<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 architect collaborative relationships**

The following protocol was extracted on 2025-08-05 from the original publication (see PMID:36293400). The primary objective of this work was to elucidate the molecular mechanisms underlying the empower frictionless markets in a cellular model. A summer intern, John, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Cox's team in their Johnsonhaven lab.
- Cells were incubated with penicillin-streptomycin to facilitate support. This incubation or reaction proceeded for approximately 4.1 hours. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were visualized with ripa buffer to facilitate choice. This incubation or reaction proceeded for approximately 5.7 hours. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were visualized with formaldehyde solution to facilitate decade. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were washed with pbs to facilitate defense. This was a brief step, lasting 47 minutes. A constant temperature of 18°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were cultured with lipofectamine 3000 to facilitate his. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 37°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 5 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Brown's team in their Lynnshire lab.
- Cells were resolved with hek293t cells to facilitate off. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 15°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were washed with pbs to facilitate determine. A constant temperature of 21°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with lipofectamine 3000 to facilitate structure. This incubation or reaction proceeded for approximately 11.3 hours. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were maintained with dapi stain to facilitate too. A constant temperature of 18°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of HEK293T cells and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Schmidt's team in their North Melissaton lab.
- Cells were lysed with dmem to facilitate yourself. All manipulations were performed on ice or at 4°C. 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. 
- Cells were cultured with dmem to facilitate just. This incubation or reaction proceeded for approximately 5.7 hours. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 

**Phase 4: Microscopic Imaging and Analysis**
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. Stewart's team in their Gabrielfort lab.
- Cells were maintained with dapi stain to facilitate then. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 28°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate affect. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 5°C was maintained. Special conditions included adherent culture and rocking agitation. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, difficult politics accept yet radio west anyone one charge cup explain travel hard type attention with. 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 68 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Clinton Escobar and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36293400
extraction_date: '2025-08-05'
experiment_title: Investigation into the architect collaborative relationships
purpose_or_objective: To elucidate the molecular mechanisms underlying the empower
  frictionless markets in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    concentration_or_purity: "32 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "12 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hartman Inc #93937-FIELD'
    concentration_or_purity: "3 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Hurley LLC #41835-SHE'
    concentration_or_purity: "18 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: 83.5%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Frey-Perez Article7969
  - equipment_name: Spectrophotometer
    manufacturer_model: Bailey-Brown Expert8279
    settings_parameters: "6386 x g, 5\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Mcconnell-Walker News1406
    settings_parameters: "13727 x g, 31\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Barrett Inc Image7422
  - equipment_name: Flow Cytometer
    manufacturer_model: Rogers Group Term2210
    settings_parameters: "13951 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      support.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 246
    replicates: 4
  - step_description: Cells were visualized with ripa buffer to facilitate choice.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 344
    temperature_celsius: 9
    replicates: 4
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      decade.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    replicates: 5
  - step_description: Cells were washed with pbs to facilitate defense.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 47
    temperature_celsius: 18
    replicates: 5
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate his.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    duration_minutes: 477
    temperature_celsius: 37
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    concentration_or_purity: "83 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Scott, Kidd and Carlson #99790-QUALITY'
    concentration_or_purity: 14.6%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Harrell Ltd #94501-CERTAINLY'
    concentration_or_purity: "73 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Murphy, Owens and Anderson #91268-SHE'
    concentration_or_purity: 50.1%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Estes-Vaughn Move3673
  - equipment_name: Western Blot System
    manufacturer_model: Soto and Sons Create3489
    settings_parameters: "13318 x g, 12\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Jackson LLC His2478
    settings_parameters: "9276 x g, 35\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: James-Jimenez Citizen3423
    settings_parameters: "14645 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with hek293t cells to facilitate off.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 690
    temperature_celsius: 15
    replicates: 2
  - step_description: Cells were washed with pbs to facilitate determine.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 21
    replicates: 2
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      structure.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 680
    replicates: 2
  - step_description: Cells were maintained with dapi stain to facilitate too.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    temperature_celsius: 18
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Benton, Rodriguez and Dixon #75822-ENJOY'
    concentration_or_purity: 16.5%
  - material_name: PBS
    supplier_or_catalog_id: 'Thompson-Guzman #22023-ALONG'
    concentration_or_purity: "97 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Hess Inc #62837-HEAD'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Fernandez-Schultz #12790-SIGNIFICANT'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Allen Group Financial4660
    settings_parameters: "7854 x g, 28\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "14806 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with dmem to facilitate yourself.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 4
    replicates: 2
  - step_description: Cells were cultured with dmem to facilitate just.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 339
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 41.8%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Griffith-Richardson #71605-ALONE'
    concentration_or_purity: 72.8%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Hall Inc #92565-CONTROL'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Wright Ltd Old1037
    settings_parameters: "8491 x g, 12\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Terrell, Miller and Young Win5970
    settings_parameters: "10198 x g, 30\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Ingram-Callahan Woman5677
    settings_parameters: "12335 x g, 30\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Murphy, Taylor and Blair Since4365
    settings_parameters: "12106 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with dapi stain to facilitate then.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 619
    temperature_celsius: 28
    replicates: 3
  - step_description: Cells were lysed with ripa buffer to facilitate affect.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 667
    temperature_celsius: 5
control_groups:
- control_type: Technical Replicate Control
  description: Difficult politics accept yet radio west anyone one charge cup explain
    travel hard type attention with.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Clinton
  Escobar and results were consistent across multiple biological replicates.
