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PSCK9 knockdown in EndoC-bH1 cells time course (DIA secretome time course)

ABSTRACT: EndoC-bH1 cells were incubated with control siRNA or PCSK9 siRNA for 24, 48 and 72 hours. Untreated baseline samples were also included. Unpowered exploratory experiment. Sample size: triplicate per condition.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Type B Pancreatic Cell, Endocrine Pancreas, Cell Culture

SUBMITTER: Maria Ryaboshapkina

LAB HEAD: Raphael Scharfmann

PROVIDER: PXD027920 | Pride | 2022-04-07

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	PE224.log.txt	Txt
	PE224.params	Other
	PE224.setup.txt	Txt
	PE224.sne	Other
	PE224_2020_GP_PCSK9_1.raw	Raw

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1 - 5 of 26

Publications

Characterization of the Secretome, Transcriptome, and Proteome of Human β Cell Line EndoC-βH1.

Ryaboshapkina Maria M Saitoski Kevin K Hamza Ghaith M GM Jarnuczak Andrew F AF Pechberty Séverine S Berthault Claire C Sengupta Kaushik K Underwood Christina Rye CR Andersson Shalini S Scharfmann Raphael R

Molecular & cellular proteomics : MCP 20220402 5

Early diabetes research is hampered by limited availability, variable quality, and instability of human pancreatic islets in culture. Little is known about the human β cell secretome, and recent studies question translatability of rodent β cell secretory profiles. Here, we verify representativeness of EndoC-βH1, one of the most widely used human β cell lines, as a translational human β cell model based on omics and characterize the EndoC-βH1 secretome. We profiled EndoC-βH1 cells using RNA-seq, ...[more]

PMID: 35378291

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PSCK9 knockdown in EndoC-bH1 cells at 72 h (DIA proteomics experiment)

Project description:EndoC-bH1 cells were incubated with control siRNA or PCSK9 siRNA for 72 hours. The experiment was powered based PCSK9 knockdown in a pilot experiment. Sample size: 12x12.

2022-04-07 | PXD027911 | Pride

PSCK9 knockdown in EndoC-bH1 cells at 72 h (DIA secretome experiment)

Project description:EndoC-bH1 cells were incubated with control siRNA or PCSK9 siRNA for 72 hours. The experiment was powered based PCSK9 knockdown in the pilot experiment [PXDxxx (PE083)]. Sample size: 12x12.

2022-04-07 | PXD027913 | Pride

PSCK9 knockdown in EndoC-bH1 cells at 72 h (pilot TMT experiment)

Project description:EndoC-bH1 cells were incubated with control siRNA or PCSK9 siRNA for 72 hours. Unpowered exploratory experiment. Sample size: 3x3.

2022-04-07 | PXD027921 | Pride

Effect of control siRNA knockdown on EndoC-bH1 cell lysate proteome (pilot TMT experiment)

Project description:EndoC-bH1 cells proteomics was assessed in untreated baseline condition and after treatment with control siRNA at 24, 48 and 72 hours. Unpowered exploratory experiment. Sample size: triplicate per condition.

2022-04-07 | PXD027898 | Pride

PSME3 Regulates Migration and Differentiation of Myoblasts

Project description:This is the second of two experiments in this project. It sought to measure the changes in the proteome following depletion of PSME3. C2C12 cells were depleted of PSME3 using specific siRNA. Controls received siRNA with a scrambled sequence. Cells were grown to confluency (Day 0 of differentiation), harvested, and the whole cell lysate was analyzed by mass spectrometry.

2025-06-17 | PXD063351 | Pride

Deep proteome coverage of microglia using a streamlined data independent acquisition-based proteomic workflow: method consideration for a phenotypically diverse cell type

Project description:As the immune cells of the brain, microglia play a key role in various homeostatic and disease-related processes. In order to carry out their numerous functions, microglia are able to adopt a wide range of phenotypic states. The proteomic landscape represents a more accurate molecular representation of these phenotypes; however, microglia present unique challenges for proteomic analysis. This study implemented a streamlined liquid- and gas-phase fractionation method with data-dependent acquisition (DDA) and parallel accumulation serial fragmentation (PASEF) analysis on a TIMS-TOF instrument to compile a comprehensive protein library obtained from adult-derived, immortalized mouse microglia with minimal starting material (10µg). The empirical library consisted of 9,140 microglial proteins and was utilized to identify an average of 7,264 proteins per run from single-shot, DIA-based analysis of microglia. Additionally, a predicted library facilitated identification of 7,519 average proteins per run from the same DIA data, revealing complementary coverage compared to the empirical library and collectively increased coverage to approximately 8,000 proteins. Importantly, several immune response pathways were uniquely identified with empirical library approach. Overall, we report a simplified, reproducible approach for deep proteome coverage of microglia with low sample input and show the importance of library optimization for this phenotypically diverse cell type.

2025-03-31 | PXD056436 | Pride

A Simplified Method for Comprehensive Capture of the Staphylococcus aureus Proteome

Project description:Staphylococcus aureus is major human pathogen causing severe and invasive infections in both community and healthcare settings. Although well studied, a comprehensive exploration of its dynamic and adaptive proteome is still somewhat lacking. Herein we employ streamlined liquid- and gas-phase fractionation with PASEF analysis on a TIMS-TOF instrument to expand coverage and explore the dark proteome of S. aureus. In so doing, we captured the most comprehensive S. aureus proteome to date, totaling 2,231 proteins (85.6% proteome coverage), and did so using a significantly simplified process, requiring less samples and input material. Furthermore, we demonstrated the utility of this library within the context of differential expression profiling by investigating the temporal dynamics of the S. aureus proteome. Notably, a significant portion of the library (94%) and related proteome (80.5%) was characterized by DIA-based proteomic analysis, where we noted alterations in metabolic/biosynthetic processes, ATP production, RNA processing, and an increase in stress response proteins such as chaperones and repair enzymes as cultures progressed into stationary phase. Collectively, our study shines new light on the hidden S. aureus proteome, generating a valuable new resource to the scientific community to facilitate further study of this dangerous human pathogen.

2025-03-31 | PXD053994 | Pride

Mass spectrometry analysis of mouse hematopoietic stem cells and their progenitors reveals differential expression within and between proteome and transcriptome throughout adult and aged hematopoiesis

Project description:mass spectrometry analysis of aged and adult hematopoietic stem cells, multipotent progenitors and oligopotent progenitors

2021-07-24 | PXD017442 | Pride

PCSK9 knockdown in EndoC-bH1 cells at 72 hours

Project description:The aim of the study was to characterize the role of PCSK9 in human beta cells. We performed siRNA-mediated knockdown of PCSK9 in human beta cell line EndoC-bH1 and compared the expression profiles against control siRNA-treated cells.

2022-03-31 | GSE182016 | GEO

Spatiotemporal profiling of the bovine oviduct fluid proteome around the time of ovulation

Project description:Unraveling the composition and regulation of the oviduct fluid (OF) is crucial to understand the microenvironment in which sperm capacitation, fertilization and early embryo development take place. Therefore, our aim was to determine the spatiotemporal changes in the OF proteome according to the anatomical region of the oviduct (ampulla vs. isthmus), the proximity of the ovulating ovary (ipsilateral vs. contralateral side) and the peri-ovulatory stage (pre-ovulatory or Pre-ov vs. post-ovulatory or Post-ov). Oviducts from adult cyclic cows were collected at a local slaughterhouse and pools of OF were analyzed by nanoLC-MS/MS and label-free protein quantification (n=32 OF pools for all region stage side conditions). A total of 3,760 proteins were identified in the OF, of which 37% were predicted to be secreted. The oviduct region was the major source of variation in protein abundance, followed by the proximity of the ovulating ovary and finally the peri-ovulatory stage. Differentially abundant proteins between regions, stages and sides were involved in a broad variety of biological functions, including protein binding, response to stress, cell-to-cell adhesion, calcium homeostasis and the immune system. This work highlights the dynamic regulation of oviduct secretions and provides new protein candidates for interactions between the maternal environment, the gametes and the early embryo.

2022-03-03 | PXD030915 | Pride

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