| dataset_type |
Allowable Value |
The specific type of dataset being produced. |
10X Multiome 2D Imaging Mass Cytometry ATACseq Auto-fluorescence Cell DIVE CODEX Confocal CosMx CyCIF DBiT DESI Enhanced Stimulated Raman Spectroscopy (SRS) GeoMx (nCounter) GeoMx (NGS) HiFi-Slide Histology LC-MS Light Sheet MALDI MERFISH MIBI Molecular Cartography MUSIC nanoSPLITS PhenoCycler Resolve RNAseq RNAseq (with probes) Second Harmonic Generation (SHG) SIMS SNARE-seq2 Stereo-seq Thick section Multiphoton MxIF Visium (no probes) Visium (with probes) Xenium |
True |
| contributors_path |
Textfield |
The path to the file with the ORCID IDs for all contributors of this dataset (e.g., “./extras/contributors.tsv” or “./contributors.tsv”). This is an internal metadata field that is just used for ingest. |
|
True |
| data_path |
Textfield |
The top level directory containing the raw and/or processed data. For a single dataset upload this might be “.” where as for a data upload containing multiple datasets, this would be the directory name for the respective dataset. For instance, if the data is within a directory called “TEST001-RK” use syntax “./TEST001-RK” for this field. If there are multiple directory levels, use the format “./TEST001-RK/Run1/Pass2” in which “Pass2” is the subdirectory where the single dataset’s data is stored. This is an internal metadata field that is just used for ingest. |
|
True |
| capture_batch_id |
Textfield |
A lab-generated ID to identify which cells were captured at the same time. This would, for example, be an ID to denote which datasets were derived from a single 10X Genomics Chromium Controller run. In the case of the 10X Controller this could be the chip ID and would allow users the ability to determine which samples were processed together in a Chromium controller. It is recommended that data providers prefix the ID with the center name, to prevent values overlapping across centers. |
|
True |
| preparation_instrument_vendor |
Allowable Value |
The manufacturer of the instrument used to prepare (staining/processing) the sample for the assay. If an automatic slide staining method was indicated this field should list the manufacturer of the instrument. |
10x Genomics Hamamatsu HTX Technologies In-House Leica Biosystems Not applicable Roche Diagnostics SunChrom Thermo Fisher Scientific |
True |
| preparation_instrument_model |
Allowable Value |
Manufacturers of a staining system instrument may offer various versions (models) of that instrument with different features. Differences in features or sensitivities may be relevant to processing or interpretation of the data. |
AutoStainer XL Chromium Connect Chromium Controller Chromium iX Chromium X Discovery Ultra EVOS M7000 M3+ Sprayer M5 Sprayer NanoZoomer S210 NanoZoomer S360 NanoZoomer S60 Not applicable ST5020 Multistainer Sublimator SunCollect Sprayer TM-Sprayer Visium CytAssist |
True |
| number_of_pre-amplification_pcr_cycles |
Numeric |
The number of PCR cycles run after the Chromium Controller step and prior to separating the suspension and initiating library construction |
|
True |
| metadata_schema_id |
Textfield |
The string that serves as the definitive identifier for the metadata schema version and is readily interpretable by computers for data validation and processing. Example: 22bc762a-5020-419d-b170-24253ed9e8d9 |
|
True |
| preparation_instrument_kit |
Allowable Value |
The reagent kit used with the preparation instrument. |
10X Genomics; Chromium Next GEM Chip G Single Cell Kit 16 rxns; PN 1000127 10X Genomics; Chromium Next GEM Chip G Single Cell Kit 48 rxns; PN 1000120 10X Genomics; Chromium Next GEM Chip K Automated Single Cell Kit 48 rxns; PN 1000289 10X Genomics; Chromium Next GEM Chip K Single Cell Kit 16 rxns; PN 1000287 10X Genomics; Chromium Next GEM Chip K Single Cell Kit 48 rxns; PN 1000286 10X Genomics; Chromium Next GEM Chip Q Single Cell Kit 16 rxns; PN 1000422 10X Genomics; Chromium NextGem Single Cell Multiome ATAC + Gene Expression Reagent Bundle 16 rxn; PN 1000283 10X Genomics; Chromium NextGem Single Cell Multiome ATAC + Gene Expression Reagent Bundle 4 rxn; PN 1000285 10X Genomics; Visium FFPE Reagent Kit v2-Small PN 1000436 Custom |
True |
| preparation_protocol_doi |
Textfield |
DOI for the protocols.io page that describes the assay or sample procurment and preparation. For example for an imaging assay, the protocol might include staining of a section through the creation of an OME-TIFF file. In this case the protocol would include any image processing steps required to create the OME-TIFF file. Example: https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1 |
|
True |
| parent_sample_id |
Textfield |
Unique HuBMAP or SenNet identifier of the sample (i.e., block, section or suspension) used to perform this assay. For example, for a RNAseq assay, the parent would be the suspension, whereas, for one of the imaging assays, the parent would be the tissue section. If an assay comes from multiple parent samples then this should be a comma separated list. Example: HBM386.ZGKG.235, HBM672.MKPK.442 or SNT232.UBHJ.322, SNT329.ALSK.102 |
|
True |
