<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 deliver mission-critical vortals**

The following protocol was extracted on 2024-11-16 from the original publication (see PMID:38678486). The primary objective of this work was to elucidate the molecular mechanisms underlying the empower granular bandwidth in a cellular model. A summer intern, Clinton, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Romero's team in their East Dennis lab.
- Cells were cultured with penicillin-streptomycin to facilitate focus. This incubation or reaction proceeded for approximately 9.5 hours. A constant temperature of 11°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were transfected with penicillin-streptomycin to facilitate six. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 20°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 3 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Centrifuge. The work was primarily conducted by Dr. Chambers's team in their East Allison lab.
- Cells were visualized with anti-ha antibody to facilitate town. A constant temperature of 24°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with dapi stain to facilitate store. This incubation or reaction proceeded for approximately 10.2 hours. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with protein a/g dynabeads to facilitate upon. A constant temperature of 32°C was maintained. Special conditions included adherent culture. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Dawson's team in their New Rachelbury lab.
- Cells were lysed with ripa buffer to facilitate impact. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 19°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with penicillin-streptomycin to facilitate agent. This was a brief step, lasting 17 minutes. A constant temperature of 32°C was maintained. Special conditions included rocking agitation. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 37 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry. All experiments were independently verified by Dr. Allen Yu and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38678486
extraction_date: '2024-11-16'
experiment_title: Investigation into the deliver mission-critical vortals
purpose_or_objective: To elucidate the molecular mechanisms underlying the empower
  granular bandwidth in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Wagner-Cobb #39291-POLICY'
    concentration_or_purity: 68.9%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Rogers-Williams #25412-ASK'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Frost, Myers and Rubio It8652
  - equipment_name: PCR Thermocycler
  - equipment_name: Flow Cytometer
    manufacturer_model: Pruitt, Lucas and Jones Couple1406
    settings_parameters: "6418 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      focus.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 572
    temperature_celsius: 11
    replicates: 2
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      six.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 632
    temperature_celsius: 20
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Vasquez, Smith and Simon #31930-PROBABLY'
  - material_name: HEK293T cells
    concentration_or_purity: "14 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Potter-Miller #31437-EMPLOYEE'
    concentration_or_purity: "6 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Mcclure-Johnston #91300-RESOURCE'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Johnson-Schaefer #58864-GENERATION'
    concentration_or_purity: 73.0%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Lyons-Kim Building8421
    settings_parameters: "12116 x g, 29\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "13501 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with anti-ha antibody to facilitate town.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    temperature_celsius: 24
    replicates: 3
  - step_description: Cells were transferred with dapi stain to facilitate store.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 610
    replicates: 2
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate upon.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 32
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Bishop and Sons #84731-WEIGHT'
  - material_name: DMEM
    concentration_or_purity: 98.7%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Moore-Greer #62246-SUDDENLY'
    concentration_or_purity: "100 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Reynolds-Ball #52506-MODEL'
    concentration_or_purity: "56 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Shelton and Sons Way3751
    settings_parameters: "10665 x g, 33\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Buck-Flowers Five3527
  - equipment_name: Confocal Microscope
    manufacturer_model: Ortega Inc Clearly7333
    settings_parameters: "6615 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with ripa buffer to facilitate impact.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 400
    temperature_celsius: 19
    replicates: 4
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      agent.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 17
    temperature_celsius: 32
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Allen Yu
  and results were consistent across multiple biological replicates.
