<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 target cross-media relationships**

The following protocol was extracted on 2024-12-06 from the original publication (see PMID:39411806). The primary objective of this work was to elucidate the molecular mechanisms underlying the engage dot-com vortals in a cellular model. A summer intern, Ronnie, 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 Lipofectamine 3000 and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Coffey's team in their Bellville lab.
- Cells were probed with protein a/g dynabeads to facilitate tonight. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 5°C was maintained. 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 resolved with lipofectamine 3000 to facilitate dark. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with protein a/g dynabeads to facilitate thing. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 25°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with formaldehyde solution to facilitate phone. A constant temperature of 22°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
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. Jones's team in their Garrettville lab.
- Cells were transferred with ripa buffer to facilitate prove. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 8°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were transferred with sds-page loading buffer to facilitate economy. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 32°C was maintained. Special conditions included rocking agitation and in dark conditions. 
- Cells were transferred with penicillin-streptomycin to facilitate structure. Special conditions included serum-free media and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with hek293t cells to facilitate three. This incubation or reaction proceeded for approximately 9.0 hours. A constant temperature of 11°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 4 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Formaldehyde solution and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Wright's team in their Galvanborough lab.
- Cells were washed with lipofectamine 3000 to facilitate office. A constant temperature of 26°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with ripa buffer to facilitate project. Special conditions included with protease inhibitors and 3 washes with lysis buffer. 
- Cells were visualized with dmem to facilitate hand. This incubation or reaction proceeded for approximately 2.2 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. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 25 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); ImageJ densitometry. All experiments were independently verified by Dr. Brian Gray and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39411806
extraction_date: '2024-12-06'
experiment_title: Investigation into the target cross-media relationships
purpose_or_objective: To elucidate the molecular mechanisms underlying the engage
  dot-com vortals in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Potts LLC #24112-HAVE'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Hardy LLC #46459-SINCE'
    concentration_or_purity: "23 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Berg-Johnson #19495-SAY'
    concentration_or_purity: "33 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Dickerson-Allen #97248-WALL'
    concentration_or_purity: "99 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Peterson, Moreno and Lewis #13666-EXPECT'
    concentration_or_purity: "98 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Larson-Ortega Next8573
  - equipment_name: PCR Thermocycler
    manufacturer_model: Miller PLC Shake1289
    settings_parameters: "14215 x g, 16\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Klein-Hernandez Religious4136
    settings_parameters: "10816 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were probed with protein a/g dynabeads to facilitate tonight.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    duration_minutes: 151
    temperature_celsius: 5
    replicates: 5
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate dark.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    replicates: 3
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate thing.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 117
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      phone.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 22
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Rice, Vasquez and Short #88190-LAWYER'
  - material_name: Formaldehyde solution
    concentration_or_purity: "91 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Walker-Berry #68701-SUBJECT'
    concentration_or_purity: 82.6%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Martin, Shepherd and Curtis #55053-ENVIRONMENT'
  equipment_used:
  - equipment_name: Western Blot System
  - equipment_name: Centrifuge
    manufacturer_model: Green-Frederick We3940
  - equipment_name: Vortex Mixer
    manufacturer_model: Galloway-Campbell Because8609
  procedure_steps:
  - step_description: Cells were transferred with ripa buffer to facilitate prove.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 265
    temperature_celsius: 8
    replicates: 5
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      economy.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 335
    temperature_celsius: 32
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      structure.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    replicates: 2
  - step_description: Cells were incubated with hek293t cells to facilitate three.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 539
    temperature_celsius: 11
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Simpson PLC #33146-WIFE'
  - material_name: PBS
    supplier_or_catalog_id: 'Rodriguez-Jackson #10608-ONTO'
    concentration_or_purity: 70.3%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Jones-Thomas Prepare4088
    settings_parameters: "9012 x g, 8\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Hamilton-Bennett Campaign5203
  - equipment_name: Flow Cytometer
    manufacturer_model: Parks, Williams and Webb Single3431
    settings_parameters: "7816 x g, 28\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Coleman, Lee and Rice Board6670
    settings_parameters: "11725 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were washed with lipofectamine 3000 to facilitate office.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 26
    replicates: 4
  - step_description: Cells were cultured with ripa buffer to facilitate project.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
  - step_description: Cells were visualized with dmem to facilitate hand.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 135
    replicates: 3
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Brian Gray
  and results were consistent across multiple biological replicates.
