Project PXD011937

PRIDE Assigned Tags:
Biological Dataset

Summary

Title

Proteomics characterization of Chromosomal Common Fragile Site (CFS) - associated proteins uncovers ATRX as a regulator of CFS stability

Description

Chromosomal Common Fragile Sites (CFSs) are conserved regions of our genome prone to break in conditions of replication stress (RS. Here, we have performed Chromatin Immunoprecipitation (ChIP) with FACND2 antibodies coupled to Mass Spectrometry to isolate CFSs from HeLa cells and identify the proteins enriched at these loci.

Sample Processing Protocol

ChIP eluates were separated by SDS-page and subjected to in-gel digestion with trypsin. Samples were stage-tipped and analysed analysed with an Easy-nLC 1000 system coupled to the Q Exactive HF-X instrument (Thermo Fisher Scientific) through a nanoelectrospray ion source.

Data Processing Protocol

All raw MS data was process using MaxQuant (v.1.6.0.1) and the integrated database search engine, Andromeda against the Uniprot database. Common contaminants were included in the database and excluded upon data analysis. False discovery rate was set to 1% for peptide spectral matches (PSMs) and protein level, calculated using the decoy database strategy.

Contact

Stephanie Munk, Copenhagen University
Andres Joaquin Lopez-Contreras, Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen 2200, Denmark ( lab head )

Submission Date

05/12/2018

Publication Date

11/06/2019

Instrument

Q Exactive

Software

Not available

Quantification

Not available

Experiment Type

Shotgun proteomics

Publication

    Pladevall-Morera D, Munk S, Ingham A, Garribba L, Albers E, Liu Y, Olsen JV, Lopez-Contreras AJ. Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability. Nucleic Acids Res. 2019 PubMed: 31180492