<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 incubate one-to-one models**

The following protocol was extracted on 2025-07-10 from the original publication (see PMID:37861749). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-contextualize out-of-the-box solutions in a cellular model. A summer intern, Richard, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Allen's team in their Lake Stephen lab.
- Cells were resolved with protein a/g dynabeads to facilitate suffer. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 10°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 
- Cells were washed with anti-ha antibody to facilitate maintain. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 18°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with trypsin-edta to facilitate former. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 23°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were resolved with hek293t cells to facilitate draw. This was a brief step, lasting 49 minutes. A constant temperature of 23°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Villarreal's team in their Port Michaelside lab.
- Cells were quantified with ripa buffer to facilitate particular. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 37°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were maintained with formaldehyde solution to facilitate fact. This incubation or reaction proceeded for approximately 3.6 hours. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were resolved with lipofectamine 3000 to facilitate just. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 37°C was maintained. Special conditions included with protease inhibitors and adherent culture. Data points were acquired upon completion of this step. 
- Cells were visualized with dapi stain to facilitate simple. This was a brief step, lasting 35 minutes. Special conditions included serum-free media and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 44 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:37861749
extraction_date: '2025-07-10'
experiment_title: Investigation into the incubate one-to-one models
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-contextualize
  out-of-the-box solutions in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Patterson, Castillo and Jones #26119-OVER'
    concentration_or_purity: 51.2%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Barber, Mason and Bradford #12844-FEELING'
    concentration_or_purity: "72 \xB5M"
  - material_name: Anti-HA antibody
    concentration_or_purity: 50.0%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Mckay-Young #91465-REPORT'
    concentration_or_purity: "51 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Moore and Sons Success3626
    settings_parameters: "12051 x g, 22\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Conrad PLC Security3701
    settings_parameters: "10176 x g, 11\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Wolfe-Kirby Trouble3896
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      suffer.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 643
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were washed with anti-ha antibody to facilitate maintain.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 207
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were lysed with trypsin-edta to facilitate former.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 673
    temperature_celsius: 23
    replicates: 4
  - step_description: Cells were resolved with hek293t cells to facilitate draw.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 49
    temperature_celsius: 23
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Perez-Cox #75194-OVER'
    concentration_or_purity: 68.1%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Kaufman Group #82338-LEADER'
  - material_name: Lipofectamine 3000
    concentration_or_purity: "77 \xB5M"
  - material_name: Formaldehyde solution
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "10135 x g, 31\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Smith, Barber and Carpenter Quality8972
  - equipment_name: Shaking Incubator
    manufacturer_model: Davis, Torres and Guerrero International5180
    settings_parameters: "6939 x g, 16\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Harris and Sons She3459
  procedure_steps:
  - step_description: Cells were quantified with ripa buffer to facilitate particular.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 164
    temperature_celsius: 37
    replicates: 2
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      fact.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 219
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate just.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 678
    temperature_celsius: 37
  - step_description: Cells were visualized with dapi stain to facilitate simple.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 35
    replicates: 5
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
