The minimum sample requirements for EGA
A Study is a container for a sequencing investigation that may comprise multiple experiments. The Study has an overall goal, but is otherwise minimally defined in the SRA. A Study is composed of a descriptor, zero or more experiments, and zero or more analyses. The submitter may decorate the Study with web links and properties.
| Field name | Cardinality | Description | Controlled vocabulary |
|---|---|---|---|
| alias | mandatory | Unique identificator for a study. this is used to link experiments to the study. | |
| title | mandatory | Title of the study as would be used in a publication. | |
| study_type | mandatory | The study_type presents a controlled vocabulary for expressing the overall purpose of the study. | Whole Genome Sequencing, Metagenomics, Transcriptome Analysis, Resequencing, Epigenetics, Synthetic Genomics, Forensic or Paleo-genomics, Gene Regulation Study, Cancer Genomics, Population Genomics, RNASeq, Exome Sequencing, Pooled Clone Sequencing, Transcriptome Sequencing, Other |
| new_study_type | optional | Optional if 'study_type' is not 'other'. to propose a new term, select other and enter a new study type. | |
| study_abstract | optional | Briefly describes the goals, purpose, and scope of the study. this need not be listed if it can be inherited from a referenced publication. |
An experiment object serves as a metadata record encapsulating essential details about a sequencing experiment, including the experimental design, sequencing type, and relevant parameters. This information enhances the interpretation and contextual understanding of nucleotide sequences submitted to the archive.
| Field name | Cardinality | Description | Controlled vocabulary |
|---|---|---|---|
| alias | mandatory | Unique identificator for each experiment. this is used to link runs to experiments. | |
| title | mandatory | Short text that can be used to call out experiment records in searches or in displays. this element is technically optional but should be used for all new records. | |
| study_alias | mandatory | Identifies the parent study. (from study metadata) | |
| sample_alias | mandatory | (from sample metadata) | |
| design_description | mandatory | Goal and setup of the individual library including library was constructed. | |
| library_name | optional | The submitter's name for this library. | |
| library_strategy | mandatory | Sequencing technique intended for this library. | WGS, WGA, WXS, RNA-Seq, ssRNA-seq, snRNA-seq, miRNA-Seq, ncRNA-Seq, FL-cDNA, EST, Hi-C, ATAC-seq, WCS, RAD-Seq, CLONE, POOLCLONE, AMPLICON, CLONEEND, FINISHING, ChIP-Seq, MNase-Seq, DNase-Hypersensitivity, Bisulfite-Seq, CTS, MRE-Seq, MeDIP-Seq, MBD-Seq, Tn-Seq, VALIDATION, FAIRE-seq, SELEX, RIP-Seq, ChIA-PET, Synthetic-Long-Read, Targeted-Capture, Tethered Chromatin Conformation Capture, NOMe-Seq, ChM-Seq, GBS, Ribo-Seq, OTHER |
| library_source | mandatory | The library_source specifies the type of source material that is being sequenced. | GENOMIC, GENOMIC SINGLE CELL, TRANSCRIPTOMIC, TRANSCRIPTOMIC SINGLE CELL, METAGENOMIC, METATRANSCRIPTOMIC, SYNTHETIC, VIRAL RNA, OTHER |
| library_selection | mandatory | Method used to enrich the target in the sequence library preparation | RANDOM, PCR, RANDOM PCR, RT-PCR, HMPR, MF, repeat fractionation, size fractionation, MSLL, cDNA, cDNA_randomPriming, cDNA_oligo_dT, PolyA, Oligo-dT, Inverse rRNA, Inverse rRNA selection, ChIP, ChIP-Seq, MNase, DNase, Hybrid Selection, Reduced Representation, Restriction Digest, 5-methylcytidine antibody, MBD2 protein methyl-CpG binding domain, CAGE, RACE, MDA, padlock probes capture method, other, unspecified |
| library_layout | mandatory | Library_layout specifies whether to expect single, paired, or other configuration of reads. in the case of paired reads, information about the relative distance and orientation is specified. | |
| insert_size | optional | Insert size for paired reads | |
| library_construction_protocol | optional | Free form text describing the protocol by which the sequencing library was constructed. | |
| platform | mandatory | The platform record selects which sequencing platform and platform-specific runtime parameters. this will be determined by the center. optional if 'instrument_model' is provided. | LS454, ILLUMINA, HELICOS, ABI_SOLID, COMPLETE_GENOMICS, BGISEQ, OXFORD_NANOPORE, PACBIO_SMRT, ION_TORRENT, CAPILLARY, DNBSEQ, ELEMENT, AVITI, ULTIMA, VELA_DIAGNOSTICS, GENAPSYS, GENEMIND, TAPESTRI |
| instrument_model | mandatory | Model of the sequencing instrument. | 454 GS, 454 GS 20, 454 GS FLX, 454 GS FLX Titanium, 454 GS FLX+, 454 GS Junior, AB 310 Genetic Analyzer, AB 3130 Genetic Analyzer, AB 3130xL Genetic Analyzer, AB 3500 Genetic Analyzer, AB 3500xL Genetic Analyzer, AB 3730 Genetic Analyzer, AB 3730xL Genetic Analyzer, AB 5500 Genetic Analyzer, AB 5500xl Genetic Analyzer, AB 5500xl-W Genetic Analysis System, AB SOLiD 3 Plus System, AB SOLiD 4 System, AB SOLiD 4hq System, AB SOLiD PI System, AB SOLiD System, AB SOLiD System 2.0, AB SOLiD System 3.0, AVITI 24, BGISEQ-50, BGISEQ-500, Complete Genomics, DNBSEQ-G400, DNBSEQ-G400 FAST, DNBSEQ-G50, DNBSEQ-G800, DNBSEQ-T10x4RS, DNBSEQ-T7, Element AVITI, FASTASeq 300, GENIUS, GS111, Genapsys Sequencer, GenoCare 1600, GenoLab M, GridION, Helicos HeliScope, HiSeq X Five, HiSeq X Ten, Illumina Genome Analyzer, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiScanSQ, Illumina HiSeq 1000, Illumina HiSeq 1500, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 3000, Illumina HiSeq 4000, Illumina HiSeq X, Illumina MiSeq, Illumina MiniSeq, Illumina NovaSeq 6000, Illumina NovaSeq X, Illumina NovaSeq X Plus, Illumina iSeq 100, Ion GeneStudio S5, Ion GeneStudio S5 Plus, Ion GeneStudio S5 Prime, Ion Torrent Genexus, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, Ion Torrent S5 XL, MGISEQ-2000RS, MinION, NextSeq 1000, NextSeq 2000, NextSeq 500, NextSeq 550, Onso, PacBio RS, PacBio RS II, PromethION, Revio, Sentosa SQ301, Sequel, Sequel II, Sequel IIe, Tapestri, UG 100, Vega, unspecified |
A run contains a group of reads generated for a particular experiment.
| Field name | Cardinality | Description | Controlled vocabulary |
|---|---|---|---|
| alias | mandatory | Unique identificator for each run. | |
| experiment_alias | mandatory | From_experiment_metadata | |
| file_name | mandatory | The name or relative pathname of a run data file. | |
| file_format | mandatory | The run data file model. | sra, srf, sff, fastq, fasta, tab, 454_native, 454_native_seq, 454_native_qual, Helicos_native, Illumina_native, Illumina_native_seq, Illumina_native_prb, Illumina_native_int, Illumina_native_qseq, Illumina_native_scarf, SOLiD_native, SOLiD_native_csfasta, SOLiD_native_qual, PacBio_HDF5, bam, cram, CompleteGenomics_native, OxfordNanopore_native |
A Sample defines an isolate of sequenceable material upon which sequencing experiments can be based. The Sample object may be a surrogate for taxonomy accession or an anonymized individual identifier. Or, it may fully specify provenance and isolation method of the starting material.
| Field name | Cardinality | Description | Controlled vocabulary |
|---|---|---|---|
| alias | mandatory | Unique identificator for each sample. | |
| title | mandatory | Short text that can be used to call out sample records in search results or in displays. | |
| taxon_id | mandatory | Ncbi taxonomy identifier. this is appropriate for individual organisms and some environmental samples. | |
| scientific_name | optional | Scientific name of sample that distinguishes its taxonomy. please use a name or synonym that is tracked in the insdc taxonomy database. also, this field can be used to confirm the taxon_id setting. | |
| common_name | optional | Genbank common name of the organism. examples: human, mouse. | |
| sample_description | optional | Free-form text describing the sample, its origin, and its method of isolation. | |
| sex | optional | Sex of the organism from which the sample was obtained | |
| subject_id | recommended | Identifier for the subject where the sample has been derived from | |
| gender | recommended | Sex | female, male, unknown |
| phenotype | mandatory | Where possible, please use the experimental factor ontology (efo) to describe your phenotypes. | |
| disease_site | optional | Affected organ | |
| sample type | optional | Affected organ | blood, bone metastases, cell line, csf, diseased tissue, lymph node metastases, metastatic, normal adjacent from prostate, normal from other tissue, normal prostate from healthy individual, normal tissue, plasma, primary sample, serum, soft tissue metastases, urine |
| donor_id | optional | Identifier of the donor where the sample has been derived from |