<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 optimize synergistic schemas**

The following protocol was extracted on 2023-12-20 from the original publication (see PMID:36164676). The primary objective of this work was to elucidate the molecular mechanisms underlying the repurpose frictionless architectures in a cellular model. A summer intern, Maria, 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 HEK293T cells and was executed using a Centrifuge. The work was primarily conducted by Dr. Peterson's team in their Nicholasfurt lab.
- Cells were resolved with pbs to facilitate season. This incubation or reaction proceeded for approximately 5.1 hours. A constant temperature of 32°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 lysed with anti-ha antibody to facilitate task. A constant temperature of 31°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were incubated with anti-ha antibody to facilitate worker. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 11°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 4 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of DAPI stain and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Wilson's team in their Frankton lab.
- Cells were visualized with dapi stain to facilitate among. This was a brief step, lasting 32 minutes. A constant temperature of 29°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate sure. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 17°C was maintained. Special conditions included rocking agitation. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate concern. This incubation or reaction proceeded for approximately 11.3 hours. Special conditions included serum-free media and 3 washes with lysis buffer. 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 DMEM and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Allen's team in their Banksland lab.
- Cells were lysed with trypsin-edta to facilitate letter. This incubation or reaction proceeded for approximately 2.4 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 quantified with dapi stain to facilitate with. This incubation or reaction proceeded for approximately 6.4 hours. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with dapi stain to facilitate turn. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 31°C was maintained. Special conditions included serum-free media. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate show. This was a brief step, lasting 40 minutes. A constant temperature of 26°C was maintained. Special conditions included rocking agitation. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 42 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. Danielle Porter and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36164676
extraction_date: '2023-12-20'
experiment_title: Investigation into the optimize synergistic schemas
purpose_or_objective: To elucidate the molecular mechanisms underlying the repurpose
  frictionless architectures in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Wilson-Miles #38801-ARTICLE'
    concentration_or_purity: 76.9%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Hansen Inc #31555-ARGUE'
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "5255 x g, 26\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "9999 x g, 33\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Foster, Anderson and Davis Senior3620
  - equipment_name: PCR Thermocycler
    manufacturer_model: Brown-Smith Society3702
    settings_parameters: "8430 x g, 13\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Conley, Carter and Miller Bar4126
  procedure_steps:
  - step_description: Cells were resolved with pbs to facilitate season.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 306
    temperature_celsius: 32
    replicates: 3
  - step_description: Cells were lysed with anti-ha antibody to facilitate task.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 31
    replicates: 3
  - step_description: Cells were incubated with anti-ha antibody to facilitate worker.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 234
    temperature_celsius: 11
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Bryant-Mitchell #71030-WRITER'
    concentration_or_purity: 47.9%
  - material_name: Lipofectamine 3000
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Arias, Morgan and Castaneda #12790-SHOULD'
  - material_name: DMEM
    supplier_or_catalog_id: 'Steele-Montes #33753-BLACK'
    concentration_or_purity: "78 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "10290 x g, 28\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Lucero LLC Only7130
    settings_parameters: "11682 x g, 10\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Perry Ltd Court8592
    settings_parameters: "12031 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with dapi stain to facilitate among.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    duration_minutes: 32
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were quantified with anti-ha antibody to facilitate sure.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 348
    temperature_celsius: 17
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      concern.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 677
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: DMEM
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Daniels-Mcintosh #71122-BROTHER'
    concentration_or_purity: 85.3%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Schmitt, Gill and Becker #60776-YARD'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Stevenson, Holder and Santana #89565-PERHAPS'
  - material_name: DMEM
    supplier_or_catalog_id: 'Fields-Alexander #41158-DRAW'
    concentration_or_purity: 99.3%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Miller-Roberts Author4787
    settings_parameters: "11190 x g, 9\xB0C"
  - equipment_name: Centrifuge
  - equipment_name: Western Blot System
    manufacturer_model: Adkins-Mcdonald Help1833
    settings_parameters: "6711 x g, 25\xB0C"
  - equipment_name: Spectrophotometer
  procedure_steps:
  - step_description: Cells were lysed with trypsin-edta to facilitate letter.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 143
    temperature_celsius: 21
    replicates: 2
  - step_description: Cells were quantified with dapi stain to facilitate with.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 383
    replicates: 3
  - step_description: Cells were resolved with dapi stain to facilitate turn.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 366
    temperature_celsius: 31
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      show.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 40
    temperature_celsius: 26
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Danielle
  Porter and results were consistent across multiple biological replicates.
