PXD050521

PXD050521 is an original dataset announced via ProteomeXchange.

Title	Cryogenic tissue homogenization as an alternative to adjacent fresh-frozen biopsy use for multi-omics analysis
Description	Background: The majority of multi-omics studies make use of adjacent fresh-frozen tissue pieces for different analyses. This approach however is not considering the intrinsic tissue heterogeneity and can lead to a biological mismatch of different omics layers. To overcome this limitation, we here propose an alternative approach where tissue is cryogenically pulverized and lyophilized, obtaining a homogenous tissue powder that can be used for subsequent omics studies. The purpose of this study was to investigate how omics analysis differ or coincide when comparing adjacent tissue slices to homogenized powder using three major mammalian organs from a wildtype mouse model. Methods: Healthy fresh-frozen and pulverized-lyophilized mouse tissue from brain, kidney, and liver was subjected to DNA methylation and genome sequencing (genomics), RNA sequencing (transcriptomics), protein (proteomics), and metabolite (metabolomics) analysis. Obtained analytical results were investigated by statistical and quality control measures, including dendrograms, correlation analysis, principal component analysis, RNA integrity, feature coverage, and energy charge estimation. Results: DNA methylation was not affected differently by the two different tissue processing methods. The RNA integrity obtained was comparable between fresh-frozen tissue slicing and pulverization-lyophilization. The coverage of gene transcripts, proteins, and metabolites was preserved similarly by both methodological approaches. Overall the pulverization-lyophilization approach resulted in a reduced heterogeneity between biological replicates. Conclusions: Cryogenically pulverized and lyophilized tissue preserves the most important cellular molecular features, such as RNA integrity, DNA methylation status, gene transcript, protein, and metabolite coverage. Therefore, it is a suitable alternative method for improved multi-omics analysis, providing reduced sample heterogeneity, beneficial for batch reproducibility, as well as easier transportation and storage conditions due to complete water removal.
HostingRepository	MassIVE
AnnounceDate	2024-03-10
AnnouncementXML	Submission_2024-03-11_00:52:40.089.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mohamed Ali Jarboui
SpeciesList	scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090;
ModificationList	Carbamidomethyl; Methyl; Acetyl; Deamidated
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-11 00:22:15	ID requested
⏵ 1	2024-03-11 00:52:40	announced

no publication

submitter keyword: Cryogenic pulverization, lyophilization, tissue omics, metabolomics, proteomics, RNA sequencing, transcriptomics, DNA methylation, genomics

Dr.Mohamed Ali Jarboui
contact affiliation	Medical Bioanalytics, University Clinic Tuebingen
contact email	mohamed-ali.jarboui@uni-tuebingen.de
lab head
Mohamed Ali Jarboui
contact affiliation	University klinikum Tuebingen
contact email	mohamed-ali.jarboui@uni-tuebingen.de
dataset submitter

MassIVE dataset URI

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