Data sheet, made-to-order program (pdf, 144 kb)

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Cycle cDNA Synthesis Kits Reagent for IVT G E N E E X P R E S S I O N M O N I T O R I N G 3’-Amplification Reagent for IVT Labeling 3’-Amplification Reagent for IVT Labeling 3’-Amplification Reagent for IVT Labeling 3’-Amplification Reagent for IVT Labeling 3’-Amplification Reagent for IVT Labeling 3’-Amplification Reagent for IVT Labeling 3’-Amplification Reagent for IVT Labeling 3’-Amplification Reagent for IVT Labeling scaffolding the ESTs and also to retrieve any rare interesting genes (e.g., Mla, Rar1, Sgt1, Rpg1) for inclusion on the GeneChip Triticeae Improvement Group (R. Wise, T.
Close, G. Muehlbauer, R. Wing, and A.
Stringent CAP3 clustering (-p95 -d60 enhanced Triticeae repeat element database -f100 -h50) was performed and resulted in (TREP), the exemplar set of 25,500 contigs 53,030 “unigenes” (26,634 contigs and community effort resulted in a significant singletons had complete 3’ ends suitable better clustering and derived annotations. v0.95 and higher). This included all 1,145 properties, pest and disease control, abiotic stress tolerance, nutritional characteristics, Array design were collected from consortia from the NCBI non-redundant database.
integrated with the EST clusters to aid in — Hybridization controls: bioB, bioC, bioD from E. coli, and cre from P1 Bacteriophage — Poly-A controls: dap, lys, phe, thr, trp from B. subtilis— Barley maintenance genes: actin, GAPDH, ubiquitin, tubulin alpha subunit, and — Matthews DE, Carollo VL, Lazo GR, Anderson OD.
GrainGenes, the genome database for small-grain crops. Nucleic Acids Res. PMID: 12519977 PubMed - indexed for MEDLINE 31(1):183-6 (2003 Jan 1).
— Ware DH, Jaiswal P, Ni J, Yap IV, Pan X, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K, Cartinhour S, Stein LD, McCouch SR.
Gramene, a tool for grass genomics. Plant Physiol. Review. PMID: 12481044 PubMed - indexed for MEDLINE 130(4):1606-13 (2002 Dec).
G E N E E X P R E S S I O N M O N I T O R I N G regions with an additional 45 control probe International, Inc. in June 1998 and made sets, and contains probes that are comple- available broadly in 2002. EST data for the Genome Array is a single array that enables target that is hybridized to the array. For Genome Sequencing Project of the Institut the relative monitoring of mRNA transcripts preparing samples for hybridization it is Pasteur, Release 10.1, December 1997.
from the bacterium B. subtilis. The array protocol, an experimental protocol available contains probe sets to interrogate approxi- completed as a custom design for Genencor — bioB, bioC, bioD, and cre from P1 Bacteriophage— Poly-A controls: dap, lys, phe, thr, trp from B. subtilis — Caldwell, R. et al. Correlation between Bacillus subtilis scoC phenotype and gene expression determined using microarrays for transcriptome analysis. Bacteriol 183: 7371–80 (2001).
8325 (OU, lab strain), and COL (TIGR).
For comprehensive monitoring of the relative The open reading frames (ORFs) in all four mRNA abundance of S. aureus sequences.
3,300 S. aureus open reading frames.
Additionally, the array also contains probes sequences in the following four strains of orientation of over 4,800 intergenic regions sequence annotation system. This array was 20 pp per ORF; additional probe pairs spaced ~26 base pairs through intergenic regions — Hybridization controls: bioB, bioC, bioD, and cre from P1 Bacteriophage— Poly-A controls: dap, lys, phe, thr, trp from B. subtilis — r2: bioB, bioC, bioD, cre, dap, phe and thr to overcome these challenges, the Paradise 2.0 Array, for a total of 47,000 transcripts on interrogating sequences located closer to probe selection criteria, the majority of the the 3' end of the transcripts compared with standard GeneChip brand arrays. Together, selected from the 300 bases at the most 3' end of the transcripts. This is different strategy which selects probe sets within the lenges for microarray analysis, including region of 600 bases proximal to the 3' ends. X3P arrays are identical to those used for G E N E E X P R E S S I O N M O N I T O R I N G In addition, 200 transcripts could not be probe set fail. In these cases, 3' probe sets represented with the new extreme 3' probe transcripts we wished to represent on the from the shorter 300 base probe selection sets. These 200 transcripts are represented X3P Array. For 4,000 transcripts, two sets region and the original probe sets from the of probes are represented on the arrays to standard Human Genome U133 Plus 2.0 11 micronInstrument and Software Requirements— GeneChip® Scanner 3000, enabled for High-Resolution Scanning — GeneChip® Operating Software (GCOS) including the GeneChip Scanner 3000 High-Resolution — Hybridization controls: bioB, bioC, bioD and cre from P1 Bacteriophage — Poly-A controls: dap, lys, phe, thr from B. subtilis— Normalization: 100 probe sets— Housekeeping: GAPDH, beta-Actin, ISGF-3 (STAT-1) clones. Affymetrix offers a second-genera- Institute, Inc. (NADII). Eighty percent of the genes represented on the array are predicted Arabidopsis array to monitor the relative sequences. Please visit www.affymetrix.com sequences used to develop this array were — Hybridization controls: bioB, bioC, bioD from E. coli and cre from P1 Bacteriophage— Poly-A controls: dap, lys, phe, thr, trp from B. subtilis— Arabidopsis maintenance genes: actin, GAPDH, ubiquitin, 25 S rRNA, 5 S rRNA — Zhu, T., Wang, X. Large-scale profiling of the Arabidopsis transcriptome. — Harmer, SL. Hogenesch, J.B., Straume, M., Chang, H.S., Han, B., Zhu, T., Wang, X., Kreps, J.A., Kay, S.A. Orchestrated transcription of key pathways in Arabidopsis by the circadian clock.
Science 290(5499): 2110–2113 (2000).
G E N E E X P R E S S I O N M O N I T O R I N G correspond to the M49 version of the E.
used for examining expression of all known intergenic sequences can be interrogated in uncharacterized intergenic transcripts. The characterization of potentially important array contains probe sets to detect the sense Poly-A controls: dap, lys, phe, thr, trp from B. subtilis — Wassarman, K.M. et al. Identification of novel small RNAs using comparative genomics and microarrays. Genes & Development 15:1637-1651 (2001).
— Rosenow, C. Saxena, R.M., Durst, M., Gingeras, T.R. Prokaryotic RNA preparation methods, useful for high density array analysis: comparison of two approaches. Nucleic Acids Research, 29(22):E112,(2001).
clusters derived from Build 95 of UniGene.
Based on this UniGene build and associated — Hybridization controls: bioB, bioC, bioD, and cre from P1 Bacteriophage — Poly-A controls: dap, lys, phe, thr, trp from B. subtilis— Human maintenance genes: actin, GAPDH, transferrin receptor and ISGF-3 — Riewald, M. et al. Activation of endothelial cell protease activated receptor 1 by the protein C pathway.
— Cicala, C. et al. HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication. Proc Natl Acad Sci USA 99(14): 9380–5 (2002).
G E N E E X P R E S S I O N M O N I T O R I N G additional genes from GenBank and TIGR.
genes. The full-length genes were selected — Hybridization controls: bioB, bioC, bioD, and cre from P1 Bacteriophage — Poly-A controls: dap, lys, phe, thr, trp from B. subtilis— Human maintenance genes: actin, GAPDH, transferrin receptor — Stamey, TA., Warrington, J.A., Caldwell, M.C., Chen, Z., Mahadevappa, M., McNeal, J.E., Nolley, R., Zhang, Z. Molecular genetic profiling of Gleason grade 4/5 prostate cancers compared to benign prostatic hyperplasia. Journal of Urology 166(6): 2171–2177 (2001). — Mutter, GL., Baak, J.P., Fitzgerald, J.T., Gray, R., Neuberg, D., Kust, G.A., Gentleman, R., Gullans, S.R., Wei, L.J., Wilcox, M. Global expression changes of constitutive and hormonally regulated genes during endometrial neoplastic transformation. Gynecologic Oncology 83(2): 177–185 (2001).
of leading cancer researchers selected the this array. Accession numbers for sequences This array enables focused and cost-effective expression studies in cancer biology. A panel — Hybridization controls: bioB, bioC, bioD from E. coli and cre from P1 Bacteriophage— Poly-A controls: dap, lys, phe, thr, trp from B. subtilis— Human maintenance genes: actin, GAPDH, transferrin receptor, transcription factor — Paxton, W. et al. Reduced HIV-1 infectability of CD+4 lymphocytes from exposed-uninfected individuals: association with low expression of CCR5 and high expression of beta-chemokines. Virology 244:66-73 (1998).
— Golub, T. et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286:531-537 (1999). — Harkin, P. et al. BRCA1 induces GADD45 and triggers JNK/SAPK-dependent apoptosis. — Lee, S.B. et al. The Wilms tumor suppressor WT1 encodes a transcriptional activator of Amphiregulin. Cell 98:663-673 (1999).
arrays, contains probe sets interrogating Set, consisting of three GeneChip® probe — Hybridization controls: bioB, bioC, bioD from E. coli and cre from P1 Bacteriophage— Poly-A controls: dap, lys, phe, thr, trp from B. subtilis— Murine maintenance genes: actin, GAPDH, hexkinase — Molecular diversity of astrocytes with implications for neurological disorders. Bachoo, R. M. et al. Proceedings of the National Academy of Sciences 101(22): 8384-9 (2004).
— Efficient isolation and gene expression profiling of small numbers of neural crest stem cells and developing Schwann cells. Buchstaller, J. et al. Journal of Neuroscience 24(10): 2357-65 (2004).
11,000 full-length genes and EST clusters — Hybridization controls: bioB, bioC, bioD from E. coli and cre from P1 Bacteriophage— Poly-A controls: dap, lys, phe, thr, trp from B. subtilis— Murine maintenance genes: actin, GAPDH, hexokinase — Voehringer, D.W. et al. Gene microarray identification of redox and mitochondrial elements that control resistance or sensitivity to apoptosis. PNAS 97:2680-2685 (2000).
— Simbulan-Rosenthal, C.M. et al. Misregulation of gene expression in primary fibroblasts lacking poly (ADP-ribose) polymerase. PNAS 97:11274-11279 (2000).
— Reilly, T.P. et al. Expression profiling of acetaminophen liver toxicity in mice using microarray technology. Biochem Biophys Res Commun 282:321-328 (2001).
ters from the UniGene database (Build 34). EST clusters. All of the sequences analyzed Array A of the set analyzes approximately contains probe sets interrogating more than — Hybridization controls: bioB, bioC, bioD from E. coli and cre from P1 Bacteriophage— Poly-A controls: dap, lys, phe, thr, trp from B. subtilis— Murine maintenance genes: actin, GAPDH, hexkinase — Gene expression analysis points to hemostasis in livers of rats cotreated with lipopolysaccharide and ranitidine. Luyendyk, J. P. et al. Toxicological Sciences 80: 203-13 (2004).
— Patterns of gene expression reveal a temporally orchestrated wound healing response in the injured spinal cord. Velardo, M. J. et al. Journal of Neuroscience 24(39): 8562-76 (2004).
G E N E E X P R E S S I O N M O N I T O R I N G receptors, cytokines, growth factors, and Array are also represented on Array A of the (including genes for kinases, cell surface collaboration with academic and industrial — Hybridization controls: bioB, bioC, bioD from E. coli and cre from P1 Bacteriophage— Poly-A controls: dap, lys, phe, thr, trp from B. subtilis— Murine maintenance genes: actin, GAPDH, hexokinase — Microarray analysis of acute and delayed gene expression profile in rats after focal ischemic brain injury and reperfusion. Lu, X. C. et al. Journal of Neuroscience Research 77(6): 843-57 (2004) Toxicology U34 Array are also represented with pharmaceutical toxicologists and from published scientific literature. All of the — Hybridization controls: bioB, bioC, bioD from E. coli and cre from P1 Bacteriophage— Poly-A controls: dap, lys, phe, thr, trp from B. subtilis— Murine maintenance genes: actin, GAPDH, hexkinase www.affymetrix.com Please visit our web site for international distributor contact information.
For research use only. Not for use in diagnostic procedures.
Part No. 701159 Rev. 92002-2005 Affymetrix, Inc. All rights reserved. Affymetrix®,GeneChip®, ®, ®, ®, HuSNP®, Jaguar™, EASI™, MicroDB™, GenFlex®, CustomExpress®, CustomSeq™, NetAffx™, ‘Tools to takeyou as far as your vision®’, and ‘The Way Ahead™’ are trademarks owned or used by Affymetrix, Inc. Array products may be covered by one or more of the following patents and/or sold under licensefrom Oxford Gene Technology: U.S. Patent No's. 5,445,934; 5,700,637; 5,744,305; 5,945,334; 6,054,270; 6,140,044; 6,261,776; 6,291,183; 6,346,413; 6,399,365; 6,420,169; 6,551,817; 6,610,482;6,733,977; and EP 619 321; 373 203 and other U.S. or foreign patents.

Source: http://cibex.nig.ac.jp/data/CBX136/array%20design.pdf