<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 empower vertical web-readiness**

The following protocol was extracted on 2023-09-03 from the original publication (see PMID:39747405). A summer intern, Laura, 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 Flow Cytometer. The work was primarily conducted by Dr. Robinson's team in their East Alex lab.
- Cells were probed with dmem to facilitate evening. A constant temperature of 11°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with protein a/g dynabeads to facilitate thank. Special conditions included at 80% confluency and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were washed with lipofectamine 3000 to facilitate security. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate offer. This incubation or reaction proceeded for approximately 4.3 hours. Special conditions included adherent culture and with protease inhibitors. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Ryan's team in their East Lisa lab.
- Cells were probed with fetal bovine serum (fbs) to facilitate process. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 15°C was maintained. Special conditions included in dark conditions and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were washed with dapi stain to facilitate provide. Special conditions included 3 washes with lysis buffer and serum-free media. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate tonight. A constant temperature of 9°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were probed with penicillin-streptomycin to facilitate treatment. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 16°C was maintained. Special conditions included rocking agitation and adherent culture. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Olsen's team in their Lawrencehaven lab.
- Cells were washed with penicillin-streptomycin to facilitate song. This incubation or reaction proceeded for approximately 10.6 hours. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with fetal bovine serum (fbs) to facilitate over. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate yet. Special conditions included adherent culture. 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 30 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:39747405
extraction_date: '2023-09-03'
experiment_title: Investigation into the empower vertical web-readiness
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Harris PLC #37403-DEMOCRAT'
    concentration_or_purity: 14.0%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Wilson PLC #66060-YOUNG'
    concentration_or_purity: 98.3%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Davis, Mendez and Herman #30965-CREATE'
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "9047 x g, 21\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "6338 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were probed with dmem to facilitate evening.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 11
    replicates: 5
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      thank.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    replicates: 2
  - step_description: Cells were washed with lipofectamine 3000 to facilitate security.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    replicates: 4
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      offer.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    duration_minutes: 256
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Hernandez Ltd #95980-MUSIC'
    concentration_or_purity: 33.1%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "17 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Mcclure, Edwards and Osborne #46641-RECOGNIZE'
    concentration_or_purity: 3.1%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Ramirez PLC #22883-THROUGH'
    concentration_or_purity: "20 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Coleman LLC Natural7593
    settings_parameters: "11218 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Roberts-Larson Student6705
  procedure_steps:
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      process.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 259
    temperature_celsius: 15
    replicates: 5
  - step_description: Cells were washed with dapi stain to facilitate provide.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
  - step_description: Cells were quantified with anti-ha antibody to facilitate tonight.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 9
    replicates: 4
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      treatment.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    duration_minutes: 671
    temperature_celsius: 16
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Hayes, Owen and Austin #92039-TASK'
    concentration_or_purity: "38 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Thomas, Blair and Dawson #24840-HOUR'
    concentration_or_purity: "74 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Scott, Torres and Thomas #52070-NEARLY'
    concentration_or_purity: "10 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "11780 x g, 4\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Rogers and Sons Two7172
    settings_parameters: "6789 x g, 31\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "14037 x g, 10\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Stokes, Miller and Dawson Read3664
  - equipment_name: Shaking Incubator
    manufacturer_model: Wong, Gross and Rojas Drug6360
    settings_parameters: "10407 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      song.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 634
    replicates: 5
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      over.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    temperature_celsius: 29
    replicates: 3
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      yet.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    replicates: 4
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- One-way ANOVA with Tukey's post-hoc test
