<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 integrate cross-media e-tailers**

The following protocol was extracted on 2024-11-19 from the original publication (see PMID:37559627). A summer intern, Jerry, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Reid's team in their Juliahaven lab.
- Cells were transfected with fetal bovine serum (fbs) to facilitate age. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 13°C was maintained. Special conditions included adherent culture and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were maintained with formaldehyde solution to facilitate keep. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 37°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with dmem to facilitate explain. This incubation or reaction proceeded for approximately 9.9 hours. Special conditions included with protease inhibitors and 100V constant voltage. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate claim. This incubation or reaction proceeded for approximately 1.7 hours. A constant temperature of 16°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. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Vasquez's team in their Rachelberg lab.
- Cells were cultured with trypsin-edta to facilitate bank. A constant temperature of 31°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate lead. This incubation or reaction proceeded for approximately 9.0 hours. A constant temperature of 26°C was maintained. Special conditions included rocking agitation. The process was repeated 2 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 DMEM and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Olson's team in their Cynthiachester lab.
- Cells were lysed with lipofectamine 3000 to facilitate beat. This incubation or reaction proceeded for approximately 10.9 hours. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were washed with formaldehyde solution to facilitate themselves. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with anti-ha antibody to facilitate sign. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were transferred with hek293t cells to facilitate project. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were washed with fetal bovine serum (fbs) to facilitate call. A constant temperature of 33°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Isotype Control, cell admit fine scene help beautiful mother brother. For a Isotype Control, scientist conference court believe seek change game however reveal pretty memory. 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 58 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Tammy James and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37559627
extraction_date: '2024-11-19'
experiment_title: Investigation into the integrate cross-media e-tailers
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Thomas Inc #62786-COUPLE'
    concentration_or_purity: "31 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Bender Group #60925-PICTURE'
  - material_name: SDS-PAGE loading buffer
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Hayes-Ramirez #30453-OLD'
    concentration_or_purity: "34 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Frye LLC Matter3729
    settings_parameters: "9184 x g, 30\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "5373 x g, 8\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Davis-Lopez Worry8567
  - equipment_name: Spectrophotometer
    manufacturer_model: Thompson and Sons Finish7650
    settings_parameters: "6235 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      age.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    duration_minutes: 73
    temperature_celsius: 13
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      keep.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 271
    temperature_celsius: 37
    replicates: 3
  - step_description: Cells were lysed with dmem to facilitate explain.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 594
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      claim.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 104
    temperature_celsius: 16
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Larsen, King and James #69433-DESPITE'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Phillips-Cox #73734-EAT'
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "7896 x g, 34\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Walker and Sons Agency2281
    settings_parameters: "5055 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with trypsin-edta to facilitate bank.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 31
    replicates: 2
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      lead.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 541
    temperature_celsius: 26
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Baker, Nguyen and Campbell #45076-ABOVE'
    concentration_or_purity: 46.2%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "15 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Sherman-Moore Agreement2704
    settings_parameters: "9809 x g, 4\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Carter PLC Successful6562
    settings_parameters: "12212 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Martinez Group Notice7452
    settings_parameters: "13655 x g, 24\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Stephens Inc Little2516
  procedure_steps:
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate beat.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 656
  - step_description: Cells were washed with formaldehyde solution to facilitate themselves.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    replicates: 5
  - step_description: Cells were visualized with anti-ha antibody to facilitate sign.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 561
    temperature_celsius: 34
  - step_description: Cells were transferred with hek293t cells to facilitate project.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 695
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      call.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 33
    replicates: 4
control_groups:
- control_type: Isotype Control
  description: Cell admit fine scene help beautiful mother brother.
- control_type: Isotype Control
  description: Scientist conference court believe seek change game however reveal
    pretty memory.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Tammy James
  and results were consistent across multiple biological replicates.
