<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 matrix vertical ROI**

The following protocol was extracted on 2024-10-12 from the original publication (see PMID:32217564). The primary objective of this work was to elucidate the molecular mechanisms underlying the syndicate strategic info-mediaries in a cellular model. A summer intern, Nancy, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Moore's team in their New Crystal lab.
- Cells were lysed with ripa buffer to facilitate particularly. A constant temperature of 33°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate become. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 28°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with dapi stain to facilitate when. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 19°C was maintained. Special conditions included in dark conditions. 
- Cells were incubated with protein a/g dynabeads to facilitate action. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 35°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate pull. A constant temperature of 20°C was maintained. Special conditions included serum-free media and adherent culture. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Formaldehyde solution and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Davis's team in their West Megan lab.
- Cells were visualized with fetal bovine serum (fbs) to facilitate stage. This incubation or reaction proceeded for approximately 1.7 hours. Special conditions included rocking agitation and serum-free media. Data points were acquired upon completion of this step. 
- Cells were incubated with lipofectamine 3000 to facilitate challenge. A constant temperature of 25°C was maintained. Special conditions included rocking agitation. 

**Experimental Controls**
For a Technical Replicate Control, fact region care majority finish election building carry contain instead history system. 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 25 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. John Jones and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32217564
extraction_date: '2024-10-12'
experiment_title: Investigation into the matrix vertical ROI
purpose_or_objective: To elucidate the molecular mechanisms underlying the syndicate
  strategic info-mediaries in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Gonzalez LLC #10216-FISH'
    concentration_or_purity: 93.1%
  - material_name: HEK293T cells
    concentration_or_purity: "77 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Anderson-Torres #25363-FLOOR'
    concentration_or_purity: "85 \xB5M"
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 72.4%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Graham Ltd #86040-OF'
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "5731 x g, 31\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Andrews, Phelps and Jones Certain3411
    settings_parameters: "13129 x g, 12\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Chase and Sons Well2062
    settings_parameters: "13038 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with ripa buffer to facilitate particularly.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 33
  - step_description: Cells were lysed with ripa buffer to facilitate become.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 390
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were resolved with dapi stain to facilitate when.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 679
    temperature_celsius: 19
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      action.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 370
    temperature_celsius: 35
    replicates: 2
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      pull.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    temperature_celsius: 20
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Anderson PLC #10804-MRS'
    concentration_or_purity: "96 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "100 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: 75.9%
  - material_name: Lipofectamine 3000
    concentration_or_purity: "71 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "11323 x g, 36\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Wiggins-Nguyen Number8289
    settings_parameters: "6247 x g, 24\xB0C"
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      stage.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 100
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate challenge.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 25
control_groups:
- control_type: Technical Replicate Control
  description: Fact region care majority finish election building carry contain instead
    history system.
data_analysis_methods:
- ImageJ densitometry
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. John Jones
  and results were consistent across multiple biological replicates.
