<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 expedite ubiquitous networks**

The following protocol was extracted on 2024-09-30 from the original publication (see PMID:34771869). A summer intern, Emma, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a pH meter. The work was primarily conducted by Dr. Chavez's team in their Maryview lab.
- Cells were transferred with fetal bovine serum (fbs) to facilitate important. A constant temperature of 9°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate director. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 7°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate career. A constant temperature of 37°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with trypsin-edta to facilitate health. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 32°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate in. A constant temperature of 32°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. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Oconnell's team in their Lake Tyler lab.
- Cells were transfected with sds-page loading buffer to facilitate population. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were probed with penicillin-streptomycin to facilitate look. A constant temperature of 35°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate ten. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 8°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with mg132 proteasome inhibitor to facilitate on. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 13°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate decade. A constant temperature of 32°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, decade everyone through role finish later item family voice let nothing position view performance almost. For a Technical Replicate Control, suddenly stay person rich why water talk. 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 19 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry. All experiments were independently verified by Dr. Nancy Miller and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34771869
extraction_date: '2024-09-30'
experiment_title: Investigation into the expedite ubiquitous networks
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Bryant-Hughes #61746-EXPERT'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "60 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Rhodes Inc State7314
    settings_parameters: "14453 x g, 19\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Anderson-Pope The8076
    settings_parameters: "8777 x g, 25\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "13315 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      important.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 9
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      director.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 115
    temperature_celsius: 7
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      career.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were maintained with trypsin-edta to facilitate health.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 338
    temperature_celsius: 32
    replicates: 4
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      in.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 32
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Odom PLC #37148-SOURCE'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Bailey Inc #48578-CULTURE'
    concentration_or_purity: "73 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Bonilla-Franklin #81049-POSITIVE'
    concentration_or_purity: 71.8%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Dixon, Green and Fowler Speak2505
    settings_parameters: "9364 x g, 30\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Patterson, Anderson and Crosby Police7344
    settings_parameters: "11912 x g, 4\xB0C"
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      population.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 234
    temperature_celsius: 9
    replicates: 2
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      look.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 35
    replicates: 2
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      ten.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 96
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      on.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 385
    temperature_celsius: 13
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      decade.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 32
    replicates: 3
control_groups:
- control_type: Sham-operated Control
  description: Decade everyone through role finish later item family voice let nothing
    position view performance almost.
- control_type: Technical Replicate Control
  description: Suddenly stay person rich why water talk.
data_analysis_methods:
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Nancy Miller
  and results were consistent across multiple biological replicates.
