DNA Methylation Metadata Attributes

Fields that are collected for DNA Methylation 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
analyte_class * The analyte class which is the target molecule that the assay is measuring. Example: DNA Chromatin Collagen DNA DNA + RNA Endogenous fluorophore Fluorochrome Lipid Lipid + metabolite Lipid + metabolite + protein Metabolite Nucleic acid + protein Peptide Polysaccharide Protein RNA RNA + protein Saturated lipid Unsaturated lipid
is_targeted * Indicates whether a specific molecule or set of molecules is targeted for detection or measurement by the assay. Example: Yes Yes No
acquisition_instrument_vendor * The company that manufactures or supplies the acquisition instrument. An acquisition instrument is a device equipped with signal detection hardware and signal processing software. It captures signals produced by assays, such as variations in light intensity or color, or signals corresponding to molecular mass. If the instrument was custom-built or developed internally, enter “In-House”. Example: Illumina 10x Genomics 3DHISTECH Akoya Biosciences Andor BGI Genomics Bruker Complete Genomics Cytek Biosciences Cytiva Element Biosciences Evident Scientific (Olympus) GE Healthcare Hamamatsu Huron Digital Pathology Illumina In-House Ionpath Keyence Leica Biosystems Leica Microsystems Microscopes International Miltenyi Biotec Motic NanoString Resolve Biosciences Revvity Sciex Singular Genomics Standard BioTools (Fluidigm) Thermo Fisher Scientific Vizgen Waters Zeiss Microscopy
acquisition_instrument_model * The specific model of the acquisition instrument, as manufacturers often offer various versions with differing features or sensitivities. These differences may be relevant to the processing or interpretation of the data. If the instrument was custom-built or developed internally, enter “In-House”. If the model is unknown, enter “Unknown”. Example: HiSeq 4000 Aperio AT2 Aperio CS2 AVITI Axio Observer 3 Axio Observer 5 Axio Observer 7 Axio Scan.Z1 Axio Zoom.V16 Biomark HD BZ-X710 BZ-X800 BZ-X810 Cell DIVE CosMx Spatial Molecular Imager Custom: Multiphoton Cytek Northern Lights CyTOF 2 CyTOF XT Digital Spatial Profiler DM6 B DMi8 DNBSEQ-T7 EVOS M7000 G4X Spatial Sequencer Helios HiSeq 2500 HiSeq 4000 Hyperion Imaging System IN Cell Analyzer 2200 In-House Juno System Lightsheet 7 LSM 710 Confocal Microscope MACSima System MALDI timsTOF Flex Prototype MERSCOPE MERSCOPE Ultra MIBIscope MoticEasyScan One NanoZoomer 2.0-HT NanoZoomer 2.0-RS NanoZoomer S210 NanoZoomer S360 NanoZoomer S60 NanoZoomer-SQ NextSeq 2000 NextSeq 500 NextSeq 550 Not applicable NovaSeq 6000 NovaSeq X NovaSeq X Plus Opera Phenix HCS Opera Phenix Plus HCS Orbitrap Eclipse Tribrid Orbitrap Fusion Lumos Tribrid Orbitrap Fusion Tribrid Pannoramic MIDI II Digital Scanner Panoramic 150 Digital Scanner Phenocycler-Fusion 1.0 Phenocycler-Fusion 2.0 PhenoImager Fusion Q Exactive Q Exactive HF Q Exactive HF-X Q Exactive UHMR QTRAP 5500 Resolve Biosciences Molecular Cartography SCN400 solariX STELLARIS 5 SYNAPT G2-Si timsTOF FleX timsTOF FleX MALDI-2 timsTOF HT timsTOF Pro timsTOF Pro 2 timsTOF SCP timsTOF Ultra timsTOF Ultra 2 TissueScope LE Slide Scanner Unknown uScopeHXII-20 VS200 Slide Scanner Xenium Analyzer Zeiss LightSheet Z.1 Zyla 4.2 sCMOS
source_storage_duration_value * The length of time the sample was stored prior to processing it. For assays performed on tissue sections, this refers to how long the tissue section (e.g., slide) was stored before the assay began (e.g., imaging). For assays performed on suspensions, such as sequencing, it refers to how long the suspension was stored before library construction started. Example: 12  
source_storage_duration_unit * The unit of measurement used to specify the source storage duration value. Example: hour day hour minute month year
time_since_acquisition_instrument_calibration_value The length of time since the acquisition instrument was last serviced or calibrated. This provides a metric for assessing drift in data capture. Example: 10  
time_since_acquisition_instrument_calibration_unit The unit of measurement used to specify the time since acquisition instrument calibration value. Example: month day month year
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  
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: d70bfe24-e82a-46cb-9369-28ae03660d97