Functional heterogeneity of immune defenses in molluscan oysters Crassostrea hongkongensis revealed by high-throughput single-cell transcriptome

2021 ◽  
Author(s):  
Meng Jie ◽  
Guofan Zhang ◽  
Wen-Xiong Wang
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Functional Heterogeneity ◽  
Crassostrea Hongkongensis ◽  
Immune Defenses ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

scholarly journals High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

Cell Reports ◽  
2019 ◽  
Vol 27 (7) ◽  
pp. 2241-2247.e4 ◽  
Author(s):  
Christine N. Shulse ◽  
Benjamin J. Cole ◽  
Doina Ciobanu ◽  
Junyan Lin ◽  
Yuko Yoshinaga ◽  
...  
Keyword(s):  
Single Cell ◽  
Plant Cell ◽  
High Throughput ◽  
Transcriptome Profiling ◽  
Cell Types ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

scholarly journals High-throughput single-cell transcriptome profiling of plant cell types

2018 ◽  
Author(s):  
Christine N. Shulse ◽  
Benjamin J. Cole ◽  
Gina M. Turco ◽  
Yiwen Zhu ◽  
Siobhan M. Brady ◽  
...  
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Transcriptome Profiling ◽  
Cell Types ◽  
Marker Genes ◽  
Single Cell Rna Sequencing ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Heterogeneous Tissues ◽  
Genomic Basis

AbstractSingle-cell transcriptome analysis of heterogeneous tissues can provide high-resolution windows into the genomic basis and spatiotemporal dynamics of developmental processes. Here we demonstrate the feasibility of high-throughput single-cell RNA sequencing of plant tissue using the Drop-seq approach. Profiling of >4,000 individual cells from the Arabidopsis root provides transcriptomes and marker genes for a diversity of cell types and illuminates the gene expression changes that occur across endodermis development.

scholarly journals Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay

2018 ◽  
Author(s):  
Eleni Mimitou ◽  
Anthony Cheng ◽  
Antonino Montalbano ◽  
Stephanie Hao ◽  
Marlon Stoeckius ◽  
...  
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Single Cells ◽  
Surface Markers ◽  
Protein Levels ◽  
Cellular Processes ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Lymphoma Sample

ABSTRACTRapid technological progress in the recent years has allowed the high-throughput interrogation of different types of biomolecules from single cells. Combining several of these readouts into integrated multi-omic assays is essential to comprehensively understand and model cellular processes. Here, we report the development of Expanded CRISPR-compatible Cellular Indexing of Transcriptomes and Epitopes by sequencing (ECCITE-seq) for the high-throughput characterization of at least five modalities of information from each single cell: transcriptome, immune receptor clonotypes, surface markers, sample identity and sgRNAs. We demonstrate the use of ECCITE-seq to directly and efficiently capture sgRNA molecules and measure their effects on gene expression and protein levels, opening the possibility of performing high throughput single cell CRISPR screens with multimodal readout using existing libraries and commonly used vectors. Finally, by utilizing the combined phenotyping of clonotype and cell surface markers in immune cells, we apply ECCITE to study a lymphoma sample to discriminate cells and define molecular signatures of malignant cells within a heterogeneous population.

scholarly journals High throughput error corrected Nanopore single cell transcriptome sequencing

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Kevin Lebrigand ◽  
Virginie Magnone ◽  
Pascal Barbry ◽  
Rainer Waldmann
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Transcriptome Sequencing ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

scholarly journals High throughput, error corrected Nanopore single cell transcriptome sequencing

2019 ◽  
Author(s):  
Kevin Lebrigand ◽  
Virginie Magnone ◽  
Pascal Barbry ◽  
Rainer Waldmann
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Rna Splicing ◽  
Transcriptome Profiling ◽  
Cell Isolation ◽  
Sequence Information ◽  
Isolation System ◽  
Single Cell Isolation ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

ABSTRACTDroplet-based high throughput single cell isolation techniques tremendously boosted the throughput of single cell transcriptome profiling experiments. However, those approaches only allow analysis of one extremity of the transcript after short read sequencing. We introduce an approach that combines Oxford Nanopore sequencing with unique molecular identifiers to obtain error corrected full length sequence information with the 10×Genomics single cell isolation system. This allows to examine differential RNA splicing and RNA editing at a single cell level.

scholarly journals Single cell transcriptome atlas of mouse mammary epithelial cells across development

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Bhupinder Pal ◽  
Yunshun Chen ◽  
Michael J. G. Milevskiy ◽  
François Vaillant ◽  
Lexie Prokopuk ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Single Cell ◽  
Developmental Stages ◽  
Mammary Epithelial Cells ◽  
Expression Profiles ◽  
Single Cells ◽  
Chromatin Accessibility ◽  
Mammary Epithelial ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Abstract Background Heterogeneity within the mouse mammary epithelium and potential lineage relationships have been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary ontogeny, we profiled single cells from nine different developmental stages spanning late embryogenesis, early postnatal, prepuberty, adult, mid-pregnancy, late-pregnancy, and post-involution, as well as the transcriptomes of micro-dissected terminal end buds (TEBs) and subtending ducts during puberty. Methods The single cell transcriptomes of 132,599 mammary epithelial cells from 9 different developmental stages were determined on the 10x Genomics Chromium platform, and integrative analyses were performed to compare specific time points. Results The mammary rudiment at E18.5 closely aligned with the basal lineage, while prepubertal epithelial cells exhibited lineage segregation but to a less differentiated state than their adult counterparts. Comparison of micro-dissected TEBs versus ducts showed that luminal cells within TEBs harbored intermediate expression profiles. Ductal basal cells exhibited increased chromatin accessibility of luminal genes compared to their TEB counterparts suggesting that lineage-specific chromatin is established within the subtending ducts during puberty. An integrative analysis of five stages spanning the pregnancy cycle revealed distinct stage-specific profiles and the presence of cycling basal, mixed-lineage, and 'late' alveolar intermediates in pregnancy. Moreover, a number of intermediates were uncovered along the basal-luminal progenitor cell axis, suggesting a continuum of alveolar-restricted progenitor states. Conclusions This extended single cell transcriptome atlas of mouse mammary epithelial cells provides the most complete coverage for mammary epithelial cells during morphogenesis to date. Together with chromatin accessibility analysis of TEB structures, it represents a valuable framework for understanding developmental decisions within the mouse mammary gland.

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