This readme file was generated on 2022-08-15 by Yu Hasegawa GENERAL INFORMATION Title of Dataset: Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models (NMR datasets, maternal plasma and infant brain) Author/Principal Investigator Information Name: Carolyn M. Slupsky ORCID: 0000-0002-5100-1594 Institution: Department of Food Science and Technology; Department of Nutrition, University of California-Davis Address: 2251 Meyer Hall, University of California Davis, One Shields Avenue, Davis, CA 95616 Email: cslupsky@ucdavis.edu Author Name: Yu Hasegawa ORCID: 0000-0002-2666-162X Institution: University of Wisconsin-Madison Address: A115 Babcock Hall 1605 Linden Dr. Madison, WI 53706 Email: yhasegawa2@wisc.edu Date of data collection: 2016-2019 Geographic location of data collection: Davis, CA, USA Information about funding sources that supported the collection of the data: This research was supported by National Institutes of Health award [grant number 1R01HD084203] to CW and CV. CMS acknowledges support from Kinsella Endowed Chair in Food, Nutrition and Health. This project was also made possible in part by support from the USDA National Institute of Food and Agriculture Hatch Project [1021411 to CMS. The CNPRC is funded through an NIH Base Grant [P51 OD011107], and the 600 MHz NMR is supported through NIH grant [1S10RR011973-01]. Citations of published research derived from these data: * Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models * Impact of Maternal Obesity on the Gestational Metabolome and Infant Metabolome, Brain, and Behavioral Development in Rhesus Macaques DATA & FILE OVERVIEW File List: 1. Metadata_ MaternalPlasma.csv (metadata for data in a folder named ÒMaternal.plasmaÓ) 2. Metadata_InfantBrain.csv (metadata for data in a folder named ÒInfant.brainÓ) Folder List: 3. Maternal.plasma (Folder that contains raw NMR acquisition files for maternal plasma samples) 4. Infant.brain (Folder that contains raw NMR acquisition files for infant brain samples) METHODOLOGICAL INFORMATION To generate the data files, proton NMR spectra were acquired on each sample at 25 C using the noesypr1d pulse sequence on a Bruker Avance 600 MHz NMR spectrometer (Bruker, Billerica, MA, USA). The unprocessed raw data is stored in a folder named ÒMaternal.plasmaÓ and ÒInfant.brainÓ. Chenomx NMRSuite (version 8.1, Chenomx Inc) was used to annotate the metabolites based on Reference Library 10. To process the raw data, 1) Download ÒMaternal.plasmaÓ and/or ÒInfant.brainÓ folders from Dryad 2) Open Chenomx (or any equivalent software of your choice) 3) Import folders you downloaded in step 1. This will automatically process the files in the subfolders (e.g., ex0010) to extract spectrum. After profiling the spectrum in each sample, export the data. For maternal plasma samples, the quantified raw metabolite concentrations were multiplied by Dilution_factor found in ÒMetadata_ MaternalPlasma.csvÓ file. For infant brain samples, raw concentration was multiplied by Dilution_factor (*) for each sample, adjusted by the volumes of buffer used in extraction (V1*V3/V2) (*), and normalized by Tissue_weight (*). Parameters indicated with (*) are summarized in ÒMetadata_InfantBrain.csvÓ file. The raw concentrations are summarized in Supplementary Data 1.xlsx of the publication: ÒMulti-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity modelsÓ by authors: Benjamin I. Laufer, Yu Hasegawa, Zhichao Zhang, Casey E. Hogrefe, Laura A. Del Rosso, Lori Haapanan, Hyeyeon Hwang, Melissa D. Bauman, Judy A. Van de Water, Ameer Y. Taha, Carolyn M. Slupsky, Mari S. Golub, John P. Capitanio, Catherine A. VandeVoort, Cheryl K. Walker, Janine M. LaSalle. People involved with sample collection, processing, analysis and/or submission: Yu Hasegawa DATA-SPECIFIC INFORMATION FOR: Metadata_ MaternalPlasma.csv Number of variables: 6 Number of rows: 95 Variable List: * FolderID: Experiment ID * MotherID: IDs assigned for individual mothers. * Batch: The experiment was done over two batches, YEAR 1 or YEAR 2. * Group: Each animal was assigned to either Control (lean control), Obese (obese control), Restriction (obese animals with gestational calorie restriction), or Pravastatin (obese animals with gestational pravastatin administration) based on Body Condition Score (BCS). * Timepoint: The samples were collected at either Trimester 1, Trimester 2, Early Trimester 3, or Late Trimester 3. * Dilution_factor: Dilution made for NMR analysis. Used to correct the concentration (see above). Missing data codes: NA. Specialized formats or other abbreviations used: NA. DATA-SPECIFIC INFORMATION FOR: Metadata_InfantBrain.csv Number of variables: 10 Number of rows: 74 Variable List: * FolderID: Experiment ID * InfantID: IDs assigned for individual mothers. * Group: Group assignment of their mothers. * Brain_weight: Weight of brain samples. * V1: Volume of solvent used to extract (uL). Used to correct the metabolite concentration. * V2: Volume of polar layer (methanol + water) collected (uL). Used to correct the metabolite concentration. * V3: Buffer added to reconstitute the sample after freeze drying (uL). Used to correct the metabolite concentration. * Dilution_factor: Dilution made for NMR analysis. * MotherID: IDs assigned for individual mothers. Missing data codes: NA. Specialized formats or other abbreviations used: NA. DATA-SPECIFIC INFORMATION FOR: Maternal.plasma A folder that contains raw NMR data. File names (e.g., ex0011, ex0020,É) correspond to the FolderID in ÒMetadata_ MaternalPlasma.csvÓ. DATA-SPECIFIC INFORMATION FOR: Infant.brain A folder that contains raw NMR data. File names (e.g., ex0010, ex0020,É) correspond to the FolderID in ÒMetadata_Infant.Brain.csvÓ.