Table 2 - Library Descriptor Terms

tagDescriptionlink
/LIBRARY_DESCRIPTOR: The LIBRARY_DESCRIPTOR specifies the origin of the material being sequenced and any treatments that the material might have undergone that affect the sequencing result. This specification is needed even if the platform does not require a library construction step per se.
/LIBRARY_DESCRIPTOR/LIBRARY_CONSTRUCTION_PROTOCOL: Free form text describing the protocol by which the sequencing library was constructed.
/LIBRARY_DESCRIPTOR/LIBRARY_LAYOUT: 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.
/LIBRARY_DESCRIPTOR/LIBRARY_LAYOUT/PAIRED/@NOMINAL_LENGTH:
/LIBRARY_DESCRIPTOR/LIBRARY_LAYOUT/PAIRED/@NOMINAL_SDEV:
/LIBRARY_DESCRIPTOR/LIBRARY_LAYOUT/PAIRED/@ORIENTATION:
/LIBRARY_DESCRIPTOR/LIBRARY_LAYOUT/SINGLE: Reads are unpaired (usual case).
/LIBRARY_DESCRIPTOR/LIBRARY_NAME: The submitter's name for this library.
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION: Whether any method was used to select for or against, enrich, or screen the material being sequenced.
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[5-methylcytidine antibody]: Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C).
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[CAGE]: Cap-analysis gene expression. <XREF_LINK> <DB>pubmed</DB> <ID>14663149</ID> </XREF_LINK>
http://www​.ncbi.nlm.nih​.gov/pubmed?term=14663149[uid]
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[CF-H]:Cot-filtered highly repetitive genomic DNA
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[CF-M]:Cot-filtered moderately repetitive genomic DNA
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[CF-S]:Cot-filtered single/low-copy genomic DNA
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[CF-T]:Cot-filtered theoretical single-copy genomic DNA
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[ChIP]:Chromatin immunoprecipitation
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[DNAse]:Deoxyribonuclease (MNase) digestion
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[HMPR]:Hypo-methylated partial restriction digest
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[Hybrid Selection]:Selection by hybridization in array or solution.
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[MBD2 protein methyl-CpG binding domain]: Enrichment by methyl-CpG binding domain.
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[MF]:Methyl Filtrated
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[MNase]:Micrococcal Nuclease (MNase) digestion
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[MSLL]:Methylation Spanning Linking Library
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[PCR]:Source material was selected by designed primers.
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[RACE]: Rapid Amplification of cDNA Ends. <XREF_LINK> <DB>pubmed</DB> <ID>2461560</ID> </XREF_LINK>
http://www​.ncbi.nlm.nih​.gov/pubmed?term=2461560[uid]
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[RANDOM PCR]:Source material was selected by randomly generated primers.
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[RANDOM]:Random selection by shearing or other method.
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[RT-PCR]:Source material was selected by reverse transcription PCR
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[Reduced Representation]:Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling.
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[Restriction Digest]: DNA fractionation using restriction enzymes.
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[cDNA]:PolyA selection or enrichment for messenger RNA (mRNA). complementary DNA.
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[other]: Other library enrichment, screening, or selection process.
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[size fractionation]: Physical selection of size appropriate targets.
/LIBRARY_DESCRIPTOR/LIBRARY_SELECTION[unspecified]: Library enrichment, screening, or selection is not specified.
/LIBRARY_DESCRIPTOR/LIBRARY_SOURCE: The LIBRARY_SOURCE specifies the type of source material that is being sequenced.
/LIBRARY_DESCRIPTOR/LIBRARY_SOURCE[GENOMIC]: Genomic DNA (includes PCR products from genomic DNA).
/LIBRARY_DESCRIPTOR/LIBRARY_SOURCE[METAGENOMIC]: Mixed material from metagenome.
/LIBRARY_DESCRIPTOR/LIBRARY_SOURCE[METATRANSCRIPTOMIC]: Transcription products from community targets
/LIBRARY_DESCRIPTOR/LIBRARY_SOURCE[OTHER]: Other, unspecified, or unknown library source material.
/LIBRARY_DESCRIPTOR/LIBRARY_SOURCE[SYNTHETIC]: Synthetic DNA.
/LIBRARY_DESCRIPTOR/LIBRARY_SOURCE[TRANSCRIPTOMIC]: Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries).
/LIBRARY_DESCRIPTOR/LIBRARY_SOURCE[VIRAL RNA]: Viral RNA.
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY: Sequencing technique intended for this library.
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[AMPLICON]: Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA . <XREF_LINK> <DB>pubmed</DB> <ID>19023400</ID> </XREF_LINK>
http://www​.ncbi.nlm.nih​.gov/pubmed?term=19023400[uid]
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[Bisulfite-Seq]:MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status. <XREF_LINK> <DB>pubmed</DB> <ID>19829295</ID> </XREF_LINK>
http://www​.ncbi.nlm.nih​.gov/pubmed?term=19829295[uid]
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[CLONEEND]: Clone end (5', 3', or both) sequencing. <XREF_LINK> <DB>pubmed</DB> <ID>18836033</ID> </XREF_LINK>
http://www​.ncbi.nlm.nih​.gov/pubmed?term=18836033[uid]
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[CLONE]: Genomic clone based (hierarchical) sequencing.
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[CTS]: Concatenated Tag Sequencing
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[ChIP-Seq]: Direct sequencing of chromatin immunoprecipitates. <XREF_LINK> <DB>pubmed</DB> <ID>18684996</ID> </XREF_LINK>
http://www​.ncbi.nlm.nih​.gov/pubmed?term=18684996[uid]
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[DNase-Hypersensitivity]: Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI.
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[EST]: Single pass sequencing of cDNA templates
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[FINISHING]: Sequencing intended to finish (close) gaps in existing coverage.
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[FL-cDNA]: Full-length sequencing of cDNA templates
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[MBD-Seq]: Direct sequencing of methylated fractions sequencing strategy.
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[MNase-Seq]: Direct sequencing following MNase digestion.
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[MRE-Seq]: Methylation-Sensitive Restriction Enzyme Sequencing strategy.
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[MeDIP-Seq]: Methylated DNA Immunoprecipitation Sequencing strategy.
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[OTHER]: Library strategy not listed.
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[POOLCLONE]: Shotgun of pooled clones (usually BACs and Fosmids).
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[RNA-Seq]: Random sequencing of whole transcriptome. <XREF_LINK> <DB>pubmed</DB> <ID>18611170</ID> </XREF_LINK>
http://www​.ncbi.nlm.nih​.gov/pubmed?term=18611170[uid]
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[WCS]: Random sequencing of a whole chromosome or other replicon isolated from a genome.
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[WGS]: Random sequencing of the whole genome.
/LIBRARY_DESCRIPTOR/LIBRARY_STRATEGY[WXS]: Random sequencing of exonic regions selected from the genome. <XREF_LINK> <DB>pubmed</DB> <ID>20111037</ID> </XREF_LINK>
http://www​.ncbi.nlm.nih​.gov/pubmed?term=20111037[uid]
/LIBRARY_DESCRIPTOR/POOLING_STRATEGY: The optional pooling strategy indicates how the library or libraries are organized if multiple samples are involved.
/LIBRARY_DESCRIPTOR/POOLING_STRATEGY[multiplexed libraries]: Multiple libraries were prepared each of which can be distinguished in the sequencing result through a molecular barcode or other indicator. Each library may be made from the same or different samples. This option is expected when the libraries are part of the same study.
/LIBRARY_DESCRIPTOR/POOLING_STRATEGY[multiplexed samples]: A library was prepared of multiplexed samples each of which can be distinguished in the sequencing result through a molecular barcode or other indicator.
/LIBRARY_DESCRIPTOR/POOLING_STRATEGY[none]: There is a one-to-one correspondence with sample and library (normal case).
/LIBRARY_DESCRIPTOR/POOLING_STRATEGY[simple pool]: The sequencing is done on a pool of identified samples which cannot be distinguished in the sequencing result.
/LIBRARY_DESCRIPTOR/POOLING_STRATEGY[spiked library]: One library is prepared with an oligonucleotide sequence included that when sequenced can help provide quality control for the library.
/LIBRARY_DESCRIPTOR/TARGETED_LOCI: Names the gene(s) or locus(loci) or other genomic feature(s) targeted by the sequence.
/LIBRARY_DESCRIPTOR/TARGETED_LOCI/LOCUS/@locus_name[16S rRNA]: Bacterial ribosomal RNA hypervariable region(s).
/LIBRARY_DESCRIPTOR/TARGETED_LOCI/LOCUS/@locus_name[exome]: All exonic regions of the genome.
/LIBRARY_DESCRIPTOR/TARGETED_LOCI/LOCUS/@locus_name[other]: Other locus, please describe.
/LIBRARY_DESCRIPTOR/TARGETED_LOCI/LOCUS/PROBE_SET: Reference to an archived primer or probe set. Example: dbProbe
/LIBRARY_DESCRIPTOR/TARGETED_LOCI/LOCUS/PROBE_SET/DB: INSDC controlled vocabulary of permitted cross references. Please see http://www.insdc.org/db_xref.html . For example, FLYBASE.
/LIBRARY_DESCRIPTOR/TARGETED_LOCI/LOCUS/PROBE_SET/ID: Accession in the referenced database. For example, FBtr0080008 (in FLYBASE).

From: SRA Glossary

Cover of SRA Handbook
SRA Handbook [Internet].

NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.