• ← Dynamics of Immune Health & Age
  • / Downloads

    • Whole Blood RNA-seq

    Researchers at the Benaroya Research Institute (BRI) conducted whole blood RNA-seq profiling of Sound Life subjects. For more details about whole blood collection and related data analyses, see this publication in Science Translational Medicine:

    Smithmyer ME, Hu A, Dufort MJ, Hocking AM, Wiedeman AE, Fasano KJ, et al. Longitudinally stable T cell function and innate immune activation distinguish healthy adult immunotypes. Sci Transl Med. 2025;17: eadt4605.
    doi:10.1126/scitranslmed.adt4605

     

    In brief, blood samples were collected at each visit directly into Tempus blood RNA tubes for later processing. Whole blood RNA-seq data are available for 836 of the 868 samples in our scRNA-seq dataset.

    Three visits per subject also included collection directly into TruCulture tubes with control or stimulation conditions (0.4 μg/mL SEB, 1 ng/mL LPS, or 20 μg/mL poly I:C). Stimulated samples were collected at the same visits as 254 samples in our scRNA-seq dataset, including samples from 47 Older Adult subjects and 45 Young Adult subjects.

    After collection, samples were processed to reverse transcribe RNA to cDNA, which was profiled using SMART-seq v4.

    Whole blood RNA-seq data are provided in AnnData format. In this structure, data from each sample, rather than each cell, are provided in the data matrix and described in observations.

    Descriptions of sample metadata provided in our files are provided below:

    Each file contains sample-level metadata. The following values are stored in the .obs section of these .h5ad files as descriptions of observations:

    Sample Identifiers
    cohort.cohortGuid: A Globally Unique Identifier (GUID) of the Cohort the subject enrolled in for our study subject.subjectGuid: A GUID for the Subject
    sample.sampleKitGuid: A GUID for the Sample Kit, representing all material collected at a visit
    barcodes: The sample identifying barcode provided in the GEO repository

    Subject Metadata
    subject.biologicalSex: The biological sex of the Subject
    subject.birthYear: The Birth Year of the Subject
    subject.ageAtFirstDraw: The Age of the Subject at their first on-study sample collection
    subject.ageGroup: The Age Group of the Subject (Young Adult or Older Adult)
    subject.race: The self-reported Race of the Subject
    subject.ethnicity: The self-reported Ethnicity of the subject
    subject.cmv: The CMV Status of the subject, as determined by an HCMV assay
    subject.bmi: The BMI of the Subject
    subject.covidVaxDose1.daysSinceFirstVisit: Timing of the first COVID-19 vaccine dose for the subject relative to the first sample draw
    subject.covidVaxDose2.daysSinceFirstVisit: Timing of the second COVID-19 vaccine dose for the subject relative to the first sample draw

    Sample Metadata
    sample.visitName: The name of the study visit (i.e. time point)
    sample.drawYear: The date of the study visit (e.g. 2021)
    sample.daysSinceFirstVisit: Timing of sample collection relative to the first sample draw
    sample.subjectAgeAtDraw: The age of the Subject in years at the time of sample collection

    GEO metadata:
    geo.accession: GEO sample accession number (e.g. GSM8573231)
    geo.title: GEO sample title (e.g. BR2038 SEB Y2 Flu Day 7-9)
    geo.timepoint: Time point name used in GEO sample metadata (e.g. Y1 Flu Day 7-9)
    geo.stimulation*: Stimulation applied to the blood sample: SEB, LPS, poly I:C, or Null (negative control)
    *Only available in the ex vivo stimulation dataset.

    Sound Life Whole Blood RNA-seq
    File Name Description Download Link
    sound-life_whole-blood_ex-vivo-stim.h5ad Whole blood RNA-seq from ex vivo stimulation of 254 samples
    sound-life_whole-blood_no-stim.h5ad Unstimulated whole blood RNA-seq from 836 samples