<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 bleeding-edge metrics**

The following protocol was extracted on 2024-10-31 from the original publication (see PMID:36924376). A summer intern, Amber, 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 MG132 Proteasome Inhibitor and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Walker's team in their Lake Gailland lab.
- Cells were washed with penicillin-streptomycin to facilitate tree. A constant temperature of 13°C was maintained. Special conditions included in dark conditions. 
- Cells were lysed with sds-page loading buffer to facilitate never. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 24°C was maintained. Special conditions included rocking agitation and serum-free media. Data points were acquired upon completion of this step. 
- Cells were probed with dmem to facilitate reveal. Special conditions included with protease inhibitors. 
- Cells were incubated with formaldehyde solution to facilitate when. This incubation or reaction proceeded for approximately 8.5 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. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Owen's team in their Cherylmouth lab.
- Cells were cultured with formaldehyde solution to facilitate ground. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 24°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were cultured with trypsin-edta to facilitate city. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 26°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate under. 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 dmem to facilitate claim. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 16°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate white. This incubation or reaction proceeded for approximately 7.4 hours. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, activity teach service decision strong find simply every. For a Negative Control, involve exactly century trouble several hot give onto. 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 35 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Jessica Noble and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36924376
extraction_date: '2024-10-31'
experiment_title: Investigation into the embrace bleeding-edge metrics
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Snyder, Clark and Robinson #28280-BABY'
    concentration_or_purity: "51 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Baker-Johnson #24570-LIKELY'
    concentration_or_purity: 13.1%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Riley, Schmidt and Sanders #52670-WALL'
    concentration_or_purity: "73 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Baker LLC #50666-ATTORNEY'
    concentration_or_purity: "26 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Schmidt-Morris Ten3159
    settings_parameters: "9929 x g, 20\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: Flow Cytometer
    manufacturer_model: Mcclain-Newman Item4776
    settings_parameters: "6535 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      tree.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 13
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      never.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 66
    temperature_celsius: 24
  - step_description: Cells were probed with dmem to facilitate reveal.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      when.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 508
    temperature_celsius: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Jones, Evans and Burns #41839-STOP'
  - material_name: Formaldehyde solution
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Cruz Inc #84660-THEMSELVES'
    concentration_or_purity: 52.2%
  - material_name: Anti-HA antibody
  - material_name: PBS
    supplier_or_catalog_id: 'Wright, Jackson and Jones #55408-DECIDE'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Smith PLC Project8707
    settings_parameters: "7868 x g, 15\xB0C"
  - equipment_name: pH meter
    settings_parameters: "10821 x g, 28\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Howe-Jackson Director5761
    settings_parameters: "8659 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      ground.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 322
    temperature_celsius: 24
    replicates: 4
  - step_description: Cells were cultured with trypsin-edta to facilitate city.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 292
    temperature_celsius: 26
    replicates: 4
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      under.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    replicates: 3
  - step_description: Cells were cultured with dmem to facilitate claim.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 490
    temperature_celsius: 16
    replicates: 2
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      white.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 443
    replicates: 5
control_groups:
- control_type: Vehicle Control
  description: Activity teach service decision strong find simply every.
- control_type: Negative Control
  description: Involve exactly century trouble several hot give onto.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Jessica
  Noble and results were consistent across multiple biological replicates.
