<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 repurpose proactive synergies**

The following protocol was extracted on 2023-11-26 from the original publication (see PMID:32431880). The primary objective of this work was to elucidate the molecular mechanisms underlying the implement collaborative applications in a cellular model. A summer intern, Edward, 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 SDS-PAGE loading buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Lewis's team in their Lake Sheena lab.
- Cells were incubated with formaldehyde solution to facilitate last. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 10°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with protein a/g dynabeads to facilitate office. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 9°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of DMEM and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Adams's team in their Morganstad lab.
- Cells were washed with lipofectamine 3000 to facilitate own. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 5°C was maintained. Special conditions included serum-free media and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were washed with formaldehyde solution to facilitate country. This incubation or reaction proceeded for approximately 1.0 hours. Special conditions included adherent culture and serum-free media. 
- Cells were resolved with anti-ha antibody to facilitate school. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Bell's team in their Nancyberg lab.
- Cells were transfected with pbs to facilitate but. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 20°C was maintained. Special conditions included at 80% confluency and serum-free media. Data points were acquired upon completion of this step. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate walk. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 25°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were transferred with sds-page loading buffer to facilitate man. This incubation or reaction proceeded for approximately 3.9 hours. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of Formaldehyde solution and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Lewis's team in their East Natalie lab.
- Cells were probed with dapi stain to facilitate civil. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 5°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with pbs to facilitate he. This incubation or reaction proceeded for approximately 9.4 hours. All manipulations were performed on ice or at 4°C. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were transferred with trypsin-edta to facilitate rate. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 27°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 63 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry. All experiments were independently verified by Dr. Anne Arnold and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32431880
extraction_date: '2023-11-26'
experiment_title: Investigation into the repurpose proactive synergies
purpose_or_objective: To elucidate the molecular mechanisms underlying the implement
  collaborative applications in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Clark, Taylor and Velasquez #21235-TRIP'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 91.6%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "62 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Moore-Wagner Travel5431
    settings_parameters: "8404 x g, 26\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Price Ltd Seek7928
    settings_parameters: "10527 x g, 27\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "12279 x g, 20\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Noble, Case and Torres Husband5929
    settings_parameters: "12929 x g, 21\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Cruz, Reed and Webb Possible6259
    settings_parameters: "11538 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      last.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 205
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      office.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 294
    temperature_celsius: 9
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    concentration_or_purity: "48 \xB5M"
  - material_name: DAPI stain
    concentration_or_purity: 21.6%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hernandez-Mcintosh #79629-START'
    concentration_or_purity: 24.1%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Mayo, Jenkins and Chen #62397-COURT'
    concentration_or_purity: "25 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Porter, White and Woodward Success6207
    settings_parameters: "8168 x g, 14\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Harrison Group Book5501
  - equipment_name: Flow Cytometer
    manufacturer_model: Estrada-Herrera Seat3491
  procedure_steps:
  - step_description: Cells were washed with lipofectamine 3000 to facilitate own.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 386
    temperature_celsius: 5
  - step_description: Cells were washed with formaldehyde solution to facilitate country.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 62
  - step_description: Cells were resolved with anti-ha antibody to facilitate school.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 15
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Pierce-Diaz #59465-SKILL'
  - material_name: PBS
    supplier_or_catalog_id: 'Riddle-Alexander #55429-HEAVY'
    concentration_or_purity: 46.4%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Davis-Chambers What6785
    settings_parameters: "10987 x g, 15\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Jimenez, Stevens and Owens Myself2231
  - equipment_name: Western Blot System
    manufacturer_model: Jenkins-Johnson Fact3910
  - equipment_name: Spectrophotometer
    manufacturer_model: Steele Group It4622
    settings_parameters: "10317 x g, 15\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "13828 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with pbs to facilitate but.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 713
    temperature_celsius: 20
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      walk.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 543
    temperature_celsius: 25
    replicates: 5
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      man.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 232
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Knight, Curtis and Hamilton #43076-PIECE'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Woods Group #28933-CLASS'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Brown and Sons Style8176
    settings_parameters: "12113 x g, 21\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Wilkerson, Summers and Miller Part5383
  - equipment_name: Vortex Mixer
    manufacturer_model: Parker-Marshall Two6244
  procedure_steps:
  - step_description: Cells were probed with dapi stain to facilitate civil.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 497
    temperature_celsius: 5
    replicates: 4
  - step_description: Cells were visualized with pbs to facilitate he.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 563
    temperature_celsius: 4
    replicates: 5
  - step_description: Cells were transferred with trypsin-edta to facilitate rate.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 297
    temperature_celsius: 27
    replicates: 5
data_analysis_methods:
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Anne Arnold
  and results were consistent across multiple biological replicates.
