PXD033840

PXD033840 is an original dataset announced via ProteomeXchange.

Title	Endogenous OCT4 interactome in hESC
Description	In two widely-cited OCT4-protein interactome papers, Ding et al. (Ding et al., 2012) used murine ESC nuclear extract to identify OCT4 interactome in nucleus and Pardo et al. (Pardo et al., 2010) used whole cell lysate to identify OCT4 interactome in murine ESCs. In both papers, Benzonase, a genetically engineered endonuclease was employed to fragment genome DNA which significantly improved the enrichment efficiency of nuclear TFs. Since our focus was on cytosolic pool of OCT4, we used mild conditions for cell lysis and modified the Pardo’s method by omitting the addition of any nucleases to the lysis buffer. Such conditions not only retained the protein/RNA interactions, but also enabled precipitation of the nuclear TFs with genome DNA, and hence a relative enrichment of the cytosolic proteins and other soluble nuclear proteins (such as splicing factors) in the supernatant, and therefore allowed us to minimize the interference of the TF roles of OCT4 and to focus more on its novel RBP roles.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_08:50:40.686.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Bo Kang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-12 04:28:02	ID requested
⏵ 1	2025-05-06 08:50:41	announced

Chen W, Chen X, Chen C, She S, Li X, Shan L, Zhang X, Dan S, Wang Y, Zhou YW, Cao Q, Wang W, Hu J, Wei Y, Xue Y, Zhang Y, Zhang S, Wang YJ, Kang B, OCT4 translationally promotes AKT signaling as an RNA-binding protein in stressed pluripotent stem cells. Stem Cell Res Ther, 16(1):84(2025) [pubmed]

10.1186/s13287-025-04229-1;

submitter keyword: OCT4,ESC,human

Ying-Jie Wang
contact affiliation	State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
contact email	yingjiewang@zju.edu.cn
lab head
Bo Kang
contact affiliation	State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 310003 Hangzhou, China
contact email	kangbo@zju.edu.cn
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/2025/05/PXD033840

PRIDE project URI

• PRIDE
  1. PXD033840
     1. Label: PRIDE project
     2. Name: Endogenous OCT4 interactome in hESC