Description:

This file describes the different steps to the quality control based on:

  • the number of UMI (transcripts) detected per cell
  • the number of genes detected per cell
  • the proportion of transcripts related to the genes encoded in the mitochondria, per cell
  • the proportion of transcripts related to the genes encoding ribosomal units, per cell
  • the proportion of transcripts related to stress signature, per cell

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

Context

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:

    • Positive selection : keeping cells that successfully develop react appropriately with MHC immune receptors of the body
    • Negative selection : keeping cells that do not react against natural proteins of the body.

  • 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 !