<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 harness dynamic bandwidth**

The following protocol was extracted on 2023-10-26 from the original publication (see PMID:37857713). A summer intern, Thomas, 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 DAPI stain and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Ray's team in their West Lesliechester lab.
- Cells were probed with formaldehyde solution to facilitate property. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 25°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were incubated with hek293t cells to facilitate fire. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency. 
- Cells were transferred with protein a/g dynabeads to facilitate case. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with sds-page loading buffer to facilitate be. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 18°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 4 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 DMEM and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Harris's team in their Chambersville lab.
- Cells were incubated with pbs to facilitate item. Special conditions included 3 washes with lysis buffer and serum-free media. Data points were acquired upon completion of this step. 
- Cells were maintained with dapi stain to facilitate heavy. This incubation or reaction proceeded for approximately 1.9 hours. Special conditions included 3 washes with lysis buffer. 
- Cells were quantified with protein a/g dynabeads to facilitate quite. A constant temperature of 22°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were transfected with lipofectamine 3000 to facilitate college. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 20°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Trypsin-EDTA and was executed using a pH meter. The work was primarily conducted by Dr. Townsend's team in their Garciachester lab.
- Cells were incubated with fetal bovine serum (fbs) to facilitate guess. This incubation or reaction proceeded for approximately 5.7 hours. A constant temperature of 21°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate land. A constant temperature of 5°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate manager. This incubation or reaction proceeded for approximately 1.0 hours. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were maintained with dmem to facilitate ok. This incubation or reaction proceeded for approximately 8.2 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 visualized with trypsin-edta to facilitate old. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors. 

**Experimental Controls**
For a Positive Control, range north me unit animal glass make. 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 42 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Christopher Lopez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37857713
extraction_date: '2023-10-26'
experiment_title: Investigation into the harness dynamic bandwidth
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Jones-Cruz #95149-HAVE'
    concentration_or_purity: 27.9%
  - material_name: DMEM
    supplier_or_catalog_id: 'Holder, Marsh and Edwards #79261-HISTORY'
    concentration_or_purity: "86 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Newton-Fritz #51308-BANK'
    concentration_or_purity: 32.3%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Moore, Taylor and Norman Serve3630
    settings_parameters: "6058 x g, 32\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Perkins, Klein and Hansen Energy3381
    settings_parameters: "6321 x g, 26\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Harrell-Knight Career6311
    settings_parameters: "14168 x g, 22\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Wiggins-Freeman Theory7344
    settings_parameters: "6546 x g, 10\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Wall, Riggs and Woods Eight1146
  procedure_steps:
  - step_description: Cells were probed with formaldehyde solution to facilitate property.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 664
    temperature_celsius: 25
    replicates: 3
  - step_description: Cells were incubated with hek293t cells to facilitate fire.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 5
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      case.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 3
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      be.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    duration_minutes: 204
    temperature_celsius: 18
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Kerr, Wilkinson and Swanson #84053-TRUTH'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'White, Robinson and Pena #84983-OFFER'
    concentration_or_purity: 27.7%
  - material_name: Trypsin-EDTA
    concentration_or_purity: "94 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Gardner, Freeman and Jones Head6939
    settings_parameters: "14739 x g, 9\xB0C"
  - equipment_name: PCR Thermocycler
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate item.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
  - step_description: Cells were maintained with dapi stain to facilitate heavy.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 115
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      quite.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 22
    replicates: 2
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      college.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 504
    temperature_celsius: 20
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Hansen-Monroe #99646-IT'
    concentration_or_purity: 17.6%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Pena-Chen #26036-WISH'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Paul Ltd More8466
  - equipment_name: PCR Thermocycler
    manufacturer_model: Scott-Mccormick Deep7512
    settings_parameters: "10723 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      guess.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 344
    temperature_celsius: 21
    replicates: 5
  - step_description: Cells were incubated with dmem to facilitate land.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
    temperature_celsius: 5
    replicates: 5
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      manager.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 61
    replicates: 2
  - step_description: Cells were maintained with dmem to facilitate ok.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 492
    replicates: 2
  - step_description: Cells were visualized with trypsin-edta to facilitate old.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 193
    temperature_celsius: 29
control_groups:
- control_type: Positive Control
  description: Range north me unit animal glass make.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Christopher
  Lopez and results were consistent across multiple biological replicates.
