Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PROTein Evolution Using Selection (PROTEUS) [Nanopore]

ABSTRACT: PROTein Evolution Using Selection (PROTEUS) [Nanopore]

PROVIDER: PRJNA1054174 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR27276546_1.fastq.gz	Fastqsanger.gz
	SRR27276547_1.fastq.gz	Fastqsanger.gz
	SRR27276548_1.fastq.gz	Fastqsanger.gz
	SRR27276549_1.fastq.gz	Fastqsanger.gz
	SRR27276550_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

PROTein Evolution Using Selection (PROTEUS) [Nanopore]

Project description:Directed evolution (DE) is a process of mutation and iterative artificial selection to breed biomolecules with new or improved activity. DE platforms are primarily prokaryotic or yeast-based, and stable highly mutagenic mammalian systems have been challenging to establish and apply. To this end, we developed PROTein Evolution Using Selection (PROTEUS), a new platform that uses chimeric virus-like vesicles (VLVs) to enable extended mammalian DE campaigns without loss of system integrity. This platform, consisting of a minimal modified Semliki Forest virus genome controlling expression of the Indiana vesiculovirus G coat protein, is stable and can generate sufficient diversity for DE in mammalian systems. Using PROTEUS, we altered the doxycycline responsiveness of tetracycline-controlled transactivators, generating a more sensitive TetON-4G tool for gene regulation. PROTEUS is also compatible with intracellular nanobody evolution, and we use it to design a novel DNA damage-responsive anti-p53 nanobody. Overall, PROTEUS is a robust, efficient, and stable platform to direct evolution of biomolecules within mammalian cells.

2025-04-03 | GSE250501 | GEO

PROTein Evolution Using Selection (PROTEUS) [Illumina]

2025-04-03 | GSE250500 | GEO

PROTein Evolution Using Selection (PROTEUS)

Project description:PROTein Evolution Using Selection (PROTEUS)

| PRJNA1054169 | ENA

PROTein Evolution Using Selection (PROTEUS) [Illumina]

Project description:PROTein Evolution Using Selection (PROTEUS) [Illumina]

| PRJNA1054172 | ENA

PROTein Evolution Using Selection (PROTEUS)

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-04-03 | GSE250502 | GEO

hMeDIP-seq of mouse cerebellum using nanopore sequencing

Project description:5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are modified versions of cytosine in DNA with roles in regulating gene expression. Using whole genomic DNA from mouse cerebellum, we benchmark 5mC and 5hmC detection by Oxford Nanopore Technologies sequencing against other standard techniques. In addition, we assess the ability of duplex base-calling to study strand asymmetric modification. Nanopore detection of 5mC and 5hmC is accurate relative to compared techniques and opens new means of studying these modifications. Strand asymmetric modification is widespread across the genome but reduced at imprinting control regions and CTCF binding sites in mouse cerebellum. Here we demonstrate the unique ability of nanopore sequencing to improve the resolution and detail of cytosine modification mapping.

2025-02-03 | GSE288331 | GEO

Epigenetic evolution of the Ly49 gene family [NanoPore]

Project description:Epigenetic evolution of the Ly49 gene family [NanoPore]

| PRJNA979148 | ENA

Proteus mirabilis mrpJ microarrays

Project description:This series of microarrays compares gene expression by the bacterial pathogen Proteus mirabilis when the transcriptional regulator mrpJ is deleted or induced to levels found during experimental urinary tract infection. The enteric bacterium Proteus mirabilis is associated with a significant number of catheter-associated urinary tract infections. Strict regulation of the antagonistic processes of adhesion and motility, mediated by fimbriae and flagella, respectively, is essential for successful disease progression. Previously, the transcriptional regulator MrpJ, which is encoded by the mrp fimbrial operon, has been shown to repress both swimming and swarming motility. Here we show that MrpJ affects a wide array of cellular processes beyond adherence and motility. Microarray analysis found that expression of mrpJ mimicking expression levels that occur during UTI leads to differential expression of 217 genes related to, among others, bacterial virulence, type VI secretion and metabolism. We probed the molecular mechanism of transcriptional regulation through MrpJ using reporter assays and chromatin immunoprecipitation (ChIP). Two virulence-associated target genes, the flagellar master regulator flhDC and mrp itself, appear to be regulated through a binding site proximal to the transcriptional start, complemented by a more distantly situated enhancer site. Furthermore, an mrpJ deletion mutant colonized the bladders of mice at significantly lower levels in a transurethral model of infection. Additionally, we observe that mrpJ is widely conserved in a collection of recent clinical isolates, leading us to conclude that our results elucidate an unanticipated role of MrpJ as a global regulator of P. mirabilis virulence. Four biological replicates were analyzed for each set of arrays (P. mirabilis HI4320 wild type vs. ΔmrpJ, and vector pLX3607 vs. mrpJ plasmid pLX3805).

2015-04-13 | E-GEOD-63321 | biostudies-arrayexpress

Deterministic evolution and stringent selection during pre-neoplasia

Project description:Deterministic evolution and stringent selection during pre-neoplasia

| PRJNA951466 | ENA

Deterministic evolution and stringent selection during pre-neoplasia

Project description:Deterministic evolution and stringent selection during pre-neoplasia

| PRJNA951465 | ENA