PXD021089

PXD021089 is an original dataset announced via ProteomeXchange.

Title	greenCUT&RUN: a rapid and efficient genome profiling approach for transcription and chromatin regulatory proteins
Description	Chromatin modifiers, transcription factors and cofactors regulate gene expression through engagement with chromatin and DNA, which can be detected by a variety of genomic techniques. Here, we describe a novel method ‘greenCUT&RUN’ for genome-wide profiling of transcription regulatory factors, which has higher sensitivity, resolution, accuracy and reproducibility than existing methods, whilst assuring specificity as assessed for the gene specific transcription factors NFY and c-FOS, and for the basal transcription factor TBP. Our strategy begins with tagging the protein of interest with GFP and utilizes a GFP-specific nanobody fused to MNase to profile genome-wide binding events. Since the nanobody targets GFP, the greenCUT&RUN approach eliminates dependency on protein-specific antibodies, which makes it widely applicable. To examine, if GFP-tagged proteins form complex with known interactors and GFP did not interfere in the formation of protein complex, mass spectrometry was performed.
HostingRepository	PRIDE
AnnounceDate	2021-01-13
AnnouncementXML	Submission_2021-01-12_23:39:01.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marc Timmers
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-24 09:06:20	ID requested
⏵ 1	2021-01-12 23:39:01	announced

Dataset with its publication pending

submitter keyword: NFYA, FOS, HeLa, GFP-tagged proteins, Affinity purification, Nanobody, Enhancer

H. Th. Marc Timmers
contact affiliation	1. German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany 2. Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany
contact email	m.timmers@dkfz-heidelberg.de
lab head
Marc Timmers
contact affiliation	German Cancer Consortium (DKTK), partner site Freiburg German Cancer Research Center (DKFZ) Foundation under Public Law c/o Department of Urology Zentrale Klinische Forschung (ZKF) Medical Center-University of Freiburg Breisacher Str. 66, 79106 Freiburg, Germany
contact email	m.timmers@dkfz-heidelberg.de
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/2021/01/PXD021089

PRIDE project URI

• PRIDE
  1. PXD021089
     1. Label: PRIDE project
     2. Name: greenCUT&RUN: a rapid and efficient genome profiling approach for transcription and chromatin regulatory proteins