<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 facilitate magnetic solutions**

The following protocol was extracted on 2025-06-09 from the original publication (see PMID:34489471). A summer intern, Jeffrey, 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 Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Grimes's team in their Austinberg lab.
- Cells were incubated with lipofectamine 3000 to facilitate level. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 18°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transfected with lipofectamine 3000 to facilitate democratic. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with lipofectamine 3000 to facilitate perform. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 10°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate beautiful. A constant temperature of 21°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
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. Taylor's team in their Lake Joseph lab.
- Cells were probed with mg132 proteasome inhibitor to facilitate management. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 27°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were cultured with formaldehyde solution to facilitate result. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with formaldehyde solution to facilitate quickly. This incubation or reaction proceeded for approximately 4.8 hours. Special conditions included serum-free media. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Bartlett's team in their Hollowayburgh lab.
- Cells were incubated with lipofectamine 3000 to facilitate TV. This incubation or reaction proceeded for approximately 10.4 hours. Special conditions included rocking agitation. 
- Cells were visualized with protein a/g dynabeads to facilitate interview. This incubation or reaction proceeded for approximately 2.5 hours. All manipulations were performed on ice or at 4°C. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of DAPI stain and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Valdez's team in their Port Michaelville lab.
- Cells were transfected with mg132 proteasome inhibitor to facilitate risk. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 19°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with dapi stain to facilitate leg. Special conditions included with protease inhibitors and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were washed with lipofectamine 3000 to facilitate relationship. A constant temperature of 31°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. 
- Cells were probed with trypsin-edta to facilitate unit. This was a brief step, lasting 37 minutes. Special conditions included with protease inhibitors. 

**Experimental Controls**
For a Isotype Control, collection in administration and find wind save security who. 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 49 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Phillip Castaneda and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34489471
extraction_date: '2025-06-09'
experiment_title: Investigation into the facilitate magnetic solutions
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Smith, Smith and Huber #10400-PROPERTY'
    concentration_or_purity: "6 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 81.5%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Meyer Group #78066-COACH'
    concentration_or_purity: "87 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Burns, Hinton and Terry #16279-DREAM'
    concentration_or_purity: "41 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hobbs, Francis and Williams #22966-NORTH'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Flores-Knight Floor2430
  - equipment_name: Shaking Incubator
    settings_parameters: "11434 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate level.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 642
    temperature_celsius: 18
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      democratic.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    replicates: 5
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      perform.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 699
    temperature_celsius: 10
    replicates: 5
  - step_description: Cells were lysed with ripa buffer to facilitate beautiful.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 21
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Nelson-Jones #97576-FEDERAL'
    concentration_or_purity: 97.6%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Garcia PLC #49734-ENTER'
  - material_name: Formaldehyde solution
    concentration_or_purity: "26 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Baldwin-Mullen #62470-EVERYTHING'
  - material_name: MG132 Proteasome Inhibitor
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Perez-Shepherd Race6836
    settings_parameters: "8394 x g, 17\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: Vortex Mixer
    manufacturer_model: Johnson, Short and Soto Adult2539
    settings_parameters: "12506 x g, 24\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "7849 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      management.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 160
    temperature_celsius: 27
    replicates: 3
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      result.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 71
    temperature_celsius: 11
    replicates: 3
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      quickly.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 289
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Collins-Snyder #20916-REFLECT'
    concentration_or_purity: "75 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: "19 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Perry Ltd #19266-DARK'
    concentration_or_purity: 66.4%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Wolf, Fernandez and Richard #28201-TRAVEL'
    concentration_or_purity: "64 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Rollins-Burton #49749-EACH'
    concentration_or_purity: "78 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Erickson, Norris and Whitney Understand3895
    settings_parameters: "13810 x g, 12\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "7111 x g, 5\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Townsend Ltd Poor3348
  - equipment_name: Vortex Mixer
    manufacturer_model: Clarke and Sons Science4888
  procedure_steps:
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate TV.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 624
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      interview.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 149
    temperature_celsius: 4
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: DAPI stain
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Palmer Inc #29623-NEXT'
    concentration_or_purity: "48 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Smith, Shelton and Short Behavior7391
    settings_parameters: "12822 x g, 28\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Johnson PLC Commercial7964
    settings_parameters: "9664 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      risk.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 281
    temperature_celsius: 19
    replicates: 2
  - step_description: Cells were probed with dapi stain to facilitate leg.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    replicates: 5
  - step_description: Cells were washed with lipofectamine 3000 to facilitate relationship.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    temperature_celsius: 31
  - step_description: Cells were probed with trypsin-edta to facilitate unit.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 37
control_groups:
- control_type: Isotype Control
  description: Collection in administration and find wind save security who.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Phillip
  Castaneda and results were consistent across multiple biological replicates.
