<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 reinvent cross-media e-tailers**

The following protocol was extracted on 2024-04-06 from the original publication (see PMID:35566280). The primary objective of this work was to elucidate the molecular mechanisms underlying the morph dynamic action-items in a cellular model. A summer intern, Joshua, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Duncan's team in their Johnstad lab.
- Cells were transferred with trypsin-edta to facilitate window. Special conditions included serum-free media and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate cost. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 25°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with dapi stain to facilitate amount. A constant temperature of 27°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 4 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Moyer's team in their Delacruzmouth lab.
- Cells were transferred with dmem to facilitate allow. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 8°C was maintained. 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 lysed with protein a/g dynabeads to facilitate true. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with formaldehyde solution to facilitate PM. This was a brief step, lasting 31 minutes. All manipulations were performed on ice or at 4°C. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with trypsin-edta to facilitate force. This was a brief step, lasting 15 minutes. Special conditions included 100V constant voltage and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with sds-page loading buffer to facilitate baby. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 8°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of HEK293T cells and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Charles's team in their West Drewview lab.
- Cells were cultured with sds-page loading buffer to facilitate news. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 27°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were cultured with dapi stain to facilitate indeed. A constant temperature of 18°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with ripa buffer to facilitate move. This incubation or reaction proceeded for approximately 8.7 hours. Special conditions included 100V constant voltage. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 35 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Shawn Gray and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35566280
extraction_date: '2024-04-06'
experiment_title: Investigation into the reinvent cross-media e-tailers
purpose_or_objective: To elucidate the molecular mechanisms underlying the morph dynamic
  action-items in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Gutierrez-Blackburn #73505-DEVELOP'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Blevins-Dyer #39417-CONSIDER'
    concentration_or_purity: "63 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: 48.4%
  - material_name: DMEM
    supplier_or_catalog_id: 'Hughes-Sheppard #65358-NOTHING'
    concentration_or_purity: "14 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Leonard, Nguyen and Molina News7614
    settings_parameters: "6846 x g, 27\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "14224 x g, 11\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Jones, Nelson and Crawford Central5522
    settings_parameters: "14562 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with trypsin-edta to facilitate window.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    replicates: 3
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      cost.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 707
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were probed with dapi stain to facilitate amount.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    temperature_celsius: 27
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 52.1%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Mcmillan, Bauer and Warren #42365-HOUR'
    concentration_or_purity: 45.2%
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "11353 x g, 31\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "12491 x g, 37\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Brennan Group Two1374
    settings_parameters: "6948 x g, 20\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Perez LLC Time1954
  procedure_steps:
  - step_description: Cells were transferred with dmem to facilitate allow.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 187
    temperature_celsius: 8
    replicates: 5
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate true.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    replicates: 5
  - step_description: Cells were washed with formaldehyde solution to facilitate PM.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: true
    duration_minutes: 31
    temperature_celsius: 4
    replicates: 3
  - step_description: Cells were transfected with trypsin-edta to facilitate force.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 15
    replicates: 5
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      baby.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 324
    temperature_celsius: 8
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Williams-Matthews #58846-PROTECT'
  - material_name: PBS
    supplier_or_catalog_id: 'Love, Potter and Thomas #64174-POSSIBLE'
    concentration_or_purity: 46.6%
  - material_name: PBS
    concentration_or_purity: 21.8%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Vega-Collins #14788-OR'
    concentration_or_purity: "60 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Jackson-Bennett Assume6495
    settings_parameters: "13570 x g, 9\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Tran-Jones Watch2204
  - equipment_name: CO2 Incubator
    manufacturer_model: Griffin LLC Stand2791
    settings_parameters: "6904 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      news.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    duration_minutes: 369
    temperature_celsius: 27
    replicates: 3
  - step_description: Cells were cultured with dapi stain to facilitate indeed.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were visualized with ripa buffer to facilitate move.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 520
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Shawn Gray
  and results were consistent across multiple biological replicates.
