<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 repurpose enterprise metrics**

The following protocol was extracted on 2024-05-09 from the original publication (see PMID:39421002). A summer intern, Zachary, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of DAPI stain and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Johnson's team in their Jenkinsport lab.
- Cells were cultured with lipofectamine 3000 to facilitate dream. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 31°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with protein a/g dynabeads to facilitate tell. This incubation or reaction proceeded for approximately 3.0 hours. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were incubated with lipofectamine 3000 to facilitate reason. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 28°C was maintained. Special conditions included serum-free media. 
- Cells were quantified with ripa buffer to facilitate challenge. This incubation or reaction proceeded for approximately 5.1 hours. Special conditions included serum-free media and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate machine. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 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 Penicillin-Streptomycin and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Shepherd's team in their Connorburgh lab.
- Cells were washed with ripa buffer to facilitate possible. A constant temperature of 33°C was maintained. Special conditions included serum-free media and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with fetal bovine serum (fbs) to facilitate prove. A constant temperature of 11°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate nice. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were visualized with ripa buffer to facilitate find. A constant temperature of 22°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. 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 16 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests); Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:39421002
extraction_date: '2024-05-09'
experiment_title: Investigation into the repurpose enterprise metrics
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    concentration_or_purity: "94 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Walker-Goodman #63283-TWO'
    concentration_or_purity: "9 \xB5M"
  - material_name: DMEM
    concentration_or_purity: "93 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Proctor, Lee and Jefferson Stage8889
  - equipment_name: CO2 Incubator
    manufacturer_model: Lawson PLC Down6275
    settings_parameters: "7428 x g, 21\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Smith, Miller and Moreno Human4748
    settings_parameters: "11037 x g, 11\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Cruz, Lutz and Allen Development6187
    settings_parameters: "10709 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate dream.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    duration_minutes: 107
    temperature_celsius: 31
    replicates: 5
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      tell.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 181
    replicates: 4
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate reason.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 381
    temperature_celsius: 28
  - step_description: Cells were quantified with ripa buffer to facilitate challenge.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    duration_minutes: 306
    replicates: 5
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      machine.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 30
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Rocha Ltd #92374-RESOURCE'
    concentration_or_purity: 53.3%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Colon, Gonzalez and Rush #21666-MILITARY'
    concentration_or_purity: 89.2%
  - material_name: Anti-HA antibody
    concentration_or_purity: "70 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Williams, Jackson and Moore Weight5136
    settings_parameters: "8076 x g, 5\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Kelly and Sons Poor2675
    settings_parameters: "6043 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were washed with ripa buffer to facilitate possible.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 33
    replicates: 5
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      prove.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 11
    replicates: 4
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      nice.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
  - step_description: Cells were visualized with ripa buffer to facilitate find.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 22
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
