PXD052787

PXD052787 is an original dataset announced via ProteomeXchange.

Title	MASH human liver - secreted proteome
Description	An approximate 1 cm3 wedge liver biopsy was collected from the left lobe of the liver during surgery. The liver was cut into two portions. One portion was placed in formalin and transported to TissuPathTM (Mount Waverley, Victoria), paraffin embedded and processed for histological analysis. Samples were graded according to the Clinical Research Network (CRN) NAFLD activity score (NAS) [36] and Kleiner classification of liver fibrosis [4] by TissuPath or Alfred Pathology. The main outcome was the diagnosis of NASH CRN where steatosis, inflammation, and ballooning scores are ≥1. The other portion of liver was placed in oxygenated Medium 199 media (M199; Gibco, USA) with 10% fetal bovine serum (FBS; Gibco, USA) and 1% penicillin-streptomycin (P/S; Gibco, USA), embedded in 3% SeaPlaque agarose (Lonza BioScience, USA) using a Tissue Embedding Unit (Alabama Research and Development, USA). Embedded livers were then sliced on the Alabama R&D Tissue Slicer (Alabama Research and Development, USA) in 500 mL of oxygenated phenol red-free Dulbecco's Modified Eagle Medium (DMEM; Gibco, USA) with 1% P/S at 300 µm thickness, as previously described [24, 37, 38]. The liver slices were washed in Phosphate Buffered Saline (PBS; Gibco USA) and cultured in oxygenated M199 medium containing 1% P/S for 1 h. Subsequently, the liver slices were washed with PBS and cultured in 1 mL EX-CELL 325 protein free medium (Sigma-Aldrich, Australia) for 16 h at 37oC. The following day, the liver slices were weighed and snap-frozen in liquid nitrogen, while the incubation medium was collected and centrifuged at 300 x g at 4 ºC for 10 min. The supernatant was snap-frozen and stored at -80 ºC for subsequent proteomics analysis.
HostingRepository	PRIDE
AnnounceDate	2025-03-25
AnnouncementXML	Submission_2025-03-24_22:00:45.304.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Benjamin Parker
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-02 23:16:44	ID requested
⏵ 1	2025-03-24 22:00:45	announced

Dataset with its publication pending

submitter keyword: liver,human, MASH, NASH

Benjamin Parker
contact affiliation	The University of Melbourne
contact email	ben.parker@unimelb.edu.au
lab head
Benjamin Parker
contact affiliation	The University of Melbourne
contact email	ben.parker@unimelb.edu.au
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/2025/03/PXD052787

PRIDE project URI

• PRIDE
  1. PXD052787
     1. Label: PRIDE project
     2. Name: MASH human liver - secreted proteome