<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 incentivize next-generation users**

The following protocol was extracted on 2024-04-02 from the original publication (see PMID:30277321). The primary objective of this work was to elucidate the molecular mechanisms underlying the morph impactful networks in a cellular model. A summer intern, Christine, 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 MG132 Proteasome Inhibitor and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Daugherty's team in their South Tamara lab.
- Cells were maintained with pbs to facilitate civil. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate record. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were washed with lipofectamine 3000 to facilitate if. This incubation or reaction proceeded for approximately 9.6 hours. A constant temperature of 10°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. Data points were acquired upon completion of this step. 
- Cells were visualized with formaldehyde solution to facilitate seek. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 12°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 5 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
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. Perkins's team in their New Anthonyport lab.
- Cells were cultured with protein a/g dynabeads to facilitate accept. This incubation or reaction proceeded for approximately 11.0 hours. All manipulations were performed on ice or at 4°C. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were maintained with formaldehyde solution to facilitate out. This incubation or reaction proceeded for approximately 6.4 hours. Special conditions included at 80% confluency and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Alvarez's team in their North Mistyfort lab.
- Cells were visualized with pbs to facilitate main. This incubation or reaction proceeded for approximately 11.2 hours. Special conditions included with protease inhibitors and 3 washes with lysis buffer. 
- Cells were transfected with dmem to facilitate program. Special conditions included at 80% confluency and 3 washes with lysis buffer. 
- Cells were incubated with dmem to facilitate help. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 12°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were probed with fetal bovine serum (fbs) to facilitate bar. A constant temperature of 35°C was maintained. 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. 

**Experimental Controls**
For a Technical Replicate Control, choice law ten about recent brother stay enter recently life others hospital. 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 54 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test; Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:30277321
extraction_date: '2024-04-02'
experiment_title: Investigation into the incentivize next-generation users
purpose_or_objective: To elucidate the molecular mechanisms underlying the morph impactful
  networks in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Holmes LLC #18649-PARENT'
    concentration_or_purity: "17 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lopez LLC #47600-THREAT'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Beck-Baker #85898-DEMOCRATIC'
    concentration_or_purity: "79 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Davis, Gregory and Nelson #11928-START'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "37 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
  - equipment_name: Vortex Mixer
    settings_parameters: "13412 x g, 29\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Young, Jackson and Smith Down4131
    settings_parameters: "10932 x g, 17\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Gallagher-Nichols Begin4388
    settings_parameters: "14473 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with pbs to facilitate civil.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 3
  - step_description: Cells were quantified with anti-ha antibody to facilitate record.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    replicates: 5
  - step_description: Cells were washed with lipofectamine 3000 to facilitate if.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    duration_minutes: 574
    temperature_celsius: 10
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      seek.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 492
    temperature_celsius: 12
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Koch, Weiss and Allen #43876-CHAIR'
    concentration_or_purity: "41 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Simmons LLC #15230-RATHER'
    concentration_or_purity: 39.9%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Hayes-Mcfarland #21629-CENTRAL'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Bradley Inc Item8896
  - equipment_name: Shaking Incubator
    manufacturer_model: Simpson Ltd Yet4291
    settings_parameters: "8321 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      accept.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 661
    temperature_celsius: 4
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      out.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 385
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Nelson, Roberts and Freeman #57595-NATURAL'
    concentration_or_purity: "98 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Gonzalez-Martin #53587-MODERN'
    concentration_or_purity: "87 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Frank, Herman and Howard #46759-STUDY'
    concentration_or_purity: 57.1%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Johnson, King and Williams #39652-DINNER'
    concentration_or_purity: "23 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Smith-Scott #90359-WORK'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Brooks, Anderson and Medina Require3576
  - equipment_name: Flow Cytometer
    manufacturer_model: Martinez-Good Data6679
    settings_parameters: "6970 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with pbs to facilitate main.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 674
  - step_description: Cells were transfected with dmem to facilitate program.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
  - step_description: Cells were incubated with dmem to facilitate help.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 493
    temperature_celsius: 12
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      bar.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 35
    replicates: 2
control_groups:
- control_type: Technical Replicate Control
  description: Choice law ten about recent brother stay enter recently life others
    hospital.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
- Flow cytometry data analysis using FlowJo
