This repostitory contains procesed TCRalpha and TCRbeta repertoire datasets (and some results as well) for the paper by Minervina et al. on mild COVID-19, arxiv, biorxiv. The paper in now published in eLife.
Table_S1.tsv - list of libraries, with approx number of cells, number of UMIs and unique clonotypes.
Table_S2.tsv - HLA-typing results.
Table_S3.tsv - TCRbeta clonotypes contracting from day 15 to day 85 post infection, for both donors, with frequencies in each timepoint.
Table_S4.tsv - TCRalpha clonotypes contracting from day 15 to day 85 post infection, for both donors, with frequencies in each timepoint.
Table_S5.tsv - TCRbeta clonotypes expanding from day 15 to day 37 post infection, for both donors, with frequencies in each timepoint.
Table_S6.tsv - TCRalpha clonotypes expanding from day 15 to day 37 post infection, for both donors, with frequencies in each timepoint.
The complete processed repertoire data is available from zenodo in mixcr format:
The raw sequencing data is available at Short Read Archive acc. PRJNA633317.
(coming soon!)
All SI tables for the initial version(v1) of preprint biorxiv could be found in old_version folder, see description below (note that contracting clones are defined as contracting from day 15 to day 45 in this version).
Two groups of TCR clones with active dynamics post-infection were identified for both donors:
contracting clones are clones contracting in the repertoire from day 15 to day 45 post-infection.
expanding clones go up from day 15 to day 37 post-infection.
Both groups were identified with edgeR (FDR-adjusted p<0.01, log2FC threshold=2). Clone counts are given as in first replicate of PBMC on day 15 (for contracting) and day 37 (for expanding group).