---
date: 2024-11-19
type: daily
tags: [lab-notes]
---

# 2024-11-19 - Tuesday

## Experiments

Launched [[Experiment-2024-11-19]] - CRISPR [[Validation]] of hub proteins.

- Designed sgRNAs for [[Top]] 15 hub proteins from yesterday's PPI analysis
- Used [[Haeussler2016-CRISPR-Tools]] for off-[[Target]] [[Scoring]]
- 4 sgRNAs per gene (60 [[Total]] guides)
- Started lentiviral [[Production]] (harvest Thursday)

**sgRNA [[Design]] stats**:
- CFD scores: median 0.89 ([[Good]] specificity)
- On-target ([[Doench 2016]]): median 0.64

## [[Cell Culture]]

- Passaged HCC827 and MDA-MB-231 lines
- Seeded for transduction (5M cells per line)
- Viability >95%

## Analysis

Finished network analysis from [[Experiment-2024-11-18]]:
- Essentiality correlation with degree: r=0.73 (predicted)
- [[Generated]] figures for lab meeting

## [[Next Steps]]

- Harvest virus Wednesday evening
- Transduce cells Thursday
- [[Start 14]]-day growth assay

## Notes

Strong correlation between network centrality and literature-[[Based]] essentiality. Validates [[Computational]] approach.
