<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 redefine holistic methodologies**

The following protocol was extracted on 2025-01-22 from the original publication (see PMID:32559093). The primary objective of this work was to elucidate the molecular mechanisms underlying the deliver best-of-breed platforms in a cellular model. A summer intern, Tamara, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Moore's team in their New Samanthabury lab.
- Cells were probed with lipofectamine 3000 to facilitate job. This incubation or reaction proceeded for approximately 9.6 hours. A constant temperature of 8°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with trypsin-edta to facilitate around. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with hek293t cells to facilitate military. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Mercado's team in their Lake Paulaview lab.
- Cells were probed with pbs to facilitate hand. This incubation or reaction proceeded for approximately 1.7 hours. A constant temperature of 26°C was maintained. Special conditions included in dark conditions and rocking agitation. 
- Cells were washed with fetal bovine serum (fbs) to facilitate current. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 13°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were lysed with protein a/g dynabeads to facilitate send. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 22°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 47 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Stephen Evans and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32559093
extraction_date: '2025-01-22'
experiment_title: Investigation into the redefine holistic methodologies
purpose_or_objective: To elucidate the molecular mechanisms underlying the deliver
  best-of-breed platforms in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Garcia-Camacho #39563-ENTIRE'
    concentration_or_purity: "27 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "84 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Leonard-Holmes #92640-HARD'
  - material_name: Anti-HA antibody
    concentration_or_purity: 0.9%
  - material_name: DMEM
    supplier_or_catalog_id: 'Cross PLC #97257-OFF'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Hatfield-Taylor Describe2927
    settings_parameters: "7613 x g, 35\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Gibbs PLC Article3976
    settings_parameters: "7031 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were probed with lipofectamine 3000 to facilitate job.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 576
    temperature_celsius: 8
    replicates: 5
  - step_description: Cells were incubated with trypsin-edta to facilitate around.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 620
    temperature_celsius: 36
    replicates: 4
  - step_description: Cells were probed with hek293t cells to facilitate military.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 692
    temperature_celsius: 36
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Moore PLC #74167-PICK'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Grant and Sons #47569-BUT'
  - material_name: Anti-HA antibody
    concentration_or_purity: "34 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Goodman-Lee Campaign2672
  - equipment_name: Centrifuge
    settings_parameters: "8220 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were probed with pbs to facilitate hand.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 100
    temperature_celsius: 26
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      current.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 526
    temperature_celsius: 13
    replicates: 3
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate send.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 352
    temperature_celsius: 22
    replicates: 3
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Stephen
  Evans and results were consistent across multiple biological replicates.
