PXD040982-1

PXD040982 is an original dataset announced via ProteomeXchange.

Title	Mass-spectrometry phosphoproteomics of Calu-3 cell lines infected with SARS-CoV-2, in comparison to non-infected and UV mock-treated cell lines
Description	To identify the proteome alterations in human epithelial cells upon SARS-CoV-2 infection, we performed an in vitro experiment, where we infected lung-adenocarcinoma cultured human airway epithelial cells (Calu-3) with an isolate of the ancestral variant and alpha variant of SARS-CoV-2 in two separate experiments. Samples were then collected 3 hours, 1 day, 3 days, and 7 days post infection. In parallel, for comparison, we collected samples on the same days from non-infected cells and cells treated with SARS-CoV-2 virus (of the corresponding variant) inactivated by ultraviolet radiation. All conditions were performed in biological triplicates and we performed phosphoproteomics analysis with high-pH fractionation and LC-MS/MS. Cell culture specifics Human lung adenocarcinoma Calu3 cells (ATCC, HTB-55) were grown in minimum essential medium (MEM) supplemented with 20% FBS, HEPES, L-glutamin, 100 U/ml penicillin, and 100 mg/ml streptomycin at 37°C and 5% CO2. The SARS-CoV-2 variants were propagated on Vero E6 cells and titrated via end point dilution assay. For UV-inactivation, the virus stock was incubated under UV-light for 3 x 1.5 min. Complete inactivation was confirmed via infection attempt and no live virus could be detected after the treatment. Cells were infected with active or UV-inactivated SARS-CoV-2 in complete MEM at a multiplicity of infection (MOI) of 1. After two  hours of incubation the virus solution was removed, the cells were washed, and fresh growth medium was added. Before the infection, the active and inactivated virus were treated with Trypsin at 1:100 dilution for one hour at 37°C.  Before sample collection at the indicated time points, the cells were washed thoroughly. Cells were lysed in lysis buffer containing 1mM DTT and boiled at 95°C for five minutes.
HostingRepository	PRIDE
AnnounceDate	2023-09-01
AnnouncementXML	Submission_2023-09-01_07:24:58.666.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	HarisBabačić
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-20 10:00:50	ID requested
⏵ 1	2023-09-01 07:24:59	announced
2	2023-11-14 06:43:26	announced	2023-11-14: Updated project metadata.
3	2024-10-22 06:02:19	announced	2024-10-22: Updated project metadata.

submitter keyword: COVID-19, phosphosites, pH fractionation, human, SARS-CoV-2, Calu-3 cell line, infection, phosphoproteomics, LC-MS/MS

JanneLehtiö
contact affiliation	Department of Oncology and Pathology, Karolinska Institute and Science for Life Laboratory
contact email	janne.lehtio@ki.se
lab head
HarisBabačić
contact affiliation	1. Department of Oncology-Pathology, Karolinska Institute, Stockholm; 2. Proteogenomics Facility, Science for Life Laboratory
contact email	haris.babacic@ki.se
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/09/PXD040982

PRIDE project URI

• PRIDE
  1. PXD040982
     1. Label: PRIDE project
     2. Name: Mass-spectrometry phosphoproteomics of Calu-3 cell lines infected with SARS-CoV-2, in comparison to non-infected and UV mock-treated cell lines