Pseudobulk Data

Sound Life Pseudobulk scRNA-seq Data

After QC, labeling, and filtering of the Sound Life scRNA-seq dataset, we assembled Pseudobulk data for each combination of L3 (high resolution) cell type and sample. We aggregated the data for each gene using 3 functions, and the results are included as layers in our AnnData (.h5ad) file, below:

sum: The sum of UMI counts for the feature across all cells in the group.
mean: The mean of normalized values across cells in the group. Normalization was performed using the NormalizeData() function in the Seurat single cell analysis package.
detect: The count of the number of cells in which the gene was detected, which can be converted to fraction of cells using the n_cells column in the cell metadata table (adata.obs).

the .h5ad file containing our pseudobulk data contains sample and subject metadata, in addition to cell type labels and QC metrics. Click the header below for descriptions of these 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
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.ageAtFirstDraw: The Age of the Subject at their first on-study sample collection
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

Sample Metadata
sample.visitName: The name of the study visit (i.e. time point)
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 unique identifier for the pooled pseudobulk cells.

*used as the primary cell index in our .h5ad files

Population Metrics
n_cells: Number of cells in the pooled pseudobulk population

Cell Labeling Results
AIFI_L1: Final broad class cell type label (9 types)
AIFI_L2: Final mid resolution cell type label (29 types)
AIFI_L3: Final high resolution cell type label (71 types)

Sound Life Pseudobulk scRNA-seq .h5ad

File Name	Description	Download Link
sound-life_AIFI_L3_pseudobulk.h5ad	Sound Life Pseudobulk data

Immunobiology of Aging Pseudobulk Data

The Immunobiology of Aging scRNA-seq dataset was assembled as Pseudobulk data for each combination of L3 (high resolution) cell type and sample. We aggregated the data for each gene using 3 functions, and the results are included as layers in our AnnData (.h5ad) file, below:

sum: The sum of UMI counts for the feature across all cells in the group.
mean: The mean of normalized values across cells in the group. Normalization was performed using the NormalizeData() function in the Seurat single cell analysis package.
detect: The count of the number of cells in which the gene was detected, which can be converted to fraction of cells using the n_cells column in the cell metadata table (adata.obs).