PXD019351
PXD019351 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Transcriptomic and Proteomic Signatures of Stemness and Differentiation in the Colon Crypt |
| Description | The intestinal epithelium is replaced weekly by non-quiescent stem cells with kinetics that rely on a rapid loss of stemness and choice for secretory or absorptive lineage differentiation. To determine how the cellular transcriptome and proteome changes during these transitions, we developed a new cell sorting method to purify stem cells, secretory and absorptive progenitor cells, and mature, differentiated cells. Transcriptome analyses revealed that as stem cells transition to the progenitor stage, alternative mRNA splicing and polyadenylation dominate changes in the transcriptome. In contrast, as progenitors differentiate into mature cell types, alterations in gene expression and mRNA levels drive the changes. RNA processing targets mRNAs encoding regulators of cell cycle, RNA regulators, cell adhesion, SUMOylation, and Wnt and Notch signaling. Additionally, carrier-assisted mass spectrometry of sorted cell populations detected >2,800 proteins and revealed RNA:protein patterns of abundance and correlation. Paired together, these data highlight new potentials for autocrine and feedback regulation and provide new insights into cell state transitions in the crypt. |
| HostingRepository | jPOST |
| AnnounceDate | 2020-07-15 |
| AnnouncementXML | Submission_2022-11-21_08:26:21.874.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Chia-Feng Tsai |
| SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
| ModificationList | L-methionine sulfoxide; alpha-amino acetylated residue; unknown modification |
| Instrument | Q Exactive |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2020-05-22 08:59:45 | ID requested | |
| 1 | 2020-07-15 13:14:15 | announced | |
| 2 | 2021-02-04 16:59:23 | announced | 2021-02-04: Updated FTP location. |
| 3 | 2022-09-18 02:34:35 | announced | 2022-09-18: Updated FTP location. |
| ⏵ 4 | 2022-11-21 08:26:22 | announced | 2022-11-22: Updated PubMed. |
Publication List
| Habowski AN, Flesher JL, Bates JM, Tsai CF, Martin K, Zhao R, Ganesan AK, Edwards RA, Shi T, Wiley HS, Shi Y, Hertel KJ, Waterman ML, Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt. Commun Biol, 3(1):453(2020) [pubmed] |
Keyword List
| submitter keyword: Colon Crypt, Stem Cells, Transcriptomics, Proteomics, Signaling, mRNA Splicing, Alternative Polyadenylation, Cell Fate |
Contact List
| Marian L. Waterman | |
|---|---|
| lab head | |
| Chia-Feng Tsai | |
| contact affiliation | Pacific Northwest National Laboratory |
| dataset submitter | |
Full Dataset Link List
| jPOST dataset URI |
| 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.jpostdb.org/JPST000853/ |
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