Browse the toolkit beneath workflows. The mechanism branch runs mechanism -> architecture -> component, while the technique branch runs from high-level approaches down to concrete methods.
9 items matching 1 filter
Mechanism Branch
Layer 1
Mechanisms
Top-level concepts: biophysical action modes such as heterodimerization, photocleavage, or RNA binding.
Layer 2
Architectures
Arrangements that realize or deploy mechanisms, including switches, construct patterns, and delivery strategies.
Layer 3
Components
Low-level parts and sequence-defined elements used inside architectures, including protein domains and RNA elements.
Technique Branch
Layer 1
Approaches
High-level engineering practices such as computational design, directed evolution, sequence verification, and functional assay.
Layer 2
Methods
Concrete methods used to design, build, verify, or characterize engineered systems.
Showing 1-9 of 9
This Bayesian computational approach is a data-analysis method developed to improve prediction of split protein behavior by contextualizing errors inherent to experimental procedures. In the cited study, it was applied to pooled, sequencing-based screening data from split Cre recombinase constructs generated with optogenetic dimers, enabling comprehensive analysis of split sites across the protein.
Bisulfite pyrosequencing is an assay method used to quantify promoter CpG DNA methylation after bisulfite treatment. In the cited study, it was used to measure methylation in the CAMK1D, CRY2, and CALM2 promoter regions in peripheral blood from patients with type 2 diabetes and matched healthy controls.
Chromatin immunoprecipitation sequencing (ChIP-seq) is an assay method that combines chromatin immunoprecipitation with sequencing-based genomic localization to map protein-associated genomic regions. In the cited study, it was used to identify genome-wide ZFHX3-binding sites in suprachiasmatic nucleus chromatin, revealing occupancy concentrated near transcription start sites and co-localization with known histone modifications.
H3K36me3 cell-free chromatin immunoprecipitation sequencing (cfChIP-seq) is a plasma-based assay that establishes a personal gene expression profile from cell-free chromatin. In the cited study context, it functions as a reference enrichment assay for active genes in liquid biopsy samples.
The light-inducible split Cre recombinase is an optogenetic multi-component switch in which split Cre recombinase fragments are coupled to light-inducible dimerization modules to achieve inducible post-translational control of Cre activity. It was characterized by comprehensive screening of split sites across the Cre protein using a pooled, sequencing-based domain insertion profiling approach.
The pooled library approach is an engineering method for rapid generation and parallel screening of nearly all possible split-protein constructs, with sequencing-based readout. In the cited application, it was used with optogenetic dimers to comprehensively map split-site behavior across Cre recombinase and support inducible post-translational control design.
RNA sequencing (RNA-seq) is a transcriptomic assay method that quantifies gene-expression changes by sequencing RNA-derived libraries. In the cited study, it was used on adult rat amygdala tissue to detect subtle expression changes associated with development, cellular function, and nervous system disease after gestational high-THC cannabis smoke exposure.
Sequencing-based solutions are proposed assay methods for detecting large-scale CRISPR-associated genomic alterations. In the cited review, they are positioned as potential approaches to identify rare events such as translocations, inversions, deletions, and chromothripsis that can be missed by current workflows.
Single-cell RNA sequencing (scRNA-seq) is a transcriptomic assay method that measures RNA molecules in individual cells by sequencing-based transcript detection. In the cited application, it detected FLiCRE transcripts within the endogenous transcriptome, enabling simultaneous readout of cell type and calcium activation history.