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This work describes the generation of a modification-free RNA library that resembles endogenous transcriptome sequence and expression level, which can be used as a negative control in epitranscriptomic sequencing methods to obtain high-confidence and quantitative maps of various RNA modifications.
Three-photon microscopy in combination with adaptive optics-based aberration correction and ECG-triggered gating allows high-resolution imaging of neurons and astrocytes up to a depth of 1.4 mm in the mouse brain.
This analysis systematically evaluates cross-linking chemistry and chromatin fragmentation strategies commonly used in 3C assays and introduces an improved Hi-C protocol for detecting loops and compartments.
This work describes nascent Ribo-Seq, which measures the speed of ribosome loading and polysome assembly on endogenous mRNA through a combination of 4-thiouridine labeling and ribosome footprint sequencing.
This work describes m6A-seq2, which utilizes multiplexed N6-methyladenosine (m6A) immunoprecipitation of pre-barcoded and pooled samples to reduce the technical variability and allows direct comparison of m6A at the site, gene and sample level.
DECODE uses deep learning for localizing single emitters in high-density two-dimensional and three-dimensional single-molecule localization microscopy data. DECODE outperforms available methods and enables fast live-cell SMLM of dynamic processes.
The LIVECell dataset comprises annotated phase-contrast images of over 1.6 million cells from different cell lines during growth from sparse seeding to confluence for improved training of deep learning-based models of image segmentation.
Mitometer enables efficient, rapid, and accurate automated segmentation and tracking of mitochondria from time-lapse images. Mitometer performs well on diverse input images and can be used to monitor dynamic fission and fusion events.
DeepCAD is a self-supervised deep-learning approach for denoising calcium imaging data. DeepCAD improved SNR and facilitates neuron extraction and spike inference.
LiftPose3D infers three-dimensional poses from two-dimensional data or from limited three-dimensional data. The approach is illustrated for videos of behaving Drosophila, mice, rats and macaques.
Long-range CRISPR activation can be enhanced by concurrent recruitment of artificial TFs to the enhancer and promoter of a target gene. This CRISPR activation system can be employed to achieve allele-selective gene upregulation by differentially targeting single-nucleotide polymorphisms embedded in enhancers or other distally located sequences.
Acoustic reporter genes can be imaged with high sensitivity using the BURST imaging sequence, allowing the detection of single cells under optimal conditions.