RNA and phosphoprotein profiles of TP53- and PTEN-knockouts in MCF10A at baseline and responding to DNA damage
Abstract A wealth of proteogenomic data has been generated using cancer samples to deepen our understanding of the mechanisms of cancer and how biological networks are altered in association with somatic mutation of tumor suppressor genes, such as TP53 and PTEN. To generate functional signatures of...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-01-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-023-02829-1 |
| _version_ | 1827388758256779264 |
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| author | ChenWei Lin Regine M. Schoenherr Uliana J. Voytovich Richard G. Ivey Jacob J. Kennedy Jeffrey R. Whiteaker Pei Wang Amanda G. Paulovich |
| author_facet | ChenWei Lin Regine M. Schoenherr Uliana J. Voytovich Richard G. Ivey Jacob J. Kennedy Jeffrey R. Whiteaker Pei Wang Amanda G. Paulovich |
| author_sort | ChenWei Lin |
| collection | DOAJ |
| description | Abstract A wealth of proteogenomic data has been generated using cancer samples to deepen our understanding of the mechanisms of cancer and how biological networks are altered in association with somatic mutation of tumor suppressor genes, such as TP53 and PTEN. To generate functional signatures of TP53 or PTEN loss, we profiled the RNA and phosphoproteomes of the MCF10A epithelial cell line, along with its congenic TP53- or PTEN-knockout derivatives, upon perturbation with the monofunctional DNA alkylating agent methyl methanesulfonate (MMS) vs. mock treatment. To enable quantitative and reproducible mass spectrometry data generation, the cell lines were SILAC-labeled (stable isotope labeling with amino acids in cell culture), and the experimental design included label swapping and biological replicates. All data are publicly available and may be used to advance our understanding of the TP53 and PTEN tumor suppressor genes and to provide functional signatures for bioinformatic analyses of proteogenomic datasets. |
| first_indexed | 2024-03-08T16:24:30Z |
| format | Article |
| id | doaj.art-a4b970c23f7e4fbc9c8e0aebd2ebfa2c |
| institution | Directory Open Access Journal |
| issn | 2052-4463 |
| language | English |
| last_indexed | 2024-03-08T16:24:30Z |
| publishDate | 2024-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj.art-a4b970c23f7e4fbc9c8e0aebd2ebfa2c2024-01-07T12:10:40ZengNature PortfolioScientific Data2052-44632024-01-0111111210.1038/s41597-023-02829-1RNA and phosphoprotein profiles of TP53- and PTEN-knockouts in MCF10A at baseline and responding to DNA damageChenWei Lin0Regine M. Schoenherr1Uliana J. Voytovich2Richard G. Ivey3Jacob J. Kennedy4Jeffrey R. Whiteaker5Pei Wang6Amanda G. Paulovich7Fred Hutchinson Cancer CenterFred Hutchinson Cancer CenterFred Hutchinson Cancer CenterFred Hutchinson Cancer CenterFred Hutchinson Cancer CenterFred Hutchinson Cancer CenterDepartment of Genetic and Genomic Sciences, Icahn School of Medicine at Mount SinaiFred Hutchinson Cancer CenterAbstract A wealth of proteogenomic data has been generated using cancer samples to deepen our understanding of the mechanisms of cancer and how biological networks are altered in association with somatic mutation of tumor suppressor genes, such as TP53 and PTEN. To generate functional signatures of TP53 or PTEN loss, we profiled the RNA and phosphoproteomes of the MCF10A epithelial cell line, along with its congenic TP53- or PTEN-knockout derivatives, upon perturbation with the monofunctional DNA alkylating agent methyl methanesulfonate (MMS) vs. mock treatment. To enable quantitative and reproducible mass spectrometry data generation, the cell lines were SILAC-labeled (stable isotope labeling with amino acids in cell culture), and the experimental design included label swapping and biological replicates. All data are publicly available and may be used to advance our understanding of the TP53 and PTEN tumor suppressor genes and to provide functional signatures for bioinformatic analyses of proteogenomic datasets.https://doi.org/10.1038/s41597-023-02829-1 |
| spellingShingle | ChenWei Lin Regine M. Schoenherr Uliana J. Voytovich Richard G. Ivey Jacob J. Kennedy Jeffrey R. Whiteaker Pei Wang Amanda G. Paulovich RNA and phosphoprotein profiles of TP53- and PTEN-knockouts in MCF10A at baseline and responding to DNA damage Scientific Data |
| title | RNA and phosphoprotein profiles of TP53- and PTEN-knockouts in MCF10A at baseline and responding to DNA damage |
| title_full | RNA and phosphoprotein profiles of TP53- and PTEN-knockouts in MCF10A at baseline and responding to DNA damage |
| title_fullStr | RNA and phosphoprotein profiles of TP53- and PTEN-knockouts in MCF10A at baseline and responding to DNA damage |
| title_full_unstemmed | RNA and phosphoprotein profiles of TP53- and PTEN-knockouts in MCF10A at baseline and responding to DNA damage |
| title_short | RNA and phosphoprotein profiles of TP53- and PTEN-knockouts in MCF10A at baseline and responding to DNA damage |
| title_sort | rna and phosphoprotein profiles of tp53 and pten knockouts in mcf10a at baseline and responding to dna damage |
| url | https://doi.org/10.1038/s41597-023-02829-1 |
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