PXD020421 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Transcriptome, proteome, and metabolome of lens fiber cells from mice exposed to cigarette smoke |
Description | We adopted an omics (transcriptome, proteome, and metabolome) approach to characterize the lens fiber cells extracted from control (CT) and cigarette smoke (CS) exposed mouse (C57BL/6) eyes. The eight pregnant female mice (gestation days 19-20) were placed in a whole-body exposure smoking chamber and served as a CS-exposed group. The mothers and newborn pups were exposed to CS for five hours/day, five days/week for 110 days. In parallel, age-matched mice were kept in normal cages and served as a control group. The ophthalmic examination revealed no sign of cataracts in CS-exposed and aged-matched CT mice. The ocular lenses were extracted and fiber cells (FC) were separated from the lens epithelium under a microscope. The CT and CS fiber cells were maintained in four biological replicates each consisting of a pool of lens fiber cells from four eyes. The eight biological replicates including four CT and four CS-exposed fiber cells were used for the next-generation-based transcriptome (RNA-Seq), mass-spectrometry-based proteome, and metabolome profiling. RNA-Seq analysis identified the expression (≥1.0 FPKM) of 9,590 and 9,531 genes in CT and CS-exposed fiber cells, respectively. The analysis identified 348 differentially expressed genes, including 186 downregulated and 162 upregulated genes in CS-exposed fiber cells. Proteome profiling revealed a total of 2,424 proteins in CT and CS exposed fiber cells. The analysis identified 42 downregulated and 59 upregulated proteins in CS exposed fiber cells. Metabolome profiling identified a total of 280 metabolites, marked with decreased levels of branched-chain amino acids (BCAAs)-related metabolites in CS exposed fiber cells. In conclusion, we have established a comprehensive omics profile of fiber cells from CS-exposed mice. To the best of our knowledge, this is the first report investigating a comprehensive omics profile of fiber cells from CS-exposed mice. |
HostingRepository | PRIDE |
AnnounceDate | 2022-02-15 |
AnnouncementXML | Submission_2022-02-15_13:16:00.440.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | OM Genetics |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-07-17 17:52:34 | ID requested | |
⏵ 1 | 2022-02-15 13:16:01 | announced | |
Publication List
Khan SY, Ali M, Jang Y, Ryu T, Schwab AJ, Ingram BO, Cable PH, Na CH, Handa JT, Riazuddin SA, Examining the effects of cigarette smoke on mouse lens through a multi OMIC approach. Sci Rep, 11(1):18801(2021) [pubmed] |
Keyword List
submitter keyword: Cigarette smoke, mouse lens fiber cells, Proteome, TMT, Mass-spectrometry |
Contact List
S. Amer Riazuddin |
contact affiliation | The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287 USA |
contact email | riazuddin@jhmi.edu |
lab head | |
OM Genetics |
contact affiliation | Johns Hopkins Wilmer Eye Institute |
contact email | omgenetics@jhmi.edu |
dataset submitter | |
Full Dataset Link List
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/2022/02/PXD020421 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD020421
- Label: PRIDE project
- Name: Transcriptome, proteome, and metabolome of lens fiber cells from mice exposed to cigarette smoke