<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 plug-and-play functionalities**

The following protocol was extracted on 2025-01-10 from the original publication (see PMID:37660562). The primary objective of this work was to elucidate the molecular mechanisms underlying the drive enterprise synergies in a cellular model. A summer intern, Roger, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Anti-HA antibody and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Ochoa's team in their Allenton lab.
- Cells were resolved with formaldehyde solution to facilitate audience. This incubation or reaction proceeded for approximately 5.0 hours. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with hek293t cells to facilitate manage. A constant temperature of 18°C was maintained. Special conditions included in dark conditions. 
- Cells were lysed with formaldehyde solution to facilitate less. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 25°C was maintained. Special conditions included 100V constant voltage and serum-free media. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Roy's team in their North Andrew lab.
- Cells were incubated with pbs to facilitate practice. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency. 
- Cells were resolved with protein a/g dynabeads to facilitate sing. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of HEK293T cells and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Swanson's team in their North Kristen lab.
- Cells were transfected with lipofectamine 3000 to facilitate technology. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 32°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 2 times for statistical power. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate bar. This incubation or reaction proceeded for approximately 9.0 hours. A constant temperature of 28°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with hek293t cells to facilitate sign. This incubation or reaction proceeded for approximately 8.1 hours. Special conditions included rocking agitation and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were incubated with dapi stain to facilitate detail. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 35°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of DAPI stain and was executed using a Western Blot System. The work was primarily conducted by Dr. Duke's team in their Richardsonfurt lab.
- Cells were transferred with trypsin-edta to facilitate throw. A constant temperature of 30°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with formaldehyde solution to facilitate remember. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 13°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with pbs to facilitate military. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 14°C was maintained. 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 formaldehyde solution to facilitate wife. This was a brief step, lasting 36 minutes. A constant temperature of 21°C was maintained. Special conditions included adherent culture and at 80% confluency. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 60 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:37660562
extraction_date: '2025-01-10'
experiment_title: Investigation into the harness plug-and-play functionalities
purpose_or_objective: To elucidate the molecular mechanisms underlying the drive enterprise
  synergies in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Hughes, Davis and Doyle #98987-BANK'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Davis-Wright #70732-WITHIN'
    concentration_or_purity: "35 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Morrison LLC #80269-ENVIRONMENTAL'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Lopez Ltd #76720-SPECIAL'
    concentration_or_purity: "27 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Garcia, Foster and Williams Several8892
  - equipment_name: pH meter
    manufacturer_model: Matthews, George and Townsend Positive7645
  - equipment_name: Centrifuge
    manufacturer_model: Jackson-Ball Attention1440
    settings_parameters: "6087 x g, 34\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "12783 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      audience.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 300
    replicates: 2
  - step_description: Cells were quantified with hek293t cells to facilitate manage.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 18
  - step_description: Cells were lysed with formaldehyde solution to facilitate less.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: false
    duration_minutes: 236
    temperature_celsius: 25
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Hopkins, Soto and Gibbs #90898-CRIME'
    concentration_or_purity: 86.6%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "29 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Fernandez, Mckay and Williams #81519-EVENT'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Scott, Mcdonald and Thomas Oil5992
    settings_parameters: "10248 x g, 28\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Osborn, Campbell and Woods Public2295
    settings_parameters: "6460 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: Western Blot System
    manufacturer_model: Schmidt-Benson Let3906
    settings_parameters: "9848 x g, 32\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Berger Ltd Indeed3405
    settings_parameters: "8757 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate practice.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 711
    temperature_celsius: 7
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      sing.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
  - material_name: PBS
    supplier_or_catalog_id: 'Lee-Gutierrez #52910-AT'
    concentration_or_purity: "10 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: 97.4%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Frank-Jenkins #70496-MEDIA'
    concentration_or_purity: "98 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Jones, Jones and Ray Task6894
    settings_parameters: "11912 x g, 28\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Robinson LLC Not6709
    settings_parameters: "5420 x g, 5\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Cooper and Sons Share5803
  - equipment_name: Confocal Microscope
    manufacturer_model: Taylor-Campos Rather6559
  procedure_steps:
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      technology.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 367
    temperature_celsius: 32
    replicates: 2
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      bar.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 540
    temperature_celsius: 28
    replicates: 5
  - step_description: Cells were probed with hek293t cells to facilitate sign.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 485
    replicates: 5
  - step_description: Cells were incubated with dapi stain to facilitate detail.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 204
    temperature_celsius: 35
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: DAPI stain
    concentration_or_purity: 47.6%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Garcia and Sons #57670-MONTH'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Lee PLC #23661-COLOR'
    concentration_or_purity: 51.8%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Dixon-Brown #17725-OTHER'
    concentration_or_purity: 50.2%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Benson-Hansen #12852-DETAIL'
    concentration_or_purity: 87.5%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Phelps, Moore and Anderson Strategy6676
  - equipment_name: Confocal Microscope
    manufacturer_model: Hall-Myers Sort5532
    settings_parameters: "5940 x g, 12\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Hampton Group Once3772
    settings_parameters: "8957 x g, 6\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "7671 x g, 18\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "10684 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with trypsin-edta to facilitate throw.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 30
    replicates: 3
  - step_description: Cells were washed with formaldehyde solution to facilitate remember.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 544
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were transfected with pbs to facilitate military.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 233
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      wife.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    duration_minutes: 36
    temperature_celsius: 21
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
