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 …

Experimental design for single-cell RNA sequencing

J Baran-Gale, T Chandra… - Briefings in functional …, 2018 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) has opened new avenues for the characterization
of heterogeneity in a large variety of cellular systems. As this is a relatively new technique …

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

JK Kim, AA Kolodziejczyk, T Ilicic… - Nature …, 2015 - nature.com
Single-cell RNA-sequencing (scRNA-seq) facilitates identification of new cell types and
gene regulatory networks as well as dissection of the kinetics of gene expression and …

Defining transcribed regions using RNA-seq

BT Wilhelm, S Marguerat, I Goodhead, J Bähler - Nature protocols, 2010 - nature.com
Next-generation sequencing technologies are revolutionizing genomics research. It is now
possible to generate gigabase pairs of DNA sequence within a week without time …

A systematic evaluation of single cell RNA-seq analysis pipelines

B Vieth, S Parekh, C Ziegenhain, W Enard… - Nature …, 2019 - nature.com
The recent rapid spread of single cell RNA sequencing (scRNA-seq) methods has created a
large variety of experimental and computational pipelines for which best practices have not …

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

CS McGinnis, DM Patterson, J Winkler, DN Conrad… - Nature …, 2019 - nature.com
Sample multiplexing facilitates scRNA-seq by reducing costs and identifying artifacts such
as cell doublets. However, universal and scalable sample barcoding strategies have not …

Technical variations in low-input RNA-seq methodologies

V Bhargava, SR Head, P Ordoukhanian, M Mercola… - Scientific reports, 2014 - nature.com
Recent advances in RNA-seq methodologies from limiting amounts of mRNA have
facilitated the characterization of rare cell-types in various biological systems. So far …

Single-cell analyses to tailor treatments

AK Shalek, M Benson - Science translational medicine, 2017 - science.org
Single-cell analyses to tailor treatments | Science Translational Medicine news careers
commentary Journals Science Science brought to you byGoogle Indexer Log in science science …

TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding

JA Schofield, EE Duffy, L Kiefer, MC Sullivan… - Nature …, 2018 - nature.com
RNA sequencing (RNA-seq) offers a snapshot of cellular RNA populations, but not temporal
information about the sequenced RNA. Here we report TimeLapse-seq, which uses …

Single-cell RNA sequencing analysis: a step-by-step overview

S Slovin, A Carissimo, F Panariello, A Grimaldi… - RNA bioinformatics, 2021 - Springer
Thanks to innovative sample-preparation and sequencing technologies, gene expression in
individual cells can now be measured for thousands of cells in a single experiment. Since its …