ATACseq

NOTE: Several versions of this metadata schema have been created over time. The (Latest) version contains most attributes, but there may be some deprecated attributes in the older versions for which data has been collected. SenNet is in the process of creating a reference which combines all of these versions into a single view. That reference will be available here once completed.

Version 3 (Latest)
Attribute Type Description Allowable Values Required
analyte_class Allowable Value Analytes are the target molecules being measured with the assay. Chromatin DNA DNA + RNA Endogenous fluorophores Fluorochrome Lipid Metabolite Nucleic acid and protein Peptide Polysaccharide Protein RNA True
acquisition_instrument_vendor Allowable Value An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. Akoya Biosciences Andor BGI Genomics Bruker Cytiva Evident Scientific (Olympus) GE Healthcare Hamamatsu Huron Digital Pathology Illumina In-House Ionpath Keyence Leica Biosystems Leica Microsystems Motic NanoString Resolve Biosciences Sciex Standard BioTools (Fluidigm) Thermo Fisher Scientific Zeiss Microscopy True
acquisition_instrument_model Allowable Value Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. Aperio AT2 Aperio CS2 Axio Observer 3 Axio Observer 5 Axio Observer 7 Axio Scan.Z1 BZ-X710 BZ-X800 BZ-X810 CosMx Spatial Molecular Imager Custom: Multiphoton Digital Spatial Profiler DM6 B DNBSEQ-T7 EVOS M7000 HiSeq 2500 HiSeq 4000 Hyperion Imaging System IN Cell Analyzer 2200 Lightsheet 7 MALDI timsTOF Flex Prototype MIBIscope MoticEasyScan One NanoZoomer 2.0-HT NanoZoomer S210 NanoZoomer S360 NanoZoomer S60 NanoZoomer-SQ NextSeq 2000 NextSeq 500 NextSeq 550 NovaSeq 6000 NovaSeq X NovaSeq X Plus Orbitrap Eclipse Tribrid Orbitrap Fusion Lumos Tribrid Phenocycler-Fusion 1.0 Phenocycler-Fusion 2.0 PhenoImager Fusion Q Exactive Q Exactive HF Q Exactive UHMR QTRAP 5500 Resolve Biosciences Molecular Cartography SCN400 STELLARIS 5 TissueScope LE Slide Scanner Unknown VS200 Slide Scanner Xenium Analyzer Zyla 4.2 sCMOS True
source_storage_duration_value Numeric How long was the source material (parent) stored, prior to this sample being processed.   True
source_storage_duration_unit Allowable Value The time duration unit of measurement hour month day minute year True
time_since_acquisition_instrument_calibration_value Numeric The amount of time since the acqusition instrument was last serviced by the vendor. This provides a metric for assessing drift in data capture.   False
time_since_acquisition_instrument_calibration_unit Allowable Value The time unit of measurement Column-by-column Not applicable Row-by-row Snake-by-columns Snake-by-rows False
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
barcode_read Allowable Value Which read file contains the cell or capture spot barcode. This should be included when constructing sequencing libraries with a non-commercial kit. This field is required if the source material is barcoded. This field is used to determine which analysis pipeline to run. Read 2 (R2) Read 1 (R1) Not applicable True
barcode_size Allowable Value Length of the cell or capture spot barcode in base pairs. Cell and capture spot barcodes are, for example, 3 x 8 bp sequences that are spaced by constant sequences, the offsets. This should be included when constructing sequencing libraries with a non-commercial kit. This field is required if the source material is barcoded. This field is used to determine which analysis pipeline to run. 14 16 40 8,8,8 8,6 Not applicable True
umi_read Allowable Value Which read file contains the UMI barcode. This should be included when constructing sequencing libraries with a non-commercial kit. Read 2 (R2) Read 1 (R1) Not applicable True
umi_size Allowable Value Length of the umi barcode in base pairs. This should be included when constructing sequencing libraries with a non-commercial kit. This field is required if UMI are present. This field is used to determine which analysis pipeline to run. 8 9 10 12 Not applicable True
assay_input_entity Allowable Value This is the entity from which the analyte is being captured. For example, for bulk sequencing this would be “tissue”, while it would be “single cell” for single cell sequencing. This field is used to determine which analysis pipeline to run. area of interest single cell single nucleus spot tissue (bulk) True
number_of_input_cells_or_nuclei Numeric How many cells or nuclei were input to the assay? This is typically not available for preparations working with bulk tissue.   False
library_adapter_sequence Textfield 5’ and/or 3’ read adapter sequences used as part of the library preparation protocol to render the library compatible with the sequencing protocol and instrumentation. This should be provided as comma-separated list of key:value pairs (adapter name:sequence).   True
library_average_fragment_size Numeric Average size of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation. Numeric value in base pairs (bp).   True
library_input_amount_value Numeric The amount of cDNA, after amplification, that was used for library construction.   False
library_input_amount_unit Allowable Value unit of library input amount value ng ul False
library_output_amount_value Numeric Total amount (eg. nanograms) of library after the clean-up step of final pcr amplification step. Answer the question: What is the Qubit measured concentration (ng/ul) times the elution volume (ul) after the final clean-up step?   False
library_output_amount_unit Allowable Value Units of library final yield. ng ul False
library_concentration_value Numeric The concentration value of the pooled library samples submitted for sequencing.   True
library_concentration_unit Allowable Value Unit of library concentration value. ng/ul nM True
library_layout Allowable Value Whether the library was generated for single-end or paired end sequencing paired-end single-end True
number_of_pcr_cycles_for_indexing Numeric Number of PCR cycles performed in order to add adapters and amplify the library. This does not include the cDNA amplification which is captured in the “number of iterations of cDNA amplification” field.   True
library_preparation_kit Allowable Value Reagent kit used for library preparation 10X Genomics; Automated Library Construction Kit 24 rxns; PN 1000428 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' 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 Fixed RNA Hybridization & Library Kit 4 rxns; PN 1000415 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; 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 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) True
sample_indexing_kit Allowable Value Indexes are needed for multiplexing sequencing libraries for simultaneous sequencing (pooling) and proper attachment to the Illumina flowcell. Each indexing kit would have a number of compatible sequences (“sample indexing sets”) that are used to label some number of samples (the number of sets depend on the kit). 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 True
sample_indexing_set Textfield The specific sequencing barcode index set used, selected from the sample indexing kit. Example: For 10X this might be “SI-GA-A1”, for Nextera “N505 - CTCCTTAC”   True
is_technical_replicate Allowable Value Is the sequencing reaction run in replicate, “Yes” or “No”. If “Yes”, FASTQ files in dataset need to be merged. Yes No True
expected_entity_capture_count Numeric Number of cells, nuclei or capture spots expected to be captured by the assay. For Visium this is the total number of spots covered by tissue, within the capture area.   False
sequencing_reagent_kit Allowable Value Reagent kit used for sequencing Custom 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 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 True
sequencing_read_format Textfield Number of sequencing cycles in each round of sequencing (i.e., Read1, i7 index, i5 index, and Read2). This is reported as a comma-delimited list. Example: For 10X snATAC-seq (R1,Index,R2,R3) this might be: 50,8,16,50. For SNARE-seq2 this might be: 75,94,8,75   True
transposition_method Allowable Value Modality of capturing accessible chromatin molecules. For example, this would be the type of kit that was used. bulkATACseq sciATACseq Custom scATACseq True
sequencing_batch_id Textfield The ID for the sequencing run. This could, for example, be the chip ID and should allow users the ability to determine which samples were processed together in a sequencing run. It is recommended that data providers prefix the ID with the center name, to prevent values overlapping across centers.   False
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.   False
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 False
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 False
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 False
preparation_protocol_doi Link 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
is_targeted Allowable Value Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay (“Yes” or “No”). The CODEX analyte is protein. Yes No True
parent_sample_id Textfield Unique SenNet 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
barcode_offset Allowable Value Positions in the read at which the cell or capture spot barcodes start. Cell and capture spot barcodes are, for example, 3 x 8 bp sequences that are spaced by constant sequences (the offsets). First barcode at position 0, then 38, then 76. This should be included when constructing sequencing libraries with a non-commercial kit. 0 8 20 1,27 0,38,76 10,48,86 Not applicable True
umi_offset Allowable Value Position in the read at which the UMI barcode starts. This should be included when constructing sequencing libraries with a non-commercial kit. 0 16 36 Not applicable True
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
SNARE-seq2 / sciATACseq / snATACseq Version 1
Attribute Type Description Allowable Values Required
version Allowable Value Version of the schema to use when validating this metadata. [‘1’] True
description Textfield Free-text description of this assay.   True
source_id Textfield SenNet Display ID of the source of the assayed tissue.   True
tissue_id Textfield SenNet Display ID of the assayed tissue.   True
execution_datetime Datetime Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.   True
protocols_io_doi Textfield DOI for protocols.io referring to the protocol for this assay.   True
operator Textfield Name of the person responsible for executing the assay.   True
operator_email Textfield Email address for the operator.   True
pi Textfield Name of the principal investigator responsible for the data.   True
pi_email Textfield Email address for the principal investigator.   True
assay_category Allowable Value Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. [‘sequence’] True
assay_type Allowable Value The specific type of assay being executed. [‘SNARE-seq2’, ‘sciATACseq’, ‘snATACseq’] True
analyte_class Allowable Value Analytes are the target molecules being measured with the assay. [‘DNA’] True
is_targeted boolean Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.   True
acquisition_instrument_vendor Textfield An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.   True
acquisition_instrument_model Textfield Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.   True
is_technical_replicate boolean If TRUE, fastq files in dataset need to be merged.   True
library_id Textfield A library ID, unique within a TMC, which allows corresponding RNA and chromatin accessibility datasets to be linked.   True
sc_isolation_protocols_io_doi Textfield Link to a protocols document answering the question: How were single cells separated into a single-cell suspension?   True
sc_isolation_entity Allowable Value The type of single cell entity derived from isolation protocol. [‘whole cell’, ‘nucleus’, ‘cell-cell multimer’, ‘spatially encoded cell barcoding’] True
sc_isolation_tissue_dissociation Textfield The method by which tissues are dissociated into single cells in suspension.   True
sc_isolation_enrichment Allowable Value The method by which specific cell populations are sorted or enriched. [‘none’, ‘FACS’] True
sc_isolation_quality_metric Textfield A quality metric by visual inspection prior to cell lysis or defined by known parameters such as wells with several cells or no cells. This can be captured at a high level. “OK” or “not OK”, or with more specificity such as “debris”, “clump”, “low clump”.   True
sc_isolation_cell_number Numeric Total number of cell/nuclei yielded post dissociation and enrichment.   True
transposition_input Numeric Number of cell/nuclei input to the assay.   True
transposition_method Allowable Value Modality of capturing accessible chromatin molecules. [‘SNARE-Seq2-AC’, ‘bulkATACseq’, ‘snATACseq’, ‘sciATACseq’] True
transposition_transposase_source Allowable Value The source of the Tn5 transposase and transposon used for capturing accessible chromatin. [‘10X snATAC’, ‘In-house’, ‘Nextera’, ‘10X multiome’] True
transposition_kit_number Textfield If Tn5 came from a kit, provide the catalog number.   False
library_construction_protocols_io_doi Textfield A link to the protocol document containing the library construction method (including version) that was used, e.g. “Smart-Seq2”, “Drop-Seq”, “10X v3”. DOI for protocols.io referring to the protocol for this assay.   True
library_layout Allowable Value State whether the library was generated for single-end or paired end sequencing. [‘single-end’, ‘paired-end’] True
library_adapter_sequence Textfield Adapter sequence to be used for adapter trimming.   True
cell_barcode_read Textfield Which read file(s) contains the cell barcode. Multiple cell_barcode_read files must be provided as a comma-delimited list (e.g. file1,file2,file3). This field is not required for barcoding by single-cell combinatorial indexing.   False
cell_barcode_offset Textfield Positions in the read at which the cell barcodes start. Cell barcodes are, for example, 3 x 8 bp sequences that are spaced by constant sequences (the offsets). First barcode at position 0, then 38, then 76. (Does not apply to sciATACseq, SNARE-seq and BulkATAC.)   False
cell_barcode_size Textfield Length of the cell barcode in base pairs. Cell barcodes are, for example, 3 x 8 bp sequences that are spaced by constant sequences, the offsets. (Does not apply to sciATACseq, SNARE-seq and BulkATAC.)   False
library_pcr_cycles Numeric Number of PCR cycles to enrich for accessible chromatin fragments.   True
library_pcr_cycles_for_sample_index Numeric Number of PCR cycles performed for library generation (figure in Descriptions section)   True
library_final_yield Numeric Total ng of library after final pcr amplification step.   True
library_final_yield_unit Allowable Value Units for library_final_yield [‘ng’] False
library_average_fragment_size Numeric Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation.   True
sequencing_reagent_kit Textfield Reagent kit used for sequencing   True
sequencing_read_format Textfield Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2.   True
sequencing_read_percent_q30 Numeric Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …)   True
sequencing_phix_percent Numeric Percent PhiX loaded to the run   True
contributors_path Textfield Relative path to file with ORCID IDs for contributors for this dataset.   True
data_path Textfield Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.   True
SNARE-seq2 / sciATACseq / snATACseq Version 0
Attribute Type Description Allowable Values Required
source_id Textfield SenNet Display ID of the source of the assayed tissue.   True
tissue_id Textfield SenNet Display ID of the assayed tissue.   True
execution_datetime Datetime Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.   True
protocols_io_doi Textfield DOI for protocols.io referring to the protocol for this assay.   True
operator Textfield Name of the person responsible for executing the assay.   True
operator_email Textfield Email address for the operator.   True
pi Textfield Name of the principal investigator responsible for the data.   True
pi_email Textfield Email address for the principal investigator.   True
assay_category Allowable Value Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. [‘sequence’] True
assay_type Allowable Value The specific type of assay being executed. [‘scRNAseq-10xGenomics’, ‘snRNAseq-10xGenomics-v2’, ‘snRNAseq-10xGenomics-v3’, ‘scRNAseq’, ‘sciRNAseq’, ‘snRNAseq’, ‘SNARE2-RNAseq’] True
analyte_class Allowable Value Analytes are the target molecules being measured with the assay. [‘RNA’] True
is_targeted boolean Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.   True
acquisition_instrument_vendor Textfield An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.   True
acquisition_instrument_model Textfield Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.   True
sc_isolation_protocols_io_doi Textfield Link to a protocols document answering the question: How were single cells separated into a single-cell suspension?   True
sc_isolation_entity Textfield The type of single cell entity derived from isolation protocol   True
sc_isolation_tissue_dissociation Textfield The method by which tissues are dissociated into single cells in suspension.   True
sc_isolation_enrichment Textfield The method by which specific cell populations are sorted or enriched.   False
sc_isolation_quality_metric Textfield A quality metric by visual inspection prior to cell lysis or defined by known parameters such as wells with several cells or no cells. This can be captured at a high level.   True
sc_isolation_cell_number Numeric Total number of cell/nuclei yielded post dissociation and enrichment   True
rnaseq_assay_input Numeric Number of cell/nuclei input to the assay   True
rnaseq_assay_method Textfield The kit used for the RNA sequencing assay   True
library_construction_protocols_io_doi Textfield A link to the protocol document containing the library construction method (including version) that was used, e.g. “Smart-Seq2”, “Drop-Seq”, “10X v3”.   True
library_layout Allowable Value State whether the library was generated for single-end or paired end sequencing. [‘single-end’, ‘paired-end’] True
library_adapter_sequence Textfield Adapter sequence to be used for adapter trimming   True
library_id Textfield A library ID, unique within a TMC, which allows corresponding RNA and chromatin accessibility datasets to be linked.   True
is_technical_replicate boolean Is the sequencing reaction run in repliucate, TRUE or FALSE   True
cell_barcode_read Textfield Which read file contains the cell barcode   True
cell_barcode_offset Textfield Position(s) in the read at which the cell barcode starts.   True
cell_barcode_size Textfield Length of the cell barcode in base pairs   True
library_pcr_cycles Numeric Number of PCR cycles to amplify cDNA   True
library_pcr_cycles_for_sample_index Numeric Number of PCR cycles performed for library indexing   True
library_final_yield_value Numeric Total number of ng of library after final pcr amplification step. This is the concentration (ng/ul) * volume (ul)   True
library_final_yield_unit Allowable Value Units of final library yield [‘ng’] False
library_average_fragment_size Numeric Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation.   True
sequencing_reagent_kit Textfield Reagent kit used for sequencing   True
sequencing_read_format Textfield Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2.   True
sequencing_read_percent_q30 Numeric Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …)   True
sequencing_phix_percent Numeric Percent PhiX loaded to the run   True
contributors_path Textfield Relative path to file with ORCID IDs for contributors for this dataset.   True
data_path Textfield Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.   True
bulkATACseq Version 1
Attribute Type Description Allowable Values Required
version Allowable Value Version of the schema to use when validating this metadata. [‘1’] True
description Textfield Free-text description of this assay.   True
source_id Textfield SenNet Display ID of the source of the assayed tissue.   True
tissue_id Textfield SenNet Display ID of the assayed tissue.   True
execution_datetime Datetime Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.   True
protocols_io_doi Textfield DOI for protocols.io referring to the protocol for this assay.   True
operator Textfield Name of the person responsible for executing the assay.   True
operator_email Textfield Email address for the operator.   True
pi Textfield Name of the principal investigator responsible for the data.   True
pi_email Textfield Email address for the principal investigator.   True
assay_category Allowable Value Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. [‘sequence’] True
assay_type Allowable Value The specific type of assay being executed. [‘bulkATACseq’] True
analyte_class Allowable Value Analytes are the target molecules being measured with the assay. [‘DNA’] True
is_targeted boolean Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.   True
acquisition_instrument_vendor Textfield An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.   True
acquisition_instrument_model Textfield Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.   True
bulk_transposition_input_number_nuclei Textfield A number (no comma separators)   True
bulk_atac_cell_isolation_protocols_io_doi Textfield Link to a protocols document answering the question: How was tissue stored and processed for cell/nuclei isolation   True
is_technical_replicate boolean Is this a sequencing replicate?   True
library_adapter_sequence Textfield Adapter sequence to be used for adapter trimming   True
library_average_fragment_size Numeric Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation.   True
library_concentration_value Numeric The concentration value of the pooled library samples submitted for sequencing.   True
library_concentration_unit Allowable Value Unit of library_concentration_value [‘nM’] False
library_construction_protocols_io_doi Textfield A link to the protocol document containing the library construction method (including version) that was used, e.g. “Smart-Seq2”, “Drop-Seq”, “10X v3”.   True
library_creation_date Datetime date and time of library creation. YYYY-MM-DD, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s.   False
library_final_yield_value Numeric Total number of ng of library after final pcr amplification step. This is the concentration (ng/ul) * volume (ul)   True
library_final_yield_unit Allowable Value Units of final library yield [‘ng’] False
library_id Textfield A library ID, unique within a TMC, which allows corresponding RNA and chromatin accessibility datasets to be linked.   True
library_layout Allowable Value State whether the library was generated for single-end or paired end sequencing. [‘single-end’, ‘paired-end’] True
library_pcr_cycles Numeric Number of PCR cycles performed in order to add adapters and amplify the library. Usually, this includes 5 pre-amplificationn cycles followed by 0-5 additional cycles determined by qPCR.   True
library_preparation_kit Textfield Reagent kit used for library preparation   True
sample_quality_metric Textfield This is a quality metric by visual inspection. This should answerthe question: Are the nuclei intact and are the nuclei free of significant amountsof debris? This can be captured at a high level, “OK” or “notOK”.   True
sequencing_phix_percent Numeric Percent PhiX loaded to the run   True
sequencing_read_format Textfield Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2.   True
sequencing_read_percent_q30 Numeric Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …)   True
sequencing_reagent_kit Textfield Reagent kit used for sequencing   True
transposition_kit_number Textfield If Tn5 came from a kit, provide the catalog number.   False
transposition_method Textfield Modality of capturing accessible chromatin molecules. The kit used, for example.   True
transposition_transposase_source Textfield The source of the Tn5 transposase and transposon used for capturing accessible chromatin.   True
contributors_path Textfield Relative path to file with ORCID IDs for contributors for this dataset.   True
data_path Textfield Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.   True
bulkATACseq 0
Attribute Type Description Allowable Values Required
version Allowable Value Version of the schema to use when validating this metadata. [‘1’] True
description Textfield Free-text description of this assay.   True
source_id Textfield SenNet Display ID of the source of the assayed tissue.   True
tissue_id Textfield SenNet Display ID of the assayed tissue.   True
execution_datetime Datetime Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.   True
protocols_io_doi Textfield DOI for protocols.io referring to the protocol for this assay.   True
operator Textfield Name of the person responsible for executing the assay.   True
operator_email Textfield Email address for the operator.   True
pi Textfield Name of the principal investigator responsible for the data.   True
pi_email Textfield Email address for the principal investigator.   True
assay_category Allowable Value Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. [‘sequence’] True
assay_type Allowable Value The specific type of assay being executed. [‘bulkATACseq’] True
analyte_class Allowable Value Analytes are the target molecules being measured with the assay. [‘DNA’] True
is_targeted boolean Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.   True
acquisition_instrument_vendor Textfield An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.   True
acquisition_instrument_model Textfield Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.   True
bulk_transposition_input_number_nuclei Textfield A number (no comma separators)   True
bulk_atac_cell_isolation_protocols_io_doi Textfield Link to a protocols document answering the question: How was tissue stored and processed for cell/nuclei isolation   True
is_technical_replicate boolean Is this a sequencing replicate?   True
library_adapter_sequence Textfield Adapter sequence to be used for adapter trimming   True
library_average_fragment_size Numeric Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation.   True
library_concentration_value Numeric The concentration value of the pooled library samples submitted for sequencing.   True
library_concentration_unit Allowable Value Unit of library_concentration_value [‘nM’] False
library_construction_protocols_io_doi Textfield A link to the protocol document containing the library construction method (including version) that was used, e.g. “Smart-Seq2”, “Drop-Seq”, “10X v3”.   True
library_creation_date Datetime date and time of library creation. YYYY-MM-DD, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s.   False
library_final_yield_value Numeric Total number of ng of library after final pcr amplification step. This is the concentration (ng/ul) * volume (ul)   True
library_final_yield_unit Allowable Value Units of final library yield [‘ng’] False
library_id Textfield A library ID, unique within a TMC, which allows corresponding RNA and chromatin accessibility datasets to be linked.   True
library_layout Allowable Value State whether the library was generated for single-end or paired end sequencing. [‘single-end’, ‘paired-end’] True
library_pcr_cycles Numeric Number of PCR cycles performed in order to add adapters and amplify the library. Usually, this includes 5 pre-amplificationn cycles followed by 0-5 additional cycles determined by qPCR.   True
library_preparation_kit Textfield Reagent kit used for library preparation   True
sample_quality_metric Textfield This is a quality metric by visual inspection. This should answerthe question: Are the nuclei intact and are the nuclei free of significant amountsof debris? This can be captured at a high level, “OK” or “notOK”.   True
sequencing_phix_percent Numeric Percent PhiX loaded to the run   True
sequencing_read_format Textfield Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2.   True
sequencing_read_percent_q30 Numeric Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …)   True
sequencing_reagent_kit Textfield Reagent kit used for sequencing   True
transposition_kit_number Textfield If Tn5 came from a kit, provide the catalog number.   False
transposition_method Textfield Modality of capturing accessible chromatin molecules. The kit used, for example.   True
transposition_transposase_source Textfield The source of the Tn5 transposase and transposon used for capturing accessible chromatin.   True
contributors_path Textfield Relative path to file with ORCID IDs for contributors for this dataset.   True
data_path Textfield Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.   True