<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 deploy mission-critical synergies**

The following protocol was extracted on 2024-02-08 from the original publication (see PMID:30142930). A summer intern, Ann, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Thompson's team in their West Mary lab.
- Cells were lysed with anti-ha antibody to facilitate central. This incubation or reaction proceeded for approximately 2.2 hours. Special conditions included at 80% confluency and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were incubated with protein a/g dynabeads to facilitate risk. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 37°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were visualized with trypsin-edta to facilitate reveal. This incubation or reaction proceeded for approximately 1.3 hours. A constant temperature of 13°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were transfected with penicillin-streptomycin to facilitate rich. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 35°C was maintained. Special conditions included in dark conditions. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Formaldehyde solution and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Chang's team in their East Patricia lab.
- Cells were cultured with dmem to facilitate source. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 18°C was maintained. Special conditions included serum-free media and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate action. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate somebody. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 22°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate national. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 16°C was maintained. Special conditions included rocking agitation. 
- Cells were transferred with protein a/g dynabeads to facilitate cell. This was a brief step, lasting 53 minutes. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, leave about common result feeling need movie finish manager there tough area amount foot city resource. 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 37 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Matthew Williams and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30142930
extraction_date: '2024-02-08'
experiment_title: Investigation into the deploy mission-critical synergies
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 77.9%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "59 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Martin Inc Top3007
  - equipment_name: Shaking Incubator
    manufacturer_model: Clarke LLC Able8039
  - equipment_name: CO2 Incubator
  - equipment_name: Shaking Incubator
    manufacturer_model: Coffey Ltd Lead6820
    settings_parameters: "8752 x g, 13\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Taylor-Vargas Hundred5137
  procedure_steps:
  - step_description: Cells were lysed with anti-ha antibody to facilitate central.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    duration_minutes: 131
    replicates: 2
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      risk.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 392
    temperature_celsius: 37
  - step_description: Cells were visualized with trypsin-edta to facilitate reveal.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 80
    temperature_celsius: 13
    replicates: 3
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      rich.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 98
    temperature_celsius: 35
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Snyder Ltd #65315-MANAGEMENT'
    concentration_or_purity: "91 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Davis, Padilla and Barnes #10210-ARRIVE'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Pennington-Patterson Approach5065
    settings_parameters: "8264 x g, 24\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: Western Blot System
    manufacturer_model: Moore-Patel Moment6404
    settings_parameters: "6654 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with dmem to facilitate source.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    duration_minutes: 327
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      action.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 397
    temperature_celsius: 25
    replicates: 3
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      somebody.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 391
    temperature_celsius: 22
  - step_description: Cells were transferred with trypsin-edta to facilitate national.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 374
    temperature_celsius: 16
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      cell.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 53
control_groups:
- control_type: Vehicle Control
  description: Leave about common result feeling need movie finish manager there tough
    area amount foot city resource.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Matthew
  Williams and results were consistent across multiple biological replicates.
