title: Single cell RNA sequencing data of the in vitro lifecycle of the kinetoplastid parasite Trypanosoma cruzi
design: Single cell RNA sequencing data of the in vitro lifecycle of the kinetoplastid parasite Trypanosoma cruzi
library_construction_protocol: For the life cycle mixes equal quantities of EP, SE/MT, ADT, AMA_6, AMA_24 and AMA_120 (for 21,000 cells in total) were pooled. For this pool, two technical replicates were collected (labelled MIX1 and MIX2) Single-cell libraries were generated using the Chromium Next GEM Single Cell 3' Reagent Kit v3.1 and the Chromium Next GEM Single Cell 3' Reagent Kit v3.1 - Dual Index (10X Genomics) for the first and second biological replicates respectively. Briefly, single-cell suspensions were loaded onto a Chromium Controller instrument in a Chromium Next GEM Chip G (10X Genomics) to obtain single‐cell Gel beads in EMulsion (GEMs). Barcoded cDNA was obtained from GEMs and amplified by PCR in a PCRmax Alpha Cycler 1 thermal cycler (Cole-Parmer, Saint Neots, UK). End repair and A‐tailing, adapter ligation, post‐ligation cleanup with SPRIselect (Beckman Coulter, Brea, CA, USA), and sample index PCR and cleanup steps were performed as per the manufacturer's instructions. Final library sample index PCR cycle parameters were selected based on quantification of barcoded cDNA samples with a Qubit 2.0 (Life technologies, Carlsbad, CA, USA), using the Qubit dsDNA HS Assay Kit (Life technologies, Eugene, OR, USA) Single-cell libraries were generated using the Chromium Next GEM Single Cell 3' Reagent Kit v3.1 and the Chromium Next GEM Single Cell 3' Reagent Kit v3.1 - Dual Index (10X Genomics) for the first and second biological replicates respectively. Briefly, single-cell suspensions were loaded onto a Chromium Controller instrument in a Chromium Next GEM Chip G (10X Genomics) to obtain single‐cell Gel beads in EMulsion (GEMs). Barcoded cDNA was obtained from GEMs and amplified by PCR in a PCRmax Alpha Cycler 1 thermal cycler (Cole-Parmer, Saint Neots, UK). End repair and A‐tailing, adapter ligation, post‐ligation cleanup with SPRIselect (Beckman Coulter, Brea, CA, USA), and sample index PCR and cleanup steps were performed as per the manufacturer's instructions. Final library sample index PCR cycle parameters were selected based on quantification of barcoded cDNA samples with a Qubit 2.0 (Life technologies, Carlsbad, CA, USA), using the Qubit dsDNA HS Assay Kit (Life technologies, Eugene, OR, USA)