Single-cell RNA sequencing provides new insights into the interaction between astrocytes and neurons after spinal cord injury in mice by Zhi Tang, Hengyang Lu, Xiao Yang, Mao Wu, Junfeng Yang, Shaoshuo Li, Heng Liu, Junkang Zhou, Bin Tang, Xinyao Du, Fei Xu, Yang Shao, Jianwei Wang

“…Methods and results: In this study, single-cell RNA sequencing (scRNA-seq) was used to analyze the transcriptome data of acute, subacute and intermediate stages of SCI in mice as well as normal tissues. …”
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Development of a prognostic model based on four genes related to exhausted CD8+ T cell in triple-negative breast cancer patients: a comprehensive analysis integrating scRNA-seq and... by Yulin Shi, Yang Yu, Jiahan Zhao, Linan Huang, Qingyang Wang, Qi Sun, Lijuan Liu, Changgang Sun

“…Initially, 398 CD8+ Tex-related genes were screened utilizing single-cell RNA sequencing (scRNA-seq) data from TNBC patients. …”
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Bulk- and single cell-RNA sequencing reveal KIF20A as a key driver of hepatocellular carcinoma progression and immune evasion by Zhixiong Su, Zhixiong Su, Yaqi Zhong, Yufang He, Lijie You, Fuli Xin, Fuli Xin, Lei Wang, Zhihua Liu

“…IntroductionKinesin family member 20A (KIF20A) is essential for cell proliferation and is implicated in promoting tumor progression, but its role in hepatocellular carcinoma (HCC) remains poorly studied.MethodsThrough the analysis of bulk RNA-sequencing (bulk RNA-seq) and single-cell RNA sequencing (scRNA-seq) data, the expression of KIF20A and its relationship with diagnosis, prognosis, and the immune microenvironment were examined. …”
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Identification of Genetic Variants Based on Single Nucleotide Polymorphisms and Insertion-Deletion Events in TLR8, IRF10b, and GAPDH Genes Related to the Immune System in Rainbow T... by Najmeh Fazeli Moghadam, Ghodrat Rahimi Miyanji, Ayoub Farhadi, Ardeshir Nejati Jawarami, Elham Younesi Melardi

“…Some variants based on single nucleotide polymorphisms (SNPs), including synonymous, non-synonymous, and non-coding, as well as insertion-deletion (InDel) events resulting in RNA sequencing data, can be used as a desirable genetic marker in genetic differentiation analysis, especially in investigating allele-specific expression. …”
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Cancer stem cells and tumor-associated macrophages as mates in tumor progression: mechanisms of crosstalk and advanced bioinformatic tools to dissect their phenotypes and interacti... by Francesco Verona, Sebastiano Di Bella, Roberto Schirano, Camilla Manfredi, Francesca Angeloro, Giulia Bozzari, Matilde Todaro, Matilde Todaro, Giuseppe Giannini, Giuseppe Giannini, Giorgio Stassi, Veronica Veschi

“…Nowadays, the integration of biological and computational data obtained by cutting-edge technologies (single-cell RNA sequencing, spatial transcriptomics, trajectory analysis) has significantly improved the comprehension of the biunivocal multicellular dialogue, providing a comprehensive view of the heterogeneity and dynamics of CSCs, and uncovering alternative mechanisms of immune evasion and therapeutic resistance. …”
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Deciphering the regulatory programs of RNA binding proteins in rheumatoid arthritis through single-cell transcriptome analysis by Hongbin Luo, Qunya Zheng, Youzheng Zhou, Weipeng Lai, Nanwen Zhang, Peng Chen

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Expression of innate immunity genes in human hematopoietic stem/progenitor cells – single cell RNA-seq analysis by Justyna Jarczak, Kannathasan Thetchinamoorthy, Diana Wierzbicka, Kamila Bujko, Mariusz Z. Ratajczak, Mariusz Z. Ratajczak, Magdalena Kucia

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Identification and multi-omics analysis of essential coding and long non-coding genes in colorectal cancer by Yanguo Li, Zixing Meng, Chengjiang Fan, Hao Rong, Yang Xi, Qi Liao

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Borreliosis and doxycycline treatment disrupt gut microbiota and immune responses in nonhuman primates by Ethan G. Napier, Isaac R. Cinco, Sheridan B. Wagner, Ethan V. Stuart, Qi Qiao, Joshua Taylor, Brian Stevenson, Ilhem Messaoudi

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Differential Response to Cisplatin between Co-cultured Cells and Pure Cultured Cells Based on Single-cell RNA Sequencing of Three-dimensional-cultured Breast Cancer Cells by Shuqing Yang, Peixian Chen, Xiaofan Mao, KaiRong Lin, Wei Li, Tiancheng He, Huiqi Huang, AiGuo Wu, Wei Luo, Guolin Ye, Guangyu Yao, Dan Zhou

“…Cisplatin was applied at a concentration of 1.25 μg/mL, and the cells were harvested after 2 days and subjected to scRNA-seq. Data were analyzed using a single-cell RNA sequencing data analysis pipeline with R language. …”
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Think twice: how single-cell suspensions from solid tissues for single-cell transcriptomics are well prepared by Meng-Meng Qu, Yan-Mei Jiao, Haijuan Wang

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Comparative transcriptome analysis of PBMCs in cats diagnosed with and recovered from FIPV by Ju Young Lee, Hyeong Ryeol Cho, Hong-Geun Oh, Jeong Ho Hwang

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Single-cell perspective on the Monocyte-to-HDL cholesterol ratio as a metastasis biomarker in papillary thyroid cancer by Zhi-kun Ning, Hao Yi, Tingting Yang, Jiang Liu, Shanshan Su, Ting He, Haoyu Huang, Minghao Xie, Hui Li, Ying Tang, Xiaoping Zhu, Xiang Min

“…Single-cell RNA sequencing (scRNA-seq) data from the GSE191288 and GSE193581 datasets were integrated to analyze various single-cell infiltration in PTC. …”
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Revolutionizing the treatment of intervertebral disc degeneration: an approach based on molecular typing by Shaofeng Chen, Wei Zhang, Yifan Liu, Runzhi Huang, Xiaoyi Zhou, Xianzhao Wei

“…Methods Chondrocyte differentiation and prognosis-related genes were extracted from single-cell RNA sequencing and multi-omics data in the Gene Expression Omnibus (GEO) database through chondrocyte trajectory analysis and non-parametric tests. …”
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Exosome-related genes influence the progression of stroke through neuroinflammatory responses by Boyan Zhao, Boyan Zhao, Jianing Wu, Mingyang Han, Xuan Rong, Jin Jin, Shiya Liu, Cheng Zhang, Ruotian Zhang, Xin Chen, Fei Peng, Xingli Dong, Shiguang Zhao, Shiguang Zhao

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Single-cell transcriptomics link gene expression signatures to clinicopathological features of gonadotroph and lactotroph PitNET by T. Elise Potthoff, Carolin Walter, Daniela Jeising, Daniel Münter, Archana Verma, Eric Suero Molina, Walter Stummer, Martin Dugas, Wolfgang Hartmann, Matthias Dottermusch, Lea Altendorf, Ulrich Schüller, Sophia Scheuermann, Christian Seitz, Thomas K. Albert, Kornelius Kerl

“…Methods We performed differential expression analysis as well as gene expression program identification based on single-cell RNA sequencing to comparatively characterize the transcriptome of seven gonadotroph and three lactotroph PitNET and correlate it with clinical features using bulk RNA-seq data from an independent cohort of 134 PitNET. …”
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TNFRSF12A expression in stomach adenocarcinoma and its preliminary role in predicting immunotherapy response by Lin-De Sun, Lin-Lin Zhang, Zheng Wan, Xiao-Dong Yang, Jing Yao, Ze-Long Yang, Lin Liu, Jun-Yan Liu

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Multi-omics analysis reveals glutathione metabolism-related immune suppression and constructs a prognostic model in lung adenocarcinoma by Yuxiang Chi, Yuxiang Chi, Guoyuan Ma, Qiang Liu, Qiang Liu, Yunzhi Xiang, Yunzhi Xiang, Defeng Liu, Jiajun Du, Jiajun Du

“…We incorporated single-cell RNA sequencing data from LUAD to compare transcription factor activity, cell communication networks, and CD8+ T cell subset distributions across distinct GSH metabolic groups, followed by pseudotime analysis. …”
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Single-cell transcriptome analysis identifies a novel tumor-associated macrophage subtype predicting better prognosis in pancreatic ductal adenocarcinoma by Xiaonan Wang, Dongyi Li, Bo Zhu, Zichun Hua, Zichun Hua, Zichun Hua, Zichun Hua

“…An in-depth understanding of TAMs is helpful to develop new strategies for immunotherapy.MethodsA large number of single-cell RNA sequencing data and bulk RNA sequencing data of PDAC were collected for systematic bioinformatics analysis. …”
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Mitochondrial DNA variant detection in over 6,500 rare disease families by the systematic analysis of exome and genome sequencing data resolves undiagnosed cases by Sarah L. Stenton, Kristen Laricchia, Nicole J. Lake, Sushma Chaluvadi, Vijay Ganesh, Stephanie DiTroia, Ikeoluwa Osei-Owusu, Lynn Pais, Emily O’Heir, Christina Austin-Tse, Melanie O’Leary, Mayada Abu Shanap, Chelsea Barrows, Seth Berger, Carsten G. Bönnemann, Kinga M. Bujakowska, Dean R. Campagna, Alison G. Compton, Sandra Donkervoort, Mark D. Fleming, Lyndon Gallacher, Joseph G. Gleeson, Goknur Haliloglu, Eric A. Pierce, Emily M. Place, Vijay G. Sankaran, Akiko Shimamura, Zornitza Stark, Tiong Yang Tan, David R. Thorburn, Susan M. White, Maha S. Zaki, Eric Vilain, Monkol Lek, Heidi L. Rehm, Anne O’Donnell-Luria

“…Here, we analyzed a cohort of 6,660 rare disease families (5,625 genetically undiagnosed [84%]) from the Genomics Research to Elucidate the Genetics of Rare diseases (GREGoR) Consortium, as well as other rare disease cohorts. Using dedicated pipelines to address the technical challenges posed by the mtDNA—circular genome, variant heteroplasmy, and nuclear misalignment—we called single nucleotide variants, small insertions/deletions, and large mtDNA deletions from exome and/or genome sequencing data, in addition to RNA sequencing data when available. …”
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