BERLIN: Basic Explorer for single-cell RNAseq analysis and cell Lineage Determination
BERLIN: Basic Explorer for single-cell RNAseq analysis and cell Lineage Determination
Abstract Single-cell RNA sequencing has revolutionized the study of immuno-oncology, cancer biology, and developmental biology by enabling the joint characterization of gene expression and cellular heterogeneity in a single platform. As of July 2023, the Gene Expression Omnibus now contains over 4000 published single-cell data sets, providing an invaluable opportunity for reanalysis to identify new cell types or cellular states as well as their defining transcriptional programs. To facilitate the reprocessing of these public datasets, we have devised a single-cell RNA sequencing analysis framework for data retrieval, quality control, expression normalization, dimension reduction, cell clustering, and data integration. Additionally, we have developed a Shiny App visualization platform that enables the exploration of gene expression, cell type annotations, and cell lineages through a user interface. We performed a re-analysis of single-cell RNAseq data generated from acute myeloid leukemia and tumor-reactive lymphocytes and found our pipeline to faithfully recapitulated the cell type assignment as well as expected lineage trajectories. Altogether, we present BERLIN, a single-cell RNAseq analysis pipeline that facilitates the integration and public dissemination of results from the reanalysis.
Conejo-Garcia Jose、Avram Dorina、Yu Xiaoqing、Chen Zhihua、Nobles Gabrielle、Nugyen Thanh N、Shaw Timothy、Zelenka Tomas、Chen Y Ann、Obermayer Alyssa、Yang Ching Yao
Department of Immunology, Duke School of Medicine Duke Cancer Institute, Duke School of MedicineImmunology Department, H Lee Moffitt Cancer CenterBiostatistics and Bioinformatics Department, H Lee Moffitt Cancer CenterBiostatistics and Bioinformatics Department, H Lee Moffitt Cancer CenterBiostatistics and Bioinformatics Department, H Lee Moffitt Cancer Center||Morsani College of Medicine, University of South FloridaBiostatistics and Bioinformatics Department, H Lee Moffitt Cancer CenterBiostatistics and Bioinformatics Department, H Lee Moffitt Cancer CenterImmunology Department, H Lee Moffitt Cancer CenterBiostatistics and Bioinformatics Department, H Lee Moffitt Cancer CenterBiostatistics and Bioinformatics Department, H Lee Moffitt Cancer CenterMorsani College of Medicine, University of South Florida
生物科学研究方法、生物科学研究技术基础医学肿瘤学
Conejo-Garcia Jose,Avram Dorina,Yu Xiaoqing,Chen Zhihua,Nobles Gabrielle,Nugyen Thanh N,Shaw Timothy,Zelenka Tomas,Chen Y Ann,Obermayer Alyssa,Yang Ching Yao.BERLIN: Basic Explorer for single-cell RNAseq analysis and cell Lineage Determination[EB/OL].(2025-03-28)[2025-08-03].https://www.biorxiv.org/content/10.1101/2023.07.13.548919.点此复制
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