PXD065221-1

PXD065221 is an original dataset announced via ProteomeXchange.

Title	The immune response against cancer is modulated by stromal cell fibronectin
Description	The data set compares murine bone marrow stromal cells that express osterix-cre (and hence cells in which the osterix promoter is active) to the cells isolated from the same animals that did not express osterix-cre (and hence do not activate the osterix promoter). To sort these cells, we used the reporter gene tdTomato. If the gene is present, the protein is not expressed because the gene is preceded by a STOP codon flanked by two floxed sites. If, on the other hand, cre is expressed (in this case osterix-cre) in the same cell that contains the tdTomato gene, activation of the promoter will lead to cre recombinase expression and removal of the gene part flanked by floxed sequences. This will remove the STOP codon and lead to expression of the tdTomato protein. Cells that are osterix-cre_tdTomatofloxed/+ therefore will express tdTomato and can be detected by flow cytometry allowing sorting. The cells were isolated from the bone marrow of adult mice. It should be noted, that in addition to the difference in osterix promoter activation, tdTomato is also expressed in the sorted osterix-cre cells. There are 4 samples that do not express osterix followed by 4 samples that do as follows: Control samples numbered 1-4 and Osterix samples numbered 5-8. Analysis results are summarized as supplementary figure 3 and supplementary table 1 in Lubosch, Pitt et al. 2025, Neoplasia
HostingRepository	PRIDE
AnnounceDate	2025-06-20
AnnouncementXML	Submission_2025-06-20_01:58:02.215.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Barbara Steigenberger
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-19 08:15:31	ID requested
⏵ 1	2025-06-20 01:58:02	announced

Dataset with its publication pending

submitter keyword: breast cancer, stromal cell, tumor microenvironment, tdTomato, bone marrow, neutrophil,Osterix, Ly6G, fibronectin, melanoma, myeloid, bone marrow., extracellular matrix, murine Additional keywords: immune response

Inaam Nakchbandi
contact affiliation	Max-Planck Institute of Biochemistry and Institute of Immunology, University of Heidelberg Im Neuenheimer Feld 305, 2. OG 69120 Heidelberg Germany
contact email	inaam.nakchbandi@immu.uni-heidelberg.de
lab head
Barbara Steigenberger
contact affiliation	MPI of Biochemistry
contact email	steigenberger@biochem.mpg.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/2025/06/PXD065221

PRIDE project URI

• PRIDE
  1. PXD065221
     1. Label: PRIDE project
     2. Name: The immune response against cancer is modulated by stromal cell fibronectin