{ "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://scischema.org/schemas/biology/crispr-cas9/1.0.0/master-schema.json", "version": "1.0.0", "title": "CRISPR-Cas9 Process Schema", "description": "A comprehensive schema representing the CRISPR-Cas9 gene-editing process, including inputs, experimental settings, instruments, outputs, and advanced CRISPR variants. This schema integrates applications in SOX gene editing, stem cell research, cancer modeling, and regenerative medicine.", "type": "object", "properties": { "inputs": { "type": "object", "description": "Components and sequences required for the CRISPR-based editing or detection process.", "properties": { "guideRNA": { "type": "object", "description": "The guide RNA (gRNA) or CRISPR RNA (crRNA) that directs the Cas nuclease to the target DNA or RNA sequence (5' to 3' direction).", "properties": { "sequence": { "type": "string", "description": "The nucleotide spacer sequence of the gRNA/crRNA. Must be 20 nucleotides for standard Cas9, variable for other nucleases like Cas12a, Cas13a, and Cas14.", "minLength": 18, "maxLength": 30, "pattern": "^[ACGTUacgtu]+$" }, "inSilicoDesigner": { "type": "string", "description": "Tool used for designing the gRNA/crRNA sequence (e.g., CHOPCHOP, CRISPOR, Benchling, IDT).", "enum": [ "CHOPCHOP", "CRISPOR", "Benchling", "IDT", "Other" ] }, "designerDetails": { "type": "string", "description": "Additional details about the in-silico designer if 'Other' is selected." }, "modifications": { "type": "array", "description": "Chemical or structural modifications applied to the gRNA/crRNA to enhance stability or specificity.", "items": { "type": "string", "enum": [ "2'-O-methyl", "Phosphorothioate", "2'-Fluoro", "Other" ] } }, "modificationDetails": { "type": "string", "description": "Additional details about gRNA/crRNA modifications if 'Other' is selected." }, "sgRNAStructure": { "type": "object", "description": "Structural features of the sgRNA that influence Cas9 conformational dynamics and cleavage activity.", "properties": { "fullLength": { "type": "boolean", "description": "Whether the sgRNA is full-length, which drives inward lobe closure of Cas9." }, "truncatedVariants": { "type": "array", "description": "Details of any truncated sgRNA variants used (e.g., Δguide1-20, Δhairpins1-2).", "items": { "type": "object", "properties": { "variantName": { "type": "string", "description": "Name of the truncated sgRNA variant (e.g., Δguide1-20)." }, "sequence": { "type": "string", "description": "Sequence of the truncated sgRNA variant." } }, "required": [ "variantName", "sequence" ] } } } }, "crRNAType": { "type": "string", "description": "Type of crRNA used, particularly relevant for Cas12, Cas13, and Cas14 systems (e.g., linear, circular).", "enum": [ "Linear", "Circular", "Other" ] }, "crRNADetails": { "type": "string", "description": "Additional details about the crRNA type if 'Other' is selected." } }, "required": [ "sequence", "inSilicoDesigner" ] }, "nucleaseSource": { "type": "object", "description": "Source and properties of the CRISPR-associated nuclease (e.g., Cas9, Cas12a, Cas13a, Cas14).", "properties": { "type": { "type": "string", "description": "Type of CRISPR nuclease used (e.g., Cas9, Cas12a, Cas13a, Cas14, BaseEditor, PrimeEditor).", "enum": [ "Cas9", "Cas12a", "Cas13a", "Cas14", "BaseEditor", "PrimeEditor", "Other" ] }, "typeDetails": { "type": "string", "description": "Additional details about the nuclease type if 'Other' is selected." }, "organism": { "type": "string", "description": "Source organism of the nuclease (e.g., Streptococcus pyogenes for SpCas9, Acidaminococcus sp. for AsCas12a).", "enum": [ "Streptococcus pyogenes (SpCas9)", "Staphylococcus aureus (SaCas9)", "Acidaminococcus sp. (AsCas12a)", "Francisella novicida (FnCas12a)", "Lachnospiraceae bacterium (LbCas12a)", "Leptotrichia buccalis (LbuCas13a)", "Leptotrichia shahii (LshCas13a)", "Other" ] }, "organismDetails": { "type": "string", "description": "Additional details about the organism if 'Other' is selected." }, "deliveryFormat": { "type": "string", "description": "Format of the nuclease and gRNA delivery (e.g., plasmid DNA, mRNA, RNP).", "enum": [ "plasmid DNA", "mRNA", "Ribonucleoprotein (RNP)", "Viral Vector", "Other" ] }, "deliveryFormatDetails": { "type": "string", "description": "Additional details about the delivery format if 'Other' is selected." }, "engineeredVariant": { "type": "string", "description": "Engineered variant of the nuclease (e.g., high-fidelity Cas9, dCas9, nCas9).", "enum": [ "Wild-type", "High-fidelity (e.g., SpCas9-HF1)", "dCas9 (dead Cas9)", "nCas9 (nickase Cas9)", "ΔHNH-Cas9", "Other" ] }, "variantDetails": { "type": "string", "description": "Additional details about the engineered variant if 'Other' is selected." }, "conformationalDynamics": { "type": "object", "description": "Conformational dynamics of the nuclease domains, particularly relevant for Cas9 and Cas12a.", "properties": { "hnhDomainState": { "type": "string", "description": "Conformational state of the HNH nuclease domain (e.g., activated, inactive, intermediate).", "enum": [ "Activated", "Inactive", "Intermediate", "Other" ] }, "hnhDomainStateDetails": { "type": "string", "description": "Additional details about the HNH domain conformational state if 'Other' is selected." }, "fretConstructs": { "type": "array", "description": "Details of FRET constructs used to monitor conformational dynamics (e.g., Cas9hinge, Cas9HNH-1, Cas9HNH-2).", "items": { "type": "object", "properties": { "constructName": { "type": "string", "description": "Name of the FRET construct (e.g., Cas9hinge, Cas9HNH-1)." }, "labeledResidues": { "type": "string", "description": "Residues labeled with FRET dyes (e.g., D435C/E945C for Cas9hinge)." }, "dyesUsed": { "type": "string", "description": "FRET dyes used (e.g., Cy3/Cy5)." }, "ratioA": { "type": "number", "description": "Observed (ratio)A value, which is proportional to FRET efficiency." } }, "required": [ "constructName", "labeledResidues", "dyesUsed" ] } }, "allostericCommunication": { "type": "boolean", "description": "Whether allosteric communication between HNH and RuvC domains was observed." }, "linkerMutations": { "type": "array", "description": "Details of mutations introduced in the HNH-RuvC linker region to study allosteric communication.", "items": { "type": "object", "properties": { "mutation": { "type": "string", "description": "Mutation introduced (e.g., E923P/T924P)." }, "effectOnCleavage": { "type": "string", "description": "Effect of the mutation on target and non-target strand cleavage." } }, "required": [ "mutation" ] } } } }, "transCleavageActivity": { "type": "boolean", "description": "Whether the nuclease exhibits trans-cleavage activity (e.g., Cas12a, Cas13a, Cas14)." } }, "required": [ "type", "organism", "deliveryFormat" ] }, "targetDNA": { "type": "object", "description": "Target DNA sequence and Protospacer Adjacent Motif (PAM), if applicable.", "properties": { "referenceGenome": { "type": "string", "description": "The specific genome build used to anchor coordinates (e.g., GRCh38, GRCm39).", "enum": [ "GRCh38 (hg38)", "GRCh37 (hg19)", "GRCm39 (Mouse)", "Other" ] }, "referenceGenomeDetails": { "type": "string", "description": "Additional details about the reference genome if 'Other' is selected." }, "genomicLocation": { "type": "string", "description": "Genomic location of the target DNA (e.g., chromosome, position, gene name). Format: 'chrX:start-end'." }, "pamSequence": { "type": "string", "description": "Protospacer Adjacent Motif (PAM) sequence required for nuclease binding (e.g., 'NGG' for SpCas9, 'TTTV' for Cas12a).", "pattern": "^[ACGTUacgtu]{3,6}$" }, "targetSequence": { "type": "string", "description": "The nucleotide target sequence adjacent to the PAM (5' to 3' direction). Length depends on the nuclease type (e.g., 20 nt for Cas9, 23 nt for Cas12a).", "minLength": 18, "maxLength": 30, "pattern": "^[ACGTUacgtu]+$" }, "strand": { "type": "string", "description": "Strand of the DNA targeted by the gRNA (plus or minus).", "enum": [ "plus", "minus" ] }, "predictedOffTargetSites": { "type": "array", "description": "Computational predictions of potential off-target activity based on sequence homology and PAM availability.", "items": { "type": "object", "properties": { "genomicLocation": { "type": "string", "description": "Genomic location of the predicted off-target site (e.g., 'chrX:start-end')." }, "sequence": { "type": "string", "description": "Sequence of the predicted off-target site." }, "mismatchPositions": { "type": "array", "description": "Positions of mismatches relative to the target sequence (1-based indexing).", "items": { "type": "integer", "minimum": 1, "maximum": 30 } }, "mismatchCount": { "type": "integer", "description": "Total number of mismatches between the gRNA and the off-target site.", "minimum": 1 }, "pam": { "type": "string", "description": "PAM sequence of the off-target site.", "pattern": "^[ACGTUacgtu]{3,6}$" } }, "required": [ "genomicLocation", "sequence", "mismatchCount", "pam" ] } }, "offTargetSites": { "type": "array", "description": "List of potential off-target sites with mismatches relative to the target sequence.", "items": { "type": "object", "properties": { "genomicLocation": { "type": "string", "description": "Genomic location of the off-target site (e.g., 'chrX:start-end')." }, "sequence": { "type": "string", "description": "Sequence of the off-target site." }, "mismatchPositions": { "type": "array", "description": "Positions of mismatches relative to the target sequence (1-based indexing).", "items": { "type": "integer", "minimum": 1, "maximum": 30 } }, "mismatchCount": { "type": "integer", "description": "Total number of mismatches between the gRNA and the off-target site.", "minimum": 1 }, "pam": { "type": "string", "description": "PAM sequence of the off-target site.", "pattern": "^[ACGTUacgtu]{3,6}$" }, "conformationalState": { "type": "string", "description": "Conformational state of the nuclease domain when bound to this off-target site (e.g., activated, inactive, intermediate).", "enum": [ "Activated", "Inactive", "Intermediate", "Other" ] } }, "required": [ "genomicLocation", "sequence", "mismatchCount", "pam" ] } } }, "required": [ "referenceGenome", "genomicLocation", "pamSequence", "targetSequence" ] }, "targetRNA": { "type": "object", "description": "Target RNA sequence for Cas13-based detection systems, if applicable.", "properties": { "genomicLocation": { "type": "string", "description": "Genomic location of the target RNA (e.g., virus, gene name)." }, "targetSequence": { "type": "string", "description": "The nucleotide target sequence for the crRNA (5' to 3' direction).", "minLength": 18, "maxLength": 30, "pattern": "^[ACGUacgu]+$" }, "preSpacerFlankingSite": { "type": "string", "description": "Pre-spacer flanking site (PFS) sequence required for Cas13 binding (e.g., 'A' for LwaCas13a).", "pattern": "^[ACGUacgu]{1,2}$" } }, "required": [ "genomicLocation", "targetSequence" ] }, "donorTemplate": { "type": "object", "description": "Donor template for Homology-Directed Repair (HDR) or base/prime editing, if applicable.", "properties": { "sequence": { "type": "string", "description": "Sequence of the donor template (ssDNA, dsDNA, or plasmid)." }, "type": { "type": "string", "description": "Type of donor template (e.g., ssDNA, dsDNA, plasmid).", "enum": [ "ssDNA", "dsDNA", "plasmid", "Other" ] }, "typeDetails": { "type": "string", "description": "Additional details about the donor template type if 'Other' is selected." }, "homologyArmLength": { "type": "integer", "description": "Length of homology arms in base pairs (bp), if applicable.", "minimum": 20, "maximum": 1000 }, "modifications": { "type": "array", "description": "Chemical or structural modifications applied to the donor template to enhance HDR efficiency.", "items": { "type": "string", "enum": [ "Phosphorothioate", "2'-O-methyl", "Locked Nucleic Acid (LNA)", "Other" ] } }, "modificationDetails": { "type": "string", "description": "Additional details about donor template modifications if 'Other' is selected." } }, "required": [ "sequence", "type" ] }, "editingStrategy": { "type": "object", "description": "Strategy used for gene editing or detection (e.g., knockout, knock-in, base editing, prime editing, SOX gene editing).", "properties": { "type": { "type": "string", "description": "Type of editing or detection strategy employed.", "enum": [ "Knockout", "Knock-in", "Base Editing", "Prime Editing", "Transcriptional Regulation", "Epigenetic Modulation", "SOX Gene Editing", "Stem Cell Differentiation", "Cancer Modeling", "Regenerative Medicine", "Other" ] }, "typeDetails": { "type": "string", "description": "Additional details about the editing or detection strategy if 'Other' is selected." }, "soxGeneTarget": { "type": "string", "description": "Specific SOX gene targeted for editing (e.g., SOX2, SOX9, SOX17).", "enum": [ "SOX1", "SOX2", "SOX3", "SOX4", "SOX5", "SOX6", "SOX7", "SOX8", "SOX9", "SOX10", "SOX11", "SOX17", "Other" ] }, "soxGeneTargetDetails": { "type": "string", "description": "Additional details about the SOX gene target if 'Other' is selected." }, "baseEditorType": { "type": "string", "description": "Type of base editor used (e.g., CBE, ABE, CGBE), if applicable.", "enum": [ "Cytosine Base Editor (CBE)", "Adenine Base Editor (ABE)", "Glycosylase Base Editor (CGBE)", "Dual Base Editor (AGBE)", "Other" ] }, "baseEditorDetails": { "type": "string", "description": "Additional details about the base editor if 'Other' is selected." }, "primeEditorType": { "type": "string", "description": "Type of prime editor used (e.g., PE2, PE3, PEmax), if applicable.", "enum": [ "PE2", "PE3", "PEmax", "Other" ] }, "primeEditorDetails": { "type": "string", "description": "Additional details about the prime editor if 'Other' is selected." }, "pegRNA": { "type": "object", "description": "Prime editing guide RNA (pegRNA) details, if applicable.", "properties": { "sequence": { "type": "string", "description": "Sequence of the pegRNA, including spacer, reverse transcriptase template, and primer binding site." }, "spacerLength": { "type": "integer", "description": "Length of the spacer sequence in the pegRNA.", "minimum": 10, "maximum": 30 }, "templateLength": { "type": "integer", "description": "Length of the reverse transcriptase template in the pegRNA.", "minimum": 10, "maximum": 50 }, "pbsLength": { "type": "integer", "description": "Length of the primer binding site (PBS) in the pegRNA.", "minimum": 8, "maximum": 15 } }, "required": [ "sequence" ] }, "detectionTarget": { "type": "string", "description": "Specific target for detection strategies (e.g., antibiotic resistance gene, antibiotic molecule).", "enum": [ "Antibiotic Resistance Gene", "Antibiotic Molecule", "Other" ] }, "detectionTargetDetails": { "type": "string", "description": "Additional details about the detection target if 'Other' is selected." }, "signalAmplification": { "type": "string", "description": "Method used for signal amplification in detection strategies (e.g., RPA, LAMP, HCR).", "enum": [ "Recombinase Polymerase Amplification (RPA)", "Loop-Mediated Isothermal Amplification (LAMP)", "Hybridization Chain Reaction (HCR)", "Strand Displacement Amplification (SDA)", "Other" ] }, "signalAmplificationDetails": { "type": "string", "description": "Additional details about the signal amplification method if 'Other' is selected." }, "biosensingMethod": { "type": "string", "description": "Biosensing method used for detection (e.g., fluorescence, colorimetric, electrochemical).", "enum": [ "Fluorescence", "Colorimetric", "Electrochemical", "Surface-Enhanced Raman Scattering (SERS)", "Metal Isotope Labeling", "Other" ] }, "biosensingMethodDetails": { "type": "string", "description": "Additional details about the biosensing method if 'Other' is selected." } }, "required": [ "type" ] } }, "required": [ "guideRNA", "nucleaseSource", "targetDNA" ] }, "deliveryExecution": { "type": "object", "description": "Groups the physical execution, molecular format, timing, and biological host for the CRISPR-Cas9 process.", "properties": { "deliveryMethod": { "type": "object", "description": "Integrated unit combining delivery method, specific instrument, and detailed protocol steps.", "properties": { "methodName": { "type": "string", "description": "Delivery method (e.g., Electroporation, Lipofection, Viral Transduction) or assay type (e.g., in vitro detection).", "enum": [ "Electroporation", "Lipofection", "Viral Transduction", "Peptide-Mediated Delivery", "Nanoparticles", "In Vitro Detection", "Other" ] }, "methodDetails": { "type": "string", "description": "Additional details about the delivery method or assay type if 'Other' is selected." }, "instrument": { "type": "object", "description": "Specific hardware used for delivery or detection.", "properties": { "manufacturer": { "type": "string", "description": "Manufacturer of the delivery or detection system (e.g., Thermo Fisher, Lonza, Bio-Rad)." }, "model": { "type": "string", "description": "Model of the delivery or detection system (e.g., Neon, Nucleofector, Lipofectamine)." } }, "required": [ "manufacturer", "model" ] }, "protocol": { "type": "object", "description": "Detailed steps and parameters for the selected delivery method or detection assay.", "oneOf": [ { "type": "object", "description": "Electroporation (Nucleofection) Protocol.", "properties": { "protocolType": { "type": "string", "enum": [ "Electroporation" ] }, "steps": { "type": "array", "description": "Steps involved in the Electroporation protocol.", "items": { "type": "object", "properties": { "stepNumber": { "type": "integer", "description": "Step number in the protocol." }, "stepName": { "type": "string", "description": "Name of the step (e.g., 'Cell Preparation', 'RNP Assembly', 'Pulse Application', 'Recovery')." }, "description": { "type": "string", "description": "Description of the step." }, "parameters": { "type": "object", "description": "Parameters specific to this step (e.g., voltage, pulse duration, cell density).", "properties": { "voltage": { "type": "number", "description": "Voltage applied during electroporation (in volts).", "minimum": 0 }, "pulseDuration": { "type": "number", "description": "Duration of the pulse (in milliseconds).", "minimum": 0 }, "numberOfPulses": { "type": "integer", "description": "Number of pulses applied.", "minimum": 1 }, "cellDensity": { "type": "number", "description": "Density of cells per reaction (e.g., cells/mL).", "minimum": 0 }, "buffer": { "type": "string", "description": "Type of electroporation buffer used (e.g., P3, SE, SF)." } } } }, "required": [ "stepNumber", "stepName", "description" ] } } }, "required": [ "protocolType", "steps" ] }, { "type": "object", "description": "Lipofection Protocol.", "properties": { "protocolType": { "type": "string", "enum": [ "Lipofection" ] }, "steps": { "type": "array", "description": "Steps involved in the Lipofection protocol.", "items": { "type": "object", "properties": { "stepNumber": { "type": "integer", "description": "Step number in the protocol." }, "stepName": { "type": "string", "description": "Name of the step (e.g., 'Seeding', 'Complex Formation', 'Transfection', 'Analysis')." }, "description": { "type": "string", "description": "Description of the step." }, "parameters": { "type": "object", "description": "Parameters specific to this step (e.g., reagent volume, incubation time).", "properties": { "reagent": { "type": "string", "description": "Lipofection reagent used (e.g., Lipofectamine CRISPRMAX, RNAiMAX)." }, "volume": { "type": "number", "description": "Volume of reagent used (in microliters).", "minimum": 0 }, "incubationTime": { "type": "number", "description": "Incubation time for complex formation (in minutes).", "minimum": 0 }, "cellConfluency": { "type": "number", "description": "Percentage confluency of cells at the time of transfection.", "minimum": 0, "maximum": 100 } } } }, "required": [ "stepNumber", "stepName", "description" ] } } }, "required": [ "protocolType", "steps" ] }, { "type": "object", "description": "Viral Transduction Protocol.", "properties": { "protocolType": { "type": "string", "enum": [ "Viral Transduction" ] }, "steps": { "type": "array", "description": "Steps involved in the Viral Transduction protocol.", "items": { "type": "object", "properties": { "stepNumber": { "type": "integer", "description": "Step number in the protocol." }, "stepName": { "type": "string", "description": "Name of the step (e.g., 'Vector Selection', 'Viral Production', 'Concentration and Titration', 'Transduction', 'Selection')." }, "description": { "type": "string", "description": "Description of the step." }, "parameters": { "type": "object", "description": "Parameters specific to this step (e.g., viral vector, MOI, incubation time).", "properties": { "vector": { "type": "string", "description": "Viral vector used (e.g., AAV, Lentivirus, Adenovirus)." }, "moi": { "type": "number", "description": "Multiplicity of Infection (MOI).", "minimum": 0 }, "incubationTime": { "type": "number", "description": "Incubation time for transduction (in hours).", "minimum": 0 }, "enhancer": { "type": "string", "description": "Enhancer used to increase transduction efficiency (e.g., polybrene, retronectin)." } } } }, "required": [ "stepNumber", "stepName", "description" ] } } }, "required": [ "protocolType", "steps" ] }, { "type": "object", "description": "Peptide-Mediated Delivery Protocol.", "properties": { "protocolType": { "type": "string", "enum": [ "Peptide-Mediated Delivery" ] }, "steps": { "type": "array", "description": "Steps involved in the Peptide-Mediated Delivery protocol.", "items": { "type": "object", "properties": { "stepNumber": { "type": "integer", "description": "Step number in the protocol." }, "stepName": { "type": "string", "description": "Name of the step (e.g., 'Complex Formation', 'Incubation', 'Wash')." }, "description": { "type": "string", "description": "Description of the step." }, "parameters": { "type": "object", "description": "Parameters specific to this step (e.g., peptide type, concentration, incubation time).", "properties": { "peptideType": { "type": "string", "description": "Type of peptide used (e.g., TAT, HA2, Nuclear Localization Signal)." }, "concentration": { "type": "number", "description": "Concentration of peptide used (in micromolar).", "minimum": 0 }, "incubationTime": { "type": "number", "description": "Incubation time (in minutes).", "minimum": 0 } } } }, "required": [ "stepNumber", "stepName", "description" ] } } }, "required": [ "protocolType", "steps" ] }, { "type": "object", "description": "Nanoparticle Delivery Protocol.", "properties": { "protocolType": { "type": "string", "enum": [ "Nanoparticles" ] }, "steps": { "type": "array", "description": "Steps involved in the Nanoparticle Delivery protocol.", "items": { "type": "object", "properties": { "stepNumber": { "type": "integer", "description": "Step number in the protocol." }, "stepName": { "type": "string", "description": "Name of the step (e.g., 'Formulation', 'Incubation', 'Wash')." }, "description": { "type": "string", "description": "Description of the step." }, "parameters": { "type": "object", "description": "Parameters specific to this step (e.g., nanoparticle type, concentration, incubation time).", "properties": { "nanoparticleType": { "type": "string", "description": "Type of nanoparticle used (e.g., Lipid Nanoparticle, Gold Nanoparticle)." }, "concentration": { "type": "number", "description": "Concentration of nanoparticles used (in nanomolar).", "minimum": 0 }, "incubationTime": { "type": "number", "description": "Incubation time (in minutes).", "minimum": 0 }, "targetingLigand": { "type": "string", "description": "Targeting ligand used to enhance specificity (e.g., antibody, peptide)." } } } }, "required": [ "stepNumber", "stepName", "description" ] } } }, "required": [ "protocolType", "steps" ] }, { "type": "object", "description": "In Vitro Detection Protocol.", "properties": { "protocolType": { "type": "string", "enum": [ "In Vitro Detection" ] }, "steps": { "type": "array", "description": "Steps involved in the in vitro detection protocol.", "items": { "type": "object", "properties": { "stepNumber": { "type": "integer", "description": "Step number in the protocol." }, "stepName": { "type": "string", "description": "Name of the step (e.g., 'Sample Preparation', 'RNP Assembly', 'Incubation', 'Signal Detection')." }, "description": { "type": "string", "description": "Description of the step." }, "parameters": { "type": "object", "description": "Parameters specific to this step (e.g., incubation time, temperature, buffer composition).", "properties": { "incubationTime": { "type": "number", "description": "Incubation time for the reaction (in minutes).", "minimum": 0 }, "temperature": { "type": "number", "description": "Temperature at which the reaction is conducted (in °C).", "default": 37 }, "buffer": { "type": "string", "description": "Type of buffer used (e.g., HEPES, Tris-HCl)." }, "reporterProbe": { "type": "string", "description": "Type of reporter probe used for signal detection (e.g., fluorescent, colorimetric)." } } } }, "required": [ "stepNumber", "stepName", "description" ] } } }, "required": [ "protocolType", "steps" ] } ] } }, "required": [ "methodName", "instrument" ] }, "deliveryFormat": { "type": "string", "description": "Format of the nuclease and gRNA delivery (e.g., plasmid DNA, mRNA, RNP).", "enum": [ "plasmid DNA", "mRNA", "Ribonucleoprotein (RNP)", "Viral Vector", "Other" ] }, "molarRatios": { "type": "object", "description": "Molar ratios of CRISPR components.", "properties": { "casToGrna": { "type": "number", "description": "Molar ratio of Cas nuclease to gRNA/crRNA (e.g., 1:1, 1:2)." }, "donorToCas": { "type": "number", "description": "Molar ratio of donor template to Cas nuclease (if applicable)." } }, "required": [ "casToGrna" ] }, "incubationTimes": { "type": "object", "description": "Incubation times for various stages of the process.", "properties": { "rnPAssembly": { "type": "number", "description": "Incubation time for RNP assembly (in minutes).", "minimum": 0 }, "postTransfection": { "type": "number", "description": "Time before assessing editing efficiency post-transfection (in hours).", "minimum": 0 }, "recovery": { "type": "number", "description": "Recovery time post-delivery before further processing (in hours).", "minimum": 0 }, "detectionReaction": { "type": "number", "description": "Incubation time for the detection reaction (in minutes).", "minimum": 0 } }, "required": [ "rnPAssembly", "postTransfection" ] }, "cellType": { "type": "object", "description": "Type and characteristics of the cells used in the experiment, if applicable.", "properties": { "type": { "type": "string", "description": "Type of cells used (e.g., primary T cells, iPSCs, cell line, embryonic stem cells).", "enum": [ "Primary T cells", "iPSCs", "Cell Line", "Embryonic Stem Cells", "Other" ] }, "typeDetails": { "type": "string", "description": "Additional details about the cell type if 'Other' is selected." }, "source": { "type": "string", "description": "Source of the cells (e.g., donor, commercial cell line)." }, "donorId": { "type": "string", "description": "Identifier for the donor, if applicable." }, "cellLine": { "type": "string", "description": "Name of the cell line, if applicable." }, "passageNumber": { "type": "integer", "description": "Passage number of the cells at the time of editing.", "minimum": 0 }, "organism": { "type": "string", "description": "Organism from which the cells are derived (e.g., human, mouse, axolotl).", "enum": [ "Human", "Mouse", "Axolotl", "Zebrafish", "Rat", "Other" ] }, "organismDetails": { "type": "string", "description": "Additional details about the organism if 'Other' is selected." } }, "required": [ "type" ] }, "cultureConditions": { "type": "object", "description": "Conditions under which the cells are cultured and expanded, if applicable.", "properties": { "medium": { "type": "string", "description": "Type of culture medium used (e.g., RPMI, X-VIVO 15)." }, "supplements": { "type": "array", "description": "Supplements added to the culture medium (e.g., FBS, cytokines).", "items": { "type": "string" } }, "temperature": { "type": "number", "description": "Temperature of incubation (in °C).", "default": 37 }, "co2Concentration": { "type": "number", "description": "CO2 concentration in the incubator (in percentage).", "default": 5 }, "humidity": { "type": "number", "description": "Humidity level in the incubator (in percentage).", "minimum": 0, "maximum": 100 } }, "required": [ "medium" ] } }, "required": [ "deliveryMethod", "deliveryFormat", "molarRatios", "incubationTimes", "cellType" ] }, "experimentalSettings": { "type": "object", "description": "Experimental parameters and protocols for delivering CRISPR components into cells or for in vitro detection assays.", "properties": { "fretExperiments": { "type": "object", "description": "Details of Förster Resonance Energy Transfer (FRET) experiments used to study nuclease conformational dynamics, if applicable.", "properties": { "experimentType": { "type": "string", "description": "Type of FRET experiment conducted (e.g., intramolecular FRET, single-molecule FRET).", "enum": [ "Intramolecular FRET", "Single-Molecule FRET", "Other" ] }, "experimentDetails": { "type": "string", "description": "Additional details about the FRET experiment if 'Other' is selected." }, "buffersUsed": { "type": "array", "description": "Buffers used in the FRET experiments (e.g., reaction buffer with heparin).", "items": { "type": "string" } }, "temperature": { "type": "number", "description": "Temperature at which FRET experiments were conducted (in °C)." }, "dataAnalysis": { "type": "object", "description": "Methods used for FRET data analysis.", "properties": { "software": { "type": "string", "description": "Software used for FRET data analysis (e.g., FluorEssence, Prism)." }, "methods": { "type": "array", "description": "Methods used for calculating FRET efficiency (e.g., (ratio)A, donor fluorescence lifetime).", "items": { "type": "string" } } } } } }, "detectionAssay": { "type": "object", "description": "Details of the detection assay used for SOX gene editing or other applications.", "properties": { "assayType": { "type": "string", "description": "Type of detection assay (e.g., DETECTR, SHERLOCK, HOLMES, CaT-SMelor).", "enum": [ "DETECTR", "SHERLOCK", "HOLMES", "CaT-SMelor", "FLASH", "Other" ] }, "assayDetails": { "type": "string", "description": "Additional details about the assay type if 'Other' is selected." }, "amplificationMethod": { "type": "string", "description": "Method used for nucleic acid amplification, if applicable (e.g., RPA, LAMP, PCR).", "enum": [ "Recombinase Polymerase Amplification (RPA)", "Loop-Mediated Isothermal Amplification (LAMP)", "Polymerase Chain Reaction (PCR)", "None", "Other" ] }, "amplificationDetails": { "type": "string", "description": "Additional details about the amplification method if 'Other' is selected." }, "signalDetectionMethod": { "type": "string", "description": "Method used for signal detection (e.g., fluorescence, colorimetric, electrochemical).", "enum": [ "Fluorescence", "Colorimetric", "Electrochemical", "Surface-Enhanced Raman Scattering (SERS)", "Metal Isotope Labeling", "Other" ] }, "signalDetectionDetails": { "type": "string", "description": "Additional details about the signal detection method if 'Other' is selected." }, "limitOfDetection": { "type": "string", "description": "Limit of detection for the assay (e.g., '10 copies/µL', '1 pM')." }, "detectionTime": { "type": "number", "description": "Time required for detection (in minutes).", "minimum": 0 }, "sampleType": { "type": "string", "description": "Type of sample used in the assay (e.g., clinical, environmental, food).", "enum": [ "Clinical", "Environmental", "Food", "Other" ] }, "sampleTypeDetails": { "type": "string", "description": "Additional details about the sample type if 'Other' is selected." } } } } }, "instruments": { "type": "object", "description": "Instruments and equipment used in the CRISPR-based process, excluding delivery systems which are now part of experimentalSettings.", "properties": { "synthesiser": { "type": "object", "description": "Oligonucleotide synthesiser for creating custom gRNAs, crRNAs, and donor templates.", "properties": { "manufacturer": { "type": "string", "description": "Manufacturer of the synthesiser (e.g., IDT, Thermo Fisher)." }, "model": { "type": "string", "description": "Model of the synthesiser." } }, "required": [ "manufacturer", "model" ] }, "validationSystem": { "type": "object", "description": "Systems used for validating the results of the CRISPR editing or detection process.", "properties": { "sequencer": { "type": "object", "description": "DNA/RNA sequencer used for confirming edits or detection results.", "properties": { "manufacturer": { "type": "string", "description": "Manufacturer of the sequencer (e.g., Illumina, Oxford Nanopore, PacBio)." }, "model": { "type": "string", "description": "Model of the sequencer." }, "sequencingMethod": { "type": "string", "description": "Sequencing method used (e.g., Sanger, NGS, Long-read).", "enum": [ "Sanger", "Next-Generation Sequencing (NGS)", "Long-read Sequencing" ] } }, "required": [ "manufacturer", "model", "sequencingMethod" ] }, "flowCytometer": { "type": "object", "description": "Flow cytometer used for sorting or analyzing edited cells (if applicable).", "properties": { "manufacturer": { "type": "string", "description": "Manufacturer of the flow cytometer (e.g., BD Biosciences, Beckman Coulter)." }, "model": { "type": "string", "description": "Model of the flow cytometer." } }, "required": [ "manufacturer", "model" ] }, "microscope": { "type": "object", "description": "Microscope used for imaging cells or detection results (if applicable).", "properties": { "manufacturer": { "type": "string", "description": "Manufacturer of the microscope (e.g., Zeiss, Leica)." }, "model": { "type": "string", "description": "Model of the microscope." }, "type": { "type": "string", "description": "Type of microscope (e.g., Confocal, Fluorescence, Brightfield).", "enum": [ "Confocal", "Fluorescence", "Brightfield", "Other" ] } }, "required": [ "manufacturer", "model" ] }, "thermocycler": { "type": "object", "description": "Thermocycler used for PCR amplification (if applicable).", "properties": { "manufacturer": { "type": "string", "description": "Manufacturer of the thermocycler (e.g., Bio-Rad, Applied Biosystems)." }, "model": { "type": "string", "description": "Model of the thermocycler." } }, "required": [ "manufacturer", "model" ] }, "fluorescenceSpectrometer": { "type": "object", "description": "Fluorescence spectrometer used for FRET experiments or fluorescence-based detection assays.", "properties": { "manufacturer": { "type": "string", "description": "Manufacturer of the fluorescence spectrometer (e.g., HORIBA Jobin Yvon)." }, "model": { "type": "string", "description": "Model of the fluorescence spectrometer." }, "settings": { "type": "object", "description": "Settings used during FRET experiments or detection assays.", "properties": { "excitationWavelength": { "type": "number", "description": "Excitation wavelength used (in nm)." }, "emissionRange": { "type": "string", "description": "Emission range collected (e.g., 550-800 nm)." }, "slitWidth": { "type": "number", "description": "Slit width used (in nm)." }, "integrationTime": { "type": "number", "description": "Integration time for fluorescence measurements (in seconds)." } } } }, "required": [ "manufacturer", "model" ] }, "massSpectrometer": { "type": "object", "description": "Mass spectrometer used for metal isotope labeling detection (e.g., ICPMS).", "properties": { "manufacturer": { "type": "string", "description": "Manufacturer of the mass spectrometer (e.g., Thermo Fisher, Agilent)." }, "model": { "type": "string", "description": "Model of the mass spectrometer." }, "type": { "type": "string", "description": "Type of mass spectrometer (e.g., ICPMS, MALDI-TOF).", "enum": [ "ICPMS", "MALDI-TOF", "Other" ] } }, "required": [ "manufacturer", "model" ] }, "electrochemicalWorkstation": { "type": "object", "description": "Electrochemical workstation used for electrochemical detection assays.", "properties": { "manufacturer": { "type": "string", "description": "Manufacturer of the electrochemical workstation (e.g., CH Instruments, Metrohm)." }, "model": { "type": "string", "description": "Model of the electrochemical workstation." } }, "required": [ "manufacturer", "model" ] } }, "required": [ "sequencer" ] } }, "required": [ "synthesiser", "validationSystem" ] }, "outputs": { "type": "object", "description": "Results and metrics from the CRISPR-based editing or detection process.", "properties": { "editingEfficiency": { "type": "number", "description": "Percentage of cells successfully modified (0-100%), if applicable.", "minimum": 0, "maximum": 100 }, "indelProfile": { "type": "object", "description": "Breakdown of insertions and deletions (indels) generated, if applicable.", "properties": { "insertions": { "type": "number", "description": "Percentage of insertions in the indel profile." }, "deletions": { "type": "number", "description": "Percentage of deletions in the indel profile." }, "sizeDistribution": { "type": "object", "description": "Distribution of indel sizes (e.g., 1 bp, 2 bp, etc.).", "unevaluatedProperties": { "type": "number", "description": "Percentage of indels of a specific size." } }, "details": { "type": "string", "description": "Additional details about the indel profile." } }, "required": [ "insertions", "deletions" ] }, "onOffTargetRatio": { "type": "object", "description": "Ratio and analysis of on-target to off-target edits, if applicable.", "properties": { "scoreType": { "type": "string", "description": "Type of score used to quantify on-target/off-target activity (e.g., E-score, S-score, CFD score).", "enum": [ "E-score", "S-score", "CFD score", "Other" ] }, "scoreValue": { "type": "number", "description": "Value of the on-target/off-target score." }, "scoreDetails": { "type": "string", "description": "Additional details about the score if 'Other' is selected." }, "offTargetSites": { "type": "array", "description": "List of identified off-target sites with their locations and editing frequencies.", "items": { "type": "object", "properties": { "genomicLocation": { "type": "string", "description": "Genomic location of the off-target site (e.g., 'chrX:start-end')." }, "sequence": { "type": "string", "description": "Sequence of the off-target site." }, "mismatches": { "type": "integer", "description": "Number of mismatches between the gRNA and the off-target site." }, "editingFrequency": { "type": "number", "description": "Frequency of editing at the off-target site (0-100%).", "minimum": 0, "maximum": 100 }, "hnhConformationalState": { "type": "string", "description": "Conformational state of the HNH domain when bound to this off-target site (e.g., activated, inactive, intermediate).", "enum": [ "Activated", "Inactive", "Intermediate", "Other" ] } }, "required": [ "genomicLocation", "sequence", "mismatches", "editingFrequency" ] } } }, "required": [ "scoreType", "scoreValue" ] }, "genomicStability": { "type": "object", "description": "Reports on large-scale structural variations resulting from the edit (e.g., translocations, large deletions), if applicable.", "properties": { "translocations": { "type": "boolean", "description": "Whether translocations were detected." }, "largeDeletions": { "type": "boolean", "description": "Whether large deletions were detected." }, "chromosomeLoss": { "type": "boolean", "description": "Whether chromosome loss was detected." }, "details": { "type": "string", "description": "Additional details about genomic stability, including methods used for detection (e.g., karyotyping, PEM-seq)." } } }, "biologicalFitnessReport": { "type": "object", "description": "A unified unit reporting on the quality, health, and functionality of the living product post-edit, if applicable.", "properties": { "cellViability": { "type": "number", "description": "Percentage of viable cells post-editing (0-100%).", "minimum": 0, "maximum": 100 }, "cellProliferation": { "type": "number", "description": "Fold change in cell proliferation post-editing relative to control.", "minimum": 0 }, "functionalAssays": { "type": "object", "description": "Results of functional assays to evaluate the edited cells (e.g., cytokine production, cytotoxicity).", "properties": { "cytokineProduction": { "type": "object", "description": "Levels of cytokines produced by edited cells (e.g., IFN-γ, IL-2).", "unevaluatedProperties": { "type": "number", "description": "Concentration of the cytokine (in pg/mL or ng/mL)." } }, "cytotoxicity": { "type": "number", "description": "Percentage of target cells killed by edited CAR-T cells (0-100%).", "minimum": 0, "maximum": 100 }, "activationMarkers": { "type": "object", "description": "Expression levels of activation markers (e.g., CD69, CD25).", "unevaluatedProperties": { "type": "number", "description": "Percentage of cells expressing the marker." } } } } }, "required": [ "cellViability" ] }, "medicalObjective": { "type": "object", "description": "Combines the targeted disease and the intended therapeutic strategy, if applicable.", "properties": { "targetDisease": { "type": "string", "description": "Disease targeted by the edited cells or detection assay (e.g., cancer, genetic disorder, bacterial infection, SOXopathies)." }, "therapeuticPotential": { "type": "string", "description": "Potential therapeutic applications of the edited cells or detection assay (e.g., CAR-T therapy, gene correction, regenerative medicine)." }, "safetyConcerns": { "type": "string", "description": "Potential safety concerns associated with the edited cells or detection assay (e.g., off-target effects, immunogenicity)." } }, "required": [ "targetDisease", "therapeuticPotential" ] }, "conformationalDynamicsResults": { "type": "object", "description": "Results from FRET experiments and other assays studying nuclease conformational dynamics, if applicable.", "properties": { "hnhActivationThreshold": { "type": "number", "description": "Threshold (ratio)A value or other metric indicating HNH domain activation." }, "offTargetCleavageCorrelation": { "type": "string", "description": "Correlation between HNH conformational state and off-target cleavage activity." }, "allostericControlEvidence": { "type": "boolean", "description": "Whether evidence of allosteric control between HNH and RuvC domains was observed." } } }, "detectionResults": { "type": "object", "description": "Results from CRISPR-based detection assays for SOX gene editing or other applications.", "properties": { "targetDetected": { "type": "boolean", "description": "Whether the target (e.g., SOX gene mutation, antibiotic resistance gene) was detected." }, "detectionSignal": { "type": "number", "description": "Quantitative signal from the detection assay (e.g., fluorescence intensity, colorimetric absorbance)." }, "concentration": { "type": "string", "description": "Concentration of the target detected (e.g., '10 copies/µL', '1 nM')." }, "sampleAnalysis": { "type": "array", "description": "Analysis of multiple samples, if applicable.", "items": { "type": "object", "properties": { "sampleId": { "type": "string", "description": "Identifier for the sample." }, "targetDetected": { "type": "boolean", "description": "Whether the target was detected in this sample." }, "detectionSignal": { "type": "number", "description": "Quantitative signal from the detection assay for this sample." }, "concentration": { "type": "string", "description": "Concentration of the target detected in this sample." } }, "required": [ "sampleId", "targetDetected" ] } } }, "required": [ "targetDetected" ] } }, "required": [ "editingEfficiency", "indelProfile", "onOffTargetRatio" ] }, "safetyAndSecurityDashboard": { "type": "object", "description": "Groups all risk-related data, uniting bio-physical variations with analytical off-target assessments.", "properties": { "genomicStability": { "type": "object", "description": "Reports on large-scale structural variations resulting from the edit (e.g., translocations, large deletions).", "properties": { "translocations": { "type": "boolean", "description": "Whether translocations were detected." }, "largeDeletions": { "type": "boolean", "description": "Whether large deletions were detected." }, "chromosomeLoss": { "type": "boolean", "description": "Whether chromosome loss was detected." }, "details": { "type": "string", "description": "Additional details about genomic stability, including methods used for detection (e.g., karyotyping, PEM-seq)." } } }, "offTargetAssessment": { "type": "object", "description": "Methods and results of off-target assessment.", "properties": { "method": { "type": "string", "description": "Method used for off-target assessment (e.g., GUIDE-seq, CIRCLE-seq, Digenome-seq).", "enum": [ "GUIDE-seq", "CIRCLE-seq", "Digenome-seq", "Other" ] }, "methodDetails": { "type": "string", "description": "Additional details about the off-target assessment method if 'Other' is selected." }, "results": { "type": "string", "description": "Summary of off-target assessment results." }, "hnhConformationalAnalysis": { "type": "string", "description": "Analysis of HNH conformational states at off-target sites." } }, "required": [ "method" ] }, "safetyAndEthics": { "type": "object", "description": "Safety and ethical considerations related to the CRISPR-based process.", "properties": { "immunogenicity": { "type": "object", "description": "Assessment of potential immunogenicity of the edited cells or detection assay.", "properties": { "assessed": { "type": "boolean", "description": "Whether immunogenicity was assessed." }, "method": { "type": "string", "description": "Method used for immunogenicity assessment (e.g., HLA typing, T-cell response assay).", "enum": [ "HLA Typing", "T-cell Response Assay", "Other" ] }, "methodDetails": { "type": "string", "description": "Additional details about the immunogenicity assessment method if 'Other' is selected." }, "results": { "type": "string", "description": "Summary of immunogenicity assessment results." } } }, "ethicalConsiderations": { "type": "object", "description": "Ethical considerations and approvals related to the CRISPR-based process.", "properties": { "institutionalReviewBoard": { "type": "boolean", "description": "Whether the study was approved by an Institutional Review Board (IRB) or Ethics Committee." }, "approvalNumber": { "type": "string", "description": "Approval number or identifier from the IRB or Ethics Committee." }, "informedConsent": { "type": "boolean", "description": "Whether informed consent was obtained from donors or participants." }, "dataPrivacy": { "type": "boolean", "description": "Whether data privacy and confidentiality measures were implemented." } }, "required": [ "institutionalReviewBoard" ] } } } }, "required": [ "offTargetAssessment" ] }, "notes": { "type": "string", "description": "Additional notes or observations about the CRISPR-based process." } }, "required": [ "inputs", "deliveryExecution", "experimentalSettings", "instruments", "outputs" ], "unevaluatedProperties": false }