Supported Data Types

The following Illumina and thrid-party data types are supported in Connected Multiomics:

Data Type	Vendor	Assay Name(s)	Secondary Analysis Pipeline	File Types	Samples per File	Datasets	Additional information
Bulk RNA-Seq	Illumina	Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus Illumina Stranded mRNA Prep Ligation TruSeq Stranded Total RNA Library Prep Gold TruSeq Stranded Total RNA Library Prep Globin TruSeq Stranded mRNA Library Prep	DRAGEN RNA	.sf .sf.gz	Multiple samples per file	Included in demo data
Bulk RNA-Seq	Various	Various	Salmon	quant.genes.sf	Multiple samples per file	Gene Expression Omnibus - Search GSM7103647
Bulk Methylation	Illumina	Illumina 5-base DNA Prep Illumina 5-base DNA Prep with Enrichment	DRAGEN Germline DRAGEN Somatic	.CX_report.txt.gz .methyl_metrics.csv .mapping_metrics.csv .wgs_coverage_metrics.csv .M-bias.txt	One sample per set of files	Included in demo data
Microarray Methylation	Illumina	Methylation Screening Array MethylationEPIC	N/A	.idat	One sample per set of files	Included in demo data	Requires 2 .idat files per sample. Red.idat and Grn.idat
Bulk Proteomics	Illumina	Illumina Protein Prep 9.5K Plasma Illumina Protein Prep 9.5K Serum	DRAGEN Protein Quantification	.adat	Multiple samples per file	Included in demo data
Bulk Proteomics	SomaLogic	SomaScan 11K and 7K assays	N/A	.adat	Multiple samples per file	SomaLogic - 11K ADAT v5.0 example
Single-cell scATAC-Seq	10X Genomics	Epi Multiome ATAC + Gene Expression	Cell Ranger ARC	.h5 .csv fragments.tsv.gz fragments.tsv.gz.tbi peaks.bed	One sample per set of files	10X - PBMC from a Healthy Donor - Granulocytes Removed Through Cell Sortings (3k)	Each file must begin with the sample name. Multiple files can be ingested at the same time
Single-cell scATAC-Seq	Various	Various	Seurat	.qs or .rds	One sample per file	Not available	R object for data processed by Seurat (ATAC)
Single-cell sc-RNA	Illumina	Illumina Single Cell 3' RNA Prep	DRAGEN Single Cell RNA	.barcodes.tsv.gz .features.tsv.gz .matrix.mtx.gz	One sample per set of files	Included in demo data	Any additional descriptors prior to main extensions are supported (eg .scRNA.filtered.matrix.mtx). Each file name must begin with the sample name. Multiple samples can be ingested at the same time.
Single-cell sc-RNA	10X Genomics Parse Biosciences	Chromium assays including: Universal 3' Gene Expression Parse assays including: Evercode WT	Cell Ranger Parse Biosciences data analysis pipeline	.tsv.gz or .csv.gz .mtx.gz	One sample per set of files	10X - 10k Human DTC Melanoma, Chromium GEM-X Single Cell 3' Parse - Performance of Evercode™ WT v3 in Adult Mouse Brain Nuclei	Sparse matrix output. Each sample has 3 files: two .csv with one .mtx or two .tsv with one .mtx. Each file name must begin with the sample name. Multiple samples can be ingested at the same time.
Single-cell sc-RNA	10X Genomics	Chromium assays including: Universal 3' Gene Expression	Cell Ranger	.h5	One sample per file	10X - 10k Human DTC Melanoma, Chromium GEM-X Single Cell 3'	This compressed binary format is preferred for 10x Genomics Cell Ranger output. One filtered .h5 file per sample. Multiple samples can be ingested at the same time.
Single-cell sc-RNA	Various	Various	Scanpy	.h5ad	One sample per file	Not available	AnnData object in the h5ad file format
Single-cell sc-RNA	Various	Various	Seurat	.qs or .rds	One sample per file	Gene Expression Omnibus - Search GSE186892	R object for data processed by Seurat (RNA)
Spatial Transcriptomics	Illumina	Ilumina Spatial Transcriptome Prep	DRAGEN Spatial Transcriptome	.h5ad .ome.tiff	One sample per set of files	Included in demo data	At least one .ome.tiff and multiple .h5ad files are required.
Spatial Transcriptomics	10X Genomics	Visium assays including: HD WT Panel Gene Expression HD 3’ Gene Expression Spatial Gene Expression	Space Ranger	.h5 or barcodes.tsv.gz features.tsv.gz matrix.mtx.gz or barcodes.csv.gz features.csv.gz matrix.mtx.gz with _spatial.tar.gz Optional: .tif	One sample per set of files	10X - Mouse Brain Serial Section 1	Either count matrix data as 1 filtered .h5 file per sample or sparse matrix files for each sample as 3 files (two .csv with one .mtx or two .tsv with one .mtx for each sample). The spatial output files should be in compressed format (.zip). The high resolution image (.tif)can be uploaded and is optional. The spatial result file name must begin with the sample name. Only 1 sample can be ingested at a time.
Spatial Transcriptomics	10X Genomics	Xenium assays including: In Situ Gene Expression	Xenium Analysis	cell_feature_matrix.h5 cells.csv.gz cell_boundaries.csv.gz nucleus_boundaries.csv.gz transcripts.csv.gz / transcripts.parquet.csv.gz morphology_focus.ome.tif	One sample per set of files	10X - Fresh Frozen Mouse Brain Hemisphere with 5K Mouse Pan Tissue and Pathways Panel	Includes the unzipped Xenium Output Bundle with the preferred input image file (.tiff) for each sample. The .h5 file name must begin with the sample name. Only 1 sample can be ingested at a time.
Metadata	Various	Various	Various	.tsv .csv	Multiple samples per file	N/A	See Sample Metadata for more detail on format.