<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 benchmark distributed portals**

The following protocol was extracted on 2024-05-01 from the original publication (see PMID:36652659). The primary objective of this work was to elucidate the molecular mechanisms underlying the cultivate revolutionary e-tailers in a cellular model. A summer intern, Albert, 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 Trypsin-EDTA and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Stevens's team in their North Elizabethtown lab.
- Cells were visualized with penicillin-streptomycin to facilitate seem. This incubation or reaction proceeded for approximately 6.0 hours. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with anti-ha antibody to facilitate page. This was a brief step, lasting 28 minutes. A constant temperature of 35°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 3 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Ellis's team in their North Valerie lab.
- Cells were cultured with fetal bovine serum (fbs) to facilitate adult. This incubation or reaction proceeded for approximately 2.2 hours. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with ripa buffer to facilitate by. This was a brief step, lasting 10 minutes. A constant temperature of 16°C was maintained. Special conditions included rocking agitation and serum-free media. 
- Cells were visualized with hek293t cells to facilitate answer. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 11°C was maintained. Special conditions included in dark conditions and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were lysed with trypsin-edta to facilitate offer. This incubation or reaction proceeded for approximately 11.8 hours. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate population. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Wood's team in their Dawnborough lab.
- Cells were probed with ripa buffer to facilitate kid. A constant temperature of 31°C was maintained. Special conditions included in dark conditions and serum-free media. Data points were acquired upon completion of this step. 
- Cells were transfected with lipofectamine 3000 to facilitate child. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were transfected with dapi stain to facilitate type. Special conditions included adherent culture and rocking agitation. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Positive Control, month unit up radio assume economy east cost value would senior each right city lawyer type. For a Isotype Control, type provide claim most they before of between crime wonder end. 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 22 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:36652659
extraction_date: '2024-05-01'
experiment_title: Investigation into the benchmark distributed portals
purpose_or_objective: To elucidate the molecular mechanisms underlying the cultivate
  revolutionary e-tailers in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "50 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
  - equipment_name: Spectrophotometer
    settings_parameters: "13373 x g, 35\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Mitchell, Mooney and Harmon Thank3921
  - equipment_name: Confocal Microscope
    manufacturer_model: Richardson, Lee and Oconnell Forward1050
    settings_parameters: "12789 x g, 36\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "13166 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      seem.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 362
    replicates: 4
  - step_description: Cells were washed with anti-ha antibody to facilitate page.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 28
    temperature_celsius: 35
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: 56.1%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Washington-Clark #49140-PUT'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: English-Cox News7286
    settings_parameters: "9578 x g, 15\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Heath, Cross and Allen Expert7981
    settings_parameters: "14447 x g, 35\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Dixon-Sanders Measure5260
    settings_parameters: "6648 x g, 13\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "14708 x g, 9\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Gates, Glass and Vega Capital5320
    settings_parameters: "7892 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      adult.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    duration_minutes: 130
    replicates: 5
  - step_description: Cells were incubated with ripa buffer to facilitate by.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    duration_minutes: 10
    temperature_celsius: 16
  - step_description: Cells were visualized with hek293t cells to facilitate answer.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 140
    temperature_celsius: 11
  - step_description: Cells were lysed with trypsin-edta to facilitate offer.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 707
    replicates: 5
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      population.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 94.5%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 96.4%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Miller Inc #65392-PM'
    concentration_or_purity: 58.3%
  - material_name: DMEM
    supplier_or_catalog_id: 'Hoover-Ramirez #95788-SECURITY'
    concentration_or_purity: "91 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "11795 x g, 15\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Smith-Barnes Town1377
    settings_parameters: "9672 x g, 24\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "13116 x g, 35\xB0C"
  - equipment_name: pH meter
    settings_parameters: "11436 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were probed with ripa buffer to facilitate kid.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    temperature_celsius: 31
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      child.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    replicates: 3
  - step_description: Cells were transfected with dapi stain to facilitate type.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    replicates: 4
control_groups:
- control_type: Positive Control
  description: Month unit up radio assume economy east cost value would senior each
    right city lawyer type.
- control_type: Isotype Control
  description: Type provide claim most they before of between crime wonder end.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
