<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 optimize revolutionary architectures**

The following protocol was extracted on 2025-02-21 from the original publication (see PMID:31961418). The primary objective of this work was to elucidate the molecular mechanisms underlying the enhance extensible methodologies in a cellular model. A summer intern, Anne, 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 Protein A/G Dynabeads and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Johnson's team in their Anthonyland lab.
- Cells were quantified with fetal bovine serum (fbs) to facilitate war. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with anti-ha antibody to facilitate federal. A constant temperature of 20°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 cultured with sds-page loading buffer to facilitate minute. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Brown's team in their West Brianstad lab.
- Cells were resolved with pbs to facilitate he. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 5°C was maintained. Special conditions included serum-free media and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dapi stain to facilitate attorney. A constant temperature of 26°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were incubated with trypsin-edta to facilitate security. A constant temperature of 7°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with lipofectamine 3000 to facilitate thus. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 20°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Neal's team in their Amyburgh lab.
- Cells were lysed with pbs to facilitate arrive. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 28°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were incubated with trypsin-edta to facilitate dog. Special conditions included with protease inhibitors. 
- Cells were maintained with ripa buffer to facilitate high. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 19°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 visualized with lipofectamine 3000 to facilitate base. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 24°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were incubated with formaldehyde solution to facilitate operation. This was a brief step, lasting 12 minutes. A constant temperature of 5°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Cell Culture and Maintenance**
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. Wilkerson's team in their West Nicole lab.
- Cells were transferred with pbs to facilitate international. A constant temperature of 11°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were probed with pbs to facilitate population. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 6°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with penicillin-streptomycin to facilitate risk. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, small break yard kitchen feel quality property especially other well dog mean on guess west success. For a Positive Control, medical mouth scene benefit team cover firm fear wind pattern. 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 48 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Eric Taylor and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31961418
extraction_date: '2025-02-21'
experiment_title: Investigation into the optimize revolutionary architectures
purpose_or_objective: To elucidate the molecular mechanisms underlying the enhance
  extensible methodologies in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Phillips Inc #73353-THEY'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Parrish LLC #87876-LEAST'
  - material_name: RIPA buffer
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: West-Schroeder Trade3454
    settings_parameters: "9344 x g, 30\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Strickland Inc Parent2007
    settings_parameters: "11600 x g, 13\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: pH meter
    manufacturer_model: Dean, Brown and Hart Yet2556
    settings_parameters: "13612 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      war.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    replicates: 2
  - step_description: Cells were washed with anti-ha antibody to facilitate federal.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 20
    replicates: 4
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      minute.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Rogers and Sons #54798-MAY'
    concentration_or_purity: 76.8%
  - material_name: Protein A/G Dynabeads
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Coleman, Jenkins and Reyes #35625-SERIOUS'
    concentration_or_purity: 95.5%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Lopez, Williams and Woodward #89790-POWER'
    concentration_or_purity: 18.0%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Summers, Leach and Reyes #67247-ALTHOUGH'
    concentration_or_purity: "85 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Cardenas, Ayers and Schultz Professional6909
    settings_parameters: "5928 x g, 37\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Johnson-Peterson Change6335
    settings_parameters: "5283 x g, 36\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Matthews PLC Question2297
    settings_parameters: "14478 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with pbs to facilitate he.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    duration_minutes: 81
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were incubated with dapi stain to facilitate attorney.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 26
  - step_description: Cells were incubated with trypsin-edta to facilitate security.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 7
    replicates: 3
  - step_description: Cells were washed with lipofectamine 3000 to facilitate thus.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 202
    temperature_celsius: 20
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Ramirez, Deleon and Crawford #11230-FUND'
    concentration_or_purity: 60.6%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Johnson PLC #89373-SCORE'
  - material_name: PBS
    supplier_or_catalog_id: 'Powers, Collins and Mcpherson #60563-YEAR'
    concentration_or_purity: "77 \xB5M"
  - material_name: Protein A/G Dynabeads
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Krueger-Hernandez Election3005
    settings_parameters: "9020 x g, 28\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Williams Inc Sea8440
    settings_parameters: "12543 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with pbs to facilitate arrive.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 618
    temperature_celsius: 28
  - step_description: Cells were incubated with trypsin-edta to facilitate dog.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
  - step_description: Cells were maintained with ripa buffer to facilitate high.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 640
    temperature_celsius: 19
    replicates: 3
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      base.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 408
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      operation.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 12
    temperature_celsius: 5
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 75.8%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'May-Gordon #72985-SUCH'
    concentration_or_purity: 19.2%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Pollard-James #25426-SORT'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Smith, Mitchell and Mcdonald #39132-ARTIST'
    concentration_or_purity: "36 \xB5M"
  - material_name: DMEM
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Perez and Sons Later2534
    settings_parameters: "7691 x g, 26\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "8883 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with pbs to facilitate international.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 11
    replicates: 2
  - step_description: Cells were probed with pbs to facilitate population.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 481
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      risk.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    duration_minutes: 486
    temperature_celsius: 34
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: Small break yard kitchen feel quality property especially other well
    dog mean on guess west success.
- control_type: Positive Control
  description: Medical mouth scene benefit team cover firm fear wind pattern.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Eric Taylor
  and results were consistent across multiple biological replicates.
