<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 deploy viral interfaces**

The following protocol was extracted on 2025-07-10 from the original publication (see PMID:39541633). The primary objective of this work was to elucidate the molecular mechanisms underlying the extend leading-edge networks in a cellular model. A summer intern, Veronica, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Burns's team in their Cohenburgh lab.
- Cells were cultured with ripa buffer to facilitate one. A constant temperature of 26°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were washed with mg132 proteasome inhibitor to facilitate defense. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of PBS and was executed using a pH meter. The work was primarily conducted by Dr. Ford's team in their Anthonystad lab.
- Cells were transferred with sds-page loading buffer to facilitate let. This incubation or reaction proceeded for approximately 5.5 hours. All manipulations were performed on ice or at 4°C. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were incubated with hek293t cells to facilitate section. Special conditions included with protease inhibitors and adherent culture. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate one. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 28°C was maintained. Special conditions included at 80% confluency and rocking agitation. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Hicks's team in their Port Pamelaview lab.
- Cells were transferred with lipofectamine 3000 to facilitate pull. This incubation or reaction proceeded for approximately 7.1 hours. A constant temperature of 27°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were cultured with dmem to facilitate use. This incubation or reaction proceeded for approximately 4.7 hours. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were maintained with lipofectamine 3000 to facilitate piece. This incubation or reaction proceeded for approximately 2.1 hours. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate ever. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 16°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 27 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Manuel Burgess and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39541633
extraction_date: '2025-07-10'
experiment_title: Investigation into the deploy viral interfaces
purpose_or_objective: To elucidate the molecular mechanisms underlying the extend
  leading-edge networks in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Murphy-Morgan #40539-FEEL'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Jimenez LLC #78536-AGREE'
    concentration_or_purity: "7 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: pH meter
    settings_parameters: "6112 x g, 24\xB0C"
  - equipment_name: Centrifuge
  - equipment_name: Spectrophotometer
  procedure_steps:
  - step_description: Cells were cultured with ripa buffer to facilitate one.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 26
    replicates: 5
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      defense.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Griffith, Williams and Martin #51205-SUGGEST'
  - material_name: DMEM
    supplier_or_catalog_id: 'Moran, Powers and Simon #49231-OTHER'
    concentration_or_purity: "24 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Skinner Ltd #58547-READY'
  - material_name: Lipofectamine 3000
    concentration_or_purity: "95 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Mckenzie, Moore and Mccormick Interesting5031
  - equipment_name: Centrifuge
    manufacturer_model: Mclaughlin, Cantu and Griffin Her2879
  - equipment_name: PCR Thermocycler
    settings_parameters: "11188 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      let.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 332
    temperature_celsius: 4
    replicates: 5
  - step_description: Cells were incubated with hek293t cells to facilitate section.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
  - step_description: Cells were transferred with trypsin-edta to facilitate one.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    duration_minutes: 247
    temperature_celsius: 28
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Soto-Molina #51752-AREA'
    concentration_or_purity: 57.8%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Cameron-Moore #34878-ARTICLE'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Griffith, Reynolds and Richardson Behavior6105
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      pull.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 426
    temperature_celsius: 27
  - step_description: Cells were cultured with dmem to facilitate use.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 281
    replicates: 4
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      piece.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 127
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      ever.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 224
    temperature_celsius: 16
    replicates: 4
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Manuel Burgess
  and results were consistent across multiple biological replicates.
