Toolkit Items

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.

Adeno-associated virus (AAV) is a viral delivery harness used to package and express CRISPR genome-editing components in vivo. In the cited literature, AAV supports single-vector delivery when smaller Cas9 orthologues and their chimeric guide RNAs fit within AAV packaging constraints, enabling robust in vivo genome editing.

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.

CLSM and super-resolution fluorescence imaging by direct stochastic optical reconstruction microscopy demonstrated homogeneous distribution of ceramide analogs in the bacterial membrane.

Immunohistochemistry is an antibody-based tissue staining assay used in the cited stroke study alongside transcriptomics and real-time polymerase chain reaction to examine post-stroke tissue in aged rats and post-stroke patients. In that context, it supported assessment of angiogenesis-related histological features such as vascular density after stroke.

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.

Multi-locus sequencing, multiplex PCR, and next-generation sequencing refined the identification of fungal and bacterial pathogens.

Chemogenetics is an engineering method in which target proteins are genetically engineered to interact with a designed chemical partner with high selectivity. It is used as a chemical-input strategy to manipulate protein or receptor function in cells and has also been used alongside optogenetics to perturb cellular structures such as specific microtubule subtypes.

Spatial transcriptomics is a transcriptomic assay method identified in the supplied review as a recent methodological advance. In that evidence, it is presented as part of a broader technology set that enables easier and more accurate visualization of cell behavior and qualitative and quantitative analysis of cell-cell interactions.

These tools include quantitative behavioral assays, calcium imaging, optogenetics and transgenics.

This review highlights the latest cutting-edge technologies driving progress in the field, including ... single-cell sequencing...

Light-controlled crRNA is a chemically modified CRISPR guide RNA in which vitamin E is attached to the 5' terminus through a photolabile linker, creating a caged crRNA that inactivates CRISPR/Cas9 until light exposure. Upon irradiation, this design restores CRISPR/Cas9 activity and supports genome editing of VEGFA and knockdown of EGFP expression in human cells.

The pUC18T-mini-Tn7T system enables IPTG-inducible, site-specific genomic integration of genes in single copy via the Ptac-lacIq regulatory system.

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.

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.

Proximity labeling is described here as a methodological approach proposed to define state-specific proteomic and post-translational signatures in studies evaluating the addivosome pathological condensate model. The supplied evidence does not identify a specific proximity-labeling enzyme, chemistry, or construct design.

We present a cheap, rapid, and versatile assay called SOSHI-seq (Screening of Self-transcribed Hormone Inducible response elements coupled to sequencing).

Sensitive detection of tobamoviruses in the field with minimal sample preparation can be achieved using latest technologies such as isothermal amplification, CRISPR/Cas-hybrid assays or next-generation sequencing.

advanced tools such as next-generation sequencing (NGS), direct stochastic optical reconstruction microscopy (dSTORM), or multiparametric flow cytometry are helping to identify novel tumor-specific targets and improve therapy designs

Multi-locus sequencing, multiplex PCR, and next-generation sequencing refined the identification of fungal and bacterial pathogens.

Here, we implement a single unique molecular identifier strategy that reduces sequencing artifacts and achieves an error rate of ~10⁻⁵, enabling single-particle-level quantification of quasi-species diversity.

Both vesicle fluid culture and next-generation sequencing (NGS) of blood samples confirmed the presence of Escherichia coli.

Both vesicle fluid culture and next-generation sequencing (NGS) of blood samples confirmed the presence of Escherichia coli.

The dual enzyme lineage tracing system is identified in a 2023 review as a recent methodological advance in lineage tracing. The supplied evidence indicates that it is intended to support visualization of cell behavior and analysis of cell-cell interactions, but no construct-level, enzyme-specific, or operational details are provided.

By using soy-absorbed, peanut-allergic patient sera on two-dimensional immunoblots and N-terminal amino-acid sequencing, about 30 protein fractions were shown to be isoforms, or fractions, of the three major peanut proteins.

While these methods, like polymerase chain reactions or whole-genome sequencing, are considered the "gold standard" for diagnostics, the development of inexpensive, rapid diagnostic assays is necessary for effective AMR detection and management.

Programmable genetic circuits are engineered genetic constructs used to create designer cells with controllable behaviors in mammalian synthetic biology. The cited literature describes circuits that can incorporate targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices to regulate complex cellular functions with high spatial and temporal resolution.

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.

mRNA-sequencing of OX lines revealed substantial upregulation of Pi starvation-responsive genes, including SPX1, PS2/PECP2, and SRG3/GDPD1.

small RNA-sequencing identified the downregulation of miR399 and miR827, which are involved in the Pi starvation response.

Sensitive detection of tobamoviruses in the field with minimal sample preparation can be achieved using latest technologies such as isothermal amplification, CRISPR/Cas-hybrid assays or next-generation sequencing.

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.

Sequencing of the samples was performed using Illumina NovaSeq X Plus platform.

high-throughput technologies such as MeRIP-seq and nanopore direct RNA sequencing have enabled the preliminary construction of RNA methylation landscapes in cucurbit species

high-throughput technologies such as MeRIP-seq and nanopore direct RNA sequencing have enabled the preliminary construction of RNA methylation landscapes in cucurbit species

this view has been challenged in the last few years with the availability of RNA sequencing, immunohistochemistry, electron microscopy, morphological reconstruction, and imaging data

this view has been challenged in the last few years with the availability of RNA sequencing, immunohistochemistry, electron microscopy, morphological reconstruction, and imaging data

The emerging tools that have translational relevance, as pointed out by the review, include... spatial proteomics...

The emerging tools that have translational relevance, as pointed out by the review, include... synaptic positron emission tomography (PET) imaging, with the capabilities of providing disease-specific and patient-level insights into the pathology of synapses.

Whole exome sequencing identified two heterozygous variants in the NPHS1 gene, as well as one heterozygous and one homozygous variant in the PLEKHG2 gene.

Light and electron microscopy have been widely used in confirming the bipolarity of somatic embryos during somatic embryogenesis.

Long non-coding RNAs (lncRNAs) are non-protein-coding RNA elements within the broader non-coding RNA landscape. In plants, available reports indicate that lncRNAs participate in light-dependent processes including photomorphogenesis, cotyledon greening, and photoperiod-regulated flowering.

Our strategy permanently inactivates VWF variants by selectively disrupting the pathogenic allele's open reading frame via the introduction of indels by Cas9. To circumvent the challenge of designing variant-specific strategies, we targeted the common single nucleotide polymorphism (SNP) rs1800378 in VWF.

The review further evaluates the clinical translational potential and challenges of innovative strategies such as vagus nerve stimulation, optogenetics, multiomics sequencing, and cytokine-targeted therapies.

The synthetic receptor system is described in a 2023 review as a methodological advance for studying cell behavior and cell-cell interactions. The available evidence indicates that it enables easier and more accurate visualization and supports qualitative and quantitative analysis in this context, but no molecular architecture or operating principle is provided.

We then develop CellChat, a tool that is able to quantitatively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data.

Here, we present CNNeoPP, an integrated computational pipeline for neoantigen discovery. CNNeoPP was rigorously validated using independent datasets, including the TESLA dataset, and experimental validation via ELISpot T-cell assays.

Personalization using advanced technologies like CRISPR screening and single-cell RNA sequencing can enhance durability and effectiveness of treatments for heavily pretreated patients

we developed Dogme to automate basecalling, alignment, modification detection, and transcript quantification. Dogme automates the reprocessing of ONT POD5 files

we have developed FragmentFinder-an intuitive, Windows-executable resource designed to require absolutely no computational background and capable of accurately characterizing all (annotated and unknown) sncRNA-derived RNAs within a raw small RNA sequencing file in real time.