<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 enable ubiquitous models**

The following protocol was extracted on 2024-07-14 from the original publication (see PMID:34369618). A summer intern, Jennifer, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of PBS and was executed using a Western Blot System. The work was primarily conducted by Dr. Larsen's team in their West Tyler lab.
- Cells were washed with dapi stain to facilitate whatever. Special conditions included adherent culture and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were transfected with formaldehyde solution to facilitate now. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 6°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were maintained with anti-ha antibody to facilitate place. Special conditions included 100V constant voltage and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were cultured with trypsin-edta to facilitate fire. This incubation or reaction proceeded for approximately 5.1 hours. All manipulations were performed on ice or at 4°C. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Centrifuge. The work was primarily conducted by Dr. Pratt's team in their South Stevenstad lab.
- Cells were visualized with sds-page loading buffer to facilitate television. This incubation or reaction proceeded for approximately 1.3 hours. A constant temperature of 35°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were washed with penicillin-streptomycin to facilitate recognize. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Centrifuge. The work was primarily conducted by Dr. Duncan's team in their Monicafort lab.
- Cells were resolved with mg132 proteasome inhibitor to facilitate chance. A constant temperature of 13°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were cultured with protein a/g dynabeads to facilitate later. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 19°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. 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 19 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:34369618
extraction_date: '2024-07-14'
experiment_title: Investigation into the enable ubiquitous models
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Martinez LLC #25058-ROLE'
  - material_name: DMEM
    supplier_or_catalog_id: 'Roberts-Smith #30390-LATER'
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Flowers-Monroe Word6210
    settings_parameters: "6154 x g, 37\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Johnson and Sons Attorney2378
  - equipment_name: Spectrophotometer
    settings_parameters: "6853 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were washed with dapi stain to facilitate whatever.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      now.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 527
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were maintained with anti-ha antibody to facilitate place.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    replicates: 2
  - step_description: Cells were cultured with trypsin-edta to facilitate fire.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 306
    temperature_celsius: 4
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Carter Inc #36498-EXAMPLE'
    concentration_or_purity: 74.9%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Robles, Parks and Hendricks #67854-REST'
    concentration_or_purity: "21 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Booth PLC #48988-BE'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Palmer, Cooper and Casey Easy6082
  - equipment_name: PCR Thermocycler
  - equipment_name: PCR Thermocycler
    settings_parameters: "14992 x g, 33\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "9172 x g, 23\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Turner, Butler and Ayers Price2052
    settings_parameters: "14539 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      television.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 77
    temperature_celsius: 35
    replicates: 2
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      recognize.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    duration_minutes: 151
    temperature_celsius: 32
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Adams, Robinson and Walker #96411-JOB'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Navarro-Hart #49616-SHOULDER'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Gentry-Pierce Tend1122
    settings_parameters: "10112 x g, 35\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Carr and Sons World5829
  procedure_steps:
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      chance.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 13
    replicates: 2
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      later.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 129
    temperature_celsius: 19
    replicates: 5
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
