DataElement

publicId 6273393 version 2 longName Molecular Analysis Library Sequencing Technique Type shortName SEQ_LIB_STRAT_TP definition The method used to determine the order of purines and pyrimidines in a nucleic acid-based sequencing library. context MCL origin MCL:Molecular and Cellular Characterization of Screened Lesions workflowStatus RELEASED registrationStatus Qualified latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription 3/1/22 jk Designated, added CDS alt name and CSI. 6/3/20 jk AQT added for caps; removed Library CSI, added MCL Genomics Core CSI. 11/19/18 jk Released per PI/Maureen at Oct 2018 Steering Comm meeting. 5/11/18 jk created for MCL Genomics based on Sequence Read Archive (SRA) data element. administrativeNotes 12/18/25 added "scDNA-Seq" (new concept C223894) per SN 5794 for HTAN data submission to GC. jk; 7/15/25 Added PVs mRNA-Seq and bulk RNA-Seq per SN request CADSR0005172 from GC/Amanda Bell, with approval of Heather Creasy via email 7/15/25. mr; 5/21/25 Classified in GDC Candidate CSI, added alt name, alt def, per June 2025 GDC DD. sl; 5/19/25 Updates are complete, CDE released to restore to CRDC Std CDE list. mr; 4/13/25 Upd OC from C177618 to C19770 to align with code map. mr; 10/29/24 per Henry/CodeMap task, add alt table LS; 10/17/24 Upd typo in def. mr; 10/16/24 Versioned DEC to 2.0 to upd OC to concept that does not specify 'double stranded DNA' in definition. Old OC C148073, new OC C177618. Upd def of CDE to reflect new OC. mr 10/7/24 Added CRDC standard CSI, alt name, alt def. mr; 9/27/24 Versioned to 2.0 to delete PVs RNA-Seq and DNA-Seq which belong in parent CDE 12373576 Experimental Strategy. mr; 7/23/24 Added CCDI-Fed alt name. mr; 1/28/24 added CCDI Federation CSI. jk; 9/18/23 Added CCDI alts, CSI. mr; 1/19/23 Added ref doc EXAMPLE; removed general CDS CSI, added CDS|Sequencing CSI; per metadata template. mr unresolvedIssues deletedIndicator No createdBy COLBERTM dateCreated 2024-09-27 modifiedBy JKNABLE dateModified 2025-12-18 DataElementConcept publicId 6273325 version 2 longName Molecular Analysis Library Sequencing Technique shortName 2626369v1.00:16069820v1.00 definition A laboratory procedure that involves the study of tissues, cells, and fluids using techniques to analyze biologically active molecules, including nucleic acids, proteins, lipids and carbohydrates, for the identification of processes, characteristics and abnormalities at the molecular level.:The method used to determine the order of purines and pyrimidines in a nucleic acid-based sequencing library._A practiced and regimented skill or series of actions. context MCL origin MCL:Molecular and Cellular Characterization of Screened Lesions workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription 10/21/20 jk per SME, moved DEC from Library CSI to MCL Genomics Core CSI. 11/19/18 jk Released per PI/Maureen at Oct 2018 Steering Comm meeting. 5/11/18 jk created for MCL Genomics based on Sequence Read Archive (SRA) data element. administrativeNotes 8/6/2026: Released and confirmed with Janice per quarterly cleanup.wz;4/13/25 Upd OC from C177618 to code map aligned C19770. mr; 10/16/24 Versioned to 2.0 to upd OC to concept that does not specify 'double stranded DNA' in definition. Old OC C148073, new OC C177618. mr unresolvedIssues deletedIndicator No createdBy COLBERTM dateCreated 2024-10-16 modifiedBy ZHWENDY dateModified 2026-08-06 ObjectClass publicId 2626369 version 1 longName Molecular Analysis shortName C19770 definition Techniques for studying or analyzing the genetic composition and mechanisms of living organisms at the molecular level. May refer to the understanding and manipulation of genes (DNA). context NCIP origin NCI Thesaurus workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2007-04-13 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy ALAIS dateCreated 2007-04-13 modifiedBy ONEDATA dateModified 2007-04-13 Concepts longName Molecular Analysis conceptCode C19770 definition A laboratory procedure that involves the study of tissues, cells, and fluids using techniques to analyze biologically active molecules, including nucleic acids, proteins, lipids and carbohydrates, for the identification of processes, characteristics and abnormalities at the molecular level. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 Property publicId 16069820 version 1 longName Library Sequencing Technique shortName C177618:C16847 definition The method used to determine the order of purines and pyrimidines in a nucleic acid-based sequencing library._A practiced and regimented skill or series of actions. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2025-04-13 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy COLBERTM dateCreated 2025-04-13 modifiedBy COLBERTM dateModified 2025-04-13 Concepts longName Sequencing Library Read Strategy conceptCode C177618 definition A method or strategy used for sequencing and analysis of reads from a nucleotide library. evsSource NCI_CONCEPT_CODE primaryIndicator No displayOrder 1 longName Technique conceptCode C16847 definition A practiced and regimented skill or series of actions. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 ConceptualDomain publicId 2435028 version 1 longName Gene Product shortName C26548 definition A protein or RNA whose structure is represented in and determined by genomic sequences. context NCIP origin NCI Thesaurus workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2005-12-06 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy CURTIST dateCreated 2005-12-06 modifiedBy SBR dateModified 2006-12-20 ValueDomain publicId 6273346 version 2 longName Library Sequencing Technique Type shortName 6273346v2.00 definition The method used to determine the order of of purines and pyrimidines in a nucleic acid-based sequencing library._A practiced and regimented skill or series of actions._Something distinguishable as an identifiable class based on common qualities. context MCL type Enumerated dataType CHARACTER minLength 3 maxLength 45 minValue maxValue decimalPlace origin MCL:Molecular and Cellular Characterization of Screened Lesions workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription 12/22/20 jk Added PV per Dec 2020 Data Dictionary review; 3 PV pending def from SME. 10/21/20 jk per SME, moved DEC from Library CSI to MCL Genomics Core CSI. 11/19/18 jk Released per PI/Maureen at Oct 2018 Steering Comm meeting. 5/11/18 jk created for MCL Genomics based on Sequence Read Archive (SRA) data element. administrativeNotes 12/18/25 added "scDNA-Seq" (new concept C223894) per SN 5794 for HTAN data submission to GC. Changed RS from Draft Mod to Released. jk; 7/15/25 Added PVs mRNA-Seq and bulk RNA-Seq per SN request CADSR0005172 from GC/Amanda Bell, with approval of Heather Creasy via email 7/15/25. mr; 10/16/24 Upd qualifer to concept that does not specify 'double stranded DNA' in definition. Old OC C148073, new OC C177618. mr 9/27/24 Versioned to delete PVs DNA-Seq, RNA-Seq that belong in parent CDE 12373576 Experimental Strategy. mr; 7/23/24 Added then deleted CCDI-Fed CSI. Meant to put it on the CDE, not the VD. mr; 1/29/24 Deleted the PV 'Validation' at suggestion/request of Pediatric Federation. mr unresolvedIssues deletedIndicator No createdBy COLBERTM dateCreated 2024-09-27 modifiedBy JKNABLE dateModified 2025-12-18 PermissibleValues publicId 9174155 value Other valueDescription Other Library strategy origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273371 version 1 longName Other Library strategy shortName 6273371v1.00 definition Different than the one(s) previously specified or mentioned. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Other conceptCode C17649 definition Different than the one(s) previously specified or mentioned. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174156 value WXS valueDescription WXS origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273372 version 1 longName WXS shortName 6273372v1.00 definition A procedure that can determine the DNA sequence for all of the exons in an individual. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Whole Exome Sequencing conceptCode C101295 definition A procedure that can determine the DNA sequence for all of the exons in an individual. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174157 value WGS valueDescription Whole Genome Sequencing origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 3463244 version 1 longName Whole Genome Sequencing shortName 3463244 definition A procedure that can determine the DNA sequence for nearly the entire genome of an individual. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2012-05-25 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy REEVESD dateCreated 2012-05-25 modifiedBy SLAUER dateModified 2026-04-22 Concepts longName Whole Genome Sequencing conceptCode C101294 definition A procedure that can determine the DNA sequence for nearly the entire genome of an individual. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 Designations languageName ENGLISH name WGS type Biomarker Synonym context NCIP id F4D4B27D-EFE4-720F-E053-731AD00A94C0 createdBy Load Job Administrator dateCreated 2023-02-16 modifiedBy ONEDATA_WA dateModified 2023-02-16 languageName ENGLISH name WGS (whole genome sequencing) type Biomarker Synonym context NCIP id F4D4B27D-EFE5-720F-E053-731AD00A94C0 createdBy Load Job Administrator dateCreated 2023-02-16 modifiedBy ONEDATA_WA dateModified 2023-02-16 languageName ENGLISH name WHOLE GENOME SEQUENCING type Biomarker Synonym context NCIP id F4D4B27D-EFE6-720F-E053-731AD00A94C0 createdBy Load Job Administrator dateCreated 2023-02-16 modifiedBy ONEDATA_WA dateModified 2023-02-16 languageName ENGLISH name Whole-Genome Sequencing type Biomarker Synonym context NCIP id F4D4B27D-EFE7-720F-E053-731AD00A94C0 createdBy Load Job Administrator dateCreated 2023-02-16 modifiedBy ONEDATA_WA dateModified 2023-02-16 languageName ENGLISH name Sequencing, Whole Genome type VM Alt Name context COG id 500DD9D7-CDBE-6D38-E063-731AD00AD17E createdBy Sarah Lauer dateCreated 2026-04-22 modifiedBy SLAUER dateModified 2026-04-22 publicId 9174158 value CLONE valueDescription CLONE origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273348 version 1 longName CLONE shortName 6273348v1.00 definition DNA sequencing where a target is cloned into a vector, physically mapped, and then shotgun sequenced. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Clone-Based Sequencing conceptCode C204814 definition DNA sequencing where a target is cloned into a vector, physically mapped, and then shotgun sequenced. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174159 value CLONEEND valueDescription CLONEEND origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273347 version 1 longName CLONEEND shortName 6273347v1.00 definition A DNA sequencing strategy where a single read is initiated from one or both ends of a cloned DNA fragment. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Clone End Sequencing conceptCode C204815 definition A DNA sequencing strategy where a single read is initiated from one or both ends of a cloned DNA fragment. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174160 value ChIP-Seq valueDescription ChIP-Seq origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273350 version 1 longName ChIP-Seq shortName 6273350 definition A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy ONEDATA dateModified 2018-05-11 Concepts longName ChIP-Seq conceptCode C106049 definition A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to map the binding sites of DNA-associated proteins in a sample of cells. First, crosslinked protein-DNA complexes are isolated using ChIP. Next, the crosslinks are broken, the proteins are removed and the purified DNA is modified with adaptor oligonucleotides to facilitate massively parallel DNA sequencing. Following sequencing, the DNA sequences that are obtained can be mapped to their genomic locations. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174161 value ChIA-PET valueDescription ChIA-PET origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273351 version 1 longName ChIA-PET shortName 6273351v1.00 definition A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with paired end tagged (PET) DNA sequencing to identify the nucleotide sequences for the binding sites occupied by DNA-associated proteins in a sample. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-19 Concepts longName Chromatin Interaction Analysis with Paired-End Tag conceptCode C172845 definition A molecular genetic technique that combines chromatin immunoprecipitation (ChIP) with paired end tagged (PET) DNA sequencing to identify the nucleotide sequences for the binding sites occupied by DNA-associated proteins in a sample. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174162 value Bisulfite-Seq valueDescription Bisulfite-Seq origin beginDate 2018-05-11 endDate deletedIndicator No createdBy COLBERTM dateCreated 2024-09-27 modifiedBy COLBERTM dateModified 2024-09-27 ValueMeaning publicId 6273352 version 1 longName Bisulfite-Seq shortName 6273352v1.00 definition A DNA sequencing technique that can differentiate cytosine from 5-methylcytosine in a DNA sample. First, a denatured DNA sample is treated with bisulfite which converts non-methylated cytosine to uracil. Next, the sample is amplified using a PCR method that does not discriminate between non-methylated and methylated sequences. The amplified DNA is subjected to nucleotide sequencing. The resulting sequence is compared to an identical control sample of DNA that was not treated with bisulfite. Unmethylated cytosines will be displayed as cytosines in the control sample and as thymines in the bisulfite-treated sample. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-19 Concepts longName Bisulfite Sequencing conceptCode C106054 definition A DNA sequencing technique that can differentiate cytosine from 5-methylcytosine in a DNA sample. First, a denatured DNA sample is treated with bisulfite which converts non-methylated cytosine to uracil. Next, the sample is amplified using a PCR method that does not discriminate between non-methylated and methylated sequences. The amplified DNA is subjected to nucleotide sequencing. The resulting sequence is compared to an identical control sample of DNA that was not treated with bisulfite. Unmethylated cytosines will be displayed as cytosines in the control sample and as thymines in the bisulfite-treated sample. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174163 value ATAC-Seq valueDescription ATAC-seq origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy COLBERTM dateModified 2024-09-27 ValueMeaning publicId 6273353 version 1 longName ATAC-seq shortName 6273353v1.00 definition A molecular genetic technique that isolates and sequences chromosomal regions that are rich in open chromatin. First, nuclei are harvested from a cellular sample. Then a hyperactive Tn5 transposase is added to the nuclei where it excises non-nucleosomal DNA strands and ligates co-administered high-throughput sequencing adapters (tagmentation). The tagged DNA fragments are isolated, amplified by PCR and sequenced. The number of reads for specific region of DNA correlate with increased chromatin accessibility and this method can identify regions of transcription factor and nucleosome binding. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy COLBERTM dateModified 2024-03-19 Concepts longName ATAC-Seq conceptCode C156056 definition A molecular genetic technique that isolates and sequences chromosomal regions that are rich in open chromatin. First, nuclei are harvested from a cellular sample. Then a hyperactive Tn5 transposase is added to the nuclei where it excises non-nucleosomal DNA strands and ligates co-administered high-throughput sequencing adapters (tagmentation). The tagged DNA fragments are isolated, amplified by PCR and sequenced. The number of reads for specific region of DNA correlate with increased chromatin accessibility and this method can identify regions of transcription factor and nucleosome binding. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174164 value AMPLICON valueDescription AMPLICON origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273354 version 1 longName AMPLICON shortName 6273354v1.00 definition A method for targeted DNA sequencing that uses oligonucleotide primers to amplify regions of interest, followed by next-generation sequencing (NGS) for deep coverage of the region. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Amplicon Sequencing conceptCode C204813 definition A method for targeted DNA sequencing that uses oligonucleotide primers to amplify regions of interest, followed by next-generation sequencing (NGS) for deep coverage of the region. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174165 value WGA valueDescription WGA origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273373 version 1 longName WGA shortName 6273373v1.00 definition Any technique designed to amplify a limited genomic DNA sample so as to generate a new sample that is indistinguishable from the original but with a higher DNA concentration. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-19 Concepts longName Whole Genome Amplification conceptCode C19590 definition Any technique designed to amplify a limited genomic DNA sample so as to generate a new sample that is indistinguishable from the original but with a higher DNA concentration. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174166 value WCS valueDescription WCS origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273374 version 1 longName WCS shortName 6273374v1.00 definition A DNA sequencing method, which involves random sequencing of clones derived from a whole chromosome or other genomic replicon. The sequences can be compared and aligned computationally to assemble the entire chromosome or replicon sequence. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Whole Chromosome Random Shotgun Sequencing conceptCode C204831 definition A DNA sequencing method, which involves random sequencing of clones derived from a whole chromosome or other genomic replicon. The sequences can be compared and aligned computationally to assemble the entire chromosome or replicon sequence. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174167 value Tn-Seq valueDescription Tn-Seq origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273375 version 1 longName Tn-Seq shortName 6273375v1.00 definition A method for accurately determining quantitative genetic interactions on a genome-wide scale in microorganisms. It is based on the assembly of a saturated Mariner transposon insertion library. After library selection, changes in frequency of each insertion mutant are determined by sequencing the flanking regions en masse. Insertion site identification can be used to link DNA mutations to phenotypic variants on a genome-wide scale. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Transposon Sequencing conceptCode C204830 definition A method for accurately determining quantitative genetic interactions on a genome-wide scale in microorganisms. It is based on the assembly of a saturated Mariner transposon insertion library. After library selection, changes in frequency of each insertion mutant are determined by sequencing the flanking regions en masse. Insertion site identification can be used to link DNA mutations to phenotypic variants on a genome-wide scale. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174168 value Tethered Chromatin Conformation Capture valueDescription Tethered Chromatin Conformation Capture origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273376 version 1 longName Tethered Chromatin Conformation Capture shortName 6273376v1.00 definition A method for genome-wide mapping of chromatin interactions. It is similar to Hi-C sequencing except that the ligations are performed on a solid substrate rather than in solution. This enhances the signal-to-noise ratio, thereby facilitating a detailed analysis of interactions within and between chromosomes. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Tethered Chromatin Conformation Capture Sequencing conceptCode C204829 definition A method for genome-wide mapping of chromatin interactions. It is similar to Hi-C sequencing except that the ligations are performed on a solid substrate rather than in solution. This enhances the signal-to-noise ratio, thereby facilitating a detailed analysis of interactions within and between chromosomes. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174169 value Targeted-Capture valueDescription Targeted-Capture origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273377 version 1 longName Targeted-Capture shortName 6273377v1.00 definition A method to enrich and sequence genomic regions of interest. Sequences are selected by oligonucleotides that are used to pull-down complementary DNA through hybridization. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Targeted Capture Sequencing conceptCode C204828 definition A method to enrich and sequence genomic regions of interest. Sequences are selected by oligonucleotides that are used to pull-down complementary DNA through hybridization. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174170 value Synthetic-Long-Read valueDescription Synthetic-Long-Read origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273378 version 1 longName Synthetic-Long-Read shortName 6273378v1.00 definition A sequence analysis method that uses sample processing and conventional sequencing to computationally reconstruct long reads from shorter sequencing reads. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Synthetic Long-Read Sequencing conceptCode C204827 definition A sequence analysis method that uses sample processing and conventional sequencing to computationally reconstruct long reads from shorter sequencing reads. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174171 value ssRNA-seq valueDescription ssRNA-seq origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273379 version 1 longName ssRNA-seq shortName 6273379v1.00 definition Bidirectional sequencing to determine the nucleotide sequence of the complementary strand and/or the transcriptional strand of a transcribed RNA. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-19 Concepts longName Strand-Specific RNA Sequencing conceptCode C172859 definition Bidirectional sequencing to determine the nucleotide sequence of the complementary strand and/or the transcriptional strand of a transcribed RNA. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174172 value SELEX valueDescription SELEX origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273380 version 1 longName SELEX shortName 6273380v1.00 definition A method for isolating single-stranded DNAs or RNAs (aptamers) with high-affinity to a target protein from a large library with random sequences. The target protein is expressed as a fusion with streptavidin-binding peptide and is the mixed with a pooled library of DNA or RNA ligands containing a 14bp randomized region (14N), and a 5 bp barcode that uniquely identifies the individual SELEX sample. Partially nested primers are used in successive SELEX rounds. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Systematic Evolution of Ligands by Exponential Enrichment conceptCode C204826 definition A method for isolating single-stranded DNAs or RNAs (aptamers) with high-affinity to a target protein from a large library with random sequences. The target protein is expressed as a fusion with streptavidin-binding peptide and is the mixed with a pooled library of DNA or RNA ligands containing a 14bp randomized region (14N), and a 5 bp barcode that uniquely identifies the individual SELEX sample. Partially nested primers are used in successive SELEX rounds. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174174 value RIP-Seq valueDescription RIP-Seq origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273382 version 1 longName RIP-Seq shortName 6273382v1.00 definition A method to recover and sequence interaction sites between RNA and specific ribosomal binding proteins. RNA-protein complexes are immunoprecipitated with antibodies targeted to the protein of interest. After RNase digestion, the RNA that was protected by the protein binding is extracted, reverse-transcribed to cDNA, and sequenced. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Direct Sequencing of RNA Immunoprecipitates conceptCode C204825 definition A method to recover and sequence interaction sites between RNA and specific ribosomal binding proteins. RNA-protein complexes are immunoprecipitated with antibodies targeted to the protein of interest. After RNase digestion, the RNA that was protected by the protein binding is extracted, reverse-transcribed to cDNA, and sequenced. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174175 value RAD-Seq valueDescription RAD-Seq origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273383 version 1 longName RAD-Seq shortName 6273383v1.00 definition A type of genome-wide sampling sequencing that reduces the complexity of the genome by subsampling only at specific sites defined by restriction enzymes. It is able to identify, verify, and score markers simultaneously and to identify which markers derive from each site. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Restriction-site Associated DNA Sequencing conceptCode C204824 definition A type of genome-wide sampling sequencing that reduces the complexity of the genome by subsampling only at specific sites defined by restriction enzymes. It is able to identify, verify, and score markers simultaneously and to identify which markers derive from each site. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174176 value POOLCLONE valueDescription POOLCLONE origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273384 version 1 longName POOLCLONE shortName 6273384v1.00 definition Shotgun sequencing of pooled DNA clones. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Pooled DNA Sequencing conceptCode C204823 definition Shotgun sequencing of pooled DNA clones. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174177 value ncRNA-Seq valueDescription ncRNA-Seq origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273385 version 1 longName ncRNA-Seq shortName 6273385v1.00 definition A molecular genetic technique that can determine the RNA sequences for all or part of the population of small and large non-protein coding RNA transcripts in a sample. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-19 Concepts longName Non-Coding RNA Sequencing conceptCode C172858 definition A molecular genetic technique that can determine the RNA sequences for all or part of the population of small and large non-protein coding RNA transcripts in a sample. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174178 value MRE-Seq valueDescription MRE-Seq origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273386 version 1 longName MRE-Seq shortName 6273386v1.00 definition A method to study DNA methylation. Genomic DNA is separately digested with different methylation sensitive restriction enzymes and the fragments are used to generate a library. Deep sequencing of the library allows for accurate detection of methylation sites in the genome. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Methylation-Sensitive Restriction Enzyme Sequencing conceptCode C204822 definition A method to study DNA methylation. Genomic DNA is separately digested with different methylation sensitive restriction enzymes and the fragments are used to generate a library. Deep sequencing of the library allows for accurate detection of methylation sites in the genome. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174179 value MNase-Seq valueDescription MNase-Seq origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273387 version 1 longName MNase-Seq shortName 6273387v1.00 definition A molecular genetic technique where genome-wide sequencing is performed on chromosomal DNA that is resistant to treatment with micrococcal nuclease. This technique identifies nucleosomal DNA sequences. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-19 Concepts longName MNase Sequencing conceptCode C106056 definition A molecular genetic technique where genome-wide sequencing is performed on chromosomal DNA that is resistant to treatment with micrococcal nuclease. This technique identifies nucleosomal DNA sequences. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174180 value miRNA-Seq valueDescription miRNA-Seq origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273388 version 1 longName miRNA-Seq shortName 6273388v1.00 definition A next-generation or massively parallel high-throughput DNA sequencing-based procedure that can identify and quantify the microRNA sequences present in a biological sample. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-19 Concepts longName MicroRNA Sequencing conceptCode C156057 definition A next-generation or massively parallel high-throughput DNA sequencing-based procedure that can identify and quantify the microRNA sequences present in a biological sample. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174181 value MeDIP-Seq valueDescription MeDIP-Seq origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273389 version 1 longName MeDIP-Seq shortName 6273389v1.00 definition A strategy to obtain DNA sequences from methylated sites. Genomic DNA is randomly sheared by sonication and immunoprecipitated with a monoclonal antibody that specifically recognizes 5-methylcytidine. The DNA fragments are then isolated and sequenced. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Methylated DNA Immunoprecipitation Sequencing conceptCode C204821 definition A strategy to obtain DNA sequences from methylated sites. Genomic DNA is randomly sheared by sonication and immunoprecipitated with a monoclonal antibody that specifically recognizes 5-methylcytidine. The DNA fragments are then isolated and sequenced. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174182 value MBD-Seq valueDescription MBD-Seq origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273390 version 1 longName MBD-Seq shortName 6273390v1.00 definition A strategy to obtain DNA sequences from (all) methylated sites. Genomic DNA is randomly fragmented with ultrasonication and then methylated fragments are captured by a protein with high affinity for double-stranded DNA harboring methylated CpGs; non-methylated DNA fragments are washed away. The methylation-enriched fraction is then barcode tagged and sequenced. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Methyl-binding Domain Sequencing conceptCode C204820 definition A strategy to obtain DNA sequences from (all) methylated sites. Genomic DNA is randomly fragmented with ultrasonication and then methylated fragments are captured by a protein with high affinity for double-stranded DNA harboring methylated CpGs; non-methylated DNA fragments are washed away. The methylation-enriched fraction is then barcode tagged and sequenced. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174183 value Hi-C valueDescription Hi-C origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273391 version 1 longName Hi-C shortName 6273391v1.00 definition A DNA sequencing strategy designed to detect genome-wide chromatin interactions in the nucleus. The method is based on Chromosome Conformation Capture, in which chromatin is crosslinked with formaldehyde, then digested, and re-ligated in such a way that only DNA fragments that are covalently linked together form ligation products. In Hi-C, a biotin-labeled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Hi-C Sequencing conceptCode C204819 definition A DNA sequencing strategy designed to detect genome-wide chromatin interactions in the nucleus. The method is based on Chromosome Conformation Capture, in which chromatin is crosslinked with formaldehyde, then digested, and re-ligated in such a way that only DNA fragments that are covalently linked together form ligation products. In Hi-C, a biotin-labeled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174184 value FL-cDNA valueDescription FL-cDNA origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273392 version 1 longName FL-cDNA shortName 6273392v1.00 definition Sequencing of cDNA to obtain a continuous full-length sequence. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Full-length cDNA Sequencing conceptCode C204817 definition Sequencing of cDNA to obtain a continuous full-length sequence. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174185 value FINISHING valueDescription FINISHING origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273356 version 1 longName FINISHING shortName 6273356v1.00 definition Targeted sequencing that uses primers chosen from a sequenced region to cover unsequenced strands or regions. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Finish Sequencing conceptCode C204818 definition Targeted sequencing that uses primers chosen from a sequenced region to cover unsequenced strands or regions. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174186 value FAIRE-seq valueDescription FAIRE-Seq origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273358 version 1 longName FAIRE-Seq shortName 6273358 definition A molecular genetic technique that depletes a biological sample of nucleosomal DNA and then subjects the non-nucleosome-associated DNA to next-generation sequencing. Since nucleosome disruption of chromatin is indicative of active sites of DNA transcription, this technique can isolate DNA sequences that are involved in transcriptional regulation. First, a sample is treated with formaldehyde to form DNA-protein crosslinks, followed by sample lysis and sonication. The processed sample is subjected to phenol/chloroform extraction and the DNA in the aqueous phase is analyzed using next-generation sequencing techniques. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy ONEDATA dateModified 2018-05-11 Concepts longName FAIRE-Seq conceptCode C106051 definition A molecular genetic technique that depletes a biological sample of nucleosomal DNA and then subjects the non-nucleosome-associated DNA to next-generation sequencing. Since nucleosome disruption of chromatin is indicative of active sites of DNA transcription, this technique can isolate DNA sequences that are involved in transcriptional regulation. First, a sample is treated with formaldehyde to form DNA-protein crosslinks, followed by sample lysis and sonication. The processed sample is subjected to phenol/chloroform extraction and the DNA in the aqueous phase is analyzed using next-generation sequencing techniques. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174187 value EST valueDescription EST origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273359 version 1 longName EST shortName 6273359v1.00 definition A random cDNA library comprised of 200-800 bp random pooled mRNA clones isolated from a specific organism, specific tissue and/or a given stage of development. Clones are randomly selected for single-pass sequencing reads, the raw sequence reads are processed to remove low-quality sequence information and contaminating vector sequence and the resulting higher-quality sequences can be aggregated and aligned with others to assemble complete genetic or genomic sequences. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName EST Library conceptCode C16208 definition A random cDNA library comprised of 200-800 bp random pooled mRNA clones isolated from a specific organism, specific tissue and/or a given stage of development. Clones are randomly selected for single-pass sequencing reads, the raw sequence reads are processed to remove low-quality sequence information and contaminating vector sequence and the resulting higher-quality sequences can be aggregated and aligned with others to assemble complete genetic or genomic sequences. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174188 value DNase-Hypersensitivity valueDescription DNase-Hypersensitivity origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273360 version 1 longName DNase-Hypersensitivity shortName 6273360v1.00 definition A molecular genetic technique where genome-wide sequencing is performed on DNA regions that are super sensitive to cleavage by DNase I to identify putative DNA regulatory sequences. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-19 Concepts longName DNase-Seq conceptCode C106052 definition A molecular genetic technique where genome-wide sequencing is performed on DNA regions that are super sensitive to cleavage by DNase I to identify putative DNA regulatory sequences. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174189 value CTS valueDescription CTS origin beginDate 2018-05-11 endDate deletedIndicator No createdBy KNABLEJ dateCreated 2024-09-27 modifiedBy ONEDATA dateModified 2024-09-27 ValueMeaning publicId 6273361 version 1 longName CTS shortName 6273361v1.00 definition A DNA sequencing strategy where a sequencing primer is chosen from a sequenced region in order to extend the sequenced region. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2018-05-11 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy KNABLEJ dateCreated 2018-05-11 modifiedBy SOKKERL dateModified 2024-03-22 Concepts longName Concatenated Tag Sequencing conceptCode C204816 definition A DNA sequencing strategy where a sequencing primer is chosen from a sequenced region in order to extend the sequenced region. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174190 value snATAC-Seq valueDescription origin beginDate 2023-03-28 endDate deletedIndicator No createdBy COLBERTM dateCreated 2024-09-27 modifiedBy COLBERTM dateModified 2024-09-27 ValueMeaning publicId 13260568 version 1 longName Single Nucleus ATAC-Seq shortName 13260568v1.00 definition A molecular genetic technique where DNA is harvested from a single cell nucleus (sn) samples and amplified to create a genomic library. Then the library is subjected to ATAC-seq, which isolates and sequences regions rich in open chromatin. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2023-03-28 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy COLBERTM dateCreated 2023-03-28 modifiedBy COLBERTM dateModified 2023-03-28 Concepts longName Single Nucleus ATAC-Seq conceptCode C198496 definition A molecular genetic technique where DNA is harvested from a single cell nucleus (sn) samples and amplified to create a genomic library. Then the library is subjected to ATAC-seq, which isolates and sequences regions rich in open chromatin. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174191 value scMultiome valueDescription origin beginDate 2024-04-18 endDate deletedIndicator No createdBy COLBERTM dateCreated 2024-09-27 modifiedBy COLBERTM dateModified 2024-09-27 ValueMeaning publicId 14900868 version 1 longName Single-cell Multiome Analysis shortName 14900868v1.00 definition Methods that simultaneously profile two or more cell states and activities, including the transcriptome, genome, epigenome, epitranscriptome, proteome, metabolome and/or other emerging omics. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2024-04-18 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy COLBERTM dateCreated 2024-04-18 modifiedBy COLBERTM dateModified 2024-04-18 Concepts longName Single-cell Multiome Analysis conceptCode C205123 definition Methods that simultaneously profile two or more cell states and activities, including the transcriptome, genome, epigenome, epitranscriptome, proteome, metabolome and/or other emerging omics. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9174192 value Spatial-tx valueDescription origin beginDate 2024-04-18 endDate deletedIndicator No createdBy COLBERTM dateCreated 2024-09-27 modifiedBy COLBERTM dateModified 2024-09-27 ValueMeaning publicId 14900867 version 1 longName Spatial Transcriptome Analysis shortName 14900867v1.00 definition Methods for assigning cell types to their tissue locations while simultaneously assessing one or more transcripts of interest expressed by each cell to characterize patterning and regulation of gene expression in tissues. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2024-04-18 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy COLBERTM dateCreated 2024-04-18 modifiedBy COLBERTM dateModified 2024-04-18 Concepts longName Spatial Transcriptome Analysis conceptCode C205121 definition Methods for assigning cell types to their tissue locations while simultaneously assessing one or more transcripts of interest expressed by each cell to characterize patterning and regulation of gene expression in tissues. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 publicId 9187935 value scRNA-Seq valueDescription origin beginDate 2024-12-18 endDate deletedIndicator No createdBy COLBERTM dateCreated 2024-12-18 modifiedBy COLBERTM dateModified 2024-12-18 ValueMeaning publicId 12373577 version 1 longName Single Cell RNA Sequencing shortName 12373577v1.00 definition A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an amplified nucleotide sample that was derived from a single cell. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2023-01-16 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy JKNABLE dateCreated 2023-01-16 modifiedBy COLBERTM dateModified 2026-04-22 Concepts longName Single Cell RNA Sequencing conceptCode C171152 definition A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an amplified nucleotide sample that was derived from a single cell. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 Designations languageName ENGLISH name scrnaseq type CIDC Alt Name context CRDC id 5010F7E8-9F42-490C-E063-731AD00AC7A5 createdBy Maureen Ryan dateCreated 2026-04-22 modifiedBy COLBERTM dateModified 2026-04-22 publicId 9220145 value mRNA-Seq valueDescription origin beginDate 2025-07-15 endDate deletedIndicator No createdBy COLBERTM dateCreated 2025-07-15 modifiedBy COLBERTM dateModified 2025-07-15 ValueMeaning publicId 3795342 version 1 longName Messenger RNA Nucleic Acid Sequencing shortName 3795342 definition A procedure that can determine the RNA sequences for all or part of the poly-A tail-containing messenger RNA transcripts in an individual. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2013-06-27 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy COLBERTM dateCreated 2013-06-27 modifiedBy ONEDATA_WA dateModified 2023-02-16 Concepts longName mRNA Sequencing conceptCode C129432 definition A procedure that can determine the RNA sequences for all or part of the poly-A tail-containing messenger RNA transcripts in an individual. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 Designations languageName ENGLISH name Messenger RNA Sequencing type Biomarker Synonym context NCIP id 07AB85B7-B47A-79FC-E050-BB89AD434450 createdBy Denise Warzel dateCreated 2014-11-12 modifiedBy ONEDATA dateModified 2014-11-12 languageName ENGLISH name Poly(A) RNA Sequencing type Biomarker Synonym context NCIP id F4D4B27D-FFB8-720F-E053-731AD00A94C0 createdBy Load Job Administrator dateCreated 2023-02-16 modifiedBy ONEDATA_WA dateModified 2023-02-16 languageName ENGLISH name Poly-A RNA Sequencing type Biomarker Synonym context NCIP id F4D4B27D-FFB9-720F-E053-731AD00A94C0 createdBy Load Job Administrator dateCreated 2023-02-16 modifiedBy ONEDATA_WA dateModified 2023-02-16 languageName ENGLISH name mRNA-Seq type Biomarker Synonym context NCIP id F4D4B27D-FFBA-720F-E053-731AD00A94C0 createdBy Load Job Administrator dateCreated 2023-02-16 modifiedBy ONEDATA_WA dateModified 2023-02-16 publicId 9220146 value Bulk RNA-Seq valueDescription origin beginDate 2025-07-15 endDate deletedIndicator No createdBy COLBERTM dateCreated 2025-07-15 modifiedBy COLBERTM dateModified 2025-07-15 ValueMeaning publicId 16310794 version 1 longName Bulk RNA Sequencing shortName 16310794v1.00 definition Transcriptome sequencing of RNA derived from pooled RNA extracted from a population of multiple cells or bulk tissue samples. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2025-07-15 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy COLBERTM dateCreated 2025-07-15 modifiedBy COLBERTM dateModified 2025-07-15 Concepts longName Bulk RNA Sequencing conceptCode C219552 definition Transcriptome sequencing of RNA derived from pooled RNA extracted from a population of multiple cells or bulk tissue samples. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 Designations languageName ENGLISH name bulk RNA-Seq type GC Alt Name context CRDC id 39F8E13A-F753-2607-E063-731AD00A6558 createdBy Maureen Ryan dateCreated 2025-07-15 modifiedBy COLBERTM dateModified 2025-07-15 publicId 9236664 value scDNA-Seq valueDescription origin beginDate 2025-12-18 endDate deletedIndicator No createdBy JKNABLE dateCreated 2025-12-18 modifiedBy JKNABLE dateModified 2025-12-18 ValueMeaning publicId 16861163 version 1 longName Single Cell DNA Sequencing shortName 16861163v1.00 definition 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. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2025-12-18 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy JKNABLE dateCreated 2025-12-18 modifiedBy JKNABLE dateModified 2025-12-18 Concepts longName Single Cell DNA Sequencing conceptCode C223894 definition 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. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 ConceptualDomain publicId 2435028 version 1 longName Gene Product shortName C26548 definition A protein or RNA whose structure is represented in and determined by genomic sequences. context NCIP origin NCI Thesaurus workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2005-12-06 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy CURTIST dateCreated 2005-12-06 modifiedBy SBR dateModified 2006-12-20 RepresentationTerm publicId 15181842 version 1 longName Library Sequencing Technique Type shortName 15181842v1.00 definition The method used to determine the order of of purines and pyrimidines in a nucleic acid-based sequencing library._A practiced and regimented skill or series of actions._Something distinguishable as an identifiable class based on common qualities. context NCIP origin workflowStatus RELEASED registrationStatus Application latestVersionIndicator Yes beginDate 2024-10-16 endDate changeDescription administrativeNotes unresolvedIssues deletedIndicator No createdBy COLBERTM dateCreated 2024-10-16 modifiedBy COLBERTM dateModified 2024-10-16 Concepts longName Sequencing Library Read Strategy conceptCode C177618 definition A method or strategy used for sequencing and analysis of reads from a nucleotide library. evsSource NCI_CONCEPT_CODE primaryIndicator No displayOrder 2 longName Technique conceptCode C16847 definition A practiced and regimented skill or series of actions. evsSource NCI_CONCEPT_CODE primaryIndicator No displayOrder 1 longName Type conceptCode C25284 definition Something distinguishable as an identifiable class based on common qualities. evsSource NCI_CONCEPT_CODE primaryIndicator Yes displayOrder 0 ClassificationSchemes publicId 5506117 version 1 longName Genomics context MCL workflowStatus RELEASED registrationStatus Application ClassificationSchemeItems publicId 7318156 version 1 longName MCL Core Genomics context MCL workflowStatus RELEASED registrationStatus Application publicId 8064110 version 1 longName GC (General Commons) context CRDC workflowStatus RELEASED registrationStatus Application ClassificationSchemeItems publicId 12177495 version 1 longName Sequencing context CRDC workflowStatus RELEASED registrationStatus Application publicId 10429357 version 1 longName GDC (Genomic Data Commons) context CRDC workflowStatus DRAFT NEW registrationStatus Application ClassificationSchemeItems publicId 14506028 version 1 longName Candidate New GDC CDEs context CRDC workflowStatus DRAFT NEW registrationStatus Application publicId 10466051 version 1 longName All CRDC Standard CDEs context CRDC workflowStatus RELEASED registrationStatus Application ClassificationSchemeItems publicId 10466056 version 1 longName Molecular context CRDC workflowStatus RELEASED registrationStatus Application publicId 13574489 version 1 longName CCDI (Childhood Cancer Data Initiative) context Pediatric Cancer workflowStatus RELEASED registrationStatus Application ClassificationSchemeItems publicId 13594094 version 1 longName Sequencing context Pediatric Cancer workflowStatus RELEASED registrationStatus Application publicId 13594223 version 1 longName Sequencing File context Pediatric Cancer workflowStatus RELEASED registrationStatus Application publicId 13594225 version 1 longName Single Cell Sequencing File context Pediatric Cancer workflowStatus RELEASED registrationStatus Application publicId 14733231 version 1 longName CCDI Federation CDEs context Pediatric Cancer workflowStatus RELEASED registrationStatus Application ClassificationSchemeItems publicId 14735767 version 1 longName Molecular context Pediatric Cancer workflowStatus RELEASED registrationStatus Application AlternateNames name CRDC type USED_BY context CRDC name library_strategy type GC Alt Name context CRDC name library_strategy type MCL Alt Name context MCL name Library Strategy type CCDI-Fed Alt Name context Pediatric Cancer name library_strategy type CCDI Alt Name context Pediatric Cancer name Sequencing Library Strategy type CRDC Alt Name context CRDC name sequencing_file type CCDI Table context Pediatric Cancer name library_strategy type GDC Alt Name context GDC ReferenceDocuments documentName PQT documentText Library strategy documentType Preferred Question Text url context MCL documentName MCL-1 documentText Library Strategy documentType Alternate Question Text url context MCL documentName MCL-Template Name documentText mcl_genomics_v0-1_20210126 documentType Data Collection Template url https://mcl.nci.nih.gov/resources/standards/mcl-cdes context MCL documentName CDS documentText Bisulfite-Seq; ChIP-Seq documentType EXAMPLE url context CRDC

apiResponse

type S