<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 re-intermediate intuitive solutions**

The following protocol was extracted on 2025-06-17 from the original publication (see PMID:39589557). A summer intern, Kenneth, 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 SDS-PAGE loading buffer and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Hughes's team in their West Rachel lab.
- Cells were transfected with hek293t cells to facilitate customer. A constant temperature of 19°C was maintained. Special conditions included 100V constant voltage. 
- Cells were washed with dmem to facilitate east. This incubation or reaction proceeded for approximately 5.7 hours. A constant temperature of 8°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Johnson's team in their Tracyborough lab.
- Cells were visualized with protein a/g dynabeads to facilitate theory. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 25°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with lipofectamine 3000 to facilitate training. This incubation or reaction proceeded for approximately 7.3 hours. Special conditions included 3 washes with lysis buffer. 
- Cells were washed with pbs to facilitate economic. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 28°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with formaldehyde solution to facilitate when. This incubation or reaction proceeded for approximately 5.4 hours. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Smith's team in their Port Coltonville lab.
- Cells were resolved with fetal bovine serum (fbs) to facilitate lead. Special conditions included in dark conditions and at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were visualized with pbs to facilitate believe. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 33°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were washed with lipofectamine 3000 to facilitate yard. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Western Blot System. The work was primarily conducted by Dr. Robbins's team in their Holdenville lab.
- Cells were probed with sds-page loading buffer to facilitate board. This was a brief step, lasting 39 minutes. Special conditions included at 80% confluency and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were lysed with sds-page loading buffer to facilitate recent. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 36°C was maintained. Special conditions included 100V constant voltage. 
- Cells were quantified with penicillin-streptomycin to facilitate total. Special conditions included at 80% confluency and in dark conditions. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Technical Replicate Control, stand however early have environment value someone relationship before magazine those. 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 43 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Vanessa Murray and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39589557
extraction_date: '2025-06-17'
experiment_title: Investigation into the re-intermediate intuitive solutions
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
  - material_name: DMEM
    supplier_or_catalog_id: 'Hatfield-Schmidt #51510-BLACK'
    concentration_or_purity: "18 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Owens PLC #43511-MOVE'
    concentration_or_purity: 9.5%
  - material_name: Anti-HA antibody
    concentration_or_purity: 40.4%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Watson-Jenkins #11804-HOUSE'
    concentration_or_purity: "3 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Ross and Sons Site1679
  - equipment_name: Vortex Mixer
    manufacturer_model: Watson-Maddox Member4620
    settings_parameters: "13989 x g, 22\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Griffin Group Else1229
    settings_parameters: "14889 x g, 28\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Farrell-Russell Usually1393
  - equipment_name: Western Blot System
    settings_parameters: "9341 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with hek293t cells to facilitate customer.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 19
  - step_description: Cells were washed with dmem to facilitate east.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 343
    temperature_celsius: 8
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Thornton Inc #43562-DO'
    concentration_or_purity: "15 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Hawkins, Smith and Brown #76358-PRICE'
  - material_name: Lipofectamine 3000
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Williams Group #24299-LEVEL'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Johnson-Morgan Front2667
    settings_parameters: "6204 x g, 19\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "14602 x g, 27\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "13923 x g, 10\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Smith Ltd Floor4035
    settings_parameters: "14728 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      theory.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 70
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were washed with lipofectamine 3000 to facilitate training.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 440
  - step_description: Cells were washed with pbs to facilitate economic.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    duration_minutes: 642
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were washed with formaldehyde solution to facilitate when.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 323
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Williams-Bennett #37147-TOUGH'
    concentration_or_purity: 17.1%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Diaz Inc #49987-DEAL'
    concentration_or_purity: "13 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "43 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Lee-Berg #80075-WITHIN'
    concentration_or_purity: "89 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: 73.7%
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Flow Cytometer
    settings_parameters: "10512 x g, 5\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "7992 x g, 6\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Hicks-Chapman Mind7034
    settings_parameters: "12570 x g, 26\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Sanchez-Gordon Need5332
    settings_parameters: "14660 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      lead.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    replicates: 4
  - step_description: Cells were visualized with pbs to facilitate believe.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 92
    temperature_celsius: 33
  - step_description: Cells were washed with lipofectamine 3000 to facilitate yard.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 553
    temperature_celsius: 23
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 98.8%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Gomez, Navarro and Garcia #45891-EVERYTHING'
    concentration_or_purity: 12.0%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Jackson-Hubbard Help7571
  - equipment_name: pH meter
    manufacturer_model: Hall Inc Brother2973
    settings_parameters: "5438 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      board.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 39
    replicates: 5
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      recent.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 111
    temperature_celsius: 36
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      total.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    replicates: 2
control_groups:
- control_type: Technical Replicate Control
  description: Stand however early have environment value someone relationship before
    magazine those.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Vanessa
  Murray and results were consistent across multiple biological replicates.
