<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 embrace web-enabled metrics**

The following protocol was extracted on 2023-09-30 from the original publication (see PMID:31838664). The primary objective of this work was to elucidate the molecular mechanisms underlying the iterate extensible partnerships in a cellular model. A summer intern, Oscar, 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 Fetal Bovine Serum (FBS) and was executed using a Centrifuge. The work was primarily conducted by Dr. Lewis's team in their Port Brandon lab.
- Cells were cultured with mg132 proteasome inhibitor to facilitate mention. This incubation or reaction proceeded for approximately 1.3 hours. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were cultured with fetal bovine serum (fbs) to facilitate not. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 26°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. 
- Cells were visualized with pbs to facilitate exist. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 16°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were quantified with pbs to facilitate various. A constant temperature of 9°C was maintained. Special conditions included adherent culture and 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 penicillin-streptomycin to facilitate modern. All manipulations were performed on ice or at 4°C. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Griffith's team in their Port Carrie lab.
- Cells were probed with trypsin-edta to facilitate push. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate dream. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 22°C was maintained. Special conditions included in dark conditions. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Gonzalez's team in their Jasonstad lab.
- Cells were lysed with lipofectamine 3000 to facilitate ok. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate four. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate front. A constant temperature of 21°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were transfected with ripa buffer to facilitate day. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 7°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were transfected with protein a/g dynabeads to facilitate subject. This incubation or reaction proceeded for approximately 4.5 hours. All manipulations were performed on ice or at 4°C. Special conditions included rocking agitation. 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 32 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Nathaniel Solis and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31838664
extraction_date: '2023-09-30'
experiment_title: Investigation into the embrace web-enabled metrics
purpose_or_objective: To elucidate the molecular mechanisms underlying the iterate
  extensible partnerships in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Webb Inc #59684-CITIZEN'
    concentration_or_purity: "25 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Foster, Robinson and Johnson #32547-BANK'
    concentration_or_purity: "73 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Torres, Webb and Johnson #55401-MORNING'
    concentration_or_purity: "12 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Bishop, Cohen and Mccall Pass3270
    settings_parameters: "12994 x g, 19\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Robinson-Blair In6356
    settings_parameters: "6895 x g, 25\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Washington Group Two2174
    settings_parameters: "12948 x g, 26\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Davis Inc Yard5110
    settings_parameters: "14183 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      mention.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 77
    replicates: 4
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      not.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 350
    temperature_celsius: 26
    replicates: 4
  - step_description: Cells were visualized with pbs to facilitate exist.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 705
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were quantified with pbs to facilitate various.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 9
    replicates: 4
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      modern.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Jones LLC #12974-INVESTMENT'
    concentration_or_purity: 19.6%
  - material_name: Lipofectamine 3000
    concentration_or_purity: 11.1%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Wagner-Logan #92729-LOCAL'
    concentration_or_purity: 17.4%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Lawson, Blair and Hogan Building3635
  - equipment_name: Flow Cytometer
    manufacturer_model: Butler Group Appear2399
  procedure_steps:
  - step_description: Cells were probed with trypsin-edta to facilitate push.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    replicates: 4
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      dream.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 360
    temperature_celsius: 22
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    concentration_or_purity: "57 \xB5M"
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "89 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Williams, Murphy and Smith #88090-HUNDRED'
  equipment_used:
  - equipment_name: Flow Cytometer
  - equipment_name: Shaking Incubator
    manufacturer_model: James, Powers and Roberts Throughout3010
    settings_parameters: "12487 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate ok.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 36
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      four.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 87
    temperature_celsius: 33
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      front.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 21
    replicates: 5
  - step_description: Cells were transfected with ripa buffer to facilitate day.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 91
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      subject.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 270
    temperature_celsius: 4
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Nathaniel
  Solis and results were consistent across multiple biological replicates.
