MassIVE MSV000087649

Complete Public PXD026758

RasimBarutcu_MingkunWu_et_al_APEX_2021

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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). [doi:10.25345/C5HJ93] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Proximity-dependent biotinylation ; APEX ; RNA ; Nuclear bodies ; Speckles ; Lamina ; Nuclear domains ; Retained introns

Contact

Principal Investigators:
(in alphabetical order) 		Anne-Claude Gingras, LTRI, Canada
Submitting User: gingraslab

Publications

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. 2022 Mar 3;82(5):1035-1052.e9. Epub 2022 Feb 18.

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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.