20 papers · ranked by Valyu relevance
Dragomirka Jovic, Xue Liang, Hua Zeng, Lin Lin + 2 more
'Yonglun Luo'] Title: Abstract Single-cell RNA sequencing (scRNA-seq) technology has become the state-of-the-art approach for unravelling the heterogeneity and complexity of RNA transcripts within individual cells, as well as revealing the composition of different cell types and functions within highly organized…
Ziye Xu, Tianyu Zhang, Hongyu Chen, Yuyi Zhu + 19 more
'Shunji Zhang' 'Jiaye Chen' 'Haide Chen' 'Lili Yang' 'Weiqin Jiang' 'Shengyu Ni' 'Fangru Lu' 'Zhaolun Wang' 'Hao Yang' 'Ling Dong' 'Feng Chen' 'Hong Zhang' 'Yu Chen' 'Jiong Liu' 'Dandan Zhang' 'Longjiang Fan' 'Guoji Guo' 'Yongcheng Wang'] Formalin-fixed paraffin-embedded (FFPE) tissues constitute a vast and valuable…
Tamer Butto, Kanak Mungikar, Peter Baumann, Jennifer Winter + 3 more
'Beat Lutz' 'Susanne Gerber' 'David Qian'] In the last decade, we have witnessed an upsurge in nuclei-based studies, particularly coupled with next-generation sequencing. Such studies aim at understanding the molecular states that exist in heterogeneous cell populations by applying increasingly more affordable…
Hattie Chung, Alexandre Melnikov, Cristin McCabe, Eugene Drokhlyansky + 8 more
Profiling cellular heterogeneity in formalin-fixed paraffin-embedded (FFPE) tissues is key to characterizing clinical specimens for biomarkers, therapeutic targets, and drug responses. Here, we optimize methods for isolating intact nuclei and single nucleus RNA-Seq from FFPE tissues in the mouse brain, and demonstrate…
Sathiya N. Manivannan, Vidu Garg
Single-cell transcriptomic analyses permit a high-resolution investigation of biological processes at the individual cell level. Single-cell transcriptomics technologies such as Drop-seq, Smart-seq, MARS-seq, sci-RNA-seq, and CELL-seq produce large volumes of data in the form of sequence reads. In general, the…
Mahmoud N. Abdelmoez, Kei Iida, Yusuke Oguchi, Hidekazu Nishikii + 5 more
'Ryuji Yokokawa' 'Hidetoshi Kotera' 'Sotaro Uemura' 'Juan G. Santiago' 'Hirofumi Shintaku'] We report a microfluidic system that physically separates nuclear RNA (nucRNA) and cytoplasmic RNA (cytRNA) from a single cell and enables single-cell integrated nucRNA and cytRNA-sequencing (SINC-seq). SINC-seq constructs two…
Albert Kuo, Kasper D Hansen, Stephanie C Hicks
Title: Summary In complex tissues containing cells that are difficult to dissociate, single-nucleus RNA-sequencing (snRNA-seq) has become the preferred experimental technology over single-cell RNA-sequencing (scRNA-seq) to measure gene expression. To accurately model these data in downstream analyses, previous work has…
Daniele Y. Sunaga-Franze, Jose M. Muino, Caroline Braeuning, Xiaocai Xu + 8 more
Single-cell genomics offers a rich potential for research on plant development and environmental responses. Here, we introduce a generic procedure for plant nuclei isolation and nanowell-based library preparation for short-read sequencing. This plant-nuclei sequencing (PN-seq) method allows for analyzing the…
Albert Kuo, Kasper D. Hansen, Stephanie C. Hicks
In complex tissues containing cells that are difficult to dissociate, single-nucleus RNA-sequencing (snRNA-seq) has become the preferred experimental technology over single-cell RNA-sequencing (scRNA-seq) to measure gene expression. To accurately model these data in downstream analyses, previous work has shown that…
Yanping Long, Zhijian Liu, Jinbu Jia, Weipeng Mo + 6 more
The broad application of large-scale single-cell RNA profiling in plants has been restricted by the prerequisite of protoplasting. We recently found that the Arabidopsis nucleus contains abundant polyadenylated mRNAs, many of which are incompletely spliced. To capture the isoform information, we combined 10x Genomics…
Gyutaek Oh, Baekgyu Choi, Jin, Seyoung + 2 more
Single-nucleus RNA sequencing (snRNA-seq) has significantly advanced our understanding of the disease etiology of neurodegenerative disorders. However, the low quality of specimens derived from postmortem brain tissues, combined with the high variability caused by disease heterogeneity, makes it challenging to…
Ricardo R. Pavan, Fabiola Diniz, Samir El-Dahr, Giovane G. Tortelote
The scale and capability of single-cell and single-nucleus RNA-sequencing technologies are rapidly growing, enabling key discoveries and large-scale cell mapping operations. However, studies directly comparing technical differences between single-cell and single-nucleus RNA sequencing are still lacking. Here, we…
Andrew Jiang, Klaus Lehnert, Suzanne J. Reid, Renee R. Handley + 6 more
The isolation of intact single cells from frozen tissue is a challenge due to the mechanical and physical stress inflicted upon the cell during the freeze-thaw process. Ruptured cells release ambient RNA into the cell suspension, which can become encapsulated into droplets during droplet based single cell RNA-seq…
Beth Martin, Chengxiang Qiu, Eva K. Nichols, M. Hoang Phung + 7 more
'Rula Green Gladden' 'Sanjay Srivatsan' 'Ronnie Blecher‐Gonen' 'Brian J. Beliveau' 'Cole Trapnell' 'Junyue Cao' 'Jay Shendure'] - 1. Department of Genome Sciences, University of Washington, Seattle, WA, USA. - 2. Department of Biology, Case Western Reserve University, Cleveland, OH, USA. - 3. Division of…
Ionut Sebastian Mihai, Sarang Chafle, Johan Henriksson
Single-cell analysis is currently one of the most high-resolution techniques to study biology. The large complex datasets that have been generated have spurred numerous developments in computational biology, in particular the use of advanced statistics and machine learning. This review attempts to explain the deeper…
Valentine Svensson, Roser Vento‐Tormo, Sarah A. Teichmann
The ability to measure the transcriptomes of single cells has only been feasible for a few years, and is becoming an extremely popular assay. While many types of analysis and questions can be answered using single cell RNA-sequencing, a central focus is the ability to survey the diversity of cell types within a sample.…
Katherine E. Prater, Kevin Lin
Acknowledgements: KEP would like to sincerely thank Drs. Ali Shojaie (UW Biostatistics) and Wei Sun (Fred Hutch Department of Biostatistics) for their helpful input and support on bioinformatics and single-cell analysis pipeline development. The authors would also like to thank Drs. Suman Jayadev, Jonathan R.…
D. Blaine Marchant, Brad Nelms, Virginia Walbot
Single-cell RNA-sequencing (scRNA-seq) can provide invaluable insight into cell development, cell type identification, and plant evolution. However, the resilience of the cell wall makes it difficult to dissociate plant tissues and release individual cells for single-cell analysis. Here, we show that plant organs can…
Juerg Straubhaar, Alexandria D’Souza, Zachary Niziolek, Bogdan Budnik
Single-cell analysis has clearly established itself in biology and biomedical fields as an invaluable tool that allows one to comprehensively understand the relationship between cells, including their types, states, transitions, trajectories, and spatial position. Scientific methods such as fluorescence labeling…
Authors not listed
Antisense oligonucleotides (ASOs) are a promising class of therapeutics designed to modulate gene expression. Both key mechanisms of action for ASOs operate in the nucleus: splice-switching ASOs modify pre-mRNA, processed in the nucleus, and mRNA-degrading ASOs require RNase H, an enzyme predominantly active in the…