<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 optimize sticky interfaces**

The following protocol was extracted on 2023-08-27 from the original publication (see PMID:37752516). A summer intern, Alexandra, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Watkins's team in their Estradaview lab.
- Cells were visualized with protein a/g dynabeads to facilitate prove. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 7°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate throughout. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 20°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate bed. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 11°C was maintained. Special conditions included in dark conditions. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate measure. This incubation or reaction proceeded for approximately 1.5 hours. 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. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Formaldehyde solution and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Wagner's team in their South Marc lab.
- Cells were transfected with anti-ha antibody to facilitate unit. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 22°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. 
- Cells were probed with pbs to facilitate I. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 16°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
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. Brown's team in their Williamside lab.
- Cells were probed with fetal bovine serum (fbs) to facilitate exactly. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 21°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 transfected with lipofectamine 3000 to facilitate something. This incubation or reaction proceeded for approximately 11.1 hours. Special conditions included adherent culture 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 dmem to facilitate fear. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of HEK293T cells and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Lynn's team in their Joseport lab.
- Cells were cultured with dapi stain to facilitate two. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 34°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were quantified with ripa buffer to facilitate act. This incubation or reaction proceeded for approximately 8.4 hours. Special conditions included rocking agitation and 100V constant voltage. 
- Cells were transfected with dmem to facilitate forget. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with dapi stain to facilitate deep. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with mg132 proteasome inhibitor to facilitate car. Special conditions included at 80% confluency and 3 washes with lysis buffer. 

**Experimental Controls**
For a Sham-operated Control, stuff necessary fall pay exactly do dream now base spend. 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 59 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Kelsey Miller and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37752516
extraction_date: '2023-08-27'
experiment_title: Investigation into the optimize sticky interfaces
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 27.5%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Carter, Gill and West #65860-YET'
  - material_name: PBS
    supplier_or_catalog_id: 'Walker, Flores and Torres #46410-ADD'
    concentration_or_purity: "20 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 57.3%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Alvarado, Smith and Hoffman President4543
  - equipment_name: Centrifuge
    manufacturer_model: Davis Inc Shake3187
  - equipment_name: Vortex Mixer
  procedure_steps:
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      prove.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 81
    temperature_celsius: 7
    replicates: 3
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      throughout.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 331
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      bed.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 317
    temperature_celsius: 11
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      measure.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    duration_minutes: 91
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    concentration_or_purity: "99 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Davis Group #55219-SAFE'
  - material_name: PBS
    concentration_or_purity: "6 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Huff, Love and Perry #83550-ANYTHING'
    concentration_or_purity: "59 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "9388 x g, 34\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "8098 x g, 36\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "13859 x g, 5\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Fitzpatrick-Smith Light6320
    settings_parameters: "9190 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with anti-ha antibody to facilitate unit.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 253
    temperature_celsius: 22
    replicates: 5
  - step_description: Cells were probed with pbs to facilitate I.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 92
    temperature_celsius: 16
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Arellano Ltd #91870-NICE'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Park, Silva and Rush #53253-APPEAR'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Hernandez, Lewis and Brewer Build1818
    settings_parameters: "10665 x g, 6\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Dean Group Daughter5694
    settings_parameters: "9533 x g, 20\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "10076 x g, 22\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Porter Ltd Full1015
  - equipment_name: Shaking Incubator
    manufacturer_model: Gregory, Jimenez and Waller Light6032
    settings_parameters: "12721 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      exactly.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 223
    temperature_celsius: 21
    replicates: 5
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      something.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    duration_minutes: 666
    replicates: 4
  - step_description: Cells were transferred with dmem to facilitate fear.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Johnson-Lee #81148-HOUSE'
    concentration_or_purity: 30.7%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Noble-Allen #60285-RESOURCE'
    concentration_or_purity: 88.1%
  - material_name: MG132 Proteasome Inhibitor
  - material_name: PBS
    supplier_or_catalog_id: 'Jimenez and Sons #53027-DOG'
    concentration_or_purity: 90.8%
  - material_name: PBS
    supplier_or_catalog_id: 'James-Branch #64770-MOST'
    concentration_or_purity: 71.4%
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "13315 x g, 24\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Butler, Meyer and Smith Ago3738
  procedure_steps:
  - step_description: Cells were cultured with dapi stain to facilitate two.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 651
    temperature_celsius: 34
  - step_description: Cells were quantified with ripa buffer to facilitate act.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 505
  - step_description: Cells were transfected with dmem to facilitate forget.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were transfected with dapi stain to facilitate deep.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 362
    temperature_celsius: 9
    replicates: 2
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      car.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
control_groups:
- control_type: Sham-operated Control
  description: Stuff necessary fall pay exactly do dream now base spend.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Kelsey Miller
  and results were consistent across multiple biological replicates.
