Enum: SequencingAssayEnum

Sequencing-based assays including RNA-seq, DNA-seq, and related methods

Permissible Values

Value	Meaning	Description
RNA_SEQ	OBI:0001271	RNA sequencing to profile transcriptome
SINGLE_CELL_RNA_SEQ	OBI:0002631	Single-cell RNA sequencing
SINGLE_NUCLEUS_RNA_SEQ	None	Single-nucleus RNA sequencing
SPATIAL_TRANSCRIPTOMICS	EFO:0008992	Spatially resolved transcriptomics
LNCRNA_SEQ	None	Long non-coding RNA sequencing
MIRNA_SEQ	OBI:0002112	MicroRNA sequencing
RIBO_SEQ	None	Ribosome profiling sequencing
WHOLE_GENOME_SEQUENCING	OBI:0002117	Whole genome sequencing
WHOLE_EXOME_SEQUENCING	OBI:0002118	Whole exome sequencing
TARGETED_EXOME_SEQUENCING	None	Targeted exome sequencing panel
NEXT_GENERATION_TARGETED_SEQUENCING	None	Next generation targeted sequencing panel
SANGER_SEQUENCING	OBI:0000695	Sanger chain termination sequencing
ATAC_SEQ	OBI:0002039	Assay for Transposase-Accessible Chromatin sequencing
SINGLE_CELL_ATAC_SEQ	None	Single-cell ATAC-seq
CHIP_SEQ	OBI:0000716	Chromatin immunoprecipitation sequencing
CUT_AND_RUN	None	Cleavage Under Targets and Release Using Nuclease
BISULFITE_SEQUENCING	OBI:0000748	Bisulfite sequencing for DNA methylation
ERR_BISULFITE_SEQUENCING	None	Enzymatic methyl-seq (EM-seq) or similar error-reduced bisulfite sequencing
OXBS_SEQ	None	Oxidative bisulfite sequencing
HI_C	OBI:0002042	High-throughput chromosome conformation capture
ISO_SEQ	None	Isoform sequencing (PacBio long-read)
NOME_SEQ	None	Nucleosome Occupancy and Methylome Sequencing
CAPP_SEQ	None	CAncer Personalized Profiling by deep Sequencing
SAFER_SEQS	None	Safe-Sequencing System
TCR_REPERTOIRE_SEQUENCING	None	T cell receptor repertoire sequencing
SCCGI_SEQ	None	Single-cell CGI sequencing
JUMPING_LIBRARY	None	Jumping library sequencing for structural variants
SNP_ARRAY	OBI:0001204	SNP genotyping array
RNA_ARRAY	OBI:0001463	RNA expression array
MIRNA_ARRAY	None	MicroRNA array
METHYLATION_ARRAY	OBI:0001332	DNA methylation array

Slots

Name	Description
sequencing_assay	Sequencing-based assay type

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/valuesets

LinkML Source

name: SequencingAssayEnum
instantiates:
- valuesets_meta:ValueSetEnumDefinition
description: Sequencing-based assays including RNA-seq, DNA-seq, and related methods
title: Sequencing Assay Types
from_schema: https://w3id.org/valuesets
see_also:
- https://nf-osi.github.io/nf-metadata-dictionary/
contributors:
- orcid:0000-0002-6601-2165
- https://github.com/anthropics/claude-code
status: DRAFT
rank: 1000
permissible_values:
  RNA_SEQ:
    text: RNA_SEQ
    description: RNA sequencing to profile transcriptome
    meaning: OBI:0001271
    aliases:
    - RNA-seq
  SINGLE_CELL_RNA_SEQ:
    text: SINGLE_CELL_RNA_SEQ
    description: Single-cell RNA sequencing
    meaning: OBI:0002631
    aliases:
    - scRNA-seq
  SINGLE_NUCLEUS_RNA_SEQ:
    text: SINGLE_NUCLEUS_RNA_SEQ
    description: Single-nucleus RNA sequencing
    aliases:
    - snRNA-seq
  SPATIAL_TRANSCRIPTOMICS:
    text: SPATIAL_TRANSCRIPTOMICS
    description: Spatially resolved transcriptomics
    meaning: EFO:0008992
  LNCRNA_SEQ:
    text: LNCRNA_SEQ
    description: Long non-coding RNA sequencing
    aliases:
    - lncRNA-seq
  MIRNA_SEQ:
    text: MIRNA_SEQ
    description: MicroRNA sequencing
    meaning: OBI:0002112
    aliases:
    - miRNA-seq
  RIBO_SEQ:
    text: RIBO_SEQ
    description: Ribosome profiling sequencing
    aliases:
    - Ribo-seq
  WHOLE_GENOME_SEQUENCING:
    text: WHOLE_GENOME_SEQUENCING
    description: Whole genome sequencing
    meaning: OBI:0002117
    aliases:
    - WGS
  WHOLE_EXOME_SEQUENCING:
    text: WHOLE_EXOME_SEQUENCING
    description: Whole exome sequencing
    meaning: OBI:0002118
    aliases:
    - WES
  TARGETED_EXOME_SEQUENCING:
    text: TARGETED_EXOME_SEQUENCING
    description: Targeted exome sequencing panel
  NEXT_GENERATION_TARGETED_SEQUENCING:
    text: NEXT_GENERATION_TARGETED_SEQUENCING
    description: Next generation targeted sequencing panel
  SANGER_SEQUENCING:
    text: SANGER_SEQUENCING
    description: Sanger chain termination sequencing
    meaning: OBI:0000695
  ATAC_SEQ:
    text: ATAC_SEQ
    description: Assay for Transposase-Accessible Chromatin sequencing
    meaning: OBI:0002039
    aliases:
    - ATAC-seq
  SINGLE_CELL_ATAC_SEQ:
    text: SINGLE_CELL_ATAC_SEQ
    description: Single-cell ATAC-seq
    aliases:
    - scATAC-seq
  CHIP_SEQ:
    text: CHIP_SEQ
    description: Chromatin immunoprecipitation sequencing
    meaning: OBI:0000716
    aliases:
    - ChIP-seq
  CUT_AND_RUN:
    text: CUT_AND_RUN
    description: Cleavage Under Targets and Release Using Nuclease
    aliases:
    - CUT&RUN
  BISULFITE_SEQUENCING:
    text: BISULFITE_SEQUENCING
    description: Bisulfite sequencing for DNA methylation
    meaning: OBI:0000748
    aliases:
    - BS-seq
  ERR_BISULFITE_SEQUENCING:
    text: ERR_BISULFITE_SEQUENCING
    description: Enzymatic methyl-seq (EM-seq) or similar error-reduced bisulfite
      sequencing
  OXBS_SEQ:
    text: OXBS_SEQ
    description: Oxidative bisulfite sequencing
    aliases:
    - oxBS-seq
  HI_C:
    text: HI_C
    description: High-throughput chromosome conformation capture
    meaning: OBI:0002042
    aliases:
    - Hi-C
  ISO_SEQ:
    text: ISO_SEQ
    description: Isoform sequencing (PacBio long-read)
    aliases:
    - Iso-Seq
  NOME_SEQ:
    text: NOME_SEQ
    description: Nucleosome Occupancy and Methylome Sequencing
    aliases:
    - NOMe-seq
  CAPP_SEQ:
    text: CAPP_SEQ
    description: CAncer Personalized Profiling by deep Sequencing
    aliases:
    - CAPP-Seq
  SAFER_SEQS:
    text: SAFER_SEQS
    description: Safe-Sequencing System
  TCR_REPERTOIRE_SEQUENCING:
    text: TCR_REPERTOIRE_SEQUENCING
    description: T cell receptor repertoire sequencing
    aliases:
    - TCR-seq
  SCCGI_SEQ:
    text: SCCGI_SEQ
    description: Single-cell CGI sequencing
    aliases:
    - scCGI-seq
  JUMPING_LIBRARY:
    text: JUMPING_LIBRARY
    description: Jumping library sequencing for structural variants
  SNP_ARRAY:
    text: SNP_ARRAY
    description: SNP genotyping array
    meaning: OBI:0001204
  RNA_ARRAY:
    text: RNA_ARRAY
    description: RNA expression array
    meaning: OBI:0001463
  MIRNA_ARRAY:
    text: MIRNA_ARRAY
    description: MicroRNA array
  METHYLATION_ARRAY:
    text: METHYLATION_ARRAY
    description: DNA methylation array
    meaning: OBI:0001332

Enum: SequencingAssayEnum

Permissible Values

Slots

See Also

Identifier and Mapping Information

Schema Source

LinkML Source