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PubMed Journals Articles About "Single Cell Genotyping CRISPR Transfected Neurons Http I2mA50uXxf7" RSS

02:42 EDT 24th August 2019 | BioPortfolio

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Showing "Single Cell Genotyping CRISPR Transfected Neurons http I2mA50uXxf7" PubMed Articles 1–25 of 36,000+

In Vivo Single-Cell Genotyping of Mouse Cortical Neurons Transfected with CRISPR/Cas9.

CRISPR/Cas-based technologies have revolutionized genetic approaches to addressing a wide range of neurobiological questions. The ability of CRISPR/Cas to introduce mutations into target genes allows us to perform in vivo loss-of-function experiments without generating genetically engineered mice. However, the lack of a reliable method to determine genotypes of individual CRISPR/Cas-transfected cells has made it impossible to unambiguously identify the genetic cause of their phenotypes in vivo. Here, we r...


SureTypeSC - A Random Forest and Gaussian Mixture predictor of high confidence genotypes in single cell data.

Accurate genotyping of DNA from a single cell is required for applications such as de novo mutation detection, linkage analysis and lineage tracing. However, achieving high precision genotyping in the single cell environment is challenging due to the errors caused by whole genome amplification. Two factors make genotyping from single cells using single nucleotide polymorphism (SNP) arrays challenging. The lack of a comprehensive single cell dataset with a reference genotype and the absence of genotyping too...

CRISPR Screening in Single Cells.

The combination of single-cell RNA-seq and CRISPR allows for efficient interrogation of possibly any number of genes, only limited by the sequencing capability. Here we describe the current protocols for CRISPR screening in single cells, from cloning and virus production to generating sequencing data.


Kinetic Measurements of Endocytosis and Exocytosis in Cultured Neurons.

The measurement of synaptic vesicle recycling in live neurons transfected with vesicular glutamate transporter fused to pHluorin (vGLUT-pHluorin) allows us to study exocytosis and endocytosis in neurons. When neurons are transfected with this protein we can measure the rate of vesicles fusing and internalizing from the membrane using live total internal reflection fluorescence (TIRF) imaging. Here, we describe transfection, culturing, and imaging of wild-type and αβγ-synuclein knockout hippocampal neuron...

Highly efficient correction of structural mutations of 450 kb KIT locus in kidney cells of Yorkshire pig by CRISPR/Cas9.

The white coat colour of Yorkshire and Landrace pig breeds is caused by the dominant white I allele of KIT, associated with 450-kb duplications and a splice mutation (G > A) at the first base in intron 17. To test whether genome editing can be employed to correct this structural mutation, and to investigate the role of KIT in the control of porcine coat colour, we designed sgRNAs targeting either intron 16 or intron 17 of KIT, and transfected Cas9/sgRNA co-expression plasmids into the kidney cells of Yo...

Single-Cell Heterogeneity Analysis and CRISPR Screen Identify Key β-Cell-Specific Disease Genes.

Identification of human disease signature genes typically requires samples from many donors to achieve statistical significance. Here, we show that single-cell heterogeneity analysis may overcome this hurdle by significantly improving the test sensitivity. We analyzed the transcriptome of 39,905 single islets cells from 9 donors and observed distinct β cell heterogeneity trajectories associated with obesity or type 2 diabetes (T2D). We therefore developed RePACT, a sensitive single-cell analysis algorithm ...

Rabies virus-mediated connectivity tracing from single neurons.

An understanding of how the brain processes information requires knowledge of its underlying wiring diagrams, as well as insights into the relationship between circuit architecture and physiological function. Notably, rabies virus based single-cell genetic manipulations that can facilitate an experimental link between physiology and genetics have recently advanced the field of systems neuroscience. It allows capturing the synaptic and the anatomical receptive fields of individual neurons. Recently, the meth...

Establishment of PITX3-mCherry knock-in reporter human embryonic stem cell line (WAe009-A-23).

Pituitary homeobox 3 (Pitx3) is a key transcription factor that plays an important role in the development and maintenance of midbrain dopaminergic (mDA) neurons. Here, we established a PITX3-mCherry knock-in reporter human embryonic stem cell (hESC) line using the CRISPR/Cas9 system. PITX3-mCherry hESCs maintained pluripotency marker expression and exhibited the capacity to generate all 3 germ layers and a normal karyotype. After differentiation into mDA neurons, most PITX3 immunoreactivity overlapped with...

A Single-Cell Model for Synaptic Transmission and Plasticity in Human iPSC-Derived Neurons.

Synaptic dysfunction is associated with many brain disorders, but robust human cell models to study synaptic transmission and plasticity are lacking. Instead, current in vitro studies on human neurons typically rely on spontaneous synaptic events as a proxy for synapse function. Here, we describe a standardized in vitro approach using human neurons cultured individually on glia microdot arrays that allow single-cell analysis of synapse formation and function. We show that single glutamatergic or GABAergic...

TARGET-seq Takes Aim at Cancer Evolution through Multi-omics Single-Cell Genotyping and Transcriptomics.

In this issue of Molecular Cell, Rodriguez-Meira et al. (2019) present TARGET-seq, an elegant single-cell method that genotypes somatic mutations and captures whole transcriptomes in the same tumor cells, thus paving the way to directly link somatic mutations with resulting transcriptional phenotypes in clonally diverse cancer populations.

Genetics of Alzheimer's Disease.

Alzheimer's disease (AD) related genes have been elucidated by advanced genetic techniques. Familial autosomal dominant AD genes founded by linkage analyses are , , , , and . Genome-wide association studies have found risk genes such as , , , , , , , , , , , , , , , , , , , , and . , , , and are proved to have high odds ratio (>2) in risk of AD using next generation sequencing studies. Thanks to the promising genetic techniques such as CRISPR-CAS9 and single-cell RNA sequencing opened a new era in genetics...

Large scale control and programming of gene expression using CRISPR.

The control of gene expression in cells and organisms allows to unveil gene to function relationships and to reprogram biological responses. Several systems, such as Zinc fingers, TALE (Transcription activator-like effectors), and siRNAs (small-interfering RNAs), have been exploited to achieve this. However, recent advances in Clustered Regularly Interspaced Short Palindromic Repeats and Cas9 (CRISPR-Cas9) have overshadowed them due to high specificity, compatibility with many different organisms, and desig...

Polymorphism of Type I-F CRISPR/Cas system in Escherichia coli of phylogenetic group B2 and its application in genotyping.

E. coli of phylogenetic group B2 is responsible for many extraintestinal infections, posing a great threat to health. The relatively polymorphic nature of CRISPR in phylogenetically related E. coli strains makes them potential markers for bacterial typing and evolutionary studies. In the current work, we investigated the occurrence and diversity of CRISPR/Cas system and explored its potential for genotyping. Type I-F CRISPR/Cas systems were found in 413 of 1190 strains of E. coli and exhibited the clusterin...

Method for Labeling and Reconstruction of Single Neurons Using Sindbis Virus Vectors.

Neuronal dendrites and axons are key substrates for the input and output of information, respectively, so establishing the precise and complete morphological description of dendritic and axonal processes of a single neuron is essential for understanding the neuron's functional role in the neuronal circuits. The whole structure of single neurons was originally revealed using Golgi staining, and later the intracellular labeling method was developed, although this is technically too difficult to stain entire n...

CRISPR-Cas9 system: A new-fangled dawn in gene editing.

Till date, only three techniques namely Zinc Finger Nuclease (ZFN), Transcription-Activator Like Effector Molecules (TALEN) and Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-Associated 9 (CRISPR-Cas9) are available for targeted genome editing. CRISPR-Cas system is very efficient, fast, easy and cheap technique for achieving knock-out gene in the cell. CRISPR-Cas9 system refurbishes the targeted genome editing approach into a more expedient and competent way, thus facilitating proficient g...

Neural effects of transcranial magnetic stimulation at the single-cell level.

Transcranial magnetic stimulation (TMS) can non-invasively modulate neural activity in humans. Despite three decades of research, the spatial extent of the cortical area activated by TMS is still controversial. Moreover, how TMS interacts with task-related activity during motor behavior is unknown. Here, we applied single-pulse TMS over macaque parietal cortex while recording single-unit activity at various distances from the center of stimulation during grasping. The spatial extent of TMS-induced activatio...

Evolution of neuronal types and families.

Major questions in the evolution of neurons and nervous systems remain unsolved, such as the origin of the first neuron, the possible convergent evolution of neuronal phenotypes, and the transition from a relatively simple decentralized nerve net to the complex, centralized nervous systems found in modern bilaterian animals. In recent years, comparative single-cell transcriptomics has opened up new research avenues addressing these issues. Here, we review recent conceptual progress toward an evolutionary de...

Directly Reprogrammed Neurons Still Have Some Growing Up to Do.

Direct lineage conversion offers a fast and simple method to study mature neurons in vitro, but its utility for investigating neurodevelopment has remained unclear. In this issue of Cell Stem Cell, Chanda et al. (2019) use Ngn2-induced neurons to elucidate the pathogenic mechanisms of the teratogenic compound valproic acid.

Progress and Challenges for Live-cell Imaging of Genomic Loci Using CRISPR-based Platforms.

Chromatin conformation, localization, and dynamics are crucial regulators of cellular behaviors. Although fluorescence in situ hybridization-based techniques have been widely utilized for investigating chromatin architectures in healthy and diseased states, the requirement for cell fixation precludes the comprehensive dynamic analysis necessary to fully understand chromatin activities. This has spurred the development and application of a variety of imaging methodologies for visualizing single chromosomal l...

Lipid heterogeneity between astrocytes and neurons revealed with single cell MALDI MS supervised by immunocytochemical classification.

Transcriptomics characterizes cells based on their potential molecular repertoire whereas direct mass spectrometry (MS) provides information on the actual compounds present within cells. Single cell matrix assisted laser desorption/ionization (MALDI) MS can measure the chemical contents of individual cells but spectra are difficult to correlate to conventional cell types, limiting the metabolic information obtained. We present a protocol that combines MALDI MS with immunocytochemistry to assay over a thousa...

Generation of a FMR1 homozygous knockout human embryonic stem cell line (WAe009-A-16) by CRISPR/Cas9 editing.

Mutations in FMR1 gene is the cause of Fragile X Syndrome (FXS) leading inherited cause of intellectual disability and autism spectrum disorders. FMR1 gene encodes Fragile X Mental Retardation Protein (FMRP) which is a RNA binding protein and play important role in synaptic plasticity and translational regulation in neurons. We have generated a homozygous FMR1 knockout (FMR1-KO) hESC line using CRISPR/Cas9 based genome editing. It created a homozygous 280 nucleotide deletion at exon1, removing the start cod...

DNA sequencing in high-throughput neuroanatomy.

Mapping brain connectivity at single cell resolution is critical for understanding brain structure. For decades, such mapping has been principally approached with microscopy techniques, aiming to visualize neurons and their connections. However, these techniques are very labor intensive and do not scale well to the complexity of mammalian brains. We recently leveraged the speed and parallelization of DNA sequencing to map the projections of thousands of single neurons in single experiments, and to map corti...

Characterization of CRISPR-Cas systems in Leptospira reveals potential application of CRISPR in genotyping of Leptospira interrogans.

Leptospirosis is a zoonotic disease caused by pathogenic Leptospira. However, understanding of the pathogenic mechanism of Leptospira is still elusive due to the limited number of genetic tools available for this microorganism. Currently, the reason for the genetic inaccessibility of Leptospira is still unknown. It is well known that as an acquired immunity of bacteria, Clustered Regularly Interspaced Short Palindromic Repeat-CRISPR-associated gene (CRISPR-Cas) systems can help bacteria against invading mob...

Diversity of CRISPR/Cas system in Clostridium perfringens.

Clostridium perfringens is an important pathogen of human and livestock infections, posing a threat to health. The horizontal gene transfer (HGT) of plasmids that carry toxin-related genes is involved in C. perfringens pathogenicity. The CRISPR/Cas system, which has been identified in a wide range of prokaryotes, provides acquired immunity against HGT. However, information about the CRISPR/Cas system in Clostridium perfringens is still limited. In this study, 111 C. perfringens strains with publicly availab...

An Agrobacterium-delivered CRISPR/Cas9 system for targeted mutagenesis in sorghum.

Clustered regularly interspaced short palindromic repeat/CRISPR-associated Cas9 (CRISPR/Cas9) systems of bacteria and archaea have engineered for genome editing in eukaryotic genomes. In such CRISPR/Cas9 system, CRISPR RNA (crRNA) and trans-activating CRISPR RNA (tracrRNA) were engineered into a simplified single guide RNA (sgRNA). Cas9 and sgRNA form a complex that scans through genome for the protospacer adjacent motif (PAM) sequence (predominantly 5'-NGG-3') and for the sequence (ca. 18-20 nucleotides) c...


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