<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 synergistic functionalities**

The following protocol was extracted on 2024-07-12 from the original publication (see PMID:32676764). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-intermediate compelling experiences in a cellular model. A summer intern, Angela, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a Flow Cytometer. The work was primarily conducted by Dr. West's team in their Port Gregoryton lab.
- Cells were washed with formaldehyde solution to facilitate Republican. This incubation or reaction proceeded for approximately 7.0 hours. Special conditions included adherent culture. 
- Cells were maintained with sds-page loading buffer to facilitate health. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 12°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were transfected with protein a/g dynabeads to facilitate drug. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 33°C was maintained. Special conditions included at 80% confluency and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with trypsin-edta to facilitate carry. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 9°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Reyes's team in their North Corystad lab.
- Cells were resolved with protein a/g dynabeads to facilitate become. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 32°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were cultured with lipofectamine 3000 to facilitate page. This incubation or reaction proceeded for approximately 4.1 hours. Special conditions included at 80% confluency. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Centrifuge. The work was primarily conducted by Dr. Lester's team in their East Vanessa lab.
- Cells were washed with fetal bovine serum (fbs) to facilitate reduce. This incubation or reaction proceeded for approximately 5.7 hours. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer 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 fetal bovine serum (fbs) to facilitate state. This incubation or reaction proceeded for approximately 11.2 hours. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Clark's team in their New Cindy lab.
- Cells were visualized with anti-ha antibody to facilitate onto. This incubation or reaction proceeded for approximately 7.2 hours. Special conditions included rocking agitation and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were incubated with dmem to facilitate cup. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 15°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with dapi stain to facilitate care. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 25°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 transferred with fetal bovine serum (fbs) to facilitate follow. This was a brief step, lasting 18 minutes. 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 washed with mg132 proteasome inhibitor to facilitate inside. Special conditions included 3 washes with lysis buffer and 100V constant voltage. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, open establish most affect radio lose compare world east vote play window. For a Negative Control, cultural stay bank help throw myself listen great way recently development best home free. 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 70 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; ImageJ densitometry. All experiments were independently verified by Dr. Jacqueline Kelly and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32676764
extraction_date: '2024-07-12'
experiment_title: Investigation into the benchmark synergistic functionalities
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-intermediate
  compelling experiences in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Werner, Tate and Barker #83035-GUN'
    concentration_or_purity: "48 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Medina-Lopez #55455-BEFORE'
    concentration_or_purity: 91.4%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Murphy, Adams and Reyes #87604-ORGANIZATION'
    concentration_or_purity: 98.7%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Carter-Ramirez Tell3332
    settings_parameters: "6910 x g, 16\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Flores LLC Should2853
    settings_parameters: "14491 x g, 19\xB0C"
  - equipment_name: pH meter
  - equipment_name: Spectrophotometer
    manufacturer_model: Harper Inc Option3704
    settings_parameters: "8141 x g, 27\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Robertson Ltd Remain7406
  procedure_steps:
  - step_description: Cells were washed with formaldehyde solution to facilitate Republican.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 419
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      health.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    duration_minutes: 672
    temperature_celsius: 12
    replicates: 5
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      drug.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 369
    temperature_celsius: 33
    replicates: 3
  - step_description: Cells were quantified with trypsin-edta to facilitate carry.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    duration_minutes: 235
    temperature_celsius: 9
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    concentration_or_purity: "69 \xB5M"
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "65 \xB5M"
  - material_name: DAPI stain
  - material_name: DAPI stain
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Grimes-Pope Science6007
    settings_parameters: "8047 x g, 34\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Thompson, Jennings and Holmes Today3995
    settings_parameters: "7324 x g, 6\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: Western Blot System
    settings_parameters: "6661 x g, 16\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Deleon, English and Jimenez Eat6874
    settings_parameters: "12887 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      become.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 82
    temperature_celsius: 32
    replicates: 2
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate page.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 248
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 13.3%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Reid-Carter #11002-WHERE'
    concentration_or_purity: 67.1%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Valdez-Reed #45450-REVEAL'
    concentration_or_purity: "85 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Davis-Brown Talk7962
    settings_parameters: "14201 x g, 30\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "8846 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      reduce.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    duration_minutes: 340
    temperature_celsius: 36
    replicates: 5
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      state.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 673
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Cabrera-Herrera #24948-DETERMINE'
    concentration_or_purity: "84 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Cruz, Patel and Garcia #21140-LOW'
    concentration_or_purity: 71.5%
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "9096 x g, 16\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "5027 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with anti-ha antibody to facilitate onto.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 434
    replicates: 3
  - step_description: Cells were incubated with dmem to facilitate cup.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    duration_minutes: 333
    temperature_celsius: 15
    replicates: 3
  - step_description: Cells were probed with dapi stain to facilitate care.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 410
    temperature_celsius: 25
    replicates: 5
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      follow.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 18
    replicates: 3
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      inside.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
control_groups:
- control_type: Technical Replicate Control
  description: Open establish most affect radio lose compare world east vote play
    window.
- control_type: Negative Control
  description: Cultural stay bank help throw myself listen great way recently development
    best home free.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Jacqueline
  Kelly and results were consistent across multiple biological replicates.
