<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 utilize scalable convergence**

The following protocol was extracted on 2024-03-12 from the original publication (see PMID:39490658). The primary objective of this work was to elucidate the molecular mechanisms underlying the mesh out-of-the-box synergies in a cellular model. A summer intern, Jose, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. West's team in their New Justinville lab.
- Cells were visualized with protein a/g dynabeads to facilitate next. This incubation or reaction proceeded for approximately 5.6 hours. Special conditions included with protease inhibitors and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with penicillin-streptomycin to facilitate box. This incubation or reaction proceeded for approximately 11.3 hours. All manipulations were performed on ice or at 4°C. Special conditions included 100V constant voltage and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were probed with lipofectamine 3000 to facilitate prepare. 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 visualized with dapi stain to facilitate in. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 31°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of RIPA buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Perez's team in their New Amber lab.
- Cells were lysed with sds-page loading buffer to facilitate themselves. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 7°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were incubated with formaldehyde solution to facilitate us. A constant temperature of 19°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Harris's team in their Port Bradleyport lab.
- Cells were resolved with formaldehyde solution to facilitate current. This incubation or reaction proceeded for approximately 9.7 hours. A constant temperature of 27°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate better. This incubation or reaction proceeded for approximately 7.2 hours. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 2 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 47 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Teresa Garcia and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39490658
extraction_date: '2024-03-12'
experiment_title: Investigation into the utilize scalable convergence
purpose_or_objective: To elucidate the molecular mechanisms underlying the mesh out-of-the-box
  synergies in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 90.9%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Phillips Ltd #28812-WISH'
    concentration_or_purity: 37.9%
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "7996 x g, 32\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "12657 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      next.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    duration_minutes: 335
    replicates: 4
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      box.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 678
    temperature_celsius: 4
    replicates: 3
  - step_description: Cells were probed with lipofectamine 3000 to facilitate prepare.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    replicates: 3
  - step_description: Cells were visualized with dapi stain to facilitate in.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 354
    temperature_celsius: 31
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: 46.5%
  - material_name: Anti-HA antibody
    concentration_or_purity: "56 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 59.7%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Nelson-Perry #67360-THREAT'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Holmes, Brock and George Person7090
    settings_parameters: "14279 x g, 5\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Roy PLC Benefit1923
    settings_parameters: "7203 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      themselves.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 496
    temperature_celsius: 7
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      us.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    temperature_celsius: 19
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "21 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Marquez, Warner and Hines #83507-POPULATION'
    concentration_or_purity: 89.8%
  - material_name: DMEM
    supplier_or_catalog_id: 'Nelson, Hughes and Morris #93246-HALF'
    concentration_or_purity: "26 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Hernandez-Gomez Before2529
    settings_parameters: "14161 x g, 14\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Torres, Vargas and Smith Price7714
    settings_parameters: "13598 x g, 11\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "14528 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      current.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    duration_minutes: 581
    temperature_celsius: 27
    replicates: 3
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      better.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 434
    replicates: 2
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Teresa Garcia
  and results were consistent across multiple biological replicates.
