Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Li et al., Xylosyltransferase Bump-and-hole Engineering to Chemically Manipulate Proteoglycans in Mammalian Cells: Decorin glycosylated in vitro with 6AzGlc and clicked with ITag

ABSTRACT: Human FLAG-tagged decorin was overexpressed in CHO pgsA-745 cells and purified. Decorin was in vitro glycosylated with BH-engineered XT1 and UDP-6AzGlc, then clicked with ITag-alkyne, digested with trypsin on S-Trap, then analysed by HCD on an Orbitrap Eclipse. Data analysis with Byonic using 6AzGlc-ITag as a custom mod.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Benjamin Schumann

PROVIDER: MSV000098982 | MassIVE | Sat Aug 30 01:52:00 BST 2025

SECONDARY ACCESSION(S): PXD067897

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Li et al., Xylosyltransferase Bump-and-hole Engineering to Chemically Manipulate Proteoglycans in Mammalian Cells: Decorin glycosylated in-cell with 6AzGlc and clicked with ITag

Project description:pgsA-745 cells stably transfected with a plasmid encoding for BH-XT1 were transfected transiently with a plasmid encoding human FLAG-tagged decorin. Cells were fed with 6AzGlc-1-phosphate precursor 1, and supernatant isolated. Decorin was purified, then clicked with ITag-alkyne, digested with trypsin on S-Trap, then analysed by HCD on an Orbitrap Eclipse. Data analysis with Byonic using 6AzGlc-ITag as a custom mod.

2025-08-30 | MSV000098981 | MassIVE

Li et al., Xylosyltransferase Bump-and-hole Engineering to Chemically Manipulate Proteoglycans in Mammalian Cells: CHO-pgs745 cells with 50 uM compound 1

Project description:CHO pgs-745 cells transfected with plasmids encoding for WT or bump-and-hole-engineered human XYLT1 or XYLT2 were fed with 6AzGlc-1-phosphate precursor (50 uM) or DMSO and secretome collected. Glycoproteins were clicked with acid-cleavable biotin-alkyne, enriched on neutravidin and on-bead digested with trypsin. Peptides were desalted and run on TIMS-ToF Pro.

2025-08-30 | MSV000098983 | MassIVE

Li et al., Xylosyltransferase Bump-and-hole Engineering to Chemically Manipulate Proteoglycans in Mammalian Cells: CHO-pgs745 cells with 250 uM compound 1

Project description:CHO pgs-745 cells transfected with plasmids encoding for WT or bump-and-hole-engineered human XYLT1 or XYLT2 were fed with 6AzGlc-1-phosphate precursor (250 uM) or DMSO and secretome collected. Glycoproteins were clicked with acid-cleavable biotin-alkyne, enriched on neutravidin and on-bead digested with trypsin. Peptides were desalted and run on TIMS-ToF Pro.

2025-08-29 | MSV000098977 | MassIVE

Engineering nuclear elasticity to manipulate somatic cell fate

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

2025-12-02 | GSE224498 | GEO

Engineering Cyclodextrin Clicked Chiral Stationary Phase for High-Efficiency Enantiomer Separation.

Project description:The separation of racemic molecules is of crucial significance not only for fundamental research but also for technical application. Enantiomers remain challenging to be separated owing to their identical physical and chemical properties in achiral environments. Chromatographic techniques employing chiral stationary phases (CSPs) have been developed as powerful tools for the chiral analysis and preparation of pure enantiomers, most of which are of biological and pharmaceutical interests. Here we report our efforts in developing high-performance phenylcarbamated cyclodextrin (CD) clicked CSPs. Insights on the impact of CD functionalities in structure design are provided. High-efficiency enantioseparation of a range of aryl alcohols and flavanoids with resolution values (Rs) over 10 were demonstrated by per(3-chloro-4-methyl)phenylcarbamated CD clicked CSP. Comparison study and molecular simulations suggest the improved enantioselectivity was attributed to higher interactions energy difference between the complexes of enantiomers and CSPs with phenylcarbamated CD bearing 3-chloro and 4-methyl functionalities.

| S-EPMC4530664 | biostudies-other

Combating viral contaminants in CHO cells by engineering innate immunity

Project description:Viral contamination in biopharmaceutical manufacturing can lead to shortages in the supply of critical therapeutics. To facilitate the protection of bioprocesses, we explored the basis for the susceptibility of CHO cells, the most commonly used cell line in biomanufacturing, to RNA virus infection. Upon infection with certain ssRNA and dsRNA viruses, CHO cells fail to generate a significant interferon (IFN) response. Nonetheless, the downstream machinery for generating IFN responses and its antiviral activity is intact in these cells: treatment of cells with exogenously-added type I IFN or poly I:C prior to infection limited the cytopathic effect from Vesicular stomatitis virus (VSV), Encephalomyocarditis virus (EMCV), and Reovirus-3 virus (Reo) in a STAT1-dependent manner. To harness the intrinsic antiviral mechanism, we used RNA-Seq to identify two upstream repressors of STAT1: Gfi1 and Trim24. By knocking out these genes, the engineered CHO cells exhibited increased resistance to the prototype RNA viruses tested. Thus, omics-guided engineering of mammalian cell culture can be deployed to increase safety in biotherapeutic protein production.

2019-05-31 | GSE119379 | GEO

Engineering nuclear elasticity to manipulate somatic cell fate [scRNA-seq]

Project description:Engineering nuclear elasticity to manipulate somatic cell fate

2025-12-02 | GSE224497 | GEO

Engineering nuclear elasticity to manipulate somatic cell fate [ATAC-seq]

Project description:Engineering nuclear elasticity to manipulate somatic cell fate

2025-12-02 | GSE224496 | GEO

Glycosylated superparamagnetic nanoparticle gradients for osteochondral tissue engineering.

Project description:In developmental biology, gradients of bioactive signals direct the formation of structural transitions in tissue that are key to physiological function. Failure to reproduce these native features in an in vitro setting can severely limit the success of bioengineered tissue constructs. In this report, we introduce a facile and rapid platform that uses magnetic field alignment of glycosylated superparamagnetic iron oxide nanoparticles, pre-loaded with growth factors, to pattern biochemical gradients into a range of biomaterial systems. Gradients of bone morphogenetic protein 2 in agarose hydrogels were used to spatially direct the osteogenesis of human mesenchymal stem cells and generate robust osteochondral tissue constructs exhibiting a clear mineral transition from bone to cartilage. Interestingly, the smooth gradients in growth factor concentration gave rise to biologically-relevant, emergent structural features, including a tidemark transition demarcating mineralized and non-mineralized tissue and an osteochondral interface rich in hypertrophic chondrocytes. This platform technology offers great versatility and provides an exciting new opportunity for overcoming a range of interfacial tissue engineering challenges.

| S-EPMC6018621 | biostudies-literature

Profiling miRNAs of high, low and non-producing CHO cells during biphasic Fed-Batch cultivations reveal interesting targets for cell line engineering

Project description:Fed-batch cultivation of recombinant Chinese hamster ovary (CHO) cell lines is one of the most widely used production mode for commercial manufacturing of recombinant protein therapeutics. Furthermore, fed-batch cultivations are often conducted as biphasic processes where culture temperature is decreased to maximize volumetric product yields. However, it still remains to be elucidated which intracellular regulatory elements actually control the observed pro-productive phenotypes. Recently, several studies have revealed microRNAs (miRNAs) to be important molecular switches of cell phenotypes since single miRNAs are capable of regulating entire physiological pathways. In this study, we analyzed miRNA profiles of two different recombinant CHO cell lines (high and low producer), and compared them to a non-producing CHO DG44 host cell line during fed-batch cultivation at 37 versus 30 Â°C culture temperature. Taking advantage of next-generation sequencing combined with cluster, correlation and differential expression analyses, we could identify 89 different miRNAs, which might be interesting for CHO cell engineering. Functional validation experiments using 19 validated target miRNAs confirmed that these miRNAs indeed induced changes in process relevant phenotypes such as recombinant protein production, apoptosis, necrosis and proliferation. Furthermore, computational miRNA target prediction combined with functional clustering identified putative target genes and cellular pathways, which might be regulated by these miRNAs. Taken together, our study systematically identified novel target miRNAs during different phases and conditions of a biphasic fed-batch process and functionally evaluated their potential for host cell engineering. 36 miRNA libraries from three different CHO cell lines and two process condition. In the control run temperature was maintained at 30Â°C, while temperature was reduced to 30Â°C after reaching mid exponential phase

2016-04-03 | E-GEOD-72945 | 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