PXD030825 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Analysis of oncogenic Kras-induced changes in the RNA-bound proteome of PDAC cells |
Description | In order to reveal the impact of oncogenic KRAS signaling on the RNA-bound proteome of Pancreatic Ductal Adenocarcinoma (PDAC), we carried out quantitative whole Transcriptome RNA Interactome Capture (RIC) analysis in tumour cells from an inducible mouse model of PDAC (iKras PDAC) (Ying et al., 2012). In this model, oncogenic Kras (G12D) expression can be controlled by administration of doxycycline (Dox). For RIC, we employed Orthogonal Organic Phase Separation (OOPS)(Queiroz et al., 2019). In this method, UV-C crosslinking coupled with phenol-chloroform based phase separation is used to isolate RNA-crosslinked proteins, which concentrate in the interface fraction, whilst free proteins concentrate in the organic fraction. SILAC was employed for quantitative analysis of Dox induced (24hrs) changes in the RNA-bound proteome. To assess the impact of ERK signalling, an independent experiment was carried out in which Trametinib (10nM) was added to the cells at the same time as Dox (both with or without Dox cells). A total of 6 biological replicates without Trametinib, and 4 biological replicates with Trametinib, were conducted, with switching the Heavy and Light SILAC labels for +Dox and -Dox conditions. Both the Interface as well as the organic phase fractions were analysed by mass spectrometry. In a separate experiment, the total proteome changes in response to dox (24hrs) were quantified from two reciprocally SILAC labelled mixes of heavy and light iKras PDAC whole cell lysates (See the READ ME.XLS for details of the experimental conditions). |
HostingRepository | PRIDE |
AnnounceDate | 2023-02-12 |
AnnouncementXML | Submission_2023-02-12_08:06:48.770.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | FarazMardakheh |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive Plus |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-01-07 13:55:40 | ID requested | |
⏵ 1 | 2023-02-12 08:06:49 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: RNA Interactome Capture |
RIC |
OOPS |
KRAS |
RNA-binding |
RBP |
SILAC |
Contact List
Faraz K.Mardakheh |
contact affiliation | Centre for Cancer Cell & Molecular Biology Barts Cancer Institute Queen Mary University of London Charterhouse Square London EC1M 6BQ U.K. |
contact email | f.mardakheh@qmul.ac.uk |
lab head | |
FarazMardakheh |
contact affiliation | Barts Cancer Institute |
contact email | f.mardakheh@qmul.ac.uk |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD030825
- Label: PRIDE project
- Name: Analysis of oncogenic Kras-induced changes in the RNA-bound proteome of PDAC cells