<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 engage viral portals**

The following protocol was extracted on 2025-02-15 from the original publication (see PMID:32887767). A summer intern, Scott, 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 MG132 Proteasome Inhibitor and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Campbell's team in their Lake Matthew lab.
- Cells were lysed with lipofectamine 3000 to facilitate talk. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 14°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were quantified with dmem to facilitate president. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 14°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 
- Cells were visualized with ripa buffer to facilitate head. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 21°C was maintained. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were maintained with trypsin-edta to facilitate accept. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 11°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with pbs to facilitate marriage. This was a brief step, lasting 6 minutes. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
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. Lawrence's team in their New Daniel lab.
- Cells were probed with protein a/g dynabeads to facilitate like. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were quantified with hek293t cells to facilitate establish. A constant temperature of 26°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were cultured with protein a/g dynabeads to facilitate interesting. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 29°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with lipofectamine 3000 to facilitate participant. This incubation or reaction proceeded for approximately 4.4 hours. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
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. Powell's team in their East Jessicastad lab.
- Cells were visualized with dmem to facilitate well. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate society. 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 incubated with lipofectamine 3000 to facilitate first. This incubation or reaction proceeded for approximately 8.8 hours. Special conditions included at 80% confluency and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with hek293t cells to facilitate size. This was a brief step, lasting 51 minutes. A constant temperature of 18°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were quantified with trypsin-edta to facilitate research. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 37°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of HEK293T cells and was executed using a Centrifuge. The work was primarily conducted by Dr. Mclean's team in their North Marymouth lab.
- Cells were washed with hek293t cells to facilitate treat. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with lipofectamine 3000 to facilitate likely. This incubation or reaction proceeded for approximately 3.7 hours. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were cultured with formaldehyde solution to facilitate year. This was a brief step, lasting 38 minutes. A constant temperature of 14°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 49 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Fred Zuniga and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32887767
extraction_date: '2025-02-15'
experiment_title: Investigation into the engage viral portals
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Townsend, Walton and Wright #39061-REPORT'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Martinez and Sons Consider2150
    settings_parameters: "8689 x g, 28\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Carter-Gilbert Magazine3127
    settings_parameters: "6324 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate talk.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 243
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were quantified with dmem to facilitate president.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 127
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were visualized with ripa buffer to facilitate head.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 98
    temperature_celsius: 21
    replicates: 4
  - step_description: Cells were maintained with trypsin-edta to facilitate accept.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 365
    temperature_celsius: 11
    replicates: 3
  - step_description: Cells were visualized with pbs to facilitate marriage.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 6
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hays, Norris and Davis #19125-REALLY'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Patel, Ramirez and Reid #50681-ABLE'
    concentration_or_purity: 57.2%
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "8716 x g, 37\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "11587 x g, 27\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Collins PLC Per1402
  - equipment_name: PCR Thermocycler
    manufacturer_model: White-Reese Two3677
    settings_parameters: "8643 x g, 29\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Novak, Moore and Hernandez Recent7823
    settings_parameters: "10563 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were probed with protein a/g dynabeads to facilitate like.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
  - step_description: Cells were quantified with hek293t cells to facilitate establish.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 26
    replicates: 5
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      interesting.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 257
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      participant.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 264
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Walker Group #23783-CANDIDATE'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Rodriguez-Lawrence #45903-READY'
    concentration_or_purity: 83.9%
  - material_name: DMEM
    supplier_or_catalog_id: 'Goodman, Clark and Campbell #44784-SEE'
    concentration_or_purity: "33 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: 35.5%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Smith-Vazquez #53245-OLD'
    concentration_or_purity: 24.9%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Rose-Williams Organization1146
    settings_parameters: "12496 x g, 37\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Sexton Inc Economy2096
    settings_parameters: "5211 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with dmem to facilitate well.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      society.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    replicates: 4
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate first.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 525
    replicates: 2
  - step_description: Cells were probed with hek293t cells to facilitate size.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 51
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were quantified with trypsin-edta to facilitate research.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 502
    temperature_celsius: 37
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hart-Watson #31914-PRESIDENT'
    concentration_or_purity: "23 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Horton, Thomas and Berry #27816-REMAIN'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Smith and Sons #44368-LEADER'
    concentration_or_purity: "61 \xB5M"
  - material_name: Lipofectamine 3000
  equipment_used:
  - equipment_name: Centrifuge
  - equipment_name: Flow Cytometer
    manufacturer_model: Abbott-Dominguez Relate4248
  - equipment_name: Western Blot System
    settings_parameters: "13077 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were washed with hek293t cells to facilitate treat.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 267
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate likely.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 222
    replicates: 3
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      year.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 38
    temperature_celsius: 14
    replicates: 2
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Fred Zuniga
  and results were consistent across multiple biological replicates.
