Project PXD003938

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Biomedical Dataset
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Summary

Title

Mouse Smooth muscle cell secretome with Anti-miR / pre-miR treatment

Description

Overexpression and inhibition of miR-29 (pre-miR and anti-miR to miR-29b) in murine aortic smooth muscle cells, analysis of their secretome (conditioned media after serum starvation), n=3 for all four groups (pre-miR control, pre-miR-29b, anti-miR control, anti-miR-29b).

Sample Processing Protocol

-Incubation in serum-free medium (72h) -Collection of the conditioned medium (“secretome”) -Gel-LC-MS of mouse smooth muscle cell secretome

Data Processing Protocol

All MS/MS samples were analyzed using Mascot (Matrix Science, London, UK; version 2.3). Mascot was set up to search the SwissProt_57.15 database (selected for Mus musculus and Bos taurus) assuming the digestion enzyme trypsin. Two missed cleavages were allowed. Mascot was searched with a fragment ion mass tolerance of 0.80 Da and a parent ion tolerance of 10.0 ppm. Iodoacetamide derivative of cysteine was specified in Mascot as a fixed modification. Oxidation of methionine was specified in Mascot as a variable modification. Scaffold (version Scaffold_3.1.4.1, Proteome Software Inc., Portland, OR) was used to validate MS/MS based peptide and protein identifications. Peptide identifications were accepted if they could be established at greater than 95.0% probability as specified by the Peptide Prophet algorithm. Protein identifications were accepted if they could be established at greater than 99.0% probability and contained at least 2 independent peptides. Protein probabilities were assigned by the Protein Prophet algorithm.

Contact

Xiaoke Yin, Cardiovascular Division, King's College London
Manuel Mayr, Cardiovascular Proteomics, Cardiology, James Black Centre, King's College University ( lab head )

Submission Date

11/04/2016

Publication Date

06/05/2016

Publication

    Ulrich V, Rotllan N, Araldi E, Luciano A, Skroblin P, Abonnenc M, Perrotta P, Yin X, Bauer A, Leslie KL, Zhang P, Aryal B, Montgomery RL, Thum T, Martin K, Suarez Y, Mayr M, Fernandez-Hernando C, Sessa WC. Chronic miR-29 antagonism promotes favorable plaque remodeling in atherosclerotic mice. EMBO Mol Med. 2016 May 2. pii: e201506031 PubMed: 27137489

Assay

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# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 63358 Mouse Smooth muscle cell secretome with Anti-miR / pre-miR treatment 128 420 224 1411 378
2 63291 Mouse Smooth muscle cell secretome with Anti-miR / pre-miR treatment 166 733 366 1461 646
3 63357 Mouse Smooth muscle cell secretome with Anti-miR / pre-miR treatment 118 595 299 1242 509
4 63290 Mouse Smooth muscle cell secretome with Anti-miR / pre-miR treatment 128 871 437 1602 764
5 63293 Mouse Smooth muscle cell secretome with Anti-miR / pre-miR treatment 132 984 480 1668 851
6 63292 Mouse Smooth muscle cell secretome with Anti-miR / pre-miR treatment 94 828 418 1670 748
7 63350 Mouse Smooth muscle cell secretome with Anti-miR / pre-miR treatment 79 790 382 1672 696
8 63352 Mouse Smooth muscle cell secretome with Anti-miR / pre-miR treatment 59 693 318 1607 604
9 63351 Mouse Smooth muscle cell secretome with Anti-miR / pre-miR treatment 46 607 259 1593 515
10 63354 Mouse Smooth muscle cell secretome with Anti-miR / pre-miR treatment 86 905 434 1732 794