Trynka group data and code

We are  committed to making our data and code publicly available. This is a collection of links to software tools, analysis code and data visualisations from our papers:

Soskic B, Cano-Gamez E, Smyth DJ, Ambridge K, Bossini-Castillo L, Kaplanis J, Ramirez-Navarro L, Nakic N, Esparza-Gordillo J, Rowan W, Wille D, Tough DF, Bronson PG & Trynka, G. (2022)  Immune disease risk variants regulate gene expression dynamics during CD4+ T cell activation Nat Genet (2022). https://doi.org/10.1038/s41588-022-01066-3  preprint   paper

Interactive data viewer (visualise scRNAseq of CD4 memory and naive cells in different timepoints after activation) + h5ad files download

eQTLs identified in this dataset

Gene expression in the time course of cell activation (pseudobulk averages)

Bossini-Castillo L,  Glinos D, Kunowska N,  Golda G,  Lamikanra A,  Spitzer M, Soskic B, Cano-Gamez E, J. Smyth D, Cattermole C,  Alasoo K, Alice Mann, Kundu K, Soranzo N, Dunham I,  Roberts D, Trynka G. Immune disease variants modulate gene expression in regulatory CD4+ T cells and inform drug targets Cell Genomics,Vol 2, Iss 4, 2022; https://doi.org/10.1016/j.xgen.2022.100117

Interactive data viewer (visualise colocalisation of Treg eQTLs and immune disease GWAS)

Code on Github

Cano-Gamez, E., Soskic, B., Roumeliotis, T.I. So E, Smyth DJ, Baldrighi M, Willé D, Nakic N, Esparza-Gordillo J, Larminie CGC, Bronson PG, Tough DF, Rowan WC, Choudhary JS, Trynka G. Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4⁺ T cells to cytokines. Nat Commun 11, 1801 (2020). doi: 10.1038/s41467-020-15543-y

Interactive data viewer (visualise bulk RNA/protein expression, as well as single-cell RNA expression profiles of resting and cytokine-polarized T cells)

Code on GitHub

Glinos DA, Soskic B, Williams C, Kennedy A, Jostins L, Sansom DM, Trynka G. Genomic profiling of T-cell activation suggests increased sensitivity of memory T cells to CD28 costimulation. Genes Immun. 2020 Dec;21(6-8):390-408. doi: 10.1038/s41435-020-00118-0

Interactive data viewer(visualise the expression of genes in response to various strength of TCR and CD28 signalling in memory and naive T cells)

Code on GitHub

Soskic B, Cano-Gamez E, Smyth DJ, Rowan WC, Nakic N, Esparza-Gordillo J, Bossini-Castillo L, Tough DF, Larminie CGC, Bronson PG, Willé D, Trynka G. Chromatin activity at GWAS loci identifies T cell states driving complex immune diseases. Nat Genet. 2019 Oct;51(10):1486-1493. doi: 10.1038/s41588-019-0493-9.

Code on Github