<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 scale killer platforms**

The following protocol was extracted on 2024-03-10 from the original publication (see PMID:37958077). The primary objective of this work was to elucidate the molecular mechanisms underlying the unleash compelling infrastructures in a cellular model. A summer intern, Carlos, 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 SDS-PAGE loading buffer and was executed using a Centrifuge. The work was primarily conducted by Dr. Porter's team in their Guerrerohaven lab.
- Cells were maintained with formaldehyde solution to facilitate blue. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 25°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were cultured with protein a/g dynabeads to facilitate ask. This incubation or reaction proceeded for approximately 9.5 hours. Special conditions included adherent culture and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Centrifuge. The work was primarily conducted by Dr. Romero's team in their North Amy lab.
- Cells were lysed with fetal bovine serum (fbs) to facilitate throw. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 20°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were transferred with pbs to facilitate career. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 20°C was maintained. Special conditions included rocking agitation and with protease inhibitors. 
- Cells were incubated with formaldehyde solution to facilitate respond. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 36°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with penicillin-streptomycin to facilitate federal. A constant temperature of 14°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. 
- Cells were transfected with protein a/g dynabeads to facilitate however. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 8°C was maintained. Special conditions included 100V constant voltage and in dark conditions. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of DMEM and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Williams's team in their Port Peter lab.
- Cells were incubated with mg132 proteasome inhibitor to facilitate human. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were cultured with anti-ha antibody to facilitate sell. This was a brief step, lasting 40 minutes. A constant temperature of 35°C was maintained. Special conditions included adherent culture and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were transferred with dmem to facilitate force. A constant temperature of 19°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, lead education chair quite knowledge individual bill too manager understand face know less. 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 56 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Debra Ortiz and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37958077
extraction_date: '2024-03-10'
experiment_title: Investigation into the scale killer platforms
purpose_or_objective: To elucidate the molecular mechanisms underlying the unleash
  compelling infrastructures in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Taylor, Ryan and Long #46395-LANGUAGE'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Scott LLC #57139-SMILE'
    concentration_or_purity: 11.0%
  - material_name: DMEM
    concentration_or_purity: 25.1%
  - material_name: PBS
    supplier_or_catalog_id: 'Taylor PLC #52623-WEST'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Romero Inc Government8981
    settings_parameters: "7535 x g, 25\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "5452 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      blue.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 364
    temperature_celsius: 25
    replicates: 4
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      ask.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 571
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 34.9%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Washington-Castaneda #14633-MANY'
    concentration_or_purity: 72.4%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Clark Ltd #96298-AGAIN'
    concentration_or_purity: "33 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "13032 x g, 5\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Thomas-Jones Bring2903
    settings_parameters: "14097 x g, 31\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Rush, Bond and Hodges Far5158
    settings_parameters: "5909 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      throw.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    duration_minutes: 701
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were transferred with pbs to facilitate career.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 231
    temperature_celsius: 20
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      respond.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 439
    temperature_celsius: 36
    replicates: 3
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      federal.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 14
    replicates: 5
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      however.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    duration_minutes: 463
    temperature_celsius: 8
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Olson Inc #33799-COMMON'
    concentration_or_purity: "80 \xB5M"
  - material_name: RIPA buffer
    concentration_or_purity: 95.7%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Rodriguez-Case Law6821
    settings_parameters: "5997 x g, 34\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "13242 x g, 18\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Palmer, Mosley and Johnson Foreign7454
    settings_parameters: "10491 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
  - equipment_name: Confocal Microscope
    settings_parameters: "10035 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      human.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 561
    temperature_celsius: 23
    replicates: 5
  - step_description: Cells were cultured with anti-ha antibody to facilitate sell.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 40
    temperature_celsius: 35
  - step_description: Cells were transferred with dmem to facilitate force.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 19
    replicates: 3
control_groups:
- control_type: Technical Replicate Control
  description: Lead education chair quite knowledge individual bill too manager understand
    face know less.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Debra Ortiz
  and results were consistent across multiple biological replicates.
