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

Publication date: Available online 20 July 2016 Source:Genomics Data Author(s): Amit Kumar Subudhi, P.A. Boopathi, Sheetal Middha, Jyoti Acharya, Sudha Narayana Rao, Raja C. Mugasimangalam, Paramendra Sirohi, Sanjay K. Kochar, Dhanpat K. Kochar, Ashis Das Malarial parasite P. falciparum, an apicomplexan protozoan has a 23.3MB nuclear genome and encodes ~5600 transcripts.The genetic diversity of the parasite within and across geographical zones is a challenge to gene expression studies which are essential for understanding of disease process, outcome and developing markers for diagnostics and prognostics.Here, we describe the strategy involved in designing a custom P. falciparum 15K array using the Agilent platform and Genotypic's Right Design methodology to study the transcriptome of Indian field isolates for which genome sequence information is limited. The array contains probes representing genome sequences of two distinct geographical isolates (i.e. 3D7 and HB3) and sub-telomeric var gene sequences of a third isolate (IT4) known to adhere in culture condition. Probes in the array have been selected based on their efficiency to detect transcripts through a 244K array experimentation. Array performance for the 15K array, was evaluated and validated using RNA materials from P. falciparum clinical isolates. A large percentage (91%) of the represented transcripts was detected from Indian P. falciparum patient isolates. Replicated probes and multiple prob...
Source: Genomics Data - Category: Genetics & Stem Cells Source Type: research