Cell & Bioscience(2024) mRNA-based precision targeting of neoantigens and tumor-associated antigens in malignant brain tumors Vrunda Trivedi Changlin Yang Duane A. Mitchell Genome Medicine(2024) scBubbletree: computational approach for visualization of single cell RNA-seq data ...
We performed single-cell RNA-sequencing (scRNA-seq) analysis using Fluidigm C1 systems to characterize human lung cancer transcriptomes at single-cell resolution. Validation of scRNA-seq differentially expressed genes (DEGs) through quantitative real time-polymerase chain reaction (qRT-PCR) found a ...
Single-cell RNA sequencing (scRNA-seq) is one approach to dissect the heterogeneity of complex biological systems (Chung et al., 2017; Darmanis et al., 2017; Tirosh et al., 2016). There is currently a paucity of single-cell studies that sample metastatic malignancies and prior scRNA-seq ...
We analyzed two distinct single-cell RNA sequencing datasets of lung cancer metastasis to analyze the evolutionary trajectory of brain metastatic tumors. In addition, a systematic comparison of cell-cell interaction between tumor cells and lymphocytes was conducted within primary and brain metastatic ...
We allocate a single CPU and 100 GB RAM in the institutional high-performance scientific computing environment. The local PC is a MacBook Pro with 2.3 GHz Quad-Core Intel Core i7 processor, 16 GB RAM). Step-by-step method details Processing the single-cell RNA-seq data Timing: ∼ 4 h...
Chicken lung isan important target organ of avian influenza virus (AIV) infection, and different pathogenic virus strains lead to opposite prognosis. Using a single-cell RNA sequencing (scRNA-seq) assay, we systematically and sequentially analyzed the tranome of 16 cell types (19 clusters) in the...
Cell-type composition analysis usingscCODA Association of single cells with phenotypes from bulk RNA-seq datasets withScissor Cell2cell communication based on differential gene expression and theCellphoneDB database. For reproducibility issues or any other requests regarding single-cell data analysis, plea...
Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles1–9, it has been difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell
Single-cell RNA-sequencing (scRNA-seq) has been recently used for the profiling of tumor microenvironments7,8. This technology allows massively parallel characterization of thousands of cells at the transcriptome level. Previous scRNA-seq studies related to lung cancer have been limited to early stage...
We provide a rich resource of 186,477 individual immune cells from 48 samples of four treatment-naive and eight neoadjuvant chemoimmunotherapy treated IIIA NSCLC patients (responders versus non-responders) by single-cell RNA-seq and TCR-seq. We observed the synergistic increase of B cells and ...