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Table S19 from Integrative Single-Cell Analysis Reveals Transcriptional and Epigenetic Regulatory Features of Clear Cell Renal Cell Carcinoma

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posted on 2023-03-31, 06:00 authored by Zhenyuan Yu, Yufang Lv, Cheng Su, Wenhao Lu, RuiRui Zhang, Jiaping Li, Bingqian Guo, Haibiao Yan, Deyun Liu, Zhanbin Yang, Hua Mi, Linjian Mo, Yi Guo, Wenyu Feng, Haotian Xu, Wenyi Peng, Jiwen Cheng, Aruo Nan, Zengnan Mo

qPCR results of the expression of 4 deferent lncRNA in cytoplasm and nucleus. Three PCR by-wells were prepared for each sample.

Funding

National Natural Science Foundation of China (NSFC)

National Key Research and Development Program of China (NKPs)

Major project of Guangxi Innovation Driven

Guangxi Key Research and Development Program (广西科技厅重点研发项目)

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ARTICLE ABSTRACT

Clear cell renal cell carcinoma (ccRCC) frequently features a high level of tumor heterogeneity. Elucidating the chromatin landscape of ccRCC at the single-cell level could provide a deeper understanding of the functional states and regulatory dynamics underlying the disease. Here, we performed single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) on 19 ccRCC samples, and whole-exome sequencing was used to understand the heterogeneity between individuals. Single-cell transcriptome and chromatin accessibility maps of ccRCC were constructed to reveal the regulatory characteristics of different tumor cell subtypes in ccRCC. Two long noncoding RNAs (RP11-661C8.2 and CTB-164N12.1) were identified that promoted the invasion and migration of ccRCC, which was validated with in vitro experiments. Taken together, this study comprehensively characterized the gene expression and DNA regulation landscape of ccRCC, which could provide new insights into the biology and treatment of ccRCC. A comprehensive analysis of gene expression and DNA regulation in ccRCC using scATAC-seq and scRNA-seq reveals the DNA regulatory programs of ccRCC at the single-cell level.

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