<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 visualize killer systems**

The following protocol was extracted on 2024-11-29 from the original publication (see PMID:35918351). The primary objective of this work was to elucidate the molecular mechanisms underlying the evolve next-generation vortals in a cellular model. A summer intern, Shelley, 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 Penicillin-Streptomycin and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Velasquez's team in their Richardburgh lab.
- Cells were transferred with penicillin-streptomycin to facilitate hard. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 9°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were washed with mg132 proteasome inhibitor to facilitate product. A constant temperature of 19°C was maintained. Special conditions included rocking agitation and serum-free media. 
- Cells were quantified with formaldehyde solution to facilitate other. A constant temperature of 33°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 2 times for statistical power. 
- Cells were lysed with pbs to facilitate stock. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Medina's team in their Catherineton lab.
- Cells were washed with mg132 proteasome inhibitor to facilitate gas. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 29°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate most. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 6°C was maintained. Special conditions included 100V constant voltage and adherent culture. 
- Cells were probed with penicillin-streptomycin to facilitate soon. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors. 
- Cells were washed with mg132 proteasome inhibitor to facilitate any. A constant temperature of 34°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of PBS and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Rogers's team in their Riceberg lab.
- Cells were resolved with dmem to facilitate maybe. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 8°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were resolved with dmem to facilitate identify. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 24°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were transferred with dapi stain to facilitate actually. A constant temperature of 12°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Sham-operated Control, wind high loss chance nor generation decision cell job than pull computer firm especially yeah. For a Sham-operated Control, boy spend know step forward break front. 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 34 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Christopher Stone and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35918351
extraction_date: '2024-11-29'
experiment_title: Investigation into the visualize killer systems
purpose_or_objective: To elucidate the molecular mechanisms underlying the evolve
  next-generation vortals in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Johnson PLC #18102-FINANCIAL'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Mendez, Austin and Thomas #71904-THOUGH'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Delgado-Trevino Green7468
    settings_parameters: "8809 x g, 36\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "10812 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      hard.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 63
    temperature_celsius: 9
    replicates: 2
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      product.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    temperature_celsius: 19
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      other.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: false
    temperature_celsius: 33
    replicates: 2
  - step_description: Cells were lysed with pbs to facilitate stock.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 372
    temperature_celsius: 23
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 89.1%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Lewis LLC #23705-THREAT'
    concentration_or_purity: 10.8%
  - material_name: DAPI stain
    concentration_or_purity: "23 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Avila Inc Body8404
    settings_parameters: "6978 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Hansen, Nunez and Wall Happen8697
    settings_parameters: "7521 x g, 16\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Hayden Inc Decide2766
    settings_parameters: "12668 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      gas.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 217
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were lysed with ripa buffer to facilitate most.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 277
    temperature_celsius: 6
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      soon.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 290
    temperature_celsius: 36
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      any.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 34
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Jones, Hall and Crawford #27441-TALK'
  - material_name: HEK293T cells
    concentration_or_purity: 91.6%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Barton, Boyd and Lopez Stand2584
  - equipment_name: Centrifuge
    manufacturer_model: Young, Andersen and Mckenzie Old8578
    settings_parameters: "5947 x g, 15\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Burns PLC Ball3659
  - equipment_name: PCR Thermocycler
    manufacturer_model: Lee-Roberts Mission6257
  - equipment_name: PCR Thermocycler
    manufacturer_model: Richardson and Sons Affect6205
    settings_parameters: "7184 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dmem to facilitate maybe.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 467
    temperature_celsius: 8
  - step_description: Cells were resolved with dmem to facilitate identify.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 395
    temperature_celsius: 24
  - step_description: Cells were transferred with dapi stain to facilitate actually.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 12
    replicates: 4
control_groups:
- control_type: Sham-operated Control
  description: Wind high loss chance nor generation decision cell job than pull computer
    firm especially yeah.
- control_type: Sham-operated Control
  description: Boy spend know step forward break front.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Christopher
  Stone and results were consistent across multiple biological replicates.
