Supported Data Types

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

Spatial Transcriptomics

Illumina Spatial Solution

Vendor	Illumina
Assay Names(s)	Illumina Spatial technology
Secondary Analysis Pipeline	DRAGEN Spatial Transcriptome
File Types	pipeline-manfiest.json or tar.gz or .h5ad .ome.tiff contour.csv (optional)
Samples Per File	One sample per set of files
Datasets	Included in demo data
Additional information	At least one of the 3 input type options must be available

10x Genomics Visium Space Ranger Output

Vendor	10x Genomics
Assay Names(s)	Visium assays including: HD WT Panel Gene Expression HD 3’ Gene Expression Spatial Gene Expression
Secondary Analysis Pipeline	Space Ranger
File Types	.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
Samples Per File	One sample per set of files
Datasets	10X - Mouse Brain Serial Section 1
Additional information	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.

10x Genomics Xenium

Vendor	10x Genomics
Assay Names(s)	Xenium assays including: In Situ Gene Expression
Secondary Analysis Pipeline	Xenium Analysis
File Types	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
Samples Per File	One sample per set of files
Datasets	10X - Fresh Frozen Mouse Brain Hemisphere with 5K Mouse Pan Tissue and Pathways Panel
Additional information	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.

Nanostring CosMx

Vendor	Nanostring
Assay Names(s)	CosMx Spatial Molecular Imager
Secondary Analysis Pipeline	N/A
File Types	exprMat_file.csv metadata_file.csv polygons.csv fov_positions_file.csv optional tx_file.csv Images contained in CellComposite or CellOverlay folder: .tiff .jpeg .jpg
Samples Per File	One sample per set of files
Datasets	NanoString - Human Frontal Cortex FFPE Dataset
Additional information	NanoString CosMx data should include 5 files (exprMat_file.csv, metadata_file.csv, polygons.csv, fov_positions_file.csv, optional tx_file.csv) and the images contained in the CellComposite/CellOverlay folder per sample. The exprMat file name must begin with the sample name. Only 1 sample can be ingested at a time.

Single-cell RNA-Seq

Illumina DRAGEN Single Cell

Vendor	Illumina
Assay Names(s)	Illumina Single Cell 3' RNA Prep
Secondary Analysis Pipeline	DRAGEN Single Cell RNA
File Types	.h5ad or .barcodes.tsv.gz .features.tsv.gz .matrix.mtx.gz
Samples Per File	One sample per set of files
Datasets	Included in demo data
Additional information	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. _matrix/_features/_barcodes and .matrix/.features/.barcodes is accepted.

scRNA feature-barcode-matrix

Vendor	10x Genomics Parse Biosciences
Assay Names(s)	Chromium assays including: Universal 3' Gene Expression Parse assays including: Evercode WT
Secondary Analysis Pipeline	Cell Ranger Parse Biosciences data analysis pipeline
File Types	.tsv.gz or .csv.gz .mtx.gz
Samples Per File	One sample per set of files
Datasets	10X - 10k Human DTC Melanoma, Chromium GEM-X Single Cell 3' Parse - Performance of Evercode™ WT v3 in Adult Mouse Brain Nuclei
Additional information	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. _matrix/_features/_barcodes and .matrix/.features/.barcodes is accepted.

10x Genomics Cell Ranger counts h5

Vendor	10x Genomics
Assay Names(s)	Chromium assays including: Universal 3' Gene Expression
Secondary Analysis Pipeline	Cell Ranger
File Types	.h5
Samples Per File	One sample per file
Datasets	10X - 10k Human DTC Melanoma, Chromium GEM-X Single Cell 3'
Additional information	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.

h5ad

Vendor	Various
Assay Names(s)	Various
Secondary Analysis Pipeline	Scanpy
File Types	.h5ad
Samples Per File	One sample per file
Datasets	Not available
Additional information	AnnData object in the h5ad file format

Single cell count matrix

Vendor	Various
Assay Names(s)	Various
Secondary Analysis Pipeline	Various
File Types	Any of the following are accepted: .txt .csv .tsv .txt.gz .csv.gz .tsv.gz
Samples Per File	One sample per file
Datasets	Not available
Additional information	This is rectangular cell by feature count full matrix. File name will be used as sample name.

Seurat (RNA)

Vendor	Various
Assay Names(s)	Various
Secondary Analysis Pipeline	Seurat
File Types	.qs or .rds
Samples Per File	One sample per file
Datasets	Gene Expression Omnibus - Search GSE186892
Additional information	R object for data processed by Seurat (RNA)

Single-cell ATAC-Seq

10x Genomics Cell Ranger

Vendor	10x Genomics
Assay Names(s)	Epi Multiome ATAC + Gene Expression
Secondary Analysis Pipeline	Cell Ranger ARC
File Types	.h5 .csv fragments.tsv.gz fragments.tsv.gz.tbi peaks.bed
Samples Per File	One sample per set of files
Datasets	10X - PBMC from a Healthy Donor - Granulocytes Removed Through Cell Sortings (3k)
Additional information	Each file must begin with the sample name. Multiple files can be ingested at the same time

Seurat (ATAC)

Vendor	Various
Assay Names(s)	Various
Secondary Analysis Pipeline	Seurat
File Types	.qs or .rds
Samples Per File	One sample per file
Datasets	Not available
Additional information	R object for data processed by Seurat (ATAC)

V(D)J

V(D)J

Vendor	10x Genomics
Assay Names(s)	V(D)J
Secondary Analysis Pipeline	Cell Ranger ARC
File Types	.csv
Samples Per File	One file per sample
Datasets	Integrated GEX and VDJ analysis of Connect generated library from mouse splenocytes
Additional information	Filtered V(D)J contig annotation file in .csv format

V(D)J + scRNA-seq

Vendor	10x Genomics
Assay Names(s)	V(D)J
Secondary Analysis Pipeline	Cell Ranger ARC
File Types	.csv .h5
Samples Per File	Two files per sample
Datasets	Not available
Additional information	Filtered V(D)J contig annotation file in .csv format with matching gene expression counts in .h5 format

Flow/Mass Cytometry

Region Count Matrix

Vendor	Various
Assay Names(s)	Various
Secondary Analysis Pipeline	Various
File Types	.fcs
Samples Per File	One file per sample
Datasets	Not available
Additional information

Bulk RNA-Seq

Illumina DRAGEN RNA

Vendor	Illumina
Assay Names(s)	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
Secondary Analysis Pipeline	DRAGEN RNA
File Types	.sf .sf.gz
Samples Per File	One sample per file
Datasets	Included in demo data
Additional information

Gene Counts in sf Format

Vendor	Various
Assay Names(s)	Various
Secondary Analysis Pipeline	Salmon
File Types	quant.genes.sf
Samples Per File	One sample per file
Datasets	Gene Expression Omnibus - Search GSM7103647
Additional information

Generic Count Matrix

Vendor	Various
Assay Names(s)	Various
Secondary Analysis Pipeline	Various
File Types	.txt .txt.gz
Samples Per File	Multiple samples per file
Datasets	GSE276756
Additional information	Multiple files can be imported at once only if they have the same format

Bulk ChIP/ATAC Seq

Region Count Matrix

Vendor	Various
Assay Names(s)	Various
Secondary Analysis Pipeline	Various including: MACS
File Types	.txt
Samples Per File	One file per sample
Datasets	Not available
Additional information	Region name contains genomic location with the format as chromosome:start-stop.

Bulk DNA-Seq

VCF

Vendor	Various
Assay Names(s)	Various
Secondary Analysis Pipeline	Various including: DRAGEN
File Types	.vcf .vcf.gz .bgz
Samples Per File	One sample per file
Datasets	Included in demo data
Additional information

Bulk Proteomics

Illumina Protein Prep

Vendor	Illumina
Assay Names(s)	Illumina Protein Prep 9.5K Plasma Illumina Protein Prep 9.5K Serum
Secondary Analysis Pipeline	DRAGEN Protein Quantification
File Types	.adat
Samples Per File	Multiple samples per file
Datasets	Included in demo data
Additional information

Somalogic ADAT

Vendor	SomaLogic
Assay Names(s)	SomaScan 11K and 7K assays
Secondary Analysis Pipeline	N/A
File Types	.adat
Samples Per File	Multiple samples per file
Datasets	SomaLogic - 11K ADAT v5.0 example
Additional information

Generic Count Matrix

Vendor	Various
Assay Names(s)	Various including: Olink Mass Spectrometry
Secondary Analysis Pipeline	N/A
File Types	.txt .txt.gz
Samples Per File	Multiple samples per file
Datasets	GSE136431 (save this .xlsx file in .txt to import)
Additional information	Multiple files can be imported at once only if they have the same format

Alamar

Vendor	Alamar Biosciences
Assay Names(s)	NULISA panels and assays
Secondary Analysis Pipeline	Alamar Analysis Solution
File Types	.csv
Samples Per File	Multiple samples per file
Datasets	Not available
Additional information

Bulk Methylation

Illumina 5-base Solution

Vendor	Illumina
Assay Names(s)	Illumina 5-base DNA Prep Illumina 5-base DNA Prep with Enrichment
Secondary Analysis Pipeline	DRAGEN Germline DRAGEN Somatic (Tumor-Normal not currently supported in ICM)
File Types	.CX_report.txt.gz .methyl_metrics.csv .mapping_metrics.csv .wgs_coverage_metrics.csv .M-bias.txt
Samples Per File	One sample per set of files
Datasets	Included in demo data
Additional information	Analysis support for DRAGEN Somatic outputs is limited to Tumor-Only

Bulk miRNA

Illumina miRNA Prep

Vendor	Illumina
Assay Names(s)	Illumina miRNA Prep
Secondary Analysis Pipeline	DRAGEN miRNA
File Types	.txt
Samples Per File	Multiple samples per file
Datasets	Included in demo data
Additional information

Generic Count Matrix

Vendor	Various
Assay Names(s)	Various
Secondary Analysis Pipeline	Various
File Types	.txt .txt.gz
Samples Per File	Multiple samples per file
Datasets	Not available
Additional information	Multiple files can be imported at once if they all have the same format

Microarray

Illumina Infinium Methylation

Vendor	Illumina
Assay Names(s)	Methylation Screening Array MethylationEPIC
Secondary Analysis Pipeline	N/A
File Types	.idat
Samples Per File	One sample per set of files
Datasets	Included in demo data
Additional information	Requires 2 .idat files per sample. Red.idat and Grn.idat

Microarray RNA

Vendor	Various
Assay Names(s)	Various
Secondary Analysis Pipeline	N/A
File Types	Any of the following are accepted: .txt .csv .tsv .txt.gz .csv.gz .tsv.gz
Samples Per File	One sample per set of files
Datasets	Not available
Additional information

Library File

scType

Vendor	Various
Assay Names(s)	Various
Secondary Analysis Pipeline	Various
File Types	.tsv .csv
Samples Per File	Multiple samples per file
Datasets	N/A
Additional information	See Sample Metadata for more detail on format.