Transcriptome of bone marrow-derived macrophages infected with T. gondii GT1 strain
Total RNA was be extracted from all infected cells 20 hrs after infection using the Qiagen RNeasy Plus kit. Integrity, sizing and concentration of RNA was checked using the Agilent 2100 Bioanalyser. The RNA was processed for high-throughput sequencing according to standard Illumina protocols. Briefly, after mRNA pull down from total RNA using Dynabeads mRNA Purifica-tion Kit (Invitrogen), mRNA was be fragmented into 200-400 base pair-long fragments  and reverse transcribed to into cDNA, before Illumina sequencing adapters were added to each end. Four samples were barcoded (each barcode unique to a sample) and multiplexed in a single lane on an Illumina sequencing flow cell for paired end sequencing on an Illumina High-seq instrument.