PXD054913

PXD054913 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Binding proteins of Hydroxymethylcytosine-modified CpG dyads
Description	Cytosine (C) modifications within CpG dyads are central regulatory elements of mammalian genomes. In addition to 5-methylcytosine (mC), genomes can also contain high levels of 5-hydroxymethylcytosine (hmC) that is read differently by nuclear proteins than mC. However, hmC can co-exist with C and mC in different combinations in the two strands of CpG dyads, and it is poorly understood, how these combinatorial marks differ in their protein interactomes and regulatory functions. To identify nuclear binding proteins, we employed DNA promoter probes with differentially modified CpG dyads in pulldown experiments. The datasets comprise three biological replicates of HEK293T nuclear proteins binding to a VEGFA promoter sequence with differentially modified CpG dyads. Each biological replicate contains five technical replicates per modified CpG dyad, resulting in a total of 15 replicates for C/C, mC/mC and hmC/mC, and 10 replicates for hmC/C and hmC/hmC.
HostingRepository	MassIVE
AnnounceDate	2025-07-25
AnnouncementXML	Submission_2025-07-25_07:03:04.060.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Petra Janning
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive Plus

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-15 01:16:02	ID requested
⏵ 1	2025-07-25 07:03:04	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: Cytosine modifications, nuclear binding proteins, binding to VEGFA promoter, interaction proteomics, bottom-up proteomics

submitter keyword: Cytosine modifications, nuclear binding proteins, binding to VEGFA promoter, interaction proteomics, bottom-up proteomics

Contact List

Petra Janning
contact affiliation	MPI of Molecular Physiology
contact email	petra.janning@mpi-dortmund.mpg.de
lab head
Petra Janning
contact affiliation	MPI f�r molekulare Physiologie
contact email	petra.janning@mpi-dortmund.mpg.de
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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MassIVE dataset URI

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://massive-ftp.ucsd.edu/v08/MSV000095609/