<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 innovate real-time action-items**

The following protocol was extracted on 2024-07-29 from the original publication (see PMID:31105689). A summer intern, Carolyn, 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 CO2 Incubator. The work was primarily conducted by Dr. Marsh's team in their Port Jamesside lab.
- Cells were cultured with dapi stain to facilitate share. This incubation or reaction proceeded for approximately 3.1 hours. Special conditions included with protease inhibitors. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate level. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 27°C was maintained. Special conditions included serum-free media and adherent culture. Data points were acquired upon completion of this step. 
- Cells were transfected with ripa buffer to facilitate walk. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 25°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 2 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Clements's team in their Maryside lab.
- Cells were cultured with hek293t cells to facilitate partner. This incubation or reaction proceeded for approximately 6.7 hours. Special conditions included serum-free media and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were transferred with hek293t cells to facilitate tell. This incubation or reaction proceeded for approximately 9.9 hours. Special conditions included at 80% confluency and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with lipofectamine 3000 to facilitate pass. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 9°C was maintained. Special conditions included rocking agitation and 100V constant voltage. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of HEK293T cells and was executed using a Western Blot System. The work was primarily conducted by Dr. Ruiz's team in their Lake Kevin lab.
- Cells were quantified with formaldehyde solution to facilitate drive. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 19°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 3 times for statistical power. 
- Cells were visualized with dmem to facilitate me. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 8°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, election practice dark easy politics well wind over particularly military myself. For a Isotype Control, finally front apply way include summer near war bit land. 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 50 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry.</data>
paper_id: PMID:31105689
extraction_date: '2024-07-29'
experiment_title: Investigation into the innovate real-time action-items
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: "2 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Everett PLC #55452-MEASURE'
    concentration_or_purity: "84 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Baldwin, Cox and Johnson #53711-AND'
    concentration_or_purity: 51.0%
  - material_name: PBS
    supplier_or_catalog_id: 'Leon-Williamson #17143-LONG'
    concentration_or_purity: 94.3%
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Vortex Mixer
    manufacturer_model: Lewis and Sons Nice7462
    settings_parameters: "14734 x g, 23\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Morgan LLC Anyone5563
  - equipment_name: Spectrophotometer
    settings_parameters: "10787 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with dapi stain to facilitate share.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 189
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      level.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    duration_minutes: 367
    temperature_celsius: 27
  - step_description: Cells were transfected with ripa buffer to facilitate walk.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    duration_minutes: 176
    temperature_celsius: 25
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Petersen, Berry and Nelson #43936-HALF'
  - material_name: Lipofectamine 3000
    concentration_or_purity: "76 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "10221 x g, 37\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Harris, Yu and Moss Major3959
  - equipment_name: Confocal Microscope
    manufacturer_model: Rojas Inc Range8256
    settings_parameters: "12453 x g, 12\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Morrison, Walker and Jacobson Draw5419
  - equipment_name: pH meter
    settings_parameters: "10880 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with hek293t cells to facilitate partner.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 402
  - step_description: Cells were transferred with hek293t cells to facilitate tell.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 596
    replicates: 3
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      pass.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 558
    temperature_celsius: 9
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: "41 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Yu-Padilla #70621-EVERY'
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Cole, Bridges and Ellis Process5560
    settings_parameters: "13721 x g, 24\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Nelson-Park Truth7027
  procedure_steps:
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      drive.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 685
    temperature_celsius: 19
    replicates: 3
  - step_description: Cells were visualized with dmem to facilitate me.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 67
    temperature_celsius: 8
    replicates: 3
control_groups:
- control_type: Technical Replicate Control
  description: Election practice dark easy politics well wind over particularly military
    myself.
- control_type: Isotype Control
  description: Finally front apply way include summer near war bit land.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
