scholarly journals Progress in Single Cell Sequencing Technology

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Qi Cai Ma ◽  
Wen Li Wu ◽  
Na Ye ◽  
Xin Dong Wang ◽  
Ping Yan ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Basic Unit ◽  
Sequencing Technology ◽  
Single Cell Sequencing ◽  
Physiological Diversity ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Whole Transcriptome ◽  
Life Structure

Cells are the basic unit of life structure and life activities. Because of the complex micro-environment of cells, the content of components that play a key role is relatively small, so single-cell analysis is extremely challenging. In recent years, single-cell sequencing technology has been developed and matured. Single-cell sequencing can reveal the composition and physiological diversity of cells, and the existing single-cell separation technology, single-cell whole genome amplification technology, single The principles and applications of cell whole transcriptome amplification technology and single cell transcriptome sequencing are summarized and summarized.

scholarly journals Single-cell transcriptome analysis reveals cell lineage specification in temporal-spatial patterns in human cortical development

2020 ◽  
Vol 6 (34) ◽  
pp. eaaz2978 ◽  
Author(s):  
Xiaoying Fan ◽  
Yuanyuan Fu ◽  
Xin Zhou ◽  
Le Sun ◽  
Ming Yang ◽  
...  
Keyword(s):  
Single Cell ◽  
Neural Progenitor Cells ◽  
Neuronal Development ◽  
Single Cell Analysis ◽  
Cortical Development ◽  
Cell Lineage ◽  
Transcriptome Profiling ◽  
Developmental Trajectory ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Neurogenesis processes differ in different areas of the cortex in many species, including humans. Here, we performed single-cell transcriptome profiling of the four cortical lobes and pons during human embryonic and fetal development. We identified distinct subtypes of neural progenitor cells (NPCs) and their molecular signatures, including a group of previously unidentified transient NPCs. We specified the neurogenesis path and molecular regulations of the human deep-layer, upper-layer, and mature neurons. Neurons showed clear spatial and temporal distinctions, while glial cells of different origins showed development patterns similar to those of mice, and we captured the developmental trajectory of oligodendrocyte lineage cells until the human mid-fetal stage. Additionally, we verified region-specific characteristics of neurons in the cortex, including their distinct electrophysiological features. With systematic single-cell analysis, we decoded human neuronal development in temporal and spatial dimensions from GW7 to GW28, offering deeper insights into the molecular regulations underlying human neurogenesis and cortical development.

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

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]

scholarly journals Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility

2019 ◽  
Author(s):  
Qiao Rui Xing ◽  
Chadi EL Farran ◽  
Yao Yi ◽  
Tushar Warrier ◽  
Pradeep Gautam ◽  
...  
Keyword(s):  
Single Cell ◽  
Target Genes ◽  
Chromatin Accessibility ◽  
Human Cell Lines ◽  
Microfluidic Chips ◽  
Primary Cells ◽  
Parallel Sequencing ◽  
Single Cell Sequencing ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

SUMMARYWe developed ASTAR-Seq (Assay for Single-cell Transcriptome and Accessibility Regions) integrated with automated microfluidic chips, which allows for parallel sequencing of transcriptome and chromatin accessibility within the same single-cell. Using ASTAR-Seq, we profiled 192 mESCs cultured in serum+LIF and 2i medium, 424 human cell lines including BJ, K562, JK1, and Jurkat, and 480 primary cells undergoing erythroblast differentiation. Integrative analysis using Coupled NMF identified the distinct sub-populations and uncovered sets of regulatory regions and the respective target genes determining their distinctions. Analysis of epigenetic regulomes further unravelled the key transcription factors responsible for the heterogeneity observed.

scholarly journals Single-cell analysis of patient-derived PDAC organoids reveals cell state heterogeneity and a conserved developmental hierarchy

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Teresa G. Krieger ◽  
Solange Le Blanc ◽  
Julia Jabs ◽  
Foo Wei Ten ◽  
Naveed Ishaque ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Ductal Adenocarcinoma ◽  
Primary Tumors ◽  
Cell State ◽  
Tumor Subtypes ◽  
Functional Hierarchy ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractPancreatic ductal adenocarcinoma (PDAC) is projected to be the second leading cause of cancer mortality by 2030. Bulk transcriptomic analyses have distinguished ‘classical’ from ‘basal-like’ tumors with more aggressive clinical behavior. We derive PDAC organoids from 18 primary tumors and two matched liver metastases, and show that ‘classical’ and ‘basal-like’ cells coexist in individual organoids. By single-cell transcriptome analysis of PDAC organoids and primary PDAC, we identify distinct tumor cell states shared across patients, including a cycling progenitor cell state and a differentiated secretory state. Cell states are connected by a differentiation hierarchy, with ‘classical’ cells concentrated at the endpoint. In an imaging-based drug screen, expression of ‘classical’ subtype genes correlates with better drug response. Our results thus uncover a functional hierarchy of PDAC cell states linked to transcriptional tumor subtypes, and support the use of PDAC organoids as a clinically relevant model for in vitro studies of tumor heterogeneity.

scholarly journals Single-cell sequencing reveals clonally expanded plasma cells during chronic viral infection produce virus-specific and cross-reactive antibodies

2021 ◽  
Author(s):  
Daniel Neumeier ◽  
Alessandro Pedrioli ◽  
Alessandro Genovese ◽  
Ioana Sandu ◽  
Roy Ehling ◽  
...  
Keyword(s):  
Viral Infection ◽  
Single Cell ◽  
Plasma Cell ◽  
Plasma Cells ◽  
Clonal Expansion ◽  
Chronic Viral Infection ◽  
Antibody Repertoire ◽  
Single Cell Sequencing ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractPlasma cells and their secreted antibodies play a central role in the long-term protection against chronic viral infection. However, due to experimental limitations, a comprehensive description of linked genotypic, phenotypic, and antibody repertoire features of plasma cells (gene expression, clonal frequency, virus specificity, and affinity) has been challenging to obtain. To address this, we performed single-cell transcriptome and antibody repertoire sequencing of the murine bone marrow plasma cell population following chronic lymphocytic choriomeningitis virus infection. Our single-cell sequencing approach recovered full-length and paired heavy and light chain sequence information for thousands of plasma cells and enabled us to perform recombinant antibody expression and specificity screening. Antibody repertoire analysis revealed that, relative to protein immunization, chronic infection led to increased levels of clonal expansion, class-switching, and somatic variants. Furthermore, antibodies from the highly expanded and class-switched (IgG) plasma cells were found to be specific for multiple viral antigens and a subset of clones exhibited cross-reactivity to non-viral- and auto-antigens. Integrating single-cell transcriptome data with antibody specificity suggested that plasma cell transcriptional phenotype was correlated to viral antigen specificity. Our findings demonstrate that chronic viral infection can induce and sustain plasma cell clonal expansion, combined with significant somatic hypermutation, and can generate cross-reactive antibodies. Graphical abstract.Single-cell sequencing reveals clonally expanded plasma cells during chronic viral infection produce virus-specific and cross-reactive antibodies.

scholarly journals Single cell analysis of spondyloarthritis regulatory T cells identifies distinct synovial gene expression patterns and clonal fates

2021 ◽  
Author(s):  
Davide Simone ◽  
Frank Penkava ◽  
Anna Ridley ◽  
Stephen Nicholas Sansom ◽  
Hussein Mohamed Al-Mossawi ◽  
...  
Keyword(s):  
T Cells ◽  
Regulatory T Cells ◽  
Single Cell ◽  
Cell Fate ◽  
Single Cell Analysis ◽  
Expression Patterns ◽  
Treg Subset ◽  
Inflammatory Site ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Regulatory T cells (Tregs) play an important role in controlling inflammation and limiting autoimmunity, but their phenotypes at inflammatory sites in human disease are poorly understood. We here analyze the single-cell transcriptome of >16,000 Tregs obtained from peripheral blood and synovial fluid of two patients with HLA-B27+ ankylosing spondylitis and three patients with psoriatic arthritis, closely related forms of inflammatory spondyloarthritis. We identify multiple Treg clusters with distinct transcriptomic profiles, including, among others, a regulatory CD8+ subset expressing cytotoxic markers/genes, and a Th17-like RORC+ Treg subset characterized by IL-10 and LAG-3 expression. Synovial Tregs show upregulation of interferon signature and TNF receptor superfamily genes, and marked clonal expansion, consistent with tissue adaptation and antigen contact respectively. Individual synovial Treg clones map to different clusters indicating cell fate divergence. Finally, we demonstrate that LAG-3 directly inhibits IL-12/23 and TNF secretion by patient-derived monocytes, a mechanism with translational potential in SpA. Our detailed characterization of Tregs at an important inflammatory site illustrates the marked specialization of Treg subpopulations.

scholarly journals Barcode identification for single cell genomics

2017 ◽  
Author(s):  
Akshay Tambe ◽  
Lior Pachter
Keyword(s):  
Single Cell ◽  
Dna Barcode ◽  
De Bruijn Graph ◽  
Rna Seq ◽  
Single Cell Genomics ◽  
Single Cell Sequencing ◽  
Processing Step ◽  
De Bruijn ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractSingle-cell sequencing experiments use short DNA barcode ‘tags’ to identify reads that originate from the same cell. In order to recover single-cell information from such experiments, reads must be grouped based on their barcode tag, a crucial processing step that precedes other computations. However, this step can be difficult due to high rates of mismatch and deletion errors that can afflict barcodes. Here we present an approach to identify and error-correct barcodes by traversing the de Bruijn graph of circularized barcode k-mers. This allows for assignment of reads to consensus fingerprints constructed from k-mers, and we show that for single-cell RNA-Seq this improves the recovery of accurate single-cell transcriptome estimates.

scholarly journals Single cell analysis of spondyloarthritis regulatory T cells identifies distinct synovial gene expression patterns and clonal fates

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Davide Simone ◽  
Frank Penkava ◽  
Anna Ridley ◽  
Stephen Sansom ◽  
M. Hussein Al-Mossawi ◽  
...  
Keyword(s):  
T Cells ◽  
Regulatory T Cells ◽  
Single Cell ◽  
Cell Fate ◽  
Single Cell Analysis ◽  
Expression Patterns ◽  
Treg Subset ◽  
Inflammatory Site ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractRegulatory T cells (Tregs) play an important role in controlling inflammation and limiting autoimmunity, but their phenotypes at inflammatory sites in human disease are poorly understood. We here analyze the single-cell transcriptome of >16,000 Tregs obtained from peripheral blood and synovial fluid of two patients with HLA-B27+ ankylosing spondylitis and three patients with psoriatic arthritis, closely related forms of inflammatory spondyloarthritis. We identify multiple Treg clusters with distinct transcriptomic profiles, including, among others, a regulatory CD8+ subset expressing cytotoxic markers/genes, and a Th17-like RORC+ Treg subset characterized by IL-10 and LAG-3 expression. Synovial Tregs show upregulation of interferon signature and TNF receptor superfamily genes, and marked clonal expansion, consistent with tissue adaptation and antigen contact respectively. Individual synovial Treg clones map to different clusters indicating cell fate divergence. Finally, we demonstrate that LAG-3 directly inhibits IL-12/23 and TNF secretion by patient-derived monocytes, a mechanism with translational potential in SpA. Our detailed characterization of Tregs at an important inflammatory site illustrates the marked specialization of Treg subpopulations.

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