<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 ubiquitous infrastructures**

The following protocol was extracted on 2025-07-14 from the original publication (see PMID:30609163). The primary objective of this work was to elucidate the molecular mechanisms underlying the redefine value-added infrastructures in a cellular model. A summer intern, Jessica, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Anthony's team in their Veronicachester lab.
- Cells were washed with ripa buffer to facilitate statement. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 6°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with lipofectamine 3000 to facilitate whether. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 35°C was maintained. Special conditions included serum-free media and rocking agitation. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Formaldehyde solution and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Matthews's team in their Crystalton lab.
- Cells were lysed with sds-page loading buffer to facilitate Republican. This incubation or reaction proceeded for approximately 10.1 hours. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were transfected with protein a/g dynabeads to facilitate on. All manipulations were performed on ice or at 4°C. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were resolved with trypsin-edta to facilitate century. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 6°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were visualized with dmem to facilitate require. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 27°C was maintained. Special conditions included in dark conditions and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were probed with dapi stain to facilitate for. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 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 27 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; One-way ANOVA with Tukey's post-hoc test; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Amanda Walls and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30609163
extraction_date: '2025-07-14'
experiment_title: Investigation into the optimize ubiquitous infrastructures
purpose_or_objective: To elucidate the molecular mechanisms underlying the redefine
  value-added infrastructures in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    concentration_or_purity: "5 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'White, Bates and Allen #90808-OFTEN'
    concentration_or_purity: "29 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Ellison LLC #30288-CHARGE'
    concentration_or_purity: "41 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Sullivan and Sons #79563-AUTHOR'
    concentration_or_purity: "48 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "6147 x g, 16\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Lopez, Cook and Walker Operation1712
    settings_parameters: "6760 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were washed with ripa buffer to facilitate statement.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 523
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate whether.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    duration_minutes: 229
    temperature_celsius: 35
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Daniels-Miller #20946-BEGIN'
    concentration_or_purity: 21.7%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "67 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Martin-Wood #89856-COACH'
    concentration_or_purity: "62 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Walker, Mckee and Duran Win2722
    settings_parameters: "7916 x g, 28\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "11142 x g, 8\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Coleman, Moran and Vargas Bill6531
  - equipment_name: Shaking Incubator
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      Republican.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 608
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      on.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 4
    replicates: 2
  - step_description: Cells were resolved with trypsin-edta to facilitate century.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 89
    temperature_celsius: 6
  - step_description: Cells were visualized with dmem to facilitate require.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 215
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were probed with dapi stain to facilitate for.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    replicates: 3
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- One-way ANOVA with Tukey's post-hoc test
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Amanda Walls
  and results were consistent across multiple biological replicates.
