Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses

CH O'Flanagan, KR Campbell, AW Zhang, F Kabeer… - Genome biology, 2019 - Springer
Background Single-cell RNA sequencing (scRNA-seq) is a powerful tool for studying
complex biological systems, such as tumor heterogeneity and tissue microenvironments …

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

M Slyper, CBM Porter, O Ashenberg, J Waldman… - Nature medicine, 2020 - nature.com
Single-cell genomics is essential to chart tumor ecosystems. Although single-cell RNA-Seq
(scRNA-Seq) profiles RNA from cells dissociated from fresh tumors, single-nucleus RNA …

XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment

Y Lee, D Bogdanoff, Y Wang, GC Hartoularos… - Science …, 2021 - science.org
Single-cell RNA sequencing (scRNA-seq) of tissues has revealed remarkable heterogeneity
of cell types and states but does not provide information on the spatial organization of cells …

Advances in single-cell RNA sequencing and its applications in cancer research

D Huang, N Ma, X Li, Y Gou, Y Duan, B Liu… - Journal of hematology & …, 2023 - Springer
Cancers are a group of heterogeneous diseases characterized by the acquisition of
functional capabilities during the transition from a normal to a neoplastic state. Powerful …

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 …

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 …

Integrating single-cell transcriptomic data across different conditions, technologies, and species

A Butler, P Hoffman, P Smibert, E Papalexi… - Nature …, 2018 - nature.com
Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied
to experiments representing a single condition, technology, or species to discover and …

CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones

S Müller, A Cho, SJ Liu, DA Lim, A Diaz - Bioinformatics, 2018 - academic.oup.com
Motivation Single-cell RNA-sequencing (scRNA-seq) has enabled studies of tissue
composition at unprecedented resolution. However, the application of scRNA-seq to clinical …

Biological and medical importance of cellular heterogeneity deciphered by single-cell RNA sequencing

RK Gupta, J Kuznicki - Cells, 2020 - mdpi.com
The present review discusses recent progress in single-cell RNA sequencing (scRNA-seq),
which can describe cellular heterogeneity in various organs, bodily fluids, and pathologies …

Single-cell transcriptomics bioinformatics and computational challenges

OB Poirion, X Zhu, T Ching, L Garmire - Frontiers in genetics, 2016 - frontiersin.org
The emerging single-cell RNA-Seq (scRNA-Seq) technology holds the promise to
revolutionize our understanding of diseases and associated biological processes at an …