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Metadata

Sequencing protocol

Information about the sequencing protocol.

View JSON source: sequencing_protocoldoneShow required fields only

Properties

Local machine namesequencing_protocol.local_machine_namefile_copy (string) Local name for the particular machine used for sequencing. For example "Machine1" or "HSMA-20".
Paired endRequiredsequencing_protocol.paired_endfile_copy (boolean) Whether the sequenced molecule was sequenced from both ends. For example "Should be one of: yes, or no.".
Sequencing protocol>10x-specific (10x) Fields specific for 10x experiments.
Drop uniformitysequencing_protocol.10x.drop_uniformityfile_copy (boolean from 10x) Whether drop uniformity was achieved as a result of visual inspection of emulsion after a 10x run. For example "Should be one of: yes, or no.".
Fastq creation methodsequencing_protocol.10x.fastq_methodfile_copy (string from 10x) Method used for the generation of fastq files from bcl files. For example "Cellranger mkfastq" or "bcl2fastq2".
Fastq creation method versionsequencing_protocol.10x.fastq_method_versionfile_copy (string from 10x) Version of the program used for fastq generation. For example "Cellranger 2.1.1" or "v2.20".
Pooled channelssequencing_protocol.10x.pooled_channelsfile_copy (number from 10x) The number of channels pooled within a sequencing lane. For example "4".
Sequencing protocol>Instrument manufacturer and modelRequired (instrument_ontology) The manufacturer and model of the sequencer.
Instrument ontology IDsequencing_protocol.instrument_manufacturer_model.ontologyfile_copy (string from instrument_ontology) An ontology term identifier in the form prefix:accession. For example "EFO:0008565" or "EFO:0008632".Graph restriction: Subclasses of EFO:0000548 from obo:efo.
Instrument ontology labelsequencing_protocol.instrument_manufacturer_model.ontology_labelfile_copy (string from instrument_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 "Illumina HiSeq 2500" or "ONT MinION".
InstrumentRequiredsequencing_protocol.instrument_manufacturer_model.textfile_copy (string from instrument_ontology) The full name of the instrument used. For example "Illumina HiSeq 2500" or "ONT MinION".
Sequencing protocol>Sequencing methodRequired (sequencing_ontology) The general method for sequencing.
Sequencing approach ontology IDsequencing_protocol.method.ontologyfile_copy (string from sequencing_ontology) An ontology term identifier in the form prefix:accession. For example "EFO:0008440" or "EFO:0008441".Graph restriction: Subclasses of OBI:0000070 from obo:efo.
Sequencing approach ontology labelsequencing_protocol.method.ontology_labelfile_copy (string from sequencing_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 "tag based single cell RNA sequencing" or "full length single cell RNA sequencing".
Sequencing approachRequiredsequencing_protocol.method.textfile_copy (string from sequencing_ontology) The name of a sequencing approach being used. For example "tag based single cell RNA sequencing" or "full length single cell RNA sequencing".
Sequencing protocol>Protocol coreRequired (protocol_core) Core protocol-level information.
Document filenamesequencing_protocol.protocol_core.documentfile_copy (string from protocol_core) A filename of a PDF document containing the details of the protocol. For example "my_cool_protocol.pdf".
Protocol descriptionsequencing_protocol.protocol_core.protocol_descriptionfile_copy (string from protocol_core) A general description of the protocol.
Protocol IDRequiredsequencing_protocol.protocol_core.protocol_idfile_copy (string from protocol_core) A unique ID for the protocol.
Protocol namesequencing_protocol.protocol_core.protocol_namefile_copy (string from protocol_core) A short name for the protocol.
protocols.io DOIsequencing_protocol.protocol_core.protocols_io_doifile_copy (string from protocol_core) The protocols.io digital object identifier (doi) for the protocol. For example "10.17504/protocols.io.mgjc3un".
Publication DOIsequencing_protocol.protocol_core.publication_doifile_copy (string from protocol_core) The publication digital object identifier (doi) for the protocol. For example "10.1101/193219".
Sequencing protocol>provenance (provenance) Provenance information provided by the system.
Accessionsequencing_protocol.provenance.accessionfile_copy (string from provenance) A unique accession for this entity, provided by the broker.
Document IDRequiredsequencing_protocol.provenance.document_idfile_copy (string from provenance) Identifier for document.
Schema major versionsequencing_protocol.provenance.schema_major_versionfile_copy (integer from provenance) The major version number of the schema. For example "4" or "10".
Schema minor versionsequencing_protocol.provenance.schema_minor_versionfile_copy (integer from provenance) The minor version number of the schema. For example "6" or "15".
Submission dateRequiredsequencing_protocol.provenance.submission_datefile_copy (string from provenance) When project was first submitted to database.
Submitter IDsequencing_protocol.provenance.submitter_idfile_copy (string from provenance) ID of individual who first submitted project.
Update datesequencing_protocol.provenance.update_datefile_copy (string from provenance) When project was last updated.
Updater IDsequencing_protocol.provenance.updater_idfile_copy (string from provenance) ID of individual who last updated project.