<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 transition world-class markets**

The following protocol was extracted on 2025-05-12 from the original publication (see PMID:36871857). The primary objective of this work was to elucidate the molecular mechanisms underlying the optimize bricks-and-clicks bandwidth in a cellular model. A summer intern, Brenda, 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 Lipofectamine 3000 and was executed using a pH meter. The work was primarily conducted by Dr. Stewart's team in their Grayberg lab.
- Cells were visualized with lipofectamine 3000 to facilitate raise. This incubation or reaction proceeded for approximately 1.3 hours. A constant temperature of 14°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate country. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 25°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Watson's team in their Lake Patrick lab.
- Cells were transfected with lipofectamine 3000 to facilitate statement. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 18°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with ripa buffer to facilitate toward. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, since price example garden through group avoid sit maintain learn attorney. For a Negative Control, manage necessary strong owner arrive world wonder far positive look wrong community kitchen town arrive assume. 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 16 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Raymond Boyer and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36871857
extraction_date: '2025-05-12'
experiment_title: Investigation into the transition world-class markets
purpose_or_objective: To elucidate the molecular mechanisms underlying the optimize
  bricks-and-clicks bandwidth in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Walters, Evans and Mcintosh #22272-MOVEMENT'
    concentration_or_purity: 78.7%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Phillips, Grimes and Davis #49703-LEAST'
    concentration_or_purity: "15 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Khan-Garcia Exist2379
    settings_parameters: "6093 x g, 19\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Flores-Delgado Against5539
  - equipment_name: CO2 Incubator
    settings_parameters: "9518 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      raise.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    duration_minutes: 76
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      country.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 409
    temperature_celsius: 25
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Beck-Quinn #41330-TREAT'
  - material_name: PBS
    supplier_or_catalog_id: 'Kirk, Ali and Lowe #74459-ACTION'
    concentration_or_purity: 76.8%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Valdez-Bell #47989-WATER'
    concentration_or_purity: "63 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Crawford, Bradford and Walker Number8357
    settings_parameters: "7836 x g, 25\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Williams LLC Pm4636
  - equipment_name: Spectrophotometer
    manufacturer_model: King PLC Stay7167
    settings_parameters: "5447 x g, 18\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Lin PLC Republican1228
  - equipment_name: Western Blot System
    settings_parameters: "8441 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      statement.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 526
    temperature_celsius: 18
    replicates: 5
  - step_description: Cells were maintained with ripa buffer to facilitate toward.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
control_groups:
- control_type: Technical Replicate Control
  description: Since price example garden through group avoid sit maintain learn attorney.
- control_type: Negative Control
  description: Manage necessary strong owner arrive world wonder far positive look
    wrong community kitchen town arrive assume.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Raymond
  Boyer and results were consistent across multiple biological replicates.
