Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Plasmid vector pSP189

ABSTRACT: Plasmid vector pSP189 Genome sequencing

PROVIDER: PRJNA302825 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR2937442_1.fastq.gz	Fastqsanger.gz
	SRR2937442_2.fastq.gz	Fastqsanger.gz
	SRR2937443_1.fastq.gz	Fastqsanger.gz
	SRR2937443_2.fastq.gz	Fastqsanger.gz
	SRR2937444_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 68

Similar Datasets

Transcriptional profiling the 150 kb linear plasmid of Borrelia turicatae implicates an important role in vector colonization and establishing mammalian infection.

Project description:As vector-borne pathogens transit between the arthropod and vertebrate, adaptation is key for survival as each host varies and initiates unique defense mechanisms. An environmental signal that relapsing fever (RF) and Lyme causing spirochetes detect is the change of temperature between vector and mammal, yet incomplete genomes have hindered progress in understanding the genetic constituents expressed during tick colonization. We conducted a combined transcriptional and genomic sequence analysis to further assemble the ~150 kb linear plasmid (lp150) of Borrelia turicatae, a causative agent of RF borreliosis. Contiguous sequences (contigs), which were originally generated by Sanger sequencing, contained open reading frames (ORFs) identified to be up-regulated by the spirochetes when grown under tick-like conditions compared to the mammal. To aid in assembling the contigs, a PacBio RS I Single Molecule Real-Time DNA sequencing approach was used, given extended nucleotide reads over several thousand base pairs. A 36 kb locus was identified toward the 3‘ end of lp150, and expression of the ORFs was verified in the tick and mammal. We report the most complete version of lp150, and this study indicates that the plasmid likely facilitates vector colonization and establishing early mammalian infection

2017-02-09 | GSE69041 | GEO

A Self-Complementary AAV Proviral Plasmid System to Reduce Aberrant Cross-Packaging and ITR Promoter Activity in AAV Vector Preparations (Long-read)

Project description:Adeno-associated viral vectors (AAV) are a leading delivery system for gene therapy in animal models and humans. With several FDA-approved AAV gene therapies on the market, issues related to vector manufacturing have become increasingly important. In this study, we focused on potentially toxic DNA contaminants that can arise from AAV proviral plasmids, the raw materials required for manufacturing recombinant AAV in eukaryotic cells. Typical AAV proviral plasmids are circular DNAs containing a therapeutic gene cassette flanked by natural AAV inverted terminal repeat (ITR) sequences, and a plasmid backbone carrying prokaryotic sequences required for plasmid replication and selection in bacteria. While the majority of AAV particles package the intended therapeutic payload, some capsids instead package the bacterial sequences located on the proviral plasmid backbone. Since ITR sequences also have promoter activity, potentially toxic bacterial open reading frames can be produced in vivo, thereby representing a safety risk. In this study, we describe a new AAV proviral plasmid for vector manufacturing that (1) significantly decreases cross-packaged bacterial sequences; (2) increases correctly packaged AAV payloads; and (3) blunts ITR-driven transcription of cross-packaged material to avoid expressing potentially toxic bacterial sequences. This system may help improve the safety of AAV vector products.

2024-07-26 | GSE272650 | GEO

A Self-Complementary AAV Proviral Plasmid System to Reduce Aberrant Cross-Packaging and ITR Promoter Activity in AAV Vector Preparations (Short-read)

2024-07-26 | GSE272649 | GEO

Synthetic plasmid

Project description:Synthetic plasmid Genome sequencing

| PRJNA209332 | ENA

Plasmid pKJK172

Project description:Plasmid pKJK172 Genome sequencing and assembly

| PRJNA432895 | ENA

Plasmid pED208

Project description:Plasmid pED208 Genome sequencing and assembly

| PRJNA871772 | ENA

Production of rAAV by plasmid transfection induces antiviral and inflammatory responses in suspension HEK293

Project description:To understand the response of host cells to rAAV vector production via plasmid transfection, samples were collected throughout the course of three 50 L production batches and analyzed by bulk RNA sequencing of polyadenylated transcripts (RNA-seq). Gene ontology analysis determined that upregulated pathways included inflammatory and antiviral responses. Systematic analyses of the cellular transcriptional response to rAAV production indicates that these host cells are not passively supporting vector manufacture, and therefore may illuminate genes and pathways that influence rAAV production, thereby enabling the rational design of next-generation manufacturing platforms to support safe, effective, and affordable AAV-based gene therapies.

2023-02-06 | GSE224405 | GEO

Gene expression profiles of dental follicle cells after 48 hours of transfection in vitro with a DLX3 plasmid and an empty vector

Project description:We analysed gene expression profiles in dental follicle cells after 48 hours of overexpression with the transcription factor DLX3. Total RNAs were isolated from dental follicle cells after 48 hours of transfection with a DLX3 expressions plasmid and for control with an empty vector.

2011-06-07 | E-GEOD-29753 | biostudies-arrayexpress

Proteomic map of the unsequenced kala-azar vector Phlebotomus papatasi

Project description:The debilitating disease kala-azar or visceral leishmaniasis (VL) is caused by the kinetoplastid protozoan parasite Leishmania donovani. The parasite is transmitted by the hematophagous sandfly vector of the genus Phlebotomus in the old world and Lutzomyia in the new world. The predominant Phlebotomine species associated with transmission of kala-azar are Phlebotomus papatasi and Phlebotomus argentipes. The infected female sandfly transmits the parasite when it takes a blood meal. Understanding the molecular interaction of the sand fly-Leishmania during the development of parasite within the gut of the sandfly is crucial to understanding parasite life cycle. The complete genome sequences of sandfly vectors (Phlebotomus and Lutzomyia) are currently not available and sequencing efforts are underway. Non-availability of genome sequence can hamper identification of proteins in the sandfly vector. In the present study we have carried out proteogenomic analysis of unsequenced sandfly vector P. paptasi cell line using high-resolution mass spectrometry and comparative homology-based searches using related dipteran protein data (mosquitoes and fruit fly). This study resulted in identification of 1,312 proteins from P. papatasi based on homology. Our study demonstrates the power of proteogenomic approaches in mapping the proteomes of unsequenced organisms.

2015-08-31 | PXD002115 | Pride

Sequence Requirements for Cascade Function in a Type I-E CRISPR System: Plasmid Loss

Project description:We generated a collection of 13 plasmids, with each plasmid containing a variant of a CRISPR protospacer targeted by spacer 8 of the E. coli CRISPR-I array. We transformed the plasmids as a pool into delta cas3 E. coli cells expressing all other cas genes constitutively. We then transformed these cells with either an empty vector or a plasmid expressing the Cas3 nuclease. DNA surrounding the protospacers was PCR-amplified and sequenced.

2017-08-24 | E-MTAB-5969 | biostudies-arrayexpress

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