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Experimental Studies

  • Data Overview
  • Data Query Tool User Guide
  • Gene Search Tool User Guide
  • Publication Search Tool User Guide
  • Cohort Browser User Guide
Experimental Studies Resource Description

Requestors who receive tissues or biospecimens from the NNTC or CHARTER enter an agreement to submit data generated from the samples they receive to the NNTC-DCC. The data submitted by requestors is documented and curated by the NNTC DCC. This process includes the development of data dictionary and methods documents, as well as harmonizing participant IDs across research and clinical studies. One benefit of this process is that the ID variables used to identify unique participants are harmonized across the CHARTER Research Study data, the NNTC Experimental data resource and the NNTC Clinical data resource. As of 2016, the NNTC-DCC began requesting CHARTER requestors submit data generated from the samples they have received. These efforts are aimed at making harmonized data generated from participants in the NNTC and CHARTER studies available for request shaping and post hoc analysis.


Experimental Data Query Tool

The NNTC-CHARTER Experimental Data Query Tool is a web-based utility that allows researchers to quickly search experimental data generated from NNTC biospecimens, including tissues, and CHARTER biospecimens. The data for the Query Tool are collected from CHARTER and NNTC requestors, who are asked to share their published (and in some cases, unpublished) raw data with the NNTC-DCC at the conclusion of their work with the samples. This effort is aimed at providing high quality data for post-hoc analysis, to allow researchers to select cases based on experimental values, and to prevent redundancy in testing.

The Query Tool allows researchers to query data types against NNTC/CHARTER participants. The results from the Query Tool indicate the data types available for each NNTC/CHARTER participant. The measured data values for each participant are not presented in the Query Tool. Requestors who would like to access the measured lab values are asked to send the results of their query to the NNTC-DCC and the data will be transferred to them.

The presence of records returned by the Experimental Data Query tool indicates whether an NNTC and/or CHARTER participant’s biospecimens were utilized in a particular research study. Generally speaking, this indicates data will be available for that participant and variable. However, in some cases, data may be missing for particular variables and/or participants within a study because data could not be generated for that biospecimen (e.g. insufficient signal was detected or insufficient sample was collected for analysis). These study specific missing data mechanisms are summarized formally in the experimental data sent to requestors.

Data present in the database can be filtered using the Query Tool along multiple variables to help researchers identify studies of interest. The Query Tool variables are summarized below:

  • Measurement: Datasets are broadly categorized into the following 8 dataset types:
    • Endo-exo chemicals:
    Datasets related to chemical concentrations in biospecimens. Exemplar data types include analyses of drug levels, steroid levels, and endotoxin levels.
    Gene expression:
    Data related to analysis of mRNA and miRNA levels in biospecimens.
    Genotype:
    Data related to participant genome sequence and attributes. Exemplar datasets include SNP analyses, mutation analyses and DNA methylation profiling.
    Morphometrics:
    (Semi)-quantitative analyses of tissue characteristics. Exemplar datasets include characterization of arterial and renal tissue specimens.
    Protein:
    Datasets related to measured protein concentrations and enzyme activity in biospecimens.
    Virology:
    Data related to viral infection. Exemplar data types include HIV DNA and RNA levels, HCV RNA levels, and levels of macrophage infectivity.
    Microbiome
    characterization:
    Data related to the functional composition of the bacteria, fungi, archaea and viruses present in tissues. Exemplar data types include levels of 16s as a marker gene to indicate the makeup of the microbiota across tissues.
    Other data:
    Data submitted to NNTC that does not fit any of the above categories. Exemplar data types include experimental group assignments, and centrally collected research data.
  • Method: This variable refines from the broad measurement classification to a broad assay type and target type. For example, within the “genotype” Measurement class, there are 8 studies related to analysis of single nucleotide polymorphisms (SNPs), 2 that utilized mutational analysis, and 1 that analyzed variable number tandem repeats. Within the Query Tool, only the methods related to the selected Measurement classes listed above will be available for selection.
  • Target: Filters available study data by the targeted molecule. Target molecules are standardized across genotype/protein data, where proteins are defined by their gene name. Within the Query Tool, only the Target classes related to the selected Measurement, Method and Tissue classes will appear in the selection box.
  • Tissue: Filters available study data by the type of biospecimen or tissue studied. Note that only the Tissue classes related to the selected Measurement and Method classes will appear in the Query Tool. Tissues are classified by the following ontology and the value assigned to each study is the most specific tissue type that can be identified from the supplied study data and publication details. The data in the “tissue” field are structured from broadest category to most narrow tissue category identified For example, a value of “CNS – brain – basal ganglia – striatum” indicates that the tissue provided can be identified most specifically as from the striatum, while “CNS – brain – basal ganglia – striatum – caudate” identifies a specific structure within the striatum. Tissue classifications are assigned according to the ontology below:

      •  Tissue:

      1. Central nervous system (CNS)
        1. Brain
          1. Deep white matter, not otherwise specified
          2. Cortex
            1. Neocortex, not otherwise specified
          3. Frontal lobe
            1. Frontal white matter and gray matter
            2. Frontal cortex
              1. Brodmann area 4
              2. Brodmann area 6
              3. Brodmann area 8
              4. Brodmann area 9 or 10
              5. Brodmann area 46
              6. Middle-frontal cortex
              7. Middle-frontal gyrus
              8. Dorsolateral prefrontal cortex
                1. Neuropil
            3. Frontal gray matter
            4. Frontal white matter
              1. White matter underlying Brodmann area 8
          4. Temporal lobe
            1. Inferior temporal lobe
            2. Hippocampus
              1. Internal capsule
              2. Neuropil
            3. Temporal cortex
          5. Occipital lobe
            1. Occipital cortex
          6. Basal ganglia (excluding substantia nigra, see midbrain)
            1. Striatum
              1. Caudate
              2. Putamen
                1. Neuropil
              3. Nucleus accumbens
            2. Globus pallidus
          7. Cerebellum
          8. Brain stem
            1. Midbrain
              1. Substantia nigra
            2. Medulla oblongata
          9. Other components and cell types
            1. Brain large arteries
            2. Oligodendrocytes
            3. Astrocytes
            4. Microglia/macrophages
            5. Brain microvascular endothelium
            6. Choroid plexus epithelium
        2. Spinal cord
          1. Dorsal horns of lumbar spinal cord
        3. Meninges
      2. Peripheral nervous system (PNS)
        1. Sural nerve
        2. Dorsal root ganglia
      3. Lymphoid system
        1. Spleen
        2. Lymph node
      4. Digestive system
        1. Esophagus
        2. Small intestine
        3. Colon
        4. Liver
      5. Kidney
      6. Lung
      7. Diaphragm
      8. Adrenal gland

       Biofluids and components:

      1. Blood
        1. Plasma
        2. Serum
        3. Peripheral blood mononuclear cells
      2. Cerebrospinal fluid
        1. Postmortem cerebrospinal fluid
      3. Urine

    Please keep the following in mind when using the Query Tool:

  • The fields above can be used to filter the Query Tool data to include only the data types of interest. As the Measurement, Method, Tissue and Target classes are selected using the drop down menus, the other menus will update dynamically to include only the relevant classes. For example, when “Genotype” is selected as the Measurement class, the Methods drop down menu will only include Method classes used in Genotype studies.
  • If multiple values are selected from a drop down menu for your query, the other drop down menus will include the relevant classes for all values selected.
  • By default, all the drop down fields are set to “None.” If the data is not filtered by any of the drop down fields, Query Tool results will summarize all of the data types available for all participants in the Experimental database.
  • Click “Submit” to generate query results and “Reset” to remove all previous criteria selections.
  • A grid summary of your query results will appear after the query is submitted.
  • Click “Download Data” to download a csv formatted file of your query results to your computer. If you would like to request the raw experimental data from the NNTC-DCC, please submit your query results and the data will be transferred to you.
    • Gene Search Tool User Guide

    The gene search tool integrates with the Expression Omnibus (GEO) to search for GEO datasets that including NNTC participants for expression of selected genes of interest. NNTC Experimental data for these studies can be accessed for specific studies using the Publication Search tool and browsed for using the Experimental Data Query tool. The data files are generally structured to match the GSM profile ID in GEO with the central NNTC participant ID. This participant ID is harmonized across all NNTC Experimental Studies, the NNTC Data Query tool, and the CHARTER Data Query tool.

    To use the Gene Search tool, select genes of interest using the “Gene Name” box. Gene names are standardized using Gene Nomenclature Committee conventions. The results of your search will be a popup window return of a GEO search across all of the NNTC-DCC experimental datasets currently on GEO that include the selected genes of interest.

    Publication Search Tool User Guide

    The Publication Search tool allows users to browse the study specific data collected in the NNTC-DCC central database and download study specific resources for studies of interest. The publication study search tool can be used to browse experimental studies in the database using keywords from the title, the PubMed ID assigned by NCBI, and author name.

    To use the Publication Search tool, enter the PubMed ID, title keyword, or author’s last name into the corresponding search box. The return will include all studies matching the search criteria. If data is available, the “download” link will return a .rar archive including the study data, a study specific data dictionary, and a description of the study methods supplied with the data submission.


    Cohort Browser User Guide

    The cohort browser allows users to browse all the experimental data available for selected NNTC/CHARTER participants using a unified participant ID. The search results will detail all of the experimental data available for the submitted list of participant IDs.

    Please format your query as a list of NNTC IDs of interest. Please delimit your list with commas (e.g. 03601, 02230, 03165, 03738, 04905, 03343, 03304, 03388, 04349, 04945). Leading “0” values are not required for the cohort browser tool (i.e. the query above may also be formatted as 3601, 2230, 3165, 3738, 4905, 3343, 3304, 3388, 4349, 4945)


    For support and general inquires please contact:

    • Address:National NeuroAIDS Tissue Consortium
      S 42nd St & Emile St. Omaha, NE 68198
    • Phone:(402) 559-7174
    • Email:nntc-dcc@unmc.edu

    Sponsored by a U24 grant mechanism from the NIMH/NIH U24MH100925