MassIVE MSV000099266

Partial Public PXD068755

Proteomic analysis of PHACTR1 overexpressing and knockdown HT1080 stable cell lines

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Description

The PHACTR1 gene to a range of vascular and neurological diseases, underscoring its pivotal role in biology. To investigate the role of PHACTR1 in cells, we used lentiviral transfection of HT1080 cells with plasmids to overexpress (O) or knockdown (K) the PHACTR1 gene or a scrambled control plasmid (S) and created stable cell lines. As part of a larger multi-omics study, we performed untargeted on cell lysates (n=6 per condition). Peptide extracts were fractionated into 8, and analysed by LC-MS/MS using a C18AQ column on an Ultimate nanoRSLC UPLC coupled to a Orbitrap Fusion Lumos. Mass spectrometry raw data files were searched using MaxQuant (v2.1.3.0) against the Uniprot human canonical proteome (downloaded April 2023). [doi:10.25345/C5XD0RB0M] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: PHACTR1 ; HT1080 ; global proteomics ; LC-MS/MS ; MaxQuant ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Jason C Kovacic, Victor Chang Cardiac Research Institute, Australia
Submitting User: kathrynwolhuter

Publications

Kathryn Wolhuter, Lijiang Ma, Nicole S Bryce, Osvaldo Contreras, Natalie Mellett, Ling Zhong, Chris Thekkedam, Corey Giles, Richard P Harvey, Thomas Hennessy, Chris Fouracre, David Bradley, Peter J Meikle, Johan L M Björkegren, Jason C Kovacic.
Multi-omic Analysis of PHACTR1 Signaling Networks in Human Cells.
Communications Biology (accepted).

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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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