Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

VEGAS Replicability

ABSTRACT: The VEGAS platform is not suitable for mammalian directed evolution

PROVIDER: PRJEB47639 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	ERR7881530_1.fastq.gz	Fastqsanger.gz
	ERR7881530_2.fastq.gz	Fastqsanger.gz
	ERR7881531_1.fastq.gz	Fastqsanger.gz
	ERR7881531_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 25

Similar Datasets

VEGAS: A Platform for Continuous Directed Evolution in Mammalian Cells (RNAseq)

Project description:VEGAS: A Platform for Continuous Directed Evolution in Mammalian Cells (RNAseq)

| PRJNA507988 | ENA

Single cell RNA-seq of BHK-21 cells carrying alphaviral RNA replication system

Project description:Directed evolution in mammalian cells can facilitate the engineering of mammalian-compatible biomolecules and can enable synthetic evolvability for mammalian cells. We engineered an orthogonal alphaviral RNA replication system to evolve synthetic RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in live mammalian cells. Toinvestigatetheexpressionheterogeneityofself-replicatingRNAsinrepRNA-v4cells,weperformedsingle-cellRNA-seqanalysisusingthe10xGenomicssequencingmethod.Ouranalysisofthesingle-cellRNA-seqprofilingdatarevealedarelativelyuniformexpressionpatternofself-replicatingRNAswithinrepRNA-v4cells.

2024-07-07 | GSE235341 | GEO

Analyzing the process of mutation accumulation in KRAS evolution experiment using amplicon sequencing

Project description:Directed evolution in mammalian cells can facilitate the engineering of mammalian-compatible biomolecules and can enable synthetic evolvability for mammalian cells. We engineered an orthogonal alphaviral RNA replication system to evolve synthetic RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in live mammalian cells. Using REPLACE, we attempted continuous intracellular evolution of the negative dominant mutant KRAS (S17N). To analyze the process of mutation accumulation, we performed amplicon sequencing on experimental materials at different stages and under different treatment conditions. The results indicated that the mutations generated by this system were primarily induced by Monanunavir, and the addition of Monanunavir significantly accelerated the rate of evolution.

2024-07-07 | GSE235327 | GEO

Project description:Vegas

| PRJNA982741 | ENA

Analyzing the process of mutation accumulation in MEK1 evolution experiment using amplicon sequencing

Project description:Directed evolution in mammalian cells can facilitate the engineering of mammalian-compatible biomolecules and can enable synthetic evolvability for mammalian cells. We engineered an orthogonal alphaviral RNA replication system to evolve synthetic RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in live mammalian cells. we employed REPLACE to drive the continuous intracellular evolution of the cancer-related protein MEK1 with the aim of conferring resistance to Cobimetinib. To investigate the accumulation of mutations during this evolutionary process, we conducted amplicon sequencing on experimental materials collected at different stages. The results revealed intricate relationships among different mutations, highlighting the complex nature of the evolutionary landscape.

2024-07-07 | GSE235328 | GEO

RNA sequencing of BHK-21 cells carrying alphaviral RNA replication system

Project description:Directed evolution in mammalian cells can facilitate the engineering of mammalian-compatible biomolecules and can enable synthetic evolvability for mammalian cells. We engineered an orthogonal alphaviral RNA replication system to evolve synthetic RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in live mammalian cells. RNA-seq of 3 different cells was performed to analyze the effect of introducing different versions of RNA replication systems (i.e., repRNA-v3 and repRNA-v4) into BHK-21 cells on endogenous gene expression. Analysis of the transcriptome profiling data indicated that repRNA-v4 stimulated lower interferon signaling and may have lower cytopathicity.

2024-07-07 | GSE217397 | GEO

Replicative RNA enables directed evolution and Darwinian adaptation in mammalian cells

Project description:Replicative RNA enables directed evolution and Darwinian adaptation in mammalian cells

| PRJNA985713 | ENA

Measurement of the degradation rate of alphaviral RNA in BHK-21 cells

Project description:Directed evolution in mammalian cells can facilitate the engineering of mammalian-compatible biomolecules and can enable synthetic evolvability for mammalian cells. We engineered an orthogonal alphaviral RNA replication system to evolve synthetic RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in live mammalian cells. To determine the degradation rate of alphaviral RNA in BHK-21 cells, 10 µg of repRNA-v4 RNA was transfected into 4 million wildtype BHK-21 cells via electroporation. Samples were collected at 1-hour, 3-hour, and 12-hour time points for subsequent RNA-seq analysis. The findings revealed that the half-life of alphaviral RNA in the cells was approximately 3.5 hours.

2024-07-07 | GSE235339 | GEO

Analysis of the accumulation of mutations in self-replicating RNAs using barcoded EGFP library

Project description:Directed evolution in mammalian cells can facilitate the engineering of mammalian-compatible biomolecules and can enable synthetic evolvability for mammalian cells. We engineered an orthogonal alphaviral RNA replication system to evolve synthetic RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in live mammalian cells. To investigate the process of mutation accumulation in REPLACE system, we constructed a repRNA-v4 plasmid library containing 64 barcodes. Using this library, we analyzed the differences in mutation accumulation for different RNAs upon entry into cells, before and after molnupiravir treatment, and before and after FACS sorting. The results demonstrated that these barcoded RNAs undergo similar processes of mutation accumulation, providing evidence that mutations are commonly accumulated across different RNAs.

2024-07-07 | GSE235338 | GEO

Project description:Ark313 Directed Evolution

| PRJNA843728 | ENA