PXD033841

PXD033841 is an original dataset announced via ProteomeXchange.

Title	Comparative Transcriptomics and Proteomics of Cancer Cell Lines Cultivated by Physiological and Commercial Media
Description	Aiming to reduce the gap between in vitro and in vivo environment, a complex culture medium, Plasmax, was introduced recently, which includes nutrients and metabolites with concentrations normally found in human plasma. Herein, to study the influence of this medium on cellular behaviors, we utilized Plasmax to cultivate another two cancer cell lines, including one breast cancer cell line, MDA-MB-231BR, and one brain cancer cell line, CRL-1620. Cancer cells were harvested and prepared for proteomics and transcriptomics analyses to assess the discrepancies caused by the different nutritional environments of Plasmax and two commercial media: DMEM, and EMEM. Total RNAs of cells were extracted using mammalian total RNA extract kits and analyzed by next-generation RNA sequencing, and proteomics analyses were performed using LC-MS/MS. Gene oncology and pathway analysis were employed to study the affected functions. The cellular invasion and cell death were inhibited in 231BR cell line when cultured in Plasmax compared to DMEM and EMEM, whereas the invasion, migration and protein synthesis of CRL cell line were activated in Plasmax in relative to both commercial media. The expression changes of some proteins were more significant compared to their corresponding transcripts, indicating that Plasmax has more influence upon regulatory processes of proteins after translation. This work provides complementary information to the original study of Plasmax, aiming to facilitate the selection of appropriate media for in vitro cancer cell studies.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:27:12.334.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Junyao Wang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-12 04:28:55	ID requested
1	2023-03-10 10:46:49	announced
⏵ 2	2023-11-14 08:27:13	announced	2023-11-14: Updated project metadata.

Wang J, Peng W, Yu A, Fokar M, Mechref Y, Comparative Transcriptomics and Proteomics of Cancer Cell Lines Cultivated by Physiological and Commercial Media. Biomolecules, 12(11):(2022) [pubmed]

submitter keyword: Culture media,Proteomics, Transcriptomics, Cancer cell line, Differential expression analysis, LC-MS/MS

Yehia Mechref
contact affiliation	Texas Tech University
contact email	Yehia.Mechref@ttu.edu
lab head
Junyao Wang
contact affiliation	Texas Tech University
contact email	junyao.wang@ttu.edu
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/2023/03/PXD033841

PRIDE project URI

• PRIDE
  1. PXD033841
     1. Label: PRIDE project
     2. Name: Comparative Transcriptomics and Proteomics of Cancer Cell Lines Cultivated by Physiological and Commercial Media