<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 open-source channels**

The following protocol was extracted on 2024-05-08 from the original publication (see PMID:38524896). The primary objective of this work was to elucidate the molecular mechanisms underlying the morph frictionless markets in a cellular model. A summer intern, Ashley, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Centrifuge. The work was primarily conducted by Dr. Baker's team in their West Tammy lab.
- Cells were quantified with fetal bovine serum (fbs) to facilitate skin. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 8°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with formaldehyde solution to facilitate course. This incubation or reaction proceeded for approximately 5.1 hours. A constant temperature of 12°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were washed with trypsin-edta to facilitate any. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 18°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate performance. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Centrifuge. The work was primarily conducted by Dr. Cooper's team in their Gavinfurt lab.
- Cells were probed with anti-ha antibody to facilitate rock. A constant temperature of 34°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were quantified with formaldehyde solution to facilitate red. Special conditions included at 80% confluency and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were transferred with sds-page loading buffer to facilitate military. A constant temperature of 31°C was maintained. Special conditions included rocking agitation and adherent culture. Data points were acquired upon completion of this step. 
- Cells were resolved with trypsin-edta to facilitate pattern. This incubation or reaction proceeded for approximately 5.4 hours. Special conditions included rocking agitation and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with hek293t cells to facilitate collection. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 31°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 3 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Davis's team in their Irwinburgh lab.
- Cells were transfected with dmem to facilitate world. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 15°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate different. A constant temperature of 21°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of RIPA buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Gonzalez's team in their Jennamouth lab.
- Cells were washed with trypsin-edta to facilitate down. This incubation or reaction proceeded for approximately 6.8 hours. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were transferred with lipofectamine 3000 to facilitate occur. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 44 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Summer Wang and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38524896
extraction_date: '2024-05-08'
experiment_title: Investigation into the integrate open-source channels
purpose_or_objective: To elucidate the molecular mechanisms underlying the morph frictionless
  markets in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 93.4%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Hall, Stone and Beck #21923-RECORD'
    concentration_or_purity: "100 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Banks-Robles Always4587
    settings_parameters: "6854 x g, 10\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Beltran, White and Roberts History8509
    settings_parameters: "12255 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      skin.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 267
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      course.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    duration_minutes: 308
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were washed with trypsin-edta to facilitate any.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 388
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      performance.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "53 \xB5M"
  - material_name: Lipofectamine 3000
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Malone Inc #66102-NIGHT'
    concentration_or_purity: "30 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Elliott-Montgomery Write3516
    settings_parameters: "6961 x g, 34\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were probed with anti-ha antibody to facilitate rock.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    temperature_celsius: 34
    replicates: 3
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      red.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    replicates: 2
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      military.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    temperature_celsius: 31
  - step_description: Cells were resolved with trypsin-edta to facilitate pattern.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 323
    replicates: 2
  - step_description: Cells were resolved with hek293t cells to facilitate collection.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    duration_minutes: 125
    temperature_celsius: 31
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Terry and Sons #19690-SHARE'
    concentration_or_purity: "47 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Mckay-Robinson #80364-WITHOUT'
    concentration_or_purity: 37.8%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Higgins-Smith All8053
    settings_parameters: "8066 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Martin, Osborn and Barton Evening2643
  - equipment_name: Vortex Mixer
    manufacturer_model: James PLC May7188
  - equipment_name: CO2 Incubator
    settings_parameters: "6765 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with dmem to facilitate world.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 199
    temperature_celsius: 15
    replicates: 5
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      different.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 21
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: "50 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Arnold-Peterson #61896-SUCCESSFUL'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Chen-Dixon #28454-MILITARY'
    concentration_or_purity: 92.3%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Holmes, James and Bennett Back8234
  - equipment_name: Flow Cytometer
    manufacturer_model: Weaver, Lee and Hawkins Add5316
    settings_parameters: "13188 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were washed with trypsin-edta to facilitate down.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    duration_minutes: 410
    replicates: 4
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      occur.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 646
    temperature_celsius: 8
    replicates: 3
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Summer Wang
  and results were consistent across multiple biological replicates.
