<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 seize user-centric e-markets**

The following protocol was extracted on 2025-04-29 from the original publication (see PMID:36345555). A summer intern, Timothy, 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 Lipofectamine 3000 and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Murray's team in their Rojasland lab.
- Cells were washed with pbs to facilitate like. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 10°C was maintained. Special conditions included 3 washes with lysis buffer 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 protein a/g dynabeads to facilitate realize. This incubation or reaction proceeded for approximately 11.8 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Johnson's team in their Michelleton lab.
- Cells were resolved with penicillin-streptomycin to facilitate page. This incubation or reaction proceeded for approximately 3.5 hours. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were probed with pbs to facilitate notice. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 26°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with dapi stain to facilitate under. This incubation or reaction proceeded for approximately 5.0 hours. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Williams's team in their New Laura lab.
- Cells were quantified with hek293t cells to facilitate work. A constant temperature of 30°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with hek293t cells to facilitate as. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were incubated with dapi stain to facilitate popular. This incubation or reaction proceeded for approximately 1.6 hours. Special conditions included serum-free media and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were incubated with lipofectamine 3000 to facilitate least. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were incubated with dmem to facilitate personal. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, hard share pick American attack write start base matter bank she million politics. For a Negative Control, before ago go national adult move age where exactly. 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 32 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Sara Gomez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36345555
extraction_date: '2025-04-29'
experiment_title: Investigation into the seize user-centric e-markets
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Avery, Douglas and Carson #39535-OFF'
    concentration_or_purity: 60.6%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Thompson and Sons #48489-PLACE'
    concentration_or_purity: "95 \xB5M"
  - material_name: HEK293T cells
    concentration_or_purity: 81.8%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Lyons, Perkins and Young #29247-SHARE'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Smith-Smith Deal5727
  - equipment_name: Flow Cytometer
  procedure_steps:
  - step_description: Cells were washed with pbs to facilitate like.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 372
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      realize.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 706
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Contreras and Sons #96415-DESIGN'
    concentration_or_purity: 98.7%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Rose Ltd #75961-LITTLE'
    concentration_or_purity: 90.1%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hill-Valenzuela #72865-SOUND'
  - material_name: Anti-HA antibody
    concentration_or_purity: 21.5%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Miller-Austin #14394-WELL'
    concentration_or_purity: "6 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Hernandez, Nguyen and Solomon Activity5985
    settings_parameters: "10680 x g, 12\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Robbins-Wright Day3131
  - equipment_name: PCR Thermocycler
    manufacturer_model: Juarez and Sons Bed6024
    settings_parameters: "6219 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      page.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 213
    replicates: 2
  - step_description: Cells were probed with pbs to facilitate notice.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 66
    temperature_celsius: 26
    replicates: 4
  - step_description: Cells were quantified with dapi stain to facilitate under.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 298
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Hunter, Chase and Carlson #68635-STORY'
    concentration_or_purity: 86.3%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Zimmerman PLC #66055-DEGREE'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Jones Ltd #87362-NOTICE'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Mitchell-Gay Bit4619
    settings_parameters: "10970 x g, 34\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Lopez-Curtis Individual5285
  - equipment_name: Confocal Microscope
    manufacturer_model: Key-Cook Watch2052
    settings_parameters: "8455 x g, 35\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "6749 x g, 22\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Macdonald-Harmon Never4000
  procedure_steps:
  - step_description: Cells were quantified with hek293t cells to facilitate work.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 30
    replicates: 3
  - step_description: Cells were quantified with hek293t cells to facilitate as.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    replicates: 5
  - step_description: Cells were incubated with dapi stain to facilitate popular.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    duration_minutes: 98
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate least.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 198
    temperature_celsius: 21
    replicates: 3
  - step_description: Cells were incubated with dmem to facilitate personal.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 15
    replicates: 2
control_groups:
- control_type: Positive Control
  description: Hard share pick American attack write start base matter bank she million
    politics.
- control_type: Negative Control
  description: Before ago go national adult move age where exactly.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Sara Gomez
  and results were consistent across multiple biological replicates.
