Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Simultaneous multifunctional transcriptome engineering by CRISPR RNA scaffold

ABSTRACT: Simultaneous multifunctional transcriptome engineering by CRISPR RNA scaffold

PROVIDER: PRJNA851969 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19792861_1.fastq.gz	Fastqsanger.gz
	SRR19792861_2.fastq.gz	Fastqsanger.gz
	SRR19792862_1.fastq.gz	Fastqsanger.gz
	SRR19792862_2.fastq.gz	Fastqsanger.gz
	SRR19792863_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

Simultaneous multifunctional transcriptome engineering by CRISPR RNA scaffold

Project description:RNA processing and metabolism are subjected to precise regulation in the cell to ensure integrity and functions of RNA. Though targeted RNA engineering has become feasible with the discovery and engineering of the CRISPR-Cas13 system, simultaneous modulation of different RNA processing steps remains unavailable. In addition, the off-target events resulting from the effectors fused with dCas13 limit its application. Here we developed a novel platform, Combinatorial RNA Engineering via Scaffold Tagged gRNA (CREST), which can simultaneously execute multiple RNA modulation functions on different RNA targets. In CREST, RNA scaffolds are appended to the 3’ end of Cas13 gRNA and their cognate RNA binding proteins are fused with enzymatic domains for manipulation. We show that CREST is capable of simultaneously manipulating RNA alternative splicing and A-to-G or C-to-U base editing. Furthermore, by fusing two split fragments of the deaminase domain of ADAR2 to dCas13 and PUFc respectively, we reconstituted its enzyme activity at target sites. This split design can reduce more than 90% of off-target events otherwise induced by a full-length effector. The flexibility of the CREST framework will enrich the transcriptome engineering toolbox for the study of RNA biology and the development of RNA-focused therapeutics

2022-06-26 | GSE206745 | GEO

Transcription profiling of human fibroblasts grown in petri dishes vs. attached to a tissue engineering scaffold sampled at 7 timepoints.

Project description:A goal of tissue engineering is to produce a scaffold material that will guide cells to differentiate and regenerate functional replacement tissue at the site of injury. Little is known about how cells respond on a molecular level to tissue engineering scaffold materials. In this work we used oligonucleotide microarrays to interrogate gene expression profiles associated with cell-biomaterial interactions. We seeded collagen-glycosaminoglycan meshes, a widely used tissue engineering scaffold material, with human IMR-90 fibroblasts and compared transcript levels with control cells grown on tissue culture polystyrene. Genes involved in cell signaling, extracellular matrix remodeling, inflammation, angiogenesis and hypoxia were all activated in cells on the collagen-GAG mesh. Understanding the impact of a scaffold on attached cells will facilitate the design of improved tissue engineering materials.

2007-10-26 | E-GEOD-6432 | biostudies-arrayexpress

Scaffold RNA engineering in type V CRISPR-Cas systems: a potent way to enhance gene expression in the yeast Saccharomyces cerevisiae.

Project description:New, orthogonal transcription factors in eukaryotic cells have been realized by engineering nuclease-deficient CRISPR-associated proteins and/or their guide RNAs. In this work, we present a new kind of orthogonal activators, in Saccharomyces cerevisiae, made by turning type V CRISPR RNA into a scaffold RNA (ScRNA) able to recruit a variable number of VP64 activation domains. The activator arises from the complex between the synthetic ScRNA and DNase-deficient type V Cas proteins: dCas12e and denAsCas12a. The transcription activation achieved via the newly engineered dCas:ScRNA system is up to 4.7-fold higher than that obtained with the direct fusion of VP64 to Cas proteins. The new transcription factors have been proven to be functional in circuits such as Boolean gates, converters, multiplex-gene and metabolic-pathway activation. Our results extend the CRISPR-Cas-based technology with a new effective tool that only demands RNA engineering and improves the current design of transcription factors based on type V Cas proteins.

2023-12-05 | GSE249355 | GEO

Transcription profiling time series of the growth of human IMR-90 cells seeded on a collagen/chondroitin sulfate tissue engineering scaffold

Project description:A series of chips with some repeated measurments. Each chip represents a pool of 4 collagen/chondroitin sulfate tissue engineering scaffold meshes seeded with 1 x 10^6 IMR-90 Human Fibroblasts. mRNA was isolated at 30 minutes, 1, 2, 4, 8, 12, 24, 48, and 72 hours after seeding.

2007-12-13 | E-GEOD-409 | biostudies-arrayexpress

Identification of Novel Scaffold Proteins for Improved Endogenous Engineering of Extracellular Vesicles

Project description:Extracellular vesicles (EVs) are gaining ground as next-generation drug delivery modalities. Genetic fusion of the protein of interest to a scaffold protein with high EV-sorting ability represents a robust cargo loading strategy. In this study 244 candidate scaffold proteins were studied, resulting in the identification of 24 proteins with conserved EV-sorting abilities across five types of producer cells. TSPAN2 and TSPAN3 were detected as the lead candidates for cargo loading, outperforming the well-known CD63 scaffold. EVs from human embryonic kidney epithelial (HEK-293T) cells, either wild type or overexpressing TSPAN2, TSPAN3 or CD63, were analyzed with label-free top-down proteomics to understand the effect of EV-engineering on protein signatures. The proteomics findings demonstrated that TSPAN2/TSPAN3-based engineering gives rise to EV subpopulations distinct from CD63. The discovery of these novel scaffolds provides a new platform for EV-based therapies.

2023-08-18 | PXD043840 | Pride

Simultaneous in vivo enzyme and host engineering through laboratory evolution

Project description:Simultaneous in vivo enzyme and host engineering through laboratory evolution

| PRJEB26704 | ENA

Scaffold RNA engineering in type V CRISPR-Cas systems: a potent way to enhance gene expression in the yeast Saccharomyces cerevisiae.

Project description:Scaffold RNA engineering in type V CRISPR-Cas systems: a potent way to enhance gene expression in the yeast Saccharomyces cerevisiae.

| PRJNA1048852 | ENA

All-in-one Engineering Multifunctional Nanoplatforms for Sensitizing Tumor Low-Temperature Photothermal Therapy in vivo

Project description:All-in-one Engineering Multifunctional Nanoplatforms for Sensitizing Tumor Low-Temperature Photothermal Therapy in vivo

| PRJNA1026142 | ENA

CRISPR Display: A modular method for locus-specific targeting of long noncoding RNAs and synthetic RNA devices in vivo [RIP-Seq]

Project description:Noncoding RNAs (ncRNAs) comprise an important class of natural regulators that mediate a vast array of biological processes, including the modulation of chromatin architecture. Moreover, artificial ncRNAs have revealed that the functional capabilities of RNA are extremely broad. To further investigate and harness these capabilities, we developed CRISPR-Display ("CRISP-Disp"), a targeted localization strategy that uses Cas9 to deploy large RNA cargos to specific DNA loci. We demonstrate that exogenous RNA domains can be functionally appended onto the CRISPR scaffold at multiple insertion points, allowing the construction of Cas9 complexes with RNAs nearing one kilobase in length, with structured RNAs, protein-binding cassettes, artificial aptamers and pools of random sequences. CRISP-Disp also allows the simultaneous multiplexing of disparate functions at multiple targets. We anticipate that this technology will provide a powerful method with which to ectopically localize functional RNAs and ribonuceloprotein complexes at specified genomic loci. RNA Immunoprecipitation (RIP) against FLAG-tagged Cas9 protein, coexpressed with a large pool of CRISPR RNAs bearing random internal insertions

2015-05-11 | E-GEOD-62305 | biostudies-arrayexpress

Lakshman scaffold

Project description:Lakshman Kund scaffold Metagenomic assembly

| PRJNA902919 | ENA