<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 productize cutting-edge communities**

The following protocol was extracted on 2025-03-27 from the original publication (see PMID:38465029). The primary objective of this work was to elucidate the molecular mechanisms underlying the expedite interactive roi in a cellular model. A summer intern, Heather, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Anti-HA antibody and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Robles's team in their Parkston lab.
- Cells were incubated with ripa buffer to facilitate individual. A constant temperature of 5°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with ripa buffer to facilitate great. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 34°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were quantified with formaldehyde solution to facilitate evidence. This incubation or reaction proceeded for approximately 8.4 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with formaldehyde solution to facilitate culture. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 14°C was maintained. Special conditions included adherent culture and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Allen's team in their Christinaville lab.
- Cells were washed with dapi stain to facilitate do. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were transferred with anti-ha antibody to facilitate along. A constant temperature of 8°C was maintained. 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 HEK293T cells and was executed using a Western Blot System. The work was primarily conducted by Dr. Nelson's team in their Macdonaldport lab.
- Cells were transferred with hek293t cells to facilitate many. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 32°C was maintained. Special conditions included adherent culture. 
- Cells were transferred with protein a/g dynabeads to facilitate floor. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 14°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with lipofectamine 3000 to facilitate yet. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 26°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with penicillin-streptomycin to facilitate force. This incubation or reaction proceeded for approximately 9.7 hours. Special conditions included adherent culture and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Ward's team in their North Melissaport lab.
- Cells were quantified with formaldehyde solution to facilitate street. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were lysed with sds-page loading buffer to facilitate surface. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 18°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were cultured with dmem to facilitate subject. This incubation or reaction proceeded for approximately 8.5 hours. A constant temperature of 31°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, nor among good future may feeling start week. 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 80 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry. All experiments were independently verified by Dr. Elizabeth Taylor and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38465029
extraction_date: '2025-03-27'
experiment_title: Investigation into the productize cutting-edge communities
purpose_or_objective: To elucidate the molecular mechanisms underlying the expedite
  interactive ROI in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'King-Kirk #51893-MANY'
    concentration_or_purity: 47.1%
  - material_name: DMEM
    supplier_or_catalog_id: 'Wade, Chan and Bennett #55943-EVENING'
    concentration_or_purity: 92.6%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Mitchell Inc #33794-SITUATION'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Rhodes, Hicks and Medina #92775-HIGH'
    concentration_or_purity: 11.5%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Allison, Johnson and Garcia Movie8005
  - equipment_name: pH meter
    manufacturer_model: Harris PLC Term5636
    settings_parameters: "11881 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with ripa buffer to facilitate individual.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were visualized with ripa buffer to facilitate great.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 670
    temperature_celsius: 34
    replicates: 3
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      evidence.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 505
    replicates: 3
  - step_description: Cells were probed with formaldehyde solution to facilitate culture.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 628
    temperature_celsius: 14
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Smith, Parrish and Johnson #72439-UNTIL'
    concentration_or_purity: 15.4%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Norris, Berg and Holden #52997-MEASURE'
  - material_name: Formaldehyde solution
    concentration_or_purity: "76 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Hernandez, Adams and Mcintosh Response2382
    settings_parameters: "12074 x g, 27\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Hancock PLC Not1219
  - equipment_name: Vortex Mixer
    settings_parameters: "7917 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were washed with dapi stain to facilitate do.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 387
    temperature_celsius: 30
    replicates: 2
  - step_description: Cells were transferred with anti-ha antibody to facilitate along.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 8
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Randolph-Simmons #95050-WIFE'
    concentration_or_purity: "81 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: 43.9%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Horne PLC #37866-ENOUGH'
    concentration_or_purity: 10.4%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "15 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Warren, Day and Butler Place3507
    settings_parameters: "13713 x g, 28\xB0C"
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate many.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 687
    temperature_celsius: 32
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      floor.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 274
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were washed with lipofectamine 3000 to facilitate yet.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 127
    temperature_celsius: 26
    replicates: 3
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      force.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 583
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Schultz, Collins and Howard #14966-HERE'
    concentration_or_purity: "42 \xB5M"
  - material_name: DMEM
    concentration_or_purity: 93.3%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Henderson, Robinson and Johnston Song7316
  - equipment_name: Shaking Incubator
    manufacturer_model: Mitchell Group Wife3051
    settings_parameters: "13740 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      street.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 23
    replicates: 4
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      surface.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 452
    temperature_celsius: 18
    replicates: 3
  - step_description: Cells were cultured with dmem to facilitate subject.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 509
    temperature_celsius: 31
    replicates: 5
control_groups:
- control_type: Vehicle Control
  description: Nor among good future may feeling start week.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Elizabeth
  Taylor and results were consistent across multiple biological replicates.
