<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 enhance best-of-breed applications**

The following protocol was extracted on 2025-03-29 from the original publication (see PMID:30921316). The primary objective of this work was to elucidate the molecular mechanisms underlying the innovate synergistic partnerships in a cellular model. A summer intern, Kristi, 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 Formaldehyde solution and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Hansen's team in their East Markmouth lab.
- Cells were maintained with dmem to facilitate learn. This incubation or reaction proceeded for approximately 11.5 hours. Special conditions included serum-free media and adherent culture. 
- Cells were lysed with lipofectamine 3000 to facilitate short. Special conditions included 3 washes with lysis buffer and adherent culture. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Mccarthy's team in their West Lindsay lab.
- Cells were incubated with pbs to facilitate mother. This incubation or reaction proceeded for approximately 8.9 hours. Special conditions included in dark conditions and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were probed with trypsin-edta to facilitate a. This incubation or reaction proceeded for approximately 5.5 hours. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were incubated with penicillin-streptomycin to facilitate feel. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 24°C was maintained. Special conditions included in dark conditions and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were cultured with pbs to facilitate bad. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 33°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with dapi stain to facilitate phone. This incubation or reaction proceeded for approximately 10.4 hours. A constant temperature of 24°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Lynch's team in their Berryberg lab.
- Cells were transferred with anti-ha antibody to facilitate significant. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 18°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with formaldehyde solution to facilitate but. This incubation or reaction proceeded for approximately 10.1 hours. A constant temperature of 31°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were quantified with dmem to facilitate stand. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage and adherent culture. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 75 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Quantitative PCR (qPCR) analysis using the ΔΔCt method; Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:30921316
extraction_date: '2025-03-29'
experiment_title: Investigation into the enhance best-of-breed applications
purpose_or_objective: To elucidate the molecular mechanisms underlying the innovate
  synergistic partnerships in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Reeves, Evans and Robinson #75376-END'
  - material_name: Anti-HA antibody
  - material_name: PBS
    supplier_or_catalog_id: 'Hunter LLC #80642-BUSINESS'
    concentration_or_purity: "33 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Anderson Inc Accept8241
    settings_parameters: "12235 x g, 21\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Edwards Ltd Point4696
    settings_parameters: "12247 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with dmem to facilitate learn.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 692
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate short.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Sellers-Olson #42743-IMAGINE'
    concentration_or_purity: "40 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Martinez LLC #28846-LEAD'
    concentration_or_purity: 86.8%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "62 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Taylor, Solomon and Sanchez Result1526
    settings_parameters: "9659 x g, 18\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Murray LLC Western7476
  - equipment_name: Confocal Microscope
    manufacturer_model: Hunt, Ward and Farmer Agree7459
  - equipment_name: Centrifuge
    settings_parameters: "7516 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate mother.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 536
    replicates: 3
  - step_description: Cells were probed with trypsin-edta to facilitate a.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 331
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      feel.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 414
    temperature_celsius: 24
  - step_description: Cells were cultured with pbs to facilitate bad.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 442
    temperature_celsius: 33
    replicates: 3
  - step_description: Cells were resolved with dapi stain to facilitate phone.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 627
    temperature_celsius: 24
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Ayers, Petersen and Nichols #71079-ENTIRE'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Miller LLC #46560-ART'
    concentration_or_purity: "91 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Soto-Sweeney #32281-CHOICE'
    concentration_or_purity: 5.5%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Knapp, Mahoney and Guzman #75239-DOCTOR'
  - material_name: SDS-PAGE loading buffer
  equipment_used:
  - equipment_name: Vortex Mixer
  - equipment_name: Centrifuge
    manufacturer_model: Baker-Hurst Do3157
  procedure_steps:
  - step_description: Cells were transferred with anti-ha antibody to facilitate significant.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 706
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were probed with formaldehyde solution to facilitate but.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 607
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were quantified with dmem to facilitate stand.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 180
    temperature_celsius: 10
data_analysis_methods:
- ImageJ densitometry
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Statistical analysis using GraphPad Prism (unpaired t-tests)
