sequencingStrategy

https://demis.rki.de/fhir/CodeSystem/sequencingStrategy

Dokumentation

Das CodeSystem SequencingStrategy enthält die Codes für die Sequenzierungsstrategie (angelehnt an ENA).

This code system https://demis.rki.de/fhir/CodeSystem/sequencingStrategy defines the following codes:

CodeDisplay
wgsWhole Genome Sequencing - random sequencing of the whole genome (see pubmed 10731132 for details)
wgaWhole Genome Amplification followed by random sequencing. (see pubmed 1631067,8962113 for details)
wxsRandom sequencing of exonic regions selected from the genome. (see pubmed 20111037 for details)
rna-seqRandom sequencing of whole transcriptome, also known as Whole Transcriptome Shotgun Sequencing, or WTSS). (see pubmed 18611170 for details)
ssrna-seqStrand-specific RNA sequencing.
mirna-seqMicro RNA sequencing strategy designed to capture post-transcriptional RNA elements and include non-coding functional elements. (see pubmed 21787409 for details)
ncrna-seqCapture 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).
fl-cdnaFull-length sequencing of cDNA templates
estSingle pass sequencing of cDNA templates
hi-cChromosome 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.
atac-seqAssay 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.
wcsRandom sequencing of a whole chromosome or other replicon isolated from a genome.
rad-seqRAD sequencing
cloneGenomic clone based (hierarchical) sequencing.
poolcloneShotgun of pooled clones (usually BACs and Fosmids).
ampliconSequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA.
cloneendClone end (5’, 3’, or both) sequencing.
finishingSequencing intended to finish (close) gaps in existing coverage.
chip-seqChIP-seq, Chromatin ImmunoPrecipitation, reveals binding sites of specific proteins, typically transcription factors (TFs) using antibodies to extract DNA fragments bound to the target protein.
mnase-seqIdentifies well-positioned nucleosomes. uses Micrococcal Nuclease (MNase) is an endo-exonuclease that processively digests DNA until an obstruction, such as a nucleosome, is reached.
dnase-hypersensitivitySequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI.
bisulfite-seqMethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status.
ctsConcatenated Tag Sequencing
mre-seqMethylation-Sensitive Restriction Enzyme Sequencing.
medip-seqMethylated DNA Immunoprecipitation Sequencing.
mbd-seqMethyl CpG Binding Domain Sequencing.
tn-seqQuantitatively 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.
validationCGHub special request
faire-seqFormaldehyde Assisted Isolation of Regulatory Elements. Reveals regions of open chromatin.
selexSystematic Evolution of Ligands by Exponential enrichment
rip-seqDirect sequencing of RNA immunoprecipitates (includes CLIP-Seq, HITS-CLIP and PAR-CLIP).
chia-petDirect sequencing of proximity-ligated chromatin immunoprecipitates.
synthetic-long-readbinning and barcoding of large DNA fragments to facilitate assembly of the fragment
targeted-captureEnrichment of a targeted subset of loci.
tethered-chromatin-conformation-captureTethered Chromatin Conformation Capture
otherLibrary strategy not listed.