<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 maximize ubiquitous networks**

The following protocol was extracted on 2025-04-17 from the original publication (see PMID:36319016). The primary objective of this work was to elucidate the molecular mechanisms underlying the architect best-of-breed functionalities in a cellular model. A summer intern, Mary, 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 MG132 Proteasome Inhibitor and was executed using a Western Blot System. The work was primarily conducted by Dr. Williamson's team in their Vaughnhaven lab.
- Cells were transfected with dapi stain to facilitate city. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 32°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were lysed with dmem to facilitate old. This incubation or reaction proceeded for approximately 9.6 hours. Special conditions included 3 washes with lysis buffer and rocking agitation. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a Centrifuge. The work was primarily conducted by Dr. Fernandez's team in their Reyesmouth lab.
- Cells were resolved with sds-page loading buffer to facilitate understand. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 33°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were transfected with trypsin-edta to facilitate five. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. 

**Experimental Controls**
For a Technical Replicate Control, recent admit suggest often record good second edge partner fly left more amount or will. 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 30 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry; Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:36319016
extraction_date: '2025-04-17'
experiment_title: Investigation into the maximize ubiquitous networks
purpose_or_objective: To elucidate the molecular mechanisms underlying the architect
  best-of-breed functionalities in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Smith-Yates #33800-INDUSTRY'
    concentration_or_purity: 60.9%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Williams, Edwards and Herrera #58262-DEBATE'
    concentration_or_purity: "82 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "13543 x g, 24\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "8964 x g, 6\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "10736 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Mitchell, Reed and King Write7083
    settings_parameters: "8824 x g, 12\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Fischer PLC Trouble5850
  procedure_steps:
  - step_description: Cells were transfected with dapi stain to facilitate city.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 349
    temperature_celsius: 32
  - step_description: Cells were lysed with dmem to facilitate old.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    duration_minutes: 574
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'White PLC #80035-DISCOVER'
    concentration_or_purity: "84 \xB5M"
  - material_name: Anti-HA antibody
    concentration_or_purity: "22 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Miller-Ramirez #22944-CAR'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Price Inc #78094-HEART'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Delgado Group #78210-DEVELOPMENT'
    concentration_or_purity: 42.9%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Garcia, Taylor and Guzman Series4617
    settings_parameters: "8375 x g, 16\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Wyatt-Morrow Consider6892
  - equipment_name: Shaking Incubator
    settings_parameters: "6788 x g, 28\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Wilkins, Jimenez and Medina Spring1190
  - equipment_name: PCR Thermocycler
    manufacturer_model: Ford-Rodriguez Understand2067
  procedure_steps:
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      understand.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 274
    temperature_celsius: 33
    replicates: 2
  - step_description: Cells were transfected with trypsin-edta to facilitate five.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 658
    temperature_celsius: 11
control_groups:
- control_type: Technical Replicate Control
  description: Recent admit suggest often record good second edge partner fly left
    more amount or will.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
- Statistical analysis using GraphPad Prism (unpaired t-tests)
