Library preparation protocol

End biasRequiredlibrary_preparation_protocol.end_bias (string enum) The type of tag or end bias the library has. Should be one of: "3 prime tag", "3 prime end bias", "5 prime tag", "5 prime end bias" or "full length".

Nominal lengthlibrary_preparation_protocol.nominal_length (integer) Average (insert) size of the fragments being sequenced. For example "250".

Nominal standard deviationlibrary_preparation_protocol.nominal_sdev (integer) Standard deviation of the (insert) size of the fragments being sequenced. For example "30".

Nucleic acid sourceRequiredlibrary_preparation_protocol.nucleic_acid_source (string enum) Source cells or organelles from which nucleic acid molecules were collected. Should be one of: "bulk cell", "single cell", "single nucleus", "bulk nuclei" or "mitochondria".

Primerlibrary_preparation_protocol.primer (string enum) Primer used for cDNA synthesis from RNA. Should be one of: "poly-dT" or "random".

Spike-in dilutionlibrary_preparation_protocol.spike_in_dilution (integer) Dilution of spike-in. For example "100".

StrandRequiredlibrary_preparation_protocol.strand (string enum) Library strandedness. Should be one of: "first", "second", "unstranded" or "not provided".

Library preparation protocol>cDNA library amplification method (library_amplification_ontology object) The method used to amplify cDNA library prior to sequencing.

Library amplification ontology IDlibrary_preparation_protocol.cdna_library_amplification_method.ontology (string from library_amplification_ontology) An ontology term identifier in the form prefix:accession. For example "OBI:0000415" or "EFO:0009013".Graph restriction: Subclasses of EFO:0009107 from obo:efo.

Library amplification ontology labellibrary_preparation_protocol.cdna_library_amplification_method.ontology_label (string from library_amplification_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "PCR" or "in vitro transcription".

Library amplificationRequiredlibrary_preparation_protocol.cdna_library_amplification_method.text (string from library_amplification_ontology) The name of a library amplification approach being used. For example "PCR" or "in vitro transcription".

Library preparation protocol>Cell barcode (barcode object) Information about cell identifier barcodes.

Barcode lengthRequiredlibrary_preparation_protocol.cell_barcode.barcode_length (integer from barcode) Length of barcode in nucleotides. For example "28".

Barcode offsetRequiredlibrary_preparation_protocol.cell_barcode.barcode_offset (integer from barcode) The 0-based offset of start of barcode in read. For example "0".

Barcode-containing readRequiredlibrary_preparation_protocol.cell_barcode.barcode_read (string enum from barcode) The read in which the barcode is found. Should be one of: "Read 1", "Read 2", "Read 3", "Read 4", "i7 Index" or "i5 Index".

White list barcode filelibrary_preparation_protocol.cell_barcode.white_list_file (string from barcode) Name of file containing legitimate barcode sequences. For example "barcode_whitelist_file.txt".

Library preparation protocol>Input nucleic acid moleculeRequired (biological_macromolecule_ontology object) Starting nucleic acid molecule isolated for sequencing.

Biological macromolecule ontology IDlibrary_preparation_protocol.input_nucleic_acid_molecule.ontology (string from biological_macromolecule_ontology) An ontology term identifier in the form prefix:accession. For example "OBI:0000869" or "CHEBI:33699".Graph restriction: Subclasses of EFO:0004446 from obo:efo or obo:chebi or obo:obi.

Biological macromolecule ontology labellibrary_preparation_protocol.input_nucleic_acid_molecule.ontology_label (string from biological_macromolecule_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "polyA RNA" or "messenger RNA".

Biological macromoleculeRequiredlibrary_preparation_protocol.input_nucleic_acid_molecule.text (string from biological_macromolecule_ontology) The name of the biological macromolecule being used. For example "polyA RNA" or "mRNA".

Library preparation protocol>Library construction kit (purchased_reagents object) Name of kit used to construct the sequencing library.

Catalog numberlibrary_preparation_protocol.library_construction_kit.catalog_number (string from purchased_reagents) The catalog number of the kit/reagent. For example "20014279".

Expiry datelibrary_preparation_protocol.library_construction_kit.expiry_date (string from purchased_reagents) The date of expiration for the kit/reagent. For example "2018-01-31" or "2018-01".

Titerlibrary_preparation_protocol.library_construction_kit.kit_titer (string from purchased_reagents) Appropriate titer and volume recommendations found in kit/reagent Certificate of Analysis. For example "3.0x10^7".

Batch/lot numberlibrary_preparation_protocol.library_construction_kit.lot_number (string from purchased_reagents) The batch or lot number of the kit/reagent. For example "10001A".

Manufacturerlibrary_preparation_protocol.library_construction_kit.manufacturer (string from purchased_reagents) The manufacturer of the kit/reagent. For example "Illumina" or "ThermoFisher Scientific".

Retail namelibrary_preparation_protocol.library_construction_kit.retail_name (string from purchased_reagents) The retail name of the kit/reagent. For example "SureCell WTA 3' Library Prep Kit" or "CytoTune iPS 2.0 Sendai Reprogramming Kit".

Library preparation protocol>Library construction methodRequired (library_construction_ontology object) The general method for sequencing library construction.

Library construction ontology IDlibrary_preparation_protocol.library_construction_method.ontology (string from library_construction_ontology) An ontology term identifier in the form prefix:accession. For example "EFO:0009310" or "EFO:0008931".Graph restriction: Subclasses of OBI:0000711 from obo:efo.

Library construction ontology labellibrary_preparation_protocol.library_construction_method.ontology_label (string from library_construction_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "10X v2 sequencing" or "Smart-seq2".

Library constructionRequiredlibrary_preparation_protocol.library_construction_method.text (string from library_construction_ontology) The name of a library construction approach being used. For example "10X v2 sequencing" or "Smart-seq2".

Library preparation protocol>Library pre-amplification method (library_amplification_ontology object) The method used to amplify RNA prior to adaptor ligation.

Library amplification ontology IDlibrary_preparation_protocol.library_preamplification_method.ontology (string from library_amplification_ontology) An ontology term identifier in the form prefix:accession. For example "OBI:0000415" or "EFO:0009013".Graph restriction: Subclasses of EFO:0009107 from obo:efo.

Library amplification ontology labellibrary_preparation_protocol.library_preamplification_method.ontology_label (string from library_amplification_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "PCR" or "in vitro transcription".

Library amplificationRequiredlibrary_preparation_protocol.library_preamplification_method.text (string from library_amplification_ontology) The name of a library amplification approach being used. For example "PCR" or "in vitro transcription".

Library preparation protocol>Nucleic acid conversion kit (purchased_reagents object) Name of kit used to convert RNA to DNA for sequencing.

Catalog numberlibrary_preparation_protocol.nucleic_acid_conversion_kit.catalog_number (string from purchased_reagents) The catalog number of the kit/reagent. For example "20014279".

Expiry datelibrary_preparation_protocol.nucleic_acid_conversion_kit.expiry_date (string from purchased_reagents) The date of expiration for the kit/reagent. For example "2018-01-31" or "2018-01".

Titerlibrary_preparation_protocol.nucleic_acid_conversion_kit.kit_titer (string from purchased_reagents) Appropriate titer and volume recommendations found in kit/reagent Certificate of Analysis. For example "3.0x10^7".

Batch/lot numberlibrary_preparation_protocol.nucleic_acid_conversion_kit.lot_number (string from purchased_reagents) The batch or lot number of the kit/reagent. For example "10001A".

Manufacturerlibrary_preparation_protocol.nucleic_acid_conversion_kit.manufacturer (string from purchased_reagents) The manufacturer of the kit/reagent. For example "Illumina" or "ThermoFisher Scientific".

Retail namelibrary_preparation_protocol.nucleic_acid_conversion_kit.retail_name (string from purchased_reagents) The retail name of the kit/reagent. For example "SureCell WTA 3' Library Prep Kit" or "CytoTune iPS 2.0 Sendai Reprogramming Kit".

Library preparation protocol>Spatial barcode (barcode object) Information about spatial barcodes.

Barcode lengthRequiredlibrary_preparation_protocol.spatial_barcode.barcode_length (integer from barcode) Length of barcode in nucleotides. For example "28".

Barcode offsetRequiredlibrary_preparation_protocol.spatial_barcode.barcode_offset (integer from barcode) The 0-based offset of start of barcode in read. For example "0".

Barcode-containing readRequiredlibrary_preparation_protocol.spatial_barcode.barcode_read (string enum from barcode) The read in which the barcode is found. Should be one of: "Read 1", "Read 2", "Read 3", "Read 4", "i7 Index" or "i5 Index".

White list barcode filelibrary_preparation_protocol.spatial_barcode.white_list_file (string from barcode) Name of file containing legitimate barcode sequences. For example "barcode_whitelist_file.txt".

Library preparation protocol>Spike-in kit (purchased_reagents object) Information about a spike-in kit.

Catalog numberlibrary_preparation_protocol.spike_in_kit.catalog_number (string from purchased_reagents) The catalog number of the kit/reagent. For example "20014279".

Expiry datelibrary_preparation_protocol.spike_in_kit.expiry_date (string from purchased_reagents) The date of expiration for the kit/reagent. For example "2018-01-31" or "2018-01".

Titerlibrary_preparation_protocol.spike_in_kit.kit_titer (string from purchased_reagents) Appropriate titer and volume recommendations found in kit/reagent Certificate of Analysis. For example "3.0x10^7".

Batch/lot numberlibrary_preparation_protocol.spike_in_kit.lot_number (string from purchased_reagents) The batch or lot number of the kit/reagent. For example "10001A".

Manufacturerlibrary_preparation_protocol.spike_in_kit.manufacturer (string from purchased_reagents) The manufacturer of the kit/reagent. For example "Illumina" or "ThermoFisher Scientific".

Retail namelibrary_preparation_protocol.spike_in_kit.retail_name (string from purchased_reagents) The retail name of the kit/reagent. For example "SureCell WTA 3' Library Prep Kit" or "CytoTune iPS 2.0 Sendai Reprogramming Kit".

Library preparation protocol>UMI barcode (barcode object) Information about unique molecular identifier (UMI) barcodes.

Barcode lengthRequiredlibrary_preparation_protocol.umi_barcode.barcode_length (integer from barcode) Length of barcode in nucleotides. For example "28".

Barcode offsetRequiredlibrary_preparation_protocol.umi_barcode.barcode_offset (integer from barcode) The 0-based offset of start of barcode in read. For example "0".

Barcode-containing readRequiredlibrary_preparation_protocol.umi_barcode.barcode_read (string enum from barcode) The read in which the barcode is found. Should be one of: "Read 1", "Read 2", "Read 3", "Read 4", "i7 Index" or "i5 Index".

White list barcode filelibrary_preparation_protocol.umi_barcode.white_list_file (string from barcode) Name of file containing legitimate barcode sequences. For example "barcode_whitelist_file.txt".

Library preparation protocol>Protocol coreRequired (protocol_core object) Core protocol-level information.

Document filenamelibrary_preparation_protocol.protocol_core.document (string from protocol_core) A filename of a PDF document containing the details of the protocol. For example "my_cool_protocol.pdf".

Protocol descriptionlibrary_preparation_protocol.protocol_core.protocol_description (string from protocol_core) A general description of the protocol.

Protocol IDRequiredlibrary_preparation_protocol.protocol_core.protocol_id (string from protocol_core) A unique ID for the protocol.

Protocol namelibrary_preparation_protocol.protocol_core.protocol_name (string from protocol_core) A short name for the protocol.

protocols.io DOIlibrary_preparation_protocol.protocol_core.protocols_io_doi (string from protocol_core) The protocols.io digital object identifier (doi) for the protocol. For example "10.17504/protocols.io.mgjc3un".

Publication DOIlibrary_preparation_protocol.protocol_core.publication_doi (string from protocol_core) The publication digital object identifier (doi) for the protocol. For example "10.1101/193219".

Library preparation protocol>provenance (provenance object) Provenance information provided by the system.

Accessionlibrary_preparation_protocol.provenance.accession (string from provenance) A unique accession for this entity, provided by the broker.

Document IDRequiredlibrary_preparation_protocol.provenance.document_id (string from provenance) Identifier for document.

Schema major versionlibrary_preparation_protocol.provenance.schema_major_version (integer from provenance) The major version number of the schema. For example "4" or "10".

Schema minor versionlibrary_preparation_protocol.provenance.schema_minor_version (integer from provenance) The minor version number of the schema. For example "6" or "15".

Submission dateRequiredlibrary_preparation_protocol.provenance.submission_date (string from provenance) When project was first submitted to database.

Submitter IDlibrary_preparation_protocol.provenance.submitter_id (string from provenance) ID of individual who first submitted project.

Update datelibrary_preparation_protocol.provenance.update_date (string from provenance) When project was last updated.

Updater IDlibrary_preparation_protocol.provenance.updater_id (string from provenance) ID of individual who last updated project.