Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states

A Isakova, N Neff, SR Quake - Proceedings of the National …, 2021 - National Acad Sciences
The ability to interrogate total RNA content of single cells would enable better mapping of
the transcriptional logic behind emerging cell types and states. However, current single-cell …

Single-cell RNA counting at allele and isoform resolution using Smart-seq3

M Hagemann-Jensen, C Ziegenhain, P Chen… - Nature …, 2020 - nature.com
Large-scale sequencing of RNA from individual cells can reveal patterns of gene, isoform
and allelic expression across cell types and states. However, current short-read single-cell …

Full-length RNA-seq from single cells using Smart-seq2

S Picelli, OR Faridani, ÅK Björklund, G Winberg… - Nature protocols, 2014 - nature.com
Emerging methods for the accurate quantification of gene expression in individual cells hold
promise for revealing the extent, function and origins of cell-to-cell variability. Different high …

Quantitative assessment of single-cell RNA-sequencing methods

AR Wu, NF Neff, T Kalisky, P Dalerba, B Treutlein… - Nature …, 2014 - nature.com
Interest in single-cell whole-transcriptome analysis is growing rapidly, especially for profiling
rare or heterogeneous populations of cells. We compared commercially available single-cell …

Exponential scaling of single-cell RNA-seq in the past decade

V Svensson, R Vento-Tormo, SA Teichmann - Nature protocols, 2018 - nature.com
Measurement of the transcriptomes of single cells has been feasible for only a few years, but
it has become an extremely popular assay. While many types of analysis can be carried out …

[HTML][HTML] Methods, challenges and potentials of single cell RNA-seq

D Hebenstreit - Biology, 2012 - mdpi.com
RNA-sequencing (RNA-seq) has become the tool of choice for transcriptomics. Several
recent studies demonstrate its successful adaption to single cell analysis. This allows new …

Entering the era of single-cell transcriptomics in biology and medicine

R Sandberg - Nature methods, 2014 - nature.com
Recent technical advances have enabled RNA sequencing (RNA-seq) in single cells.
Exploratory studies have already led to insights into the dynamics of differentiation, cellular …

[HTML][HTML] SingleCellNet: a computational tool to classify single cell RNA-Seq data across platforms and across species

Y Tan, P Cahan - Cell systems, 2019 - cell.com
Single-cell RNA-seq has emerged as a powerful tool in diverse applications, from
determining the cell-type composition of tissues to uncovering regulators of developmental …

Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning

Y Deng, F Bao, Q Dai, LF Wu, SJ Altschuler - Nature methods, 2019 - nature.com
Recent advances in large-scale single-cell RNA-seq enable fine-grained characterization of
phenotypically distinct cellular states in heterogeneous tissues. We present scScope, a …

Single-cell mRNA quantification and differential analysis with Census

X Qiu, A Hill, J Packer, D Lin, YA Ma, C Trapnell - Nature methods, 2017 - nature.com
Single-cell gene expression studies promise to reveal rare cell types and cryptic states, but
the high variability of single-cell RNA-seq measurements frustrates efforts to assay …