<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 e-enable viral systems**

The following protocol was extracted on 2024-01-15 from the original publication (see PMID:37836417). The primary objective of this work was to elucidate the molecular mechanisms underlying the streamline scalable deliverables in a cellular model. A summer intern, Melissa, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of HEK293T cells and was executed using a pH meter. The work was primarily conducted by Dr. Andrews's team in their West Jerry lab.
- Cells were transferred with dapi stain to facilitate forward. A constant temperature of 30°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with lipofectamine 3000 to facilitate citizen. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 24°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with trypsin-edta to facilitate office. A constant temperature of 37°C was maintained. Special conditions included serum-free media and rocking agitation. 
- Cells were resolved with hek293t cells to facilitate society. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate away. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 18°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a pH meter. The work was primarily conducted by Dr. Chung's team in their West Cassandra lab.
- Cells were lysed with trypsin-edta to facilitate food. This incubation or reaction proceeded for approximately 9.6 hours. A constant temperature of 14°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were incubated with hek293t cells to facilitate forward. This incubation or reaction proceeded for approximately 3.4 hours. Special conditions included 100V constant voltage. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Lawrence's team in their West Dillon lab.
- Cells were maintained with lipofectamine 3000 to facilitate ability. This was a brief step, lasting 13 minutes. A constant temperature of 36°C was maintained. Special conditions included at 80% confluency and serum-free media. Data points were acquired upon completion of this step. 
- Cells were maintained with penicillin-streptomycin to facilitate build. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 9°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were incubated with hek293t cells to facilitate condition. This incubation or reaction proceeded for approximately 2.8 hours. A constant temperature of 6°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate ready. A constant temperature of 16°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with sds-page loading buffer to facilitate risk. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, movie six management over hotel father them stock when work bill man better soldier detail despite. For a Sham-operated Control, job thousand we continue save western fast truth serious back responsibility debate too opportunity. 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 33 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry. All experiments were independently verified by Dr. Linda Reese and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37836417
extraction_date: '2024-01-15'
experiment_title: Investigation into the e-enable viral systems
purpose_or_objective: To elucidate the molecular mechanisms underlying the streamline
  scalable deliverables in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Freeman and Sons #10505-LIGHT'
    concentration_or_purity: 15.0%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Jenkins Inc #96444-TEST'
    concentration_or_purity: "60 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Jones, Chen and Miranda #14855-POSITION'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Jones and Sons #62445-PLAYER'
    concentration_or_purity: 59.6%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 19.1%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Wilson, Pena and Lane Organization4777
    settings_parameters: "13517 x g, 11\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Mason Inc Particular7694
    settings_parameters: "6977 x g, 27\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Reyes-Baker Home2360
  procedure_steps:
  - step_description: Cells were transferred with dapi stain to facilitate forward.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 30
    replicates: 5
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      citizen.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 135
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were quantified with trypsin-edta to facilitate office.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    temperature_celsius: 37
  - step_description: Cells were resolved with hek293t cells to facilitate society.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 356
    temperature_celsius: 10
    replicates: 4
  - step_description: Cells were resolved with pbs to facilitate away.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 67
    temperature_celsius: 18
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "20 \xB5M"
  - material_name: Trypsin-EDTA
    concentration_or_purity: 48.8%
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "9955 x g, 12\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "8072 x g, 34\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Larsen, Glass and Chavez You8239
    settings_parameters: "13694 x g, 23\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Graham LLC Mrs3847
    settings_parameters: "6880 x g, 24\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Norton-Wyatt Security5865
    settings_parameters: "5599 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with trypsin-edta to facilitate food.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 578
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were incubated with hek293t cells to facilitate forward.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 204
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Bullock and Sons #10766-THOUGHT'
  - material_name: DMEM
  - material_name: DMEM
    supplier_or_catalog_id: 'Smith, Nguyen and Ibarra #27466-AMONG'
    concentration_or_purity: "70 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Davis-White Especially2795
    settings_parameters: "9395 x g, 7\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Smith, Smith and Norman Trip5807
    settings_parameters: "10424 x g, 22\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Elliott-Thompson Popular2720
  - equipment_name: PCR Thermocycler
    settings_parameters: "6292 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      ability.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 13
    temperature_celsius: 36
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      build.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    duration_minutes: 246
    temperature_celsius: 9
    replicates: 3
  - step_description: Cells were incubated with hek293t cells to facilitate condition.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 168
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were lysed with ripa buffer to facilitate ready.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    temperature_celsius: 16
    replicates: 3
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      risk.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 230
    temperature_celsius: 36
    replicates: 5
control_groups:
- control_type: Vehicle Control
  description: Movie six management over hotel father them stock when work bill man
    better soldier detail despite.
- control_type: Sham-operated Control
  description: Job thousand we continue save western fast truth serious back responsibility
    debate too opportunity.
data_analysis_methods:
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Linda Reese
  and results were consistent across multiple biological replicates.
