Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Exploring roles of the chitinase ChiC in modulating Pseudomonas aeruginosa virulence phenotypes

ABSTRACT: Proteins were precipitated using chloroform and methanol, by the protocol described by Wessel and Flügge (1984). Following precipitation, the proteins were reduced and alkylated before being digested, cleaned and desalted using STrap tips (Zougman A, Selby PJ, Banks RE. 2014). The peptide samples were analyzed by a nano UPLC (nanoElute, Bruker) coupled to a trapped ion mobility spectrometry and a quadrupole time of flight mass spectrometer (timsTOF Pro, Bruker).

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Pseudomonas Aeruginosa (strain Ucbpp-pa14) Bacteria

SUBMITTER: Per Kristian Edvardsen

LAB HEAD: Gustav Vaaje-Kolstad

PROVIDER: PXD048597 | Pride | 2024-04-30

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20230114_2h_1_Slot2-20_1_3175.d.zip	Other
	20230114_2h_2_Slot2-21_1_3176.d.zip	Other
	20230114_2h_3_Slot2-22_1_3177.d.zip	Other
	20230114_2h_ctrl_1_Slot2-23_1_3178.d.zip	Other
	20230114_2h_ctrl_1_Slot2-24_1_3179.d.zip	Other

Items per page:

1 - 5 of 14

Similar Datasets

SiTrap versus STrap comparison

Project description:These are supporting RAW files for the 'Detergent-free simultaneous sample preparation method for proteomics and metabolomics' SiTrap method manuscript. MDA-MB-231 cells were processed either by SiTrap methodology using SiTrap cellulose tips and two different extraction solutions or by STrap method using STrap quartz tips and SDS for extraction. 30 ug of protein was digested with trypsin in six replicates in each case. The peptides were eluted from the tips and concentrated for proteomics analysis.

2019-10-02 | MSV000084406 | MassIVE

GNPS - SiTrap versus STrap comparison

2019-10-02 | MSV000084406 | GNPS

Exploring roles of the chitinase ChiC in modulating Pseudomonas aeruginosa virulence phenotypes

Project description:Chitinases are ubiquitous enzymes involved in biomass degradation and chitin turnover in nature. Pseudomonas aeruginosa (PA), an opportunistic human pathogen, expresses ChiC, a secreted glycoside hydrolase 18 (GH18) family chitinase. Despite speculation about ChiC's role in PA disease pathogenesis, there is scant evidence supporting this hypothesis. Since PA cannot catabolize chitin, we investigated the potential function(s) of ChiC in PA pathophysiology

2024-04-30 | PXD048320 | Pride

Serine-Threonine Kinase Receptor-Associated Protein (STRAP) Knockout Decreases the Malignant Phenotype in Neuroblastoma

Project description:Purpose: Serine-threonine kinase receptor-associated protein (STRAP) plays an important role in neural development but also in tumor growth. Neuroblastoma, a tumor of neural crest origin, is the most common extracranial malignancy of childhood, and it continues to carry a poor prognosis. The recent discovery of the role of STRAP in another pediatric solid tumor, osteosarcoma, and its known function in neural development, led us to investigate the role of STRAP in neuroblastoma tumorigenesis. Methods: STRAP protein expression was abrogated in two human neuroblastoma cell lines, SK-N-AS (AS) and SK-N-BE(2). Methods included transient knockdown with siRNA, stable knockdown with shRNA lentiviral transfection, and CRISPR-Cas9 genetic knockout of STRAP. STRAP knockdown and knockout cells were examined for phenotypic alterations in vitro and tumor growth in vivo. Results: Cell proliferation, viability, motility, and growth were significantly decreased in STRAP knockout compared to wild-type cells. Indicators of stemness, including mRNA abundance of common stem cell markers Oct4, Nanog, and Nestin, the percentage of cells expressing CD133 on their surface, and the ability to form tumorspheres, were significantly decreased in the STRAP KO cells. In vivo, AS STRAP knockout cells formed tumors less readily than wild-type tumor cells. Conclusion: These novel findings demonstrated that STRAP plays a role in tumorigenesis and maintenance of neuroblastoma stemness.

2021-07-14 | GSE169322 | GEO

Transcriptome-wide maps of STRAP-RNA interactions in mouse early embryo and lineage-committed cells.

Project description:We report the application of enhanced cross-linking immunoprecipitation (eCLIP) sequencing technology for high-throughput profiling of STRAP-RNA interactions in mouse embryos (E9.5) or embryoid body (EB) cells. Based on the eCLIP-seq data, we computationally identified a transcriptome-wide set of high-confidence peaks (over ten thousands) and most of STRAP-peaks distributed in the murine genome by defining certain exons and introns as well as their intersection. STRAP eCLIP signals in embryos were dramatically enriched at exon/intron and intron/exon borders. Numerous STRAP peaks are significantly enriched on the genes with critical roles in early organ development. Finally, we show two examples of STRAP-RNA binding that link to its regulated genes at the alternative splicing level. Together, we uncover the position- and context- dependent effects of STRAP on splicing regulation during mouse embryonic stem cells lineage commitment. Our studies provide a very useful platform to decipher STRAP’s role in the many steps in RNA biogenesis for future studies.

2020-09-16 | GSE131472 | GEO

STRAP is involved in mutated Apc-induced stemness and tumorigenesis in colon cancer

Project description:To identify pathways mediating the effects of Strap in colon cancer development, we established the mRNA expression proﬁles of intestinal adenomas that formed in ApcMin/+ mice with and without Strap deletion.

2021-09-20 | GSE160428 | GEO

Oncogenic Serine-Threonine Kinase Receptor Associated Protein Supports Hepatocellular Carcinoma Cell Growth by Enhancing Wnt/β-catenin Signaling

Project description:Serine-threonine kinase receptor-associated protein (STRAP) is upregulated in breast, colorectal and lung cancers, promoting their growth. We identify the upregulation of STRAP in hepatocellular carcinomas. Elevated STRAP endows tumor cells with growth advantage by reprograming a variety of metabolic processes and signaling pathways critical for hepatocellular carcinoma progression. Especially, enhanced Wnt/β-catenin signaling is likely to be a major effector of its tumor-promoting role.

2018-09-03 | GSE101061 | GEO

Next generation sequencing facilitates quantitative analysis of STRAP-dependent alternative splicing events

Project description:We report the application of next generation sequencing for evaluating alternative splicing (AS) events on lineage-committed WT and Strap-KO embryoid body (EB) cells. We also analyzed AS during mouse embryo development using RNA-seq data. Of all STRAP-regulated AS, exon-skipping events were the most frequent ones with significant changes in 49% (240 out of 489) cases. Retained introns were also overrepresented (20%, 97 out of 489) as compared to other types of AS STRAP appears to function in promoting both exon inclusion and skipping at different exons. GO function revealed STRAP-regulated AS events involve in protein catabolism, molecular binding and cell motility. More specifically, they included neuronal migration and development. Together, these analyses uncovered the previous unknown role of STRAP involved in the substantial transcriptional diversity at the exon level in certain development stage. Our study also represents the first detailed analysis of AS events in the mouse early organogenesis with biologic replicates, generated by RNA-seq technology.

2020-09-16 | GSE131471 | GEO

Native Purification of yeast Met30 in the absence and presence of Cadmium followed by DSSO crosslinking and Mass spec analysis

Project description:HBTHMet30 cells were cultured in YEP + 2% galactose + 4µM Biotin at 30˚C and treated with 100 µM CdCl2 for 30 minutes. Native whole cells lysates were prepared in lysis buffer (50mM Hepes pH7.5, 200mM NaCl, 10% glycerol, 40mM imidazole, 0.2% Triton1mM dithiothreitol, 0.1mM orthovanadate, 1mM phenylmethylsulfonyl floride [PMSF], and 1mg/ml each leupeptin and pepstatin) and bound to Ni-resin. Proteins were eluted in the presence of 250mM imidazole. For cross-linking analysis, eluted HBTHMet30 was first bound to Streptavidin beads and then on-bead cross-linked with 0.5 mM DSSO in PBS buffer for 1 h at 37 °C. Bead-bound proteins were reduced with TCEP and alkylated with iodocetamide, digested by trypsin and cleaned-up with C18 tips prior to LC MSn analysis.

2024-06-22 | PXD048194 | Pride

Systems biology of blood and tissue for comprehensive analysis of immune response to hepatitis B vaccine in adults

Project description:Protein concentrations of both lysed WBC and plasma samples were measured by the PierceTM Bradford Assay and normalized to contain 10 μg per sample before proceeding with sample digestion using the procedure as previously described44. Peptides were desalted using STop-And-Go Extraction tips (STAGE tips)45, dried using the Vacufuge Plus (Eppendorf) for 45 minutes, then chemically dimethylated with light, medium, and heavy formaldehyde46 for triplex analysis of each timepoint per individual (i.e. two triplex samples were prepared for each individual, with sample from one of the timepoints spiked into both triplexed samples to use a reference). After labeling, samples for each triplex was combined and desalted and dried again using STAGE tips and the Vacufuge Plus. Peptides were resuspended in 30μl of 0.1% formic acid for liquid chromatography and mass spectrometry analysis (LC-MS). A total of 2 μg per sample was injected into the EasynLC-1000 chromatography system (Thermo) with a 50 cm analytical column, packed in-house with C18, coupled to an Impact II Q-TOF mass spectrometer (Bruker Daltonics, Bremen, Germany), with detailed parameters as previously described47. Data was analysed using MaxQuant (v1.5.5.1) with default values and “Match Between Runs” activated, searched against the human Uniprot database (downloaded on 15 July, 2017).

2020-12-01 | PXD020474 | Pride