Near term bovine placenta proteome
Description
Data was generated to analyze the proteome of near-term bovine cotyledons (10.17632/bc4y39gy8w.1) in comparison with term cloned delivery pregnancies (10.17632/bc8yr2xkp7.1). Also, the near term bovine cotyledons proteome was compared with decellularized counterpart (10.17632/4yjygxyy6x.1).
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Cotyledons from three near-term bovine placenta (control group) obtained from local abattoir, and three term placentas derived by cloning by somatic cell nuclear transfer (clone group) (10.1371/journal.pone.0101022) were used in this experiment. Some cotyledons from control group were decellularized (decel group) according Barreto et al. (10.1002/term.2618). All experimental procedures were under rules of Ethics Committee number 9050171115 from this University of Sao Paulo. The biological replicates from control, clone and decell groups were homogenized, precipitated, reduced, alkylated, digested and purificated as established by HEDRICK et al. (doi.org/10.1038/nrm3902). After, 3 µg of total protein diluted in 15 µL of ABC was loaded into the reading tubes and then read on the mass spectrometer Orbitrap Fusion Lumos (Thermo Scientific). The generated data were deposited in Mendeley Data Database in different datasets for control (10.17632/bc4y39gy8w.1), clone (10.17632/bc8yr2xkp7.1) and decell (10.17632/4yjygxyy6x.1) groups. Data were exported to MaxQuant software (version v1.6.10.43) and combined to bovine protein database (Uniprot). MaxQuant LFQ intensity were exported to Inferno software (version 1.1.6970) based on R software (version 3.6.2). Data quality was analyzed by means of correction graphs and principal component analysis (PCA), and statistical analysis was performed using fold change values (threshold of ±0.5). Only proteins primarily related to extracellular matrix or cell junction ontologies were filtered. PCA were performed using the R-statistics built in functions of princomp (https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/princomp) and FactoMineR package for graphical visualization. The Proteome fold change quantification data of bovine placenta were grouped by two (Control x Decel, Control x Clone and Decel x Clone) and were used for Enrichment analysis and functional classification for Gene ontology terms. There was used the "enrichGO" function from R package clusterProfiler to identify differentially regulated terms into Cellular components, Biology processes and molecular functions. The GeneSymbol identifiers were converted to Entrez identifiers with bitR and then used "enrichKEGG" function from R package clusterProfiler to compute enrichment of proteins in KEGG pathways using an FDR cutoff of 0.05. The significant pathway results and respective proteins were used to create the Pathway diagrams with the Pathviews package. STRING v11.0 was used to explore the biological interactions of proteins identified as differentially abundant on those three groups of bovine placenta with Bos taurus reference databases, using all active interaction sources with evidence and medium interaction confidence of 0.4. NetworkAnalyst with the protein-protein interaction (PPI) database based on Uterus Tissue Specific data collected from DifferentialNet for PPI interactions across human tissues using filter=15.