Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PiggyBac (PB) genetic screening allows identification of putative metastatic genes

ABSTRACT: PiggyBac (PB) genetic screening allows identification of putative metastatic genes

PROVIDER: PRJNA605234 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11040024_1.fastq.gz	Fastqsanger.gz
	SRR11040024_2.fastq.gz	Fastqsanger.gz
	SRR11040025_1.fastq.gz	Fastqsanger.gz
	SRR11040025_2.fastq.gz	Fastqsanger.gz
	SRR11040026_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 68

Similar Datasets

PiggyBac (PB) genetic screening allows identification of putative metastatic genes

Project description:Next-Generation Sequencing was applied to investigate candidate breast cancer metastatic genes. PB targeted sequencing of primary tumours and metastases (3 lung metastases, 6 lung macro-metastases and 9 LM cell lines) allowed to identify Nfib as a candidate metastasis inducer.

2021-01-15 | GSE144898 | GEO

Identification of phosphorylation sites in piggyBac transposase N-terminus

Project description:The piggyBac transposon system is widely used for biotechnology and genome engineering and is the founding member of a large superfamily of piggyBac-like elements. We investigated the role in transpositon of the nonconserved N-terminus in the piggyBac transposase, including the impact of predicted casein kinase phosphorylation sites within it.

2023-03-11 | PXD037132 | Pride

Investigating the role of Lef1 in mouse embryonic stem cells.

Project description:Genome-wide analysis of gene expression in piggybac empty vector and piggybac-lef1 transfected mouse embryonic stem cells (46C mouse ESCs) Analysis of genes regulated by lef1, and we found that lef1 acts biphasically in mouse embryonic stem cells. Total RNA obtained from empty vector (PB)-transfected 46 ESCs or different states (passage 2 and passage 5) of lef1-transfected (PB-Lef1 P2, PB-Lef1 P5) 46C mouse ESCs.

2016-01-29 | E-GEOD-77330 | biostudies-arrayexpress

RNA Microarray of 36H liver stages of Pb WT and Pb SSPELD Knock out parasites

Project description:Global gene expression profiling of P. berghei liver stages at 36h from WT and Pb SSPELD KO parasites to investigate the changes in RNA expression levels in Pb SSPELD parasites.

2016-09-01 | GSE72399 | GEO

A PiggyBac transposon screen in pancreatic cancer

Project description:A PiggyBac transposon based screen in a murine pancreatic cancer model.This data has been described in the following article [doi:10.1038/ng.3164] and its further analysis can be freely submitted for publication. For information on the proper use of data shared by the Wellcome Trust Sanger Institute (including information on acknowledgement), please see http://www.sanger.ac.uk/datasharing/

2016-07-04 | E-ERAD-514 | biostudies-arrayexpress

piggyBac-Mediated Genomic Integration of Linear dsDNA-Based Library for Deep Mutational Scanning in Mammalian Cells

Project description:Deep mutational scanning (DMS) makes it possible to perform massively parallel quantification of the relationship between genetic variants and phenotypes of interest. However, the difficulties in introducing large variant libraries into mammalian cells greatly hinder DMS under physiological states. Here we developed two novel strategies for DMS library construction in mammalian cells, namely ‘piggyBac-in-vitro ligation’ and ‘piggyBac-in-vitro ligation-PCR’. For the first strategy, we took the ‘in-vitro ligation’ approach to prepare high-diversity linear dsDNAs, and integrate them into the mammalian genome with a piggyBac transposon system. For the second strategy, we further added a PCR step using the in-vitro ligation dsDNAs as templates, for the construction of high-content genome-integrated libraries via large-scale transfection. Both strategies could successfully establish genome-integrated EGFP-chromophore randomized libraries in HEK293T cells and enrich the green fluorescence-chromophore amino acid sequences. And we further identified a novel transcriptional activator peptide with the ‘piggyBac-in-vitro ligation-PCR’ strategy. Our novel strategies greatly facilitate the construction of large variant DMS library in mammalian cells, and may have great application potential in the future.

2023-10-05 | GSE226719 | GEO

PB enrichment culture

Project description:PB enrichment culture Raw sequence reads

| PRJNA774086 | ENA

RNA-sequencing of human peripheral blood mononuclear cells (PB MNCs) and induced neural progenitor cells derived from PB MNCs

Project description:We have successfully generated human induced neural progenitor cells (iNPCs) from peripheral blood mononuclear cells (PB MNCs). To gain further insights into the transcriptional activation and cellular identity of human iNPCs, we compared the transcriptome of human iNPCs with PB MNCs and published database CORTECON and BrainSpan.

2019-11-21 | GSE107806 | GEO

Transposase N-terminal phosphorylation and asymmetric transposon ends inhibit piggyBac transposition in mammalian cells

Project description:DNA transposon systems are widely used in mammalian cells for genetic modification experiments, but their regulation remains poorly understood. We used biochemical and cell-based assays together with AlphaFold modeling and rational protein redesign to evaluate aspects of piggyBac transposition including the previously unexplained role of the transposase N-terminus and the need for asymmetric transposon ends for cellular activity. We found that phosphorylation at predicted casein kinase II sites in the transposase N-terminus inhibits transposition, most likely by preventing transposase-DNA interactions. Deletion of the region containing these sites releases inhibition thereby enhancing activity. We also found that the N-terminal domain promotes transposase dimerization in the absence of transposon DNA. When the N-terminus is deleted, the transposase gains the ability to carry out transposition using symmetric transposon left ends. This novel activity is also conferred by appending a second C-terminal domain. When combined, these modifications together result in a transposase that is highly active when symmetric transposon ends are used. Our results demonstrate that transposase N-terminal phosphorylation and the requirement for asymmetric transposon ends both negatively regulate piggyBac transposition in mammalian cells. These novel insights into the mechanism and structure of the piggyBac transposase expand its potential use for genomic applications.

2022-11-10 | GSE201914 | GEO

DIGE of Pb stress in Rhoeo discolor (L. Her.) Hance

Project description:Proteome analysis of leaves from Rhoeo discolor (L. Her.) Hance leaves streesed with Pb against untreated control group via DIGE

2022-02-22 | PXD003873 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data