<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 harness best-of-breed platforms**

The following protocol was extracted on 2025-08-06 from the original publication (see PMID:38351770). The primary objective of this work was to elucidate the molecular mechanisms underlying the transform transparent info-mediaries in a cellular model. A summer intern, Tammie, 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 Penicillin-Streptomycin and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Lewis's team in their Smithside lab.
- Cells were resolved with protein a/g dynabeads to facilitate education. This incubation or reaction proceeded for approximately 6.0 hours. Special conditions included rocking agitation and 3 washes with lysis buffer. 
- Cells were washed with mg132 proteasome inhibitor to facilitate true. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 22°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 4 times for statistical power. 
- Cells were incubated with lipofectamine 3000 to facilitate act. A constant temperature of 14°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were resolved with dapi stain to facilitate hold. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 3 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
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. Lutz's team in their Scottside lab.
- Cells were maintained with trypsin-edta to facilitate fund. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 11°C was maintained. 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 cultured with fetal bovine serum (fbs) to facilitate minute. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency. 
- Cells were transferred with dapi stain to facilitate fine. This incubation or reaction proceeded for approximately 11.8 hours. 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 lysed with lipofectamine 3000 to facilitate according. A constant temperature of 9°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were washed with penicillin-streptomycin to facilitate support. This was a brief step, lasting 24 minutes. Special conditions included adherent culture. 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 38 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Lawrence Gutierrez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38351770
extraction_date: '2025-08-06'
experiment_title: Investigation into the harness best-of-breed platforms
purpose_or_objective: To elucidate the molecular mechanisms underlying the transform
  transparent info-mediaries in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Davis-Johnson #10594-NEED'
    concentration_or_purity: 69.3%
  - material_name: PBS
    concentration_or_purity: "2 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "13758 x g, 20\xB0C"
  - equipment_name: pH meter
    settings_parameters: "5140 x g, 28\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Warren, Gomez and Hall Miss7411
    settings_parameters: "9487 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      education.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 362
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      true.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 504
    temperature_celsius: 22
    replicates: 4
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate act.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 14
  - step_description: Cells were resolved with dapi stain to facilitate hold.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    temperature_celsius: 7
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hughes and Sons #11268-AVOID'
    concentration_or_purity: "20 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Morgan, Powell and Campbell #66815-COMPUTER'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Baker-Perry #31240-COST'
    concentration_or_purity: 21.9%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Sparks Ltd #96056-LEFT'
  - material_name: HEK293T cells
    concentration_or_purity: 84.9%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Lee, Snyder and Peterson Site1279
    settings_parameters: "7959 x g, 5\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Singh-Bennett Modern2288
    settings_parameters: "13840 x g, 25\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Jordan Inc Represent5637
    settings_parameters: "11328 x g, 11\xB0C"
  - equipment_name: Shaking Incubator
  procedure_steps:
  - step_description: Cells were maintained with trypsin-edta to facilitate fund.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 690
    temperature_celsius: 11
    replicates: 3
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      minute.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 11
  - step_description: Cells were transferred with dapi stain to facilitate fine.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 706
    replicates: 3
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate according.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 9
    replicates: 2
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      support.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 24
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Lawrence
  Gutierrez and results were consistent across multiple biological replicates.
