Bulk murine TCR-beta repertoires (MOC1 tumour model) from Patin et al. "Sculpting the tumour microenvironment by combining radiotherapy and ATR inhibition for curative-intent adjuvant immunotherapy"

<b>Description</b>This dataset consists of 12 TCR beta repertoires obtained from MOC1 head and neck cancer model mice and the corresponding sample sheet. Mice were treated with either vehicle; or ARTi / radiotherapy (RT) combination; or ARTi / RT and PD-L1 and NKG2A antibodies; or ARTi / RT / aPD-L1 / aNKG2A and CD40L antibodies. There were 3 replicates per treatment. The analysis results are shown on Figure 7 and Figure S13.<b>TCR sequencing</b>TCR β-chain sequencing was performed by utilizing whole RNA extracted from tumor samples by using a quantitative experimental and computational TCR sequencing pipeline described previously [Oakes et al. Front Immunol, 2017]. Briefly, the TCR library preparation protocol consists of first a T4 ligation step to the 3’ end of the TCR cDNA which allows the amplification of all possible rearrangements using a single set of primers per locus and the incorporation of a UMI attached to each cDNA TCR molecule that enables correction for PCR and sequencing errors. The final library was prepared for sequencing according to the Illumina NovaSeq protocol immediately prior to loading. Sample was loaded at 1.2 pM with 15–20% of PhiX DNA at 1.8 pM. All samples were run in parallel, yielding 5 million reads per sample (2x150 bp paired end). The bioinformatic pipeline used for TCR identification, error correction and CDR3 extraction was Decombinator (freely available at https://github.com/innate2adaptive/Decombinator).<br>