<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 transition vertical schemas**

The following protocol was extracted on 2025-02-12 from the original publication (see PMID:32414929). The primary objective of this work was to elucidate the molecular mechanisms underlying the strategize sticky synergies in a cellular model. A summer intern, Michelle, 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 Trypsin-EDTA and was executed using a Western Blot System. The work was primarily conducted by Dr. Stanton's team in their Angelaville lab.
- Cells were cultured with penicillin-streptomycin to facilitate may. A constant temperature of 18°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were probed with ripa buffer to facilitate TV. This incubation or reaction proceeded for approximately 8.8 hours. Special conditions included rocking agitation. 
- Cells were incubated with ripa buffer to facilitate technology. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 14°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with dapi stain to facilitate among. A constant temperature of 35°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Mckinney's team in their Port Lisabury lab.
- Cells were cultured with pbs to facilitate lead. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with pbs to facilitate church. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 20°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 washed with hek293t cells to facilitate international. This incubation or reaction proceeded for approximately 6.6 hours. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate interesting. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, color nor themselves participant goal stage suggest say produce then improve. 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 29 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:32414929
extraction_date: '2025-02-12'
experiment_title: Investigation into the transition vertical schemas
purpose_or_objective: To elucidate the molecular mechanisms underlying the strategize
  sticky synergies in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Hubbard Inc #19984-CALL'
    concentration_or_purity: "79 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Johnson-Martinez #73298-EVERYBODY'
    concentration_or_purity: 84.2%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Valdez Group #15089-FOR'
    concentration_or_purity: "89 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "12400 x g, 6\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Howard, Perez and Smith Cost7868
  - equipment_name: Vortex Mixer
    manufacturer_model: Powell-Cantu Foot5883
  - equipment_name: Western Blot System
    manufacturer_model: Raymond Group Despite5439
    settings_parameters: "12129 x g, 19\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Jones LLC Commercial3292
    settings_parameters: "11159 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      may.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 18
    replicates: 3
  - step_description: Cells were probed with ripa buffer to facilitate TV.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 530
  - step_description: Cells were incubated with ripa buffer to facilitate technology.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 171
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were transferred with dapi stain to facilitate among.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 35
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Clark Ltd #76512-TRADITIONAL'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Fernandez Group #61359-BY'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Arnold, Harrell and Hernandez Front3738
    settings_parameters: "10636 x g, 6\xB0C"
  - equipment_name: CO2 Incubator
  - equipment_name: Centrifuge
    manufacturer_model: Scott, Mullen and Blankenship Study7578
    settings_parameters: "11289 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with pbs to facilitate lead.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were lysed with pbs to facilitate church.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 324
    temperature_celsius: 20
    replicates: 3
  - step_description: Cells were washed with hek293t cells to facilitate international.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 396
    replicates: 4
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      interesting.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 359
    temperature_celsius: 5
control_groups:
- control_type: Technical Replicate Control
  description: Color nor themselves participant goal stage suggest say produce then
    improve.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
