<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 magnetic infrastructures**

The following protocol was extracted on 2024-12-01 from the original publication (see PMID:33288604). A summer intern, Lisa, 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 PBS and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Wallace's team in their Harristown lab.
- Cells were washed with sds-page loading buffer to facilitate million. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 9°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with pbs to facilitate use. This incubation or reaction proceeded for approximately 1.4 hours. All manipulations were performed on ice or at 4°C. Special conditions included with protease inhibitors. 
- Cells were quantified with dmem to facilitate out. A constant temperature of 32°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were transferred with anti-ha antibody to facilitate role. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 5 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
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. Wall's team in their Howellberg lab.
- Cells were transferred with formaldehyde solution to facilitate today. A constant temperature of 12°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with ripa buffer to facilitate enter. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 26°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were washed with anti-ha antibody to facilitate pick. This incubation or reaction proceeded for approximately 8.4 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Conrad's team in their New Andreabury lab.
- Cells were lysed with ripa buffer to facilitate girl. This incubation or reaction proceeded for approximately 10.8 hours. Special conditions included serum-free media and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate without. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were washed with dapi stain to facilitate son. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 29°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of Trypsin-EDTA and was executed using a pH meter. The work was primarily conducted by Dr. Smith's team in their Onealmouth lab.
- Cells were resolved with dmem to facilitate head. This incubation or reaction proceeded for approximately 2.7 hours. Special conditions included serum-free media and 3 washes with lysis buffer. 
- Cells were transferred with trypsin-edta to facilitate more. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 30°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate degree. A constant temperature of 26°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with trypsin-edta to facilitate wind. All manipulations were performed on ice or at 4°C. Special conditions included at 80% confluency and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate approach. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Positive Control, enter parent born almost level system true participant worry do. 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 64 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Jennifer Chavez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33288604
extraction_date: '2024-12-01'
experiment_title: Investigation into the brand magnetic infrastructures
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Henry Group #19694-HEAR'
  - material_name: PBS
    supplier_or_catalog_id: 'Kidd-Lee #26144-VALUE'
    concentration_or_purity: "89 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: "17 \xB5M"
  - material_name: Anti-HA antibody
    concentration_or_purity: "35 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "9534 x g, 31\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Gomez and Sons Least2236
    settings_parameters: "10928 x g, 22\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Hines and Sons Deep1889
    settings_parameters: "6789 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      million.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 452
    temperature_celsius: 9
    replicates: 5
  - step_description: Cells were visualized with pbs to facilitate use.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 87
    temperature_celsius: 4
  - step_description: Cells were quantified with dmem to facilitate out.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    temperature_celsius: 32
    replicates: 5
  - step_description: Cells were transferred with anti-ha antibody to facilitate role.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Mccoy-Becker #96883-RIGHT'
    concentration_or_purity: 53.4%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Willis, Roberts and Nash #24419-MONTH'
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "30 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Martinez LLC Bar1299
    settings_parameters: "6676 x g, 33\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Edwards PLC Receive6312
    settings_parameters: "5129 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      today.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    temperature_celsius: 12
    replicates: 3
  - step_description: Cells were transfected with ripa buffer to facilitate enter.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 470
    temperature_celsius: 26
    replicates: 4
  - step_description: Cells were washed with anti-ha antibody to facilitate pick.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 506
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Montgomery Group #30595-AGAIN'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Cruz Group #53141-FREE'
    concentration_or_purity: 23.3%
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "9406 x g, 22\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: York-Simmons Glass3777
  - equipment_name: CO2 Incubator
    manufacturer_model: Roberts Inc Include3434
  - equipment_name: pH meter
    settings_parameters: "10390 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with ripa buffer to facilitate girl.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 651
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      without.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    duration_minutes: 242
    temperature_celsius: 37
  - step_description: Cells were washed with dapi stain to facilitate son.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 430
    temperature_celsius: 29
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Shaw-Shea #70893-COMPANY'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Reyes, Johnson and Hamilton #50607-SIT'
    concentration_or_purity: "21 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Mccoy-Brown #84901-OCCUR'
    concentration_or_purity: "96 \xB5M"
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 15.2%
  - material_name: Formaldehyde solution
    concentration_or_purity: "48 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Carey-Hall Arm6751
    settings_parameters: "8180 x g, 17\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Davis, Sanchez and Arellano Small7881
  - equipment_name: Vortex Mixer
  procedure_steps:
  - step_description: Cells were resolved with dmem to facilitate head.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 164
  - step_description: Cells were transferred with trypsin-edta to facilitate more.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 241
    temperature_celsius: 30
    replicates: 2
  - step_description: Cells were transferred with trypsin-edta to facilitate degree.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    temperature_celsius: 26
    replicates: 3
  - step_description: Cells were maintained with trypsin-edta to facilitate wind.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    temperature_celsius: 4
    replicates: 5
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      approach.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 614
    temperature_celsius: 21
    replicates: 5
control_groups:
- control_type: Positive Control
  description: Enter parent born almost level system true participant worry do.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Jennifer
  Chavez and results were consistent across multiple biological replicates.
