Abstract
The rapid development of high-throughput single-cell RNA sequencing technology offers a good opportunity to dissect cell heterogeneity of animals. A large number of organism-wide single-cell ...atlases have been constructed for vertebrates such as
Homo sapiens
,
Macaca fascicularis
,
Mus musculus
and
Danio rerio
. However, an intermediate taxon that links mammals to vertebrates of more ancient origin is still lacking. Here, we construct the first
Xenopus
cell landscape to date, including larval and adult organs. Common cell lineage-specific transcription factors have been identified in vertebrates, including fish, amphibians and mammals. The comparison of larval and adult erythrocytes identifies stage-specific hemoglobin subtypes, as well as a common type of cluster containing both larval and adult hemoglobin, mainly at NF59. In addition, cell lineages originating from all three layers exhibits both antigen processing and presentation during metamorphosis, indicating a common regulatory mechanism during metamorphosis. Overall, our study provides a large-scale resource for research on
Xenopus
metamorphosis and adult organs.
Current single-cell visualisation techniques project high dimensional data into ‘map’ views to identify high-level structures such as cell clusters and trajectories. New tools are needed to allow the ...transversal through the high dimensionality of single-cell data to explore the single-cell local neighbourhood. StarmapVis is a convenient web application displaying an interactive downstream analysis of single-cell expression or spatial transcriptomic data. The concise user interface is powered by modern web browsers to explore the variety of viewing angles unavailable to 2D media. Interactive scatter plots display clustering information, while the trajectory and cross-comparison among different coordinates are displayed in connectivity networks. Automated animation of camera view is a unique feature of our tool. StarmapVis also offers a useful animated transition between two-dimensional spatial omic data to three-dimensional single cell coordinates. The usability of StarmapVis is demonstrated by four data sets, showcasing its practical usability. StarmapVis is available at: https://holab-hku.github.io/starmapVis.
Display omitted
Tumor heterogeneity and its drivers impair tumor progression and cancer therapy. Single‐cell RNA sequencing is used to investigate the heterogeneity of tumor ecosystems. However, most methods of ...scRNA‐seq amplify the termini of polyadenylated transcripts, making it challenging to perform total RNA analysis and somatic mutation analysis.Therefore, a high‐throughput and high‐sensitivity method called snHH‐seq is developed, which combines random primers and a preindex strategy in the droplet microfluidic platform. This innovative method allows for the detection of total RNA in single nuclei from clinically frozen samples. A robust pipeline to facilitate the analysis of full‐length RNA‐seq data is also established. snHH‐seq is applied to more than 730 000 single nuclei from 32 patients with various tumor types. The pan‐cancer study enables it to comprehensively profile data on the tumor transcriptome, including expression levels, mutations, splicing patterns, clone dynamics, etc. New malignant cell subclusters and exploring their specific function across cancers are identified. Furthermore, the malignant status of epithelial cells is investigated among different cancer types with respect to mutation and splicing patterns. The ability to detect full‐length RNA at the single‐nucleus level provides a powerful tool for studying complex biological systems and has broad implications for understanding tumor pathology.
In this study, snHH‐seq, a high‐throughput, and high‐sensitivity snRNA‐seq method, is applied to pan‐cancer samples from 32 patients, comprising > 700 000 nuclei from various cancer types. The comprehensive analysis of gene expression, somatic mutations, splicing patterns, and clonal behavior shows broad implications for understanding tumor pathology.
Abstract
Motivation
Scalable clustering algorithms are needed to analyze millions of cells in single cell RNA-seq (scRNA-seq) data.
Results
Here, we present an open source python package called ...FlowGrid that can integrate into the Scanpy workflow to perform clustering on very large scRNA-seq datasets. FlowGrid implements a fast density-based clustering algorithm originally designed for flow cytometry data analysis. We introduce a new automated parameter tuning procedure, and show that FlowGrid can achieve comparable clustering accuracy as state-of-the-art clustering algorithms but at a substantially reduced run time for very large single cell RNA-seq datasets. For example, FlowGrid can complete a one-hour clustering task for one million cells in about five min.
Availability and implementation
https://github.com/holab-hku/FlowGrid.
Supplementary information
Supplementary data are available at Bioinformatics online.
Individual cells are basic units of life. Despite extensive efforts to characterize the cellular heterogeneity of different organisms, cross-species comparisons of landscape dynamics have not been ...achieved. Here, we applied single-cell RNA sequencing (scRNA-seq) to map organism-level cell landscapes at multiple life stages for mice, zebrafish and Drosophila. By integrating the comprehensive dataset of > 2.6 million single cells, we constructed a cross-species cell landscape and identified signatures and common pathways that changed throughout the life span. We identified structural inflammation and mitochondrial dysfunction as the most common hallmarks of organism aging, and found that pharmacological activation of mitochondrial metabolism alleviated aging phenotypes in mice. The cross-species cell landscape with other published datasets were stored in an integrated online portal-Cell Landscape. Our work provides a valuable resource for studying lineage development, maturation and aging.
Electrical Impedance Tomography has been recently applied to image fast neural activity in the somatosensory cerebral cortex. This non-invasive imaging modality has the unique advantage of high ...spatial-temporal resolution in millimeters over milliseconds. This work was designed to test an existing 32-channel EIT system, a modified UCL ScouseTom, and to discuss the feasibility of imaging neural activity in retinal tissue through computer simulation. The finite element method was used to model a retinal slice with a realistic conductivity-depth profile of the macaque eye. The conductivity perturbation was simulated in five different layers of the model. 5μV RMS white noise was added to boundary voltages. Simulation results showed that it is feasible to apply EIT in retinal tissue but the injection current is near threshold of unwanted phosphenes induction. Therefore the suggested future work are validating threshold current through animal experiments, developing electrodes with low contact impedance and mitigating noise through averaging.
Shotgun metagenomics has enabled the discovery of antibiotic resistance genes (ARGs). Although there have been numerous studies benchmarking the bioinformatics methods for shotgun metagenomic data ...analysis, there has not yet been a study that systematically evaluates the performance of different experimental protocols on metagenomic species profiling and ARG detection. In this study, we generated 35 whole genome shotgun metagenomic sequencing data sets for five samples (three human stool and two microbial standard) using seven experimental protocols (KAPA or Flex kits at 50ng, 10ng, or 5ng input amounts; XT kit at 1ng input amount). Using this comprehensive resource, we evaluated the seven protocols in terms of robust detection of ARGs and microbial abundance estimation at various sequencing depths. We found that the data generated by the seven protocols are largely similar. The inter-protocol variability is significantly smaller than the variability between samples or sequencing depths. We found that a sequencing depth of more than 30M is suitable for human stool samples. A higher input amount (50ng) is generally favorable for the KAPA and Flex kits. This systematic benchmarking study sheds light on the impact of sequencing depth, experimental protocol, and DNA input amount on ARG detection in human stool samples.
PDF