The metadata specifictaion for Bisulfite Seq experiments is as defined below
BISULFITE_CONVERSION_PERCENT:The bisulfite conversion percent and how it was determined. At most 1 instance(s) are allowed.
BISULFITE_CONVERSION_PROTOCOL:The bisulfite conversion protocol. At most 1 instance(s) are allowed.
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL:The protocol used for adaptor ligation. At most 1 instance(s) are allowed.
DNA_PREPARATION_ADAPTOR_SEQUENCE:The sequence of the adaptor used in preparation. At most 1 instance(s) are allowed.
DNA_PREPARATION_FRAGMENT_SIZE_RANGE:The DNA fragment size range used in preparation. At most 1 instance(s) are allowed.
DNA_PREPARATION_INITIAL_DNA_QNTY:The initial DNA quantity used in preparation. At most 1 instance(s) are allowed.
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION:The fragment size selection after adaptor ligation. At most 1 instance(s) are allowed.
EXPERIMENT_ONTOLOGY_CURIE:undef.
EXPERIMENT_TYPE:undef. Allowed values are: "DNA Methylation". At most 1 instance(s) are allowed.
EXTRACTION_PROTOCOL:The protocol used to isolate the extract material. At most 1 instance(s) are allowed.
EXTRACTION_PROTOCOL_SONICATION_CYCLES:The number of sonication cycles used for extraction. At most 1 instance(s) are allowed.
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR:The type of sonicator used for extraction. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE:The sequence of the PCR forward primer used for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES:The number of PCR cycles used for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE:The PCR polymerase used for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_PRIMER_CONC:The concentration of the PCR primers used for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL:The protocol for isolating PCR products used for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE:The sequence of the PCR reverse primer used for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_TEMPLATE_CONC:The PCR template concentration for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM:The thermocycling program used for library generation. At most 1 instance(s) are allowed.
LIBRARY_STRATEGY:undef. Allowed values are: "Bisulfite-Seq". At most 1 instance(s) are allowed.
MOLECULE:undef. Allowed values are: "genomic DNA". At most 1 instance(s) are allowed.
MOLECULE_ONTOLOGY_CURIE:undef.
The metadata specifictaion for ChIP-Seq experiments is as defined below
CHIP_ANTIBODY:The specific antibody used in the ChIP protocol. At most 1 instance(s) are allowed.
CHIP_ANTIBODY_CATALOG:The catalog from which the antibody was purchased. At most 1 instance(s) are allowed.
CHIP_ANTIBODY_LOT:The lot identifier of the antibody. At most 1 instance(s) are allowed.
CHIP_ANTIBODY_PROVIDER:The name of the company, laboratory or person that provided the antibody. At most 1 instance(s) are allowed.
CHIP_PROTOCOL:The ChIP protocol used. At most 1 instance(s) are allowed.
CHIP_PROTOCOL_ANTIBODY_AMOUNT:The amount of antibody used in the ChIP protocol. At most 1 instance(s) are allowed.
CHIP_PROTOCOL_BEAD_AMOUNT:The amount of beads used in the ChIP protocol. At most 1 instance(s) are allowed.
CHIP_PROTOCOL_BEAD_TYPE:The type of bead used in the ChIP protocol. At most 1 instance(s) are allowed.
CHIP_PROTOCOL_CHROMATIN_AMOUNT:The amount of chromatin used in the ChIP protocol. At most 1 instance(s) are allowed.
CHIP_PROTOCOL_CROSSLINK_TIME:The timespan in which the chromatin is crosslinked. At most 1 instance(s) are allowed.
EXPERIMENT_ONTOLOGY_CURIE:undef.
EXPERIMENT_TARGET_HISTONE:Target histone mark. Allowed values are: "H2AFZ", "H2AK5ac", "H2AK9ac", "H2BK120ac", "H2BK12ac", "H2BK15ac", "H2BK20ac", "H2BK5ac", "H3F3A", "H3K14ac", "H3K18ac", "H3K23ac", "H3K23me2", "H3K27ac", "H3K27me3", "H3K36me3", "H3K4ac", "H3K4me1", "H3K4me2", "H3K4me3", "H3K56ac", "H3K79me1", "H3K79me2", "H3K9ac", "H3K9me1", "H3K9me2", "H3K9me3", "H3T11ph", "H4K12ac", "H4K20me1", "H4K5ac", "H4K8ac", "H4K91ac". At most 1 instance(s) are allowed.
EXPERIMENT_TARGET_TF:(Controlled vocabulary) An HGNC gene symbol. At most 1 instance(s) are allowed.
EXPERIMENT_TARGET_TF_MODIFICATION:Post-transcriptional modification of the target protein. At most 1 instance(s) are allowed.
EXPERIMENT_TYPE:undef. At most 1 instance(s) are allowed.
EXTRACTION_PROTOCOL:The protocol used to isolate the extract material. At most 1 instance(s) are allowed.
EXTRACTION_PROTOCOL_SONICATION_CYCLES:The number of sonication cycles used for extraction. At most 1 instance(s) are allowed.
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR:The type of sonicator used for extraction. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_FRAGMENT_SIZE_RANGE:The fragment size range of the preparation. At most 1 instance(s) are allowed.
LIBRARY_STRATEGY:undef. Allowed values are: "ChIP-Seq". At most 1 instance(s) are allowed.
MOLECULE:undef. Allowed values are: "genomic DNA". At most 1 instance(s) are allowed.
MOLECULE_ONTOLOGY_CURIE:undef.
The metadata specifictaion for Chromatin Accessibility experiments is as defined below
DNASE_PROTOCOL:The protocol used for DNAse treatment. At most 1 instance(s) are allowed.
EXPERIMENT_ONTOLOGY_CURIE:undef.
EXPERIMENT_TYPE:undef. Allowed values are: "Chromatin Accessibility". At most 1 instance(s) are allowed.
EXTRACTION_PROTOCOL:The protocol used to isolate the extract material. At most 1 instance(s) are allowed.
LIBRARY_STRATEGY:undef. Allowed values are: "ATAC-seq", "DNase-Hypersensitivity", "NOME-Seq". At most 1 instance(s) are allowed.
MOLECULE:undef. Allowed values are: "genomic DNA". At most 1 instance(s) are allowed.
MOLECULE_ONTOLOGY_CURIE:undef.
The metadata specifictaion for MeDIP-Seq experiments is as defined below
EXPERIMENT_ONTOLOGY_CURIE:undef.
EXPERIMENT_TYPE:undef. Allowed values are: "DNA Methylation". At most 1 instance(s) are allowed.
EXTRACTION_PROTOCOL:The protocol used to isolate the extract material. At most 1 instance(s) are allowed.
EXTRACTION_PROTOCOL_SONICATION_CYCLES:The number of sonication cycles used for extraction. At most 1 instance(s) are allowed.
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR:The type of sonicator used for extraction. At most 1 instance(s) are allowed.
LIBRARY_STRATEGY:undef. Allowed values are: "MeDIP-Seq". At most 1 instance(s) are allowed.
MEDIP_ANTIBODY:The specific antibody used in the MeDIP protocol. At most 1 instance(s) are allowed.
MEDIP_ANTIBODY_CATALOG:The catalog from which the antibody was purchased. At most 1 instance(s) are allowed.
MEDIP_ANTIBODY_LOT:The lot identifier of the antibody. At most 1 instance(s) are allowed.
MEDIP_ANTIBODY_PROVIDER:The name of the company, laboratory or person that provided the antibody. At most 1 instance(s) are allowed.
MEDIP_PROTOCOL:The MeDIP protocol used. At most 1 instance(s) are allowed.
MEDIP_PROTOCOL_ANTIBODY_AMOUNT:The amount of antibody used in the MeDIP protocol. At most 1 instance(s) are allowed.
MEDIP_PROTOCOL_BEAD_AMOUNT:The amount of beads used in the MeDIP protocol. At most 1 instance(s) are allowed.
MEDIP_PROTOCOL_BEAD_TYPE:The type of bead used in the MeDIP protocol. At most 1 instance(s) are allowed.
MEDIP_PROTOCOL_DNA_AMOUNT:The amount of DNA used in the MeDIP protocol. At most 1 instance(s) are allowed.
MOLECULE:undef. Allowed values are: "genomic DNA". At most 1 instance(s) are allowed.
MOLECULE_ONTOLOGY_CURIE:undef.
The metadata specifictaion for MRE-Seq experiments is as defined below
EXPERIMENT_ONTOLOGY_CURIE:undef.
EXPERIMENT_TYPE:undef. Allowed values are: "DNA Methylation". At most 1 instance(s) are allowed.
LIBRARY_STRATEGY:undef. Allowed values are: "MRE-Seq". At most 1 instance(s) are allowed.
MOLECULE:undef. Allowed values are: "genomic DNA". At most 1 instance(s) are allowed.
MOLECULE_ONTOLOGY_CURIE:undef.
MRE_PROTOCOL:The MRE protocol. At most 1 instance(s) are allowed.
MRE_PROTOCOL_CHROMATIN_AMOUNT:The amount of chromatin used in the MRE protocol. At most 1 instance(s) are allowed.
MRE_PROTOCOL_RESTRICTION_ENZYME:The restriction enzyme(s) used in the MRE protocol. At most 1 instance(s) are allowed.
MRE_PROTOCOL_SIZE_FRACTION:The size of the fragments selected in the MRE protocol. At most 1 instance(s) are allowed.
The metadata specifictaion for Other experiments is as defined below
EXPERIMENT_ONTOLOGY_CURIE:undef.
EXPERIMENT_TYPE:undef. Allowed values are: "Other". At most 1 instance(s) are allowed.
The metadata specifictaion for RNA-Seq experiments is as defined below
AMPLIFIED:(Controlled Vocabulary) True or False - Is the sample amplified?. At most 1 instance(s) are allowed.
EXPERIMENT_ONTOLOGY_CURIE:undef.
EXPERIMENT_TYPE:undef. Allowed values are: "RNA-Seq", "mRNA-Seq", "smRNA-Seq", "total-RNA-Seq". At most 1 instance(s) are allowed.
- If 'experiment_type' is 'smRNA-Seq', then 'library_strategy' must be set to 'miRNA-Seq'
EXTRACTION_PROTOCOL:The protocol used to isolate the extract material. At most 1 instance(s) are allowed.
EXTRACTION_PROTOCOL_FRAGMENTATION:The fragmentation method used in the extraction protocol. At most 1 instance(s) are allowed.
EXTRACTION_PROTOCOL_RNA_ENRICHMENT:The mRNA enrichment method used in the extraction protocol. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_3'_ADAPTER_SEQUENCE:The sequence of the 3' adapter used for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_5'_ADAPTER_SEQUENCE:The sequence of the 5' adapter used for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_FRAGMENT_SIZE_RANGE:The fragment size range of the preparation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_FRAGMENTATION:The fragmentation method used in the library protocol. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE:The sequence of the PCR forward primer used for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES:The number of PCR cycles used for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE:The PCR polymerase used for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_PRIMER_CONC:The concentration of the PCR primers used for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL:The protocol for isolating PCR products used for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE:The sequence of the PCR reverse primer used for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_TEMPLATE_CONC:The PCR template concentration for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM:The thermocycling program used for library generation. At most 1 instance(s) are allowed.
LIBRARY_GENERATION_PROTOCOL:The protocol used to generate the library. At most 1 instance(s) are allowed.
LIBRARY_STRATEGY:undef. Allowed values are: "RNA-Seq", "miRNA-Seq". At most 1 instance(s) are allowed.
MOLECULE:undef. Allowed values are: "cytoplasmic RNA", "nuclear RNA", "polyA RNA", "small RNA", "total RNA". At most 1 instance(s) are allowed.
MOLECULE_ONTOLOGY_CURIE:undef.
PREPARATION_INITIAL_RNA_QNTY:The initial RNA quantity used in preparation. At most 1 instance(s) are allowed.
PREPARATION_PCR_NUMBER_CYCLES:The number of PCR cycles used to amplify. At most 1 instance(s) are allowed.
PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL:The protocol for reverse transcription used in preparation. At most 1 instance(s) are allowed.
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL:The protocol for 3’ adapter ligation used in preparation. At most 1 instance(s) are allowed.
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE:The sequence of the 3’ RNA adapter used in preparation. At most 1 instance(s) are allowed.
RNA_PREPARATION_5'_DEPHOSPHORYLATION:The protocol for 5’ dephosphorylation used in preparation. At most 1 instance(s) are allowed.
RNA_PREPARATION_5'_PHOSPHORYLATION:The protocol for 5’ phosphorylation used in preparation. At most 1 instance(s) are allowed.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL:The protocol for 5’ adapter ligation used in preparation. At most 1 instance(s) are allowed.
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE:The sequence of the 5’ RNA adapter used in preparation. At most 1 instance(s) are allowed.
RNA_PREPARATION_FRAGMENT_SIZE_RANGE:The mRNA fragment size range of the preparation. At most 1 instance(s) are allowed.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE:The sequence of the primer for reverse transcription used in preparation. At most 1 instance(s) are allowed.
TEMPLATE_TYPE:(Controlled Vocabulary) mRNA or cDNA - The type of template, if applicable. At most 1 instance(s) are allowed.
The metadata specifictaion for WGS experiments is as defined below
EXPERIMENT_TYPE:undef. Allowed values are: "WGS". At most 1 instance(s) are allowed.
EXTRACTION_PROTOCOL:The protocol used to isolate the extract material. At most 1 instance(s) are allowed.
LIBRARY_STRATEGY:undef. Allowed values are: "WGS". At most 1 instance(s) are allowed.
MOLECULE:undef. Allowed values are: "genomic DNA". At most 1 instance(s) are allowed.