Proteomics

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RasimBarutcu_MingkunWu_et_al_APEX_2021

ABSTRACT: 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).

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Anne-Claude Gingras  

PROVIDER: MSV000087649 | MassIVE | Thu Jun 17 13:06:00 BST 2021

SECONDARY ACCESSION(S): PXD026758

REPOSITORIES: MassIVE

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Publications

Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns.

Barutcu A Rasim AR   Wu Mingkun M   Braunschweig Ulrich U   Dyakov Boris J A BJA   Luo Zheng Z   Turner Kyle M KM   Durbic Tanja T   Lin Zhen-Yuan ZY   Weatheritt Robert J RJ   Maass Philipp G PG   Gingras Anne-Claude AC   Blencowe Benjamin J BJ  

Molecular cell 20220218 5

The nucleus is highly compartmentalized through the formation of distinct classes of membraneless domains. However, the composition and function of many of these structures are not well understood. Using APEX2-mediated proximity labeling and RNA sequencing, we surveyed human transcripts associated with nuclear speckles, several additional domains, and the lamina. Remarkably, speckles and lamina are associated with distinct classes of retained introns enriched in genes that function in RNA proces  ...[more]

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