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Series GSE171572 Query DataSets for GSE171572
Status Public on Nov 20, 2023
Title RNA and phosphoprotein profiles of TP53- and PTEN-knockouts in MCF10A at baseline and responding to DNA damage
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Overall design Cells from 3 MCF10A cell lines (WT, p53-KO, PTEN-KO) were treated with 0.5 mM methyl methanesulfonate and harvested after 3 hours of treatment. The experiment was repeated on three days. RNAs were extracted for RNAseq. More details about cell treatments and RNA extraction and sequencing are provided on the sample pages.
Contributor(s) Lin C, Schoenherr RM, Voytovich UJ, Ivey RG, Kennedy JJ, Whiteaker JR, Wang P, Paulovich AG
Citation(s) 38177134
Submission date Apr 06, 2021
Last update date Feb 21, 2024
Contact name Amanda Paulovich
Organization name Fred Hutchinson Cancer Research Center
Street address 1100 Fairview Ave. N.
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (18)
GSM5227563 MCF10A_p53-KO_mock_r1
GSM5227564 MCF10A_p53-KO_MMC_r1
GSM5227565 MCF10A_PTEN-KO_mock_r1
BioProject PRJNA720113
SRA SRP313680

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Supplementary file Size Download File type/resource
GSE171572_MCF10A_exons.cpm.gct.gz 1.6 Mb (ftp)(http) GCT
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Raw data are available in SRA
Processed data are available on Series record

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