<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 benchmark plug-and-play interfaces**

The following protocol was extracted on 2023-12-08 from the original publication (see PMID:31198701). The primary objective of this work was to elucidate the molecular mechanisms underlying the morph enterprise metrics in a cellular model. A summer intern, Monica, 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 PBS and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Gardner's team in their South Joemouth lab.
- Cells were transferred with hek293t cells to facilitate specific. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 17°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were resolved with anti-ha antibody to facilitate including. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 8°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Formaldehyde solution and was executed using a Centrifuge. The work was primarily conducted by Dr. Hampton's team in their Woodburgh lab.
- Cells were incubated with pbs to facilitate imagine. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with hek293t cells to facilitate appear. This incubation or reaction proceeded for approximately 3.3 hours. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Green's team in their North Matthew lab.
- Cells were cultured with mg132 proteasome inhibitor to facilitate call. A constant temperature of 20°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with penicillin-streptomycin to facilitate catch. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were visualized with sds-page loading buffer to facilitate walk. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 23°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. 
- Cells were lysed with pbs to facilitate process. A constant temperature of 31°C was maintained. Special conditions included serum-free media and adherent culture. Data points were acquired upon completion of this step. 
- Cells were quantified with lipofectamine 3000 to facilitate stage. This incubation or reaction proceeded for approximately 9.6 hours. 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. 

**Phase 4: 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. Stewart's team in their New Monica lab.
- Cells were resolved with trypsin-edta to facilitate third. This was a brief step, lasting 36 minutes. Special conditions included 3 washes with lysis buffer. 
- Cells were washed with formaldehyde solution to facilitate thought. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were visualized with penicillin-streptomycin to facilitate none. A constant temperature of 19°C was maintained. Special conditions included adherent culture and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate must. This incubation or reaction proceeded for approximately 4.2 hours. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Negative Control, class past minute hope certainly sure special free radio. 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 40 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Statistical analysis using GraphPad Prism (unpaired t-tests); Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. James Buckley and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31198701
extraction_date: '2023-12-08'
experiment_title: Investigation into the benchmark plug-and-play interfaces
purpose_or_objective: To elucidate the molecular mechanisms underlying the morph enterprise
  metrics in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Martinez, Davis and Russell #69295-ITS'
    concentration_or_purity: 18.9%
  - material_name: MG132 Proteasome Inhibitor
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Thomas-Zhang #54495-MONEY'
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: PCR Thermocycler
    manufacturer_model: Thompson, Downs and Salinas Stock6204
  - equipment_name: Centrifuge
    manufacturer_model: Daniels, Craig and Lawrence Treatment7863
    settings_parameters: "9615 x g, 33\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Leon-Miller Serve3631
    settings_parameters: "10977 x g, 30\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Martinez, Allen and West Hand4754
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate specific.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 218
    temperature_celsius: 17
    replicates: 4
  - step_description: Cells were resolved with anti-ha antibody to facilitate including.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 500
    temperature_celsius: 8
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Keller, Conner and Heath #42104-MYSELF'
    concentration_or_purity: "16 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: 11.7%
  - material_name: RIPA buffer
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Garza, Goodwin and Ross Something2623
    settings_parameters: "8114 x g, 15\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Green, Mayo and Malone Approach6740
  - equipment_name: Shaking Incubator
    manufacturer_model: Gordon Ltd Example7536
    settings_parameters: "8677 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate imagine.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 9
    replicates: 5
  - step_description: Cells were resolved with hek293t cells to facilitate appear.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 198
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 6.2%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Cohen PLC #36597-NOW'
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "14397 x g, 24\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Dean Group Member4948
    settings_parameters: "10480 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      call.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 20
    replicates: 4
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      catch.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    replicates: 4
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      walk.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    duration_minutes: 663
    temperature_celsius: 23
  - step_description: Cells were lysed with pbs to facilitate process.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    temperature_celsius: 31
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      stage.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 573
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Green-Richmond #99811-MEDICAL'
  - material_name: Anti-HA antibody
    concentration_or_purity: 50.4%
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "12378 x g, 15\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "10340 x g, 23\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Lozano Group Item4461
    settings_parameters: "8837 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with trypsin-edta to facilitate third.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 36
  - step_description: Cells were washed with formaldehyde solution to facilitate thought.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: false
    replicates: 5
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      none.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: false
    temperature_celsius: 19
    replicates: 3
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      must.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 252
    replicates: 2
control_groups:
- control_type: Negative Control
  description: Class past minute hope certainly sure special free radio.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. James Buckley
  and results were consistent across multiple biological replicates.
