The code files in this repository were created and used to analyze three pairs of patient tissue samples collected during carotid endarterectomy procedures. For more details of the experiment, please see our bioRxiv paper:
Tom Alsaigh, Doug Evans, David Frankel, Ali Torkamani bioRxiv 2020.03.03.968123; doi: with GEO Data
It is expected that this archive version of the paper will be updated and formally published in a recognized journal (after 11/01/2021). Interested parties should look for it's formal publication for the authoritative presentation of the experiment.
The data used in this analysis was taken from 3 pairs of samples that were collected at different times and processed as independent pairs. Within each pair are samples of the carotid artery where an atherosclerotic lesion had formed (Atherosclerotic Core or AC) and nearby carotid tissue relatively devoid of plaque (Proximal Adjacent or PA). AC and PA sample pairs were processed using a 10x Genomics single cell platform. The sample pairs were NGS processed as multiplexed pairs.
The resulting NGS data from these experiments were processed using the 10x Genomics Cellranger suite of software. Those files (NGS and Cellranger) serve as the primary input to the analytic programs found in this repository. These source data files are available via GEO. When running the 10x software, default parameters and the latest reference transcriptome were always used, so no documentation is included here showing the Cellranger commands. The NGS input files for Cellranger can be found on GEO and should be sufficient for an interested researcher to reproduce the Cellranger results, also found on GEO.
Analysis was performed through a sequence of steps, and the numbering of the Jupyter note files (code folder) are reflective of the order of processing. Files are indexed as nnnn.nn.nn, where the first 4 digits are primary, and the second and third sets of digits (nn.nn) are indicative in incremental recoding of the primary notebook.
The first two notebooks are of special interest. The first, 0000.00.00... holds an index of all the notebooks in this repository, as well as the platform versioning (at the end of the notebook). The second notebook, 0100.00.000... sets up the data and file structure of the analysis. The file structure is dependent upon the infrastructure upon which the analysis takes place. Those interested in reproducing the results of this analysis are advised to review this notebook carefully and recode it as necessary to match the new infrastructure