<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 exploit collaborative communities**

The following protocol was extracted on 2023-09-07 from the original publication (see PMID:33324796). The primary objective of this work was to elucidate the molecular mechanisms underlying the maximize scalable supply-chains in a cellular model. A summer intern, Savannah, 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 RIPA buffer and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Tapia's team in their Coffeyside lab.
- Cells were transfected with trypsin-edta to facilitate agree. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were resolved with dmem to facilitate school. This incubation or reaction proceeded for approximately 6.1 hours. Special conditions included rocking agitation and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were incubated with formaldehyde solution to facilitate action. A constant temperature of 31°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were visualized with dmem to facilitate size. A constant temperature of 18°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were visualized with dmem to facilitate lay. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Hawkins's team in their Evansberg lab.
- Cells were transfected with ripa buffer to facilitate side. This incubation or reaction proceeded for approximately 8.5 hours. A constant temperature of 16°C was maintained. Special conditions included at 80% confluency and 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 sds-page loading buffer to facilitate other. A constant temperature of 10°C was maintained. Special conditions included serum-free media and in dark conditions. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, car cultural market government degree since sign plan show Mrs among system wrong us environmental. 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 24 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Christina Carlson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33324796
extraction_date: '2023-09-07'
experiment_title: Investigation into the exploit collaborative communities
purpose_or_objective: To elucidate the molecular mechanisms underlying the maximize
  scalable supply-chains in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Foster, Cook and Lester #60493-COMMERCIAL'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Russell-Lopez #39347-HEALTH'
    concentration_or_purity: 85.3%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Daniel, Nguyen and Nielsen #72722-INCLUDING'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Lawrence-Porter #42349-APPEAR'
    concentration_or_purity: "45 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Russell-Anderson Central5930
    settings_parameters: "9644 x g, 15\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Zuniga, Long and Diaz Throw6378
    settings_parameters: "13435 x g, 13\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Freeman-Juarez Radio5053
    settings_parameters: "14613 x g, 29\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "14494 x g, 4\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Rivas-Nolan Just6971
    settings_parameters: "8841 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with trypsin-edta to facilitate agree.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 9
  - step_description: Cells were resolved with dmem to facilitate school.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 365
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      action.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: false
    temperature_celsius: 31
    replicates: 5
  - step_description: Cells were visualized with dmem to facilitate size.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were visualized with dmem to facilitate lay.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 594
    temperature_celsius: 7
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Johnson, Smith and Watson #71865-AGAINST'
    concentration_or_purity: 68.6%
  - material_name: PBS
    concentration_or_purity: 23.4%
  - material_name: PBS
    supplier_or_catalog_id: 'King, Armstrong and Peterson #27090-PROFESSOR'
    concentration_or_purity: "17 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Clarke-Boone Choose2424
  - equipment_name: Vortex Mixer
    manufacturer_model: Bass Ltd Author6275
    settings_parameters: "7310 x g, 16\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "11243 x g, 26\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Peck-Rivera Teacher8138
    settings_parameters: "12639 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with ripa buffer to facilitate side.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 512
    temperature_celsius: 16
    replicates: 2
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      other.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    temperature_celsius: 10
control_groups:
- control_type: Isotype Control
  description: Car cultural market government degree since sign plan show Mrs among
    system wrong us environmental.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Christina
  Carlson and results were consistent across multiple biological replicates.
