 42,708 un-annotated singlets (labeled as s). 11,137 un-annotated singlets were spotted on the 2nd DAA array and the remaining 31,571 un-annotated singlets were spotted on the 3rd array (we did not test this array in the current study). In summary the 2nd DAA array has 1325 + 29,572 + 11,137 = 42,034 features. Finally, each array has 2,000 random Agilent designed sequences that have been used in control tests. |
| 4 |
GPL3635 |
Aplysia Annotated Array AAA |
44,247 |
University of Florida |
2006-04-06 |
Agilent Technologies |
Aplysia californica
|
Oligo Array |
in situ oligonucleotide, Aplysia Annotated Array AAA, Microarray Probe Design and Aplysia Oligo-array Fabrication. We constructed two custom 44,000 oligonucleotide arrays in collaboration with Agilent TechnologiesTM. The 60-mer oligonucleotide sequences were designed from a set of 56,071 non-redundant Aplysia sequences from the current assembly, based on bioinformatics criteria such as melting temperature and secondary structure. Based on the content of the arrays we distinguish between an annotated and discovery array. While the annotated array primarily contains probes originating from assembled sequences or full length clones with known identity, the majority of probes on the discovery array are unknown. Briefly, the first 44,000 features array called the Aplysia Annotated Array (AAA) had all annotated sequences consisting of: full length clones from the table 4S (labeled as f), 32 sequences which were truncated sequence from these same clones that were over 1.5 Kb in length (labeled as d); 67 NCBI Aplysia californica specific sequences (labeled as n); and 90 truncated sequences from NCBI (labeled as b). All these sequences have their ‘1st best’ selected probes spotted 3 times, 2nd best probe spotted once, and 3rd best probe spotted once giving (76+67+32+90)*5 = 1325 features which are also spotted on all 2 custom arrays. In addition, AAA represents Aplysia sequences from our EST assembly that have any of the following terms in their blast hit definition: “receptorâ€Â, “hormoneâ€Â, “channelâ€Â, “transcriptionâ€Â, “factorâ€Â, “RNAâ€Â, “Hoxâ€Â, “Homeoboxâ€Â, “neuro*â€Â, “synap*â€Â, “calciumâ€Â, “cyclicâ€Â, “CREBâ€Â. These terms are matched as either complete word or part of the word in the transcriptome annotation and account for 6188 sequences. These sequences have their “1st best†probes spotted 3 times, and “2nd best probes†spotted once, occupying 6188*4 = 24,744 features (labeled as m). For all the remaining sequences with nr blastx e-value < 4e-6, their “1st best probes were spotted twice giving 7961 such sequences. They occupy 7961*2 = 15,922 features and are labeled as a. Thus, on AAA we have 1325 + 24,744 + 15,922 = 41,991 features. All the rest of the Aplysia sequences are regarded as un-annotated sequences and their best probe was spotted once on the 2nd Aplysia array that we named as DAA. There were 72,280 (including both plus and minus directions because direction is unknown) un-annotated Aplysia sequences and if they were contigs, they were spotted on DAA. There were 29,572 un-annotated contigs (labeled as c) leaving 42,708 un-annotated singlets (labeled as s). 11,137 un-annotated singlets were spotted on the 2nd DAA array and the remaining 31,571 un-annotated singlets were spotted on the 3rd array (we did not test this array in the current study). In summary the 2nd DAA array has 1325 + 29,572 + 11,137 = 42,034 features. Finally, each array has 2,000 random Agilent designed sequences that have been used in control tests. |
| 5 |
GPL3825 |
UI Squid EST 30K cDNA array |
30,000 |
The University of Iowa |
2006-05-30 |
The University of Iowa |
Euprymna scolopes
 |
cDNA Array |
spotted DNA/cDNA, UI Squid EST 30K cDNA array, Glass slide with 30,005 spots (13,978 unique cDNA clone inserts) in 48 blocks consisting of 25 columns and 25 rows. Blocks are arranged in 12 rows and 4 columns. The set of 13,978 cDNA clone inserts was identified form the University of Iowa EST collection. The clone inserts were amplified with T7 and T3 primers and printed with 50% DMSO on UltraGaps slides (Corning) using a ProSys 5510 Microarray Printer. |
| 6 |
GPL3809 |
Whole Genome, Alternative Splicing Drosophila Chip v3 |
22,575 |
University of Florida |
2006-05-25 |
Agilent Technologies |
Drosophila melanogaster
|
Oligo Array |
spotted oligonucleotide, Whole Genome, Alternative Splicing Drosophila Chip v3, |
| 7 |
GPL3884 |
Whole Genome, Alternative Splicing Drosophila Chip v2 |
22,575 |
University of Florida |
2006-06-19 |
Agilent Technologies |
Drosophila melanogaster
|
Oligo Array |
spotted oligonucleotide, Whole Genome, Alternative Splicing Drosophila Chip v2, |
| 8 |
GPL3821 |
QIMR Schistosoma 22k oligonucleotide array |
20,301 |
Agilent Technologies |
2006-05-29 |
Agilent Technologies |
Schistosoma japonicum,Schistosoma mansoni
 |
Oligo Array |
in situ oligonucleotide, QIMR Schistosoma 22k oligonucleotide array, This microarray contains 19,221 non-control 60-mer probes designed to sequences sourced from the Chinese sequencing team (http://schistosoma.chgc.sh.cn/) as of Dec 2004 and from the TIGR Schistosoma mansoni Gene Index (SmGI) release 5.0. Agilent's 22k control grid with eQC targets is also implemented. |
| 9 |
GPL3859 |
elegans_Dprint_YMD |
19,660 |
Yale University School of Medicine |
2006-06-08 |
Gene Pix |
Caenorhabditis elegans
 |
cDNA Array |
spotted DNA/cDNA, elegans_Dprint_YMD, fourth print of sjj primer set 1st PCR |
| 10 |
GPL3860 |
elegans_Fprint_YMD |
19,213 |
Yale University School of Medicine |
2006-06-08 |
Gene Pix |
Caenorhabditis elegans
|
cDNA Array |
spotted DNA/cDNA, elegans_Fprint_YMD, 6th print of sjj primer 1st PCR |
| 11 |
GPL3861 |
elegans_Cprint_YMD |
19,213 |
Yale University School of Medicine |
2006-06-09 |
Gene Pix |
Caenorhabditis elegans
|
cDNA Array |
spotted DNA/cDNA, elegans_Cprint_YMD, the third print run at Yale using the 1st PCR of the sjj primer set |
| 12 |
GPL3880 |
DGRC-D. melanogaster-DGRC2-17328-v1 |
17,328 |
Drosophila Genomics Resource Center (DGRC) |
2006-06-15 |
Drosophila Genomics Resource Center (DGRC) |
Drosophila melanogaster
|
Oligo Array |
spotted oligonucleotide, DGRC-D. melanogaster-DGRC2-17328-v1, DGRC-2 transcriptome microarrays are spotted with gene-specific Drosophila melanogaster 70 N long oligonucleotides. The oligos were designed against release 4.1 of the genome annotation using a custom implementation of OligoArray2. Oligos selected have minimal sequence similarity to other genes, size range between 65-69 nucleotides with a minimal Tm window, and locations biased towards the 3'-ends of transcripts. Oligo Synthesis was completed by Illumina. The array also contains the following controls: a ubiquitously expressed gene (actin 5C), a spotting buffer-only control (150 mM NaPO4, pH 8.5), exogenous (non-Drosophila) probes: 9 from Arabidopsis, 2 from soybean, 1 from apple and Ambion’s Array Control Sense Oligo Spots bacterial sequences that can be utilized with spiking RNAs, four exogenous markers - GAL4, lacZ, modified GFP, and FLPase, and a 70mer probe degradation long oligonucleotide set. DGRC-2 arrays are printed using an Omnigrid 300 contact-printing instrument and 48 silicon split-pins on Corning UltraGAPS slides. |
| 13 |
GPL3797 |
01_Drosophila_16K_Universitat_Barcelona |
16,416 |
Universitat de Barcelona |
2006-05-23 |
Departament de Genètica (Universitat de Barcelona) i Plataforma de Transcriptòmica (SCT-PCB-UB) |
Drosophila melanogaster
|
Oligo Array |
spotted oligonucleotide, 01_Drosophila_16K_Universitat_Barcelona, Oligonucleotide Drosophila microarray platform containing virtually all genes from the genome. In addition to the Operon Drosophila Genome Oligo Set Version 1.1, a number of positive and negative controls have been printed so that quality of hybridizations and analysis procedures can be assessed. |
| 14 |
GPL3826 |
DGRC-D. melanogaster-DGRC1-15552-v1 |
15,552 |
Drosophila Genomics Resource Center (DGRC) |
2006-05-31 |
Drosophila Genomics Resource Center (DGRC) |
Drosophila melanogaster
|
cDNA Array |
spotted DNA/cDNA, DGRC-D. melanogaster-DGRC1-15552-v1, DGRC-1 amplicon transcriptome microarrays are spotted with DNA fragments amplified from genomic DNA of the Oregon R strain of Drosophila melanogaster using gene-specific oligonucleotide primer pairs made by Incyte Genomics. The primers were designed against release 1 of the annotated genome sequence and were selected to amplify fragments which have minimal sequence similarity to other genes, size range between 100-600 bp, and location biased towards the 3'-end of transcripts. The array also contains the following controls: a ubiquitously expressed gene (actin 5C), a spotting buffer-only control (3XSSC plus 1.5M Betaine), exogenous(non-Drosophila) probes (7 from Arabidopsis and 8 Ambion array control PCR spots from bacteria that can be used with spiking RNAs), and three exogenous markers: GAL4, lacZ, and FLP. The DGRC arrays are printed using an Omnigrid 300 contact-printing instrument and 48 silicon split-pins on Corning GAPS II slides. |
| 15 |
GPL3827 |
DGRC-D. melanogaster-DGRC1-15552-v2 |
15,552 |
Drosophila Genomics Resource Center (DGRC) |
2006-05-31 |
Drosophila Genomics Resource Center (DGRC) |
Drosophila melanogaster
|
cDNA Array |
spotted DNA/cDNA, DGRC-D. melanogaster-DGRC1-15552-v2, DGRC-1 amplicon transcriptome microarrays are spotted with DNA fragments amplified from genomic DNA of the Oregon R strain of Drosophila melanogaster using gene-specific oligonucleotide primer pairs made by Incyte Genomics. The primers were designed against release 1 of the annotated genome sequence and were selected to amplify fragments which have minimal sequence similarity to other genes, size range between 100-600 bp, and location biased towards the 3'-end of transcripts. The array also contains the following controls: a ubiquitously expressed gene (actin 5C), a spotting buffer-only control (3XSSC plus 1.5M Betaine), exogenous(non-Drosophila) probes (7 from Arabidopsis and 8 Ambion array control PCR spots from bacteria that can be used with spiking RNAs), and three exogenous markers: GAL4, lacZ, and FLP. The DGRC arrays are printed using an Omnigrid 300 contact-printing instrument and 48 silicon split-pins on Corning GAPS II slides. |
| 16 |
GPL3828 |
DGRC-D. melanogaster-DGRC1-15552-v3 |
15,552 |
Drosophila Genomics Resource Center (DGRC) |
2006-05-31 |
Drosophila Genomics Resource Center (DGRC) |
Drosophila melanogaster
|
cDNA Array |
spotted DNA/cDNA, DGRC-D. melanogaster-DGRC1-15552-v3, DGRC-1 amplicon transcriptome microarrays are spotted with DNA fragments amplified from genomic DNA of the Oregon R strain of Drosophila melanogaster using gene-specific oligonucleotide primer pairs made by Incyte Genomics. The primers were designed against release 1 of the annotated genome sequence and were selected to amplify fragments which have minimal sequence similarity to other genes, size range between 100-600 bp, and location biased towards the 3'-end of transcripts. The array also contains the following controls: a ubiquitously expressed gene (actin 5C), a spotting buffer-only control (3XSSC plus 1.5M Betaine), exogenous(non-Drosophila) probes (7 from Arabidopsis and 8 Ambion array control PCR spots from bacteria that can be used with spiking RNAs), and three exogenous markers: GAL4, lacZ, and FLP. The DGRC arrays are printed using an Omnigrid 300 contact-printing instrument and 48 silicon split-pins on Corning GAPS II slides. |
| 17 |
GPL3829 |
DGRC-D. melanogaster-DGRC1-15552-v4 |
15,552 |
Drosophila Genomics Resource Center (DGRC) |
2006-05-31 |
Drosophila Genomics Resource Center (DGRC) |
Drosophila melanogaster
|
cDNA Array |
spotted DNA/cDNA, DGRC-D. melanogaster-DGRC1-15552-v4, DGRC-1 amplicon transcriptome microarrays are spotted with DNA fragments amplified from genomic DNA of the Oregon R strain of Drosophila melanogaster using gene-specific oligonucleotide primer pairs made by Incyte Genomics. The primers were designed against release 1 of the annotated genome sequence and were selected to amplify fragments which have minimal sequence similarity to other genes, size range between 100-600 bp, and location biased towards the 3'-end of transcripts. The array also contains the following controls: a ubiquitously expressed gene (actin 5C), a spotting buffer-only control (3XSSC plus 1.5M Betaine), exogenous(non-Drosophila) probes (7 from Arabidopsis and 8 Ambion array control PCR spots from bacteria that can be used with spiking RNAs), and three exogenous markers: GAL4, lacZ, and FLP. The DGRC arrays are printed using an Omnigrid 300 contact-printing instrument and 48 silicon split-pins on Corning GAPS II slides. |
| 18 |
GPL3830 |
DGRC-D. melanogaster-DGRC1-15552-v5 |
15,552 |
Drosophila Genomics Resource Center (DGRC) |
2006-05-31 |
Drosophila Genomics Resource Center (DGRC) |
Drosophila melanogaster
|
cDNA Array |
spotted DNA/cDNA, DGRC-D. melanogaster-DGRC1-15552-v5, DGRC-1 amplicon transcriptome microarrays are spotted with DNA fragments amplified from genomic DNA of the Oregon R strain of Drosophila melanogaster using gene-specific oligonucleotide primer pairs made by Incyte Genomics. The primers were designed against release 1 of the annotated genome sequence and were selected to amplify fragments which have minimal sequence similarity to other genes, size range between 100-600 bp, and location biased towards the 3'-end of transcripts. The array also contains the following controls: a ubiquitously expressed gene (actin 5C), a spotting buffer-only control (3XSSC plus 1.5M Betaine), exogenous(non-Drosophila) probes (7 from Arabidopsis and 8 Ambion array control PCR spots from bacteria that can be used with spiking RNAs), and three exogenous markers: GAL4, lacZ, and FLP. The DGRC arrays are printed using an Omnigrid 300 contact-printing instrument and 48 silicon split-pins on Corning GAPS II slides. |
| 19 |
GPL3770 |
SAGE:17:NlaIII:Palaemonetes pugio |
13,754 |
|
2006-05-16 |
|
Palaemonetes pugio
 |
SAGE NlaIII |
SAGE NlaIII, SAGE:17:NlaIII:Palaemonetes pugio, This is a virtual platform for SAGE libraries generated for Palaemonetes pugio using NlaIII as an anchor enzyme. |
| 20 |
GPL3833 |
YUSM (K. White) D. melanogaster cDNA array |
13,745 |
University of California, San Diego, School of Medicine |
2006-06-01 |
Dr. Kevin P. White Lab at Yale University School of Medicine |
Drosophila melanogaster
|
cDNA Array |
spotted DNA/cDNA, YUSM (K. White) D. melanogaster cDNA array, PCR fragment array for Drosophila melanogaster |
|