Nature Protocols | Stepwise

Single-cell analysis techniques

Here we present a collection of just a few of our single-cell analysis protocols for your interest, in advance of our attendance at the upcoming Select Biosciences Single Cell Analysis Europe conference in Edinburgh from the 28th-29th March. 

As you will see, the methods range from gene expression and copy number profiling to isolation and imaging of single cells, as examples of the content we have published on this topic over the years. 

These protocols will be free to access until the end of March and we hope you will find them useful!

  Microarray analysis of copy number variation in single cells
Konings et al.
This protocol enables reliable detection of DNA copy number aberrations in a single cell, by hybridizing multiple displacement-amplified DNA to BAC- and SNP-arrays.    
Comprehensive qPCR profiling of gene expression in single neuronal cells
Citri et al.
This protocol describes a single-cell assay to characterize lineage-specific reprogrammed human neuronal cells, using qPCR gene expression profiling.  
Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy
Young et al.
Quantitative single-cell time-lapse microscopy forms the basis of this protocol, enabling gene expresion and regulation to be quantified in individual E. coli cells.  
Rapid isolation of single malaria parasite–infected red blood cells by cell sorting
Miao & Cui
In this protocol, a method for efficient cloning of the malaria parasite is presented that uses a cell sorter to rapidly isolate single P. falciparum–infected red blood cells.  

Quantifying cellular adhesion to extracellular matrix components by single-cell force spectroscopy
Friedrichs, Helenius & Muller
Here, a protocol to study integrin-mediated adhesion of HeLa cells to collagen type I using atomic force microscopy-based single-cell force spectroscopy is presented. 

RNA-Seq analysis to capture the transcriptome landscape of a single cell
Tang et al.
This digital transcriptome analysis protocol uses a deep-sequencing approach to analyze the functional readout of the genome from a single mouse oocyte.
Targeted single-cell electroporation of mammalian neurons in vivo
Hausser et al.
This protocol for single-cell electroporation provides a method for delivering plasmid DNA into single identified mammalian neurons in vivo.
Single-cell isolation from cell suspensions and whole genome amplification from single cells to provide templates for CGH analysis
Giegl & Speicher
Here, the authors describe various options for single-cell isolation and whole genome amplification, allowing a comprehensive genomic analysis of single cells.
Global single-cell cDNA amplification to provide a template for representative high-density oligonucleotide microarray analysis
Kurimoto et al.
The representative amplification of global mRNAs from typical single mammalian cells is achieved using this protocol, providing a template for microarray analysis.
Adult mouse hematopoietic stem cells: purification and single-cell assays
Ema et al.
In this protocol, the authors present their single-cell colony assay and single-cell transplantation procedures to characterize purified haematopoietic stem cells.


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