PXD038502

PXD038502 is an original dataset announced via ProteomeXchange.

Title	BANC-seq to identify genome-wide transcription factor binding affinities to native chromatin
Description	BANC-seq (Binding Affinities to Native Chromatin by sequencing) allows determination of absolute apparent binding affinites of transcription factors to native chromatin in a genome-wide manner. In this study, we establish the method and show that chromatin and DNA sequence define binding affinites of FOXA1, SP1, YY1 and MYC/MAX complex. To relate the identified binding affinities to the actual transcriptional levels of these transcription factors in the cells used in this study, and to confirm that the nuclear isolation protocol used in the study does not lead to loss of nuclear proteins, we have generated whole proteomes including proteomics standards for absolute quantification of proteins. In addition, to validate some of the findings of the study, we have performed PAQMAN (Protein-nucleic acid affinity quantification by MAss spectrometry in nuclear extracts), as well as DNA pulldowns followed by mass spec.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:44:34.173.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hannah Neikes
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480; Q Exactive HF-X; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-01 16:33:05	ID requested
1	2023-02-09 06:50:49	announced
2	2023-04-06 03:49:02	announced	2023-04-06: Updated project metadata.
⏵ 3	2023-11-14 08:44:42	announced	2023-11-14: Updated project metadata.

Neikes HK, Kliza KW, Gr, ä, we C, Wester RA, Jansen PWTC, Lamers LA, Baltissen MP, van Heeringen SJ, Logie C, Teichmann SA, Lindeboom RGH, Vermeulen M, Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq. Nat Biotechnol, 41(12):1801-1809(2023) [pubmed]

submitter keyword: DNA pulldowns,Transcription factors, TMT, proteomes, binding affinity, absolute quantification

Michiel Vermeulen
contact affiliation	Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands.
contact email	Michiel.Vermeulen@science.ru.nl
lab head
Hannah Neikes
contact affiliation	Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands.
contact email	h.neikes@science.ru.nl
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/2023/02/PXD038502

PRIDE project URI

• PRIDE
  1. PXD038502
     1. Label: PRIDE project
     2. Name: BANC-seq to identify genome-wide transcription factor binding affinities to native chromatin