Metadata Reporting Standards
10X Multiome
A multimodal single-cell sequencing technology that simultaneously captures both gene expression (RNA-seq) and chromatin accessibility (ATAC-seq) from the same individual nucleus. Both RNA molecules and open-chromatin DNA fragments are labeled with a unique per-nucleus barcode using the 10x Genomics Chromium platform, allowing paired readouts to be linked to the same cell of origin.
* This reporting standard requires the inclusion of RNAseq and ATACseq dataset metadata for completeness.
DOI: https://doi.org/10.35079/HBM528.GWLG.472
Published: August 25, 2026
Schema
Legend:
Text field
Allowable value
Radio
Numeric
* Required
| Attribute | Type | Description | Allowable Values |
|---|---|---|---|
| Parent sample ID * | The unique identifier from HuBMAP or SenNet for the sample (such as a block, section, or suspension) used to perform the assay. For instance, in an RNAseq assay, the parent sample would be the suspension, while in imaging assays, it would be the tissue section. If the assay is derived from multiple parent samples, this field should contain a comma-separated list of identifiers. Example: HBM386.ZGKG.235, HBM672.MKPK.442 | ||
| Lab ID | A locally assigned identifier provided by the data provider for the dataset. It is used to reference an external metadata record that may be maintained independently, enabling traceability and supporting provenance tracking. Example: Visium_9OLC_A4_S1 | ||
| Preparation protocol DOI * | The DOI for the protocols.io page that details the assay or the procedures used for sample procurement and preparation. For example, in the case of an imaging assay, the protocol may start with tissue section staining and end with the generation of an OME-TIFF file. The documented protocol should also include any image processing steps involved in producing the final OME-TIFF. Example: https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1 | ||
| Dataset type * | The specific type of dataset being produced. Example: RNAseq | HiFi-Slide SNARE-seq2 COMET Visium (no probes) DESI Confocal Stereo-seq Visium (with probes) Molecular Cartography DBiT-seq Seq-Scope CosMx Transcriptomics CyCIF Light Sheet seqFISH ATACseq CosMx Proteomics Singular Genomics G4X Visium HD MERFISH 10X Multiome 4i PhenoCycler Second Harmonic Generation (SHG) Thick section Multiphoton MxIF CyTOF Olink MIBI Auto-fluorescence FACS Xenium SIMS Cell DIVE CODEX GeoMx (NGS) MUSIC Pixel-seqV2 MALDI 2D Imaging Mass Cytometry Histology Enhanced Stimulated Raman Spectroscopy (SRS) DART-FISH Resolve RNAseq LC-MS nanoSPLITS GeoMx (nCounter) RNAseq (with probes) MS Lipidomics MPLEx |
|
| Contributors path * | The name of the file containing the ORCID IDs for all contributors to this dataset. Example: ./contributors.csv | ||
| Data path * | The top-level directory containing the raw and/or processed data. For a single dataset upload, this might be represented as “.”, whereas for a data upload containing multiple datasets, this would be the directory name for the respective dataset. For example, if the data is within a directory named “TEST001-RK”, use the syntax “./TEST001-RK” for this field. If there are multiple directory levels, use the format “./TEST001-RK/Run1/Pass2”, where “Pass2” is the subdirectory where the single dataset’s data is stored. This is an internal metadata field used solely for data ingestion. Example: ./TEST001-RK | ||
| Capture batch ID * | A lab-assigned identifier used to indicate which cells or nuclei were captured together in the same run. For example, in a 10X Genomics Chromium Controller workflow, this could be the chip ID used to trace datasets derived from a single capture event. This ID helps users identify samples processed together on the same device. To avoid conflicts across institutions, it is recommended to prefix the ID with the name of the sequencing center. Example: Broad_Batch1234 | ||
| Preparation instrument vendor * | The company that manufactures the instrument used to prepare the sample (e.g., for staining or other processing steps) prior to the assay. If the instrument was custom-built or developed internally, enter “In-House”. If no sample preparation occurred, enter “Not applicable”. Example: 10X Genomics | In-House Leica Biosystems Not applicable Thermo Fisher Scientific Roche Diagnostics HTX Technologies 10x Genomics Hamamatsu SunChrom |
|
| Preparation instrument model * | The specific model of the instrument used for sample preparation, such as staining. Manufacturers may offer multiple models with varying features or sensitivities, which can influence how the sample is processed and how the resulting data is interpreted. If no sample preparation occurred, enter “Not applicable”. Example: Chromium X | NanoZoomer S210 Not applicable Sublimator EVOS M7000 Chromium Controller NanoZoomer S360 NanoZoomer S60 Chromium X AutoStainer XL Visium CytAssist SunCollect Sprayer M3+ Sprayer Discovery Ultra ST5020 Multistainer Chromium iX Chromium Connect M5 Sprayer TM-Sprayer |
|
| Preparation instrument kit * | The reagent kit used in conjunction with the preparation instrument for sample processing (e.g., staining or labeling). If the reagent kit was prepared using a custom protocol, enter “Custom”. Example: 10X Genomics; Chromium Next GEM Chip G Single Cell Kit, 48 rxns; PN 1000120 | 10X Genomics; Chromium Next GEM Chip G Single Cell Kit, 16 rxns; PN 1000127 10X Genomics; Chromium Next GEM Chip K Automated Single Cell Kit, 48 rxns; PN 1000289 10X Genomics; Chromium NextGem Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxn; PN 1000283 10x Genomics; Chromium Single Cell B Chip Kit, 16 rxns; PN 1000074 10X Genomics; Chromium NextGem Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 4 rxn; PN 1000285 10x Genomics; Chromium GEM-X Single Cell 3' Kit v4, 16 rxns; PN 1000691 10X Genomics; Chromium Next GEM Chip K Single Cell Kit, 48 rxns; PN 1000286 10X Genomics; Chromium Next GEM Chip G Single Cell Kit, 48 rxns; PN 1000120 10X Genomics; Visium FFPE Reagent Kit v2-Small, PN 1000436 Custom 10X Genomics; Chromium Next GEM Chip Q Single Cell Kit, 16 rxns; PN 1000422 10X Genomics; Chromium Next GEM Chip K Single Cell Kit, 16 rxns; PN 1000287 |
|
| Number of pre-amplification PCR cycles * | The number of PCR cycles performed following the Chromium Controller step and before the suspension is separated and library construction begins. Example: 7 | ||
| Metadata schema ID * | The unique string identifier for the metadata specification version, which is easily interpretable by computers for purposes of data validation and processing. Example: 22bc762a-5020-419d-b170-24253ed9e8d9 |
Definitions
| Pattern | Required? | Description |
|---|---|---|
| extras/ | ✓ | Folder for general lab-specific files related to the dataset. |
| extras/expected_cell_count.txt$ | The expected cell count for the RNA sequencing dataset. This is an optional file that, if present, will be used by the HIVE’s RNA sequencing analysis pipeline. With some datasets, knowing the expected cell count has improved the output of the HIVE analysis pipeline. | |
| raw/ | ✓ | All raw data files for the experiment. |
| raw/fastq/ | ✓ | Raw sequencing files for the experiment. |
| raw/fastq/RNA/ | ✓ | Directory containing fastq files pertaining to RNAseq sequencing. |
| raw/fastq/RNA/*_R*.fastq.gz$ | ✓ | This is a GZip’d version of the forward and reverse fastq files from RNAseq sequencing (R1 and R2). |
| raw/fastq/ATAC/ | ✓ | Directory containing fastq files pertaining to ATACseq sequencing. |
| raw/fastq/ATAC/*_R*.fastq.gz$ | ✓ | This is a GZip’d version of the fastq files containing the forward, reverse and barcode reads from ATACseq sequencing (R1, R2 and R3). Further, if the barcodes are in R3 (as with 10X) then the metadata field “barcode reads” would be set to “Read 2 (R2)” and the fastq file named “*_R2*.fastq.gz” would be expected. |
| lab_processed/ | Experiment files that were processed by the lab generating the data. |
Example
. ├── extras/ │ └── expected_cell_count.txt ├── raw/ │ └── fastq/ │ ├── RNA/ │ │ └── foobar_10xmultiome_R.fastq.gz │ └── ATAC/ │ └── foobar_10xmultiome_R.fastq.gz └── lab_processed/
HuBMAP Datasets
The HuBMAP Data Portal is an open platform to discover, visualize, and download standardized healthy single-cell and spatial tissue data.
View HuBMAP Datasets
Citation
Fisher SA, Hardi J, Morgan R, Nordgren E, Kant PM, Honick B, Rosario J, O'Connor MJ, Turner ML, DCWG Members, Gehlenborg N, Blood PD, Silverstein JC, Musen MA. 2026. The HuBMAP Framework for Advancing Data FAIRness. submitted. https://doi.org/10.64898/2026.06.01.728946
Reuse
This standard may be reused, expanded, or referenced by external repositories. It represents version 2.0 of the metadata schema and version 2.2 of the file directory structure. If you are uploading data, the latest versions of both are available at the "Latest Versions" link below. If you are querying or using HuBMAP or SenNet metadata, a harmonized view of the metadata specification is available at the "Harmonized Version" link below.
Latest Versions Harmonized Version
Contributors
Below is the information for the individuals who contributed to the HuBMAP and SenNet metadata reporting standards.
For questions about this standard, email HuBMAP Helpdesk. You can alternatively reach out to the individuals listed below, either via the email address listed in the table or via contact information provided on their ORCID profile page.
| Name | Affiliation | Contact | ORCID |
|---|---|---|---|
| Stephen A Fisher | University of Pennsylvania, Philadelphia PA, USA | safisher@upenn.edu | 0000-0001-8034-7685 |
| Josef Hardi | Stanford University, Stanford, CA, USA | johardi@stanford.edu | 0000-0002-2533-6681 |
| Richard Morgan | University of Pittsburgh, Pittsburgh, PA, USA | rsm66@pitt.edu | 0009-0003-1800-8545 |
| Mark A Musen | Stanford University, Stanford, CA, USA | musen@stanford.edu | 0000-0003-3325-793X |
| Jonathan C Silverstein | University of Pittsburgh, Pittsburgh, PA, USA | j.c.s@pitt.edu | 0000-0002-9252-6039 |
| Erik Nordgren | University of Pennsylvania, Philadelphia PA, USA | 0000-0002-5024-0278 | |
| Peter M Kant | University of Pittsburgh, Pittsburgh, PA, USA; Currently - Otsuka Precision Health, Princeton, NJ, USA | 0009-0002-6510-5041 | |
| Brendan John Honick | Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, USA | 0000-0001-6128-9854 | |
| Martin J O’Connor | Stanford University, Stanford, CA, USA | 0000-0002-2256-2421 | |
| Jean G Rosario | University of Pennsylvania, Philadelphia PA, USA | 0000-0002-6116-5058 | |
| Nils Gehlenborg | Harvard Medical School, Boston, MA, USA | 0000-0003-0327-8297 | |
| Philip D Blood | Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, USA | 0000-0002-9129-1223 | |
| Kyung Jin Ahn | Children’s Hospital of Philadelphia, Philadelphia, PA, USA | 0000-0002-4184-482X | |
| Christopher R Anderton | Pacific Northwest National Laboratory, Richland, WA, USA | 0000-0002-6170-1033 | |
| Shovik Bandyopadhyay | Children’s Hospital of Philadelphia, Philadelphia, PA, USA; Brigham and Women’s Hospital, Boston, MA, USA | 0000-0003-3919-3914 | |
| Kenneth C Bedi | University of Pennsylvania, Philadelphia PA, USA | 0000-0003-3588-9324 | |
| Maigan Brusko | University of Florida, Gainesville, FL, USA | 0000-0002-4331-2202 | |
| Martha Campbell-Thompson | University of Florida, Gainesville, FL, USA | 0000-0001-6878-1235 | |
| James Carson | The University of Texas at Austin, Austin, TX, USA | 0000-0001-9009-5645 | |
| Chase M Carver | Mayo Clinic, Rochester, MN, USA | 0000-0003-4002-2418 | |
| Jing Chen | University of Florida, Gainesville, FL, USA | 0000-0001-8008-8062 | |
| Anthony M Corbett | University of Rochester Medical Center, Rochester, NY, USA | 0000-0001-9545-0853 | |
| Alexandra E Cuaycal | University of Florida, Gainesville, FL, USA | 0000-0002-9060-6326 | |
| Penny Cuda | Carnegie Mellon University, Pittsburgh, PA, USA | 0009-0002-6547-2650 | |
| Dinh Diep | University of California, San Diego, CA, USA; Currently - Altos Labs, San Diego, CA, USA | 0000-0001-6057-4119 | |
| Sergii Domanskyi | The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA | 0000-0002-6847-6019 | |
| Sean Donahue | Carnegie Mellon University, Pittsburgh, PA, USA | 0000-0002-4072-2046 | |
| Michael P Duffy | University of Pennsylvania, Philadelphia PA, USA | 0000-0001-5325-3683 | |
| Michael T Eadon | Indiana University School of Medicine, Indianapolis, IN, USA | 0000-0003-3066-2876 | |
| Jean Fan | Johns Hopkins University, Baltimore, MD, USA | 0000-0002-0212-5451 | |
| Melissa A Farrow | Vanderbilt University, Nashville, TN, USA | 0000-0002-1602-2082 | |
| Kathleen M Fisch | University of California San Diego, La Jolla, CA, USA | 0000-0002-0117-7444 | |
| William F Flynn | The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA | 0000-0001-6533-0340 | |
| James M Fulcher | Pacific Northwest National Laboratory, Richland, WA, USA | 0000-0001-9033-3623 | |
| Soumya Ghose | GE HealthCare, Niskayuna, NY, USA | 0000-0002-2730-1482 | |
| Fiona Ginty | GE HealthCare, Niskayuna, NY, USA | 0000-0001-6638-683X | |
| Joana P Gonçalves | Delft University of Technology, Delft, The Netherlands | 0000-0001-6072-9627 | |
| Yongqun He | University of Michigan, Ann Arbor, MI, USA | 0000-0001-9189-9661 | |
| Po Hu | Children’s Hospital of Philadelphia, Philadelphia, PA, USA; University of Pennsylvania, Philadelphia, PA, USA | 0000-0003-2422-1652 | |
| Sanjay Jain | Washington University School of Medicine, St. Louis, MO, USA | 0000-0003-2804-127X | |
| Thomas V Karathanos | Stanford University, Stanford, CA, USA | 0000-0003-1754-3872 | |
| Madhurima Kaushal | Washington University School of Medicine | 0000-0003-2760-0586 | |
| Angela RS Kruse | Vanderbilt University, Nashville, TN, USA; Currently - The Ohio State University, Columbus, OH, USA | 0000-0001-8776-2769 | |
| Yumi Kwon | Pacific Northwest National Laboratory, Richland, WA, USA | 0000-0003-0523-6197 | |
| Blue B Lake | University of California San Diego, La Jolla, CA, USA; Currently - Altos Labs, San Diego, CA, USA | 0000-0002-8637-9044 | |
| Roy Lardenoije | Delft University of Technology, Delft, The Netherlands | 0000-0002-9026-7870 | |
| Shin Lin | Emory University, Atlanta, GA, USA | 0000-0003-0118-0413 | |
| Yiing Lin | Washington University, St. Louis, MO, USA | 0000-0002-0317-7608 | |
| Scott A Lindsay | University of California, San Diego, CA, USA | 0000-0002-2929-7755 | |
| Peiran Lu | Children’s Hospital of Philadelphia, Philadelphia, PA, USA; University of Pennsylvania, Philadelphia, PA, USA | 0009-0001-5096-3046 | |
| Clayton Mathews | University of Florida, Gainesville, FL, USA | 0000-0002-8817-6355 | |
| Elizabeth McDonough | GE HealthCare, Niskayuna, NY, USA | 0000-0001-7524-8260 | |
| Ricardo Melo Ferreira | Indiana University School of Medicine, Indianapolis, IN, USA | 0000-0003-2063-9744 | |
| Emma M Monte | Stanford University, Stanford, CA, USA | 0000-0003-2566-1967 | |
| Kathleen O’Neill | University of Pennsylvania, Philadelphia PA, USA | 0000-0003-1980-6840 | |
| Minxing Pang | University of Pennsylvania, Philadelphia PA, USA | 0000-0001-5208-5972 | |
| Mana Parast | University of California San Diego, La Jolla, CA, USA | 0000-0001-5963-2246 | |
| Liming Pei | Children’s Hospital of Philadelphia, Philadelphia, PA, USA; University of Pennsylvania, Philadelphia, PA, USA | 0000-0002-1924-0333 | |
| Samuel Peters | University of Minnesota, Minneapolis, MN, USA | 0000-0003-1479-8087 | |
| Ajay Pillai | National Institute of Health, Bethesda, MD, USA | 0000-0002-9789-7189 | |
| Gloria Pryhuber | University of Rochester Medical Center, Rochester, NY, USA | 0000-0002-9185-3994 | |
| Ling Qin | University of Pennsylvania, Philadelphia PA, USA | 0000-0002-2582-0078 | |
| Presha Rajbhandari | Columbia University, NYC, NY, USA | 0000-0003-2184-7238 | |
| Matthew M Ruffalo | Carnegie Mellon University, Pittsburgh, PA, USA | 0000-0003-2222-6169 | |
| Pinaki Sarder | University of Florida, Gainesville, FL, USA | 0000-0003-2450-5233 | |
| Diane C Saunders | Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA; Northwestern University, Chicago, IL, USA | 0000-0002-8849-6746 | |
| Kevin Schneider | Buck Institute, Novato, CA, USA | 0009-0001-8046-0167 | |
| Lingyan Shi | University of California San Diego, La Jolla, CA, USA | 0000-0003-1373-3206 | |
| Santhosh Sivajothi | The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA | 0000-0002-8854-4517 | |
| David Smith | Children’s Hospital of Philadelphia, Philadelphia, PA, USA | 0000-0001-7858-3785 | |
| Jeff M Spraggins | Vanderbilt University, Nashville, TN, USA | 0000-0001-9198-5498 | |
| Valentina Stanley | University of California, San Diego, CA, USA | 0000-0002-2212-7796 | |
| Kai Tan | Children’s Hospital of Philadelphia, Philadelphia, PA, USA; University of Pennsylvania, Philadelphia, PA, USA | 0000-0002-9104-5567 | |
| Anusha Thadi | Children’s Hospital of Philadelphia, Philadelphia, PA, USA | 0000-0002-1271-0398 | |
| Hua Tian | Columbia University Medical Center, NYC, NY, USA | 0000-0002-3598-0219 | |
| Morgan L Turner | Harvard Medical School, Boston, MA, USA | 0000-0002-1512-9742 | |
| Ioannis S Vlachos | Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Cancer Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Boston, MA, USA | 0000-0002-8849-808X | |
| Seth Winfree | University of Nebraska Medical Center, Omaha, NE, USA; Currently - QCDx Inc, Farmington, CT, USA | ||
| Pei-Hsun Wu | Johns Hopkins University, Baltimore, MD, USA | 0000-0002-7371-2960 | |
| Kevin J Zemaitis | Pacific Northwest National Laboratory, Richland, WA, USA | 0000-0002-3524-9776 | |
| Mowei Zhou | Pacific Northwest National Laboratory, Richland, WA, USA; Currently - Zhejiang University, Hangzhou, Zhejiang 310058, China | 0000-0003-3575-3224 | |
| Chenchen Zhu | Department of Genetics, Stanford University, Stanford, CA, USA | 0000-0003-2165-9456 |