PXD004652 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | A Systems-Level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells |
Description | Mesenchymal stem/stromal cells (MSCs) are self-renewing multipotent cells with regenerative, secretory and immunomodulatory capabilities that are beneficial for the treatment of various diseases. To avoid the issues that come with using tissue-derived MSCs in therapy, MSCs may be generated by the differentiation of human embryonic stems cells (hESCs) in culture. However, the changes that occur during the differentiation process have not been comprehensively characterized. Here, we combined transcriptome, proteome and phosphoproteome profiling to perform an in-depth, multi-omics study of the hESCs-to-MSCs differentiation process. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation. Among the earliest and strongest induced proteins with extensive differential phosphorylation was AHNAK, which we hypothesized to be a defining factor in MSC biology. We observed two distinct expression waves of developmental HOX genes and an AGO2-to-AGO3 switch in gene silencing. Exploring the kinetic of non-coding ORFs during differentiation, we mapped new functions to well annotated long non-coding RNAs (CARMN, MALAT, NEAT1, LINC00152) as well as new candidates which we identified to be important to the differentiation process. Phosphoproteome analysis revealed ESC and MSC-specific phosphorylation motifs with PAK2 and RAF1 as top predicted upstream kinases in MSCs. Our data represent a rich systems-level resource on ESC-to-MSC differentiation that will be useful for the study of stem cell biology. |
HostingRepository | PRIDE |
AnnounceDate | 2019-07-26 |
AnnouncementXML | Submission_2019-08-01_04:42:24.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Johannes Graumann |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2016-07-25 05:39:19 | ID requested | |
1 | 2019-07-23 14:40:56 | announced | |
2 | 2019-07-24 00:30:26 | announced | Updated project metadata. |
3 | 2019-07-26 00:30:17 | announced | Updated project metadata. |
⏵ 4 | 2019-08-01 04:42:25 | announced | Updated project metadata. |
5 | 2021-10-29 04:35:27 | announced | 2021-10-29: Updated project metadata. |
Publication List
Billing AM, Dib SS, Bhagwat AM, da Silva IT, Drummond RD, Hayat S, Al-Mismar R, Ben-Hamidane H, Goswami N, Engholm-Keller K, Larsen MR, Suhre K, Rafii A, Graumann J, A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells. Mol Cell Proteomics, 18(10):1950-1966(2019) [pubmed] |
Keyword List
curator keyword: Biomedical |
submitter keyword: Human embryonic stem cells, human mesenchymal stem cells, bone marrow, differentiation, transcriptome, proteome, phosphoproteome, quantitative proteomics, LC-MS/MS, RNA-seq |
Contact List
Johannes Graumann |
contact affiliation | Weill Cornell Medicine - Qatar |
contact email | jog2030@qatar-med.cornell.edu |
lab head | |
Johannes Graumann |
contact affiliation | Max Planck Institute for Heart and Lung Research |
contact email | johannes.graumann@mpi-bn.mpg.de |
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/2019/07/PXD004652 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD004652
- Label: PRIDE project
- Name: A Systems-Level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells