Sequencing Level 1
Attribute: NGS Sequencing Platform¶
| Valid Value | Description |
|---|---|
| 454 GS | nan |
| 454 GS 20 | nan |
| 454 GS FLX | nan |
| 454 GS FLX Titanium | nan |
| 454 GS FLX+ | nan |
| 454 GS Junior | nan |
| AB 310 Genetic Analyzer | nan |
| AB 3130 Genetic Analyzer | nan |
| AB 3130xL Genetic Analyzer | nan |
| AB 3500 Genetic Analyzer | nan |
| AB 3500xL Genetic Analyzer | nan |
| AB 3730 Genetic Analyzer | nan |
| AB 3730xL Genetic Analyzer | nan |
| AB 5500 Genetic Analyzer | A proprietary next-generation DNA sequencing system from Applied Biosystems that utilizes DNA ligase. DNA fragments attached to beads are clonally amplified and ligated to fluorescently labeled "interrogation probes". Ligation frees the fluor, which is detected and identifies the specific probe. The marker of the attached probe is then removed and a 5'-phosphate group is regenerated. Multiple cycles of ligation, detection, and cleavage are performed. |
| AB 5500x-Wl Genetic Analyzer | A proprietary next-generation DNA sequencing system from Applied Biosystems that utilizes DNA ligase. DNA fragments attached to beads are clonally amplified and ligated to fluorescently labeled "interrogation probes". Ligation frees the fluor, which is detected and identifies the specific probe. The marker of the attached probe is then removed and a 5'-phosphate group is regenerated. Multiple cycles of ligation, detection, and cleavage are performed. |
| AB 5500xl Genetic Analyzer | A proprietary next-generation DNA sequencing system from Applied Biosystems that utilizes DNA ligase. DNA fragments attached to beads are clonally amplified and ligated to fluorescently labeled "interrogation probes". Ligation frees the fluor, which is detected and identifies the specific probe. The marker of the attached probe is then removed and a 5'-phosphate group is regenerated. Multiple cycles of ligation, detection, and cleavage are performed. |
| AB SOLiD 2 | nan |
| AB SOLiD 3 | nan |
| AB SOLiD 3 Plus System | A proprietary next-generation DNA sequencing system from Applied Biosystems that utilizes DNA ligase. DNA fragments attached to beads are clonally amplified and ligated to fluorescently labeled "interrogation probes". Ligation frees the fluor, which is detected and identifies the specific probe. The marker of the attached probe is then removed and a 5'-phosphate group is regenerated. Multiple cycles of ligation, detection, and cleavage are performed. |
| AB SOLiD 4 | nan |
| AB SOLiD 4hq System | A proprietary next-generation DNA sequencing system from Applied Biosystems that utilizes DNA ligase. DNA fragments attached to beads are clonally amplified and ligated to fluorescently labeled "interrogation probes". Ligation frees the fluor, which is detected and identifies the specific probe. The marker of the attached probe is then removed and a 5'-phosphate group is regenerated. Multiple cycles of ligation, detection, and cleavage are performed. |
| AB SOLiD PI System | A proprietary next-generation DNA sequencing system from Applied Biosystems that utilizes DNA ligase. DNA fragments attached to beads are clonally amplified and ligated to fluorescently labeled "interrogation probes". Ligation frees the fluor, which is detected and identifies the specific probe. The marker of the attached probe is then removed and a 5'-phosphate group is regenerated. Multiple cycles of ligation, detection, and cleavage are performed. |
| AB SOLiD System | A proprietary next-generation DNA sequencing system from Applied Biosystems that utilizes DNA ligase. DNA fragments attached to beads are clonally amplified and ligated to fluorescently labeled "interrogation probes". Ligation frees the fluor, which is detected and identifies the specific probe. The marker of the attached probe is then removed and a 5'-phosphate group is regenerated. Multiple cycles of ligation, detection, and cleavage are performed. |
| BGISEQ-500 | The BGISEQ-500 is a model type of the BGISEQ sequencing library platform. |
| Complete Genomics | nan |
| DNBSEQ-G400 | The DNBSEQ-G400 is a model type of the BGISEQ sequencing library platform. |
| DNBSEQ-G50 | The DNBSEQ-G50 is a model type of the BGISEQ sequencing library platform. |
| DNBSEQ-T7 | The DNBSEQ-T7 is a model type of the BGISEQ sequencing library platform. |
| GridION | nan |
| Helicos HeliScope | nan |
| Illumina Genome Analyzer | nan |
| Illumina Genome Analyzer II | nan |
| Illumina Genome Analyzer IIx | nan |
| Illumina HiScanSQ | nan |
| Illumina HiSeq 1000 | nan |
| Illumina HiSeq 1500 | nan |
| Illumina HiSeq 2000 | nan |
| Illumina HiSeq 2500 | nan |
| Illumina HiSeq 3000 | nan |
| Illumina HiSeq 4000 | nan |
| Illumina HiSeq X Five | nan |
| Illumina HiSeq X Ten | nan |
| Illumina iSeq 100 | The Illumina iSeq 100 is a model type of the Illumina sequencing library platform. |
| Illumina MiniSeq | nan |
| Illumina MiSeq | nan |
| Illumina NextSeq | nan |
| Illumina NextSeq 2500 | nan |
| Illumina NextSeq 500 | nan |
| Illumina NextSeq 550 | nan |
| Illumina NovaSeq | nan |
| Illumina NovaSeq 6000 | nan |
| Illumina NovaSeq X Plus | nan |
| Ion Torrent PGM | nan |
| Ion Torrent Proton | nan |
| Ion Torrent S5 | nan |
| Ion Torrent S5 XL | nan |
| MGISEQ-2000RS | The MGISEQ-2000RS is a model type of the BGISEQ sequencing library platform. |
| MinION | nan |
| Not Reported | nan |
| Other | nan |
| PacBio RS | nan |
| PacBio RS II | nan |
| PacBio Sequel | The PacBio Sequel is a model type of the PacBio SMRT sequencing library platform. |
| PacBio Sequel II | The PacBio Sequel II is a model type of the PacBio SMRT sequencing library platform. |
| PromethION | nan |
| Ultima Genomics UG100 | nan |
| Unknown | nan |
Attribute: NGS Read Indicator¶
| Valid Value | Description |
|---|---|
| R1 | nan |
| R2 | nan |
| R1&R2 | nan |
| I1 | nan |
| Other | nan |
Attribute: NGS Library Layout¶
| Valid Value | Description |
|---|---|
| Paired-end | nan |
| Single-indexed | nan |
Attribute: NGS Library Strategy¶
| Valid Value | Description |
|---|---|
| AMPLICON | Sequencing of overlapping or distinct PCR or RT-PCR products |
| ATAC-seq | 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 |
| Bisulfite-Seq | Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status |
| ChIA-PET | Direct sequencing of proximity-ligated chromatin immunoprecipitates. |
| ChIP-Seq | Direct sequencing of chromatin immunoprecipitates |
| CLONE | Genomic clone based (hierarchical) sequencing |
| CLONEEND | Clone end (5', 3', or both) sequencing |
| CTS | Concatenated Tag Sequencing |
| Spatial-tx | nan |
| snATAC-Seq | nan |
| DNase-Hypersensitivity | Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI |
| scMultiome | nan |
| EST | Single pass sequencing of cDNA templates |
| FAIRE-seq | Formaldehyde Assisted Isolation of Regulatory Elements. reveals regions of open chromatin |
| FINISHING | Sequencing intended to finish (close) gaps in existing coverage |
| FL-cDNA | Full-length sequencing of cDNA templates |
| Hi-C | 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 |
| MBD-Seq | Direct sequencing of methylated fractions sequencing strategy |
| MeDIP-Seq | Methylated DNA Immunoprecipitation Sequencing strategy |
| miRNA-Seq | Random sequencing of small miRNAs |
| MNase-Seq | Direct sequencing following MNase digestion |
| MRE-Seq | Methylation-Sensitive Restriction Enzyme Sequencing strategy |
| ncRNA-Seq | 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). |
| Other | Library strategy not listed (please include additional info in the “design description”) |
| POOLCLONE | Shotgun of pooled clones (usually BACs and Fosmids) |
| RAD-Seq | nan |
| RIP-Seq | Direct sequencing of RNA immunoprecipitates (includes CLIP-Seq, HITS-CLIP and PAR-CLIP). |
| RNA-Seq | Random sequencing of whole transcriptome |
| SELEX | Systematic Evolution of Ligands by EXponential enrichment |
| DNA-Seq | nan |
| ssRNA-seq | strand-specific RNA sequencing |
| Synthetic-Long-Read | nan |
| Targeted-Capture | nan |
| Tethered Chromatin Conformation Capture | nan |
| Tn-Seq | Sequencing from transposon insertion sites |
| WCS | Random sequencing of a whole chromosome or other replicon isolated from a genome |
| WGA | Random sequencing of the whole genome following non-pcr amplification |
| WGS | Random sequencing of the whole genome |
| WXS | Random sequencing of exonic regions selected from the genome |
Attribute: NGS Library Source Material¶
| Valid Value | Description |
|---|---|
| Bulk Cells | nan |
| Bulk Tissue | nan |
| Bulk Nuclei | nan |
| Single-nuclei | nan |
| Single-cells | nan |
| Not Reported | nan |
Attribute: NGS Library Source Molecule¶
| Valid Value | Description |
|---|---|
| Genomic DNA | nan |
| Metagenomic | nan |
| Metatranscriptomic | nan |
| Not Reported | nan |
| Transcriptome | nan |
| Viral RNA | nan |
Attribute: NGS Library Selection Method¶
| Valid Value | Description |
|---|---|
| 5-methylcytidine antibody | Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C) |
| CAGE | Cap-analysis gene expression |
| rRNA Depletion | nan |
| cDNA | complementary DNA |
| cDNA oligo_dT | nan |
| cDNA random priming | nan |
| CF-H | Cot-filtered highly repetitive genomic DNA |
| CF-M | Cot-filtered moderately repetitive genomic DNA |
| CF-S | Cot-filtered single/low-copy genomic DNA |
| CF-T | Cot-filtered theoretical single-copy genomic DNA |
| Poly-T Enrichment | nan |
| ChIP | Chromatin immunoprecipitation |
| DNAse | Deoxyribonuclease (MNase) digestion |
| HMPR | Hypo-methylated partial restriction digest |
| Hybrid Selection | Selection by hybridization in array or solution |
| Not applicable | nan |
| Inverse rRNA | depletion of ribosomal RNA by oligo hybridization. |
| MBD2 protein methyl-CpG binding domain | Enrichment by methyl-CpG binding domain |
| miRNA Size Fractionation | nan |
| MDA | Multiple displacement amplification |
| MF | Methyl Filtrated |
| MNase | Micrococcal Nuclease (MNase) digestion |
| MSLL | Methylation Spanning Linking Library |
| Oligo-dT | enrichment of messenger RNA (mRNA) by hybridization to Oligo-dT. |
| Other | Other library enrichment, screening, or selection process (please include additional info in the “design description”) |
| Padlock probes capture method | Circularized oligonucleotide probes |
| PCR | Source material was selected by designed primers |
| PolyA | PolyA selection or enrichment for messenger RNA (mRNA); should replace cDNA enumeration. |
| RACE | Rapid Amplification of cDNA Ends |
| Random | Random selection by shearing or other method |
| Random PCR | Source material was selected by randomly generated primers |
| Reduced Representation | Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling |
| Repeat fractionation | Selection for less repetitive (and more gene rich) sequence through Cot filtration (CF) or other fractionation techniques based on DNA kinetics. |
| Restriction Digest | DNA fractionation using restriction enzymes |
| RT-PCR | Source material was selected by reverse transcription PCR |
| Size fractionation | Physical selection of size appropriate targets |
| Affinity Enrichment | nan |
| Unspecified | Library enrichment, screening, or selection is not specified (please include additional info in the “design description”) |