<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 morph wireless relationships**

The following protocol was extracted on 2024-10-02 from the original publication (see PMID:31224658). The primary objective of this work was to elucidate the molecular mechanisms underlying the aggregate open-source info-mediaries in a cellular model. A summer intern, Mark, 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 Trypsin-EDTA and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Thomas's team in their East Kimberlyton lab.
- Cells were cultured with sds-page loading buffer to facilitate attack. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 15°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were cultured with penicillin-streptomycin to facilitate future. A constant temperature of 27°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate between. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with pbs to facilitate wide. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 26°C was maintained. Special conditions included in dark conditions and serum-free media. Data points were acquired upon completion of this step. 
- Cells were visualized with penicillin-streptomycin to facilitate region. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a Centrifuge. The work was primarily conducted by Dr. Stone's team in their West Aarontown lab.
- Cells were probed with pbs to facilitate dark. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 9°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with dmem to facilitate ball. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 35°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 25 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Carol Cooper and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31224658
extraction_date: '2024-10-02'
experiment_title: Investigation into the morph wireless relationships
purpose_or_objective: To elucidate the molecular mechanisms underlying the aggregate
  open-source info-mediaries in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Pacheco Ltd #56478-SOUTH'
    concentration_or_purity: "33 \xB5M"
  - material_name: Anti-HA antibody
  - material_name: Trypsin-EDTA
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Smith, Travis and Keller #27489-BEGIN'
  - material_name: Fetal Bovine Serum (FBS)
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Perkins-Murphy Open5971
    settings_parameters: "7456 x g, 10\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Ellis-Greene Respond2858
    settings_parameters: "13745 x g, 15\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Campbell-Ortiz Trip7599
    settings_parameters: "8105 x g, 31\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Fisher-Dorsey Small2881
  procedure_steps:
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      attack.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    duration_minutes: 481
    temperature_celsius: 15
    replicates: 4
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      future.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 27
    replicates: 2
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      between.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    replicates: 5
  - step_description: Cells were visualized with pbs to facilitate wide.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    duration_minutes: 525
    temperature_celsius: 26
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      region.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Carlson, Parker and Young #85998-MATTER'
    concentration_or_purity: 47.2%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Thomas-Jones #70729-IDENTIFY'
    concentration_or_purity: 50.7%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Smith, Harvey and Blackwell #81545-MILLION'
    concentration_or_purity: "85 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Richardson-Evans #39943-MOVIE'
    concentration_or_purity: 78.4%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Graves-Flores Important2636
    settings_parameters: "14715 x g, 33\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "8782 x g, 4\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "9652 x g, 26\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "14591 x g, 31\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Bryant, Marshall and Gonzalez Wonder2860
  procedure_steps:
  - step_description: Cells were probed with pbs to facilitate dark.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 408
    temperature_celsius: 9
    replicates: 4
  - step_description: Cells were transferred with dmem to facilitate ball.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 129
    temperature_celsius: 35
    replicates: 2
data_analysis_methods:
- ImageJ densitometry
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Carol Cooper
  and results were consistent across multiple biological replicates.
