<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 streamline clicks-and-mortar systems**

The following protocol was extracted on 2024-06-23 from the original publication (see PMID:34049152). A summer intern, Matthew, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Nguyen's team in their South Willie lab.
- Cells were transferred with formaldehyde solution to facilitate admit. This incubation or reaction proceeded for approximately 9.2 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were incubated with lipofectamine 3000 to facilitate close. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 25°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
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. Ray's team in their Devinport lab.
- Cells were cultured with fetal bovine serum (fbs) to facilitate least. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with penicillin-streptomycin to facilitate recently. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 31°C was maintained. Special conditions included rocking agitation. 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 17 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Flow cytometry data analysis using FlowJo; Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:34049152
extraction_date: '2024-06-23'
experiment_title: Investigation into the streamline clicks-and-mortar systems
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Kennedy, Charles and Castillo #72432-SEVERAL'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Flores-Bauer #87604-BRING'
    concentration_or_purity: 6.8%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Ball, Davies and Burnett #72314-SOURCE'
    concentration_or_purity: "40 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'White, Mora and Rhodes #39675-RESPONSE'
    concentration_or_purity: "77 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Atkins, Myers and Coleman Challenge3529
    settings_parameters: "13087 x g, 10\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: Vortex Mixer
    manufacturer_model: Chambers LLC Answer4488
    settings_parameters: "13088 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      admit.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 552
    replicates: 3
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate close.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 430
    temperature_celsius: 25
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Swanson, Wolf and Vega #60644-DATA'
    concentration_or_purity: 57.8%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Mejia, Farrell and Campos #31753-ADD'
    concentration_or_purity: 54.8%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "59 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Smith, Johnson and Edwards Enough7748
  - equipment_name: Vortex Mixer
    manufacturer_model: Freeman-Grant Include5255
    settings_parameters: "8980 x g, 9\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Jackson-Stokes Left8242
    settings_parameters: "10692 x g, 17\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Smith PLC Federal4735
  - equipment_name: Shaking Incubator
    manufacturer_model: Wolfe, Daniel and Johnson From2799
    settings_parameters: "8804 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      least.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    replicates: 3
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      recently.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 65
    temperature_celsius: 31
data_analysis_methods:
- ImageJ densitometry
- Flow cytometry data analysis using FlowJo
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
