Impact of p53 knockdown on protein dataset of HaCaT cells.

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These cells maintain a stable keratinocyte phenotype, do not require specific growth factors during cultivation, and respond to keratinocyte differentiation stimuli. HaCaT cells bear two mutant p53 alleles - R282Q and H179Y. At least two mechanisms of GOF (gain-of-function) of mutant p53 are known: it affects functions of p63/p73 by inhibiting their binding to DNA; or it binds to new DNA sites by interacting with other transcription factors (NF-Y, E2F1, NF-KB, VDR, p63). Proteins of the P53 family play an important role in the regulation of proliferation and differentiation processes of human keratinocytes. Proteomic study of HaCaT cells with TP53 gene knockdown provides new data for understanding the limitations of HaCaT cells when using them as an experimental model of normal human keratinocytes. In this article we present datasets obtained through the high-throughput shotgun proteomics analysis of human immortalized HaCaT keratinocytes and p53 knockdown HaCaT keratinocytes. As a protocol for proteomic profiling of cells, we used the approach of obtaining LC-MS/MS measurements followed by their processing with MaxQuant software (version 1.6.3.4). The \"RAW\" files were deposited to the ProteomeXchange with identifier PXD033538.", "claims": [{"id": "claim-method", "statement": "Difference between the groups was tested using Student's t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35647242", "locator": "sections[8] \"ELISA\" paragraph 2", "quote": "Difference between the groups was tested using Student's t-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Protein dataset of immortalized HaCaT cells p53 knock down HaCaT keratinocytes (Original data) (ProteomeXchange).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35647242", "locator": "sections[20] \"Data Availability\" paragraph 2", "quote": "Protein dataset of immortalized HaCaT cells p53 knock down HaCaT keratinocytes (Original data) (ProteomeXchange)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Comparison of wild-type and p53 knockdown HaCaT protein profiles resulted in the identification of 2875 proteins, out of which 320 were significantly changed, including 222 and 98 proteins that were up- and downregulated in p53 knockdown HaCaT, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35647242", "locator": "sections[3] \"Data Description\" paragraph 8", "quote": "Comparison of wild-type and p53 knockdown HaCaT protein profiles resulted in the identification of 2875 proteins, out of which 320 were significantly changed, including 222 and 98 proteins that were up- and downregulated in p53 knockdown HaCaT, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Comparison of wild-type and p53 knockdown HaCaT protein profiles resulted in the identification of 2875 proteins, out of which 320 were significantly changed, including 222 and 98 proteins that were up- and downregulated in p53 knockdown HaCaT, respectively.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:35647242"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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