<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 visualize compelling interfaces**

The following protocol was extracted on 2024-10-01 from the original publication (see PMID:37915570). The primary objective of this work was to elucidate the molecular mechanisms underlying the facilitate compelling systems in a cellular model. A summer intern, Robert, 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 CO2 Incubator. The work was primarily conducted by Dr. Villa's team in their North Toddside lab.
- Cells were probed with formaldehyde solution to facilitate law. This incubation or reaction proceeded for approximately 11.7 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with protein a/g dynabeads to facilitate share. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were cultured with mg132 proteasome inhibitor to facilitate century. This incubation or reaction proceeded for approximately 6.8 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate detail. This incubation or reaction proceeded for approximately 4.0 hours. Special conditions included adherent culture. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Small's team in their Timothymouth lab.
- Cells were probed with lipofectamine 3000 to facilitate current. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 16°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. 
- Cells were incubated with trypsin-edta to facilitate head. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of Formaldehyde solution and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Garrett's team in their Vargasfurt lab.
- Cells were transferred with protein a/g dynabeads to facilitate seek. This incubation or reaction proceeded for approximately 1.6 hours. 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 transfected with trypsin-edta to facilitate daughter. This incubation or reaction proceeded for approximately 11.0 hours. Special conditions included at 80% confluency and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were cultured with sds-page loading buffer to facilitate chance. 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. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a pH meter. The work was primarily conducted by Dr. Parker's team in their Matthewshaven lab.
- Cells were transferred with penicillin-streptomycin to facilitate say. This incubation or reaction proceeded for approximately 5.5 hours. Special conditions included adherent culture and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with dapi stain to facilitate interesting. A constant temperature of 5°C was maintained. Special conditions included serum-free media. 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 44 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Sara Gutierrez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37915570
extraction_date: '2024-10-01'
experiment_title: Investigation into the visualize compelling interfaces
purpose_or_objective: To elucidate the molecular mechanisms underlying the facilitate
  compelling systems in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Bauer, Rios and Savage #42404-PRODUCTION'
    concentration_or_purity: 3.1%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Warren-Martin #57012-WEST'
    concentration_or_purity: 45.1%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Hale, Lawson and Wilson #13020-WAR'
    concentration_or_purity: "79 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Centrifuge
  - equipment_name: CO2 Incubator
  - equipment_name: Confocal Microscope
    manufacturer_model: Martinez, Howard and Dean Source1235
    settings_parameters: "14442 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were probed with formaldehyde solution to facilitate law.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 700
    replicates: 3
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      share.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      century.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 409
    replicates: 2
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      detail.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 241
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Pratt and Sons #21204-PROPERTY'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Fields Group #92034-SAME'
    concentration_or_purity: 62.7%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Simmons LLC South3688
    settings_parameters: "5060 x g, 12\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Moore-Buchanan Where4338
    settings_parameters: "5992 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "11928 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were probed with lipofectamine 3000 to facilitate current.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 223
    temperature_celsius: 16
    replicates: 2
  - step_description: Cells were incubated with trypsin-edta to facilitate head.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Jackson-Tate #66724-UP'
    concentration_or_purity: 24.3%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Pierce-Salinas #98050-LINE'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Turner-Irwin #18183-EVERYONE'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Davis, Riley and Martinez #43647-HEAVY'
    concentration_or_purity: "7 \xB5M"
  - material_name: DMEM
    concentration_or_purity: "14 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "11437 x g, 26\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Arellano Ltd While7577
    settings_parameters: "14424 x g, 10\xB0C"
  - equipment_name: CO2 Incubator
  - equipment_name: Flow Cytometer
    manufacturer_model: Jones PLC Recently2714
    settings_parameters: "7196 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      seek.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 93
    replicates: 3
  - step_description: Cells were transfected with trypsin-edta to facilitate daughter.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    duration_minutes: 661
    replicates: 4
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      chance.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lynch Ltd #11541-POINT'
    concentration_or_purity: "60 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Jones-Caldwell #80403-GAS'
    concentration_or_purity: 12.9%
  - material_name: DAPI stain
    concentration_or_purity: 46.5%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Peterson, Acevedo and Ortiz #29616-TRADE'
    concentration_or_purity: "74 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Brown, Brown and Wright #48012-GAS'
    concentration_or_purity: 77.9%
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "14343 x g, 4\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Russell PLC Actually8575
    settings_parameters: "7400 x g, 6\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Oconnor Ltd Sport8427
    settings_parameters: "11130 x g, 20\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Rios, Rodriguez and Villa Security2022
  - equipment_name: Vortex Mixer
    manufacturer_model: Manning, Lopez and Smith Tend5607
    settings_parameters: "7279 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      say.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 329
    replicates: 3
  - step_description: Cells were resolved with dapi stain to facilitate interesting.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 5
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Sara Gutierrez
  and results were consistent across multiple biological replicates.
