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Understanding cellular and molecular dynamics after treatment is crucial for elucidating resistance mechanisms. Single-cell RNA sequencing (scRNA-seq) of paired pre- and post-treatment patient samples enables high-resolution exploration of such dynamics, but rapidly accumulated relevant data bring challenges for easy data access, integration, and reuse. Therefore, we present the Cancer Treatment-related Single-Cell transcriptome DataBase (scCT-DB, http:\/\/scctdb.ncpsb.org.cn). scCT-DB has comprehensively collected 266 patient-derived paired pre- and post-treatment scRNA-seq datasets processed by a uniform pipeline and with detailed and structured metadata, most of which simultaneously include information on primary\/acquired drug response. scCT-DB includes 6.19 million cells from 1142 original patient samples, 27 major cancer types, 96 therapeutic regimens, and 102 drugs (involving chemotherapy, immunotherapy, hormone therapy, and targeted therapy). scCT-DB also provides 48 dataset pairs with opposite primary response groupings and 41 longitudinal datasets with \u22653 sampling timepoints. Besides data browsing, download, and search, scCT-DB also supports single-dataset analysis (including cell abundance, gene, cell state, and intercellular communication perturbation analyses), dataset comparative and re-combination analyses, providing insights into drug perturbation mechanisms and their heterogeneity in patients, drug resistance mechanisms, and discovery of biomarkers predictive of treatment response, etc.<\/jats:p>","DOI":"10.1093\/nar\/gkaf1065","type":"journal-article","created":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T12:24:13Z","timestamp":1761222253000},"page":"D1616-D1633","source":"Crossref","is-referenced-by-count":3,"title":["scCT-DB, an omnibus for cancer patient-derived paired pre- and post-treatment single-cell transcriptomes to reveal drug perturbation and drug resistance mechanisms"],"prefix":"10.1093","volume":"54","author":[{"given":"Shurui","family":"Ma","sequence":"first","affiliation":[{"name":"School of Basic Medical Sciences, Anhui 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