TEA-seq Data

TEA-seq is a trimodal single-cell assay used to simultaneously measure transcripts, surface epitopes, and chromatin accessibility, as described in (Swanson, et al., 2021).

Below, we provide labeled and annotated PBMC TEA-seq data from healthy and at-risk subjects from the ALTRA cohort.

TEA-seq data is provided using the MuData (.h5mu) format. This format allows storage of multiple layers of information for each cell, called 'modalities', which can originate from multimodal data or from secondary analyses. See the MuData documentation for additional information about access to and use of these results. This dataset contains five modalities:

rna: The transcriptomic measures (scRNA-seq) from the TEA-seq assay
prot: The surface antigent (antigen-derived tags, or ADTs) from the TEA-seq assay
atac: The chromatin accessibility (ATAC-seq) from the TEA-seq assay
genescores: GeneScores computed from ATAC-seq data using the ArchR package
tf: ChromVar scores from ATAC-seq data generated using the ArchR package

The MuData filecontains sample and subject metadata, in addition to cell type labels and QC metrics. In addition to global metrics that apply to all assays, the rna and atac assays have additional assay-specific QC measures stored in assay-specific observations tables. 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 .h5mu 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
specimen.specimenGuid: A GUID for the specific aliquot used for the experiment

Subject Metadata
subject.subjectGuid: A GUID for the Subject
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.diseaseGroup: The disease group in the ALTRA study (ARI or HC2)

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)
chip_id: A GUID for the 10x Genomics chip the cells were loaded into (e.g. B039-P1C2)
well_id: A GUID for the 10x Genomics well the cells were loaded into within the chip (e.g. B039-P1C2W4)
*barcodes: A GUID for the individual cell
original_barcodes: The original, sequence-based barcode generated by 10x Genomics Cell Ranger software
cell_name: A quasi-unique, memorable cell identifier generated using an adjective-adjective-animal structure

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

Cell Labeling Results
AIFI_L1: Final broad class cell type label (9 types)
AIFI_L1_score: AIFI_L1 prediction score generated by CellTypist
AIFI_L2: Final mid resolution cell type label (29 types)
AIFI_L2_score: AIFI_L2 prediction score generated by CellTypist
AIFI_L3: Final high resolution cell type label (71 types)
AIFI_L3_score: AIFI_L3 prediction score generated by CellTypist
manual_labels: Manually reviewed cell type labels based on AIFI_L3

scRNA-specific metrics, stored in modality-specific observations (rna.obs):

barcodes: A GUID for the individual cell
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
n_mito_umis: Total number of UMIs that were assigned to mitochondrial genes
total_counts: Total read counts
total_counts_mt: Total number of reads that were assigned to mitochondrial genes
pct_counts_mt: Percent of reads that were assigned to mitochondrial genes

scATAC-specific metrics, stored in modality-specific observations (atac.obs):

barcodes: A GUID for the individual cell
n_fragments: Number of ATAC-seq fragments associated with the cell
n_unique: Number of Unique ATAC-seq framents
n_duplicate: Number of Duplicate ATAC-seq fragments
n_mito: Number of ATAC-seq fragments aligning to mitochondrial chromosomes (chrMT)
ReadsInPeaks: Number of reads found within peak regions called by ArchR
ReadsInPromoter: Number of reads found within promoter regions called by ArchR
ReadsInBlacklist: Number of reads found within Blacklist regions called by ArchR
ReadsInTSS: Number of reads found within TSS regions called by ArchR
FRIP: Fraction of Reads In Peaks (computed by ArchR)
TSSEnrichment: Enrichment of reads in TSS regions (computed by ArchR)
PromoterRatio: Ratio of reads in promoter regions (computed by ArchR)
NucleosomeRatio: Ratio of reads from fragments with nucleosomal length (computed by ArchR)

Download links

File Name N Subjects N Samples N Cells File Size
altra_ARI-HC2_tea-seq.h5mu 12 12 88,967 15 GB
ALTRA and Sound Life TEA-seq .h5mu
File Name Description Download Link
altra_ARI-HC2_tea-seq.h5mu TEA-seq data from ARI and control subjects