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Deciphering H3K4me3 Broad Domains Associated With Gene Regulatory Networks and Conserved Epigenomic Landscapes in the Human Brain

ABSTRACT: ChIP-seq and RNA-seq datasets newly generated for this manuscript are included in the SubSeries listed below. For previously published datasets, see accession no. GSE21172 and additional links provided in references 16, 18, 20. For references 16, 18: https://zlab.umassmed.edu/zlab/publications/ShulhaPLOSGen2013.html https://zlab.umassmed.edu/zlab/publications/ShulhaAGP2011.html For reference 20, sequences are accessible through: http://www.umassmed.edu/zlab/publications/

ORGANISM(S): Homo sapiens

PROVIDER: GSE71238 | GEO | 2016/07/21

SECONDARY ACCESSION(S): PRJNA295363

REPOSITORIES: GEO

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Project description:INTRODUCTION: Differences in the metabolite profiles between serum and plasma are incompletely understood. OBJECTIVES: To evaluate metabolic profile differences between serum and plasma and among plasma sample subtypes. METHODS: We analyzed serum, platelet rich plasma (PRP), platelet poor plasma (PPP), and platelet free plasma (PFP), collected from 8 non-fasting apparently healthy women, using untargeted standard 1D and CPMG 1H NMR and reverse phase and hydrophilic (HILIC) UPLC-MS. Differences between metabolic profiles were evaluated using validated principal component and orthogonal partial least squares discriminant analysis. RESULTS: Explorative analysis showed the main source of variation among samples was due to inter-individual differences with no grouping by sample type. After correcting for inter-individual differences, lipoproteins, lipids in VLDL/LDL, lactate, glutamine, and glucose were found to discriminate serum from plasma in NMR analyses. In UPLC-MS analyses, lysophosphatidylethanolamine (lysoPE)(18:0) and lysophosphatidic acid(20:0) were higher in serum, and phosphatidylcholines (PC)(16:1/18:2, 20:3/18:0, O-20:0/22:4), lysoPC(16:0), PE(O-18:2/20:4), sphingomyelin(18:0/22:0), and linoleic acid were lower. In plasma subtype analyses, isoleucine, leucine, valine, phenylalanine, glutamate, and pyruvate were higher among PRP samples compared with PPP and PFP by NMR while lipids in VLDL/LDL, citrate, and glutamine were lower. By UPLC-MS, PE(18:0/18:2) and PC(P-16:0/20:4) were higher in PRP compared with PFP samples. CONCLUSIONS: Correction for inter-individual variation was required to detect metabolite differences between serum and plasma. Our results suggest the potential importance of inter-individual effects and sample type on the results from serum and plasma metabolic phenotyping studies. NMR protocols and data are reported in the current study MTBLS470. UPLC-MS protocols and data associated to this study are reported in MTBLS465. Linked Studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS465' target='_blank'>MTBLS465</a>

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Deciphering H3K4me3 Broad Domains Associated With Gene Regulatory Networks and Conserved Epigenomic Landscapes in the Human Brain

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