A cross strain Plasmodium falciparum microarray optimized for the transcriptome analysis of Plasmodium falciparum patient derived isolates

Aurrecoechea, 2009, PlasmoDB: a functional genomic database for malaria parasites, Nucleic Acids Res., 37, D539, 10.1093/nar/gkn814 Balu, 2005, High-efficiency transformation of Plasmodium falciparum by the lepidopteran transposable element piggyBac, Proc. Natl. Acad. Sci. U. S. A., 102, 16391, 10.1073/pnas.0504679102 Bartfai, 2010, H2A.Z demarcates intergenic regions of the Plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3, PLoS Pathog., 6, 10.1371/journal.ppat.1001223 Bozdech, 2003, The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum, PLoS Biol., 1, 10.1371/journal.pbio.0000005 Caro, 2012, Plate-based transfection and culturing technique for genetic manipulation of Plasmodium falciparum, Malar. J., 11, 22, 10.1186/1475-2875-11-22 Daily, 2007, Distinct physiological states of Plasmodium falciparum in malaria-infected patients, Nature, 450, 1091, 10.1038/nature06311 Das, 1995, Species-specific 18S rRNA gene amplification for the detection of Plasmodium falciparum and Plasmodium vivax malaria parasites, Mol. Cell. Probes, 9, 161, 10.1006/mcpr.1995.0025 Duraisingh, 2005, Heterochromatin silencing and locus repositioning linked to regulation of virulence genes in Plasmodium falciparum, Cell, 121, 13, 10.1016/j.cell.2005.01.036 Flueck, 2009, Plasmodium falciparum heterochromatin protein 1 marks genomic loci linked to phenotypic variation of exported virulence factors, PLoS Pathog., 5, 10.1371/journal.ppat.1000569 Gardner, 2002, Genome sequence of the human malaria parasite Plasmodium falciparum, Nature, 419, 498, 10.1038/nature01097 Hay, 2010, Estimating the global clinical burden of Plasmodium falciparum malaria in 2007, PLoS Med., 7, 10.1371/journal.pmed.1000290 Hayward, 2000, Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria, Mol. Microbiol., 35, 6, 10.1046/j.1365-2958.2000.01730.x Hu, 2010, Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum, Nat. Biotechnol., 28, 91, 10.1038/nbt.1597 Imwong, 2010, Exploring the contribution of candidate genes to artemisinin resistance in Plasmodium falciparum, Antimicrob. Agents Chemother., 54, 2886, 10.1128/AAC.00032-10 Joannin, 2008, Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family, BMC Genomics, 9, 19, 10.1186/1471-2164-9-19 Kafsack, 2012, New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community, Malar. J., 11, 187, 10.1186/1475-2875-11-187 Kochar, 2010, Clinical features of children hospitalized with malaria—a study from Bikaner, northwest India, Am.J.Trop. Med. Hyg., 83, 981, 10.4269/ajtmh.2010.09-0633 Le Roch, 2003, Discovery of gene function by expression profiling of the malaria parasite life cycle, Science, 301, 1503, 10.1126/science.1087025 Mackinnon, 2009, Comparative transcriptional and genomic analysis of Plasmodium falciparum field isolates, PLoS Pathog., 5, 10.1371/journal.ppat.1000644 Maier, 2008, Exported proteins required for virulence and rigidity of Plasmodium falciparum-infected human erythrocytes, Cell, 134, 48, 10.1016/j.cell.2008.04.051 Mamoun, 2001, Plasmodium protein phosphatase 2C dephosphorylates translation elongation factor 1beta and inhibits its PKC-mediated nucleotide exchange activity in vitro, Mol. Microbiol., 39, 973, 10.1046/j.1365-2958.2001.02289.x Miller, 2002, The pathogenic basis of malaria, Nature, 415, 673, 10.1038/415673a Natalang, 2008, Dynamic RNA profiling in Plasmodium falciparum synchronized blood stages exposed to lethal doses of artesunate, BMC Genomics, 9, 388, 10.1186/1471-2164-9-388 Oakley, 2007, Molecular factors and biochemical pathways induced by febrile temperature in intraerythrocytic Plasmodium falciparum parasites, Infect. Immun., 75, 2012, 10.1128/IAI.01236-06 Olszewski, 2009, Host-parasite interactions revealed by Plasmodium falciparum metabolomics, Cell Host Microbe, 5, 191, 10.1016/j.chom.2009.01.004 Otto, 2010, New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq, Mol. Microbiol., 76, 12, 10.1111/j.1365-2958.2009.07026.x Pakalapati, 2013, Development and evaluation of a 28S rRNA gene-based nested PCR assay for Plasmodium falciparum and Plasmodium vivax, Pathog. Glob. Health, 107, 180, 10.1179/2047773213Y.0000000090 Pakalapati, 2013, Comparative evaluation of microscopy, OptiMAL((R)) and 18S rRNA gene based multiplex PCR for detection of Plasmodium falciparum & Plasmodium vivax from field isolates of Bikaner, India, Asian Pac J Trop Med, 6, 346, 10.1016/S1995-7645(13)60037-1 Petter, 2007, Variant proteins of the Plasmodium falciparum RIFIN family show distinct subcellular localization and developmental expression patterns, Mol. Biochem. Parasitol., 156, 51, 10.1016/j.molbiopara.2007.07.011 Sargeant, 2006, Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites, Genome Biol., 7, R12, 10.1186/gb-2006-7-2-r12 Scherf, 2008, Antigenic variation in Plasmodium falciparum, Annu. Rev. Microbiol., 62, 445, 10.1146/annurev.micro.61.080706.093134 Silvestrini, 2005, Genome-wide identification of genes upregulated at the onset of gametocytogenesis in plasmodium falciparum, Mol. Biochem. Parasitol., 143, 100, 10.1016/j.molbiopara.2005.04.015 Subudhi, 2014, Natural antisense transcripts in Plasmodium falciparum isolates from patients with complicated malaria, Exp. Parasitol., 141C, 39, 10.1016/j.exppara.2014.03.008 Subudhi, 2015, Disease specific modules and hub genes for intervention strategies: a co-expression network based approach for Plasmodium falciparum clinical isolates, Infect. Genet. Evol., 35, 96, 10.1016/j.meegid.2015.08.007 Subudhi, 2015, Plasmodium falciparum complicated malaria: modulation and connectivity between exportome and variant surface antigen gene families, Mol. Biochem. Parasitol., 201, 31, 10.1016/j.molbiopara.2015.05.005 Tamez, 2008, An erythrocyte vesicle protein exported by the malaria parasite promotes tubovesicular lipid import from the host cell surface, PLoS Pathog., 4, 10.1371/journal.ppat.1000118 Tuikue Ndam, 2008, Plasmodium falciparum transcriptome analysis reveals pregnancy malaria associated gene expression, PLoS One, 3, 10.1371/journal.pone.0001855 World Health, O., 2000, Severe falciparum malaria, Trans. R. Soc. Trop. Med. Hyg., 94, 1, 10.1016/S0035-9203(00)90300-6 2015 Ye, 2012, Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction, BMC Bioinformatics, 13, 134, 10.1186/1471-2105-13-134 Young, 2005, The Plasmodium falciparum sexual development transcriptome: a microarray analysis using ontology-based pattern identification, Mol. Biochem. Parasitol., 143, 67, 10.1016/j.molbiopara.2005.05.007