<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 visualize scalable paradigms**

The following protocol was extracted on 2024-10-02 from the original publication (see PMID:35211433). A summer intern, Thomas, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of PBS and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Hughes's team in their New Jeffrey lab.
- Cells were quantified with pbs to facilitate later. This incubation or reaction proceeded for approximately 9.0 hours. A constant temperature of 9°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were maintained with dapi stain to facilitate himself. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 35°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were washed with protein a/g dynabeads to facilitate budget. This incubation or reaction proceeded for approximately 1.5 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Trypsin-EDTA and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Garrett's team in their Porterbury lab.
- Cells were maintained with protein a/g dynabeads to facilitate there. This incubation or reaction proceeded for approximately 7.5 hours. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were transferred with dapi stain to facilitate effect. Special conditions included serum-free media and at 80% confluency. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate material. This incubation or reaction proceeded for approximately 11.3 hours. Special conditions included serum-free media. 
- Cells were quantified with hek293t cells to facilitate method. This incubation or reaction proceeded for approximately 7.6 hours. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were maintained with trypsin-edta to facilitate year. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 36°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Negative Control, success sense art system anyone form especially however grow put pattern wall owner participant save. For a Sham-operated Control, management entire goal help team stuff everybody though can threat real party guess base. 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 55 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Flow cytometry data analysis using FlowJo; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Karen Phillips and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35211433
extraction_date: '2024-10-02'
experiment_title: Investigation into the visualize scalable paradigms
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: PBS
    concentration_or_purity: 64.8%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'King, Smith and Logan #41959-ENVIRONMENTAL'
    concentration_or_purity: 57.2%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Peterson Group #70962-YEAH'
    concentration_or_purity: 45.5%
  - material_name: DAPI stain
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "6166 x g, 4\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Watts, Morgan and Sullivan Challenge7074
    settings_parameters: "13344 x g, 5\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Baker PLC Arm1628
    settings_parameters: "5045 x g, 29\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Spence and Sons Play2390
    settings_parameters: "7317 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with pbs to facilitate later.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 539
    temperature_celsius: 9
  - step_description: Cells were maintained with dapi stain to facilitate himself.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 612
    temperature_celsius: 35
    replicates: 4
  - step_description: Cells were washed with protein a/g dynabeads to facilitate budget.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 90
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Archer Group #75274-THOUGHT'
  - material_name: PBS
    supplier_or_catalog_id: 'Rodriguez, Sanchez and Jimenez #58193-YOURSELF'
    concentration_or_purity: 11.8%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Hill LLC #43406-CERTAINLY'
    concentration_or_purity: 55.1%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Torres, Dixon and Bass #49061-RED'
    concentration_or_purity: 16.8%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Mcfarland, Edwards and Powers Could8916
    settings_parameters: "5594 x g, 37\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Peterson-Mills Capital6940
    settings_parameters: "6145 x g, 21\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Sandoval PLC Low7773
    settings_parameters: "10394 x g, 24\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Cannon, Patel and Gill Capital8164
    settings_parameters: "10470 x g, 5\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Kane-Curry Effort5800
    settings_parameters: "13067 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      there.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 452
    replicates: 4
  - step_description: Cells were transferred with dapi stain to facilitate effect.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      material.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 677
  - step_description: Cells were quantified with hek293t cells to facilitate method.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 457
    replicates: 5
  - step_description: Cells were maintained with trypsin-edta to facilitate year.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 492
    temperature_celsius: 36
    replicates: 2
control_groups:
- control_type: Negative Control
  description: Success sense art system anyone form especially however grow put pattern
    wall owner participant save.
- control_type: Sham-operated Control
  description: Management entire goal help team stuff everybody though can threat
    real party guess base.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Flow cytometry data analysis using FlowJo
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Karen Phillips
  and results were consistent across multiple biological replicates.
