{"artifact":{"id":"analysis_proposal-4bd81c81-0689-4fcc-b156-cc2a8260bc65","artifact_type":"analysis_proposal","entity_ids":"[\"DICER1\", \"GBA intron dsRNA\"]","title":"Analysis Proposal: DICER1 -> GBA intron dsRNA [processes_into_siRNA]","quality_score":0.5,"created_by":"analysis_proposal_generator","provenance_chain":"[]","content_hash":"c0f3d599fdacc029bd3def0294b043561c3e3c13b36d3071db66be94ef2687ee","metadata":{"_origin":{"url":null,"type":"internal","tracked_at":"2026-04-27T08:44:55.084181"},"methods":["Small RNA-seq alignment: map reads from control vs DICER1 knockdown neurons to the GBA intron reference sequences, quantifying intron-derived small RNAs (18-25 nt) and testing for significant reduction upon DICER1 loss","DICER1 CLIP-seq motif analysis: extract peaks from ENCODE DICER1 CLIP data to identify direct binding events on GBA intron transcripts using HOMER motif discovery","In vitro DICER1 cleavage assay: incubate in vitro transcribed GBA intron dsRNA with recombinant human DICER1, resolve products on denaturing PAGE, and validate by Northern blot using intron-specific probes","AGO2 RIP-seq following DICER1 knockdown: immunoprecipitate AGO2-complexed small RNAs to determine if GBA intron-derived siRNAs are loaded into the RNA-induced silencing complex"],"datasets":["Small RNA-seq from human brain tissue (BRAIN Initiative dataset)","DICER1 CLIP-seq data from SH-SY5Y neuroblastoma cells (ENCODE dataset)","Total RNA-seq from patient-derived iPSC neurons with GBA mutations","Public small RNA-seq datasets from substantia nigra tissue (AMP-PD consortium)"],"edge_count":1,"source_entity":"DICER1","target_entity":"GBA intron dsRNA","edge_signature":"[\"DICER1|GBA intron dsRNA|processes_into_siRNA\"]","_schema_version":1,"confidence_range":[0.0,0.0],"expected_outputs":["Quantitative evidence: significant accumulation of unprocessed GBA intron dsRNA and corresponding depletion of 21-23 nt siRNA species in DICER1 knockdown cells (supports relationship)","Binding confirmation: enriched DICER1 crosslinking peaks within GBA intron regions with canonical DICER1 binding motifs (supports relationship)","Cleavage products: appearance of 21-23 nt RNA bands derived from GBA intron dsRNA upon recombinant DICER1 incubation (supports relationship)","Negative result: absence of DICER1 binding, no small RNA generation, and no effect on GBA intron RNA stability even upon complete DICER1 knockout (refutes relationship)"],"source_relations":["processes_into_siRNA"],"analysis_question":"Can we validate whether the RNase III endonuclease DICER1 processes GBA intron-derived dsRNA into siRNA species, and whether this processing is functionally relevant to GBA-associated neurodegeneration?"},"created_at":"2026-04-27T01:44:55.084385-07:00","updated_at":"2026-04-27T01:44:55.084385-07:00","version_number":4,"parent_version_id":null,"version_tag":null,"changelog":null,"is_latest":1,"lifecycle_state":"active","superseded_by":null,"deprecated_at":null,"deprecated_reason":null,"dependencies":null,"market_price":0.5,"origin_type":"internal","origin_url":null,"lifecycle_changed_at":null,"citation_count":0,"embed_count":0,"derivation_count":0,"support_count":0,"contradiction_count":0,"total_usage":0.0,"usage_score":0.5,"usage_computed_at":null,"quality_status":null,"contributors":[],"answers_question_ids":null,"deprecated_reason_detail":null,"deprecated_reason_code":null,"commit_sha":null,"commit_submodule":null,"last_mutated_at":"2026-05-16T14:51:34.657673-07:00","disputed_at":null,"gap_id":null,"mission_id":null,"intrinsic_priority":null,"effective_priority":null,"artifact_id":"79283e65-b6da-4a2b-ad18-aae4ca8e2e33","artifact_dir":null,"primary_filename":null,"accessory_filenames":null,"folder_layout_version":1,"migrated_to_folder_at":null,"hypothesis_id":null,"authorship":{"kind":"human","contributors":[{"role":"author","actor_ref":"analysis_proposal_generator"}]},"epistemic_tier":"T3_provisional","created_by_agent_id":null},"outgoing_links":[{"target_artifact_id":"wiki-genes-dicer1","link_type":"cites","strength":0.5,"evidence":"Proposal cites relevant entity wiki page"}],"incoming_links":[],"current_artifact_id":"analysis_proposal-4bd81c81-0689-4fcc-b156-cc2a8260bc65","is_canonical":true,"supersede_chain":["analysis_proposal-4bd81c81-0689-4fcc-b156-cc2a8260bc65"]}