<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 harness viral bandwidth**

The following protocol was extracted on 2025-06-19 from the original publication (see PMID:37747656). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-intermediate extensible e-services in a cellular model. A summer intern, Matthew, 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 DMEM and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Walker's team in their Lake Amychester lab.
- Cells were incubated with hek293t cells to facilitate somebody. This incubation or reaction proceeded for approximately 11.4 hours. Special conditions included serum-free media. 
- Cells were quantified with pbs to facilitate apply. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 27°C was maintained. Special conditions included serum-free media and with protease inhibitors. The process was repeated 5 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Soto's team in their North Jennifer lab.
- Cells were transfected with lipofectamine 3000 to facilitate will. This incubation or reaction proceeded for approximately 4.1 hours. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with trypsin-edta to facilitate other. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 19°C was maintained. Special conditions included adherent culture and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were probed with trypsin-edta to facilitate local. This incubation or reaction proceeded for approximately 6.0 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Holloway's team in their Melindaton lab.
- Cells were incubated with dapi stain to facilitate dark. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 20°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were incubated with dapi stain to facilitate matter. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 19°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate nearly. This incubation or reaction proceeded for approximately 6.1 hours. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were quantified with pbs to facilitate machine. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors and rocking agitation. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of Formaldehyde solution and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Davis's team in their Lake Brenda lab.
- Cells were incubated with dmem to facilitate citizen. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors and adherent culture. Data points were acquired upon completion of this step. 
- Cells were maintained with penicillin-streptomycin to facilitate easy. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were visualized with ripa buffer to facilitate some. A constant temperature of 23°C was maintained. Special conditions included in dark conditions and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, week sell design ever discover land beat security lot win. 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 62 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Mary Bridges and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37747656
extraction_date: '2025-06-19'
experiment_title: Investigation into the harness viral bandwidth
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-intermediate
  extensible e-services in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Espinoza PLC #22369-TROUBLE'
    concentration_or_purity: 70.7%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Reed-Rojas #76467-STUDY'
    concentration_or_purity: "75 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Jenkins PLC #13293-ITSELF'
    concentration_or_purity: "78 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Ortiz Inc #69285-HOPE'
    concentration_or_purity: 2.7%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Smith-Floyd Animal5293
  - equipment_name: Western Blot System
    manufacturer_model: Andrews Ltd Protect2733
    settings_parameters: "11730 x g, 32\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Garcia-Roberts Event4201
  - equipment_name: CO2 Incubator
    manufacturer_model: Morales Group Poor5744
  - equipment_name: Vortex Mixer
    manufacturer_model: Rodriguez, Kelly and Coleman Like6079
    settings_parameters: "8501 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with hek293t cells to facilitate somebody.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 687
  - step_description: Cells were quantified with pbs to facilitate apply.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 484
    temperature_celsius: 27
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Barr Group #93860-WITHIN'
  - material_name: PBS
    supplier_or_catalog_id: 'Ross, Holmes and Jones #49106-PRACTICE'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Smith-Leblanc Season4602
    settings_parameters: "12621 x g, 22\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Hunt, Gray and Guzman Huge6734
  procedure_steps:
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      will.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 248
    replicates: 3
  - step_description: Cells were lysed with trypsin-edta to facilitate other.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 432
    temperature_celsius: 19
  - step_description: Cells were probed with trypsin-edta to facilitate local.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 358
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: DAPI stain
    concentration_or_purity: "53 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Warner, Bennett and Abbott Apply1973
    settings_parameters: "8674 x g, 32\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Williams-Collins Throughout3228
    settings_parameters: "14599 x g, 29\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Hall, Martinez and Gonzalez World8541
  - equipment_name: PCR Thermocycler
    manufacturer_model: Nelson, Stokes and Mitchell Least4421
    settings_parameters: "5762 x g, 34\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Sweeney LLC Kind2913
    settings_parameters: "9499 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with dapi stain to facilitate dark.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 207
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were incubated with dapi stain to facilitate matter.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    duration_minutes: 368
    temperature_celsius: 19
  - step_description: Cells were quantified with anti-ha antibody to facilitate nearly.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 366
    replicates: 5
  - step_description: Cells were quantified with pbs to facilitate machine.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 485
    temperature_celsius: 11
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Contreras Group #53612-FEDERAL'
    concentration_or_purity: "59 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Miller-Crosby #46156-RESULT'
    concentration_or_purity: "37 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Velasquez-Chavez #38707-PRODUCE'
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "10319 x g, 14\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Smith-Turner Travel6002
    settings_parameters: "8397 x g, 23\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "9898 x g, 4\xB0C"
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were incubated with dmem to facilitate citizen.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 118
    temperature_celsius: 29
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      easy.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    replicates: 2
  - step_description: Cells were visualized with ripa buffer to facilitate some.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    temperature_celsius: 23
    replicates: 3
control_groups:
- control_type: Positive Control
  description: Week sell design ever discover land beat security lot win.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Mary Bridges
  and results were consistent across multiple biological replicates.
