| 1 |
GPL2707 |
Mouse Exons |
837,251 |
University of Toronto |
2005-07-31 |
Agilent |
Mus musculus
 |
Oligo Array |
in situ oligonucleotide, Mouse Exons, |
| 2 |
GPL2678 |
Tiling design for D. melanogaster |
390,919 |
Fred Hutchinson Cancer Research Center |
2005-07-27 |
NimbleGen Systems Inc. |
Drosophila melanogaster
 |
Tiling Array |
in situ oligonucleotide, Tiling design for D. melanogaster, All of Chr 4, 2L, pericentric regions on 2, first 2MB on X and part of 2R. Based on FlyBase release 3.2.2. One 60mer per 100 bases. |
| 3 |
GPL2699 |
Populus 2.0 |
388,340 |
USDA Forest Service |
2005-07-28 |
NimbleGen |
Populus trichocarpa
 |
Oligo Array |
in situ oligonucleotide, Populus 2.0, This array has probes designed from gene models taken from the Joint Genome Institute Populus trichocarpa genome sequence, as well as probes designed using aspen ESTs. |
| 4 |
GPL2845 |
Applied Biosystems TaqMan Gene Expression Assays (human) |
210,442 |
Life Technologies |
2005-09-13 |
Applied Biosystems |
Homo sapiens
 |
RT-PCR |
RT-PCR, Applied Biosystems TaqMan Gene Expression Assays (human), Pre-designed TaqMan probe and primer sets for quantitative gene expression studies of human genes. |
| 5 |
GPL2618 |
Populus 1.0 |
194,344 |
USDA Forest Service |
2005-07-11 |
NimbleGen |
Populus trichocarpa
|
Oligo Array |
in situ oligonucleotide, Populus 1.0, This array has probes designed from gene models taken from the Joint Genome Institute Populus trichocarpa genome sequence, as well as probes designed using aspen ESTs. |
| 6 |
GPL2675 |
Small RNA identification in Arabidopsis thaliana using modified MPSS |
181,582 |
University of Delaware |
2005-07-26 |
|
Arabidopsis thaliana
 |
MPSS |
MPSS, Small RNA identification in Arabidopsis thaliana using modified MPSS, All MPSS was performed essentially as described by Brenner et al. (Nat Biotechnol. 2000 18:630). The specific modifications to the method for the MPSS sequencing of small RNAs are described in the paper associated with this dataset (Lu et al., 2005). The signatures with "flag = 1" match to tRNAs, rRNAs, snoRNAs and snRNAs. |
| 7 |
GPL2850 |
Applied Biosystems TaqMan Gene Expression Assays (mouse) |
175,755 |
Life Technologies |
2005-09-15 |
Applied Biosystems |
Mus musculus
|
RT-PCR |
RT-PCR, Applied Biosystems TaqMan Gene Expression Assays (mouse), Pre-designed TaqMan probe and primer sets for quantitative gene expression studies of mouse genes. |
| 8 |
GPL2847 |
Applied Biosystems TaqMan Gene Expression Assays (rat) |
150,478 |
Life Technologies |
2005-09-14 |
Applied Biosystems |
Rattus norvegicus
 |
RT-PCR |
RT-PCR, Applied Biosystems TaqMan Gene Expression Assays (rat), Pre-designed TaqMan probe and primer sets for quantitative gene expression studies of rat genes. |
| 9 |
GPL2735 |
BCCRC Lam SMRT array 32k_1.2 |
98,208 |
BCCRC |
2005-08-09 |
British Columbia Cancer Research Center |
Homo sapiens
|
Tiling Array |
spotted DNA/cDNA, BCCRC Lam SMRT array 32k_1.2, A tiling resolution array of 32,433 overlapping BAC clones spanning the human genome (NOTE: this is the same clone-set as the "BCCRC Lam SMRT array 32k" except that clones with insufficient annotation data have been removed; genome coverage remains the same). |
| 10 |
GPL2720 |
ares_ucsc_mouse_59198_affyMouseA |
59,198 |
UC Santa Cruz |
2005-08-04 |
Affymetrix |
Mus musculus
|
GeneChip |
in situ oligonucleotide, ares_ucsc_mouse_59198_affyMouseA, |
| 11 |
GPL2761 |
Human 58K oligonucleotide chip |
58,268 |
Odense University Hospital |
2005-08-16 |
Human MicroArray Centre, University of Southern Denmark |
Homo sapiens
|
Oligo Array |
spotted oligonucleotide, Human 58K oligonucleotide chip, 29,134 oligonuclaotides recognising 28,800 genes or EST designed by Compugene and produced by Sigma |
| 12 |
GPL2895 |
GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray |
56,448 |
GE Healthcare Life Sciences |
2005-09-26 |
GE Healthcare |
Homo sapiens
|
Oligo Array |
spotted oligonucleotide, GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray, CodeLink Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55 000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55 000 probes represent well annotated, full length, and partial human gene sequences from major public databases. CodeLink Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release). Some sequences for design were derived from Incyte LifeSeqâ„¢ Gold and Foundation databases. Well-annotated mRNA or coding sequences were chosen to ensure usefulness for a large range of applications in basic research, biotechnology, and drug development. Each sequence was carefully screened to ensure high-quality, specific probe design, and to reduce redundancy of gene targets. All of the probes designed to these sequences were functionally tested, and over 80% were functionally validated against 25 human tissues to ensure best representation of the gene and biologically relevant results. As a result of their high-quality probe content and design, CodeLink Human Whole Genome Bioarrays are useful for performing differential expression studies of many important biological processes in a single experiment. For instance, CodeLink Human Whole Genome Bioarray can be used to study unique gene expression profiles at different stages of oncogenesis. These studies help to characterize and understand tumor types and tumor progression for use in drug target identification and personalized medicine. In addition, this bioarray enables the investigation of cell and tissue reactions to their environment from stimulus reception to signal transduction processing and response. This bioarray comprehensively covers cell differentiation, development, apoptosis, and metabolism for drugs and other cellular biomolecules. Expression profiling of the genes involved in these types of biological processes can be directly applied to target identification, pathway characterization, and drug effect prediction in basic research and drug development. CodeLink users can submit data to GEO by exporting tab-delimited text files from the CodeLink software. The "Feature_id" header will need to be renamed to "ID_REF", and the "Normalized_intensity" header to "VALUE" before uploading the exported tables. In addition, users are encouraged to include additional raw data columns in their data uploads. These additional columns do not need to be renamed. |
| 13 |
GPL2616 |
BCCRC Lam SMRTr array |
53,856 |
National Human Genome Research Institute |
2005-07-10 |
Lam Lab, BC Cancer Agency |
Homo sapiens
|
Tiling Array |
spotted DNA/cDNA, BCCRC Lam SMRTr array , A tiling resolution array of 26, 928 overlapping BAC clones spanning the human genome Keywords = SMRTr tiling array |
| 14 |
GPL2897 |
GE Healthcare/Amersham Biosciences CodeLinkâ„¢ Mouse Whole Genome Bioarray |
45,920 |
GE Healthcare Life Sciences |
2005-09-26 |
GE Healthcare |
Mus musculus
|
Oligo Array |
spotted oligonucleotide, GE Healthcare/Amersham Biosciences CodeLinkâ„¢ Mouse Whole Genome Bioarray, Mice exhibit high similarity to many human biological pathways, making it a key model system for human physiological and toxicological studies in drug discovery applications. The probe sequences, representing well annotated, full length and partial mouse gene sequences, were designed based on sequences selected from the NCBI UniGene build #139, RefSeq database (April 1, 2004 release) and dbEST database (July 31, 2004 release).Well-annotated mRNA or coding sequences were chosen to ensure usefulness for a large range of applications in basic research, biotechnology, and drug development. Each sequence was carefully screened to ensure high-quality, specific probe design, and to reduce redundancy of gene targets. All of the probes designed to these sequences were functionally tested, and over 97% were functionally validated against 14 mouse tissues to ensure best representation of the gene and biologically relevant results. For flexibility and data preservation, CodeLink Mouse Whole Genome Bioarrays are compatible with lower density CodeLink mouse bioarrays. This means that existing data from CodeLink UniSet Mouse 20K Bioarrays can be continuously used in future studies along with newly generated data from CodeLink Mouse Whole Genome Bioarrays. CodeLink users can submit data to GEO by exporting tab-delimited text files from the CodeLink software. The "Feature_id" header will need to be renamed to "ID_REF", and the "Normalized_intensity" header to "VALUE" before uploading the exported tables. In addition, users are encouraged to include additional raw data columns in their data uploads. These additional columns do not need to be renamed. |
| 15 |
GPL2871 |
Agilent-012600 Arabidopsis 3 Oligo Microarray (4142A (Feature Number version) |
44,290 |
Agilent Technologies |
2005-09-23 |
Agilent Technologies |
Arabidopsis thaliana
|
MPSS |
in situ oligonucleotide, Agilent-012600 Arabidopsis 3 Oligo Microarray (4142A (Feature Number version), The content on this microarray is derived from the ATH1 v.5 database of The Institute for Genomic Research (TIGR) and from the Arabidopsis MPSS database at the University of Delaware. Nearly 40,000 features represents 28,500 genes from TIGR and more than 10,000 unannotated transcripts from University of Delaware. This microarray will be useful for scientists studying gene activity associated with various plant organ functions, stages of growth, and biotic and abiotic stresses. Arrays of this design have barcodes that begin with 16012600 or 2512600. 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. *** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7270. |
| 16 |
GPL2872 |
Agilent-012694 Whole Mouse Genome G4122A (Feature Number version) |
44,290 |
Agilent Technologies |
2005-09-23 |
Agilent Technologies |
Mus musculus
|
Oligo Array |
in situ oligonucleotide, Agilent-012694 Whole Mouse Genome G4122A (Feature Number version), Designed to truly represent all known genes in the mouse genome and their resulting transcripts, Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts. Content for this microarray was generated from leading public databases, including RefSeq, RIKEN, NIA, Ensembl, RIKEN, UCSC Goldenpath, and Unigene. Arrays of this design have barcodes that begin with 16012694 or 2512694. 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. *** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7042. |
| 17 |
GPL2873 |
Agilent-012750 Human Genome CGH Microarray 44A (Feature number version) |
44,290 |
Agilent Technologies |
2005-09-23 |
Agilent Technologies |
Homo sapiens
|
Oligo Array |
in situ oligonucleotide, Agilent-012750 Human Genome CGH Microarray 44A (Feature number version), Human Genome CGH Microarray 44A is a high-resolution, high performance 60-mer oligonucleotide-based microarray that contains over 40,000 probes sourced from the NCBI genome (Build 34). The probes, empirically validated in multiple model systems, span coding and noncoding sequences of the human genome with an average spatial resolution of 35kb. Coupled with Agilents optimized assay protocols and CGH Analytics software, this microarray enables genome-wide survey and molecular profiling of genomic aberrations (i.e. copy number changes) on a single chip. Arrays of this design have barcodes that begin with 16012750 or 2512750. 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. *** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL11069. |
| 18 |
GPL2876 |
Agilent-012799 Mouse Developmental Microarray 44K G2519A Option 002 (Feature Number version) |
44,290 |
Agilent Technologies |
2005-09-23 |
Agilent Technologies |
Mus musculus
|
Oligo Array |
in situ oligonucleotide, Agilent-012799 Mouse Developmental Microarray 44K G2519A Option 002 (Feature Number version), The Mouse Development Oligo Microarray 44K array represents the first commercial whole mouse genome microarray based on the NIA (National Institute on Aging) Mouse Gene Index, which is optimized for stem cell and developmental research. Arrays of this design have barcodes that begin with 16012799 or 2512799. 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. *** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7273. |
| 19 |
GPL2877 |
Agilent-013162 Whole Rat Genome Microarray G4131A (Feature Number version) |
44,290 |
Agilent Technologies |
2005-09-23 |
Agilent Technologies |
Rattus norvegicus
|
Oligo Array |
in situ oligonucleotide, Agilent-013162 Whole Rat Genome Microarray G4131A (Feature Number version), With a focus on well known rat genes and homologues to human and mouse genes with useful annotation, Agilent's Whole Rat Genome Oligo Microarray provides researchers with a new tool for modeling human biology in the rat model organism. For researchers, this means they now have access to a microarray made up of relevant content that has been empirically validated by Agilent. Arrays of this design have barcodes that begin with 16013162 or 2513162. 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. *** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7289. |
| 20 |
GPL2879 |
Agilent-013282 Human Genome CGH Microarray 44B (Feature number version) |
44,290 |
Agilent Technologies |
2005-09-23 |
Agilent Technologies |
Homo sapiens
|
Oligo Array |
in situ oligonucleotide, Agilent-013282 Human Genome CGH Microarray 44B (Feature number version), Human Genome CGH Microarray 44B, high-resolution, high performance 60-mer oligonucleotide, allowing genome-wide survey and molecular profiling of DNA copy number changes on a single chip. It provides comprehensive genome-wide coverage with emphasis on the most commonly studied genomic regions and cancer-related genes. It consists of ~43,000 60-mer oligonucleotide probes, empirically validated in multiple model systems, spanning coding and noncoding sequences with average spatial resolution of 35kb. It replaces 44A (G4410A), includes all biological probes from 44A, mapped to the latest NCBI build, 35), plus an additional ~ 2,500 probes to expand coverage in the human genome. Agilent has taken extra measures to design the microarray that truly represents the coverage and performance needed for this application. Agilent has developed and optimized assay protocols that enable researchers to use nanogram levels of total genomic DNA without genome complexity reduction. Arrays of this design have barcodes that begin with 16013282 or 2513282. 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. *** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL11068. |
|