MassIVE MSV000096277

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Alternative Polyadenylation is Essential for Tissue Homeostasis by Safeguarding Nuclear Pore Integrity

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Description

Dataset1: In vitro cultured stem cells of the esophageal epithelium (basal cells). This experiment aimed to characterize changes in global protein expression during differentiation of esophageal basal cells that express different levels of Nudt21. For this, conditional Nudt21 KO or hypomorphic Nudt21 esophageal basal cells were treated for four days with ETOH (control), 4OHT (Nudt21 KO) or 4OHT+Dox (hypomorph) under self-renewing conditions. On the fourth day calcium was added to induce differentiation. Cells were collected 6 days post calcium exposure and subjected to proteomic analysis (n=3 biol. replicates per condition). Proteome mapping was performed using multiplexed quantitative proteomics with TMTpro reagents (PMID: 33900084) on a Orbitrap Lumos mass spectrometer using an SPS-MS3 method. Prior to mass spectrometry analysis the TMTset was fractionated off-line by basic pH reversed-phase chromatography (bRPLC) into 16 fractions. Samples were labeled as follows: 131N - Control_1_Diff 131C - Control_2_Diff 132N - Control_3_Diff 132C - KO_1_Diff 133N - KO_2_Diff 133C - KO_3_Diff 134N - Hypomorph_1_Diff 134C - Hypomorph_2_Diff 135N - Hypomorph_3_Diff Dataset 2: In vitro cultured stem cells of the esophageal epithelium (basal cells). This experiment aimed to characterize changes in global protein expression during self-renewal of esophageal basal cells that express different levels of Nudt21.For this, conditional Nudt21 KO or hypomorphic Nudt21 esophageal basal cells were treated for a total of six days with ETOH (control), 4OHT (Nudt21 KO) or 4OHT+Dox (hypomorph) under self-renewing conditions. Cells were collected at day0 (control) day2 (KO), day 4 (KO and hypomorph) and day6 (KO and hypomorph). and subjected to proteomic analysis (n=3 biol. replicates per condition and timepoints). The analysis was performed as described for dataset 1 - 14 bRPLC were analyzed. Samples were labeled as follows: 126 - Control_d0_1 127N - Control_d0_2 127C - Control_d0_3 128N - KO_d2_1 128C - KO_d2_2 129N - KO_d2_3 129C - KO_d4_1 130N - KO_d4_2 130C - KO_d4_3 131N - KO_d6_1 131C - KO_d6_2 132N - KO_d6_3 132C - Hypo_d4_1 133N - Hypo_d4_2 133C - Hypo_d4_3 134N - Hypo_d6_1 134C - Hypo_d6_2 135N - Hypo_d6_3 [doi:10.25345/C51G0J63D] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: TMTpro ; Orbitrap ; Lumos ; SPS-MS3 ; Nudt21 ; Stem Cells ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Konrad Hochedlinger, Massachusetts General Hospital and Harvard Medical School, United States
Wilhelm Haas, Massachusetts General Hospital and Harvard Medical School, United States
Submitting User: ericzaniewski
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Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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