A searchable and exportable tab-separated table of the following metadata is now available.
🔹 italics = potential considerations
| metadata | definition | examples | source |
|---|---|---|---|
| sample_name | Identifier of the sample | e.g. ISDsoil1 | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”) |
| seq_meth | Sequencing method used | e.g. 454 Genome Sequencer FLX [OBI:0000702] | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”), ENA Metadata Validation: Instrument (“ENA Metadata Validation: Instrument”) |
| lib_layout | Specify whether to expect single, paired, or other configuration of reads | e.g. single-end, paired end or others | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”) |
| lib_source | The lib_source specifies the type of source material that is being sequenced | e.g. genomic, metagenomic, transcriptomic, etc. | ENA Metadata Validation: Source (“ENA Metadata Validation: Source”) |
| lib_strategy | Sequencing technique intended for this library | e.g. WGS, Amplicon, etc. | ENA Metadata Validation: Strategy (“ENA Metadata Validation: Strategy”) |
| lib_selection | Whether any method was used to select and/or enrich the material being sequenced | e.g. Random, PCR, etc. | ENA Metadata Validation: Selection (“ENA Metadata Validation: Selection”) |
| nucl_acid_ext | Literature reference or SOP describing nucleic extraction | e.g. CTAB extraction, Phenol-Cloroform Extraction | The FAIR Cookbook (Rocca-Serra et al. 2022) |
| nucl_acid_ext_treat | Treatment of nucleic acid after extraction | e.g. DNase, RNase | Adapted from The FAIR Cookbook (Rocca-Serra et al. 2022) |
| 🔹 insert_length | for inner dist. calc. (or incl. in lib_layout?)(Array Express parameter: insert “Nominal Length” | ||
| sequence_count | Number of reads in the library (sequencing depth) or ‘spots’ | e.g. 32,283,453 | Adapted from NCBI-SRA (Leinonen et al. 2011) |
| basepairs_count | Number of base pairs (nucleotides) in the library or ‘bases’ | e.g. 6,400,000,000 | Adapted from NCBI-SRA (Leinonen et al. 2011) |
| average_length | As basepairs_count divided by sequence_count | e.g. 198 | Calculated as basepairs_count/sequence_count |
| sequence_count_qual | Number of reads in the library (sequencing depth) after quality filtering | SRA-Tinder (NCBI Hackathons) | |
| basepairs_count_qual | Number of base pairs (nucleotides) in the library after quality filtering | SRA-Tinder (NCBI Hackathons) | |
| rRNA treatment | Depletion (Pre-seq, molecular), Removal (Post-seq data), None | Advances and Challenges in Metatranscriptomic Analysis (Shakya et al. 2019) | |
| cDNA_ampl_meth | Technique used to amplify a cDNA library | e.g. MMLV, AMV | The FAIR Cookbook (Rocca-Serra et al. 2022) |
| cDNA_oligo | Type of primer used for cDNA synthesis from RNA | e.g. polyA or random | The FAIR Cookbook (Rocca-Serra et al. 2022) |
| checksum | Hash value for data integrity | e.g. MD5: cbc41d0e49636872a765b950cb7f410a | Data transfer and data integrity |
| Comments/questions: |
|---|
| Added cDNA_ampl_meth and cDNA_oligo to the table -MB 11AUG23 |
| metadata | definition | examples | source |
|---|---|---|---|
| run_ref | Accessions/identifiers linking to the raw data (FASTQ) | e.g. accession = “ERR178314” | ENA Submitting Transcriptome Assemblies (“ENA Submitting Transcriptome Assemblies”) |
| Locus | Physical location of a gene on a chromosome | e.g. “GAAA01000000 93507 rc mRNA”, “11q1.4-q2.1” | Adapted from ENA Submitting Transcriptome Assemblies (“ENA Submitting Transcriptome Assemblies”) |
| Description | Sample description | e.g. TSA: Latimeria chalumnae voucher 08118, transcriptome shotgun assembly | Adapted from ENA Submitting Transcriptome Assemblies (“ENA Submitting Transcriptome Assemblies”) |
| DB Link | BioProject/Biosample/SRA | e.g. PRJNA1035062 | Adapted from ENA Submitting Transcriptome Assemblies (“ENA Submitting Transcriptome Assemblies”) |
| Reference | Author/Consortium/Title/Journal | Adapted from ENA Submitting Transcriptome Assemblies (“ENA Submitting Transcriptome Assemblies”) | |
| Seq length | Number of nucleotides in a transcript. Sequences should be greater than 200 bp in length. | Adapted from ENA Submitting Transcriptome Assemblies (“ENA Submitting Transcriptome Assemblies”) | |
| Seq quality | The accuracy and reliability of the nucleotide sequence information obtained from RNA sequencing | Adapted from ENA Submitting Transcriptome Assemblies (“ENA Submitting Transcriptome Assemblies”) | |
| Protocols | Links to protocol accessions |
| Comments/questions: |
|---|
| Don’t know which protocol accessions were meant here, was it SOP, and protocol for what, so I left it empty for the time being -MB 11AUG23 |
The publications describing the reasons for formation of The minimum information about a genome sequence (MIGS) (Field et al. 2008), Advances and Challenges in Metatranscriptomic Analysis (Shakya et al. 2019) can be found online. We also highly encourage the readers of this GitHub to read The FAIR cookbook recipes (Rocca-Serra et al. 2022), and look for examples of submitted Transcriptomic samples in Transcriptome Shotgun Assembly Sequence Database (“Transcriptome Shotgun Assembly Sequence Database”).
“ENA Metadata Validation: Instrument.” https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#instrument.
“ENA Metadata Validation: Selection.” https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#selection.
“ENA Metadata Validation: Source.” https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#source.
“ENA Metadata Validation: Strategy.” https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#strategy.
“ENA Submitting Transcriptome Assemblies.” https://ena-docs.readthedocs.io/en/latest/submit/assembly/transcriptome.html.
Field, D., G. Garrity, T. Gray, N. Morrison, J. Selengut, P. Sterk, T. Tatusova, et al. 2008. “The Minimum Information about a Genome Sequence (MIGS) Specification.” Nature Biotechnology. 2008. https://doi.org/10.1038/nbt1360.
“GSC MIXS: MIGSBacteria.” https://genomicsstandardsconsortium.github.io/mixs/MIGSBacteria/.
Leinonen, R., H. Sugawara, M. Shumway, and International Nucleotide Sequence Database Collaboration. 2011. “The Sequence Read Archive.” Nucleic Acids Research 39 (Database issue): D19–21. https://doi.org/10.1093/nar/gkq1019.
NCBI Hackathons. “SRA-Tinder: A Tool to Discover Related Sequence Read Archive (SRA) Experiments.” https://github.com/NCBI-Hackathons/SRA_Tinder.
Rocca-Serra, Philippe, Alasdair J G Gray, Alejandra Delfin Rossaro, Andrea Splendiani, Andrea Zaliani, Andreas Pippow, Anne Cambon-Thomsen, et al. 2022. “The FAIR Cookbook.” https://github.com/FAIRplus/the-fair-cookbook/.
Shakya, Migun, Christopher Quince, James H Campbell, and Zamin K Yang. 2019. “Advances and Challenges in Metatranscriptomic Analysis.” Frontiers in Genetics 10 (September): 904. https://doi.org/10.3389/fgene.2019.00904.
“Transcriptome Shotgun Assembly Sequence Database.” https://www.ncbi.nlm.nih.gov/genbank/tsa/.