Entamoeba histolytica sequencing from TSS identification  experiment TEX treatment
Total RNA (10-100 g) was polyA enriched  twice using Sera-Mag Magnetic Particles Oligo(dT) coated (Thermo Scientific  ref. 28152103011150) and fragmented 5 minutes (Ambion ref. AM8740). According  to manufacturer's instructions, Transcription Start Site enrichment was  achieved with Terminator 5'-Phosphate-Dependant Exonuclease (TEBU ref.  TER51020) followed by Tobacco Acid Pyrophosphatase (TEBU ref. T81050)  treatment. For CapSeq, total  RNA was similarly treated with an additional 15% TBE-urea gel size selection. RNA was treated with Terminator  5-phosphate-dependent Exonuclease (Epicenter ref. TER51020), calf intestinal  phosphatase (New England Biolab ref. M0290) and Tobacco Acid Pyrophosphatase (Epicenter ref. T19050). Libraries were constructed following manufacturer's  recommendations using TruSeq Small RNA Sample Prep Kit (Illumina, ref.  RS-200-0012). The libraries were purified with AMPure XP beads (Agencourt  ref. A63880) and controlled by Bioanalyzer DNA High Sensitivity Chips  (Agilent ref. 5065-4626). Sequencing has been performed on a HiSeq 2000  (Illumina) in a multiplexed 51+7 bases single read using a TruSeq SR Cluster  kit v2 cBot HS (Illumina, ref. GD-401-2510) and a TruSeq SBS kit v2 HS 50  cycles (Illumina, ref. FC-401-1002).