3-1. Experiment

M: Mandatory field

Experiment Metadata

No	Field	M/O	Description
1	Library ID	M	Short unique identifier for the sequencing library. Each Library ID must be unique in a single BioProject Format: [Sample name]_[Library strategy or source] If there are multiple same sample and strategy/source, write as follows. [Sample name]_[Library strategy or source]_[number]
2	Title	M	A clear and concise auto-generated description to identify the dataset on public pages Format: [Instrument Model] [Library layout] Sequencing of [Sample name]
3	Library strategy	M	This has drop-down menus that allow you to select from a controlled vocabulary. See the Library strategy from for details
4	Library source	M	This has drop-down menus that allow you to select from a controlled vocabulary. See the Library source from for details
5	Library selection	M	This has drop-down menus that allow you to select from a controlled vocabulary. See the Library selection from for details
6	Library layout	M	This has drop-down menus that allow you to select from a controlled vocabulary. See the Library layout from for details
7	Platform	M	This has drop-down menus that allow you to select from a controlled vocabulary. See the Platform & Instrument model from for details
8	Instrument model	M	This has drop-down menus that allow you to select from a controlled vocabulary. See the Platform & Instrument model from for details
9	Library construction protocol	M	Free form description of the methods used to create the sequencing library; a brief ‘materials and methods’ section
10	Release date	M	Data release date

Library strategy

No	Value	Description
1	AMPLICON	Sequencing of overlapping or distinct PCR or RT-PCR products
2	ATAC-seq	Assay for Transposase-Accessible Chromatin (ATAC) strategy is used to study genome-wide chromatin accessibility. Alternative method to DNase-seq that uses an engineered Tn5 transposase to cleave DNA and to integrate primer DNA sequences into the cleaved genomic DNA
3	Bisulfite-Seq	Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status
4	ChIA-PET	Direct sequencing of proximity-ligated chromatin immunoprecipitates
5	ChIP-Seq	Direct sequencing of chromatin immunoprecipitates
6	CLONE	Genomic clone based (hierarchical) sequencing
7	CLONEEND	Clone end (5', 3', or both) sequencing
8	CTS	Concatenated Tag Sequencing
9	DIP-Seq	DNA immunoprecipitation sequencing
10	DNase-Hypersensitivity	Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNase I
11	EST	Single pass sequencing of cDNA templates
12	FAIRE-seq	Formaldehyde Assisted Isolation of Regulatory Elements. reveals regions of open chromatin
13	FINISHING	Sequencing intended to finish (close) gaps in existing coverage
14	FL-cDNA	Full-length sequencing of cDNA templates
15	GBS	Targeted sequencing of specific genomic regions for genotyping
16	Hi-C	Chromosome Conformation Capture technique where a biotin-labeled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing
17	MBD-Seq	Methyl-CpG-Binding Domain Sequencing strategy
18	MeDIP-Seq	Methylated DNA Immunoprecipitation Sequencing strategy
19	miRNA-Seq	Random sequencing of small miRNAs
20	MNase-Seq	Direct sequencing following MNase digestion
21	MRE-Seq	Methylation-Sensitive Restriction Enzyme Sequencing strategy
22	ncRNA-Seq	Capture of other non-coding RNA types, including post-translation modification types such as snRNA (small nuclear RNA) or snoRNA (small nucleolar RNA), or expression regulation types such as siRNA (small interfering RNA) or piRNA/piwi/RNA (piwi-interacting RNA)
23	NOMe-Seq	Simultaneous sequencing of DNA methylation and chromatin accessibility
24	OTHER	Library strategy not listed. Please include additional info in the field 9(Library construction protocol)
25	POOLCLONE	Shotgun of pooled clones (usually BACs and Fosmids)
26	RAD-Seq	A technique to analyze the sequence of the genome cut with restriction enzymes
27	Ribo-Seq	Ribosome footprinting of mRNAs followed by sequencing
28	RIP-Seq	Direct sequencing of RNA immunoprecipitates (includes CLIP-Seq, HITS-CLIP and PAR-CLIP)
29	RNA-Seq	Random sequencing of whole transcriptome
30	SELEX	Systematic Evolution of Ligands by Exponential enrichment
31	ssRNA-seq	strand-specific RNA sequencing
32	Synthetic-Long-Read	A technique for analyzing synthetic long reads made by assembled short sequence reads
33	Targeted-Capture	Random sequencing of targeted regions selected from the genome
34	Tethered Chromatin Conformation Capture	A technique to capture chromosomal structures by immobilizing them on a solid surface rather than a solution
35	Tn-Seq	Sequencing from transposon insertion sites
36	VALIDATION	CGHub special request: Independent experiment to re-evaluate putative variants
37	WCS	Random sequencing of a whole chromosome or other replicon isolated from a genome
38	WGA	Random sequencing of the whole genome following non-PCR amplification
39	WGS	Random sequencing of the whole genome
40	WXS	Random sequencing of exonic regions selected from the genome

Library source

No	Value
1	GENOMIC	Genomic DNA (includes PCR products from genomic DNA)
2	GENOMIC SINGLE CELL	Single cell genomic DNA (includes PCR products from genomic DNA)
3	METAGENOMIC	Mixed material from metagenome
4	METATRANSCRIPTOMIC	Transcription products from community targets
5	SYNTHETIC	Synthetic DNA
6	OTHER	Other, unspecified, or unknown library source material. Please include additional info in the field 9 (Library construction protocol)
7	TRANSCRIPTOMIC	Transcription products or non-genomic DNA (EST, cDNA, RT-PCR, screened libraries)
8	TRANSCRIPTOMIC SINGLE CELL	Single cell transcription products or non-genomic DNA (EST, cDNA, RT-PCR, screened libraries)
9	VIRAL RNA	Viral RNA

Library selection

No	Value
1	5-methylcytidine antibody	Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C)
2	CAGE	Cap-analysis gene expression
3	ChIP	Chromatin immunoprecipitation
4	DNase	Deoxyribonuclease (DNase) digestion
5	HMPR	Hypo-methylated partial restriction digest
6	Hybrid Selection	Selection by hybridization in array or solution
7	Inverse rRNA	Depletion of ribosomal RNA by oligo hybridization
8	MBD2 protein methyl-CpG binding domain	Enrichment by methyl-CpG binding domain
9	MDA	Multiple displacement amplification
10	MF	Methyl Filtrated
11	MNase	Micrococcal Nuclease (MNase) digestion
12	MSLL	Methylation Spanning Linking Library
13	Oligo-dT	Enrichment of messenger RNA (mRNA) by hybridization to Oligo-dT
14	PCR	Source material was selected by designed primers
15	Poly-A	PolyA selection or enrichment for messenger RNA (mRNA); should replace cDNA enumeration
16	RACE	Rapid Amplification of cDNA Ends
17	RANDOM	Random selection by shearing or other method
18	RANDOM PCR	Source material was selected by randomly generated primers
19	RT-PCR	Source material was selected by reverse transcription PCR
20	Reduced Representation	Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling
21	Restriction Digest	DNA fractionation using restriction enzymes
22	cDNA	complementary DNA
23	cDNA_oligo_dT	cDNA to analyze mRNA by binding to poly-A tail
24	cDNA_randomPriming	cDNA made up of random sequences so that it can attach anywhere to RNA
25	other	Other library enrichment, screening, or selection process. Please include additional info in the field 9 (Library construction protocol)
26	padlock probes capture method	Circularized oligonucleotide probes
27	repeat fractionation	Selection for less repetitive (and more gene rich) sequence through Cot filtration (CF) or other fractionation techniques based on DNA kinetics
28	size fractionation	Physical selection of size appropriate targets

Library layout

No	Value
1	single
2	Paired

Platform & Instrument model

No (Platform)	Value (Platform)	Value (Instrument model)
1	ABI_SOLID	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
2	BGISEQ	BGISEQ-50 BGISEQ-500 MGISEQ-2000RS
3	CAPILLARY	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
4	COMPLETE_GENOMICS	Complete Genomics
5	DNBSEQ	DNBSEQ-G400 DNBSEQ-G400 FAST DNBSEQ-G50 DNBSEQ-T7
6	ELEMENT	Element AVITI
7	GENAPSYS	GS111
8	GENEMIND	FASTASeq 300 GenoCare 1600 GenoLab M
9	HELICOS	Helicos HeliScope
10	ILLUMINA	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 iSeq 100 Illumina MiSeq Illumina MiniSeq Illumina NovaSeq 6000 Illumina NovaSeq X Illumina NovaSeq X Plus NextSeq 500 NextSeq 550 NextSeq 1000 NextSeq 2000
11	ION_TORRENT	Ion GeneStudio S5 Ion GeneStudio S5 Plus Ion GeneStudio S5 Prime Ion Torrent PGM Ion Torrent Genexus Ion Torrent Proton Ion Torrent S5 Ion Torrent S5 XL
12	LS454	454 GS 454 GS 20 454 GS FLX 454 GS FLX Titanium 454 GS FLX+ 454 GS Junior
13	OXFORD_NANOPORE	GridION MinION PromethION
14	PACBIO_SMRT	PacBio RS PacBio RS II Revio Sequel Sequel II Sequel IIe Onso
15	TAPESTRI	Tapestri
16	ULTIMA	UG 100
17	VELA_DIAGNOSTICS	Sentosa SQ301
18	unspecified	Please specify