A5033045017- CRISPR and Genetic Engineering
- Single-cell and spatial transcriptomics
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Cancer Genomics and Diagnostics
- Genomics and Rare Diseases
- Monoclonal and Polyclonal Antibodies Research
- Advanced Biosensing Techniques and Applications
- Advanced biosensing and bioanalysis techniques
- Genetic Associations and Epidemiology
- Microtubule and mitosis dynamics
- Chromosomal and Genetic Variations
- Skin and Cellular Biology Research
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- Cell Image Analysis Techniques
- RNA regulation and disease
- Cellular Mechanics and Interactions
- Genomic variations and chromosomal abnormalities
- Anodic Oxide Films and Nanostructures
Applied Genetic Technologies (United States)
2022-2025
Duke University
2022-2025
Durham Technical Community College
2024
Abstract The ENCODE Consortium’s efforts to annotate noncoding cis -regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, CRISPR screens offer a systematic approach investigate mechanisms. ENCODE4 Functional Characterization Centers conducted 108 in human cell lines, comprising >540,000 perturbations across 24.85 megabases the genome. Using 332 functionally confirmed CRE–gene links K562 cells, we established guidelines for screening endogenous...
Highlights•CRISPR barnyard screens characterize the distribution of ambient gRNAs•CRISPR identify factors influencing abundance gRNAs•CLEANSER is open-source software that assigns gRNAs to cells in perturb-seq screens•CLEANSER demonstrates increased accuracy calling hits published datasetsSummarySingle-cell RNA sequencing CRISPR (perturb-seq) enable high-throughput investigation genome, allowing for characterization thousands genomic perturbations on gene expression. Ambient gRNAs, which are...
Epigenetic control of cellular transcription and phenotype is influenced by changes in the microenvironment, yet how mechanical cues from these microenvironments precisely influence epigenetic state to regulate remains largely unmapped. Here, we combine genome-wide epigenome profiling, editing, phenotypic single-cell RNA-seq CRISPR screening identify a new class genomic enhancers that responds microenvironment. These ‘mechanoenhancers’ could be active on either soft or stiff extracellular...
Abstract The ENCODE Consortium’s efforts to annotate non-coding, cis -regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes which play a major role in health and disease. Pooled, non-coding CRISPR screens are promising approach for systematically investigating mechanisms. Here, the Functional Characterization Centers report 109 comprising 346,970 individual perturbations across 13.3Mb genome, using variety methods, readouts, statistical analyses. Across 332...
Recent technological developments in single-cell RNA-seq CRISPR screens enable high-throughput investigation of the genome. Through transduction a gRNA library to cell population followed by transcriptomic profiling scRNA-seq, it is possible characterize effects thousands genomic perturbations on global gene expression. A major source noise scRNA-seq are ambient gRNAs, which contaminating gRNAs that likely originate from other cells. If not properly filtered, can result an excess false...
CRISPR epigenomic editing technologies enable functional interrogation of non-coding elements. However, current computational methods for guide RNA (gRNA) design do not effectively predict the power potential, molecular and cellular impact to optimize efficient gRNAs, which are crucial successful applications these technologies. We present "launch-dCas9" (machine LeArning based UNified CompreHensive framework CRISPR-dCas9) gRNA from multiple perspectives, including cell fitness, wildtype...
This protocol describes methods for a CRISPR screen to identify motifs in the MYH9 intron 3 mechanoenhancer that control expression.
This protocol describes methods for a CRISPR interference screen to identify open chromatin regions that function as stiffness-responsive modulators of cell growth and migration.
This protocol describes methods for a CRISPR interference screen to identify open chromatin regions that function as stiffness-responsive modulators of MYH9 expression.
This protocols describes methods for Omni ATAC-seq to characterize the chromatin structural responses changes in extracellular matrix stiffness cues.
This protocols describes methods for RNA-seq to characterize the cellular gene expression responses changes in extracellular matrix stiffness cues.