The 18.4 Data Release includes human and model studies. A new annotation key “chromosome” was added to the Portal annotation schema. This key will allow users to query for files associated with a particular chromosome, e.g. VCFs or imputed genotype dosages.

Human

  • The MindPhenomeKB Study 

    This study provides analysis files associated with the construction of two large-scale knowledge bases, the MindDiseasePhenome and the MindDrugPhenome, using natural language processing, information extraction, and data integration of 30 million biomedical articles, with a focus on Alzheimer’s disease. 

  • The ADMC_ADNI_NightingaleNMR Study

    This study provides metabolomics data generated on the Nightingale Health NMR Platform from serum from the Alzheimer’s Disease Neuroimaging Initiative – 1, GO, and 2 cohorts. Quantified metabolites include lipoproteins, fatty acids, glycerides, phospholipids, amino acids, ketones, and cholesterol.

  • The ADMC_ADNI_BakerLipidomics Study
    This study provides metabolomics data generated using the Baker Institute targeted lipidomics platform from serum samples from the ADNI 1, GO, and 2 cohorts.. The data was generated from samples collected at the baseline visit. Quantified metabolites include sphingolipids, phosphatidylcholine, lysophosphatidylcholine, phosphatidylethanolamine, cholesterol, bile acids, fatty acids, acylcarnitines, and acylglycerols.

  • The eQTLmetaAnalysis Study
    This is a brain cis-eQtL meta-analysis study ustilizing data from the AMP-AD program and the CommonMind Consortium. The analysis is described in the Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions paper and was previously released under the RNAseq Harmonization Study.

  • The DiseasePseudotime Study
    This study provides pseudotime source data as described in Molecular estimation of neurodegeneration pseudotime in older brains 

    • This release provides an update of the ‘rosmap_pseudotimes_states_F.csv’ file. This file contains unadjusted Pseudotimes and States for the ROSMAP DLPFC female samples. The States in the first version of the file did not match the figures and downstream analyses described in the manuscript due to a coding error (a small section of code which updates the States was not run before the download into Synapse). This update fixes the error, so that the States match the figures and downstream analyses described in the manuscript.

Models

  • The Jax.IU.Pitt.Proteomics_Metabolomics_Pilot Study
    This study provides label-free proteomics data and metabolomics data from APOE4.Trem2*R47H and 5XFAD mouse models of late-onset Alzheimer’s disease. This release provides:

    • Label-free proteomics data from brain homogenate, including raw files and MaxQuant search output files
    • Metabolomics data generated on the Biocrates P180 platform on brain homogenate and serum from the same mice as the proteomics data

  • The 5XFAD Study
    This study provides deep phenotyping data from the 5XFAD mouse model

    • This release provides an update of the following files:
      • The individual metadata file: This update provides the age of death, in addition to the previous date of birth and date of death. It also provides an additional variable called ‘modelCommonName’, which comprise the variant and the LOAD platform strain (i.e. LOAD1 or LOAD2). LOAD1= APOE4_HOMOZYGOUS; TREM2R47H_HOMOZYGOUS. LOAD2=APOE4_HOMOZYGOUS; TREM2R47H_HOMOZYGOUS; HTAU_HOMOZYGOUS
      • An update of the Immunofluorescence file using the anti-LAMP1 primary antibody. Data from 2 groups of mice had been switched:  individualIDs 572 with 570 (vice versa) 277 with 279 (vice versa)

  • The UCI_3xTg-AD Study
    This study provides RNAseq data from the hippocampus of mice at age 4, 12, or 18 months.

    • This update provides an update of the individual metadata file by including the age of death, in addition to the previous date of birth and date of death. It also provides an additional variable called ‘modelCommonName’, which comprise the variant and the LOAD platform strain (i.e. LOAD1 or LOAD2). LOAD1= APOE4_HOMOZYGOUS; TREM2R47H_HOMOZYGOUS. LOAD2=APOE4_HOMOZYGOUS; TREM2R47H_HOMOZYGOUS; HTAU_HOMOZYGOUS

  • The UCI_hAbeta_KI) Study
    This study provides RNAseq data from the hippocampus of mice at age 2 and 22 months.

      • This update provides an update of the individual metadata file by including the age of death, in addition to the previous date of birth and date of death. It also provides an additional variable called ‘modelCommonName’, which comprise the variant and the LOAD platform strain (i.e. LOAD1 or LOAD2). LOAD1= APOE4_HOMOZYGOUS; TREM2R47H_HOMOZYGOUS. LOAD2=APOE4_HOMOZYGOUS; TREM2R47H_HOMOZYGOUS; HTAU_HOMOZYGOUS