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E-PROT-34

ABSTRACT: Allele-Specific Protein Abundance in Human Brain

PROVIDER: E-PROT-34 | ExpressionAtlas | 2022-01-06

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-PROT-34-analysis-methods.tsv	Tabular
	E-PROT-34-configuration.xml	Xml
	E-PROT-34-factors.xml	Xml
	E-PROT-34-zoomifications-log.tsv	Tabular
	E-PROT-34.condensed-sdrf.tsv	Tabular

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Allele-Specific Protein Abundance in Human Brain

Project description:We describe a method for identifying peptides that result from missense changes and identify peptides among 2 human brains that would have otherwise not been detected. Next, we use this data to estimate of allele-specific protein abundance in human brain for an average per individual, and to estimate apolipoprotein E allele specific abundance in human brain across individuals. Finally, we estimate the heritability of allele-specific protein abundance.

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Project description:Systematic survey of gene and isoform allele-specific expression in human brain and liver tissues, and description of optimised bioinformatic and statistical methods to accurately measure allele-specific expression. DNA-seq data for the same set of samples have been deposited at the European Nucleotide Archive under project accessino PRJEB5279 ( http://www.ebi.ac.uk/ena/data/view/PRJEB5279 ).

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Project description:Brain ureido degenerative protein modifications in Alzheimer's disease with cerebrovascular disease

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Human SMARCA5 interactome in transgenic SMARCA5 mouse model

Project description:We hypothesize that the ISWI ATPase Smarca5 plays a role in hematopoietic stem cell development via its interaction partners, and to study the role, we used a mouse model with transgenic expression of SMARCA5 coupled with mass spectrometry analysis. The study uses transgenic SMARCA5 mouse model with conditional hypomorphic allele (lower expression on protein level compared to controls) incorporated into Rosa26 locus, transgenic allele uses endogenous Rosa26 promoter. The transgenic human SMARCA5 protein has a FLAG tag at its C-terminus, which allows specific immunoprecipitation and also differentiation from the endogenous protein (human and mouse SMARCA5 are almost identical at the protein level). To ensure the highest possible expression of the transgenic allele, we used a model that also had one endogenous Smarca5 allele deleted. Various organs (thymus, spleen, brain, kidney, liver, testes, muscle, fetal liver) were isolated from transgenic mice, lysed and then immunoprecipitated using anti-FLAG antibody. The immunoprecipitates were then analyzed using mass spectrometry to determine SMARCA5 interactomes in various tissues. Transgenic human SMARCA5 was confirmed to form all the expected complexes and capable of replacing the functions of the mouse protein. For details, see the publication of Turkova et al. 2024 in Communications Biology.

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