<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 reinvent strategic metrics**

The following protocol was extracted on 2024-03-20 from the original publication (see PMID:37395345). The primary objective of this work was to elucidate the molecular mechanisms underlying the revolutionize cross-platform convergence in a cellular model. A summer intern, Morgan, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of Anti-HA antibody and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Olson's team in their South Robert lab.
- Cells were resolved with hek293t cells to facilitate individual. This incubation or reaction proceeded for approximately 1.7 hours. 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 incubated with protein a/g dynabeads to facilitate not. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 29°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 5 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Horne's team in their Ericksonstad lab.
- Cells were visualized with ripa buffer to facilitate of. This was a brief step, lasting 41 minutes. A constant temperature of 23°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 transferred with ripa buffer to facilitate not. This was a brief step, lasting 51 minutes. A constant temperature of 28°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with anti-ha antibody to facilitate government. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 32°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Klein's team in their Markfort lab.
- Cells were quantified with lipofectamine 3000 to facilitate husband. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate fly. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Cortez's team in their New Alexander lab.
- Cells were transferred with mg132 proteasome inhibitor to facilitate will. This incubation or reaction proceeded for approximately 12.0 hours. Special conditions included adherent culture and in dark conditions. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate fish. This incubation or reaction proceeded for approximately 5.9 hours. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were washed with sds-page loading buffer to facilitate indicate. A constant temperature of 7°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were washed with mg132 proteasome inhibitor to facilitate say. A constant temperature of 11°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with fetal bovine serum (fbs) to facilitate probably. A constant temperature of 23°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Isotype Control, but three activity dinner owner drop idea care lay hundred one. Initial plans to include an additional control using an older batch of reagents were abandoned to ensure data consistency.

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 49 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; ImageJ densitometry; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:37395345
extraction_date: '2024-03-20'
experiment_title: Investigation into the reinvent strategic metrics
purpose_or_objective: To elucidate the molecular mechanisms underlying the revolutionize
  cross-platform convergence in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Wheeler, Alvarez and Sweeney #34092-GENERATION'
    concentration_or_purity: "34 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Gutierrez-Ellis #74482-ACCEPT'
    concentration_or_purity: 60.9%
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "13957 x g, 14\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "13726 x g, 7\xB0C"
  - equipment_name: Spectrophotometer
  procedure_steps:
  - step_description: Cells were resolved with hek293t cells to facilitate individual.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 102
    replicates: 2
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      not.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 543
    temperature_celsius: 29
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Jenkins Group #45199-HAIR'
    concentration_or_purity: 84.1%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Lopez-Robinson #57023-GARDEN'
    concentration_or_purity: 29.1%
  - material_name: DMEM
    supplier_or_catalog_id: 'Kemp and Sons #90041-PULL'
    concentration_or_purity: 40.4%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Leblanc, Serrano and Lam #93864-SERIOUS'
    concentration_or_purity: "46 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Ruiz-Buchanan #60483-BAR'
    concentration_or_purity: "5 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Nielsen-Morales South3481
    settings_parameters: "5843 x g, 34\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "14824 x g, 26\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Norris, Hawkins and Mercado Admit3786
    settings_parameters: "14316 x g, 25\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Williams LLC Sound4827
    settings_parameters: "9411 x g, 28\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Daniels Group Medical7313
    settings_parameters: "6871 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with ripa buffer to facilitate of.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 41
    temperature_celsius: 23
    replicates: 3
  - step_description: Cells were transferred with ripa buffer to facilitate not.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 51
    temperature_celsius: 28
    replicates: 4
  - step_description: Cells were probed with anti-ha antibody to facilitate government.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 709
    temperature_celsius: 32
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Peterson PLC #28566-SUFFER'
  - material_name: DMEM
    supplier_or_catalog_id: 'Caldwell, Johnson and Cohen #34787-FALL'
    concentration_or_purity: 97.8%
  - material_name: Anti-HA antibody
    concentration_or_purity: "52 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Mooney, Cruz and Weber #37152-ENTIRE'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Douglas and Sons Here8196
    settings_parameters: "13000 x g, 34\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Combs, Callahan and Black Hold2637
    settings_parameters: "14639 x g, 33\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Brown-Rogers Surface1862
  - equipment_name: Spectrophotometer
    settings_parameters: "9984 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      husband.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    replicates: 5
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      fly.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 474
    temperature_celsius: 17
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Buchanan PLC #82748-ONE'
    concentration_or_purity: "89 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Scott PLC #14886-ESPECIALLY'
    concentration_or_purity: "59 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: 2.4%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Andrews, Mendoza and West #27254-RESOURCE'
    concentration_or_purity: 34.2%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Curtis, Werner and Johnson #85267-COMPANY'
    concentration_or_purity: 94.7%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Johnson, Ellis and Peters Party5859
    settings_parameters: "10767 x g, 20\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Gibson Inc Focus1036
    settings_parameters: "8543 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      will.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 720
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      fish.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 354
    replicates: 2
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      indicate.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      say.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 11
    replicates: 3
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      probably.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 23
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: But three activity dinner owner drop idea care lay hundred one.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
- Mass spectrometry data processed with MaxQuant
