Single-cell Genomics

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2011 Apr 1

PMID 21451520

Citations 120

Authors

Tomer Kalisky

Stephen R Quake

Affiliations

Soon will be listed here.

Abstract

Methods for genomic analysis at single-cell resolution enable new understanding of complex biological phenomena. Single-cell techniques, ranging from flow cytometry and microfluidics to PCR and sequencing, are used to understand the cellular composition of complex tissues, find new microbial species and perform genome-wide haplotyping.

Citing Articles

Genetically encoded protein oscillators for FM streaming of single-cell data.

Rajasekaran R, Galateo T, Xu Z, Bolshakov D, Weix E, Coyle S bioRxiv. 2025; .

PMID: 40060462 PMC: 11888400. DOI: 10.1101/2025.02.28.640587.

A simple guideline for designing droplet microfluidic chips to achieve an improved single (bio)particle encapsulation rate using a stratified flow-assisted particle ordering method.

Nguyen T, Ezzo N, Chan S, Yim E, Ren C Biomicrofluidics. 2024; 18(5):054110.

PMID: 39397893 PMC: 11466506. DOI: 10.1063/5.0219528.

Single Cell mass spectrometry: Towards quantification of small molecules in individual cells.

Lan Y, Zou Z, Yang Z Trends Analyt Chem. 2024; 174.

PMID: 39391010 PMC: 11465888. DOI: 10.1016/j.trac.2024.117657.

Revalidation of DNA Fragmentation Analyses for Human Sperm-Measurement Principles, Comparative Standards, Calibration Curve, Required Sensitivity, and Eligibility Criteria for Test Sperm.

Kaneko S, Okada Y Biology (Basel). 2024; 13(7).

PMID: 39056679 PMC: 11274034. DOI: 10.3390/biology13070484.

Gene expression model inference from snapshot RNA data using Bayesian non-parametrics.

Kilic Z, Schweiger M, Moyer C, Shepherd D, Presse S Nat Comput Sci. 2023; 3(2):174-183.

PMID: 38125199 PMC: 10732567. DOI: 10.1038/s43588-022-00392-0.

References

Frumkin D, Wasserstrom A, Itzkovitz S, Stern T, Harmelin A, Eilam R . Cell lineage analysis of a mouse tumor. Cancer Res. 2008; 68(14):5924-31. DOI: 10.1158/0008-5472.CAN-07-6216. View

Blainey P, Quake S . Digital MDA for enumeration of total nucleic acid contamination. Nucleic Acids Res. 2010; 39(4):e19. PMC: 3045575. DOI: 10.1093/nar/gkq1074. View

Blainey P, Mosier A, Potanina A, Francis C, Quake S . Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLoS One. 2011; 6(2):e16626. PMC: 3043068. DOI: 10.1371/journal.pone.0016626. View

Bandura D, Baranov V, Ornatsky O, Antonov A, Kinach R, Lou X . Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. Anal Chem. 2009; 81(16):6813-22. DOI: 10.1021/ac901049w. View

Raj A, Bogaard P, Rifkin S, van Oudenaarden A, Tyagi S . Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods. 2008; 5(10):877-9. PMC: 3126653. DOI: 10.1038/nmeth.1253. View

Marcy Y, Ouverney C, Bik E, Losekann T, Ivanova N, Garcia Martin H . Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci U S A. 2007; 104(29):11889-94. PMC: 1924555. DOI: 10.1073/pnas.0704662104. View

Tietjen I, Rihel J, Cao Y, Koentges G, Zakhary L, Dulac C . Single-cell transcriptional analysis of neuronal progenitors. Neuron. 2003; 38(2):161-75. DOI: 10.1016/s0896-6273(03)00229-0. View

Ottesen E, Hong J, Quake S, Leadbetter J . Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science. 2006; 314(5804):1464-7. DOI: 10.1126/science.1131370. View

Luo L, Salunga R, Guo H, Bittner A, Joy K, Galindo J . Gene expression profiles of laser-captured adjacent neuronal subtypes. Nat Med. 1999; 5(1):117-22. DOI: 10.1038/4806. View

10.

Sykes P, Neoh S, Brisco M, Hughes E, Condon J, Morley A . Quantitation of targets for PCR by use of limiting dilution. Biotechniques. 1992; 13(3):444-9. View

11.

Chiang M, Melton D . Single-cell transcript analysis of pancreas development. Dev Cell. 2003; 4(3):383-93. DOI: 10.1016/s1534-5807(03)00035-2. View

12.

Zhang K, Martiny A, Reppas N, Barry K, Malek J, Chisholm S . Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol. 2006; 24(6):680-6. DOI: 10.1038/nbt1214. View

13.

Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N . mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods. 2009; 6(5):377-82. DOI: 10.1038/nmeth.1315. View

14.

Irish J, Hovland R, Krutzik P, Perez O, Bruserud O, Gjertsen B . Single cell profiling of potentiated phospho-protein networks in cancer cells. Cell. 2004; 118(2):217-28. DOI: 10.1016/j.cell.2004.06.028. View

15.

Bengtsson M, Stahlberg A, Rorsman P, Kubista M . Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels. Genome Res. 2005; 15(10):1388-92. PMC: 1240081. DOI: 10.1101/gr.3820805. View

16.

Leslie M . Cell biology. The power of one. Science. 2011; 331(6013):24-6. DOI: 10.1126/science.331.6013.24-a. View

17.

Lambolez B, Audinat E, Bochet P, Crepel F, Rossier J . AMPA receptor subunits expressed by single Purkinje cells. Neuron. 1992; 9(2):247-58. DOI: 10.1016/0896-6273(92)90164-9. View

18.

Eberwine J, Yeh H, Miyashiro K, Cao Y, Nair S, Finnell R . Analysis of gene expression in single live neurons. Proc Natl Acad Sci U S A. 1992; 89(7):3010-4. PMC: 48793. DOI: 10.1073/pnas.89.7.3010. View

19.

Maryanski J, Jongeneel C, Bucher P, Casanova J, Walker P . Single-cell PCR analysis of TCR repertoires selected by antigen in vivo: a high magnitude CD8 response is comprised of very few clones. Immunity. 1996; 4(1):47-55. DOI: 10.1016/s1074-7613(00)80297-6. View

20.

Liu J, Hansen C, Quake S . Solving the "world-to-chip" interface problem with a microfluidic matrix. Anal Chem. 2003; 75(18):4718-23. DOI: 10.1021/ac0346407. View