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TMT proteomics and phosphoproteomics of SARS-CoV-2 infected Calu-3 cells

ABSTRACT: Proteomics and phosphoproteomics measurments of human a lung epithelial cell line (Calu-3 cells) infected with the novel coronavirus SARS-CoV-2 over a time-course of 4,8 and 12 hours.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung Epithelial Cell

SUBMITTER: Tommaso Mari

LAB HEAD: Matthias Selbach

PROVIDER: PXD030395 | Pride | 2022-07-08

REPOSITORIES: pride

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			Action	DRS
	MQ_search_results_TXT.zip	Other
	Rowlf_20200720_TM_HStmtpro_Calu3_tot_fr1.raw	Raw
	Rowlf_20200720_TM_HStmtpro_Calu3_tot_fr10.raw	Raw
	Rowlf_20200720_TM_HStmtpro_Calu3_tot_fr11.raw	Raw
	Rowlf_20200720_TM_HStmtpro_Calu3_tot_fr12.raw	Raw

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Publications

In Vitro Kinase-to-Phosphosite Database (iKiP-DB) Predicts Kinase Activity in Phosphoproteomic Datasets.

Mari Tommaso T Mösbauer Kirstin K Wyler Emanuel E Landthaler Markus M Drosten Christian C Selbach Matthias M

Journal of proteome research 20220524 6

Phosphoproteomics routinely quantifies changes in the levels of thousands of phosphorylation sites, but functional analysis of such data remains a major challenge. While databases like PhosphoSitePlus contain information about many phosphorylation sites, the vast majority of known sites is not assigned to any protein kinase. Assigning changes in the phosphoproteome to the activity of individual kinases therefore remains a key challenge. A recent large-scale study systematically identified in vit ...[more]

PMID: 35608653

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2021-11-29 | PXD022709 | Pride

RNA-seq analysis of vorinostat-resistant HCT116 cells following gene knockdown of GLI1 or PSMD13 with or without vorinostat treatment

Project description:Transcriptome analysis was conducted on vorinostat resistant HCT116 cells (HCT116-VR) upon knockdown of potential vorinostat resistance candidate genes in the presence and absence of vorinostat. Potential vorinostat resistance candidate genes chosen for this study were GLI1 and PSMD13, which were identified through a genome-wide synthetic lethal RNA interference screen. To understand the transcriptional events underpinning the effect of GLI1 and PSMD13 knockdown (sensitisation to vorinostat-induced apoptosis), cells were first subjected to gene knockdown, then to treatment with vorinsotat or the solvent control. Two timepoints for drug treatment were assessed: a timepoint before induction of apoptosis (4hrs for siGLI1 and 8hrs for siPSMD13) and a timepoint when apoptosis could be detected (8hrs for siGLI1 and 12hrs for siPSMD13). There are 42 samples in total, from triplicate independent biological experiments of 14 samples each.

2016-06-30 | E-GEOD-57871 | biostudies-arrayexpress

Transcription profiling of reversibly switchable transgenic model of Myc-mediated cell tumorigenesis treated with tamoxifen sacrificed after 2, 4, 8, 24 h of treatment (activation cohort) or 2, 4, 6, days after a 21 day tamoxifen treatment regime ended (regression cohort)

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Omental adipose tissue metaboproteome: differential dysregulation by chronic binge alcohol and ovariectomy in simian immunodeficiency virus-infected female macaques

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Roles and Programming of Arabidopsis ARGONAUTE Proteins During Turnip Mosaic Virus Infection

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