Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

PROVIDER: PRJNA985719 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR24971020_subreads.fastq.gz	Fastqsanger.gz
	SRR24971021_subreads.fastq.gz	Fastqsanger.gz
	SRR24971022_subreads.fastq.gz	Fastqsanger.gz
	SRR24971023_subreads.fastq.gz	Fastqsanger.gz
	SRR24971024_subreads.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 5

Similar Datasets

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

Transcription profling of a yeast molecular barcoded ORF library

Project description:I used Affy Tag4 array as a readout of the molecular barcoded yeast orf library<br>

2009-07-02 | E-MEXP-2077 | biostudies-arrayexpress

Analysis of diversity in barcoded plasmid library

Project description:Analysis of diversity in barcoded plasmid library

| PRJNA630750 | ENA

Analysis of diversity in barcoded virus library

Project description:Analysis of diversity in barcoded virus library

| PRJNA630756 | ENA

CRISPR Anchor screening of a barcoded library in cells treated with standard of care neuroblastoma drugs

Project description:Neuroblastoma cells were treated with a barcoded library of >600 genes and one of several standrard of care neuroblastoma compounds (or vehicle control)

2023-09-28 | GSE223991 | GEO

Immunoprecipitated proteins associated with foci-forming Eno2p-EGFP-FLAG or non-forming Eno2V22Ap-EGFP-FLAG in yeast Saccharomyces cerevisiae under hypoxia

Project description:Yeast enolase (Eno2p) conjugated with EGFP and Flag-tag (Eno2p-EGFP-FLAG) and Eno2p with V22A substitution (Eno2V22Ap) conjugated with EGFP and Flag-tag (Eno2V22Ap-EGFP-FLAG) were produced in baker's yeast S. cerevisiae. After semi-anaerobic culture at 30 ˚C for 12h, cells producing Eno2p-EGFP-FLAG formed fluorescent foci, while cells producing Eno2V22Ap-EGFP-FLAG did not. The cells were collected and lysed, and proteins Eno2p-EGFP-FLAG or Eno2V22Ap-EGFP-FLAG and the associated proteins were coimmunoprecipitated using ANTI-FLAG M2 affinity gel and analyzed. Data contain two biological replicates and two technical replicates (n = 4). As the results, 96 proteins were detected with both recombinant Eno2p-EGFP-FLAG and Eno2V22Ap-EGFP-FLAG protein, 29 proteins were detected only with recombinant Eno2p-EGFP-FLAG protein, and 16 proteins were detected only with recombinant Eno2V22Ap-EGFP-FLAG protein. Data Processing/Data Analysis: The separated analytes were detected on an LTQ Velos linear ion trap mass spectrometer (Thermo Scientific). For data-dependent acquisition, the method was set to automatically analyze the five most intense ions observed in the MS scan. The mass spectrometry data were used for protein identification by the Mascot search engine on Protein Discoverer software (ver. 1.2, Thermo Scientific) against the information in the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org). Search parameters for peptide identification included a precursor mass tolerance of 1.2 Da, a fragment mass tolerance of 0.8 Da, a minimum of one tryptic terminus, and a maximum of one internal trypsin cleavage site. Cysteine carbamidomethylation (+57.021 Da) and methionine oxidation (+15.995 Da) were set as a differential amino acid modification. The data were then filtered at a q value ≤ 0.01 corresponding to 1% FDR at the spectral level.

2014-02-25 | PXD000173 | Pride

Transcriptome analysis of Mapt-EGFP+ and Mapt-EGFP- myenteric cells

Project description:Transcriptome analysis of Mapt-EGFP+ and Mapt-EGFP- myenteric cells

| PRJNA822404 | ENA

Interaction protein of Ptc1::eGFP and Ptc2::eGFP in Aspergillus flavus

Project description:There are the Mass spectrum original data of Ptc1 and Ptc2. The immunoprecipitated proteins from Ptc1::eGFP and Ptc2::eGFP stains in Aspergillus flavus were detected with SDS-PAGE. Next, in-gel tryptic digestion, and the peptides were obtained and detected by liquid chromatog-raphy coupled with tandem mass spectrometry (LC-MS/MS) on a Q-Exactive (QE) mass spectrometer (Thermo Fisher Scientific)

2023-07-06 | PXD038079 |

Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes

Project description:Calling cards technology using self-reporting transposons enables the identification of DNA-protein interactions through RNA sequencing . Here, we have drastically reduced the cost and labor requirements of calling card experiments in bulk populations of cells by introducing a DNA barcode into the calling card itself. An additional barcode incorporated during reverse transcription enables simultaneous transcriptome measurement in a facile and affordable protocol. We demonstrate that barcoded self-reporting transposons recover in vitro binding sites for four basic helix-loop-helix transcription factors with important roles in cell fate specification: ASCL1, MYOD1, NEUROD2, and NGN1. Further, simultaneous calling cards and transcriptional profiling during transcription factor overexpression identified both binding sites and gene expression changes for two of these factors. In sum, RNA-based identification of transcription factor binding sites and gene expression through barcoded self-reporting transposon calling cards and transcriptomes is an efficient and powerful method to infer gene regulatory networks in a population of cells.

2022-02-04 | GSE195992 | GEO

BM-eGFP+ MSC expression arrays

Project description:original population (oMSC) and highly migrative subpopulation (sMSC) of murine eGFP+ bone marrow MSC

| EGAD00010001265 | EGA