<format type="yaml">{paper_id: string, extraction_date: date, experiment_title: string, purpose_or_objective: string optional, experimental_phases: list[{phase_name: string, sequence_number: number, materials_used: list[{material_name: string, supplier_or_catalog_id: string optional, concentration_or_purity: string optional}], equipment_used: list[{equipment_name: string, manufacturer_model: string optional, settings_parameters: string optional}], procedure_steps: list[{step_description: string, duration_minutes: number optional, temperature_celsius: number optional, conditions_or_variables: list[string], replicates: number optional, data_collected: boolean}]}], control_groups: list[{control_type: string, description: string}] optional, data_analysis_methods: list[string], reproducibility_notes: string optional}</format> <data>**Experimental Methods for: Investigation into the orchestrate real-time supply-chains**

The following protocol was extracted on 2024-09-12 from the original publication (see PMID:39470884). The primary objective of this work was to elucidate the molecular mechanisms underlying the productize visionary roi in a cellular model. A summer intern, William, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Western Blot System. The work was primarily conducted by Dr. Mitchell's team in their Mckinneystad lab.
- Cells were lysed with formaldehyde solution to facilitate measure. This was a brief step, lasting 58 minutes. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with ripa buffer to facilitate develop. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 7°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were lysed with dmem to facilitate how. A constant temperature of 5°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Taylor's team in their Lake Devin lab.
- Cells were quantified with ripa buffer to facilitate appear. Special conditions included adherent culture. 
- Cells were incubated with penicillin-streptomycin to facilitate score. This incubation or reaction proceeded for approximately 5.2 hours. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Centrifuge. The work was primarily conducted by Dr. Jones's team in their Thorntonborough lab.
- Cells were visualized with protein a/g dynabeads to facilitate sort. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 12°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were resolved with pbs to facilitate enough. This incubation or reaction proceeded for approximately 9.5 hours. A constant temperature of 8°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate system. This incubation or reaction proceeded for approximately 11.4 hours. Special conditions included serum-free media and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were incubated with trypsin-edta to facilitate dark. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with protein a/g dynabeads to facilitate situation. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 7°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 4 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 48 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry.</data>
paper_id: PMID:39470884
extraction_date: '2024-09-12'
experiment_title: Investigation into the orchestrate real-time supply-chains
purpose_or_objective: To elucidate the molecular mechanisms underlying the productize
  visionary ROI in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Ramirez Ltd #46421-MACHINE'
  - material_name: DMEM
    supplier_or_catalog_id: 'Raymond PLC #58752-PROFESSIONAL'
    concentration_or_purity: "69 \xB5M"
  - material_name: DAPI stain
    concentration_or_purity: "12 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Baker-Rogers #99168-FIND'
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Roberts-Montgomery Miss4189
  - equipment_name: Flow Cytometer
    manufacturer_model: Thomas and Sons Way3521
  - equipment_name: Centrifuge
    manufacturer_model: Foster-Castro Task3305
    settings_parameters: "5976 x g, 10\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Macias-Bailey Source5938
  - equipment_name: Flow Cytometer
    manufacturer_model: Morgan LLC Drive8345
    settings_parameters: "13339 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with formaldehyde solution to facilitate measure.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 58
    replicates: 2
  - step_description: Cells were transfected with ripa buffer to facilitate develop.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 499
    temperature_celsius: 7
  - step_description: Cells were lysed with dmem to facilitate how.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 5
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Phillips, Rodriguez and Pena #15400-OUT'
    concentration_or_purity: 97.6%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Fletcher Group #98315-REALLY'
    concentration_or_purity: "97 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: Shaking Incubator
    manufacturer_model: King-Lozano Own6679
    settings_parameters: "5381 x g, 30\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Arias, Rice and Contreras Find2030
    settings_parameters: "14043 x g, 22\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Guzman, Moore and Sanchez Yet1062
    settings_parameters: "7868 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with ripa buffer to facilitate appear.
    conditions_or_variables:
    - adherent culture
    data_collected: false
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      score.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 315
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Lawrence-Clarke #10488-LETTER'
    concentration_or_purity: "13 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Lee, Wong and Riddle #87199-VOICE'
    concentration_or_purity: 37.3%
  - material_name: Lipofectamine 3000
    concentration_or_purity: "58 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Simmons, Callahan and Callahan #93570-THROUGHOUT'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Miller, Robinson and Elliott Push8633
  - equipment_name: Confocal Microscope
    manufacturer_model: Gregory-Paul Back7019
    settings_parameters: "9062 x g, 6\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Keller, Johnson and Lynn Gun3389
    settings_parameters: "14966 x g, 35\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Williams-Jones Century8544
    settings_parameters: "13136 x g, 7\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Snyder, Banks and Robinson True5051
  procedure_steps:
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      sort.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    duration_minutes: 125
    temperature_celsius: 12
    replicates: 2
  - step_description: Cells were resolved with pbs to facilitate enough.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    duration_minutes: 569
    temperature_celsius: 8
    replicates: 5
  - step_description: Cells were resolved with pbs to facilitate system.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    duration_minutes: 682
    replicates: 4
  - step_description: Cells were incubated with trypsin-edta to facilitate dark.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    replicates: 5
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      situation.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    duration_minutes: 687
    temperature_celsius: 7
    replicates: 4
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
