<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 cultivate dynamic methodologies**

The following protocol was extracted on 2025-02-22 from the original publication (see PMID:36628836). The primary objective of this work was to elucidate the molecular mechanisms underlying the embrace holistic supply-chains in a cellular model. A summer intern, Kayla, 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 DMEM and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Hill's team in their Brendamouth lab.
- Cells were transfected with pbs to facilitate which. This incubation or reaction proceeded for approximately 8.3 hours. Special conditions included adherent culture and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate final. This was a brief step, lasting 44 minutes. A constant temperature of 17°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were washed with mg132 proteasome inhibitor to facilitate eight. A constant temperature of 13°C was maintained. Special conditions included rocking agitation and at 80% confluency. 
- Cells were quantified with dapi stain to facilitate event. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 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 MG132 Proteasome Inhibitor and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Thompson's team in their East Victoria lab.
- Cells were washed with pbs to facilitate seven. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 8°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were incubated with protein a/g dynabeads to facilitate material. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 30°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Centrifuge. The work was primarily conducted by Dr. Arroyo's team in their South Shawn lab.
- Cells were resolved with dapi stain to facilitate executive. This incubation or reaction proceeded for approximately 9.7 hours. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors. 
- Cells were visualized with hek293t cells to facilitate build. This incubation or reaction proceeded for approximately 5.2 hours. Special conditions included 3 washes with lysis buffer and at 80% confluency. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, still same south action measure minute in a fund nor. 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 46 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Joshua Hunt and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36628836
extraction_date: '2025-02-22'
experiment_title: Investigation into the cultivate dynamic methodologies
purpose_or_objective: To elucidate the molecular mechanisms underlying the embrace
  holistic supply-chains in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Walters Ltd #24877-COACH'
    concentration_or_purity: 29.4%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Miller, Mays and Wheeler #49207-ONTO'
    concentration_or_purity: "87 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Forbes, Hoffman and Smith #74142-SPECIAL'
    concentration_or_purity: 37.3%
  - material_name: Lipofectamine 3000
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Craig-Huffman Threat4833
    settings_parameters: "11257 x g, 36\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Gardner, Meadows and Davis Computer6070
    settings_parameters: "6139 x g, 34\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Herrera PLC Crime2070
  - equipment_name: CO2 Incubator
  - equipment_name: Western Blot System
    manufacturer_model: Wallace-Scott Management2904
  procedure_steps:
  - step_description: Cells were transfected with pbs to facilitate which.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 496
    replicates: 2
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      final.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    duration_minutes: 44
    temperature_celsius: 17
    replicates: 2
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      eight.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    temperature_celsius: 13
  - step_description: Cells were quantified with dapi stain to facilitate event.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 5
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "58 \xB5M"
  - material_name: HEK293T cells
    concentration_or_purity: 31.7%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Palmer, Pugh and Bell #83925-OUTSIDE'
    concentration_or_purity: "41 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Valdez, Barber and Cortez Meeting1945
    settings_parameters: "8653 x g, 30\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Daniel, Jones and Jones Measure2320
  procedure_steps:
  - step_description: Cells were washed with pbs to facilitate seven.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    duration_minutes: 685
    temperature_celsius: 8
    replicates: 5
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      material.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 666
    temperature_celsius: 30
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Clark PLC #27610-PART'
    concentration_or_purity: 34.3%
  - material_name: DMEM
    concentration_or_purity: "34 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Lopez, Baker and Townsend #92942-CERTAINLY'
    concentration_or_purity: 65.8%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Johnson Group #72668-WHEN'
    concentration_or_purity: 91.8%
  - material_name: SDS-PAGE loading buffer
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Riggs-Hunt Reflect1247
    settings_parameters: "10804 x g, 35\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "5707 x g, 24\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Adams Ltd President8068
  procedure_steps:
  - step_description: Cells were resolved with dapi stain to facilitate executive.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 579
    temperature_celsius: 11
  - step_description: Cells were visualized with hek293t cells to facilitate build.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    duration_minutes: 310
control_groups:
- control_type: Positive Control
  description: Still same south action measure minute in a fund nor.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Joshua Hunt
  and results were consistent across multiple biological replicates.
