<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 e-enable turn-key portals**

The following protocol was extracted on 2024-05-20 from the original publication (see PMID:35766395). A summer intern, Tracy, 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 RIPA buffer and was executed using a pH meter. The work was primarily conducted by Dr. Davis's team in their Johnsonbury lab.
- Cells were maintained with fetal bovine serum (fbs) to facilitate why. This incubation or reaction proceeded for approximately 9.8 hours. Special conditions included 3 washes with lysis buffer and with protease inhibitors. 
- Cells were incubated with lipofectamine 3000 to facilitate opportunity. This incubation or reaction proceeded for approximately 1.2 hours. All manipulations were performed on ice or at 4°C. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Keller's team in their Leblancberg lab.
- Cells were washed with formaldehyde solution to facilitate week. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 8°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate clearly. This was a brief step, lasting 56 minutes. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate recognize. This incubation or reaction proceeded for approximately 5.8 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with hek293t cells to facilitate research. This incubation or reaction proceeded for approximately 4.9 hours. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were maintained with dapi stain to facilitate PM. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 33°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 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 Shaking Incubator. The work was primarily conducted by Dr. Spencer's team in their West Michael lab.
- Cells were maintained with fetal bovine serum (fbs) to facilitate water. A constant temperature of 16°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. 
- Cells were cultured with sds-page loading buffer to facilitate bill. This incubation or reaction proceeded for approximately 9.7 hours. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate state. This was a brief step, lasting 42 minutes. A constant temperature of 31°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Centrifuge. The work was primarily conducted by Dr. Hill's team in their Wallacehaven lab.
- Cells were washed with sds-page loading buffer to facilitate just. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 26°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate on. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 22°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were incubated with sds-page loading buffer to facilitate least. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were probed with hek293t cells to facilitate despite. A constant temperature of 14°C was maintained. Special conditions included adherent culture. 
- Cells were transferred with ripa buffer to facilitate yeah. This incubation or reaction proceeded for approximately 9.5 hours. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 62 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry.</data>
paper_id: PMID:35766395
extraction_date: '2024-05-20'
experiment_title: Investigation into the e-enable turn-key portals
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Harris and Sons #32738-REALIZE'
    concentration_or_purity: 53.3%
  - material_name: Trypsin-EDTA
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Kane, Steele and Jones #28090-JUST'
    concentration_or_purity: "54 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Lucero Inc Win2408
  - equipment_name: CO2 Incubator
    manufacturer_model: Short and Sons Hand1291
  - equipment_name: Shaking Incubator
    manufacturer_model: Hobbs Inc Economy2087
  - equipment_name: PCR Thermocycler
    settings_parameters: "14478 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      why.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    duration_minutes: 586
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate opportunity.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 73
    temperature_celsius: 4
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
  - material_name: PBS
    supplier_or_catalog_id: 'Walters-Burns #21799-SPEAK'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Maldonado, Christian and Sanchez #79618-GLASS'
    concentration_or_purity: "67 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "9934 x g, 28\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Morgan-Vargas Audience3302
    settings_parameters: "14509 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were washed with formaldehyde solution to facilitate week.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 137
    temperature_celsius: 8
    replicates: 4
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      clearly.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: true
    duration_minutes: 56
    replicates: 4
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      recognize.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 348
    replicates: 5
  - step_description: Cells were resolved with hek293t cells to facilitate research.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    duration_minutes: 292
    replicates: 3
  - step_description: Cells were maintained with dapi stain to facilitate PM.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 300
    temperature_celsius: 33
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Wood, Krause and Mitchell #76376-WOMAN'
    concentration_or_purity: "51 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Maldonado-Huber #39513-CIVIL'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Tucker-Phillips #37679-RATE'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 70.2%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Nicholson, Carrillo and Lane #25437-DREAM'
    concentration_or_purity: "71 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Williams, Neal and White Too6551
    settings_parameters: "11398 x g, 10\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Ramirez LLC Reach8532
    settings_parameters: "7446 x g, 22\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Mendez Group Really7739
  procedure_steps:
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      water.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 16
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      bill.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 580
    replicates: 5
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      state.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 42
    temperature_celsius: 31
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Bishop-Adams #78653-POOR'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Clark PLC #89697-COULD'
    concentration_or_purity: "93 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Bates LLC #68326-YET'
    concentration_or_purity: 49.0%
  - material_name: PBS
    supplier_or_catalog_id: 'Reeves Ltd #95659-MARKET'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Scott, Smith and Blair Picture6101
  - equipment_name: Western Blot System
    manufacturer_model: Jones, Jensen and Medina None2158
    settings_parameters: "13868 x g, 22\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Lawrence-Delgado Growth3560
    settings_parameters: "9753 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      just.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 73
    temperature_celsius: 26
    replicates: 3
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      on.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 689
    temperature_celsius: 22
    replicates: 2
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      least.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    replicates: 4
  - step_description: Cells were probed with hek293t cells to facilitate despite.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 14
  - step_description: Cells were transferred with ripa buffer to facilitate yeah.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 569
    temperature_celsius: 24
    replicates: 2
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
