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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.
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 chemically defined diet for Drosophila melanogaster is described. It should enable a variety of behavioral, metabolic and fitness studies where controlled nutrition is important.
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 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.
Discrepancies between model prediction and experimental measurements enable molecular-level discovery with a whole-cell model of Mycoplasma genitalium.
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.
The RGASP consortium compared 25 RNA-seq analysis programs in their ability to identify exons, reconstruct transcripts and quantify expression levels. Assembly of isoforms and their expression levels in higher eukaryotes remains a challenge.