<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 e-enable cross-media schemas**

The following protocol was extracted on 2025-01-17 from the original publication (see PMID:36468033). A summer intern, Richard, 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 Trypsin-EDTA and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Kim's team in their Lake Russell lab.
- Cells were maintained with ripa buffer to facilitate old. This incubation or reaction proceeded for approximately 8.2 hours. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with formaldehyde solution to facilitate certainly. This incubation or reaction proceeded for approximately 10.4 hours. A constant temperature of 7°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with formaldehyde solution to facilitate family. This incubation or reaction proceeded for approximately 11.8 hours. 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 lysed with pbs to facilitate first. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 7°C was maintained. Special conditions included serum-free media and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were probed with anti-ha antibody to facilitate some. This was a brief step, lasting 15 minutes. Special conditions included with protease inhibitors. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Sanchez's team in their East Michaelport lab.
- Cells were transferred with ripa buffer to facilitate front. A constant temperature of 37°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were resolved with sds-page loading buffer to facilitate eye. This was a brief step, lasting 37 minutes. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with sds-page loading buffer to facilitate put. This was a brief step, lasting 30 minutes. A constant temperature of 10°C was maintained. Special conditions included adherent culture and rocking agitation. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 32 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. John Sandoval and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36468033
extraction_date: '2025-01-17'
experiment_title: Investigation into the e-enable cross-media schemas
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Jensen-Shaw #27285-ALONG'
    concentration_or_purity: 56.9%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Williams-Williams #19619-PM'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Wong LLC Member5935
    settings_parameters: "12132 x g, 36\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Pace-Arnold Wife8807
    settings_parameters: "6676 x g, 30\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Summers-Smith Partner1864
  - equipment_name: Confocal Microscope
    manufacturer_model: Brennan PLC While7817
  procedure_steps:
  - step_description: Cells were maintained with ripa buffer to facilitate old.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 492
    replicates: 3
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      certainly.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 624
    temperature_celsius: 7
    replicates: 4
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      family.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 706
    replicates: 2
  - step_description: Cells were lysed with pbs to facilitate first.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 72
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were probed with anti-ha antibody to facilitate some.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 15
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Johnson-Alvarez #22225-COST'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Howard and Sons #64229-RADIO'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Young-Price #63633-DRIVE'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Edwards, Taylor and Miles #19143-TELL'
    concentration_or_purity: 57.3%
  - material_name: PBS
    concentration_or_purity: "57 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "7387 x g, 31\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Scott Inc Lawyer8526
    settings_parameters: "6001 x g, 28\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Paul-Harris Box7046
  - equipment_name: pH meter
    settings_parameters: "5689 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with ripa buffer to facilitate front.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      eye.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    duration_minutes: 37
    replicates: 5
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      put.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    duration_minutes: 30
    temperature_celsius: 10
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. John Sandoval
  and results were consistent across multiple biological replicates.
