Identification and functional analysis of long non-coding RNAs in human and mouse early embryos based on single-cell transcriptome data

AbstractAdvances of single-cell technologies allow scrutinizing of heterogeneous cell states, however, analyzing transitions from snap-shot single-cell transcriptome data remains challenging. To investigate cells with transient properties or mixed identities, we present MuTrans, a method based on multiscale reduction technique for the underlying stochastic dynamical systems that prescribes cell-fate transitions. By iteratively unifying transition dynamics across multiple scales, MuTrans constructs the cell-fate dynamical manifold that depicts progression of cell-state transition, and distinguishes meta-stable and transition cells. In addition, MuTrans quantifies the likelihood of all possible transition trajectories between cell states using the coarse-grained transition path theory. Downstream analysis identifies distinct genes that mark the transient states or drive the transitions. Mathematical analysis reveals consistency of the method with the well-established Langevin equation and transition rate theory. Applying MuTrans to datasets collected from five different single-cell experimental platforms and benchmarking with seven existing tools, we show its capability and scalability to robustly unravel complex cell fate dynamics induced by transition cells in systems such as tumor EMT, iPSC differentiation and blood cell differentiation. Overall, our method bridges data-driven and model-based approaches on cell-fate transitions at single-cell resolution.

Download Full-text

Dr.seq2: a quality control and analysis pipeline for parallel single cell transcriptome and epigenome data

10.1101/143271 ◽

2017 ◽

Author(s):

Chengchen Zhao ◽

Sheng’en Hu ◽

Xiao Huo ◽

Yong Zhang

Keyword(s):

Quality Control ◽

Single Cell ◽

Cell Heterogeneity ◽

Transcriptome Data ◽

Analysis Pipeline ◽

Link Type ◽

Data Application ◽

Heterogeneity Analysis ◽

Cell Transcriptome ◽

Single Cell Transcriptome

AbstractAn increasing number of single cell transcriptome and epigenome technologies, including single cell ATAC-seq (scATAC-seq), have been recently developed as powerful tools to analyze the features of many individual cells simultaneously. However, the methods and software were designed for one certain data type and only for single cell transcriptome data. A systematic approach for epigenome data and multiple types of transcriptome data is needed to control data quality and to perform cell-to-cell heterogeneity analysis on these ultra-high-dimensional transcriptome and epigenome datasets. Here we developed Dr.seq2, a Quality Control (QC) and analysis pipeline for multiple types of single cell transcriptome and epigenome data, including scATAC-seq and Drop-ChIP data. Application of this pipeline provides four groups of QC measurements and different analyses, including cell heterogeneity analysis. Dr.seq2 produced reliable results on published single cell transcriptome and epigenome datasets. Overall, Dr.seq2 is a systematic and comprehensive QC and analysis pipeline designed for parallel single cell transcriptome and epigenome data. Dr.seq2 is freely available at: http://www.tongji.edu.cn/~zhanglab/drseq2/ and https://github.com/ChengchenZhao/DrSeq2.

Download Full-text

Single Cell Transcriptome Data Analysis Defines the Heterogeneity of Peripheral Nerve Cells in Homeostasis and Regeneration

Frontiers in Cellular Neuroscience ◽

10.3389/fncel.2021.624826 ◽

2021 ◽

Vol 15 ◽

Author(s):

Bing Chen ◽

Matthew C. Banton ◽

Lolita Singh ◽

David B. Parkinson ◽

Xin-peng Dun

Keyword(s):

Endothelial Cells ◽

Data Analysis ◽

Single Cell ◽

Schwann Cells ◽

Peripheral Nerves ◽

Cell Types ◽

Transcriptome Data ◽

Single Cell Rna Sequencing ◽

Cell Transcriptome ◽

Single Cell Transcriptome

The advances in single-cell RNA sequencing technologies and the development of bioinformatics pipelines enable us to more accurately define the heterogeneity of cell types in a selected tissue. In this report, we re-analyzed recently published single-cell RNA sequencing data sets and provide a rationale to redefine the heterogeneity of cells in both intact and injured mouse peripheral nerves. Our analysis showed that, in both intact and injured peripheral nerves, cells could be functionally classified into four categories: Schwann cells, nerve fibroblasts, immune cells, and cells associated with blood vessels. Nerve fibroblasts could be sub-clustered into epineurial, perineurial, and endoneurial fibroblasts. Identified immune cell clusters include macrophages, mast cells, natural killer cells, T and B lymphocytes as well as an unreported cluster of neutrophils. Cells associated with blood vessels include endothelial cells, vascular smooth muscle cells, and pericytes. We show that endothelial cells in the intact mouse sciatic nerve have three sub-types: epineurial, endoneurial, and lymphatic endothelial cells. Analysis of cell type-specific gene changes revealed that Schwann cells and endoneurial fibroblasts are the two most important cell types promoting peripheral nerve regeneration. Analysis of communication between these cells identified potential signals for early blood vessel regeneration, neutrophil recruitment of macrophages, and macrophages activating Schwann cells. Through this analysis, we also report appropriate marker genes for future single cell transcriptome data analysis to identify cell types in intact and injured peripheral nerves. The findings from our analysis could facilitate a better understanding of cell biology of peripheral nerves in homeostasis, regeneration, and disease.

Download Full-text

singleCellHaystack: Finding surprising genes in 2-dimensional representations of single cell transcriptome data

10.1101/557967 ◽

2019 ◽

Author(s):

Alexis Vandenbon ◽

Diego Diez

Keyword(s):

Single Cell ◽

Expression Patterns ◽

R Package ◽

Biological Knowledge ◽

Transcriptome Data ◽

Sequencing Data ◽

Single Cell Sequencing ◽

Leibler Divergence ◽

Cell Transcriptome ◽

Single Cell Transcriptome

AbstractSummarySingle-cell sequencing data is often visualized in 2-dimensional plots, including t-SNE plots. However, it is not straightforward to extract biological knowledge, such as differentially expressed genes, from these plots. Here we introduce singleCellHaystack, a methodology that addresses this problem. singleCellHaystack uses Kullback-Leibler Divergence to find genes that are expressed in subsets of cells that are non-randomly positioned on a 2D plot. We illustrate the usage of singleCellHaystack through applications on several single-cell datasets. singleCellHaystack is implemented as an R package, and includes additional functions for clustering and visualization of genes with interesting expression patterns.Availability and implementationhttps://github.com/alexisvdb/[email protected]

Download Full-text