PubMed

Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species.

Hammond JP, Broadley MR, Craigon DJ, Higgins J, Emmerson ZF, Townsend HJ, White PJ, May ST.

Plant Methods. 2005 Nov 9;1(1):10.PMID: 16280083 [PubMed]Related articlesFree article

Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection.

Graham NS, Broadley MR, Hammond JP, White PJ, May ST.

BMC Genomics. 2007 Oct 1;8:344.PMID: 17908303 [PubMed - indexed for MEDLINE]Related articlesFree article

Heterologous oligonucleotide microarrays for transcriptomics in a non-model species; a proof-of-concept study of drought stress in Musa.

Davey MW, Graham NS, Vanholme B, Swennen R, May ST, Keulemans J.

BMC Genomics. 2009 Sep 16;10:436.PMID: 19758430 [PubMed - indexed for MEDLINE]Related articlesFree article

Equine transcriptome quantification using human GeneChip arrays can be improved using genomic DNA hybridisation and probe selection.

Graham NS, Clutterbuck AL, James N, Lea RG, Mobasheri A, Broadley MR, May ST.

Vet J. 2009 Sep 26. [Epub ahead of print]PMID: 19786357 [PubMed - as supplied by publisher]Related articles

A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences.

Trick M, Cheung F, Drou N, Fraser F, Lobenhofer EK, Hurban P, Magusin A, Town CD, Bancroft I.

BMC Plant Biol. 2009 May 8;9:50.PMID: 19426481 [PubMed - indexed for MEDLINE]Related articlesFree article

AffyMAPSDetector: a software tool to characterize Affymetrix GeneChip expression arrays with respect to SNPs.

Kumari S, Verma LK, Weller JW.

BMC Bioinformatics. 2007 Jul 30;8:276.PMID: 17663786 [PubMed - indexed for MEDLINE]Related articlesFree article

A statistical method for predicting splice variants between two groups of samples using GeneChip expression array data.

Fan W, Khalid N, Hallahan AR, Olson JM, Zhao LP.

Theor Biol Med Model. 2006 Apr 7;3:19.PMID: 16603076 [PubMed - indexed for MEDLINE]Related articlesFree article

Arabidopsis transcript profiling on Affymetrix GeneChip arrays.

Hennig L, Menges M, Murray JA, Gruissem W.

Plant Mol Biol. 2003 Nov;53(4):457-65.PMID: 15010612 [PubMed - indexed for MEDLINE]Related articles

Exploration, normalization, and summaries of high density oligonucleotide array probe level data.

Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP.

Biostatistics. 2003 Apr;4(2):249-64.PMID: 12925520 [PubMed - indexed for MEDLINE]Related articlesFree article

Expression profiling using affymetrix genechip probe arrays.

Schinke-Braun M, Couget JA.

Methods Mol Biol. 2007;366:13-40.PMID: 17568117 [PubMed - indexed for MEDLINE]Related articles

Probe selection for high-density oligonucleotide arrays.

Mei R, Hubbell E, Bekiranov S, Mittmann M, Christians FC, Shen MM, Lu G, Fang J, Liu WM, Ryder T, Kaplan P, Kulp D, Webster TA.

Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11237-42. Epub 2003 Sep 19.PMID: 14500916 [PubMed - indexed for MEDLINE]Related articlesFree article

A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes.

Hammond JP, Bowen HC, White PJ, Mills V, Pyke KA, Baker AJ, Whiting SN, May ST, Broadley MR.

New Phytol. 2006;170(2):239-60.PMID: 16608451 [PubMed - indexed for MEDLINE]Related articles

A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat.

Alberts R, Terpstra P, Hardonk M, Bystrykh LV, de Haan G, Breitling R, Nap JP, Jansen RC.

BMC Bioinformatics. 2007 Apr 20;8:132.PMID: 17448222 [PubMed - indexed for MEDLINE]Related articlesFree article

GST-PRIME: an algorithm for genome-wide primer design.

Leister D, Varotto C.

Methods Mol Biol. 2007;402:141-58. Review.PMID: 17951794 [PubMed - indexed for MEDLINE]Related articles

Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays.

Chudin E, Walker R, Kosaka A, Wu SX, Rabert D, Chang TK, Kreder DE.

Genome Biol. 2002;3(1):RESEARCH0005. Epub 2001 Dec 14.PMID: 11806828 [PubMed - indexed for MEDLINE]Related articlesFree article

Benchmarking the CATMA microarray. A novel tool for Arabidopsis transcriptome analysis.

Allemeersch J, Durinck S, Vanderhaeghen R, Alard P, Maes R, Seeuws K, Bogaert T, Coddens K, Deschouwer K, Van Hummelen P, Vuylsteke M, Moreau Y, Kwekkeboom J, Wijfjes AH, May S, Beynon J, Hilson P, Kuiper MT.

Plant Physiol. 2005 Feb;137(2):588-601.PMID: 15710687 [PubMed - indexed for MEDLINE]Related articlesFree article

Development and evaluation of an Arabidopsis whole genome Affymetrix probe array.

Redman JC, Haas BJ, Tanimoto G, Town CD.

Plant J. 2004 May;38(3):545-61.PMID: 15086809 [PubMed - indexed for MEDLINE]Related articles

Genes involved in biosynthesis and signalisation of ethylene in Brassica oleracea and Arabidopsis thaliana: identification and genome comparative mapping of specific gene homologues.

Babula D, Misztal LH, Jakubowicz M, Kaczmarek M, Nowak W, Sadowski J.

Theor Appl Genet. 2006 Feb;112(3):410-20. Epub 2005 Nov 26.PMID: 16311726 [PubMed - indexed for MEDLINE]Related articles

How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results.

Millenaar FF, Okyere J, May ST, van Zanten M, Voesenek LA, Peeters AJ.

BMC Bioinformatics. 2006 Mar 15;7:137.PMID: 16539732 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide analysis of Arabidopsis responsive transcriptome to nitrogen limitation and its regulation by the ubiquitin ligase gene NLA.

Peng M, Bi YM, Zhu T, Rothstein SJ.

Plant Mol Biol. 2007 Dec;65(6):775-97. Epub 2007 Sep 21.PMID: 17885809 [PubMed - indexed for MEDLINE]Related articles