MassIVE MSV000094396

Partial Public PXD050949

Thivierge_etal_Drosha_BioID_2024

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Description

This dataset consists of the files for 22 BioID samples: .wiff and .wiff.scan raw MS files, .mzML peak files, and MSPLIT results files; all acquired on TripleTOF 6600 mass spectrometers operated in Data Independent Acquisition mode (SWATH). It also includes the sequence database used for analysis and the MSPLIT spectral library which was generated from paired samples acquired in Data Dependent Acquisition (DDA) mode. All streptavidin affinity purification, mass spectrometric acquisition, and data analysis was performed by Boris Dyakov. Samples were provided by Thomas Duchaine's lab (McGill University). The files are associated with a manuscript in Cell Reports by Thivierge et al. that explores the paraspeckle-independent co-transcriptional regulation of nuclear microRNA biogenesis by SFPQ, wherein SFPQ is identified as a proximally-associated protein for DROSHA. Only the Wildtype DROSHA bait data is used in the publication, but all files used in statistical analysis are provided. Thomas Duchaine is the corresponding author of the manuscript (thomas.duchaine@mcgill.ca) Anne-Claude Gingras should be contacted for questions about this dataset (gingras@lunenfeld.ca) [doi:10.25345/C57M04B4Z] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: BioID ; Proximity-dependent biotinylation ; SFPQ ; miRNA ; Drosha ; paraspeckles ; lncRNA ; nuclear exosome ; RNA stability ; transcription

Contact

Principal Investigators:
(in alphabetical order) 		Anne-Claude Gingras, LTRI, Canada
Submitting User: gingraslab
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Owner Reanalyses
Experimental Design
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Identification Results
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Quantification Results
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When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
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.

"N/A" means no results of this type were submitted.
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.

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

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) 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 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.