<status value="active" /> <experimental value="false" /> <date value="2025-10-31" /> <publisher value="Robert Koch-Institut" /> <contact> <telecom> <system value="email" /> <value value="demis-support@rki.de" /> </telecom> </contact> <description value="Das CodeSystem SequencingStrategy enthält die Codes der Sequenzierungsstrategien (angelehnt an ENA)." /> <jurisdiction> <coding> <system value="urn:iso:std:iso:3166" /> <version value="ALPHA-2" /> <code value="DE" /> </coding> </jurisdiction> <copyright value="(C) 2021-2025 Robert Koch-Institut" /> <caseSensitive value="false" /> <valueSet value="https://demis.rki.de/fhir/igs/ValueSet/sequencingStrategy" /> <content value="complete" /> <count value="36" /> <concept> <code value="amplicon" /> <display value="Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA." /> </concept> <concept> <code value="atac-seq" /> <display value="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." /> </concept> <concept> <code value="bisulfite-seq" /> <display value="MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status." /> </concept> <concept> <code value="chia-pet" /> <display value="Direct sequencing of proximity-ligated chromatin immunoprecipitates." /> </concept> <concept> <code value="chip-seq" /> <display value="ChIP-seq, Chromatin ImmunoPrecipitation, reveals binding sites of specific proteins, typically transcription factors (TFs) using antibodies to extract DNA fragments bound to the target protein." /> </concept> <concept> <code value="clone" /> <display value="Genomic clone based (hierarchical) sequencing." /> </concept> <concept> <code value="cloneend" /> <display value="Clone end (5’, 3’, or both) sequencing." /> </concept> <concept> <code value="cts" /> <display value="Concatenated Tag Sequencing" /> </concept> <concept> <code value="dnase-hypersensitivity" /> <display value="Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI." /> </concept> <concept> <code value="est" /> <display value="Single pass sequencing of cDNA templates" /> </concept> <concept> <code value="faire-seq" /> <display value="Formaldehyde Assisted Isolation of Regulatory Elements. Reveals regions of open chromatin." /> </concept> <concept> <code value="finishing" /> <display value="Sequencing intended to finish (close) gaps in existing coverage." /> </concept> <concept> <code value="fl-cdna" /> <display value="Full-length sequencing of cDNA templates" /> </concept> <concept> <code value="hi-c" /> <display value="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." /> </concept> <concept> <code value="mbd-seq" /> <display value="Methyl CpG Binding Domain Sequencing." /> </concept> <concept> <code value="medip-seq" /> <display value="Methylated DNA Immunoprecipitation Sequencing." /> </concept> <concept> <code value="mirna-seq" /> <display value="Micro RNA sequencing strategy designed to capture post-transcriptional RNA elements and include non-coding functional elements. (see pubmed 21787409 for details)" /> </concept> <concept> <code value="mnase-seq" /> <display value="Identifies well-positioned nucleosomes. uses Micrococcal Nuclease (MNase) is an endo-exonuclease that processively digests DNA until an obstruction, such as a nucleosome, is reached." /> </concept> <concept> <code value="mre-seq" /> <display value="Methylation-Sensitive Restriction Enzyme Sequencing." /> </concept> <concept> <code value="ncrna-seq" /> <display value="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)." /> </concept> <concept> <code value="other" /> <display value="Library strategy not listed." /> </concept> <concept> <code value="poolclone" /> <display value="Shotgun of pooled clones (usually BACs and Fosmids)." /> </concept> <concept> <code value="rad-seq" /> <display value="RAD sequencing" /> </concept> <concept> <code value="rip-seq" /> <display value="Direct sequencing of RNA immunoprecipitates (includes CLIP-Seq, HITS-CLIP and PAR-CLIP)." /> </concept> <concept> <code value="rna-seq" /> <display value="Random sequencing of whole transcriptome, also known as Whole Transcriptome Shotgun Sequencing, or WTSS). (see pubmed 18611170 for details)" /> </concept> <concept> <code value="selex" /> <display value="Systematic Evolution of Ligands by Exponential enrichment" /> </concept> <concept> <code value="ssrna-seq" /> <display value="Strand-specific RNA sequencing." /> </concept> <concept> <code value="synthetic-long-read" /> <display value="binning and barcoding of large DNA fragments to facilitate assembly of the fragment" /> </concept> <concept> <code value="targeted-capture" /> <display value="Enrichment of a targeted subset of loci." /> </concept> <concept> <code value="tethered-chromatin-conformation-capture" /> <display value="Tethered Chromatin Conformation Capture" /> </concept> <concept> <code value="tn-seq" /> <display value="Quantitatively determine fitness of bacterial genes based on how many times a purposely seeded transposon gets inserted into each gene of a colony after some time." /> </concept> <concept> <code value="validation" /> <display value="CGHub special request" /> </concept> <concept> <code value="wcs" /> <display value="Random sequencing of a whole chromosome or other replicon isolated from a genome." /> </concept> <concept> <code value="wga" /> <display value="Whole Genome Amplification followed by random sequencing. (see pubmed 1631067,8962113 for details)" /> </concept> <concept> <code value="wgs" /> <display value="Whole Genome Sequencing - random sequencing of the whole genome (see pubmed 10731132 for details)" /> </concept> <concept> <code value="wxs" /> <display value="Random sequencing of exonic regions selected from the genome. (see pubmed 20111037 for details)" /> </concept> </CodeSystem>