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docs/TASKS.md
james-m-jordan 4ab492fffd Update project structure and add experiment files
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Lab Task List

This file tracks all ongoing lab and dev tasks. Issues created via GitHub and the Lab Agent are appended automatically below.

TASKS

Note: This file is now automatically updated by the agent/task-runner. Tasks are marked done when experiments are completed, and new tasks may be added as needed.

Lab Tasks

Ybx1 Knockdown mRNA Stability Experiment (EXP-0225)

  • Day 1 (May 6, 2025): Complete reverse transfection setup
    • Thaw HEK293T cells and check viability
    • Prepare transfection master mixes (siRNA targeting Ybx1 and Control siRNA)
    • Set up reverse transfection in 24-well plates
    • Update experiment status in repository
  • Day 3 (May 8, 2025): Verify Ybx1 knockdown by qPCR
  • Day 3 (May 8, 2025): Begin actinomycin D time course experiment
    • Collect t=0 samples before actinomycin D addition
    • Add actinomycin D (5 μg/ml) to remaining wells
    • Collect samples at 2h, 4h, and 8h timepoints
  • Day 4 (May 9, 2025): Complete RNA extractions
  • Day 4 (May 9, 2025): Synthesize cDNA and perform qPCR
  • Submit final data to repository and link to experimental record

YBX1-CEBPA Co-Immunoprecipitation (EXP-0226)

  • Day 1 (May 8, 2025): Set up 3T3 cells
    • Seed 3T3 cells in six 10 cm dishes
    • Prepare stock solutions for adipogenic induction
  • Day 2 (May 9, 2025): Begin adipogenic treatment
    • Prepare fresh adipogenic induction medium
    • Treat cells with control or adipogenic medium
  • Day 3 (May 10, 2025): Harvest and process cells
    • Collect cell lysates from all conditions
    • Measure protein concentrations
    • Set up antibody incubation for co-immunoprecipitation
  • Day 4 (May 11, 2025): Complete Co-IP and Western blotting
    • Process IP samples with protein A/G beads
    • Run SDS-PAGE gels and transfer to membranes
    • Blot for protein interactions
    • Image and quantify results
  • Analyze protein interaction data and prepare figures

Materials and Resources

  • Confirm Actinomycin D stock availability
  • Ensure sufficient RNA extraction reagents are available
  • Check qPCR primer stocks for all target genes
  • Order YBX1 and C/EBPα antibodies for Co-IP
  • Verify Invitrogen gel and transfer system availability

Development Tasks

  • Reorganize repository structure: convert "projects" to "aims" and "subprojects" to "projects" for better GitHub integration
  • Improve GitHub issue integration with short hash identifiers for future-proofing
  • Update documentation to reflect new naming conventions
  • Evaluate need for TASKS.md file in the new structure (consider GitHub issues as primary task tracker)

This file will be updated as tasks are added or completed during implementation. - [ ] #9 Pre-build Dev Container for instant Agent boot (added 2025-05-07 10:37)

  • #10 Add repo-level OPENAI_API_KEY secret & document (added 2025-05-07 10:37)
  • #11 Rewrite README Quick-Start for students (added 2025-05-07 10:37)
  • #12 Implement automated ISSUE → TASKS.md hook (added 2025-05-07 10:37)
  • #13 Add GitLens default issue view configuration (added 2025-05-07 10:37)
  • #14 CI: Codespace headless smoke test (added 2025-05-07 10:37)
  • #15 [Wet-Lab] Complete HEK293T thaw & viability check (added 2025-05-07 10:37)
  • #16 [Wet-Lab] Prepare Ybx1 & control siRNA mixes (added 2025-05-07 10:37)