[HTML][HTML] Experimental considerations for single-cell RNA sequencing approaches

QH Nguyen, N Pervolarakis, K Nee… - Frontiers in cell and …, 2018 - frontiersin.org
Single-cell transcriptomic technologies have emerged as powerful tools to explore cellular
heterogeneity at the resolution of individual cells. Previous scientific knowledge in cell …

bigSCale: an analytical framework for big-scale single-cell data

G Iacono, E Mereu, A Guillaumet-Adkins… - Genome …, 2018 - genome.cshlp.org
Single-cell RNA sequencing (scRNA-seq) has significantly deepened our insights into
complex tissues, with the latest techniques capable of processing tens of thousands of cells …

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 …

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

I Gupta, PG Collier, B Haase, A Mahfouz… - Nature …, 2018 - nature.com
Full-length RNA sequencing (RNA-Seq) has been applied to bulk tissue, cell lines and
sorted cells to characterize transcriptomes,,,,,,,,,,, but applying this technology to single cells …

MARS-seq2. 0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing

H Keren-Shaul, E Kenigsberg, DA Jaitin, E David… - Nature protocols, 2019 - nature.com
Human tissues comprise trillions of cells that populate a complex space of molecular
phenotypes and functions and that vary in abundance by 4–9 orders of magnitude. Relying …

Single-cell biology: beyond the sum of its parts

AF Schier - Nature methods, 2020 - nature.com
The field of single-cell RNA sequencing (scRNA-seq) has been paired with genomics,
epigenomics, spatial omics, proteomics and imaging to achieve multimodal measurements …

Stem cell transcriptome profiling via massive-scale mRNA sequencing

N Cloonan, ARR Forrest, G Kolle, BBA Gardiner… - Nature …, 2008 - nature.com
We developed a massive-scale RNA sequencing protocol, short quantitative random RNA
libraries or SQRL, to survey the complexity, dynamics and sequence content of …

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

JT Gaublomme, B Li, C McCabe, A Knecht… - Nature …, 2019 - nature.com
Single-nucleus RNA-seq (snRNA-seq) enables the interrogation of cellular states in
complex tissues that are challenging to dissociate or are frozen, and opens the way to …

Comparative analysis of RNA sequencing methods for degraded or low-input samples

X Adiconis, D Borges-Rivera, R Satija, DS DeLuca… - Nature …, 2013 - nature.com
RNA-seq is an effective method for studying the transcriptome, but it can be difficult to apply
to scarce or degraded RNA from fixed clinical samples, rare cell populations or cadavers …

Simultaneous epitope and transcriptome measurement in single cells

M Stoeckius, C Hafemeister, W Stephenson… - Nature …, 2017 - nature.com
High-throughput single-cell RNA sequencing has transformed our understanding of complex
cell populations, but it does not provide phenotypic information such as cell-surface protein …