PXD036968-1

PXD036968 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	SARS-CoV-2 variants evolve convergent strategies to remodel the host response: Infection proteomics
Description	We sought to compare differences in the human cellular response to distinct SARS-CoV-2 variants of concern. Here, we infected Calu-3 lung epithelial cells with each of the SARS-CoV-2 variants of concern (Alpha, Beta, Gamma, Delta, and Omicron) compared to two early-lineage controls (VIC and IC19). We performed global abundance proteomics and phosphoproteomics at 10, 24, and, for certain samples, 48 hours post infection to comprehensively characterize the host response to infection.
HostingRepository	PRIDE
AnnounceDate	2024-02-16
AnnouncementXML	Submission_2024-02-15_23:14:30.112.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mehdi Bouhaddou
SpeciesList	scientific name: Severe acute respiratory syndrome coronavirus 2; NCBI TaxID: 2697049;
ModificationList	phosphorylated residue; acetylated residue
Instrument	Orbitrap Fusion Lumos; Orbitrap Exploris 480

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-25 14:13:43	ID requested
⏵ 1	2024-02-15 23:14:31	announced
2	2024-10-22 06:30:52	announced	2024-10-22: Updated project metadata.

Publication List

10.1016/j.cell.2023.08.026;
Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, Furnon W, De Lorenzo G, Cowton V, Syed AM, Ciling A, Deutsch N, Pirak D, Dowgier G, Mesner D, Turner JL, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Dunham AS, Zhong X, Eckhardt M, Fossati A, Liotta NF, Kehrer T, Cupic A, Rutkowska M, Mena I, Aslam S, Hoffert A, Foussard H, Olwal CO, Huang W, Zwaka T, Pham J, Lyons M, Donohue L, Griffin A, Nugent R, Holden K, Deans R, Aviles P, Lopez-Martin JA, Jimeno JM, Obernier K, Fabius JM, Soucheray M, H, ü, ttenhain R, Jungreis I, Kellis M, Echeverria I, Verba K, Bonfanti P, Beltrao P, Sharan R, Doudna JA, Martinez-Sobrido L, Patel AH, Palmarini M, Miorin L, White K, Swaney DL, Garcia-Sastre A, Jolly C, Zuliani-Alvarez L, Towers GJ, Krogan NJ, SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell, 186(21):4597-4614.e26(2023) [pubmed]

10.1016/j.cell.2023.08.026;

Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, Furnon W, De Lorenzo G, Cowton V, Syed AM, Ciling A, Deutsch N, Pirak D, Dowgier G, Mesner D, Turner JL, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Dunham AS, Zhong X, Eckhardt M, Fossati A, Liotta NF, Kehrer T, Cupic A, Rutkowska M, Mena I, Aslam S, Hoffert A, Foussard H, Olwal CO, Huang W, Zwaka T, Pham J, Lyons M, Donohue L, Griffin A, Nugent R, Holden K, Deans R, Aviles P, Lopez-Martin JA, Jimeno JM, Obernier K, Fabius JM, Soucheray M, H, ü, ttenhain R, Jungreis I, Kellis M, Echeverria I, Verba K, Bonfanti P, Beltrao P, Sharan R, Doudna JA, Martinez-Sobrido L, Patel AH, Palmarini M, Miorin L, White K, Swaney DL, Garcia-Sastre A, Jolly C, Zuliani-Alvarez L, Towers GJ, Krogan NJ, SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell, 186(21):4597-4614.e26(2023) [pubmed]

Keyword List

ProteomeXchange project tag: Sars-cov-2, Covid-19
submitter keyword: lung, omics, SARS-CoV-2, host response, host, infection, COVID-19

ProteomeXchange project tag: Sars-cov-2, Covid-19

submitter keyword: lung, omics, SARS-CoV-2, host response, host, infection, COVID-19

Contact List

Nevan J
contact affiliation	Department of Cellular and Molecular Pharmacology University of California San Francisco (UCSF)
contact email	nevan.krogan@ucsf.edu
lab head
Mehdi Bouhaddou
contact affiliation	UCSF
contact email	mehdibouhaddou@gmail.com
dataset submitter

Full Dataset Link List

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/2024/02/PXD036968
PRIDE project URI

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/2024/02/PXD036968

PRIDE project URI

Repository Record List

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