Description:
This file describes the different steps to the quality control based on:
Input data: Seurat object containing all cells (filtered count matrix)
Output data: Seurat object annotated for the cells
to filter out for downstream analysis, called
sobj_TD3A_qc_annotated.rds
Next steps: Cells annotation for cell type, doublet status and cell cycle status
In this file, we used a dataset from the Paiva et al. publication.
The study concerns thymus autonomy:
The thymus is an “organ of passage”, critical in its function to the adaptive immune system for the maturation of T cell lymphocytes.
This maturation involves two main steps, performed thanks to macrophages:
Thymus autonomy is a natural mechanism that allows to create T cells in the thymus by differentiation and cell competition, even when normal progenitors from the bone marrow are lacking, in critical conditions.
This mechanism is known in its effects, but the cells involved in are not.
This study is of importance in the health field, as this mechanism relies on a temporary loss of control of the cell normal functions.
The consequence is that if thymus is in autonomy for too long (few weeks), this is a prelude for leukemia !