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ProtocolCore

Suggested Protocols

Exploratory MVP
All protocol fields

CRISPR / Genome Editing

Source-bound CRISPR / Genome Editing starter protocols

Compose common planning, SpCas9 knockout, CBE, ABE, HDR, prime editing, and outcome validation from exact source profiles with explicit boundaries. Delivery conditions are finalized only through the Gene Delivery handoff.

Editable starter protocols

7 source-bound starters

What do these protocols do?

They select one editing chemistry after the common identity contract and preserve its exact geometry, mode-specific controls, Gene Delivery handoff, unintended products, and orthogonal validation in one record.

Supported editing workflows

  • • Common identity, controls & handoffs
  • • SpCas9 nuclease knockout
  • • Cytosine base editing
  • • Adenine base editing
  • • HDR precise editing
  • • Prime editing
  • • Outcome validation

Scope boundary

They do not mix numbers across editors, donors, or papers and do not supply delivery recipes, pooled screens, CRISPRi/a, germline, in-vivo, clinical execution, or universal PASS thresholds.

PRT-GE-COMMON-001Common identity, controls & handoffs

Genome-editing identity, source, control, delivery, and validation foundation

CRISPR / Genome Editing · GE-COMMON-CONTRACT-1.0

Official guidance reviewed
EXACT_SOURCE_PROFILE_REQUIREDGE_COORD_1_REQUIREDNO_CROSS_SOURCE_NUMERIC_MIXINGDELIVERY_HANDOFF_REQUIREDCHEMISTRY_SPECIFIC_OUTCOMESNO_UNIVERSAL_ACCEPTANCE_THRESHOLDRESEARCH_USE_ONLY

Lock the target, source profile, and delivery handoff before execution

This MVP starter creates no target sequence or delivery recipe. Enter your reference, transcript, edit intent, and exact guide/editor/donor/pegRNA artifacts, then finalize every condition against the actual Gene Delivery profile and analysis evidence.

1

1. LOCK MODEL, REFERENCE, AND EDIT INTENT

Record model provenance, assembly and patch, contig, 1-based closed coordinate, strand, HGNC ID, transcript accession/version, allele state, exact intended edit, and claim before composing execution.

2

2. LOCK ONE EXACT SOURCE PROFILE

Attach one admitted profile and GE-COORD-1.0 receipt; never borrow a missing editor, guide, donor, pegRNA, kit, or numeric condition from another lineage.

Condition: One profile ID, source cluster, publication/revision, rights rule, applicability, and exclusion set.
3

3. FREEZE GUIDE AND MODE-SPECIFIC DESIGN

Select one edit mode, preserve guide/PAM orientation and model-versioned scores, and hash the guide, donor or pegRNA artifacts plus explicit specialist handoffs.

4

4. PREDECLARE CONTROLS AND REPLICATES

Assign untreated/parental, delivery/mock, non-targeting, positive/benchmark, and every mode-specific control role before execution.

5

5. EXECUTE ONLY THE TYPED GENE DELIVERY HANDOFF

Use one resolved delivery profile and record actual cargo identities, amount basis and units, model/vessel, reagent or device revision, exposure, recovery, viability, harvest timing, and deviations. ProtocolCore supplies no delivery recipe.

Duration: USER REQUIRED — source-defined exposure, recovery, and harvest checkpoints.Temperature: USER REQUIRED — model and assay-specific handling condition.Reagent: USER REQUIRED — exact Gene Delivery/Transfection profile ID or UNRESOLVED.
6

6. COLLECT VERSIONED ANALYSIS MATERIAL

Collect every biological replicate at its source-defined time and preserve sample, extraction, amplicon, raw-file, guide/editor/donor/pegRNA, software, and parameter identities.

7

7. CLASSIFY COMPLETE OUTCOMES

Use the selected child chemistry taxonomy and keep intended, bystander, indel, other, unmodified, compound, and unclassified outcomes separate.

8

8. COMPLETE ORTHOGONAL AND RISK REVIEW

Predeclare on-target, orthogonal genotype, structural/dropout, off-target, molecular/function, analytical-sensitivity, and uncertainty dispositions.

9

9. ISSUE A FAIL-CLOSED DISPOSITION

Assign ACCEPT, CONDITIONAL, REPEAT, REJECT, or SPECIALIST REVIEW with critical loss, uncertainty, allowed claim, responsible owner, and immutable evidence links; never collapse discordant evidence into one score.