scholarly journals Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering

2019 ◽  
Author(s):  
Andres F. Vallejo ◽  
James Davies ◽  
Amit Grover ◽  
Ching-Hsuan Tsai ◽  
Robert Jepras ◽  
...  
Keyword(s):  
Dendritic Cell ◽  
Single Cell ◽  
Cellular Systems ◽  
Sequencing Depth ◽  
Powerful Method ◽  
Library Preparation ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Magnitude Sensitivity ◽  
Transcript Identification

AbstractSingle-cell transcriptomics has sensitivity limits that restrict low abundance transcript identification, affects clustering and introduce artefact. Here, we describe Constellation DropSeq (C-DropSeq), a molecular transcriptome filter that delivers two orders of magnitude sensitivity gains by maximising read utility while reducing sequencing depth and costs. The simple and powerful method is broadly compatible with library preparation routines and was demonstrated by identifying and characterizing the activation of rare dendritic cell sub-populations.

scholarly journals Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering

iScience ◽  
2021 ◽  
Vol 24 (3) ◽  
pp. 102147
Author(s):  
Andres F. Vallejo ◽  
James Davies ◽  
Amit Grover ◽  
Ching-Hsuan Tsai ◽  
Robert Jepras ◽  
...  
Keyword(s):  
Single Cell ◽  
Cellular Systems ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

scholarly journals A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle

2020 ◽  
Author(s):  
Karen Davey ◽  
Daniel Wong ◽  
Filip Konopacki ◽  
Eugene Kwa ◽  
Heike Fiegler ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Single Cell ◽  
Regulatory Networks ◽  
Single Cells ◽  
Transcriptome Profiling ◽  
Cost Effective ◽  
Microfluidic System ◽  
Cellular Systems ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

SummarySingle cell transcriptome profiling has emerged as a breakthrough technology for the high-resolution understanding of complex cellular systems. Here we report a flexible, cost-effective and user-friendly droplet-based microfluidics system, called the Nadia Instrument, that can allow 3’ mRNA capture of ∼50,000 single cells or individual nuclei in a single run. The precise pressure-based system demonstrates highly reproducible droplet size, low doublet rates and high mRNA capture efficiencies that compare favorably in the field. Moreover, when combined with the Nadia Innovate, the system can be transformed into an adaptable setup that enables use of different buffers and barcoded bead configurations to facilitate diverse applications. Finally, by 3’ mRNA profiling asynchronous human and mouse cells at different phases of the cell cycle, we demonstrate the system’s ability to readily distinguish distinct cell populations and infer underlying transcriptional regulatory networks. Notably this identified multiple transcription factors that had little or no known link to the cell cycle (e.g. DRAP1, ZKSCAN1 and CEBPZ). In summary, the Nadia platform represents a promising and flexible technology for future transcriptomic studies, and other related applications, at cell resolution.

scholarly journals A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Karen Davey ◽  
Daniel Wong ◽  
Filip Konopacki ◽  
Eugene Kwa ◽  
Tony Ly ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Single Cell ◽  
Regulatory Networks ◽  
Single Cells ◽  
Transcriptome Profiling ◽  
Cost Effective ◽  
Microfluidic System ◽  
Cellular Systems ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractSingle cell transcriptome profiling has emerged as a breakthrough technology for the high-resolution understanding of complex cellular systems. Here we report a flexible, cost-effective and user-friendly droplet-based microfluidics system, called the Nadia Instrument, that can allow 3′ mRNA capture of ~ 50,000 single cells or individual nuclei in a single run. The precise pressure-based system demonstrates highly reproducible droplet size, low doublet rates and high mRNA capture efficiencies that compare favorably in the field. Moreover, when combined with the Nadia Innovate, the system can be transformed into an adaptable setup that enables use of different buffers and barcoded bead configurations to facilitate diverse applications. Finally, by 3′ mRNA profiling asynchronous human and mouse cells at different phases of the cell cycle, we demonstrate the system's ability to readily distinguish distinct cell populations and infer underlying transcriptional regulatory networks. Notably this provided supportive evidence for multiple transcription factors that had little or no known link to the cell cycle (e.g. DRAP1, ZKSCAN1 and CEBPZ). In summary, the Nadia platform represents a promising and flexible technology for future transcriptomic studies, and other related applications, at cell resolution.

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.

scholarly journals Single-Cell Transcriptome Analyses Reveal Signals to Activate Dormant Neural Stem Cells

Cell ◽  
2015 ◽  
Vol 161 (5) ◽  
pp. 1175-1186 ◽  
Author(s):  
Yuping Luo ◽  
Volkan Coskun ◽  
Aibing Liang ◽  
Juehua Yu ◽  
Liming Cheng ◽  
...  
Keyword(s):  
Stem Cells ◽  
Neural Stem Cells ◽  
Single Cell ◽  
Transcriptome Analyses ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome
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