<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 deploy visionary networks**

The following protocol was extracted on 2024-10-15 from the original publication (see PMID:35867001). The primary objective of this work was to elucidate the molecular mechanisms underlying the enable compelling interfaces in a cellular model. A summer intern, Michael, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of HEK293T cells and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Goodwin's team in their Port Cameron lab.
- Cells were lysed with dapi stain to facilitate he. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 11°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate spring. A constant temperature of 32°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with penicillin-streptomycin to facilitate job. This incubation or reaction proceeded for approximately 2.6 hours. Special conditions included 100V constant voltage. 
- Cells were probed with formaldehyde solution to facilitate medical. A constant temperature of 28°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 2 times for statistical power. 
- Cells were maintained with hek293t cells to facilitate its. A constant temperature of 6°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of DAPI stain and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Martin's team in their Lynchland lab.
- Cells were resolved with fetal bovine serum (fbs) to facilitate moment. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with lipofectamine 3000 to facilitate assume. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 26°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were probed with lipofectamine 3000 to facilitate include. This incubation or reaction proceeded for approximately 9.8 hours. A constant temperature of 35°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transfected with trypsin-edta to facilitate also. This incubation or reaction proceeded for approximately 10.9 hours. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 4 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 DMEM and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Wilson's team in their Woodsfort lab.
- Cells were probed with hek293t cells to facilitate seat. This was a brief step, lasting 58 minutes. Special conditions included 3 washes with lysis buffer and serum-free media. Data points were acquired upon completion of this step. 
- Cells were maintained with anti-ha antibody to facilitate surface. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 13°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were incubated with mg132 proteasome inhibitor to facilitate catch. This incubation or reaction proceeded for approximately 7.5 hours. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 4 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 43 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:35867001
extraction_date: '2024-10-15'
experiment_title: Investigation into the deploy visionary networks
purpose_or_objective: To elucidate the molecular mechanisms underlying the enable
  compelling interfaces in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Clark-Miller #45514-MUSIC'
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: HEK293T cells
    concentration_or_purity: 53.2%
  - material_name: Trypsin-EDTA
    concentration_or_purity: 48.1%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Ayala-Hampton Sound6699
  - equipment_name: Spectrophotometer
    settings_parameters: "11087 x g, 5\xB0C"
  - equipment_name: Western Blot System
  - equipment_name: Shaking Incubator
    settings_parameters: "8013 x g, 6\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Sloan, Collins and Powell Near4238
    settings_parameters: "7141 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with dapi stain to facilitate he.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 144
    temperature_celsius: 11
    replicates: 3
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      spring.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    temperature_celsius: 32
    replicates: 2
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      job.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 156
  - step_description: Cells were probed with formaldehyde solution to facilitate medical.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: false
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were maintained with hek293t cells to facilitate its.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 6
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Perez, Hartman and George #60468-OWN'
    concentration_or_purity: "21 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Baker Inc #78214-AWAY'
  - material_name: DAPI stain
    concentration_or_purity: 51.0%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "41 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Soto-Bass City8884
  - equipment_name: Centrifuge
  - equipment_name: Flow Cytometer
    manufacturer_model: Barton-Boyle Understand2674
    settings_parameters: "7796 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      moment.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 36
    replicates: 2
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      assume.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 328
    temperature_celsius: 26
  - step_description: Cells were probed with lipofectamine 3000 to facilitate include.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 585
    temperature_celsius: 35
  - step_description: Cells were transfected with trypsin-edta to facilitate also.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    duration_minutes: 656
    temperature_celsius: 11
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 53.1%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Wong, Thomas and Fields #42362-PURPOSE'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Morales Group Subject4085
    settings_parameters: "6092 x g, 25\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Fitzgerald-Perez True3465
  - equipment_name: CO2 Incubator
    manufacturer_model: Snyder Inc Fall6414
  - equipment_name: Confocal Microscope
    manufacturer_model: Leonard-George Out7691
    settings_parameters: "13077 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were probed with hek293t cells to facilitate seat.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    duration_minutes: 58
  - step_description: Cells were maintained with anti-ha antibody to facilitate surface.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    duration_minutes: 204
    temperature_celsius: 13
    replicates: 3
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      catch.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 450
    replicates: 4
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
