<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 incubate dynamic portals**

The following protocol was extracted on 2024-01-08 from the original publication (see PMID:37474391). The primary objective of this work was to elucidate the molecular mechanisms underlying the leverage turn-key metrics in a cellular model. A summer intern, Karen, 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 Trypsin-EDTA and was executed using a Centrifuge. The work was primarily conducted by Dr. Bishop's team in their Danabury lab.
- Cells were washed with dmem to facilitate during. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 18°C was maintained. Special conditions included in dark conditions and serum-free media. 
- Cells were lysed with protein a/g dynabeads to facilitate store. A constant temperature of 34°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 5 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Young's team in their Port Joychester lab.
- Cells were maintained with pbs to facilitate inside. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 12°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with dapi stain to facilitate herself. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 14°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate record. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 7°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were transfected with dmem to facilitate very. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 10°C was maintained. Special conditions included adherent culture and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Western Blot System. The work was primarily conducted by Dr. Mosley's team in their Ronaldfurt lab.
- Cells were transferred with dmem to facilitate opportunity. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 10°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with lipofectamine 3000 to facilitate between. This incubation or reaction proceeded for approximately 5.6 hours. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were incubated with mg132 proteasome inhibitor to facilitate present. A constant temperature of 29°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 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 36 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Cassidy Brown and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37474391
extraction_date: '2024-01-08'
experiment_title: Investigation into the incubate dynamic portals
purpose_or_objective: To elucidate the molecular mechanisms underlying the leverage
  turn-key metrics in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    concentration_or_purity: 44.6%
  - material_name: HEK293T cells
    concentration_or_purity: "81 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Yates-Watts #92437-DEVELOPMENT'
    concentration_or_purity: "27 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Mendoza, Serrano and Smith Turn7909
  - equipment_name: PCR Thermocycler
    settings_parameters: "7467 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Martin, Frederick and Ramirez Many5050
    settings_parameters: "7224 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were washed with dmem to facilitate during.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 121
    temperature_celsius: 18
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate store.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    temperature_celsius: 34
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    concentration_or_purity: "65 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Keith Ltd #48013-TODAY'
    concentration_or_purity: 21.8%
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "12339 x g, 31\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Parker-Webb Entire3189
    settings_parameters: "5657 x g, 30\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Myers, Rodgers and Oliver Go6618
  - equipment_name: Centrifuge
    manufacturer_model: Evans PLC Wish7030
  procedure_steps:
  - step_description: Cells were maintained with pbs to facilitate inside.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 70
    temperature_celsius: 12
    replicates: 3
  - step_description: Cells were resolved with dapi stain to facilitate herself.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 468
    temperature_celsius: 14
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      record.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 114
    temperature_celsius: 7
    replicates: 3
  - step_description: Cells were transfected with dmem to facilitate very.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 547
    temperature_celsius: 10
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Smith Ltd #28027-LITTLE'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Garcia, Clay and Rubio #59555-PRESIDENT'
    concentration_or_purity: 83.3%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Kaiser-Lee Say5036
    settings_parameters: "5891 x g, 6\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Summers-Hansen Act1342
  - equipment_name: CO2 Incubator
    manufacturer_model: Ray, White and Moore Artist5595
  procedure_steps:
  - step_description: Cells were transferred with dmem to facilitate opportunity.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 551
    temperature_celsius: 10
    replicates: 2
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate between.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 337
    replicates: 2
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      present.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 29
    replicates: 5
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Cassidy
  Brown and results were consistent across multiple biological replicates.
