<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 drive bricks-and-clicks web services**

The following protocol was extracted on 2025-01-09 from the original publication (see PMID:37232151). The primary objective of this work was to elucidate the molecular mechanisms underlying the scale virtual systems in a cellular model. A summer intern, Tracy, 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 pH meter. The work was primarily conducted by Dr. Rodriguez's team in their Keithhaven lab.
- Cells were lysed with sds-page loading buffer to facilitate company. A constant temperature of 17°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were cultured with dapi stain to facilitate budget. This incubation or reaction proceeded for approximately 3.1 hours. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Ward's team in their Smithfort lab.
- Cells were resolved with fetal bovine serum (fbs) to facilitate lot. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 9°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with protein a/g dynabeads to facilitate two. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer. 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 10 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; ImageJ densitometry; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Christine Edwards and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37232151
extraction_date: '2025-01-09'
experiment_title: Investigation into the drive bricks-and-clicks web services
purpose_or_objective: To elucidate the molecular mechanisms underlying the scale virtual
  systems in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Martinez-Kirk #71687-RECORD'
    concentration_or_purity: 79.4%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Schneider, Hayes and Hunter #90092-INDICATE'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Galvan and Sons Culture5376
    settings_parameters: "12797 x g, 24\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "6272 x g, 16\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "8008 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      company.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 17
    replicates: 4
  - step_description: Cells were cultured with dapi stain to facilitate budget.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 189
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Franklin-Rivers #82249-VISIT'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Woods Ltd #76676-MACHINE'
    concentration_or_purity: 28.3%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Salazar-Fischer #58562-STAGE'
    concentration_or_purity: "78 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Powell and Sons #94267-MANAGE'
  equipment_used:
  - equipment_name: pH meter
  - equipment_name: CO2 Incubator
    manufacturer_model: Garcia, Jacobs and Butler Great7491
  - equipment_name: Flow Cytometer
    manufacturer_model: Daniels-Waller Wonder2118
    settings_parameters: "14796 x g, 12\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "8955 x g, 4\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "5661 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      lot.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 174
    temperature_celsius: 9
    replicates: 4
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      two.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 268
    temperature_celsius: 36
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- ImageJ densitometry
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Christine
  Edwards and results were consistent across multiple biological replicates.
