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As most VSA genes are unique, the variability among sequences has impeded the functional study of VSA across different <jats:italic>P. falciparum<\/jats:italic> strains. However, many <jats:italic>P. falciparum<\/jats:italic> genomes have recently been sequenced, allowing the development of specific microarray probes for each VSA gene.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Methods<\/jats:title>\n            <jats:p>All VSA sequences from the HB3, Dd2 and IT\/FCR3 genomes were extracted using HMMer software. Oligonucleotide probes were designed with OligoRankPick and added to the 3D7-based microarray chip. As a proof of concept, IT\/R29 parasites were selected for and against rosette formation and the transcriptomes of isogenic rosetting and non-rosetting parasites were compared by microarray.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>From each parasite strain 50-56 <jats:italic>var<\/jats:italic> genes, 125-132 <jats:italic>rif<\/jats:italic> genes, 26-33 <jats:italic>stevor<\/jats:italic> genes and 3-8 <jats:italic>pfmc-2tm<\/jats:italic> genes were identified. Bioinformatic analysis of the new VSA sequences showed that 13 <jats:italic>rif genes<\/jats:italic> and five <jats:italic>stevor<\/jats:italic> genes were well-conserved across at least three strains (83-100% amino acid identity). The ability of the VSA-supplemented microarray chip to detect cytoadherence-related genes was assessed using <jats:italic>P. falciparum<\/jats:italic> clone IT\/R29, in which rosetting is known to be mediated by PfEMP1 encoded by <jats:italic>ITvar9<\/jats:italic>. Whole transcriptome analysis showed that the most highly up-regulated gene in rosetting parasites was <jats:italic>ITvar9<\/jats:italic> (19 to 429-fold up-regulated over six time points). Only one <jats:italic>rif<\/jats:italic> gene (<jats:italic>IT4rifA_042<\/jats:italic>) was up-regulated by more than four fold (five fold at 12 hours post-invasion), and no <jats:italic>stevor<\/jats:italic> or <jats:italic>pfmc-2tm<\/jats:italic> genes were up-regulated by more than two fold. 377 non-VSA genes were differentially expressed by three fold or more in rosetting parasites, although none was as markedly or consistently up-regulated as <jats:italic>ITvar9<\/jats:italic>.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Probes for the VSA of newly sequenced <jats:italic>P. falciparum<\/jats:italic> strains can be added to the 3D7-based microarray chip, allowing the analysis of the entire transcriptome of multiple strains. For the rosetting clone IT\/R29, the striking transcriptional upregulation of <jats:italic>ITvar9<\/jats:italic> was confirmed, and the data did not support the involvement of other VSA families in rosette formation.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1475-2875-10-180","type":"journal-article","created":{"date-parts":[[2011,7,1]],"date-time":"2011-07-01T18:44:32Z","timestamp":1309545872000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Design of a variant surface antigen-supplemented microarray chip for whole transcriptome analysis of multiple Plasmodium falciparum cytoadherent strains, and identification of strain-transcendent rif and stevor genes"],"prefix":"10.1186","volume":"10","author":[{"given":"Antoine","family":"Claessens","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashfaq","family":"Ghumra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Archna P","family":"Gupta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sachel","family":"Mok","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zbynek","family":"Bozdech","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J Alexandra","family":"Rowe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2011,6,30]]},"reference":[{"key":"1778_CR1","doi-asserted-by":"publisher","first-page":"e16","DOI":"10.1017\/S1462399409001082","volume":"11","author":"JA Rowe","year":"2009","unstructured":"Rowe JA, Claessens A, Corrigan RA, Arman M: Adhesion of Plasmodium falciparum-infected erythrocytes to human cells: molecular mechanisms and therapeutic implications. 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