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PXD054300

PXD054300 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleRAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues, cancer cells, and macrophages - label-free MS RAPIDASH of L36-FLAG and S17-FLAG E14 mESCs
DescriptionRibosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translation. Nevertheless, a lack of technologies to enrich RAPs across sample types has prevented systematic analysis of RAP identities, dynamics, and functions. We have developed a label-free methodology called RAPIDASH to enrich ribosomes and RAPs from any sample. We applied RAPIDASH to mouse embryonic tissues and identified hundreds of potential RAPs, including DHX30 and LLPH, two forebrain RAPs important for neurodevelopment. We identified a critical role of LLPH in neural development linked to the translation of genes with long coding sequences. In addition, we showed RAPIDASH can identify ribosome changes in cancer cells. Finally, we characterized ribosome composition remodeling during immune cell activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs in multiple cell types, tissues, and stimuli and is adaptable to characterize ribosome remodeling in several contexts. This dataset refers to label-free identification of RAPs enriched by RAPIDASH from L36-FLAG and S17-FLAG mouse embryonic stem cells (mESCs). This dataset is used for comparison with Ribo-FLAG IP and elaborated in Figures 1G-H.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_06:58:07.454.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD054300
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterTeodorus Theo Susanto
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListacetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
InstrumentLTQ Orbitrap Elite
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-07-27 23:28:16ID requested
12024-09-11 18:51:46announced
22024-10-22 06:58:07announced2024-10-22: Updated project metadata.
Publication List
10.6019/PXD054300;
10.1016/J.MOLCEL.2024.08.023;
Keyword List
submitter keyword: acquity UPLC M-class system, embryonic stem cell, orbitrap elite, Ribo-FLAG immunoprecipitation,ribosome, ribosome-associated proteins, mouse
Contact List
Maria Barna
contact affiliationAssociate Professor of Genetics Stanford University USA
contact emailmbarna@stanford.edu
lab head
Teodorus Theo Susanto
contact affiliationScientist
contact emailtheosusanto@protonmail.com
dataset submitter
Full Dataset Link List
Dataset FTP location
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