PXD034143

PXD034143 is an original dataset announced via ProteomeXchange.

Title	Proteomic profiling of mouse Paneth cells microdissected from small intestinal tissue
Description	Paneth cells are antimicrobial peptide-secreting cells located at the base of the crypts of the small intestine. The proteome of Paneth cells is not well defined because of their co-existence with stem cells making it difficult to culture Panth cells alone in vitro. Using a simplied toluidine blue O method for staining mouse intestinal tissue, laser capture microdissection (LCM) to isolate cells from the crypt region and surfactant assisted one pot protein digestion, we identified more than 1,300 proteins from crypts equivalent to 18,000 cells. Compared with the proteomes of villi and smooth muscle regions, the crypt proteome is highly enriched in defensins, lysozymes and other antimicrobial peptides that are characteristic of Paneth cells. The sensitivity of the LCM-based proteomics approach was also assessed using a smaller number of cell equivalent tissues, a comparable proteomic coverage can be achieved with 3,600 cells. This work is the first proteomics study of intestinal tissue enriched with Paneth cells. The simplied workflow enables profiling of Paneth cell associated pathological changes at the proteome level directly from frozen intestinal tissue. It may also be useful for proteomics studies of other spatially resolved cell types from other tissues.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:30:51.401.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jongmin Woo
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-26 01:32:33	ID requested
1	2022-10-12 07:10:30	announced
⏵ 2	2023-11-14 08:30:52	announced	2023-11-14: Updated project metadata.

Woo J, Schoenfeld M, Sun X, Iraguha T, Zhou Z, Zhang Q, Mouse Paneth Cell-Enriched Proteome Enabled by Laser Capture Microdissection. J Proteome Res, 21(10):2435-2442(2022) [pubmed]

submitter keyword: Paneth cell, mouse small intestine, proteomics, laser capture microdissection, toluidine blue, villi

Qibin Zhang
contact affiliation	1. Center for Translational Biomedical Research, University of North Carolina at Greensboro 2. Department of Chemistry & Biochemistry, University of North Carolina at Greensboro
contact email	q_zhang2@uncg.edu
lab head
Jongmin Woo
contact affiliation	The University of North Carolina at Greensboro
contact email	jongminw@gmail.com
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/2022/10/PXD034143

PRIDE project URI

• PRIDE
  1. PXD034143
     1. Label: PRIDE project
     2. Name: Proteomic profiling of mouse Paneth cells microdissected from small intestinal tissue