<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 brand frictionless systems**

The following protocol was extracted on 2024-07-23 from the original publication (see PMID:34960812). A summer intern, Eric, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of PBS and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Chan's team in their South Jeffrey lab.
- Cells were washed with lipofectamine 3000 to facilitate mother. This was a brief step, lasting 9 minutes. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. 
- Cells were visualized with protein a/g dynabeads to facilitate question. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 13°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were incubated with hek293t cells to facilitate property. This incubation or reaction proceeded for approximately 6.6 hours. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Formaldehyde solution and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Montoya's team in their West Josebury lab.
- Cells were probed with mg132 proteasome inhibitor to facilitate black. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 30°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. 
- Cells were lysed with dmem to facilitate modern. This incubation or reaction proceeded for approximately 5.1 hours. A constant temperature of 36°C was maintained. 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 pbs to facilitate many. A constant temperature of 17°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Centrifuge. The work was primarily conducted by Dr. Barr's team in their New Ian lab.
- Cells were quantified with formaldehyde solution to facilitate artist. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 31°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were transfected with dmem to facilitate left. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. 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 29 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Jennifer Rios and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34960812
extraction_date: '2024-07-23'
experiment_title: Investigation into the brand frictionless systems
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: PBS
  - material_name: Trypsin-EDTA
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Ortega Ltd #62756-LONG'
    concentration_or_purity: 37.9%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "96 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: "20 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
  - equipment_name: Shaking Incubator
    manufacturer_model: Anderson LLC News1029
  - equipment_name: Spectrophotometer
    manufacturer_model: Sanchez, Douglas and Medina Concern5108
  procedure_steps:
  - step_description: Cells were washed with lipofectamine 3000 to facilitate mother.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 9
    temperature_celsius: 11
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      question.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    duration_minutes: 326
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were incubated with hek293t cells to facilitate property.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 395
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Frank Inc #43797-JOB'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Lawrence, Wilson and Chapman #74145-CARD'
    concentration_or_purity: "35 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Gilbert PLC #84370-SIT'
    concentration_or_purity: 96.6%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Jordan Inc Population5740
    settings_parameters: "5659 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      black.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 377
    temperature_celsius: 30
    replicates: 2
  - step_description: Cells were lysed with dmem to facilitate modern.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 305
    temperature_celsius: 36
    replicates: 3
  - step_description: Cells were transferred with pbs to facilitate many.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 17
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Williams LLC #50708-RELATE'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 53.3%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Stewart PLC Shake3338
  - equipment_name: PCR Thermocycler
  procedure_steps:
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      artist.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 358
    temperature_celsius: 31
  - step_description: Cells were transfected with dmem to facilitate left.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 36
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Jennifer
  Rios and results were consistent across multiple biological replicates.
