Paired Tag Metadata Attributes

Fields that are collected for Paired Tag data, available at dataset.metadata.<attribute>  

* indicates a required field

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 10X Multiome 2D Imaging Mass Cytometry 4i ATACseq Auto-fluorescence Cell DIVE CODEX COMET Confocal CosMx Proteomics CosMx Transcriptomics CyCIF CyTOF DART-FISH DBiT-seq DESI DNA Methylation Enhanced Stimulated Raman Spectroscopy (SRS) FACS GeoMx (nCounter) GeoMx (NGS) HiFi-Slide Histology iCLAP Illumina Spatial ver0 LC-MS Light Sheet MACSima MALDI MERFISH MIBI Molecular Cartography MPLEx MS Lipidomics MUSIC nanoSPLITS Olink PhenoCycler Pixel-seqV2 Raman Imaging Resolve RNAseq RNAseq (with probes) Second Harmonic Generation (SHG) Seq-Scope seqFISH SIMS Singular Genomics G4X SNARE-seq2 STARmap Stereo-seq Thick section Multiphoton MxIF Virtual Histology Visium (no probes) Visium (with probes) Visium HD Xenium
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 10x Genomics Akoya Biosciences Hamamatsu HTX Technologies In-House Ionpath Leica Biosystems Not applicable Roche Diagnostics SunChrom Thermo Fisher Scientific
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 AutoStainer XL Chromium Connect Chromium Controller Chromium iX Chromium X Custom 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
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 Chip E Single Cell ATAC Kit, 48 rxns; PN 1000155 10x Genomics; Chromium GEM-X Single Cell 3' Kit v4, 16 rxns; PN 1000691 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; Chromium Single Cell B Chip Kit, 16 rxns; PN 1000074 10X Genomics; Visium FFPE Reagent Kit v2-Small, PN 1000436 Custom
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  
non_global_files A semicolon separated list of non-shared files to be included in the dataset. The path assumes the files are located in the “TOP/non-global/” directory. For example, for the file is TOP/non-global/lab_processed/images/1-tissue-boundary.geojson the value of this field would be “./lab_processed/images/1-tissue-boundary.geojson”. After ingest, these files will be copied to the appropriate locations within the respective dataset directory tree.  
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