Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Production and Characterization of an AAV1-VP3 Only Capsid: An Analytical Benchmark Standard

ABSTRACT: This dataset contains mass spectra of AAV particles analyzed by ensemble measurement and Direct Mass Technology mode.

INSTRUMENT(S): Q Exactive UHMR

ORGANISM(S): Adeno-associated Virus (ncbitaxon:272636)

SUBMITTER: Weijing Liu

PROVIDER: MSV000091640 | MassIVE | Tue Apr 04 15:55:00 BST 2023

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Production and characterization of an AAV1-VP3-only capsid: An analytical benchmark standard.

Project description: Not available

| S-EPMC10238842 | biostudies-literature

Native mass spectrometry prescreening of G protein-coupled receptor complexes for cryo-EM structure determination

Project description:This dataset contains mass spectra of GPCR complex analyzed by ensemble measurement and Direct Mass Technology mode.

2023-12-14 | MSV000093671 | MassIVE

Establishing analytical validity of BeadChip array genotype data by comparison to whole-genome sequence and standard benchmark datasets.

Project description: Not available

| S-EPMC8919546 | biostudies-literature

AAV capsid prioritization in machine-perfused normal and steatotic human livers

Project description:Adeno-associated virus (AAV) vectors generated with five different capsids were intravenously injected into human livers undergoing normothermic machine perfusion (NMP). To assess the tropism of the five AAV vectors in the human livers, single-cell suspensions of hepatocytes and non-parenchymal cells (NPCs) were analyzed by single-cell RNA sequencing (scRNAseq). Differentially expressed genes were identified in AAV vector-transduced hepatocytes and unique cell populations.

2024-11-12 | GSE228000 | GEO

Cell-mediated Immune Response Signature to AAV Capsid in Cynomolgus Monkeys

Project description:Cell-mediated immune (CMI) responses to adeno-associated virus (AAV) can lead to both tissue damage and loss of therapeutic transgene expression. Identifying robust biomarkers of CMI and understanding CMI mechanisms can be help to helpful in clinical practice and in advancement of AAV gene therapies. The present work evaluated PBMCs from non-human primates (NHP) before and 14 days following immunization with AAV9 capsid. PBMCs were stimulated in vitro with AA9 capsid peptides to evaluate CMI responses by IFN- ELISPOT, intracellular cytokines and activation markers by flow cytometry, secreted cytokines by ELISAMSD, and transcriptional responses by RNAseq. AAV peptide stimulation produced a robust IFN- ELISPOT response at 14 days. Flow cytometry revealed an increase in IFN- positive CD4 and CD8 cells, IL2 positive CD4 cells, and TNF positive CD4 cells. An increase in the CXCR3 ligands IP-10 and I-TAC were detected both inas secreted proteins. The most robust changes in response to AAV stimulation and strongest correlations to ELISPOT response were revealed by RNAseq, including transcripts encoding IFN- and transcripts encoding , IP-10 and I-TAC , and many downstream transcripts and several IFN-independent pathways. These data provide evidence that a gene signature, or CXCR3 ligand transcripts or protein could serve as robust and sensitive alternatives to ELISPOT for detection of CMI, andCMI and warrant further benchmarking in human samples.

2024-02-26 | GSE256418 | GEO

Characterization of Residual MicroRNAs in AAV Vector Batches Produced in HEK293 Mammalian Cells and Sf9 Insect Cells

Project description:With more than 130 clinical trials and eight approved gene therapy products, AAVs stand as one of the most popular vehicles to deliver therapeutic DNA in vivo. One critical quality attribute analyzed in AAV batches is the presence of residual DNA, as it could pose genotoxic risks or induce immune responses. Surprisingly, the presence of small cell‑derived RNAs, such as micro‑RNAs, has not been previously investigated. In this study, we examined the presence of miRNAs in purified AAV batches produced in mammalian or in insect cells. Our findings revealed that miRNAs were present in all batches, regardless of the production cell line or capsid serotype (2 and 8). Quantitative assays indicated that miRNAs were co‑purified with the rAAV particles in a proportion correlated with their abundance in the production cells. The level of residual miRNAs was reduced via an immunoaffinity chromatography purification process including a tangential flow filtration step or by RNase treatment, suggesting that most miRNA contaminants are likely non encapsidated into AAV particles. In summary, we demonstrate, for the first time, that miRNAs are co-purified with AAV particles. Further investigations are required to determine whether these miRNAs could interfere with the safety or efficacy of AAV-mediated gene therapy.

2024-06-30 | GSE270691 | GEO

Expression data from mouse liver

Project description:HBV-transgenic mice were treated i.v. with 1x10e11 particles AAV serotype 8 vectors expressing different RNAi-triggers targeting the HBV transcripts. To determine possible toxicities caused by the different vectors (including off-target activity against endogenous genes) we performed a whole transcriptome analysis of RNA of livers harvested 15 days after injection. 4 replicates per treatment group were analyzed. As controls, one group of mice was treated with 0.9% saline (mock) and another group of animals was treated with an empty AAV8 vector (1x10e11 particles i.v.).

2015-08-25 | E-GEOD-72335 | biostudies-arrayexpress

PIA - Yeast Gold Standard Benchmark Dataset

Project description:This Dataset is no actual new study but the Yeast Gold Standard benchmark dataset used in the PIA manuscript.

2015-05-08 | PXD000792 | Pride

Quantum chemical benchmark databases of gold-standard dimer interaction energies.

Project description: Not available

| S-EPMC7876112 | biostudies-literature

The AAV capsid can influence the epigenetic marking of rAAV delivered episomal genomes in a species dependent manner [Tn5_InVivo]

Project description:Recombinant adeno-associated viral vectors (rAAVs) are among the most commonly used vehicles for in vivo based gene therapies. However, it is hard to predict which AAV capsid will provide the most robust expression in human subjects due to the observed discordance in vector-mediated transduction between species. We used a primate specific capsid, AAV-LK03, and demonstrated that the limitation of this capsid towards transduction of mouse cells was unrelated to cell entry and nuclear transport but rather due to depleted histone H3 chemical modifications related to active transcription, namely H3K4me3 and H3K27ac, on the vector DNA itself. A single-amino acid insertion into the AAV-LK03 capsid enabled efficient transduction and the accumulation of active-related epigenetic marks on the vector chromatin in mouse without compromising transduction efficiency in human cells. Our study suggests that the capsid protein itself is involved in driving the epigenetic status of the vector genome, most likely during the process of uncoating. Programming viral chromatin states by capsid design may enable facile DNA transduction between vector and host species and ultimately led to rationale selection of AAV capsids for use in humans.

2023-02-28 | GSE226165 | GEO

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