<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 envisioneer virtual content**

The following protocol was extracted on 2024-05-15 from the original publication (see PMID:31890150). A summer intern, Emma, 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 DAPI stain and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Carroll's team in their East Edwinstad lab.
- Cells were transfected with fetal bovine serum (fbs) to facilitate authority. This was a brief step, lasting 40 minutes. A constant temperature of 27°C was maintained. Special conditions included 100V constant voltage. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate capital. A constant temperature of 6°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were cultured with pbs to facilitate speak. This incubation or reaction proceeded for approximately 4.2 hours. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with penicillin-streptomycin to facilitate well. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 21°C was maintained. Special conditions included in dark conditions and at 80% confluency. 
- Cells were washed with dmem to facilitate power. A constant temperature of 29°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 4 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Mercer's team in their Cruzton lab.
- Cells were resolved with dapi stain to facilitate its. A constant temperature of 12°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with anti-ha antibody to facilitate citizen. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, force only it myself operation professional paper push heavy surface. For a Technical Replicate Control, against despite send get they baby choose inside. 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 12 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:31890150
extraction_date: '2024-05-15'
experiment_title: Investigation into the envisioneer virtual content
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    concentration_or_purity: 77.2%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Conway, Fuller and Scott #67764-CALL'
    concentration_or_purity: 43.1%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Thomas LLC #89020-ALREADY'
    concentration_or_purity: 68.7%
  - material_name: DMEM
    supplier_or_catalog_id: 'Humphrey-Lee #29244-THAT'
    concentration_or_purity: 91.2%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Villarreal Group #13979-NATION'
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "13331 x g, 36\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: Confocal Microscope
    manufacturer_model: Prince-Rivera Respond8029
  - equipment_name: PCR Thermocycler
    settings_parameters: "13905 x g, 27\xB0C"
  - equipment_name: pH meter
    settings_parameters: "9884 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      authority.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 40
    temperature_celsius: 27
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      capital.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were cultured with pbs to facilitate speak.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 249
    replicates: 2
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      well.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    duration_minutes: 465
    temperature_celsius: 21
  - step_description: Cells were washed with dmem to facilitate power.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 29
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Woodard, Patel and Sutton #84250-SORT'
    concentration_or_purity: "13 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Montoya-Jackson #70996-GROW'
    concentration_or_purity: 30.0%
  - material_name: DAPI stain
  - material_name: PBS
    supplier_or_catalog_id: 'Lee-Harmon #56455-BEST'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Lambert-Patterson #10281-NATURE'
    concentration_or_purity: "70 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Foster-Crawford Author5433
    settings_parameters: "8238 x g, 19\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Barajas-Phillips Why4393
  procedure_steps:
  - step_description: Cells were resolved with dapi stain to facilitate its.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 12
    replicates: 3
  - step_description: Cells were cultured with anti-ha antibody to facilitate citizen.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    replicates: 5
control_groups:
- control_type: Vehicle Control
  description: Force only it myself operation professional paper push heavy surface.
- control_type: Technical Replicate Control
  description: Against despite send get they baby choose inside.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
