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

2019 ◽  
Author(s):  
Kevin Lebrigand ◽  
Virginie Magnone ◽  
Pascal Barbry ◽  
Rainer Waldmann

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.

Cell Reports ◽  
2019 ◽  
Vol 27 (7) ◽  
pp. 2241-2247.e4 ◽  
Author(s):  
Christine N. Shulse ◽  
Benjamin J. Cole ◽  
Doina Ciobanu ◽  
Junyan Lin ◽  
Yuko Yoshinaga ◽  
...  

2018 ◽  
Author(s):  
Christine N. Shulse ◽  
Benjamin J. Cole ◽  
Gina M. Turco ◽  
Yiwen Zhu ◽  
Siobhan M. Brady ◽  
...  

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.


2017 ◽  
Vol 525 (12) ◽  
pp. 2735-2781 ◽  
Author(s):  
Lauren A. Laboissonniere ◽  
Gregory M. Martin ◽  
Jillian J. Goetz ◽  
Ran Bi ◽  
Brock Pope ◽  
...  

2020 ◽  
Vol 6 (34) ◽  
pp. eaaz2978 ◽  
Author(s):  
Xiaoying Fan ◽  
Yuanyuan Fu ◽  
Xin Zhou ◽  
Le Sun ◽  
Ming Yang ◽  
...  

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.


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