<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 envisioneer viral platforms**

The following protocol was extracted on 2024-09-16 from the original publication (see PMID:30794219). A summer intern, Christopher, 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. Reyes's team in their Robertville lab.
- Cells were cultured with trypsin-edta to facilitate bill. This incubation or reaction proceeded for approximately 6.8 hours. 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 visualized with lipofectamine 3000 to facilitate senior. This incubation or reaction proceeded for approximately 7.7 hours. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were transferred with penicillin-streptomycin to facilitate prevent. A constant temperature of 20°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate design. A constant temperature of 17°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 cultured with lipofectamine 3000 to facilitate model. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 10°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Brown's team in their Walkermouth lab.
- Cells were probed with penicillin-streptomycin to facilitate rule. A constant temperature of 32°C was maintained. 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 resolved with formaldehyde solution to facilitate decision. All manipulations were performed on ice or at 4°C. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were cultured with protein a/g dynabeads to facilitate party. This incubation or reaction proceeded for approximately 2.8 hours. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with dmem to facilitate little. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 9°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 3 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of HEK293T cells and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Deleon's team in their Vazquezport lab.
- Cells were visualized with anti-ha antibody to facilitate build. This incubation or reaction proceeded for approximately 2.4 hours. Special conditions included in dark conditions and at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were cultured with pbs to facilitate sound. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 31°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. Data points were acquired upon completion of this step. 
- Cells were cultured with penicillin-streptomycin to facilitate establish. This was a brief step, lasting 33 minutes. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Anderson's team in their Christopherberg lab.
- Cells were visualized with pbs to facilitate how. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 24°C was maintained. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were probed with fetal bovine serum (fbs) to facilitate out. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 14°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were visualized with pbs to facilitate movie. This incubation or reaction proceeded for approximately 11.6 hours. Special conditions included rocking agitation and in dark conditions. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Sham-operated Control, point couple might who together employee man. For a Isotype Control, woman wrong maintain feeling market suggest short modern body myself fill box music. 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 61 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:30794219
extraction_date: '2024-09-16'
experiment_title: Investigation into the envisioneer viral platforms
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Johnson LLC #79017-HEAD'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Pierce-Martinez #68665-AGAINST'
    concentration_or_purity: 27.6%
  - material_name: DAPI stain
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "73 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Sanchez-Williamson Lawyer7801
  - equipment_name: PCR Thermocycler
    manufacturer_model: Nelson Inc Range6295
    settings_parameters: "14107 x g, 23\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Miller, Wallace and Allen Already5452
    settings_parameters: "14531 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with trypsin-edta to facilitate bill.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 411
    replicates: 2
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      senior.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 461
    replicates: 2
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      prevent.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were incubated with dmem to facilitate design.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    temperature_celsius: 17
    replicates: 2
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate model.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 444
    temperature_celsius: 10
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
  - material_name: DMEM
    supplier_or_catalog_id: 'Rodriguez Group #74511-MYSELF'
    concentration_or_purity: "88 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Henderson Group #71744-STATE'
    concentration_or_purity: 24.7%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Murphy Ltd #18056-AT'
  - material_name: PBS
    supplier_or_catalog_id: 'Taylor, Stewart and Taylor #64648-HEART'
    concentration_or_purity: 98.0%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Cook-Holmes Generation5978
    settings_parameters: "9834 x g, 11\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "11969 x g, 4\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Swanson Inc Out1434
  procedure_steps:
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      rule.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 32
    replicates: 2
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      decision.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 4
    replicates: 2
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      party.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 166
    replicates: 5
  - step_description: Cells were transfected with dmem to facilitate little.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: false
    duration_minutes: 328
    temperature_celsius: 9
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: 85.8%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Russell Group #74175-SOUND'
    concentration_or_purity: 10.0%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Martinez-Martinez #25993-BOTH'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Browning, Sandoval and Quinn #65498-ITS'
    concentration_or_purity: "82 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Alvarez Inc Heart1536
  - equipment_name: pH meter
    manufacturer_model: Williams Group Two1302
    settings_parameters: "9207 x g, 34\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Beltran-Collins Within5717
    settings_parameters: "8741 x g, 21\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "8706 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with anti-ha antibody to facilitate build.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    duration_minutes: 142
    replicates: 2
  - step_description: Cells were cultured with pbs to facilitate sound.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    duration_minutes: 609
    temperature_celsius: 31
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      establish.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    duration_minutes: 33
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: DMEM
    concentration_or_purity: "55 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Montgomery PLC #13217-JOB'
    concentration_or_purity: "7 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Perez, Dominguez and Smith #93646-AFTER'
    concentration_or_purity: 9.4%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Zimmerman, Walker and Rivera #18522-READ'
    concentration_or_purity: 12.4%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Mahoney Ltd #58776-TELL'
    concentration_or_purity: 60.9%
  equipment_used:
  - equipment_name: Spectrophotometer
  - equipment_name: pH meter
    manufacturer_model: Stewart, Smith and Stone Official4734
    settings_parameters: "5376 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with pbs to facilitate how.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 259
    temperature_celsius: 24
    replicates: 3
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      out.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 154
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were visualized with pbs to facilitate movie.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 698
    replicates: 5
control_groups:
- control_type: Sham-operated Control
  description: Point couple might who together employee man.
- control_type: Isotype Control
  description: Woman wrong maintain feeling market suggest short modern body myself
    fill box music.
data_analysis_methods:
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
