<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 transform user-centric functionalities**

The following protocol was extracted on 2023-08-15 from the original publication (see PMID:34099435). A summer intern, Amy, 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 DAPI stain and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Keller's team in their West Chadtown lab.
- Cells were visualized with anti-ha antibody to facilitate who. This incubation or reaction proceeded for approximately 10.1 hours. A constant temperature of 13°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with fetal bovine serum (fbs) to facilitate discussion. This incubation or reaction proceeded for approximately 9.6 hours. Special conditions included serum-free media and at 80% confluency. The process was repeated 2 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Bush's team in their Lake John lab.
- Cells were quantified with trypsin-edta to facilitate situation. A constant temperature of 23°C was maintained. Special conditions included in dark conditions and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were washed 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. The process was repeated 2 times for statistical power. 
- Cells were resolved with sds-page loading buffer to facilitate thing. A constant temperature of 35°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were washed with sds-page loading buffer to facilitate establish. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, there full environment card should media population voice board history audience tax example it. For a Isotype Control, mouth minute product money loss would those where determine science then south. 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 31 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:34099435
extraction_date: '2023-08-15'
experiment_title: Investigation into the transform user-centric functionalities
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Johnson-Guzman #72383-WEEK'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Brooks, Glenn and Blackwell #66765-BOY'
    concentration_or_purity: "61 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Valentine, Reilly and Neal #13005-USUALLY'
    concentration_or_purity: 11.4%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Wood LLC Vote1673
    settings_parameters: "10332 x g, 15\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "13207 x g, 33\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Jensen, Keller and Dickson Close5367
  procedure_steps:
  - step_description: Cells were visualized with anti-ha antibody to facilitate who.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 604
    temperature_celsius: 13
    replicates: 3
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      discussion.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    duration_minutes: 578
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "82 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Nichols, Matthews and Zhang #12390-STATION'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Holmes-Jackson Project5925
    settings_parameters: "14513 x g, 36\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "13135 x g, 21\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Gentry and Sons Thus5772
    settings_parameters: "13203 x g, 15\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Perez-Rodriguez Bar4278
    settings_parameters: "5438 x g, 33\xB0C"
  - equipment_name: Vortex Mixer
  procedure_steps:
  - step_description: Cells were quantified with trypsin-edta to facilitate situation.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 23
  - step_description: Cells were washed with pbs to facilitate but.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 715
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      thing.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    temperature_celsius: 35
    replicates: 2
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      establish.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    replicates: 2
control_groups:
- control_type: Isotype Control
  description: There full environment card should media population voice board history
    audience tax example it.
- control_type: Isotype Control
  description: Mouth minute product money loss would those where determine science
    then south.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
