MARS_Sequence_Set_Template
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Structured Comment NameItemDefinitionExpected value
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unique_sequence_set_idUnique Sequence Set IDDesignate a unique identifier for each sequence set (that comes from a sample) that will not be duplicated for a separate set. For next gen sequencing sets you might want to use the SRA sample identifier (what you would designate in the barcode file).For example you could use a combination of place/name, date and sequencing method; or some other system that will result in unique identifiers for your samples (e.g. sequence set identifiers assigned by Genbank).
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collection_dateCollection DateThe time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliantdate and time
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study_typeStudy typeEnter the type of study, enter ONLY the terms defined here(marker gene, genome, metagenome, metatransciptome, metaproteome, metabolome)
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target_genetarget geneTargeted gene or locus name for marker gene studiesFor example: 16S rRNA
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target_taxaTarget taxaThis is the same field as the Investigation_Type on the MIMARKS list, though accepts more terms if your study targeted specific groups. List which domains of life (Bacteria, Archaea, Eukarya), or specific taxa (taxonomic subgroup or functional group) your study has targetedCould be a combination of domains (e.g. Archaea and Bacteria) or a subgroup e.g. methanogens, or Flavobacteriaceae
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region_targetedRegion targetedSpecific region of the targeted by the primers - typically this refers to the 16S rRNA, though other molecules could be specified if appropriate.For example: V6, D-Loop
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forward_primerForward primerList the forward primer identifierFor example: BACT27F
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reverse_primerReverse primerList the reverse primer identifierFor example: UNIV1391R
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forward_primer_sequenceForward primer sequenceEnter in 5'-3' format the DNA sequence that encodes the primer
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reverse_primer_sequenceReverse primer sequenceEnter in 5'-3' format the DNA sequence that encodes the primer
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primer_55' Sequence position of the targeted amplicon regionIf there is a known sequence position (e.g. in E. coli 16S rRNA gene), list the base that follows the last base (3' end) of the 5' primer; for example the primer 27F hits E. coli positions 8-27. Note that usage of this context is not consistant in the field of molecular microbial ecology (for example in a number of cases primer BACT27F is the same as BACT8F), but in order to represent the mARS data to the user community accurately, it will help if all users utilize the same position referencing (regardless of how your primers are named).In this example the correct position would be 27
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primer_33' base of primer target in marker geneIf there is a known sequence position (e.g. in E. coli 16S rRNA gene) list the base that follows the last base (3' end) of the 3' primer; for example the primer 1391R hits E. coli positions 1407-1391 (in reverse orientation)In this example the correct position would be 1391
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genbank_contigsNumber of sequences or contigs in Genbank data set or raw reads in short read archiveThis is the number of reads or contigs that you are providing reference to in mARSinteger
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metagenome_sequencing_approachSequencing approach for metagenomeIf your project is NOT an amplicon study and the DNA was sequenced directly, what approach was used to sequence the metagenome?For example: direct shotgun, small or large insert library
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sequencing_technologySequencing technologyEnter the most appropriate technology, or combination fo technologies used in your study.For example: 454 GS20, 454 FLX, 454FLX+, Illumina MiSeq, Illumina HiSeq, Sanger, Ion Torrent PGM, Ion Proton, Pacific BIosciences
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seq_yrYear that sequening was performedEnter the year that your sequencing was perfomed (this will help identify compatibility issues with early technologies)Enter the year, e.g. 2014
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run_typeType of run200 bp, 250 bp paired end, 400 bpEnter the type of run, e.g. 250 bp paired end
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output_filetype_for_next_generation_sequence_dataOutput filetype for next generation sequence dataEnter the file type for your sequence dataFor example: SFF, iseq, qseq, fastaq
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has_next_generation_sequence_output_dataIs the next generation sequence output data file(s) available to link to?YES/NO?
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sequence_data_repositorySequence data repository(s)Where have your data been deposited?For Example: GenBank, SRA, IMG-M, VAMPS, MG-RAST
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url_data_repositoryWebsite where data is deposited (if GenBank, not necessary)Enter the URL lik to your data if other than GenBank
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genbank_accession_numbersGenBank accession number(s), accession number range, or other project identifier(s)List the accession number(s) or range or sequence set identifier in the repository that links to your sequence data setFor example: EF069336-EF069388
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sra_accession_numberSequence Read Archive (SRA) Accession numberTo accomodate for slight differences in the way that investigators report their data records in the Sequence Read Archive, we minimally require that the SRA# or the Bioproject# are entered here IN ADDITION to the SRA run number so that the database can access these data for downstream analyses.For example: SRA067787
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sra_project_numberSRA project number (Bioproject)Enter the SRA project accession numberFor example: PRJNA208431 (for the record above)
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sra_run_numberSRA run numberEach biological sample in your data set should have a unique SRA run number - THIS IS ESSENTIALFor example: SRAR952925
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sra_sample_accession_numbersSRA Sample Accession number(s) (Biosample)Enter the SRA sample ID.For example: SAMN02203916
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number_of_spots_in_sraNumber of spots in your SRA runThis value is in the value in the SRA for your sequence setFor example: 90,795 (for the record above)
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number_of_bases_predictedNumber of bases predictedThis value is in the value in the SRA for your sequence setFor example: 44.4 Mbp (for the record above)
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