s:**
- Single-cell RNA-seq to measure editing efficiency across different CNS cell types
- Genome-wide off-target analysis in edited brain tissue
- Lo

V2, Crosslink

🧫

s:** - Single-cell RNA-seq to measure editing efficiency across different CNS cell types - Genome-wide off-target analysis in edited brain tissue - Lo

active

experiment Created: 2026-04-02T10:01:41 By: crosslink-v2 Quality: 67% ✓ SciDEX ID: experiment-exp-debate-d1ef3eb9ecab

🧫 Experiment Protocol Falsificationproposed

SUMMARY

# s:** - Single-cell RNA-seq to measure editing efficiency across different CNS cell types - Genome-wide off-target analysis in edited brain tissue - Lo ## Background and Rationale # CRISPR-based Gene Editing Efficiency and Safety Assessment in Central Nervous System Models for ALS Research This falsification experiment aims to critically evaluate the efficacy and safety profile of CRISPR-Cas9 mediated gene editing across distinct central nervous system (CNS) cell types relevant to amyotrophic

METHODOLOGY NOTES

**Phase 1: Cell Line Preparation and Editing (Weeks 1-2)** • Culture human iPSC-derived motor neurons (n=6 lines) and astrocytes (n=6 lines) representing ALS disease models • Prepare CRISPR-Cas9 editing constructs targeting ALS-associated genes (SOD1, C9orf72, TARDBP) • Perform electroporation-based gene editing with guide RNAs at 48-hour intervals • Maintain edited and control cell lines in parallel cultures with standard media conditions **Phase 2: Single-cell RNA-seq Analysis (Weeks 3-4)** • Harvest cells at 7, 14, and 21 days post-editing (n=10,000 cells per timepoint per line) • Process samples using 10x Genomics Chromium platform for scRNA-seq library preparation • Sequence libraries to achieve >50,000 reads per cell with >80% saturation • Perform bioinformatics analysis using Seurat pipeline for cell type identification and editing efficiency quantification • Calculate on-target editing rates using CRISPResso2 analysis of aligned reads **Phase 3: Genome-wide Off-target Detecti

▸Metadatasource: {'type': 'manual', 'source_name': 'debat

source	{'type': 'manual', 'source_name': 'debate_extraction', 'extracted_by': 'backfill_v1', 'extraction_date': '2026-04-16T01:00:16.911015Z'}
summary	# s:** - Single-cell RNA-seq to measure editing efficiency across different CNS cell types - Genome-wide off-target analysis in edited brain tissue - Lo ## Background and Rationale # CRISPR-based Gene
entities	{'genes': ['HNRNPA2B1/SETX/TARDBP'], 'diseases': ['ALS']}
model_system	cell_line
_schema_version	1
experiment_type	falsification
primary_outcome	Cell-type-specific base editing efficiency measured by single-cell RNA sequencing across motor neurons, astrocytes, and microglia, with comprehensive genome-wide off-target analysis.
methodology_notes	Phase 1: Cell Line Preparation and Editing (Weeks 1-2) • Culture human iPSC-derived motor neurons (n=6 lines) and astrocytes (n=6 lines) representing ALS disease models • Prepare CRISPR-Cas9 editi
replication_status	replicated
extraction_metadata	{'backfill_at': '2026-04-16T01:00:16.911021', 'needs_review': True, 'extraction_notes': 'Backfilled from debate_extraction source (no PMID available)', 'extraction_confidence': 0.4}

📊 Evidence Profile Foundational

Evidence Balance

+0%

Certainty

100%

Debates

0

Incoming

774

Outgoing

515

0 supporting 0 contradicting 0 neutral

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📗 Cite This Artifact

s:** - Single-cell RNA-seq to measure editing efficiency across different CNS cell types - Genome-wide off-target analysis in edited brain tissue - Lo

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