Single-nucleus methyl-3C sequencing Metadata Attributes

The attributes shown here have been colleced for Single-nucleus methyl-3C sequencing data, available from the HuBMAP Search and Entity APIs at Dataset.metadata.<attribute>.
These attributes are harmonized across all versions of the Single-nucleus methyl-3C sequencing metadata specifications. See the latest version of the Single-nucleus methyl-3C sequencing Metadata Specifications for the schema and directory structure needed when ingesting Segmentation Mask metadata.

* 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 An identifier assigned by the data provider to reference an external metadata record for the dataset. The external record may be maintained independently and can support dataset traceability and provenance tracking. Leave this field empty if no such identifier exists.  
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  
barcode_offset * The position within a sequencing read where a barcode sequence begins. In sequencing libraries, barcodes—short DNA sequences used to tag individual cells or molecules—are often arranged in a pattern where each barcode is separated by a constant sequence of known length. These constant sequences create predictable spacing between barcodes, known as offsets. For example, if barcodes are 8 base pairs (bp) long and separated by 30 bp constant regions, the barcodes might start at positions 0, 38, and 76 within the read. If the source material is not barcoded, this field should be marked as “Not applicable”. Example: 0,38,76 0 1 8 20 0,14 1,27 0,38,76 10,48,78 10,48,86 0,20-23,51-54 Not applicable
barcode_read * The sequencing read file contains the cell or capture spot barcode sequences. This information is essential when constructing sequencing libraries with a non-commercial kit, as it ensures that barcodes are correctly extracted during data processing. If the source material is not barcoded, this field should be marked as “Not applicable”. Example: Read 1 (R1) Not applicable Read 1 (R1) Read 2 (R2)
barcode_size * The length of each cell or capture spot barcode in base pairs (bp). If the source material is not barcoded, enter “Not applicable”. Example: 16 8 14 16 40 8,6 10,10 8,8,8 14-17,14,14 Not applicable
assay_input_entity * The entity from which the analyte is captured. For example, in bulk sequencing, the source entity would be “tissue” while in single-cell sequencing, it would be “single cell”. Example: single cell area of interest single cell single nucleus spot tissue (bulk)
number_of_input_cells_or_nuclei * The number of cells or nuclei that were input into the assay. This information is typically not available for assays performed on bulk tissue preparations, and therefore this field may be left blank. Example: 1000  
library_adapter_sequence * The 5’ and/or 3’ adapter sequences used during library preparation to make the library compatible with the sequencing protocol and instrumentation. Adapter sequences should be provided as a comma-separated list of key-value pairs in the format: “adapter name: sequence”. Example: Nextera Read 1: CTGTCTCTTATACACATCT  
library_average_fragment_size * The average size of sequencing library fragments, measured in base pairs (bp), as estimated by gel electrophoresis, BioAnalyzer, or TapeStation. Example: 200  
library_output_amount_value * The total amount of library following the clean-up step after the final PCR amplification. To calculate, multiply the Qubit-measured concentration (ng/µl) by the elution volume (µl) obtained after the final clean-up. Example: 125  
library_output_amount_unit * The unit of measurement used to specify the library output amount value. Example: ng ng ul
library_concentration_value * The concentration of the pooled library submitted for sequencing. Example: 2.5  
library_concentration_unit * Unit of library concentration value. ng/ul nM pg/ul
library_layout * Indicates whether the sequencing library was prepared for single-end or paired-end sequencing. This information determines how reads are generated and aligned during data processing. Example: single-end paired-end single-end
number_of_pcr_cycles_for_indexing * The number of PCR cycles used specifically to add sequencing adapters and amplify the library during the indexing step. This count does not include earlier cDNA amplification cycles, which are recorded separately under the “Number of iterations of cDNA amplification” field. Example: 8  
library_preparation_kit * The reagent kit used to construct the sequencing library, including both the kit name and, if available, version and product number. If the library was prepared using a custom protocol, enter “Custom”. Example: 10X Genomics; Chromium Next GEM Single Cell 5’ Kit v2, 16 rxns; PN 1000263 10X Genomics; Automated Library Construction Kit, 24 rxns; PN 1000428 10x Genomics; Chromium GEM-X Single Cell 5' Kit v3, 16 rxns; PN 1000699 10X Genomics; Chromium Next GEM Automated Single Cell 5' Kit v2, 24 rxns; PN 1000290 10X Genomics; Chromium Next GEM Automated Single Cell 5' Kit v2, 4 rxns; PN 1000298 10X Genomics; Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, 16 rxns; PN 1000121 10X Genomics; Chromium Next GEM Single Cell 3' HT Kit v3.1, 48 rxns; PN 1000348 10X Genomics; Chromium Next GEM Single Cell 3' HT Kit v3.1, 8 rxns; PN 1000370 10X Genomics; Chromium Next GEM Single Cell 3' Kit v3.1, 16 rxns; PN 1000268 10X Genomics; Chromium Next GEM Single Cell 3' Kit v3.1, 4 rxns; PN 1000269 10x Genomics; Chromium Next GEM Single Cell 5' HT Kit v2, 48 rxns; PN 1000356 10x Genomics; Chromium Next GEM Single Cell 5' HT Kit v2, 8 rxns; PN 1000374 10X Genomics; Chromium Next GEM Single Cell 5' Kit v2, 16 rxns; PN 1000263 10X Genomics; Chromium Next GEM Single Cell 5' Kit v2, 4 rxns; PN 1000265 10x Genomics; Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit, 16 rxns; PN 1000175 10X Genomics; Chromium Next GEM Single Cell Fixed RNA Hybridization & Library Kit, 4 rxns; PN 1000415 10x Genomics; Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit, 16 rxns; PN 1000414 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 3' GEM, Library & Gel Bead Kit v3, 4 rxns; PN 1000092 10X Genomics; Chromium Single Cell 3' Library & Gel Bead Kit, 4 rxns; PN 120267 10x Genomics; Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, 16 rxns; PN 1000075 10x Genomics; Chromium Single Cell ATAC Library & Gel Bead Kit, 16 rxns; PN 1000110 10x Genomics; Library Construction Kit C, 16 rxns; PN 1000694 10x Genomics; Library Construction Kit C, 4 rxns; PN 1000689 10x Genomics; Library Construction Kit, 16 rxns; PN 1000190 10X Genomics; Visium CytAssist Spatial Gene Expression for FFPE, Human Transcriptome, 11 mm, 2 reactions; PN 1000522 10X Genomics; Visium CytAssist Spatial Gene Expression for FFPE, Human Transcriptome, 6.5mm, 4 reactions; PN 1000520 10x Genomics; Visium CytAssist Spatial Gene Expression for FFPE, Mouse Transcriptome, 6.5mm, 4 rxns; PN 1000521 10X Genomics; Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome, 1 slides, 4 reactions; PN 1000338 10X Genomics; Visium Spatial for FFPE Gene Expression Kit, Mouse Transcriptome, 4 rxns; PN 1000339 10X Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 1 slides, 4 reactions; PN 1000187 10X Genomics; Visium Spatial Gene Expression Slide and Reagent Kit, 4 slides, 16 reactions; PN 1000184 Custom Illumina; TruSeq Stranded mRNA Library Prep (48 samples); PN 20020594 Illumina; TruSeq Stranded mRNA Library Prep (96 samples); PN 20020595 New England BioLabs; NEBNext Ultra II RNA Library Prep Kit for Illumina; PN E7770 Parse Biosciences; Evercode WT Mini v2 Kit, 12 rxns; PN ECW02010 Parse Biosciences; Evercode WT v2 Kit, 48 rxns; PN ECW02030
sample_indexing_kit * The reagent kit used to add index sequences to samples. Indexes enable multiplexing, allowing multiple libraries to be pooled and sequenced together on the same Illumina flow cell. Each indexing kit includes a set of compatible index sequences (often called “indexing sets”) used to uniquely label a specific number of samples, depending on the kit’s design. If the library was prepared using a custom protocol, enter “Custom”. If no indexing was performed, enter “Not applicable”. Example: 10X Genomics; Dual Index Kit TS, Set A; PN 1000251 10x Genomics; Chromium i7 Multiplex Kit N, Set A, 96 rxn; PN 1000084 10x Genomics; Chromium i7 Multiplex Kit, 96 rxns; PN 120262 10X Genomics; Chromium i7 Sample Index Plate (96 rxn); PN 220103 10X Genomics; Dual Index Kit TS, Set A; PN 1000251 10X Genomics; Dual Index Kit TT, Set A (96 rxn); PN 1000215 10X Genomics; Single Index Kit N, Set A (96 rxn); PN 1000212 Custom Illumina; IDT for Illumina - TruSeq RNA UD Indexes v2 (96 Indexes, 96 Samples); PN 20040871 Illumina; TruSeq RNA CD Index Plate (96 Indexes, 96 Samples); PN 20019792 Illumina; TruSeq RNA Single Indexes Set A (12 Indexes, 48 Samples); PN 20020492 Illumina; TruSeq RNA Single Indexes Set B (12 Indexes, 48 Samples); PN 20020493 Integrated DNA Technologies: Custom DNA Oligos NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-AB NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-CD NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-EF NanoString Technologies; GeoMx Seq Code Pack; PN GMX-NGS-SEQ-GH Not applicable Parse Biosciences; Fragmentation Reagents; PN WX100 Parse Biosciences; UDI Plate - WT; PN UDI1001
sample_indexing_set * The specific sequencing barcode index set used, chosen from the sample indexing kit. For example, in the case of 10x, this might be “SI-GA-A1”, whereas for Nextera, it could be “N505 - CTCCTTAC”. Example: SI-GA-A1  
is_technical_replicate * Indicates whether the sequencing reaction was run in replicate. If “Yes,” the corresponding FASTQ files in the dataset should be merged for analysis. Example: Yes Yes No
expected_entity_capture_count * The number of cells, nuclei, or capture spots expected to be captured by the assay. Example: 14336  
sequencing_reagent_kit * The reagent kit used to perform the sequencing run, including the platform, kit name, version, and product number when available. If the reagent kit was prepared using a custom protocol, enter “Custom”. Example: Illumina; NextSeq 500/550 Hi Output Kit 150 Cycles; v2.5; PN 20024907 Custom Element Biosciences; AVITI 2x75 Sequencing Kit Cloudbreak FS High Output (184 Cycles); PN 860-00015 Illumina; HiSeq 3000/4000 PE Cluster Kit PE-410-1001; PN 1000283 Illumina; NextSeq 1000/2000 P2 Reagent v3 Kit (100 Cycles); PN 20046811 Illumina; NextSeq 1000/2000 P2 Reagent v3 Kit (200 Cycles); PN 20046812 Illumina; NextSeq 1000/2000 P2 Reagent v3 Kit (300 Cycles); PN 20046813 Illumina; NextSeq 2000 P3 Reagent Kit (300 Cycles); PN 20040561 Illumina; NextSeq 2000 P3 Reagents Kit (100 Cycles); PN 20040559 Illumina; NextSeq 500/550 Hi Output Kit 150 Cycles; v2.5; PN 20024907 Illumina; NextSeq 500/550 Hi Output Kit 75 Cycles v2.5; PN 20024906 Illumina; NextSeq 500/550 Mid Output Kit 150 Cycles v2.5; PN 20024904 Illumina; NovaSeq 6000 S1 Reagent Kit (200 Cycles); PN 20012864 Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (100 Cycles); PN 20028319 Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (200 Cycles); PN 20028318 Illumina; NovaSeq 6000 S1 Reagent v1.5 Kit (300 Cycles); PN 20028317 Illumina; NovaSeq 6000 S2 Reagent v1.5 Kit (100 Cycles); PN 20028316 Illumina; NovaSeq 6000 S4 Reagent Kit v1.5 (300 cycles); PN 20028312 Illumina; NovaSeq 6000 S4 Reagent v1.5 Kit (200 Cycles); PN 20028313 Illumina; NovaSeq 6000 SP Reagent v1.5 Kit (100 Cycles); PN 20028401 Illumina; NovaSeq 6000 SP Reagent v1.5 Kit (300 Cycles); PN 20028400 Illumina; NovaSeq X Series 1.5B Reagent Kit (100 Cycle); PN 20104703 Illumina; NovaSeq X Series 1.5B Reagent Kit (200 Cycle); PN 20104704 Illumina; NovaSeq X Series 1.5B Reagent Kit (300 Cycle); PN 20104705 Illumina; NovaSeq X Series 10B Reagent Kit (100 Cycle); PN 20085596 Illumina; NovaSeq X Series 10B Reagent Kit (200 Cycle); PN 20085595 Illumina; NovaSeq X Series 10B Reagent Kit (300 Cycle); PN 20085594 Illumina; NovaSeq X Series 25B Reagent Kit (100 Cycle); PN 20125967 Illumina; NovaSeq X Series 25B Reagent Kit (200 Cycle); PN 20125968 Illumina; NovaSeq X Series 25B Reagent Kit (300 Cycle); PN 20104706
sequencing_read_format * The number of sequencing cycles for each read and index in the sequencing run, typically reported as a comma-separated list in the order: Read 1, i7 index, i5 index, and Read 2. Example: 50,8,16,50  
sequencing_batch_id * A lab-assigned identifier for the sequencing run, such as a chip ID, that enables users to determine which samples were processed together. To avoid ID conflicts across institutions, it is recommended to prefix the ID with the name of the sequencing center. Example: Broad_Chip1234  
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
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