| 1 |
GPL1425 |
Rat 2K Array |
4,608 |
Medical College of Wisconsin |
2004-08-30 |
|
Rattus norvegicus
 |
GeneChip |
spotted DNA/cDNA, Rat 2K Array, The custom microarrays were manufactured by the Department of Physiology at the Medical College of Wisconsin. Microarrays were printed with a GMS 417 robotic arrayer from Affymetrix (made by Genetic Microsystems) that has a printhead with 4 pin-and-ring print tips. Arrays were prepared from the first 18 of 88 plates of a rat cDNA library from Research Genetics. The clone set represents 1631 known genes and 192 ESTs. We included 506 negative control spots and 456 positive control spots. Following amplification, PCR amplicons were distributed into 384-well polypropylene plates (Genetix, 384 micro array), resuspended in 50% DMSO and printed onto poly-L-lysine coated glass slides. Print configuration is 8 blocks in a 2 x 4 arrangement. Positive controls were printed in each block, and included beta-actin and GAPDH. Negative controls were also printed in each block, and included 5 Arabidopsis gene fragments, mouse COT-1, DMSO, poly dA, yeast tRNA, and PCR buffer with and without primers. The microarray spot density is 250 microns (center-to-center). Spot diameters are approximately 120-150 microns. After printing, DNA was cross-linked to the slides by UV irradiation at 65 mJ (Stratalinker UV Crosslinker, Stratagene). The microarrays were post-processed according to the procedures on the Stanford website (http://cmgm.stanford.edu/pbrown/protocols/index.html) and subsequently stored at room temperature in a desiccated chamber until use. |
| 2 |
GPL1405 |
CCF Cancer cDNA Array |
9,984 |
Lerner Research Inst., The Cleveland Clinic |
2004-08-11 |
|
Homo sapiens
 |
GeneChip |
spotted DNA/cDNA, CCF Cancer cDNA Array, The Cancer cDNA Array contains probes for 9241 cDNA clones corresponding to ~4900 unigenes or unclustered ESTs relevant to cancer biology. These include: 1) 1800 genes implicated in metastasis or tumor development in general from the literature and Affymetrix cancer G110 array (www.affymetrix.com/analysis/index.affx); 2) 1809 genes involved in kidney development (golgi.ana.ed.ac.uk/kidhome.html) or showing more than 3-fold variation of expression among 4 primary Wilms tumors and fetal kidney in our previous Affymetrix GeneChip experiments (unpublished data); 3) 1400 potential downstream targets of p53 transcriptional regulation; 4) 950 genes with AU-rich elements in their 3’ and/or 5’ UTR; 5) 1245 cytokine responsive genes, genes for zinc finger proteins or genes implicated in apoptosis. |
| 3 |
GPL1394 |
GAP_M_Ia |
2,496 |
Duke University Medical Center |
2004-08-05 |
|
Aspergillus flavus
 |
GeneChip |
spotted DNA/cDNA, GAP_M_Ia, PCR products were generated using approximately 5 ng plasmid DNA isolated from unique cDNA clones. T3 and T7 primers were used to generate amplicons. PCR products were then purified by isopropanol precipation followed by a 70% ethanol wash. The presence of amplicons was verified by agarose gel electrophoresis. PCR products at approximately 250 ng/ul in 50% DMSO were spotted in triplicate onto Corning GAPSII slides (Corning, NY) using an Affymetrix 417 Arrayer (Santa Clara, CA). Spots were allowed to air dry before being fixed following manufacturer’s recommendation. Keywords = aspergillus Keywords = aflatoxin |
| 4 |
GPL1355 |
[Rat230_2] Affymetrix Rat Genome 230 2.0 Array |
31,099 |
Affymetrix, Inc. |
2004-07-20 |
Affymetrix |
Rattus norvegicus
|
GeneChip |
in situ oligonucleotide, [Rat230_2] Affymetrix Rat Genome 230 2.0 Array, 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 June 03, 2009: annotation table updated with netaffx build 28 June 07, 2012: annotation table updated with netaffx build 32 |
| 5 |
GPL1352 |
[U133_X3P] Affymetrix Human X3P Array |
61,359 |
Affymetrix, Inc. |
2004-07-19 |
Affymetrix |
Homo sapiens
|
GeneChip |
in situ oligonucleotide, [U133_X3P] Affymetrix Human X3P Array, 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 The GeneChip X3P Array was designed specifically for whole-genome expression profiling of formalin-fixed, paraffin-embedded (FFPE) samples, and is now available via the GeneChip Made-to-Order program. Resulting from a collaboration between Affymetrix and Arcturus, this array is optimized as part of a system solution together with the Paradise Reagent System from Arcturus for expression analysis of FFPE samples. FFPE samples introduce unique challenges for microarray analysis, including potential fragmentation and chemical modification of RNA molecules. In order to overcome these challenges, the Paradise Reagent System was developed to provide RNA isolation and amplification reagents optimized for FFPE samples. In addition, the X3P Array is designed to focus on interrogating sequences located closer to the 3' end of the transcripts compared with standard GeneChip arrays. Together, the reagents and array accommodate the characteristics of the FFPE RNA samples, enabling genome-wide profiling. The target sequences on the X3P Arrays are identical to those used for designing the Human Genome U133 Plus 2.0 Array, for a total of 47,000 transcripts with 61,000 probe sets, although the probes on the two types of arrays are significantly different. As a result of the modification to the probe selection criteria, the majority of the probe sets on the X3P arrays are selected from the 300 bases at the most 3' end of the transcripts. This is different from the standard Affymetrix design strategy which selects probe sets within the region of 600 bases proximal to the 3' ends. To select probes for the 47,000 transcripts, it was not possible to identify high-performance probe sets within the shorter 300 base probe selection region for approximately 4,000 transcripts. For these transcripts, two sets of probes are represented on the arrays: 1) the original probe sets from the standard HG-U133 Plus design are replicated on the X3P arrays, and 2) the new, more 3' probe sets are also included although they fell below the minimum probe score selection threshold. In addition, fewer than 200 transcripts from the HG-U133 Plus design are only represented by the HG-U133 Plus probe sets, where no probe sets within the smaller (300 bps) probe selection region could be found. Annotations derived from Affymetrix CSV file dated 6/23/2004 |
| 6 |
GPL1340 |
[Barley1] Affymetrix Barley Genome Array |
22,840 |
Affymetrix, Inc. |
2004-07-09 |
Affymetrix |
Hordeum vulgare
 |
GeneChip |
in situ oligonucleotide, [Barley1] Affymetrix Barley Genome Array, 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 The GeneChip Barley Genome Array was designed and funded by the USDA-IFAFS Triticeae Improvement group (R. Wise, T. Close, G. Muehlbauer, R. Wing, and A. Kleinhofs) in collaboration with Affymetrix and the international barley community. A community effort resulted in a significant improvement to sequence quality through better clustering and derived annotations. Sequences used for the Barley Genome Array design were collected from consortia labs submitting EST sequences and by collecting sequences from the NCBI/GenBank non-redundant database. Approximately 400,000 raw barley ESTs were submitted from 84 libraries, and about 350,000 survived quality pruning. Stringent CAP3 clustering (-p95 -d60 -f100 -h50) was performed and resulted in 53,030 "unigenes" (26,634 contigs and 26,396 singletons). 25,500 contigs and singletons had complete 3' ends suitable for array design (see HarvEST Triticeae v0.95 and higher). This included all 1,145 known barley genes (including alleles) from the NCBI non-redundant database. The nonredundant cloned gene set was integrated with the EST clusters to aid in scaffolding the ESTs and also to retrieve any rare interesting genes (e.g., Mla, Rar1, Sgt1, Rpg1) for inclusion on the GeneChip microarray. After pruning against an enhanced Triticeae repeat element database (TREP), the exemplar set of 25,500 contigs and singletons was submitted to Affymetrix for initial computation. Potential applications for the barley array include analysis of malting properties, pest and disease control, abiotic stress tolerance, nutritional characteristics, and reproductive development. The GeneChip Barley Genome Array was released in June, 2003. Annotations derived from Affymetrix CSV file dated 6/23/2004 |
| 7 |
GPL1339 |
[S_aureus] Affymetrix S. aureus Genome Array |
7,775 |
Affymetrix, Inc. |
2004-07-09 |
Affymetrix |
Staphylococcus aureus
 |
GeneChip |
in situ oligonucleotide, [S_aureus] Affymetrix S. aureus Genome Array, 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 June 03, 2009: annotation table updated with netaffx build 28 Oct 18, 2012: annotation table updated with netaffx build 32 |
| 8 |
GPL1321 |
[Plasmodium_Anopheles] Affymetrix Plasmodium/Anopheles Genome Array |
22,769 |
Affymetrix, Inc. |
2004-07-01 |
Affymetrix |
Plasmodium falciparum,Anopheles gambiae
 |
GeneChip |
in situ oligonucleotide, [Plasmodium_Anopheles] Affymetrix Plasmodium/Anopheles Genome Array, 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 June 03, 2009: annotation table updated with netaffx build 28 Oct 12, 2009: annotation table updated with netaffx build 32 |
| 9 |
GPL1322 |
[Drosophila_2] Affymetrix Drosophila Genome 2.0 Array |
18,952 |
Affymetrix, Inc. |
2004-07-01 |
Affymetrix |
Drosophila melanogaster
 |
GeneChip |
in situ oligonucleotide, [Drosophila_2] Affymetrix Drosophila Genome 2.0 Array, 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 June 03, 2009: annotation table updated with netaffx build 28 June 08, 2012: annotation table updated with netaffx build 32 |
| 10 |
GPL1320 |
[Vitis_Vinifera] Affymetrix Vitis vinifera (Grape) Genome Array |
16,602 |
Affymetrix, Inc. |
2004-07-01 |
Affymetrix |
Vitis vinifera
 |
GeneChip |
in situ oligonucleotide, [Vitis_Vinifera] Affymetrix Vitis vinifera (Grape) Genome Array, 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 The GeneChip® Vitis vinifera Genome Array is the first array to provide comprehensive coverage of the V. vinifera genome. 14,000 V. vinifera transcripts and 1,700 transcripts from other Vitis species can be interrogated. Oligonucleotide probes complementary to each corresponding sequence are synthesized in situ on the arrays. Sixteen pairs of oligonucleotide probes are used to measure the level of transcription of each sequence represented on the GeneChip® Vitis vinifera (Grape) Genome Array. Sequences used in the design of the V. vinifera Genome Array were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 7, Oct 2003). Annotations derived from Affymetrix CSV file dated 6/23/2004 |
| 11 |
GPL1319 |
[Zebrafish] Affymetrix Zebrafish Genome Array |
15,617 |
Affymetrix, Inc. |
2004-07-01 |
Affymetrix |
Danio rerio
 |
GeneChip |
in situ oligonucleotide, [Zebrafish] Affymetrix Zebrafish Genome Array, 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 The Affymetrix GeneChip Zebrafish Genome Array can be used to study gene expression of over 14,900 Danio rerio transcripts. Sequence information for this array was selected from the following public data sources: RefSeq (July 2003), GenBank (release 136.0, June 2003), dbEST (July 2003), and UniGene (Build 54, June 2003). Probe sets on the array were designed with 16 oligonucleotide pairs to detect each transcript. This array was designed in collaboration with representative members of the Zebrafish community and the National Institutes of Health. Note: The DsRed probe set is provided with permission from BD Biosciences, and BD Biosciences grants users a limited license to utilize this probe set only on the Affymetrix array. Other uses of the probe set, or other DsRed sequence or sequences requires a license from BD Biosciences. Annotations derived from Affymetrix CSV file dated 6/23/2004 |
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