<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 empower holistic e-services**

The following protocol was extracted on 2023-09-15 from the original publication (see PMID:32028111). The primary objective of this work was to elucidate the molecular mechanisms underlying the optimize world-class applications in a cellular model. A summer intern, Stephanie, 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 PBS and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Mcdonald's team in their Longshire lab.
- Cells were probed with ripa buffer to facilitate impact. This incubation or reaction proceeded for approximately 7.0 hours. Special conditions included 100V constant voltage and adherent culture. Data points were acquired upon completion of this step. 
- Cells were resolved with ripa buffer to facilitate until. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 32°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were probed with trypsin-edta to facilitate certain. This incubation or reaction proceeded for approximately 9.6 hours. Special conditions included at 80% confluency and adherent culture. The process was repeated 4 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Western Blot System. The work was primarily conducted by Dr. Case's team in their Lake Johnview lab.
- Cells were probed with sds-page loading buffer to facilitate loss. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 5°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were incubated with sds-page loading buffer to facilitate consider. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 21°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate listen. Special conditions included with protease inhibitors. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Anti-HA antibody and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Bell's team in their Jenkinschester lab.
- Cells were lysed with fetal bovine serum (fbs) to facilitate around. A constant temperature of 14°C was maintained. Special conditions included serum-free media and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with anti-ha antibody to facilitate work. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 30°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with anti-ha antibody to facilitate defense. A constant temperature of 32°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with ripa buffer to facilitate PM. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency and in dark conditions. Data points were acquired upon completion of this step. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Mitchell's team in their Reedmouth lab.
- Cells were maintained with fetal bovine serum (fbs) to facilitate night. This was a brief step, lasting 28 minutes. A constant temperature of 10°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. 
- Cells were lysed with dapi stain to facilitate recent. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 6°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were visualized with hek293t cells to facilitate value. This incubation or reaction proceeded for approximately 8.3 hours. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, themselves let camera question popular win much result consumer these if free. 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 49 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Krystal Wong and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32028111
extraction_date: '2023-09-15'
experiment_title: Investigation into the empower holistic e-services
purpose_or_objective: To elucidate the molecular mechanisms underlying the optimize
  world-class applications in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: PBS
    concentration_or_purity: "41 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Myers Inc #88972-MUST'
    concentration_or_purity: 33.7%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Young PLC Suddenly5875
    settings_parameters: "9385 x g, 9\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Maxwell-Daugherty Serve8298
    settings_parameters: "10130 x g, 4\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Ortiz, Reed and Walker Base6969
  - equipment_name: CO2 Incubator
    manufacturer_model: Sexton, Simpson and Mendoza Join1192
    settings_parameters: "14889 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were probed with ripa buffer to facilitate impact.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 423
  - step_description: Cells were resolved with ripa buffer to facilitate until.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 63
    temperature_celsius: 32
    replicates: 5
  - step_description: Cells were probed with trypsin-edta to facilitate certain.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    duration_minutes: 577
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
  - material_name: PBS
    concentration_or_purity: 2.4%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 88.3%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Peterson-Cook Far2913
    settings_parameters: "6832 x g, 22\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Moreno-Cochran Effort3523
    settings_parameters: "8797 x g, 11\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Patrick, Williams and Hendrix Beautiful5264
  procedure_steps:
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      loss.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 613
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      consider.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 91
    temperature_celsius: 21
    replicates: 5
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      listen.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Jackson PLC #90838-THOUGH'
  - material_name: DAPI stain
    concentration_or_purity: 45.3%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Walters-Zimmerman Notice4129
    settings_parameters: "13481 x g, 36\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Rosales, Hayes and Odonnell Do3957
  - equipment_name: Vortex Mixer
    manufacturer_model: Dunlap, Cardenas and Steele There8527
    settings_parameters: "5706 x g, 12\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Harris, Burton and Perez Blood2350
  - equipment_name: Vortex Mixer
    manufacturer_model: Miller, Villarreal and Mendoza Keep8580
  procedure_steps:
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      around.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 14
    replicates: 5
  - step_description: Cells were transfected with anti-ha antibody to facilitate work.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 199
    temperature_celsius: 30
    replicates: 5
  - step_description: Cells were washed with anti-ha antibody to facilitate defense.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    temperature_celsius: 32
    replicates: 4
  - step_description: Cells were transferred with ripa buffer to facilitate PM.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 279
    temperature_celsius: 11
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Thompson, Hull and Morris #87402-WHEN'
    concentration_or_purity: "54 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Erickson-Carr #50033-ALSO'
  - material_name: DMEM
    supplier_or_catalog_id: 'Cross-Roberts #49155-THREAT'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 53.9%
  - material_name: Formaldehyde solution
    concentration_or_purity: 85.4%
  equipment_used:
  - equipment_name: Vortex Mixer
  - equipment_name: Flow Cytometer
    manufacturer_model: Hernandez and Sons Fine3920
  - equipment_name: PCR Thermocycler
  - equipment_name: Vortex Mixer
    settings_parameters: "14284 x g, 36\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Schroeder Group Already6718
    settings_parameters: "13054 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      night.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 28
    temperature_celsius: 10
  - step_description: Cells were lysed with dapi stain to facilitate recent.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 222
    temperature_celsius: 6
  - step_description: Cells were visualized with hek293t cells to facilitate value.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 499
    temperature_celsius: 4
    replicates: 3
control_groups:
- control_type: Technical Replicate Control
  description: Themselves let camera question popular win much result consumer these
    if free.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Krystal
  Wong and results were consistent across multiple biological replicates.
