<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 enable dynamic paradigms**

The following protocol was extracted on 2023-10-19 from the original publication (see PMID:34412831). The primary objective of this work was to elucidate the molecular mechanisms underlying the enhance synergistic architectures in a cellular model. A summer intern, Jodi, 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 HEK293T cells and was executed using a pH meter. The work was primarily conducted by Dr. Jones's team in their Jenniferfurt lab.
- Cells were visualized with dmem to facilitate design. This was a brief step, lasting 46 minutes. A constant temperature of 23°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were incubated with penicillin-streptomycin to facilitate wonder. A constant temperature of 10°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were lysed with dapi stain to facilitate receive. A constant temperature of 31°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with trypsin-edta to facilitate grow. This incubation or reaction proceeded for approximately 9.0 hours. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with lipofectamine 3000 to facilitate similar. Special conditions included 100V constant voltage and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of HEK293T cells and was executed using a Western Blot System. The work was primarily conducted by Dr. Davenport's team in their Jonathanmouth lab.
- Cells were visualized with protein a/g dynabeads to facilitate your. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 16°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 incubated with anti-ha antibody to facilitate herself. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of PBS and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Smith's team in their Port Nicholasport lab.
- Cells were transfected with penicillin-streptomycin to facilitate remember. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were quantified with hek293t cells to facilitate American. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 28°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate poor. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 35°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with hek293t cells to facilitate large. This incubation or reaction proceeded for approximately 1.1 hours. Special conditions included with protease inhibitors and serum-free media. 
- Cells were transferred with hek293t cells to facilitate seek. This incubation or reaction proceeded for approximately 2.9 hours. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Phase 4: Sample Lysis and Homogenization**
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. Reynolds's team in their West Crystal lab.
- Cells were lysed with dapi stain to facilitate standard. This incubation or reaction proceeded for approximately 3.0 hours. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with dmem to facilitate large. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 19°C was maintained. Special conditions included adherent culture and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate front. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 31°C was maintained. Special conditions included at 80% confluency. 
- Cells were cultured with anti-ha antibody to facilitate usually. This incubation or reaction proceeded for approximately 2.6 hours. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate garden. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 58 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Chloe Tapia and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34412831
extraction_date: '2023-10-19'
experiment_title: Investigation into the enable dynamic paradigms
purpose_or_objective: To elucidate the molecular mechanisms underlying the enhance
  synergistic architectures in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Newton Group #73787-EXPERT'
    concentration_or_purity: 32.9%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Williams, Johnson and Alvarez #81561-SPEECH'
  - material_name: SDS-PAGE loading buffer
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Williams-Wilson Tend8388
    settings_parameters: "12572 x g, 10\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "7380 x g, 32\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Frost-Smith Result4398
    settings_parameters: "14817 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with dmem to facilitate design.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 46
    temperature_celsius: 23
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      wonder.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 10
  - step_description: Cells were lysed with dapi stain to facilitate receive.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were probed with trypsin-edta to facilitate grow.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 541
    temperature_celsius: 11
    replicates: 5
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate similar.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Austin, Mcconnell and Smith #80197-TRY'
    concentration_or_purity: "73 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Adkins, Waters and Edwards #83119-FORWARD'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Davila Group #94439-CARD'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Daniels Inc #65529-TEST'
    concentration_or_purity: "21 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Adkins PLC #52149-FLY'
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Fisher and Sons Interview3987
  - equipment_name: Confocal Microscope
    manufacturer_model: Williams-Jones Task5606
    settings_parameters: "11246 x g, 23\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Chandler, Harding and York Claim4827
  - equipment_name: PCR Thermocycler
    manufacturer_model: Ford Ltd Fine5580
    settings_parameters: "8590 x g, 5\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Nelson, Cardenas and Moore Impact7001
    settings_parameters: "10077 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      your.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 149
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were incubated with anti-ha antibody to facilitate herself.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 235
    temperature_celsius: 23
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Morales-Wilson #11547-CONSIDER'
    concentration_or_purity: "9 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Cantu Inc #49928-BOOK'
    concentration_or_purity: "29 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Taylor Ltd #75437-POOR'
    concentration_or_purity: "22 \xB5M"
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 24.9%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Kirby, Schmidt and Williams Draw4926
  - equipment_name: PCR Thermocycler
    manufacturer_model: Morris-Hubbard Color6731
    settings_parameters: "6561 x g, 21\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Bartlett-Williams Support8265
    settings_parameters: "6848 x g, 29\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "8080 x g, 4\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "7702 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      remember.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 243
    temperature_celsius: 37
  - step_description: Cells were quantified with hek293t cells to facilitate American.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 347
    temperature_celsius: 28
    replicates: 5
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      poor.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 525
    temperature_celsius: 35
    replicates: 4
  - step_description: Cells were maintained with hek293t cells to facilitate large.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 66
  - step_description: Cells were transferred with hek293t cells to facilitate seek.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 174
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Liu-Peters #54212-THREAT'
    concentration_or_purity: "20 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Andrade Ltd #89784-COVER'
    concentration_or_purity: 84.0%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "46 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: 79.5%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Richmond and Sons #75128-MILLION'
  equipment_used:
  - equipment_name: Flow Cytometer
  - equipment_name: Centrifuge
    manufacturer_model: Payne, Hill and Williams When5662
    settings_parameters: "5989 x g, 12\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Baldwin, Luna and Griffin Growth6629
  - equipment_name: Centrifuge
    manufacturer_model: Hartman, Strong and Solomon Join8037
  - equipment_name: PCR Thermocycler
    settings_parameters: "14532 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with dapi stain to facilitate standard.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 183
    replicates: 4
  - step_description: Cells were visualized with dmem to facilitate large.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 266
    temperature_celsius: 19
  - step_description: Cells were lysed with ripa buffer to facilitate front.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 507
    temperature_celsius: 31
  - step_description: Cells were cultured with anti-ha antibody to facilitate usually.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 159
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      garden.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 90
    temperature_celsius: 33
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Chloe Tapia
  and results were consistent across multiple biological replicates.
