AIRRWAS integrates TCR-microbiome data to reveal how the gut microbiome shapes the circulating and mucosal T cell repertoire

Prevotella/Peptoniphilus: TCR sequencing data after stimulation with bacterial lysates of Prevotella bivia (PB) or Peptoniphilus lacrimalis (PL). PBMCs were stimulated for either 24 h or 7 days. Six samples were stimulated with PB lysate, four with PL lysate, and three with both lysates separately. Activated CD154highOX40highCD4+ and CD137highCD69highCD8+ T cells were sorted using a FACSAria II (BD Biosciences) and subjected to bulk TCR sequencing using the QIAseq Immune Repertoire RNA Library Kit (Qiagen).

vb: CO010_PB_1d_S13_L001.clones_TRA.tsv  = [individual]_[bacterium]_[timeframe]_[run]_[details].clones_[TRA/B].tsv

Treg/Tconv: PBMC samples (n = 6) were stimulated with PL lysate and sorted into activated conventional (Tconv; CD154highCD137lowCD4+) and regulatory T cells (Tregs; CD154lowCD137highCD4+) after 6 h of stimulation using an Aurora CS (Cytek Biosciences). Activated T cells were sequenced using a modified TIRTL-seq protocol to generate bulk TRA and TRB sequencing data without pairing information. (See file 2_PL_validation_IDs.xlsx for Treg/Tconv mapping)

vb: 5009_PedRheum_196_PedRheum_I13_S200_TRA.tsv  = 5009_PedRheum_[individual]_PedRheum_[run]_[details]_[TRA/B].tsv

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AIRRWAS integrates TCR-microbiome data to reveal how the gut microbiome shapes the circulating and mucosal T cell repertoire