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    • scRNA-seq Data

    PBMC scRNA-seq

    scRNA-seq data from peripheral blood mononuclear cells (PBMCs) was generated on the 10x Genomics Flex scRNA-seq Platform (v1). For data collection and processing details, see the Experimental Methods sections.

    Below, we provide labeled and annotated PBMC scRNA-seq data from the HIRISA dataset.

    All .h5ad files for this project contain sample and subject metadata, in addition to cell type labels and QC metrics. Click the header below for descriptions of these metadata:

    Each file contains sample-level metadata, as well as cell-level cell type labels and QC metrics. The following values are stored in the .obs section of these .h5ad files as descriptions of observations:

    Sample Identifiers
    subject.subjectGuid: A Globally Unique Identifier (GUID) for the Subject
    sample.sampleKitGuid: A GUID for the Sample Kit, representing all material collected at a visit
    specimen.specimenGuid: A GUID for the specific aliquot used for the experiment

    Subject Metadata
    subject.biologicalSex: The biological sex of the Subject
    subject.birthYear: The Birth Year of the Subject
    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 (Negative or Positive)

    Sample Metadata
    sample.drawYear: The year of the study visit (e.g. 2021)
    sample.subjectAgeAtDraw: The age of the Subject in years at the time of sample collection

    Process Identifiers
    batch_id: A GUID for the batch of samples processed together (e.g. B039)
    pool_id: A GUID for the pool of samples combined for Cell Hashing (e.g. B039-P1)
    *barcodes: A GUID for the individual cell
    *used as the primary cell index in our .h5ad files

    Cell QC Metrics
    n_reads: Number of reads assigned to the cell barcode
    n_umis: Number of Unique Molecular Identifiers (unique molecules) detected
    n_genes: Number of genes with at least 1 UMI detected

    Cell Labeling Results
    AIFI_L1: Final broad class cell type label (9 types)
    L1 Label: Broad cell type labels used in figures
    L2 Label: Higher resolution cell type labels used in figures and apps

    Experimental Parameters
    Treatment: The IFN treatment used on the cells, or "none" for negative controls

    Cell Class .h5ad files

    We are providing our scRNA-seq data in AnnData (.h5ad) format. For more details about AnnData, see the AnnData Documentation Page.

    By default, normalized and log-transformed data are provided in the adata.X matrix. To recover raw values for your own normalization, use:

    adata = adata.raw.to_adata()

    Each file provided below contains a subset of the full > 1.2 million cell dataset. Sample counts, cell counts, and approximate file sizes are below:

    File NameN SubjectsN SamplesN CellsFile Size
    hirisaall-cellsifn-stim.h5ad51051,232,89968 GB
    hirisat-cellifn-stim.h5ad530360,55612 GB
    hirisab-cellifn-stim.h5ad525291,53711 GB
    hirisamonocyteifn-stim.h5ad525304,10813 GB
    hirisank-cellifn-stim.h5ad525276,6989 GB
    HIRISA scRNA-seq .h5ad Files
    File NameDescriptionDownload Link
    hirisa_all-cell_ifn-stim.h5ad HIRISA data for all classes
    hirisa_b-cell_ifn-stim.h5ad HIRISA data for B cells
    hirisa_monocyte_ifn-stim.5had HIRISA data for Monocytes
    hirisa_nk-cell_ifn-stim.h5ad HIRISA data for NK cells
    hirisa_t-cell_ifn-stim.h5ad HIRISA data for T cells