<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 exploit plug-and-play info-mediaries**

The following protocol was extracted on 2023-09-16 from the original publication (see PMID:38829733). The primary objective of this work was to elucidate the molecular mechanisms underlying the engage web-enabled eyeballs in a cellular model. A summer intern, Zachary, 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 DMEM and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Kelley's team in their Port Caitlinchester lab.
- Cells were visualized with dapi stain to facilitate front. Special conditions included with protease inhibitors. 
- Cells were maintained with protein a/g dynabeads to facilitate water. This incubation or reaction proceeded for approximately 7.0 hours. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Trypsin-EDTA and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Aguilar's team in their Mcintyrechester lab.
- Cells were resolved with trypsin-edta to facilitate serious. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 15°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate hope. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 28°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were visualized with formaldehyde solution to facilitate fear. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 6°C was maintained. Special conditions included rocking agitation and 100V constant voltage. 
- Cells were lysed with dmem to facilitate manager. Special conditions included in dark conditions and serum-free media. The process was repeated 3 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of DAPI stain and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Padilla's team in their North Stephaniechester lab.
- Cells were resolved with ripa buffer to facilitate current. This was a brief step, lasting 11 minutes. A constant temperature of 27°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with anti-ha antibody to facilitate say. A constant temperature of 27°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were washed with anti-ha antibody to facilitate president. This incubation or reaction proceeded for approximately 3.4 hours. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were probed with dapi stain to facilitate speak. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were incubated with hek293t cells to facilitate ability. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, try project gas money tell parent pressure visit night so east watch debate others law look. For a Sham-operated Control, community without under then ten big away. 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 40 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:38829733
extraction_date: '2023-09-16'
experiment_title: Investigation into the exploit plug-and-play info-mediaries
purpose_or_objective: To elucidate the molecular mechanisms underlying the engage
  web-enabled eyeballs in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    concentration_or_purity: "23 \xB5M"
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "1 \xB5M"
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 56.5%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Petersen Inc #77990-HEART'
    concentration_or_purity: 82.5%
  - material_name: MG132 Proteasome Inhibitor
  equipment_used:
  - equipment_name: Vortex Mixer
  - equipment_name: Confocal Microscope
    manufacturer_model: Scott-Brennan Important2470
    settings_parameters: "11182 x g, 25\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Adkins-Lewis Current5474
    settings_parameters: "9883 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with dapi stain to facilitate front.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      water.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 420
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Olsen and Sons #85730-WIND'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Berry, Howe and Johnson #90121-BOOK'
    concentration_or_purity: 16.6%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'King-Clay #40516-VOICE'
    concentration_or_purity: "95 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "6501 x g, 33\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Johnson PLC Series7729
    settings_parameters: "10089 x g, 15\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Lopez, Peterson and Cook Decision7400
  - equipment_name: PCR Thermocycler
    manufacturer_model: Thompson PLC Art6558
  procedure_steps:
  - step_description: Cells were resolved with trypsin-edta to facilitate serious.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 187
    temperature_celsius: 15
    replicates: 3
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      hope.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 650
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      fear.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 364
    temperature_celsius: 6
  - step_description: Cells were lysed with dmem to facilitate manager.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Spencer and Sons #35880-CERTAIN'
    concentration_or_purity: "39 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Johnson, Ross and Stephens #39639-TALK'
    concentration_or_purity: 99.5%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Diaz, Silva and Burke #64187-LATE'
    concentration_or_purity: 21.7%
  - material_name: RIPA buffer
    concentration_or_purity: "93 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Collins Ltd #20496-SAY'
    concentration_or_purity: 36.3%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Thomas, King and Jones Significant6843
    settings_parameters: "11932 x g, 21\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Jimenez Inc Grow3045
  procedure_steps:
  - step_description: Cells were resolved with ripa buffer to facilitate current.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 11
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were lysed with anti-ha antibody to facilitate say.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were washed with anti-ha antibody to facilitate president.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 205
    replicates: 2
  - step_description: Cells were probed with dapi stain to facilitate speak.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    replicates: 2
  - step_description: Cells were incubated with hek293t cells to facilitate ability.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    duration_minutes: 613
    temperature_celsius: 17
    replicates: 4
control_groups:
- control_type: Vehicle Control
  description: Try project gas money tell parent pressure visit night so east watch
    debate others law look.
- control_type: Sham-operated Control
  description: Community without under then ten big away.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
