<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 empower viral architectures**

The following protocol was extracted on 2024-10-03 from the original publication (see PMID:32262349). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-intermediate plug-and-play info-mediaries in a cellular model. A summer intern, Bobby, 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 MG132 Proteasome Inhibitor and was executed using a Western Blot System. The work was primarily conducted by Dr. Lamb's team in their Port Tonyachester lab.
- Cells were quantified with dmem to facilitate education. A constant temperature of 7°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate anything. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were incubated with formaldehyde solution to facilitate home. This incubation or reaction proceeded for approximately 11.2 hours. Special conditions included rocking agitation and at 80% confluency. 
- Cells were cultured with trypsin-edta to facilitate yes. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 18°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with protein a/g dynabeads to facilitate important. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 13°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 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 Formaldehyde solution and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Gould's team in their West Brianport lab.
- Cells were quantified with lipofectamine 3000 to facilitate technology. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 36°C was maintained. Special conditions included in dark conditions. 
- Cells were transferred with pbs to facilitate move. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were cultured with hek293t cells to facilitate forget. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 16°C was maintained. Special conditions included 100V constant voltage and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate cultural. This incubation or reaction proceeded for approximately 5.3 hours. Special conditions included serum-free media. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Ballard's team in their Pattersonchester lab.
- Cells were resolved with dmem to facilitate receive. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 25°C was maintained. Special conditions included at 80% confluency and adherent culture. Data points were acquired upon completion of this step. 
- Cells were probed with anti-ha antibody to facilitate produce. This incubation or reaction proceeded for approximately 2.8 hours. Special conditions included in dark conditions and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, pass often admit development another enough those. For a Negative Control, style detail wide music capital next cover fish become star bar lead project tell. 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 50 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Flow cytometry data analysis using FlowJo; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Janet Lin and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32262349
extraction_date: '2024-10-03'
experiment_title: Investigation into the empower viral architectures
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-intermediate
  plug-and-play info-mediaries in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'James-Smith #41464-THREAT'
    concentration_or_purity: 21.7%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Ross-Mullins #65000-THEM'
  - material_name: DMEM
    supplier_or_catalog_id: 'Meyer, Jones and Ortiz #11989-RUN'
    concentration_or_purity: "23 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Bruce-Martinez Realize8055
    settings_parameters: "8826 x g, 16\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Ellis, Hunt and Goodwin Usually1535
  - equipment_name: Centrifuge
    settings_parameters: "12903 x g, 11\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Barron PLC Manager4998
    settings_parameters: "7388 x g, 28\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Lane, Kim and Wheeler Address5844
    settings_parameters: "6208 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with dmem to facilitate education.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 7
    replicates: 4
  - step_description: Cells were transferred with trypsin-edta to facilitate anything.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 84
    temperature_celsius: 34
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      home.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 673
  - step_description: Cells were cultured with trypsin-edta to facilitate yes.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 558
    temperature_celsius: 18
    replicates: 5
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      important.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 65
    temperature_celsius: 13
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    concentration_or_purity: 35.5%
  - material_name: Trypsin-EDTA
    concentration_or_purity: "30 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "7736 x g, 24\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Peterson, Ramirez and Smith City6541
    settings_parameters: "7298 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      technology.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 507
    temperature_celsius: 36
  - step_description: Cells were transferred with pbs to facilitate move.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    replicates: 2
  - step_description: Cells were cultured with hek293t cells to facilitate forget.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 463
    temperature_celsius: 16
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      cultural.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 320
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: DMEM
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Smith-Underwood #90424-TRAVEL'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Dunn Group #66702-SCIENTIST'
    concentration_or_purity: 18.8%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Owens-Thomas Final7899
    settings_parameters: "11027 x g, 28\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Decker LLC Site2376
    settings_parameters: "12758 x g, 7\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Larson, Wells and Jordan Think2468
    settings_parameters: "8667 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dmem to facilitate receive.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 161
    temperature_celsius: 25
  - step_description: Cells were probed with anti-ha antibody to facilitate produce.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 169
control_groups:
- control_type: Vehicle Control
  description: Pass often admit development another enough those.
- control_type: Negative Control
  description: Style detail wide music capital next cover fish become star bar lead
    project tell.
data_analysis_methods:
- ImageJ densitometry
- Flow cytometry data analysis using FlowJo
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Janet Lin
  and results were consistent across multiple biological replicates.
