E-MTAB-14406:Sample 4 (cycle_metacyc2)
2025-08-27
ENA first public
ERC000011
ENA-CHECKLIST
University of Glasgow University of Edinburgh
INSDC center name
public
INSDC status
ERS20928733
SRA accession
E-MTAB-14406:Sample 4 (cycle_metacyc2)
Submitter Id
ArrayExpress
broker name
metacyclic trypomastigotes
cell_type
not collected
collection date
Protocols: A mixture of stationary phase epimastigotes and metacyclic trypomastigotes (SE/MT) was obtained from a 10 days-old culture initiated with 3x10/1^5 epimastigotes/ml. 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)
description
not collected
geographic location (country and/or sea)
not applicable
isolate
Trypanosoma cruzi
organism
Trypanosoma cruzi
organism
Trypanosoma cruzi
scientific_name
Sample 4 (cycle_metacyc2)
title