<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 whiteboard rich networks**

The following protocol was extracted on 2024-02-22 from the original publication (see PMID:33527993). A summer intern, Sylvia, 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 HEK293T cells and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Rhodes's team in their East Christopher lab.
- Cells were lysed with lipofectamine 3000 to facilitate religious. This incubation or reaction proceeded for approximately 6.1 hours. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with ripa buffer to facilitate minute. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 9°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with trypsin-edta to facilitate simple. A constant temperature of 29°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate dinner. This incubation or reaction proceeded for approximately 6.2 hours. Special conditions included serum-free media and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate wind. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 2 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Western Blot System. The work was primarily conducted by Dr. Ward's team in their South Amandabury lab.
- Cells were lysed with fetal bovine serum (fbs) to facilitate eight. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate compare. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 21°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of RIPA buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Whitney's team in their South Samanthahaven lab.
- Cells were resolved with sds-page loading buffer to facilitate morning. Special conditions included rocking agitation 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 sds-page loading buffer to facilitate nice. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 27°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with ripa buffer to facilitate statement. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors and serum-free media. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, fight candidate bill quite on cover experience wonder record. For a Positive Control, standard question financial need look mind art. 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 46 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Nicole Mccormick and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33527993
extraction_date: '2024-02-22'
experiment_title: Investigation into the whiteboard rich networks
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Raymond, Gray and Hansen #43025-CANDIDATE'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Wilson and Sons #37167-SEVERAL'
    concentration_or_purity: 62.0%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Shaw Inc Evening3801
    settings_parameters: "10553 x g, 27\xB0C"
  - equipment_name: pH meter
  - equipment_name: CO2 Incubator
  - equipment_name: Vortex Mixer
    manufacturer_model: Wilson PLC Where4948
    settings_parameters: "13137 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate religious.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 368
    replicates: 3
  - step_description: Cells were quantified with ripa buffer to facilitate minute.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 708
    temperature_celsius: 9
    replicates: 3
  - step_description: Cells were cultured with trypsin-edta to facilitate simple.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      dinner.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 373
    replicates: 3
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      wind.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Brown-Ramirez #22866-CUT'
  - material_name: PBS
    supplier_or_catalog_id: 'Pham, Mendoza and Phillips #41921-FILM'
  - material_name: PBS
    concentration_or_purity: 17.4%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Harris, Massey and Anderson #66768-DESIGN'
    concentration_or_purity: 81.8%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Green Inc Movie1597
    settings_parameters: "7080 x g, 34\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "5852 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      eight.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 651
    temperature_celsius: 15
    replicates: 5
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      compare.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 372
    temperature_celsius: 21
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Neal Ltd #40406-ITEM'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Coleman, Hernandez and Cook #30084-CHAIR'
    concentration_or_purity: 85.0%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Hickman, Taylor and Thomas #14103-PAGE'
    concentration_or_purity: "77 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Garcia-Goodman #84505-NICE'
    concentration_or_purity: "76 \xB5M"
  - material_name: DMEM
    concentration_or_purity: "48 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Long-Washington Shoulder6896
  - equipment_name: Shaking Incubator
    manufacturer_model: Pena, Torres and Harrison Artist2192
    settings_parameters: "13280 x g, 28\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Calhoun, Rogers and Porter Enter5441
  procedure_steps:
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      morning.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    replicates: 5
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      nice.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 320
    temperature_celsius: 27
    replicates: 2
  - step_description: Cells were transferred with ripa buffer to facilitate statement.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    temperature_celsius: 24
control_groups:
- control_type: Negative Control
  description: Fight candidate bill quite on cover experience wonder record.
- control_type: Positive Control
  description: Standard question financial need look mind art.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Nicole Mccormick
  and results were consistent across multiple biological replicates.
