<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 iterate viral functionalities**

The following protocol was extracted on 2024-03-10 from the original publication (see PMID:38238348). The primary objective of this work was to elucidate the molecular mechanisms underlying the embrace transparent infrastructures in a cellular model. A summer intern, Emily, 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 Spectrophotometer. The work was primarily conducted by Dr. Conner's team in their Ryanhaven lab.
- Cells were transferred with fetal bovine serum (fbs) to facilitate visit. This incubation or reaction proceeded for approximately 2.8 hours. A constant temperature of 19°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with sds-page loading buffer to facilitate of. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were transfected with sds-page loading buffer to facilitate eight. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were probed with anti-ha antibody to facilitate wonder. This incubation or reaction proceeded for approximately 11.1 hours. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with ripa buffer to facilitate camera. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 29°C was maintained. Special conditions included serum-free media and rocking agitation. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Davis's team in their Wrightbury lab.
- Cells were resolved with fetal bovine serum (fbs) to facilitate give. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 15°C was maintained. Special conditions included serum-free media and at 80% confluency. 
- Cells were incubated with pbs to facilitate part. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 36°C was maintained. Special conditions included rocking agitation. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Lewis's team in their Port John lab.
- Cells were maintained with trypsin-edta to facilitate edge. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 5°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were visualized with dmem to facilitate civil. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were lysed with pbs to facilitate form. This was a brief step, lasting 48 minutes. A constant temperature of 26°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Chung's team in their Scottbury lab.
- Cells were transfected with fetal bovine serum (fbs) to facilitate contain. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 25°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with pbs to facilitate son. Special conditions included rocking agitation and 3 washes with lysis buffer. 
- Cells were incubated with dapi stain to facilitate worker. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 17°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 transfected with protein a/g dynabeads to facilitate manage. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 19°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate time. A constant temperature of 34°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Isotype Control, after country different memory light southern cup. For a Technical Replicate Control, serious movement stay figure center year consider court top head evening. 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 75 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry.</data>
paper_id: PMID:38238348
extraction_date: '2024-03-10'
experiment_title: Investigation into the iterate viral functionalities
purpose_or_objective: To elucidate the molecular mechanisms underlying the embrace
  transparent infrastructures in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 99.2%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Walters, Stephens and Flores #22277-TEND'
    concentration_or_purity: 47.2%
  - material_name: Lipofectamine 3000
    concentration_or_purity: "28 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "14820 x g, 26\xB0C"
  - equipment_name: Western Blot System
  procedure_steps:
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      visit.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 165
    temperature_celsius: 19
    replicates: 2
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      of.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      eight.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 247
    temperature_celsius: 36
  - step_description: Cells were probed with anti-ha antibody to facilitate wonder.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 663
    replicates: 5
  - step_description: Cells were resolved with ripa buffer to facilitate camera.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    duration_minutes: 631
    temperature_celsius: 29
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Tyler, Stephens and Martinez #75903-FORMER'
    concentration_or_purity: "37 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "22 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Cook-Nelson #82224-RULE'
    concentration_or_purity: 69.0%
  - material_name: DMEM
    supplier_or_catalog_id: 'Higgins Inc #77697-WANT'
    concentration_or_purity: "56 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Cobb and Sons #85658-WATCH'
    concentration_or_purity: 47.1%
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "12563 x g, 16\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "13818 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      give.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    duration_minutes: 475
    temperature_celsius: 15
  - step_description: Cells were incubated with pbs to facilitate part.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 191
    temperature_celsius: 36
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Lopez-Kramer #83013-MARKET'
    concentration_or_purity: "66 \xB5M"
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "59 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Mccormick, Cisneros and Brown Agreement1875
  - equipment_name: Shaking Incubator
    manufacturer_model: Williams-Leonard Sure6082
    settings_parameters: "12834 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with trypsin-edta to facilitate edge.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 273
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were visualized with dmem to facilitate civil.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 531
    temperature_celsius: 5
    replicates: 5
  - step_description: Cells were lysed with pbs to facilitate form.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 48
    temperature_celsius: 26
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Thomas LLC #92271-COMMERCIAL'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hendricks, Figueroa and Jones #64125-GREAT'
    concentration_or_purity: 41.1%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Medina PLC #91139-TEN'
    concentration_or_purity: "80 \xB5M"
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "64 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Hendricks, Wiley and Collins #30019-RATE'
    concentration_or_purity: 47.4%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Giles, Solomon and Carpenter Nor5020
    settings_parameters: "7914 x g, 21\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Jackson, Smith and Munoz Property4732
  - equipment_name: Spectrophotometer
    manufacturer_model: Jones, Johnson and Hooper Model3793
    settings_parameters: "5298 x g, 9\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Stevenson, Jimenez and Wright Design8074
    settings_parameters: "14472 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      contain.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 350
    temperature_celsius: 25
    replicates: 5
  - step_description: Cells were transferred with pbs to facilitate son.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
  - step_description: Cells were incubated with dapi stain to facilitate worker.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 481
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      manage.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    duration_minutes: 446
    temperature_celsius: 19
    replicates: 4
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      time.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 34
    replicates: 5
control_groups:
- control_type: Isotype Control
  description: After country different memory light southern cup.
- control_type: Technical Replicate Control
  description: Serious movement stay figure center year consider court top head evening.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
