Paired Vgamma9Vdelta2 T-cell receptor sequences from pigtail macaques (Macaca nemestrina) following in vivo pharmacological expansion

Dataset related to the following manuscript:
-Barber-Axthelm IM, Wragg KM, Esterbauer R, Amarasena TH, Barber-Axthelm VRB, Wheatley AK, Gibbon AM, Kent SJ, and Juno JA. Phenotypic and functional characterization of pharmacologically expanded Vgamma9Vdelta2 T-cells in pigtail macaques (2023)

The included datasets are related to in vivo pharmacologically expanded Vgamma9Vdelta2 T-cells in pigtail macaques (Macaca nemistrina). Gamma and delta T-cell receptor (TCR) sequences were taken from peripheral blood Vgamma9Vdelta2 T-cells collected per-expansion (day -14) or at peak expansion (day 4), from 4 animals (NM11, NM89, NM251, NM295). Sequencing data from Day 15 is also included from 1 animal (NM89). Sequences were amplified by single-cell, multiplex RT-PCR, prior to capillary electrophoresis sequencing. Details on RT-PCR amplification conditions and primers can be found in the associated manuscript. The sequences were subsequently aligned using the MiXCR software package (v3.0.13; species: Macaca mulatta).

Dataset description:
-Combined_TCR_sequence_alignments_MiXCR.csv: Aligned, paired, single-cell TCRG and TCRD sequences, with associated FACS sort data (from BD FACSAria III cell sorter), for 4 animals (NM11, NM89, NM251, NM295) and 2 timepoints (pre-expansion and peak expansion). Sequencing data from Day 15 is also included from 1 animal (NM89). Rows without TCRG/TCRD alignment information indicate an RT-PCR sequencing product that could not be aligned. Initial RT-PCR TCRG/TCRD nucleotide sequences are included.
-TCRG_Functional.clones.csv: Assembled list of functional TCRG clones recovered across 4 animals (NM11, NM89, NM251, NM295) and 2 timepoints (pre-expansion and peak expansion), generated through the MiXCR assemble function. TCRG sequences from Day 15 is also included from 1 animal (NM89). TCRG clone list is used to filter out non-functional clones from the Combined_TCR_sequence_alignments_MiXCR.csv in R.
-TCRD_Functional.clones.csv: Assembled list of functional TCRD clones recovered across 4 animals (NM11, NM89, NM251, NM295) and 2 timepoints (pre-expansion and peak expansion), generated through the MiXCR assemble function. TCRG sequences from Day 15 is also included from 1 animal (NM89). TCRD clone list is used to filter out non-functional clones from the Combined_TCR_sequence_alignments_MiXCR.csv in R.

The code used for downstream TCR sequence analysis has been deposited at GitHub (https://github.com/BarberAxthelm/Vd2-Vg9_TCR_Analysis) and is publicly available as of the date of publication.