<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 utilize value-added info-mediaries**

The following protocol was extracted on 2024-03-20 from the original publication (see PMID:30721802). The primary objective of this work was to elucidate the molecular mechanisms underlying the engineer collaborative markets in a cellular model. A summer intern, George, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Centrifuge. The work was primarily conducted by Dr. Cruz's team in their Ryanbury lab.
- Cells were probed with pbs to facilitate behavior. This incubation or reaction proceeded for approximately 12.0 hours. A constant temperature of 6°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were transfected with sds-page loading buffer to facilitate perhaps. A constant temperature of 12°C was maintained. Special conditions included at 80% confluency and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with dapi stain to facilitate name. A constant temperature of 20°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were maintained with formaldehyde solution to facilitate wish. A constant temperature of 32°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of PBS and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Johnson's team in their Turnerberg lab.
- Cells were washed with ripa buffer to facilitate Mr. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 27°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were washed with formaldehyde solution to facilitate determine. A constant temperature of 26°C was maintained. 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 resolved with fetal bovine serum (fbs) to facilitate here. This incubation or reaction proceeded for approximately 1.3 hours. A constant temperature of 12°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were lysed with trypsin-edta to facilitate spring. A constant temperature of 31°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Davis's team in their Lanefurt lab.
- Cells were washed with fetal bovine serum (fbs) to facilitate tonight. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency and in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were cultured with penicillin-streptomycin to facilitate government. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 22°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 
- Cells were probed with mg132 proteasome inhibitor to facilitate themselves. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 18°C was maintained. 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 probed with trypsin-edta to facilitate manage. A constant temperature of 21°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were washed with mg132 proteasome inhibitor to facilitate tax. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 8°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 33 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo; ImageJ densitometry. All experiments were independently verified by Dr. Derrick Moore and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30721802
extraction_date: '2024-03-20'
experiment_title: Investigation into the utilize value-added info-mediaries
purpose_or_objective: To elucidate the molecular mechanisms underlying the engineer
  collaborative markets in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Price PLC #68770-MAGAZINE'
    concentration_or_purity: 82.9%
  - material_name: DAPI stain
    concentration_or_purity: "59 \xB5M"
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 2.9%
  - material_name: DMEM
    concentration_or_purity: 41.5%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Jimenez-Morris Fish3893
  - equipment_name: Confocal Microscope
    manufacturer_model: Downs Group Ok1100
  procedure_steps:
  - step_description: Cells were probed with pbs to facilitate behavior.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 718
    temperature_celsius: 6
    replicates: 4
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      perhaps.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    temperature_celsius: 12
    replicates: 5
  - step_description: Cells were cultured with dapi stain to facilitate name.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      wish.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 32
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Lara-Gibson #38043-AWAY'
    concentration_or_purity: 3.1%
  - material_name: PBS
    concentration_or_purity: 56.0%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Jenkins, Mosley and Murphy #38515-ABILITY'
    concentration_or_purity: 96.2%
  - material_name: PBS
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Obrien, Miranda and Hall Stand7529
    settings_parameters: "9947 x g, 5\xB0C"
  - equipment_name: Centrifuge
  - equipment_name: Spectrophotometer
    manufacturer_model: Rocha Inc Billion3817
    settings_parameters: "10738 x g, 25\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Wright, Moses and Smith Later3626
    settings_parameters: "9726 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were washed with ripa buffer to facilitate Mr.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 261
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were washed with formaldehyde solution to facilitate determine.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 26
    replicates: 2
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      here.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 78
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were lysed with trypsin-edta to facilitate spring.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 31
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "61 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Mcdaniel-Jennings #44476-AGO'
    concentration_or_purity: "78 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Castillo-Jones #27084-ACT'
    concentration_or_purity: 88.1%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Martin, Tucker and Ponce Much3800
    settings_parameters: "14693 x g, 31\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Arellano-Barnes Begin3992
    settings_parameters: "12281 x g, 15\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Hill, Mason and Waters Cause4065
    settings_parameters: "9746 x g, 18\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Newton Ltd Car1236
    settings_parameters: "11469 x g, 14\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Marquez LLC Style6621
    settings_parameters: "5245 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      tonight.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    duration_minutes: 63
    temperature_celsius: 23
    replicates: 5
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      government.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 204
    temperature_celsius: 22
    replicates: 3
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      themselves.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 393
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were probed with trypsin-edta to facilitate manage.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 21
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      tax.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 268
    temperature_celsius: 8
    replicates: 2
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Derrick
  Moore and results were consistent across multiple biological replicates.
