{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Ma WF"],"funding":["American Heart Association","NCATS NIH HHS","Fondation Leducq","NHLBI NIH HHS","National Institutes of Health"],"pagination":["12-22"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8919504"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["340"],"pubmed_abstract":["<h4>Background and aims</h4>The atherosclerotic plaque microenvironment is highly complex, and selective agents that modulate plaque stability are not yet available. We sought to develop a scRNA-seq analysis workflow to investigate this environment and uncover potential therapeutic approaches. We designed a user-friendly, reproducible workflow that will be applicable to other disease-specific scRNA-seq datasets.<h4>Methods</h4>Here we incorporated automated cell labeling, pseudotemporal ordering, ligand-receptor evaluation, and drug-gene interaction analysis into a ready-to-deploy workflow. We applied this pipeline to further investigate a previously published human coronary single-cell dataset by Wirka et al. Notably, we developed an interactive web application to enable further explorati"],"journal":["Atherosclerosis"],"pubmed_title":["Enhanced single-cell RNA-seq workflow reveals coronary artery disease cellular cross-talk and candidate drug targets."],"pmcid":["PMC8919504"],"funding_grant_id":["R01 HL155165","UL1 TR001873","R01 HL156849","R01 HL132904","R01 HL136314","R01 HL150359","K12HL143959","T32HL007284","R01 HL148239","R00 HL125912","R01HL148239","POST35120545","R00HL125912","T32 HL007284","K12 HL143959"],"pubmed_authors":["Miller CL","Gancayco C","Reilly MP","Mosquera JV","Ligay AV","Hodonsky CJ","Slenders L","Li M","Turner AW","Wong D","Pan H","Ma WF","Barrientos NB","Mai D","van der Laan SW","Pasterkamp G","Owsiany K","Alencar GF","Owens GK","Mokry M","Khomtchouk BB","Song Y"],"additional_accession":[]},"is_claimable":false,"name":"Enhanced single-cell RNA-seq workflow reveals coronary artery disease cellular cross-talk and candidate drug targets.","description":"<h4>Background and aims</h4>The atherosclerotic plaque microenvironment is highly complex, and selective agents that modulate plaque stability are not yet available. We sought to develop a scRNA-seq analysis workflow to investigate this environment and uncover potential therapeutic approaches. We designed a user-friendly, reproducible workflow that will be applicable to other disease-specific scRNA-seq datasets.<h4>Methods</h4>Here we incorporated automated cell labeling, pseudotemporal ordering, ligand-receptor evaluation, and drug-gene interaction analysis into a ready-to-deploy workflow. We applied this pipeline to further investigate a previously published human coronary single-cell dataset by Wirka et al. Notably, we developed an interactive web application to enable further explorati","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 Jan","modification":"2026-05-28T12:54:44.142Z","creation":"2025-02-18T22:34:38.274Z"},"accession":"S-EPMC8919504","cross_references":{"pubmed":["34871816"],"doi":["10.1016/j.atherosclerosis.2021.11.025"]}}