Replication Data for: "Single-cell T-cell Receptor sequencing of paired human atherosclerotic plaques and blood reveals autoimmune-like features of expanded effector T-cells."

These are the single-cell TCR sequencing (scTCRseq) on human carotid artery plaques from the Athero-Express Biobank Study as used after quality control in the paper referenced below; below the abstract.
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<b>Abstract</b></br>
We applied single-cell TCR sequencing (scTCRseq) on human carotid artery plaques and patient matched PBMC samples to assess the extent of TCR clonality and antigen specific activation within the various T-cell subsets on 3 patients, and applied bulk CDR3b sequencing of matched PBMC and plaque material of 10 patients. CellChat was used to analyze potential interactions of effector CD4+ T-cells with foam cells in the plaque. Finally, we integrated a published scTCRseq dataset of the autoimmune disease psoriatic arthritis to assess commonalities and differences between the two diseases. In this repository we provide the raw atherosclerosis TCRseq data, the bulk sequencing data, and the code that was used for the analysis of the data. </br ></br></br >

<b>GitHub</b></br>
A link to the <em>public</em> GitHub repository: <a href="" target="_blank">link</a>. This contains all scripts used for the data, which is pseudonymized and shared here. </br></br>

<strong>Athero-Express Biobank Study</strong></br>
The AE started in 2002 and now includes over 3,500 patients who underwent surgery to remove atherosclerotic plaques (endarterectomy) from one (or more) of their major arteries (majority carotids and femorals); this is further described <a href="https://doi.org/10.34894/4IKE3T" target="_blank">here</a>. The study design and staining protocols are described by <a href="https://pubmed.ncbi.nlm.nih.gov/15678794/" target="_blank">Verhoeven <em>et al.</em></a></br></br>

<b>Additional data</b></br>
Additional clinical data is available upon discussion and signing a Data Sharing Agreement (see Terms of Access).</br></br>

<b>PlaqView</b></br>
<b>Please note, that we will also integrate these data through PlaqView, but they are not available yet.</b><br>In collaboration with the <a href="http://millerlab.org" target="_blank">http://millerlab.org</a> from the University of Virginia (USA) we created <a href="https://www.plaqview.com" target="_blank">PlaqView.com</a>. You can query any gene of interest in many carotid-plaque datasets, including ours. From our experience we know that usually this suffices most research questions and prevents the lengthy process of obtaining these data through a DSA.