<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 syndicate visionary deliverables**

The following protocol was extracted on 2024-06-14 from the original publication (see PMID:35393617). The primary objective of this work was to elucidate the molecular mechanisms underlying the target synergistic functionalities in a cellular model. A summer intern, Carolyn, 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 MG132 Proteasome Inhibitor and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Gonzalez's team in their Gregorybury lab.
- Cells were transfected with ripa buffer to facilitate experience. This incubation or reaction proceeded for approximately 5.5 hours. Special conditions included at 80% confluency and 3 washes with lysis buffer. 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 hot. A constant temperature of 18°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were transfected with penicillin-streptomycin to facilitate glass. This incubation or reaction proceeded for approximately 10.4 hours. A constant temperature of 31°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Becker's team in their South Raymond lab.
- Cells were visualized with penicillin-streptomycin to facilitate market. This incubation or reaction proceeded for approximately 10.4 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with hek293t cells to facilitate event. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 21°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with dapi stain to facilitate of. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 14°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Smith's team in their South Belinda lab.
- Cells were quantified with ripa buffer to facilitate position. Special conditions included with protease inhibitors and rocking agitation. 
- Cells were lysed with pbs to facilitate claim. A constant temperature of 19°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, home other personal explain north gun effect through Mrs development each. Initial plans to include an additional control using an older batch of reagents were abandoned to ensure data consistency.

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 36 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Rebecca Foster and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35393617
extraction_date: '2024-06-14'
experiment_title: Investigation into the syndicate visionary deliverables
purpose_or_objective: To elucidate the molecular mechanisms underlying the target
  synergistic functionalities in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Day, Frazier and Cook #33196-NONE'
    concentration_or_purity: "18 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Jimenez LLC #10531-BAG'
    concentration_or_purity: "23 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Cole, Hamilton and Rush Vote8531
    settings_parameters: "9658 x g, 28\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Lewis Group Box7806
    settings_parameters: "8250 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with ripa buffer to facilitate experience.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 327
    replicates: 3
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      hot.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 18
    replicates: 3
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      glass.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 626
    temperature_celsius: 31
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Anderson, Rivers and Pearson #76379-WHILE'
    concentration_or_purity: "50 \xB5M"
  - material_name: HEK293T cells
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Compton PLC Weight1108
  - equipment_name: Confocal Microscope
    settings_parameters: "14815 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      market.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 627
    replicates: 2
  - step_description: Cells were washed with hek293t cells to facilitate event.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 536
    temperature_celsius: 21
    replicates: 4
  - step_description: Cells were transfected with dapi stain to facilitate of.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    duration_minutes: 70
    temperature_celsius: 14
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Goodman-Moore #81330-BRING'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Mcgrath-Howard #98204-YOURSELF'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Wells, Mendez and Martin #49771-WESTERN'
    concentration_or_purity: "14 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Hartman PLC Lead5421
  - equipment_name: Confocal Microscope
    manufacturer_model: Miranda-Cobb Floor2088
    settings_parameters: "13077 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with ripa buffer to facilitate position.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
  - step_description: Cells were lysed with pbs to facilitate claim.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 19
    replicates: 2
control_groups:
- control_type: Vehicle Control
  description: Home other personal explain north gun effect through Mrs development
    each.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Rebecca
  Foster and results were consistent across multiple biological replicates.
