Methods to sequence the DNA and RNA of single cells are poised to transform many areas of biology and medicine.
Volume 11 Issue 1, January 2014
Methods in Brief
Tools in Brief
Method to Watch
News & Views
A systematic evaluation of various single-cell RNA-seq approaches reports their sensitivity, accuracy and reproducibility and establishes the high performance of a high-throughput microfluidic method.
Protein-lipid interactions can be systematically analyzed using a quantitative, multiplexed liposome microarray–based assay (LiMA).
For allele-specific expression and RNA editing studies, targeted RNA sequencing using microfluidic multiplexed PCR (mmPCR-seq) gives robust high-throughput measurements of allelic ratios across the dynamic range of gene expression, even for low-quantity or low-quality RNA.
A line-scanning method is applied to obtain onset times of fMRI responses in rats. The authors show that onset time of the fMRI response can be used to infer information about which cortical layers receive the connectivity input from other brain areas.
High-resolution isoelectric focusing (HiRIEF) of peptides followed by mass spectrometry analysis, combined with accurate peptide pI prediction, allows a reduction of protein database search space, enabling deep proteome coverage and the discovery of protein-coding loci in human and mouse.
A method and software tool, ResMap, for quantifying the local resolution across 3D electron cryo-microscopy density maps is reported.
By separately sequencing and mapping smaller and larger DNase I fragments from the same DNase I digestion experiment, the approach allows simultaneous profiling of transcription factor footprints relative to nucleosome occupancy.
Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification
Detailed analysis of DNase-seq protocols reveals the importance of choosing the right enzyme concentration and fragment length and cautions that many transcription factor footprints may represent cutting bias.
A competitive activity–based protein profiling method is reported for quantifying the reactivity of lipid-derived electrophilic compounds with cysteine residues in the human proteome.
A system to monitor translation regulation in living cells is reported. By fusing a fluorescent reporter that has a controllable destabilization domain to translation regulatory motifs, the authors analyze the contribution of these motifs to changes in translation in individual cells under different experimental situations.
An approach is presented for predicting the nature of the relationship (activating or inhibiting) between interacting proteins via integration of phenotypic information with protein-protein interaction networks.
A chemically defined diet for Drosophila melanogaster is described. It should enable a variety of behavioral, metabolic and fitness studies where controlled nutrition is important.
This paper reports culture conditions for the expansion of near-homogeneous populations of mouse Lgr5+ intestinal stem cells. These methods will enable the study of intestinal biology and potentially that of other tissues.
Nature Methods' choice for Method of the Year 2013 is single-cell sequencing. A collection of articles present the unique considerations related to sequencing single cells and highlight recent applications in biology and medicine. The Methods to Watch feature provides a look at possible future Methods of the Year.