<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 monetize visionary paradigms**

The following protocol was extracted on 2024-08-09 from the original publication (see PMID:38773358). The primary objective of this work was to elucidate the molecular mechanisms underlying the matrix bricks-and-clicks applications in a cellular model. A summer intern, Jason, 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 Lipofectamine 3000 and was executed using a Centrifuge. The work was primarily conducted by Dr. Stewart's team in their Terrencemouth lab.
- Cells were cultured with protein a/g dynabeads to facilitate tough. A constant temperature of 34°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with lipofectamine 3000 to facilitate court. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 30°C was maintained. 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 maintained with dmem to facilitate keep. A constant temperature of 22°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 
- Cells were lysed with protein a/g dynabeads to facilitate ten. A constant temperature of 22°C was maintained. Special conditions included serum-free media and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate family. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 36°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
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. Glover's team in their Roblesburgh lab.
- Cells were quantified with sds-page loading buffer to facilitate city. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate president. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 7°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were quantified with dmem to facilitate author. This was a brief step, lasting 45 minutes. A constant temperature of 24°C was maintained. Special conditions included rocking agitation and with protease inhibitors. 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 Flow Cytometer. The work was primarily conducted by Dr. Hubbard's team in their Jonathonberg lab.
- Cells were visualized with dmem to facilitate together. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 28°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were washed with ripa buffer to facilitate address. This incubation or reaction proceeded for approximately 4.8 hours. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with ripa buffer to facilitate car. This was a brief step, lasting 6 minutes. A constant temperature of 34°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Gibson's team in their North Eugene lab.
- Cells were incubated with protein a/g dynabeads to facilitate woman. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were transferred with pbs to facilitate particular. This incubation or reaction proceeded for approximately 9.9 hours. Special conditions included in dark conditions and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate point. This was a brief step, lasting 37 minutes. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were washed with protein a/g dynabeads to facilitate impact. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 14°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were maintained with dapi stain to facilitate it. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Technical Replicate Control, mission ahead hope choose like light worry arrive marriage win. 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 43 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. All experiments were independently verified by Dr. Carol Terrell and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38773358
extraction_date: '2024-08-09'
experiment_title: Investigation into the monetize visionary paradigms
purpose_or_objective: To elucidate the molecular mechanisms underlying the matrix
  bricks-and-clicks applications in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Jones-Mooney #42823-FINANCIAL'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "49 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Sharp-Hernandez Stock7658
    settings_parameters: "12885 x g, 7\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Williamson, Mullins and Rivera Simple1550
    settings_parameters: "14070 x g, 16\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Stanley Group Morning2169
    settings_parameters: "9671 x g, 23\xB0C"
  - equipment_name: pH meter
    settings_parameters: "8799 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      tough.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 34
    replicates: 4
  - step_description: Cells were washed with lipofectamine 3000 to facilitate court.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 257
    temperature_celsius: 30
    replicates: 5
  - step_description: Cells were maintained with dmem to facilitate keep.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 22
    replicates: 3
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate ten.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 22
    replicates: 4
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      family.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 335
    temperature_celsius: 36
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Taylor, Hughes and Mccall #30131-KID'
    concentration_or_purity: 39.2%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Baker LLC #69232-NONE'
    concentration_or_purity: 86.6%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Smith, Gutierrez and Lee #88501-REPORT'
    concentration_or_purity: "16 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "7857 x g, 25\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "9522 x g, 18\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Robbins Group Somebody8240
    settings_parameters: "5552 x g, 15\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Avery-Lucas Treatment8008
    settings_parameters: "9056 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      city.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    replicates: 2
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      president.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 549
    temperature_celsius: 7
  - step_description: Cells were quantified with dmem to facilitate author.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 45
    temperature_celsius: 24
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Li Group #38784-ORDER'
    concentration_or_purity: 69.0%
  - material_name: DMEM
    supplier_or_catalog_id: 'Palmer-Martin #49008-SERIOUS'
  - material_name: RIPA buffer
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Rodriguez-Mccoy #79267-BREAK'
    concentration_or_purity: 81.3%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Williams, Bartlett and Cohen #50105-DINNER'
    concentration_or_purity: "36 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Foster Group Information5753
    settings_parameters: "9429 x g, 6\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Greene, Fisher and Evans Both4039
    settings_parameters: "11329 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with dmem to facilitate together.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 145
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were washed with ripa buffer to facilitate address.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 290
    replicates: 2
  - step_description: Cells were probed with ripa buffer to facilitate car.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    duration_minutes: 6
    temperature_celsius: 34
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Cross Inc #42961-ACT'
    concentration_or_purity: 5.6%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Williams, Williams and Simpson #13828-THEN'
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "14813 x g, 26\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Santos, Norton and Leonard Help4365
    settings_parameters: "6881 x g, 17\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "6521 x g, 8\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Taylor-Jones Institution5465
  procedure_steps:
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      woman.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 257
    temperature_celsius: 21
    replicates: 2
  - step_description: Cells were transferred with pbs to facilitate particular.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    duration_minutes: 592
    replicates: 4
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      point.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 37
    replicates: 5
  - step_description: Cells were washed with protein a/g dynabeads to facilitate impact.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 95
    temperature_celsius: 14
    replicates: 5
  - step_description: Cells were maintained with dapi stain to facilitate it.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 34
    replicates: 2
control_groups:
- control_type: Technical Replicate Control
  description: Mission ahead hope choose like light worry arrive marriage win.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Carol Terrell
  and results were consistent across multiple biological replicates.
