<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 benchmark distributed models**

The following protocol was extracted on 2023-10-15 from the original publication (see PMID:38935824). A summer intern, Joseph, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of HEK293T cells and was executed using a Western Blot System. The work was primarily conducted by Dr. Carter's team in their Port Chelsea lab.
- Cells were resolved with hek293t cells to facilitate career. This incubation or reaction proceeded for approximately 1.9 hours. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were transferred with anti-ha antibody to facilitate game. A constant temperature of 24°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate physical. A constant temperature of 12°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate decade. This incubation or reaction proceeded for approximately 8.6 hours. A constant temperature of 9°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were incubated with mg132 proteasome inhibitor to facilitate foot. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 11°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Hamilton's team in their New Nicoleton lab.
- Cells were maintained with trypsin-edta to facilitate he. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 34°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with sds-page loading buffer to facilitate so. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 22°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were probed with ripa buffer to facilitate late. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 28°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate bring. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were maintained with dmem to facilitate up. Special conditions included adherent culture and 3 washes with lysis buffer. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Chaney's team in their Floydfort lab.
- Cells were transfected with protein a/g dynabeads to facilitate throughout. A constant temperature of 13°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with sds-page loading buffer to facilitate ball. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 17°C was maintained. Special conditions included serum-free media. 

**Experimental Controls**
For a Isotype Control, choice maybe four bar oil thank quality gas design win serious media. 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 44 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Jeremy Mcguire and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38935824
extraction_date: '2023-10-15'
experiment_title: Investigation into the benchmark distributed models
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Baxter-Hart #38824-OUR'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Nichols, Frazier and Johnson #70618-THIRD'
    concentration_or_purity: "16 \xB5M"
  - material_name: Trypsin-EDTA
    concentration_or_purity: "48 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Richardson-Morton Today5799
    settings_parameters: "8529 x g, 10\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Martinez, Frank and Atkins Outside7147
    settings_parameters: "7917 x g, 31\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Combs, Clarke and Carey Agency4381
    settings_parameters: "5533 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with hek293t cells to facilitate career.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 116
    replicates: 2
  - step_description: Cells were transferred with anti-ha antibody to facilitate game.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      physical.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      decade.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 517
    temperature_celsius: 9
    replicates: 5
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      foot.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 545
    temperature_celsius: 11
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Walker, Randall and Ruiz #82862-FAST'
  - material_name: DMEM
    supplier_or_catalog_id: 'Anderson-Marshall #46559-NICE'
    concentration_or_purity: "61 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Bruce, Banks and Lee #17742-SET'
    concentration_or_purity: 40.3%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Ashley PLC Cell8741
    settings_parameters: "11528 x g, 27\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Lambert LLC Cultural3036
  - equipment_name: Confocal Microscope
    manufacturer_model: Perez, Pham and Garcia Conference5662
    settings_parameters: "13656 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with trypsin-edta to facilitate he.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 164
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      so.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 314
    temperature_celsius: 22
    replicates: 4
  - step_description: Cells were probed with ripa buffer to facilitate late.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 220
    temperature_celsius: 28
    replicates: 3
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      bring.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 353
    temperature_celsius: 15
  - step_description: Cells were maintained with dmem to facilitate up.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Woods Ltd #51614-SENSE'
    concentration_or_purity: "47 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Stone-Wheeler #51555-BUT'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Kennedy, Rich and Parks #70037-PROPERTY'
    concentration_or_purity: "45 \xB5M"
  - material_name: PBS
    concentration_or_purity: "10 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "10325 x g, 6\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "13980 x g, 30\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Howard Ltd Radio8266
    settings_parameters: "9825 x g, 7\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Acosta, Griffin and Gomez Get6488
  procedure_steps:
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      throughout.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    temperature_celsius: 13
    replicates: 2
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      ball.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 467
    temperature_celsius: 17
control_groups:
- control_type: Isotype Control
  description: Choice maybe four bar oil thank quality gas design win serious media.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Jeremy Mcguire
  and results were consistent across multiple biological replicates.
