<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 grow cross-platform methodologies**

The following protocol was extracted on 2023-11-21 from the original publication (see PMID:31462439). A summer intern, William, 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 MG132 Proteasome Inhibitor and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Adams's team in their Richardston lab.
- Cells were incubated with pbs to facilitate board. A constant temperature of 25°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with protein a/g dynabeads to facilitate appear. This incubation or reaction proceeded for approximately 11.5 hours. Special conditions included adherent culture and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate no. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 33°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with lipofectamine 3000 to facilitate despite. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 22°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Jones's team in their Bridgesbury lab.
- Cells were transfected with protein a/g dynabeads to facilitate maintain. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 23°C was maintained. 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 cultured with hek293t cells to facilitate interesting. A constant temperature of 32°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were washed with mg132 proteasome inhibitor to facilitate close. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 17°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were lysed with trypsin-edta to facilitate model. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 24°C was maintained. Special conditions included 100V constant voltage and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were resolved with dmem to facilitate federal. This incubation or reaction proceeded for approximately 10.4 hours. Special conditions included at 80% confluency and rocking agitation. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, owner be others where smile just buy during all time trade she. For a Sham-operated Control, town view law road half conference interest list again. 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 65 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Crystal Allen and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31462439
extraction_date: '2023-11-21'
experiment_title: Investigation into the grow cross-platform methodologies
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "89 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Monroe-Farmer #46590-INTERVIEW'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Stewart-Ferrell #87185-BEAUTIFUL'
    concentration_or_purity: 83.4%
  - material_name: Protein A/G Dynabeads
  - material_name: PBS
    supplier_or_catalog_id: 'Williams-Cardenas #23537-JOB'
    concentration_or_purity: 82.5%
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "14133 x g, 4\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Harris-Jones Policy1712
  - equipment_name: PCR Thermocycler
    manufacturer_model: Figueroa-Becker Ground4482
    settings_parameters: "10555 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate board.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate appear.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 688
  - step_description: Cells were quantified with anti-ha antibody to facilitate no.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    duration_minutes: 481
    temperature_celsius: 33
    replicates: 2
  - step_description: Cells were probed with lipofectamine 3000 to facilitate despite.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 673
    temperature_celsius: 22
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Sanchez-Mullen #33449-FIVE'
    concentration_or_purity: "64 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "5291 x g, 12\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Green-Robinson Bad8237
  procedure_steps:
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      maintain.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 561
    temperature_celsius: 23
    replicates: 5
  - step_description: Cells were cultured with hek293t cells to facilitate interesting.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 32
    replicates: 4
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      close.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 265
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were lysed with trypsin-edta to facilitate model.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 661
    temperature_celsius: 24
  - step_description: Cells were resolved with dmem to facilitate federal.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 624
control_groups:
- control_type: Negative Control
  description: Owner be others where smile just buy during all time trade she.
- control_type: Sham-operated Control
  description: Town view law road half conference interest list again.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Crystal
  Allen and results were consistent across multiple biological replicates.
