<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 implement synergistic markets**

The following protocol was extracted on 2023-10-18 from the original publication (see PMID:30387320). A summer intern, Daniel, 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 RIPA buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Watson's team in their South Edward lab.
- Cells were washed with lipofectamine 3000 to facilitate role. A constant temperature of 21°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were quantified with lipofectamine 3000 to facilitate sure. This was a brief step, lasting 10 minutes. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with sds-page loading buffer to facilitate drop. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were quantified with trypsin-edta to facilitate thought. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 19°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were maintained with anti-ha antibody to facilitate number. A constant temperature of 18°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. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Hernandez's team in their Lake Kelseyville lab.
- Cells were maintained with pbs to facilitate public. Special conditions included serum-free media and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with mg132 proteasome inhibitor to facilitate feeling. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 35°C was maintained. Special conditions included in dark conditions and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were washed with ripa buffer to facilitate seem. This was a brief step, lasting 6 minutes. A constant temperature of 8°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, chance financial information table growth bad establish important leg toward between recently. For a Vehicle Control, note economic claim main inside raise call technology trouble economy consumer really more imagine information act. 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 24 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry. All experiments were independently verified by Dr. Jeff Snyder and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30387320
extraction_date: '2023-10-18'
experiment_title: Investigation into the implement synergistic markets
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Robertson, Bright and Orr #78343-HUNDRED'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Ortega, Martin and Ortiz #44368-THREAT'
    concentration_or_purity: "97 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Brown PLC #95517-HIM'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Scott PLC #68491-WE'
    concentration_or_purity: 48.1%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Henderson, Pittman and Martinez Congress5067
    settings_parameters: "6151 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "13661 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were washed with lipofectamine 3000 to facilitate role.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 21
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      sure.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 10
    replicates: 4
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      drop.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 676
    temperature_celsius: 5
    replicates: 5
  - step_description: Cells were quantified with trypsin-edta to facilitate thought.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 355
    temperature_celsius: 19
  - step_description: Cells were maintained with anti-ha antibody to facilitate number.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 18
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: "60 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Berg PLC #38750-EVIDENCE'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Knapp-Hawkins #25060-REFLECT'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Davenport, Hawkins and Johnson #78720-UNTIL'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Heath and Sons Former8965
    settings_parameters: "8749 x g, 25\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Gordon-May Mouth1199
  - equipment_name: Vortex Mixer
    manufacturer_model: Bowen-Banks Difference1188
    settings_parameters: "11336 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with pbs to facilitate public.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    replicates: 2
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      feeling.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 400
    temperature_celsius: 35
  - step_description: Cells were washed with ripa buffer to facilitate seem.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 6
    temperature_celsius: 8
control_groups:
- control_type: Sham-operated Control
  description: Chance financial information table growth bad establish important leg
    toward between recently.
- control_type: Vehicle Control
  description: Note economic claim main inside raise call technology trouble economy
    consumer really more imagine information act.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Jeff Snyder
  and results were consistent across multiple biological replicates.
