Tu, A. A. et al. TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures. Nat. Immunol. 2019 2012 20, 1692–1699 (2019).

Landing page for computational scripts and other supplementary information related to TCR recovery from Seq-Well libraries related to the Nat. Immunol manuscript.

GEO

Gene expression matrices can be found on GSE136028. Seurat objest will be included as rds files.

Rscripts

Contains basic R scripts used to produce Figure 3 and 4 in the manuscript. Also includes tests and other exploratory analysis that ultimately did not get included.

Figure 3

The E7_combined script contains analysis that compares TCRs from mice that were immunized with E7, and sorted with tetramers.

Figure 4

PNOIT_TCR script contains analysis regarding peanut allergy patients shown in figure 4.

src

Contains supplemental files (such as gene lists, scripts for helper functions), as well as msigdb results that were obtained via web portal. The MsigDb folder contains results obtained from querying MsigDb portal. Include data for both figure 3 and 4.

Preprocess

Contains script for combining raw TCR data (as made available in supplement of manuscript) with the relevant seurat files

TCR_fastqprocessing

Shell scripts for mapping sequencing fastq to TCR reference to produce the relevant bam files. Reference files included for both human and mouse

Seqwell_TCR_processing

Instruction for analyzing mapped bam files into compiled TCR summary files, which contains TCR sequences along with the single-cell barcodes that they are mapped to. Implemented as a docker image. Raw scripts included in this folder

Local_processing

Running the processing program locally just using MatLab. This is not recommended, as it can take a really long time.

Docker_associated_scripts

Scripts included and used in the docker image environment

TCR_recovery_protocol

Laboratory protocol on how to perform the recovery procedure to construct the TCR sequencing libraries.