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New methods for measuring the sensitivity of chromatin to DNase digestion and Tn5 transposition help us map and interpret the genome's regulatory sequences.
Individual cells of the same phenotype are commonly viewed as identical functional units of a tissue or organ. However, the deep sequencing of DNA and RNA from single cells suggests a more complex ecology of heterogeneous cell states that together produce emergent system-level function. Continuing development of high-content, real-time, multimodal single-cell measurement technologies will lead to the ultimate goal of understanding the function of an individual cell in the context of its microenvironment.
Emerging technologies are bringing single-cell genome sequencing into the mainstream; this field has already yielded insights into the genetic architecture and variability between cells that highlight the dynamic nature of the genome.
Recent technical advances have enabled RNA sequencing (RNA-seq) in single cells. Exploratory studies have already led to insights into the dynamics of differentiation, cellular responses to stimulation and the stochastic nature of transcription. We are entering an era of single-cell transcriptomics that holds promise to substantially impact biology and medicine.
Single-cell genome and transcriptome sequencing methods are generating a fresh wave of biological insights into development, cancer and neuroscience. Kelly Rae Chi reports.
With an optimized protocol and unique molecular identifiers (UMIs) to tag individual transcripts, the mRNA complement of a single cell can be quantified on an absolute scale with almost no amplification bias.
A recently described red-shifted channelrhodopsin permits control of complex behaviors in freely moving adult flies and reveals the functional modulation of courtship behavior by social experience.
A data-independent acquisition (DIA) mass spectrometry approach, ultradefinition (UD)MSE, offers high reproducibility and improved proteome coverage over alternative DIA and data-dependent acquisition workflows.
This Analysis reports the development and assessment of 645 multiple reaction monitoring (MRM) mass spectrometry assays to quantify 319 targeted human breast cancer proteins. The results of this pilot project coordinated among three individual groups suggest that an organized international effort to generate MRM assays to the human proteome will be possible.
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.
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.