PXD026758

PXD026758 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	RasimBarutcu_MingkunWu_et_al_APEX_2021
Description	This dataset consists of 26 raw MS files and associated peak lists and result files, acquired on a TripleTOF 6600 mass spectrometer operated in Data Dependent Acquisition mode. Samples were generated by Rasim Barutcu and Mingkun Wu (some clones also generated by Boris Dyakov). Streptavidin affinity purification and mass spectrometric acquisition was performed by Zhen-Yuan Lin. Mass Spectrometry data analysis was performed by Boris Dyakov. The files are associated with a manuscript submitted for publication by Barutcu et al. that identifies functionally distinct proteins and retained intron RNAs associated with nuclear domains (speckles and lamina) using APEX2-mediated proximity labeling. ("Systematic mapping of nuclear domain associated transcripts reveals speckles and lamina as hubs of functionally distinct populations of retained introns") Benjamin Blencowe is the corresponding author of the manuscript (b.blencowe@utoronto.ca). Anne-Claude Gingras should be contacted for questions about this dataset (gingras@lunenfeld.ca).
HostingRepository	MassIVE
AnnounceDate	2023-01-10
AnnouncementXML	Submission_2023-01-10_10:41:38.027.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Gingras Lab
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	deamidated L-asparagine; deamidated L-glutamine; L-methionine sulfoxide
Instrument	TripleTOF 6600

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2021-06-17 13:06:36	ID requested
⏵ 1	2023-01-10 10:41:38	announced

Publication List

Barutcu AR, Wu M, Braunschweig U, Dyakov BJA, Luo Z, Turner KM, Durbic T, Lin ZY, Weatheritt RJ, Maass PG, Gingras AC, Blencowe BJ, Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns. Mol Cell, 82(5):1035-1052.e9(2022) [pubmed]

Barutcu AR, Wu M, Braunschweig U, Dyakov BJA, Luo Z, Turner KM, Durbic T, Lin ZY, Weatheritt RJ, Maass PG, Gingras AC, Blencowe BJ, Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns. Mol Cell, 82(5):1035-1052.e9(2022) [pubmed]

Keyword List

submitter keyword: Proximity-dependent biotinylation, APEX, RNA, Nuclear bodies, Speckles, Lamina, Nuclear domains, Retained introns

submitter keyword: Proximity-dependent biotinylation, APEX, RNA, Nuclear bodies, Speckles, Lamina, Nuclear domains, Retained introns

Contact List

Anne-Claude Gingras
contact affiliation	LTRI
contact email	gingras@lunenfeld.ca
lab head
Gingras Lab
contact affiliation	Samuel Lunenfeld Research Institute
contact email	gingras@mshri.on.ca
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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MassIVE dataset 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://massive.ucsd.edu/MSV000087649/