PXD025194

PXD025194 is an original dataset announced via ProteomeXchange.

Title	RNA-interactome capture in human embryonic stem cells (hESCs)
Description	Embryonic stem cell (ESC) self-renewal and cell-fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carried out a proteome-wide screen and identified 810 proteins that directly bind RNA in hESCs. We determined the RBP catalog by using RNA-interactome capture (RIC), a method based on UV light-mediated cross-linking (CL) of RNAs to proteins in living cells, followed by oligo(dT) purification of poly(A)-RNA-protein complexes and mass spectrometry analysis of captured proteins. As control, we applied a similar strategy to non-cross-linked (non-CL) samples. To uncover the identity of the eluted proteins, we performed in-solution tryptic digestion of CL and non-CL eluates and analyzed their contents by a high-resolution mass spectrometer (Q-Exactive Plus). We then performed differential proteome analysis between CL and non-CL eluates, resulting in a set of 810 high-confidence protein groups, defined as the hESC RNA-interactome. RIC was carried out in four independent biological replicates. This data accompanies the manuscript: "Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells".
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:45:30.362.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shlomi Dvir
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-06 04:01:52	ID requested
1	2023-05-04 18:41:56	announced
⏵ 2	2023-11-14 08:45:40	announced	2023-11-14: Updated project metadata.

Dvir S, Argoetti A, Lesnik C, Roytblat M, Shriki K, Amit M, Hashimshony T, Mandel-Gutfreund Y, Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells. Cell Rep, 35(9):109198(2021) [pubmed]

submitter keyword: RNA-interactome capture, RIC, hESCs, RNA-binding proeins, RBPs, human embryonic stem cells

Yael Mandel-Gutfreund
contact affiliation	1. Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel 2. Computer Science Department, Technion - Israel Institute of Technology, Haifa 320003, Israel
contact email	yaelmg@technion.ac.il
lab head
Shlomi Dvir
contact affiliation	Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
contact email	shlomidvir1@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/05/PXD025194

PRIDE project URI

• PRIDE
  1. PXD025194
     1. Label: PRIDE project
     2. Name: RNA-interactome capture in human embryonic stem cells (hESCs)