Sigma wta2 whole transcriptome amplification kit

300ηg of RNA was used as starting material for cDNA synthesis using the Sigma WTA2 whole transcriptome amplification kit as previously described [17 (link)].
1μg of cDNA was labeled with Cy3 dye using 65% AT rich pre-labeled random hexamers as primers for cDNA synthesis by Klenow fragment of DNA polymerase I. Hybridizations on the Nimblegen array were performed for 18 hours followed by washing of the arrays as described according to standard protocol (Roche NimbleGen Inc., Madison, WI). The microarray image was obtained using a 2μM scanner and probe intensity values extracted using NimbleScan software (Roche NimbleGen Inc., Madison, WI). For the Agilent HD exon array, hybridizations were performed for 17 hours. Images were obtained on the same 2uM scanner and probe intensity values extracted using Agilent Feature Extraction software.

The microarray measurements were performed as described in [36 (link)]. Briefly, RNA was extracted using TriZol reagent (Invitrogen, Carlsbad, CA) and the quality and quantity determined by NanoDrop (NanoDrop Technologies). 300 ηg of RNA was used for cDNA synthesis using Sigma WTA2 whole transcriptome amplification kit. 1 μg of cDNA was labeled with Cy3 dye and allowed to hybridize to a custom Agilent array for 17 h followed by washing. The microarray image was taken using a 2 μM scanner and probe intensity values obtained using Agilent Feature Extraction software. Normalization of probe intensities was done using the robust multichip average (RMA) method. The time points were obtained as described above for the RNA-seq measurements and include the time points 6 (n = 3), 24 (n = 3) and 38 (n = 3) hours after time zero.
Ethical approval for the use of human blood in this study was granted by the Institutional Review Boards of the University of South Florida and the University of Notre Dame. All of the blood used for the in vitro culturing of parasites was obtained from healthy adult volunteers and drawn by trained personal from Interstate Blood Bank.
The NF54 strain was originally obtained from the Naval Medical Research Center.