Experimental Considerations for Single-Cell RNA Sequencing Approaches

Frontiers in Cell and Developmental Biology
Quy H NguyenKai Kessenbrock

Abstract

Single-cell transcriptomic technologies have emerged as powerful tools to explore cellular heterogeneity at the resolution of individual cells. Previous scientific knowledge in cell biology is largely limited to data generated by bulk profiling methods, which only provide averaged read-outs that generally mask cellular heterogeneity. This averaged approach is particularly problematic when the biological effect of interest is limited to only a subpopulation of cells such as stem/progenitor cells within a given tissue, or immune cell subsets infiltrating a tumor. Great advances in single-cell RNA sequencing (scRNAseq) enabled scientists to overcome this limitation and allow for in depth interrogation of previously unexplored rare cell types. Due to the high sensitivity of scRNAseq, adequate attention must be put into experimental setup and execution. Careful handling and processing of cells for scRNAseq is critical to preserve the native expression profile that will ensure meaningful analysis and conclusions. Here, we delineate the individual steps of a typical single-cell analysis workflow from tissue procurement, cell preparation, to platform selection and data analysis, and we discuss critical challenges in each of these steps...Continue Reading

References

Apr 1, 1995·Current Opinion in Immunology·A Radbruch, D Recktenwald
Jan 10, 2002·The Journal of Biological Chemistry·Liming XiongJian-Kang Zhu
Feb 2, 2006·BMC Molecular Biology·Andreas SchroederThomas Ragg
Nov 30, 2010·Best Practice & Research. Clinical Haematology·Britta Will, Ulrich Steidl
Mar 15, 2011·Nature·Nicholas NavinMichael Wigler
Jul 24, 2012·Nature Biotechnology·Daniel RamsköldRickard Sandberg
Nov 20, 2013·Proceedings of the National Academy of Sciences of the United States of America·Rashel V GrindbergRoger S Lasken
Dec 24, 2013·Nature Methods·Saiful IslamSten Linnarsson
Jan 5, 2014·Nature Protocols·Simone PicelliRickard Sandberg
Jun 14, 2014·Science·Anoop P PatelBradley E Bernstein
Jun 18, 2015·Nature·Jason D BuenrostroWilliam J Greenleaf
Dec 17, 2015·Nature Reviews. Drug Discovery·James R HeathPaul S Mischel
Feb 20, 2016·Nature Protocols·Suguna Rani KrishnaswamiRoger S Lasken
Apr 20, 2016·Nature Communications·Benjamin LacarFred H Gage
May 15, 2016·Nucleic Acids Research·Zhicheng Ji, Hongkai Ji
Jul 28, 2016·BMC Obesity·Suresh AmbatiRichard B Meagher
Nov 9, 2016·Nature Biotechnology·Allon WagnerNir Yosef
Jan 4, 2017·Scientific Reports·Po-Yuan TungYoav Gilad
Jan 17, 2017·Nature Communications·Grace X Y ZhengJason H Bielas
Jan 20, 2017·Nature·Amos Tanay, Aviv Regev
May 10, 2017·Genome Biology·Guo-Cheng YuanItay Tirosh
May 21, 2017·BMC Biology·Jonathan AllesNikolaus Rajewsky
Aug 11, 2017·Nature Communications·Ruli GaoNicholas Navin
Aug 22, 2017·Nature Methods·Xiaojie QiuCole Trapnell
Aug 29, 2017·Nature Methods·Naomi HabibAviv Regev
Sep 30, 2017·Nature Methods·Susanne C van den BrinkAlexander van Oudenaarden
Oct 27, 2017·Nature·Orit Rozenblatt-RosenSarah A Teichmann
Dec 12, 2017·Nature Biotechnology·Hyun Min KangChun Jimmie Ye
Feb 24, 2018·Cell·Xiaoping HanGuoji Guo

❮ Previous
Next ❯

Citations

Feb 29, 2020·JCI Insight·Rajasree MenonUNKNOWN Nephrotic Syndrome Study Network (NEPTUNE)
Apr 24, 2020·Circulation Research·Jesse W WilliamsKlaus Ley
May 28, 2019·APMIS : Acta Pathologica, Microbiologica, Et Immunologica Scandinavica·Thomas Litman
Jan 12, 2020·Briefings in Bioinformatics·Meichen DongYuchao Jiang
Apr 2, 2020·Nature Reviews. Cardiology·David T PaikJoseph C Wu
Jul 6, 2020·European Respiratory Review : an Official Journal of the European Respiratory Society·Michael J AlexanderPaul A Reyfman
Aug 9, 2019·Cell & Bioscience·Xiaoning TangXiao Zhu
Jul 1, 2020·Laryngoscope Investigative Otolaryngology·Madeline P Pyle, Michael Hoa
Dec 20, 2019·Nature Reviews. Nephrology·Deepak A RaoBetty Diamond
Jul 9, 2020·APL Bioengineering·Aditya Kumar, Prashant Mali
Feb 12, 2020·ELife·Laura Ferrer-FontJohannes U Mayer
Aug 11, 2020·Cancer Metastasis Reviews·Robert ClarkeYue Wang
Jul 17, 2020·Nature·UNKNOWN Tabula Muris Consortium
Nov 30, 2018·Nature Cell Biology·Devon A LawsonZena Werb
Nov 5, 2020·Journal of Cellular and Molecular Medicine·Haotong LiShengshou Hu
Apr 15, 2020·Cancer Cell·Bora LimNicholas Navin
Dec 11, 2019·Journal of Neuroscience Methods·Kamil Sebastian RosiewiczVolker Siffrin
Jan 9, 2021·Cell Death & Disease·Tamaki KurosawaAkiyoshi Uezumi
Mar 7, 2021·International Journal of Molecular Sciences·Viktoria FuhrHilka Rauert-Wunderlich
Feb 22, 2021·Genes, Chromosomes & Cancer·Ulrich PfistererThoas Fioretos
Mar 4, 2021·FEBS Letters·Mirjana Gusic, Holger Prokisch
Apr 13, 2021·Biochimica Et Biophysica Acta. Proteins and Proteomics·Livia Goto-Silva, Magno Junqueira
Oct 21, 2020·The Korean Journal of Internal Medicine·Jisoo Kim, Jihwan Park
May 13, 2021·Nature Communications·Frederique Ruf-ZamojskiStuart C Sealfon
Apr 23, 2021·Journal of the Chinese Medical Association : JCMA·Zhi-Xiong ChongHan-Kiat Ong
Jun 3, 2021·Methods and Protocols·Daniele MercatelliFederico Manuel Giorgi
May 12, 2021·Molecular Human Reproduction·E R FrostJ M Sutherland
Jul 17, 2021·Nature Reviews. Cardiology·Dawn M Fernandez, Chiara Giannarelli
Oct 1, 2021·Nature Communications·Daniel E RussAriel J Levine

❮ Previous
Next ❯

Methods Mentioned

BETA
RNAseq
scRNAseq
single-cell sequencing
PCR
flow cytometry
snRNAseq
genotyping

Software Mentioned

snRNAseq
Monocle
MAST
Nanogrid
Demuxlet
Fluidigm
CellTree
Seurat
TSCAN

Related Concepts

Related Feeds

Cell-Type-Specific Viral Vectors (ASM)

Viral vectors are used in biological research and therapy to deliver genetic material into cells. However, the efficiency of viral vectors varies depending on the cell type. Here is the latest research on cell-type-specific viral vectors.

Cell-Type-Specific Viral Vectors

Viral vectors are used in biological research and therapy to deliver genetic material into cells. However, the efficiency of viral vectors varies depending on the cell type. Here is the latest research on cell-type-specific viral vectors.

Cell-Type Specific Viral Vectors

Viral vectors are used in biological research and therapy to deliver genetic material into cells. However, the efficiency of viral vectors varies depending on the cell type. Here is the latest research on cell-type-specific viral vectors.

Related Papers

Current Opinion in Lipidology
Holger WinkelsKlaus Ley
Nature Reviews. Immunology
Efthymia Papalexi, Rahul Satija
© 2022 Meta ULC. All rights reserved