prep_data sheets
Contextual data about how the samples were prepared for sequencing. Includes how they were extracted, what molecular protocols were used, how they were sequenced. Two prep_data sheets are provided: one for amplicon preps (amplicon_prep_data) and one for metagenomic preps (metag_prep_data). All of terms in the metag_prep_data sheet are also in the amplicon_prep_data sheet. The 1st section of these sheets is in the format for an NCBI SRA upload and should NOT be rearranged or renamed. Each row is a separate sequencing library preparation, distinguished by a unique library_id. One sample from sample_prep could be represented multiple times on these sheets if multiple marker genes were amplified or multiple replicate sequencing libraries were prepared.
Terms
| Term | Definition | Required By |
|---|---|---|
| sample_name | Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. Suggested format: PROJECT_REGION_STATION_DEPTH_REPLICATE | NCBI+OBIS |
| title | Short description that will identify the dataset on public pages. A clear and concise formula for the title would be like: {methodology} of {organism}: {sample info} | NCBI+OBIS |
| biosample_accession | BioSample accession from NCBI, provided after creating a biosample on NCBI, such as during the SRA submission process | Recommended |
| samp_vol_we_dna_ext | Volume (ml) or mass (g) of total collected sample processed for DNA extraction | Recommended |
| samp_mat_process | Any processing applied to the sample during or after retrieving the sample from environment. | Recommended |
| size_frac | Filtering pore size used in sample preparation | Optional |
| library_id | Short unique identifier for the sequencing library. Each library_ID must be unique! | NCBI |
| library_strategy | NCBI | |
| library_source | NCBI | |
| library_selection | NCBI | |
| lib_layout | Specify whether to expect single, paired, or other configuration of reads | NCBI |
| platform | NCBI | |
| instrument_model | NCBI | |
| design_description | Free-form description of the methods used to create the sequencing library; a brief 'materials and methods' section. | NCBI |
| drive_location | Internal storage location of sequencing files | Recommended |
| sra_accession | Provide the NCBI SRA accession once generated by NCBI. | Recommended |
| date_dna_extracted | Add date that DNA was extracted. Used for internal data management. | Internal |
| extraction_personnel | Add names of personnel who did extraction, separated by a space | | Internal |
| date_pcr | Add date that PCR was run. Used for internal data management. | Internal |
| pcr_personnel | Add names of personnel who did extraction, separated by a space | | Internal |
| seq_facility | Name of facility that did the sequencing | Recommended |
| seq_meth | Sequencer and read length | Recommended |
| nucl_acid_ext | A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample | Recommended |
| target_gene | Targeted gene or marker name for marker-based studies | Recommended |
| target_subfragment | Name of subfragment of a gene or markerImportant to e.g. identify special regions on marker genes like the hypervariable V6 region of the 16S rRNA gene | Recommended |
| pcr_primer_forward | Forward PCR primer that was used to amplify the sequence of the targeted gene, locus or subfragment. | Recommended |
| pcr_primer_reverse | Reverse PCR primer that was used to amplify the sequence of the targeted gene, locus or subfragment. | Recommended |
| pcr_primer_name_forward | Name of the forward PCR primer | Recommended |
| pcr_primer_name_reverse | Name of the reverse PCR primer | Recommended |
| pcr_primer_reference | Reference for the primers | Recommended |
| pcr_cond | Description of reaction conditions and components of PCR in the form of ´initial denaturation:94degC_1.5min; annealing=...´ Examples: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 | Recommended |
| nucl_acid_amp | A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids | Optional |
| adapters | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters | Recommended |
| mid_barcode | Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters. MIXS term: mid | Optional |