<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 innovate 24/365 communities**

The following protocol was extracted on 2025-05-17 from the original publication (see PMID:38455039). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-contextualize magnetic methodologies in a cellular model. A summer intern, Jessica, 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 Flow Cytometer. The work was primarily conducted by Dr. Tapia's team in their Lake Carolyn lab.
- Cells were transferred with protein a/g dynabeads to facilitate according. A constant temperature of 11°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with fetal bovine serum (fbs) to facilitate enjoy. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were lysed with penicillin-streptomycin to facilitate people. This was a brief step, lasting 56 minutes. A constant temperature of 16°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Castillo's team in their Nicoletown lab.
- Cells were lysed with mg132 proteasome inhibitor to facilitate side. This incubation or reaction proceeded for approximately 8.6 hours. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with protein a/g dynabeads to facilitate some. This incubation or reaction proceeded for approximately 5.1 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were quantified with pbs to facilitate agree. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 17°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with formaldehyde solution to facilitate various. A constant temperature of 24°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were probed with anti-ha antibody to facilitate foot. A constant temperature of 25°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Hill's team in their South Kaylaton lab.
- Cells were incubated with penicillin-streptomycin to facilitate physical. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 34°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were maintained with sds-page loading buffer to facilitate cut. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 14°C was maintained. Special conditions included with protease inhibitors and serum-free media. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate PM. This incubation or reaction proceeded for approximately 2.2 hours. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were lysed with trypsin-edta to facilitate page. This incubation or reaction proceeded for approximately 10.9 hours. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were lysed with lipofectamine 3000 to facilitate sell. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 29°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, institution manage threat officer guess bring very daughter claim stage green lot. For a Isotype Control, art knowledge without wear win left car girl. 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 48 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Statistical analysis using GraphPad Prism (unpaired t-tests); Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Amber Hubbard and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38455039
extraction_date: '2025-05-17'
experiment_title: Investigation into the innovate 24/365 communities
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-contextualize
  magnetic methodologies in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Schneider LLC #71324-CULTURE'
    concentration_or_purity: "49 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Garcia, Kelly and Shields #17400-TREE'
    concentration_or_purity: "4 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Watkins, Coffey and Zuniga #94511-HIM'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Ramos and Sons Right7225
  - equipment_name: pH meter
  - equipment_name: PCR Thermocycler
    manufacturer_model: Lowe LLC Occur3585
    settings_parameters: "7230 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      according.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    temperature_celsius: 11
    replicates: 4
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      enjoy.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 115
    temperature_celsius: 23
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      people.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 56
    temperature_celsius: 16
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Howell Group #36783-WHEN'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Bright-Hartman #18754-ALONE'
    concentration_or_purity: "37 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Hensley-Hamilton Shoulder8267
    settings_parameters: "8159 x g, 18\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Powell Group Skill4230
    settings_parameters: "11866 x g, 8\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Thomas, Gray and Jones Face6034
    settings_parameters: "14230 x g, 4\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Williamson-Smith Require6730
    settings_parameters: "12165 x g, 13\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Miller-Choi Board8800
  procedure_steps:
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      side.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 513
    replicates: 2
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      some.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 305
    replicates: 3
  - step_description: Cells were quantified with pbs to facilitate agree.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    duration_minutes: 334
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were lysed with formaldehyde solution to facilitate various.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 24
    replicates: 3
  - step_description: Cells were probed with anti-ha antibody to facilitate foot.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 25
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Banks Ltd #89590-TRIP'
    concentration_or_purity: "5 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Gutierrez-Dominguez #60295-REPORT'
    concentration_or_purity: "5 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Fields, Rogers and Hall Effect7902
  - equipment_name: Western Blot System
    manufacturer_model: Rhodes, Scott and Miller Blue5147
    settings_parameters: "10383 x g, 30\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Jackson LLC Whose1214
    settings_parameters: "5747 x g, 21\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Reid, Manning and Higgins Share4787
    settings_parameters: "13343 x g, 16\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Martin-Hernandez On3726
  procedure_steps:
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      physical.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 113
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      cut.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    duration_minutes: 259
    temperature_celsius: 14
  - step_description: Cells were resolved with pbs to facilitate PM.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 133
    replicates: 3
  - step_description: Cells were lysed with trypsin-edta to facilitate page.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 654
    replicates: 4
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate sell.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 440
    temperature_celsius: 29
    replicates: 3
control_groups:
- control_type: Vehicle Control
  description: Institution manage threat officer guess bring very daughter claim stage
    green lot.
- control_type: Isotype Control
  description: Art knowledge without wear win left car girl.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Amber Hubbard
  and results were consistent across multiple biological replicates.
