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CREST-seq allows functional screening of cis-regulatory elements through the use of sgRNA pairs to introduce tiled deletions in regions of interest. The analysis of a 2-megabase target region shows that promoters can act as distal enhancers for unrelated genes.
Iterative expansion microscopy (iExM) is a strategy that achieves high resolution expansion microscopy by expanding samples multiple times. Expanding a sample twice enables ∼4.5 × 4.5 ∼20× physical expansion and ∼25 nm resolution.
An ultrafast, fragment-ion indexing–based database search tool, MSFragger, makes open searching practical and enables comprehensive identification of modified peptides in mass spectrometry–based proteomics data sets.
This paper describes a fully defined, nonxenogeneic in vitro niche for the differentiation of haematopoietic stem and progenitor cells to progenitor T cells in mouse and human.
iTango confers access to neuromodulation-sensitive subsets of neurons in a functionally defined and temporally controlled manner. The tool allows for manipulating the subset of neurons that are activated by dopamine during a behavior of interest.
This paper describes an in vitro method to generate human T cells from hematopoietic stem and progenitor cells (HSPCs). It should be useful for both basic and applied studies using T cells.
vTwINS enables high-speed volumetric calcium imaging via a V-shaped point spread function and a dedicated data-processing algorithm. Song et al. apply this strategy to image population activity in the mouse visual cortex and hippocampus.
A lysine-less, internally affinity-tagged ubiquitin construct is deployed to discover linear polyubiquitinated substrates via a mass-spectrometry-based proteomics approach.
New fluorescent biosensors enable the first super-resolution imaging of enzyme activity in live cells via fluorescence fluctuation increase by contact (FLINC).
Selection-linked integration in the Plasmodium genome allows for rapid selection of genes inserted at a genomic locus or induction of the inactivation of gene products.
A robust acoustic droplet ejection–drop-on-tape method delivers samples to an X-ray free-electron laser source for combined serial femtosecond crystallography and X-ray emission spectroscopy analysis, providing detailed insights into macromolecular reaction dynamics.
SyConn is a computational framework that infers the synaptic wiring of neurons in volume electron microscopy data sets with machine learning. It has been applied to zebra finch, mouse and zebrafish neuronal tissue samples.
A software tool, cryoSPARC, addresses the speed bottleneck in cryo-EM image processing, enabling automated macromolecular structure determination in hours on a desktop computer without requiring a starting model.
Single-cell combinatorial indexed sequencing (SCI-seq) resolves genomic heterogeneity by generating thousands of low-pass single-cell libraries at once for somatic copy number variant detection.
The Census tool converts single-cell RNA-seq relative read counts to relative transcript counts for more accurate differential gene expression and analysis in the absence of spike-ins or molecular barcodes.
The Microfluidic-based Ligand Enrichment (SMiLE) sequencing strategy probes DNA binding of single and heterodimeric transcription factors over a wide affinity range.
Direct library preparation (DLP) is a robust and economic method for preparing large numbers of single-cell whole-genome sequencing libraries without preamplification, to study copy-number heterogeneity at the cell level and other variant types at the clone or population level.