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 Identifierscohort.cohortGuid:
A Globally Unique Identifier (GUID) of the Cohort the subject enrolled in for our studysubject.subjectGuid:
A GUID for the Subjectspecimen.specimenGuid:
A GUID for the specific aliquot used for the experiment
Subject Metadatasubject.subjectGuid:
A GUID for the Subjectsubject.biologicalSex:
The biological sex of the Subjectsubject.birthYear:
The Birth Year of the Subjectsubject.race:
The self-reported Race of the Subjectsubject.ethnicity:
The self-reported Ethnicity of the subjectsubject.diseaseGroup:
The disease group in the ALTRA study (ARI or HC2)
Process Identifiersbatch_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 celloriginal_barcodes:
The original, sequence-based barcode generated by 10x Genomics Cell Ranger softwarecell_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 ResultsAIFI_L1:
Final broad class cell type label (9 types)AIFI_L1_score:
AIFI_L1 prediction score generated by CellTypistAIFI_L2:
Final mid resolution cell type label (29 types)AIFI_L2_score:
AIFI_L2 prediction score generated by CellTypistAIFI_L3:
Final high resolution cell type label (71 types)AIFI_L3_score:
AIFI_L3 prediction score generated by CellTypistmanual_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 celln_reads:
Number of reads assigned to the cell barcoden_umis:
Number of Unique Molecular Identifiers (unique molecules) detectedn_genes:
Number of genes with at least 1 UMI detectedn_mito_umis:
Total number of UMIs that were assigned to mitochondrial genestotal_counts:
Total read countstotal_counts_mt:
Total number of reads that were assigned to mitochondrial genespct_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 celln_fragments:
Number of ATAC-seq fragments associated with the celln_unique:
Number of Unique ATAC-seq framentsn_duplicate:
Number of Duplicate ATAC-seq fragmentsn_mito:
Number of ATAC-seq fragments aligning to mitochondrial chromosomes (chrMT)ReadsInPeaks:
Number of reads found within peak regions called by ArchRReadsInPromoter:
Number of reads found within promoter regions called by ArchRReadsInBlacklist:
Number of reads found within Blacklist regions called by ArchRReadsInTSS:
Number of reads found within TSS regions called by ArchRFRIP:
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 |