Sequencing Level 1

Attribute: NGS Sequencing Platform

Valid Value	Description	Ontology
454 GS	The Roche/454 GS (Genome Sequencer) is a high-throughput pyrosequencing instrument developed by 454 Life Sciences, one of the first commercially available next-generation DNA sequencing platforms.	EFO:0004431
454 GS 20	The 454 GS 20 is a high-throughput pyrosequencing instrument developed by 454 Life Sciences, the first commercially released model in the GS sequencer line.	EFO:0004206
454 GS FLX	The 454 GS FLX is a next-generation pyrosequencing instrument developed by 454 Life Sciences (later Roche) that uses emulsion PCR-amplified beads and sequencing-by-synthesis with bioluminescent detection.	EFO:0004432
454 GS FLX Titanium	The 454 GS FLX Titanium sequencer is a GS high-throughput sequencing machine developed by 454 Life Sciences, an upgraded version of the GS FLX offering increased read length and throughput.	EFO:0004433
454 GS FLX+	The 454 GS FLX+ is an upgraded version of the 454 GS FLX Titanium pyrosequencing instrument from 454 Life Sciences (Roche), offering extended read lengths of up to approximately 1,000 bp.	GENEPIO:0100968
454 GS Junior	The 454 GS Junior is a benchtop high-throughput pyrosequencing machine developed by 454 Life Sciences, a smaller-scale version of the GS FLX system.	EFO:0004434
AB 310 Genetic Analyzer	An Applied Biosystems sequencing instrument that uses a single-capillary electrophoresis system to perform automated Sanger sequencing and fragment analysis.	GENEPIO:0100975
AB 3130 Genetic Analyzer	An Applied Biosystems sequencing instrument that performs capillary electrophoresis-based Sanger sequencing using 4 capillaries; successor to the AB PRISM 310.	GENEPIO:0100976
AB 3130xL Genetic Analyzer	An Applied Biosystems sequencing instrument that performs capillary electrophoresis-based Sanger sequencing using 16 capillaries; successor to the AB PRISM 310.	GENEPIO:0100977
AB 3500 Genetic Analyzer	An Applied Biosystems sequencing instrument that performs capillary electrophoresis-based Sanger sequencing using 8 capillaries and can run 96-well plates; successor to the 3130 series.	GENEPIO:0100978
AB 3500xL Genetic Analyzer	An Applied Biosystems sequencing instrument that performs capillary electrophoresis-based Sanger sequencing using 24 capillaries and can run 384-well plates; successor to the 3130 series.	GENEPIO:0100979
AB 3730 Genetic Analyzer	An Applied Biosystems sequencing instrument that uses a 48-capillary array electrophoresis system for Sanger sequencing; successor to the 3500 series.	GENEPIO:0100980
AB 3730xL Genetic Analyzer	An Applied Biosystems sequencing instrument that uses a 96-capillary array electrophoresis system for Sanger sequencing; successor to the 3500 series.	GENEPIO:0100981
AB 5500 Genetic Analyzer	A proprietary next-generation DNA sequencing system from Applied Biosystems that utilizes DNA ligase. DNA fragments attached to beads are clonally amplified and ligated to fluorescently labeled "interrogation probes". Ligation frees the fluor, which is detected and identifies the specific probe. The marker of the attached probe is then removed and a 5'-phosphate group is regenerated. Multiple cycles of ligation, detection, and cleavage are performed.	EFO:0004440
AB 5500x-Wl Genetic Analyzer	A proprietary next-generation DNA sequencing system from Applied Biosystems that utilizes DNA ligase. DNA fragments attached to beads are clonally amplified and ligated to fluorescently labeled "interrogation probes". Ligation frees the fluor, which is detected and identifies the specific probe. The marker of the attached probe is then removed and a 5'-phosphate group is regenerated. Multiple cycles of ligation, detection, and cleavage are performed.	GENEPIO:0100970
AB 5500xl Genetic Analyzer	A proprietary next-generation DNA sequencing system from Applied Biosystems that utilizes DNA ligase. DNA fragments attached to beads are clonally amplified and ligated to fluorescently labeled "interrogation probes". Ligation frees the fluor, which is detected and identifies the specific probe. The marker of the attached probe is then removed and a 5'-phosphate group is regenerated. Multiple cycles of ligation, detection, and cleavage are performed.	EFO:0004436
AB SOLiD 2	A proprietary next-generation DNA sequencing system from Applied Biosystems (the second-generation SOLiD platform) that utilizes DNA ligase-based sequencing-by-ligation chemistry on clonally amplified, bead-attached DNA fragments.	EFO:0004442
AB SOLiD 3	A proprietary next-generation DNA sequencing system from Applied Biosystems (the third-generation SOLiD platform) that utilizes DNA ligase-based sequencing-by-ligation chemistry on clonally amplified, bead-attached DNA fragments.	EFO:0004439
AB SOLiD 3 Plus System	A proprietary next-generation DNA sequencing system from Applied Biosystems that utilizes DNA ligase. DNA fragments attached to beads are clonally amplified and ligated to fluorescently labeled "interrogation probes". Ligation frees the fluor, which is detected and identifies the specific probe. The marker of the attached probe is then removed and a 5'-phosphate group is regenerated. Multiple cycles of ligation, detection, and cleavage are performed.	Not available
AB SOLiD 4	A proprietary next-generation DNA sequencing system from Applied Biosystems (the fourth-generation SOLiD platform) that utilizes DNA ligase-based sequencing-by-ligation chemistry on clonally amplified, bead-attached DNA fragments.	EFO:0004438
AB SOLiD 4hq System	A proprietary next-generation DNA sequencing system from Applied Biosystems that utilizes DNA ligase. DNA fragments attached to beads are clonally amplified and ligated to fluorescently labeled "interrogation probes". Ligation frees the fluor, which is detected and identifies the specific probe. The marker of the attached probe is then removed and a 5'-phosphate group is regenerated. Multiple cycles of ligation, detection, and cleavage are performed.	EFO:0004441
AB SOLiD PI System	A proprietary next-generation DNA sequencing system from Applied Biosystems that utilizes DNA ligase. DNA fragments attached to beads are clonally amplified and ligated to fluorescently labeled "interrogation probes". Ligation frees the fluor, which is detected and identifies the specific probe. The marker of the attached probe is then removed and a 5'-phosphate group is regenerated. Multiple cycles of ligation, detection, and cleavage are performed.	EFO:0004437
AB SOLiD System	A proprietary next-generation DNA sequencing system from Applied Biosystems that utilizes DNA ligase. DNA fragments attached to beads are clonally amplified and ligated to fluorescently labeled "interrogation probes". Ligation frees the fluor, which is detected and identifies the specific probe. The marker of the attached probe is then removed and a 5'-phosphate group is regenerated. Multiple cycles of ligation, detection, and cleavage are performed.	OBI:0000696
BGISEQ-500	The BGISEQ-500 is a model type of the BGISEQ sequencing library platform.	GENEPIO:0100145
Complete Genomics	A life sciences subsidiary of a Chinese biotechnology company that has developed and commercialized a DNA sequencing platform for human genome sequencing and analysis.	NCIT:C215818
DNBSEQ-G400	The DNBSEQ-G400 is a model type of the BGISEQ sequencing library platform.	GENEPIO:0100148
DNBSEQ-G50	The DNBSEQ-G50 is a model type of the BGISEQ sequencing library platform.	GENEPIO:0100150
DNBSEQ-T7	The DNBSEQ-T7 is a model type of the BGISEQ sequencing library platform.	GENEPIO:0100147
Affymetrix SNP 6.0	A high-density microarray platform manufactured by Affymetrix for genome-wide detection of single nucleotide polymorphisms and copy number variation.	NCIT:C202277
GeneChip U133 Plus 2.0	A gene expression microarray manufactured by Affymetrix covering over 47000 transcripts on the human genome.	NCIT:C206467
GeneChip U133A	A gene expression microarray manufactured by Affymetrix covering a subset of well-characterized human genes.	NCIT:C206468
GridION	A DNA sequencer manufactured by Oxford Nanopore Technologies that can run and analyze up to five individual flow cells, producing up to 150 Gb of data per run, using real-time nanopore sequencing.	GENEPIO:0100141
Helicos HeliScope	The HeliScope is a DNA sequencer manufactured by Helicos BioSciences that performs single-molecule sequencing of unamplified DNA templates using reversible-terminator chemistry.	OBI:0000717
Illumina Human Methylation 27	A DNA methylation microarray manufactured by Illumina interrogating approximately 27000 CpG sites across the human genome.	Not available
Illumina Human Methylation 450	A DNA methylation microarray manufactured by Illumina interrogating approximately 450000 CpG sites across the human genome.	Not available
Illumina Genome Analyzer	A DNA sequencer manufactured by Solexa (later acquired by Illumina) as one of its first sequencer lines, launched in 2006, capable of sequencing 1 gigabase (Gb) of data in a single run.	GENEPIO:0100106
Illumina Genome Analyzer II	A DNA sequencer developed by Illumina; an upgraded version of the original Genome Analyzer supporting single- or paired-end sequencing by synthesis.	EFO:0004201
Illumina Genome Analyzer IIx	An upgraded Illumina Genome Analyzer II model that supports sequencing of single, long, or short-insert paired-end clone libraries using sequencing-by-synthesis technology; one of the most widely adopted early next-generation sequencing platforms.	OBI:0002000
Illumina HiScanSQ	A DNA sequencer manufactured by Illumina using sequencing-by-synthesis chemistry, containing a HiScan Reader for sequencing and microarray-based analyses as well as an SQ Module supporting microfluidics.	GENEPIO:0100109
Illumina HiSeq 1000	The Illumina HiSeq 1000 is a sequencing machine developed by Illumina with a single flow cell and a throughput of up to 35 Gb per day.	EFO:0004204
Illumina HiSeq 1500	The Illumina HiSeq 1500 is a sequencing machine developed by Illumina, with a single flow cell and dual surface imaging offering high-output and rapid-run modes.	EFO:0011027
Illumina HiSeq 2000	The Illumina HiSeq 2000 is a sequencing machine developed by Illumina with two flow cells and a throughput of up to 55 Gb per day, optimized for multi-sample sequencing.	EFO:0004203
Illumina HiSeq 2500	The Illumina HiSeq 2500 is a sequencing machine developed by Illumina with two flow cells and a throughput of up to 160 Gb per day, supporting both high-output batch runs and rapid-run modes.	EFO:0008565
Illumina HiSeq 3000	The Illumina HiSeq 3000 is a high-throughput sequencing machine developed by Illumina with a single flow cell and a throughput of more than 200 Gb per day.	EFO:0008564
Illumina HiSeq 4000	The Illumina HiSeq 4000 is a high-throughput sequencing machine developed by Illumina with two flow cells and a throughput of more than 400 Gb per day.	EFO:0008563
Illumina HiSeq X Five	A DNA sequencer manufactured by Illumina using sequencing-by-synthesis chemistry, consisting of a set of five HiSeq X ultra-high-throughput sequencing systems configured for population-scale whole-genome sequencing.	GENEPIO:0100112
Illumina HiSeq X Ten	A DNA sequencer manufactured by Illumina consisting of a set of ten HiSeq X ultra-high-throughput sequencing systems configured for population-scale whole-genome sequencing.	GENEPIO:0100113
Illumina iSeq 100	The Illumina iSeq 100 is a model type of the Illumina sequencing library platform.	GENEPIO:0100121
Illumina Methylation Epic	A DNA methylation microarray (BeadChip) manufactured by Illumina interrogating over 850000 methylation sites across the genome.	OBI:0002131
Illumina Methylation Epic v2	The second-generation version of the Illumina Infinium MethylationEPIC BeadChip, interrogating over 900000 methylation sites across the genome.	OBI:0003650
Illumina MiniSeq	A benchtop DNA sequencer manufactured by Illumina using sequencing-by-synthesis chemistry, with an output capacity of approximately 1.65-7.5 Gb per run.	GENEPIO:0100124
Illumina MiSeq	The Illumina MiSeq is a high-throughput sequencing machine developed by Illumina; primary applications include small whole-genome sequencing, targeted gene sequencing, and 16S metagenomic sequencing.	EFO:0004205
Illumina NextSeq	A benchtop DNA sequencer manufactured by Illumina using sequencing-by-synthesis chemistry; the NextSeq series succeeded the HiSeq/MiSeq lines with high throughput in a compact benchtop format.	GENEPIO:0100126
Illumina NextSeq 1000	The Illumina NextSeq 1000 is a benchtop high-throughput sequencing machine developed by Illumina using XLEAP-SBS chemistry.	EFO:0010962
Illumina NextSeq 2000	The Illumina NextSeq 2000 is a benchtop high-throughput sequencing machine developed by Illumina using XLEAP-SBS chemistry with onboard data analysis.	EFO:0010963
Illumina NextSeq 2500	This name does not correspond to a standard commercially released Illumina platform; it appears to conflate the Illumina NextSeq (500/550) benchtop sequencer series with the HiSeq 2500. If used, it should be treated as an Illumina sequencing-by-synthesis benchtop instrument similar to the NextSeq 500/550.	Not available
Illumina NextSeq 500	The Illumina NextSeq 500 is a benchtop high-throughput sequencing machine developed by Illumina using sequencing-by-synthesis chemistry.	EFO:0009173
Illumina NextSeq 550	The Illumina NextSeq 550 is a benchtop high-throughput sequencing machine developed by Illumina; primary applications include exome sequencing, targeted gene sequencing, whole-transcriptome sequencing, and cytogenomic arrays.	EFO:0008566
Illumina NovaSeq	A DNA sequencer manufactured by Illumina using sequencing-by-synthesis chemistry with an output capacity of up to 6 Tb and 20 billion reads in dual flow-cell mode.	GENEPIO:0100122
Illumina NovaSeq 6000	The Illumina NovaSeq 6000 is a high-throughput sequencing machine developed by Illumina, with two flow cells and an output of up to 6000 Gb using patterned flow-cell sequencing-by-synthesis technology.	EFO:0008637
Illumina NovaSeq S4	The S4 flow-cell configuration of the Illumina NovaSeq 6000, offering the platform's highest throughput mode.	EFO:0008637
Illumina NovaSeq X Plus	The Illumina NovaSeq X Plus is a high-throughput sequencing machine developed by Illumina with a dual flow-cell configuration and an output of up to 16 Tb per run using XLEAP-SBS chemistry.	EFO:0022841
Ion Torrent PGM	A DNA sequencer manufactured by Ion Torrent (Thermo Fisher) that utilizes ion semiconductor sequencing and has an output capacity of 300 Mb to 1 Gb.	GENEPIO:0100136
Ion Torrent Proton	A DNA sequencer manufactured by Ion Torrent (Thermo Fisher) that utilizes ion semiconductor sequencing and has an output capacity of up to 15 Gb.	GENEPIO:0100137
Ion Torrent S5	A DNA sequencer manufactured by Ion Torrent (Thermo Fisher) that utilizes ion semiconductor sequencing and requires only a small amount of input material.	GENEPIO:0100139
Ion Torrent S5 XL	A DNA sequencer manufactured by Ion Torrent (Thermo Fisher) that utilizes ion semiconductor sequencing, requiring only a small amount of input material while producing data faster than the standard S5 model.	GENEPIO:0100138
MGISEQ-2000RS	The MGISEQ-2000RS is a model type of the BGISEQ sequencing library platform.	EFO:0700018
MinION	A portable DNA sequencer manufactured by Oxford Nanopore Technologies that uses consumable flow cells producing up to 30 Gb of sequence data per flow cell, generating real-time results via nanopore sequencing.	GENEPIO:0100142
Not Reported	Not provided or available.	NCIT:C43234
Other	A value indicating that the sequencing platform used is not among the listed controlled vocabulary options.	NCIT:C17649
PacBio RS	A DNA sequencer manufactured by Pacific Biosciences that utilizes SMRT (single-molecule real-time) cells for sequencing; the first commercial model produced by the company.	GENEPIO:0100131
PacBio RS II	The PacBio RS II is a high-throughput sequencing machine developed by Pacific Biosciences; primary applications are whole-genome sequencing of smaller organisms and targeted sequencing of DNA and RNA.	EFO:0008631
PacBio Sequel	The PacBio Sequel is a model type of the PacBio SMRT sequencing library platform.	GENEPIO:0100133
PacBio Sequel II	The PacBio Sequel II is a model type of the PacBio SMRT sequencing library platform.	GENEPIO:0100134
PromethION	The ONT PromethION is a high-throughput, high-sample-number benchtop sequencing machine developed by Oxford Nanopore Technologies.	EFO:0008634
Ultima Genomics UG100	The Ultima UG100 is a high-throughput sequencing machine developed by Ultima Genomics, designed for large-scale sequencing projects including single-cell RNA sequencing and human genome sequencing, using emulsion-based PCR amplification.	EFO:0920005
Unknown	Not known, observed, recorded, or reported as unknown by the data contributor.	NCIT:C17998

Attribute: NGS Read Indicator

Valid Value	Description	Ontology
R1	The read direction identified as number 1 in a paired-end nucleotide sequencing reaction.	NCIT:C172301
R2	The read direction identified as number 2 in a paired-end nucleotide sequencing reaction.	NCIT:C172302
R1&R2	Indicates that both Read 1 and Read 2, the forward and reverse reads of a paired-end sequencing reaction, are represented or applicable.	Not available
I1	The first index read in a sequencing run, used to identify the sample-specific barcode (e.g., i7 index) for demultiplexing pooled libraries.	Not available
Other	Different than the one(s) previously specified or mentioned.	NCIT:C17649

Attribute: NGS Library Layout

Valid Value	Description	Ontology
Paired-end	A DNA sequencing strategy where a single read is initiated from each end of a DNA fragment.	NCIT:C150423
Single-indexed	An indexed sequencing method that includes one index read.	NCIT:C165444

Attribute: NGS Library Strategy

Valid Value	Description	Ontology
AMPLICON	Sequencing of overlapping or distinct PCR or RT-PCR products	NCIT:C204813
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	NCIT:C156056
Bisulfite-Seq	Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status	NCIT:C106054
ChIA-PET	Direct sequencing of proximity-ligated chromatin immunoprecipitates.	NCIT:C172845
ChIP-Seq	Direct sequencing of chromatin immunoprecipitates	NCIT:C106049
CLONE	Genomic clone based (hierarchical) sequencing	NCIT:C204814
CLONEEND	Clone end (5', 3', or both) sequencing	NCIT:C204815
CTS	Concatenated Tag Sequencing	NCIT:C204816
Spatial-tx	A method that measures and maps gene expression in a biological sample while preserving the spatial context of the cells.	NCIT:C205121
snATAC-Seq	A molecular genetic technique where DNA is harvested from a single cell nucleus and subjected to ATAC-seq to isolate and sequence regions rich in open chromatin.	NCIT:C198496
DNase-Hypersensitivity	Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI	NCIT:C106052
scMultiome	A sequencing strategy that simultaneously profiles two or more molecular modalities, such as the transcriptome and chromatin accessibility, from the same individual cell to capture a more complete picture of cellular state.	NCIT:C205123
EST	Single pass sequencing of cDNA templates	NCIT:C18155
FAIRE-seq	Formaldehyde Assisted Isolation of Regulatory Elements. reveals regions of open chromatin	NCIT:C106051
FINISHING	Sequencing intended to finish (close) gaps in existing coverage	NCIT:C204818
FL-cDNA	Full-length sequencing of cDNA templates	NCIT:C204817
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	NCIT:C204819
MBD-Seq	Direct sequencing of methylated fractions sequencing strategy	NCIT:C204820
MeDIP-Seq	Methylated DNA Immunoprecipitation Sequencing strategy	NCIT:C204821
miRNA-Seq	Random sequencing of small miRNAs	NCIT:C156057
MNase-Seq	Direct sequencing following MNase digestion	NCIT:C106056
MRE-Seq	Methylation-Sensitive Restriction Enzyme Sequencing strategy	NCIT:C204822
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).	NCIT:C172858
Other	Library strategy not listed (please include additional info in the “design description”)	NCIT:C17649
POOLCLONE	Shotgun of pooled clones (usually BACs and Fosmids)	NCIT:C204823
RAD-Seq	A type of genome-wide sampling sequencing that reduces the complexity of the genome by subsampling only at specific sites defined by restriction enzymes.	NCIT:C204824
RIP-Seq	Direct sequencing of RNA immunoprecipitates (includes CLIP-Seq, HITS-CLIP and PAR-CLIP).	NCIT:C204825
RNA-Seq	Random sequencing of whole transcriptome	NCIT:C124261
mRNA-Seq	A procedure that can determine the RNA sequences for all or part of the poly-A tail-containing messenger RNA transcripts in an individual.	NCIT:C129432
Bulk RNA-Seq	RNA sequencing performed on a population of cells in aggregate rather than at single-cell resolution.	NCIT:C219552
scRNA-Seq	A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an amplified nucleotide sample derived from a single cell.	NCIT:C171152
SELEX	Systematic Evolution of Ligands by EXponential enrichment	NCIT:C204826
DNA-Seq	The determination of the sequence of purine and pyrimidine bases in a strand of DNA.	NCIT:C153598
scDNA-Seq	A procedure that can determine the nucleotide sequence of specific regions or the entire genome in an amplified nucleotide sample derived from a single cell.	NCIT:C223894
ssRNA-seq	strand-specific RNA sequencing	NCIT:C172859
Synthetic-Long-Read	A sequencing strategy that uses specialized sample processing combined with conventional short-read sequencing to computationally reconstruct long sequencing reads.	NCIT:C204827
Targeted-Capture	A technique that determines the nucleotide sequence of a pre-specified region of DNA or RNA by using primers that are specific for that region.	NCIT:C130177
Tethered Chromatin Conformation Capture	A method for genome-wide mapping of chromatin interactions, similar to Hi-C sequencing except that the ligations are performed on a solid substrate rather than in solution, enhancing the signal-to-noise ratio.	NCIT:C204829
Tn-Seq	Sequencing from transposon insertion sites	NCIT:C204830
WCS	Random sequencing of a whole chromosome or other replicon isolated from a genome	NCIT:C204831
WGA	Random sequencing of the whole genome following non-pcr amplification	NCIT:C19590
WGS	Random sequencing of the whole genome	NCIT:C101294
WXS	Random sequencing of exonic regions selected from the genome	NCIT:C101295

Attribute: NGS Library Source Material

Valid Value	Description	Ontology
Bulk Cells	A biospecimen consisting of multiple cells intended to be analyzed as a pool.	NCIT:C178223
Bulk Tissue	A biospecimen either derived from a whole tissue specimen or tissue section, which may consist of heterogeneous cells or tissues.	NCIT:C178225
Bulk Nuclei	A biospecimen consisting of multiple nuclei intended to be analyzed as a pool.	NCIT:C178224
Single-nuclei	A biospecimen that contains the contents of a single nucleus.	NCIT:C178227
Single-cells	A biospecimen that contains the contents of a single cell.	NCIT:C178226
Not Reported	Not provided or available.	NCIT:C43234

Attribute: NGS Library Source Molecule

Valid Value	Description	Ontology
Genomic DNA	The DNA that is part of the normal chromosomal complement of an organism.	NCIT:C95940
Metagenomic	Derived from or associated with material collected from an environmental sample.	NCIT:C201925
Metatranscriptomic	Derived from or associated with transcripts from an environmental sample.	NCIT:C201926
Not Reported	Not provided or available.	NCIT:C43234
Transcriptome	The complete set of RNA transcripts that are produced by the genome, under specific circumstances or in a specific cell.	NCIT:C153194
Viral RNA	The RNA that originates from a virus.	NCIT:C204811

Attribute: NGS Library Selection Method

Valid Value	Description	Ontology
5-methylcytidine antibody	Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C)	NCIT:C204821
CAGE	Cap-analysis gene expression	NCIT:C180697
rRNA Depletion	A library selection method in which ribosomal RNA (rRNA) is selectively removed from a nucleic acid sample prior to sequencing, enriching for non-ribosomal RNA species such as messenger RNA and other transcripts.	GENEPIO:0101020
cDNA	complementary DNA	NCIT:C324
cDNA oligo_dT	A library selection method using oligo-dT primers to select for polyadenylated mRNA during cDNA synthesis, enriching for mature eukaryotic transcripts.	NCIT:C201929
cDNA random priming	A library selection method using random-sequence oligonucleotides to prime cDNA synthesis, allowing unbiased coverage of RNA transcripts including non-polyadenylated species.	NCIT:C201930
CF-H	Cot-filtered highly repetitive genomic DNA	GENEPIO:0001943
CF-M	Cot-filtered moderately repetitive genomic DNA	GENEPIO:0001944
CF-S	Cot-filtered single/low-copy genomic DNA	GENEPIO:0001945
CF-T	Cot-filtered theoretical single-copy genomic DNA	GENEPIO:0001946
Poly-T Enrichment	A library selection method using poly-T (oligo-dT) oligonucleotides to capture polyadenylated mRNA, enriching for mature eukaryotic transcripts with poly(A) tails.	NCIT:C201929
ChIP	Chromatin immunoprecipitation	NCIT:C106048
DNAse	Deoxyribonuclease (MNase) digestion	GENEPIO:0001948
HMPR	Hypo-methylated partial restriction digest	GENEPIO:0001949
Hybrid Selection	Selection by hybridization in array or solution	GENEPIO:0001950
Not applicable	Determination of a value is not relevant in the current context.	NCIT:C48660
Inverse rRNA	depletion of ribosomal RNA by oligo hybridization.	Not available
MBD2 protein methyl-CpG binding domain	Enrichment by methyl-CpG binding domain	GENEPIO:0001951
miRNA Size Fractionation	A library selection method that isolates small RNA species, such as microRNAs, from a nucleic acid sample based on their characteristically small size, typically using gel- or column-based size-exclusion techniques.	NCIT:C163991
MDA	Multiple displacement amplification	NCIT:C19590
MF	Methyl Filtrated	GENEPIO:0001952
MNase	Micrococcal Nuclease (MNase) digestion	GENEPIO:0001953
MSLL	Methylation Spanning Linking Library	GENEPIO:0001954
Oligo-dT	enrichment of messenger RNA (mRNA) by hybridization to Oligo-dT.	NCIT:C201929
Other	Other library enrichment, screening, or selection process (please include additional info in the “design description”)	NCIT:C17649
Padlock probes capture method	Circularized oligonucleotide probes	Not available
PCR	Source material was selected by designed primers	NCIT:C17003
PolyA	PolyA selection or enrichment for messenger RNA (mRNA); should replace cDNA enumeration.	GENEPIO:0102191
RACE	Rapid Amplification of cDNA Ends	NCIT:C180698
Random	Random selection by shearing or other method	NCIT:C201930
Random PCR	Source material was selected by randomly generated primers	NCIT:C17003
Reduced Representation	Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling	NCIT:C167284
Repeat fractionation	Selection for less repetitive (and more gene rich) sequence through Cot filtration (CF) or other fractionation techniques based on DNA kinetics.	EFO:0004455
Restriction Digest	DNA fractionation using restriction enzymes	GENEPIO:0001961
RT-PCR	Source material was selected by reverse transcription PCR	NCIT:C18136
Size fractionation	Physical selection of size appropriate targets	GENEPIO:0001963
Affinity Enrichment	A library selection method that enriches for specific nucleic acid or protein targets through binding to an antibody, protein, or other affinity reagent prior to sequencing or analysis.	NCIT:C163987
Unspecified	Library enrichment, screening, or selection is not specified (please include additional info in the “design description”)	NCIT:C38046