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Identification of TIMPs signatures in Randall plaque from single-cell RNA sequencing (scRNA-Seq) analysis
BackgroundTissue inhibitors of metalloproteinases (TIMPs) are essential for controlling the dynamics of the extracellular matrix. Although their role...
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scSNPdemux: a sensitive demultiplexing pipeline using single nucleotide polymorphisms for improved pooled single-cell RNA sequencing analysis
BackgroundHere we present scSNPdemux, a sample demultiplexing pipeline for single-cell RNA sequencing data using natural genetic variations in...
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Comparison of transformations for single-cell RNA-seq data
The count table, a numeric matrix of genes × cells, is the basic input data structure in the analysis of single-cell RNA-sequencing data. A common...
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RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations
Single-cell RNA-seq analysis coupled with CRISPR-based perturbation has enabled the inference of gene regulatory networks with causal relationships....
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Single Cell RNA-Seq: Cell Isolation and Data Analysis
Single-cell RNA-sequencing technologies have revolutionized the way that researchers can interrogate cellular relationships and the level of detail...
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Plant Nuclei Isolation for Single-Nucleus RNA Sequencing
Transcriptome profiling has been significantly hampered by the heterogeneity among individual cells within a tissue or an organ. Recent advances in...
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High-throughput total RNA sequencing in single cells using VASA-seq
Most methods for single-cell transcriptome sequencing amplify the termini of polyadenylated transcripts, capturing only a small fraction of the total...
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Single-cell RNA-seq integrated with multi-omics reveals SERPINE2 as a target for metastasis in advanced renal cell carcinoma
Tumor growth, metastasis and therapeutic response are believed to be regulated by the tumor and its microenvironment (TME) in advanced renal cell...
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Complex Analysis of Single-Cell RNA Sequencing Data
AbstractSingle-cell RNA sequencing (scRNA-seq) is a revolutionary tool for studying the physiology of normal and pathologically altered tissues. This...
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Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN
Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of...
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Comprehensive analysis of single-cell RNA-seq and bulk RNA-seq revealed the heterogeneity and convergence of the immune microenvironment in renal cell carcinoma
Substantial progress has been made in cancer biology and treatment in recent years, but the clinical outcome of patients with renal cell carcinoma...
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Isolation of Murine Articular Chondrocytes for Single-Cell RNA or Bulk RNA Sequencing Analysis
Single-cell RNA sequencing (scRNA-seq) is highly dependent on cellular composition of a tissue of interest. For soft tissues, isolation of individual...
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Detection of cell markers from single cell RNA-seq with sc2marker
BackgroundSingle-cell RNA sequencing (scRNA-seq) allows the detection of rare cell types in complex tissues. The detection of markers for rare cell...
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Probe-based bacterial single-cell RNA sequencing predicts toxin regulation
Clonal bacterial populations rely on transcriptional variation across individual cells to produce specialized states that increase fitness....
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Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis
Ulcerative colitis (UC) is a significant inflammatory bowel disease caused by an abnormal immune response to gut microbes. However, there are still...
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eSVD-DE: cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings
BackgroundSingle-cell RNA-sequencing (scRNA) datasets are becoming increasingly popular in clinical and cohort studies, but there is a lack of...
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Beyond benchmarking and towards predictive models of dataset-specific single-cell RNA-seq pipeline performance
BackgroundThe advent of single-cell RNA-sequencing (scRNA-seq) has driven significant computational methods development for all steps in the...
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CRISPR/Cas9-based depletion of 16S ribosomal RNA improves library complexity of single-cell RNA-sequencing in planarians
BackgroundSingle-cell RNA-sequencing (scRNA-seq) relies on PCR amplification to retrieve information from vanishingly small amounts of starting...
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Using “Galaxy-rCASC”: A Public Galaxy Instance for Single-Cell RNA-Seq Data Analysis
rCASC is a modular workflow providing an integrated environment for single-cell RNA-seq (scRNA-Seq) data analysis exploiting Docker containers to...
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Profiling Transcriptional Heterogeneity with Seq-Well S3: A Low-Cost, Portable, High-Fidelity Platform for Massively Parallel Single-Cell RNA-Seq
Seq-Well is a high-throughput, picowell-based single-cell RNA-seq technology that can be used to simultaneously profile the transcriptomes of...