Transcriptomics tool for the human Schistosoma blood flukes using microarray gene expression profiling

• Published in: Experimental parasitology 2006-11, Vol.114 (3), p.160-172
• Main Authors: Gobert, Geoffrey N., McInnes, Russell, Moertel, Luke, Nelson, Charles, Jones, Malcolm K., Hu, Wei, McManus, Donald P.
• Format: Article
• Language: English
• Subjects: Animals; Biological and medical sciences; Biomphalaria; CTP; Cy3; Cy5; cyanine3; cyanine5; cytidine 5′-triphosphate; Female; Fertility - genetics; Fundamental and applied biological sciences. Psychology; GEML; Gene expression; gene expression markup language; Gene Expression Profiling - methods; Gene Expression Regulation - genetics; Gene Ontologies; Helminth; Host-Parasite Interactions - immunology; hours; In Situ Hybridization, Fluorescence; Invertebrates; Life cycle. Host-agent relationship. Pathogenesis; locally weighed scatter plot smoothing; LOWESS; Male; Mice; Microarray; min; minute; nanogram; Nemathelminthia. Plathelmintha; Oligonucleotide Array Sequence Analysis - methods; Oligonucleotide Array Sequence Analysis - standards; PBS; phosphate buffer saline; photomultiplier tube; PMT; Protozoa; QIMR; Queensland Institute of Medical Research; reverse transcriptase; Reverse Transcriptase Polymerase Chain Reaction; revolutions per minute; RNA, Helminth - analysis; RNA, Helminth - genetics; RNA, Messenger - analysis; RNA, Messenger - genetics; rpm; Schistosoma; Schistosoma japonicum; Schistosoma japonicum - genetics; Schistosoma japonicum - immunology; Schistosoma japonicum - physiology; Schistosoma mansoni; Schistosoma mansoni - genetics; Schistosoma mansoni - immunology; Schistosoma mansoni - physiology; second; Signal Transduction - genetics; sodium chloride/sodium phosphate/EDTA buffer; SSPE; TAE; Transcription, Genetic; Transcriptome; Trematoda; Tris/acetate/EDTA buffer; w/v; weight/volume
• ISSN: 0014-4894; 1090-2449
• DOI: 10.1016/j.exppara.2006.03.003

We report the design, fabrication, and validation of a microarray covering the majority of the Schistosoma japonicum and Schistosoma mansoni transcriptomes. The oligonucleotide microarray contains 12,166 S. mansoni and 7055 S. japonicum target sequences. A confidence threshold of ⩽0.001 ( P value) was used in all analyses. The cross hybridization potential of the microarray was representative of 10,362 probes detected in both channels, while 12,052 probes hybridised to S. japonicum and 11,254 probes hybridised to S. mansoni. Differential hybridisation consisted of 3422 probes to S. mansoni mRNA and 3103 probes to S. japonicum mRNA. Important biological functions, such as transport, metabolism, immune evasion and host–parasite immunological interplay, cell communication, and sexual maturation are represented on this microarray. This is the first microarray commercially manufactured for studying schistosomes, and the large size and verified quality of the resource demonstrate its power for characterising the schistosome transcriptome.