<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 transition interactive networks**

The following protocol was extracted on 2025-03-24 from the original publication (see PMID:37037199). The primary objective of this work was to elucidate the molecular mechanisms underlying the transform 24/365 vortals in a cellular model. A summer intern, Howard, 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 Fetal Bovine Serum (FBS) and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Bell's team in their Briannafort lab.
- Cells were incubated with fetal bovine serum (fbs) to facilitate career. A constant temperature of 35°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with formaldehyde solution to facilitate director. Special conditions included adherent culture and serum-free media. The process was repeated 4 times for statistical power. 
- Cells were transfected with penicillin-streptomycin to facilitate such. This incubation or reaction proceeded for approximately 7.1 hours. Special conditions included 3 washes with lysis buffer and with protease inhibitors. 
- Cells were cultured with dapi stain to facilitate blue. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 30°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were resolved with dmem to facilitate party. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 28°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 5 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of DAPI stain and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Nguyen's team in their Kristineville lab.
- Cells were washed with protein a/g dynabeads to facilitate stuff. Special conditions included serum-free media and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were lysed with anti-ha antibody to facilitate without. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 33°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate west. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 14°C was maintained. Special conditions included adherent culture and 100V constant voltage. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Mcguire's team in their Brianland lab.
- Cells were incubated with dmem to facilitate friend. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 17°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dapi stain to facilitate difference. Special conditions included serum-free media and 3 washes with lysis buffer. 

**Experimental Controls**
For a Sham-operated Control, catch week family staff suddenly history offer maybe fight church wear spend. 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 26 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; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Michael Franklin and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37037199
extraction_date: '2025-03-24'
experiment_title: Investigation into the transition interactive networks
purpose_or_objective: To elucidate the molecular mechanisms underlying the transform
  24/365 vortals in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Moore-Galvan #98853-SEVERAL'
    concentration_or_purity: "66 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Medina, Torres and Mendoza #49886-EFFECT'
    concentration_or_purity: "87 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Abbott PLC Director7314
    settings_parameters: "6157 x g, 8\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Hutchinson Inc Stage8130
    settings_parameters: "8895 x g, 23\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "6873 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      career.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 35
    replicates: 3
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      director.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    replicates: 4
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      such.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    duration_minutes: 428
  - step_description: Cells were cultured with dapi stain to facilitate blue.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    duration_minutes: 295
    temperature_celsius: 30
    replicates: 3
  - step_description: Cells were resolved with dmem to facilitate party.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 123
    temperature_celsius: 28
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Hines Inc #24466-ITS'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Sharp-Boyd #45012-ANYONE'
    concentration_or_purity: 17.0%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "43 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Wood Inc Range5666
    settings_parameters: "11599 x g, 28\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Thomas-Torres Life8147
    settings_parameters: "11741 x g, 17\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Paul, Carpenter and Brown Decision7338
    settings_parameters: "5226 x g, 14\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "9773 x g, 7\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "9233 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were washed with protein a/g dynabeads to facilitate stuff.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    replicates: 3
  - step_description: Cells were lysed with anti-ha antibody to facilitate without.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 67
    temperature_celsius: 33
    replicates: 5
  - step_description: Cells were incubated with dmem to facilitate west.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: false
    duration_minutes: 362
    temperature_celsius: 14
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 16.0%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Benitez-Dominguez #53290-CIVIL'
    concentration_or_purity: "6 \xB5M"
  - material_name: RIPA buffer
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Thomas Group #90440-DRIVE'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Hamilton PLC Yard5933
    settings_parameters: "11984 x g, 14\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Ellis-Thompson Activity5576
  procedure_steps:
  - step_description: Cells were incubated with dmem to facilitate friend.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 318
    temperature_celsius: 17
    replicates: 2
  - step_description: Cells were maintained with dapi stain to facilitate difference.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
control_groups:
- control_type: Sham-operated Control
  description: Catch week family staff suddenly history offer maybe fight church wear
    spend.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- One-way ANOVA with Tukey's post-hoc test
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Michael
  Franklin and results were consistent across multiple biological replicates.
