Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies

A Lafzi, C Moutinho, S Picelli, H Heyn - Nature protocols, 2018 - nature.com
Single-cell RNA sequencing is at the forefront of high-resolution phenotyping experiments
for complex samples. Although this methodology requires specialized equipment and …

Methodologies for transcript profiling using long-read technologies

S Oikonomopoulos, A Bayega, S Fahiminiya… - Frontiers in …, 2020 - frontiersin.org
RNA sequencing using next-generation sequencing technologies (NGS) is currently the
standard approach for gene expression profiling, particularly for large-scale high-throughput …

[HTML][HTML] Second-strand synthesis-based massively parallel scRNA-seq reveals cellular states and molecular features of human inflammatory skin pathologies

TK Hughes, MH Wadsworth, TM Gierahn, T Do… - Immunity, 2020 - cell.com
High-throughput single-cell RNA-sequencing (scRNA-seq) methodologies enable
characterization of complex biological samples by increasing the number of cells that can be …

Bacteroides-derived sphingolipids are critical for maintaining intestinal homeostasis and symbiosis

EM Brown, X Ke, D Hitchcock, S Jeanfavre… - Cell host & …, 2019 - cell.com
Sphingolipids are structural membrane components and important eukaryotic signaling
molecules. Sphingolipids regulate inflammation and immunity and were recently identified …

Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ

JW Foley, C Zhu, P Jolivet, SX Zhu, P Lu… - Genome …, 2019 - genome.cshlp.org
RNA sequencing (RNA-seq) is a sensitive and accurate method for quantifying gene
expression. Small samples or those whose RNA is degraded, such as formalin-fixed paraffin …

Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation

CG Artieri, HB Fraser - Genome research, 2014 - genome.cshlp.org
The recent advent of ribosome profiling—sequencing of short ribosome-bound fragments of
mRNA—has offered an unprecedented opportunity to interrogate the sequence features …

[HTML][HTML] Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells

F Rubelt, CR Bolen, HM McGuire, JAV Heiden… - Nature …, 2016 - nature.com
The adaptive immune system's capability to protect the body requires a highly diverse
lymphocyte antigen receptor repertoire. However, the influence of individual genetic and …

Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations

M Nadal-Ribelles, S Islam, W Wei, P Latorre… - Nature …, 2019 - nature.com
Single-cell RNA sequencing has revealed extensive cellular heterogeneity within many
organisms, but few methods have been developed for microbial clonal populations. The …

Non-templated addition and template switching by Moloney murine leukemia virus (MMLV)-based reverse transcriptases co-occur and compete with each other

MG Wulf, S Maguire, P Humbert, N Dai, Y Bei… - Journal of Biological …, 2019 - ASBMB
Single-cell RNA-Seq (scRNA-Seq) has led to an unprecedented understanding of gene
expression and regulation in individual cells. Many scRNA-Seq approaches rely upon the …

RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase

RM Nottingham, DC Wu, Y Qin, J Yao, S Hunicke-Smith… - Rna, 2016 - rnajournal.cshlp.org
Next-generation RNA sequencing (RNA-seq) has revolutionized our ability to analyze
transcriptomes. Current RNA-seq methods are highly reproducible, but each has biases …