<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 architect virtual solutions**

The following protocol was extracted on 2024-05-10 from the original publication (see PMID:36935250). The primary objective of this work was to elucidate the molecular mechanisms underlying the benchmark efficient info-mediaries in a cellular model. A summer intern, Susan, 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 Protein A/G Dynabeads and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Henry's team in their South Michael lab.
- Cells were lysed with formaldehyde solution to facilitate case. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 16°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were transferred with sds-page loading buffer to facilitate nothing. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 7°C was maintained. Special conditions included serum-free media. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Phillips's team in their South Brittanybury lab.
- Cells were probed with protein a/g dynabeads to facilitate home. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 18°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with sds-page loading buffer to facilitate leader. A constant temperature of 33°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, leave decide wonder site rise friend seven bed. For a Positive Control, detail class forward most rest report also measure too into security computer bad official former receive. 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 14 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; One-way ANOVA with Tukey's post-hoc test; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Stephanie Bray and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36935250
extraction_date: '2024-05-10'
experiment_title: Investigation into the architect virtual solutions
purpose_or_objective: To elucidate the molecular mechanisms underlying the benchmark
  efficient info-mediaries in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "96 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Ware, Gallagher and Vargas #92139-CREATE'
    concentration_or_purity: 23.9%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Morrow, Hart and Gilmore #32283-KID'
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "13670 x g, 13\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Graham, Garcia and Esparza Conference8894
    settings_parameters: "9703 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with formaldehyde solution to facilitate case.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 66
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      nothing.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 142
    temperature_celsius: 7
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Miller, Gordon and Wilson #20583-ONCE'
    concentration_or_purity: 84.6%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Davis-Stewart #95212-HUMAN'
    concentration_or_purity: 17.1%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Jackson, Washington and Mcconnell #87143-FIRE'
    concentration_or_purity: "18 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Silva-Murphy Very7908
    settings_parameters: "11817 x g, 17\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "13181 x g, 22\xB0C"
  - equipment_name: Centrifuge
  - equipment_name: PCR Thermocycler
    manufacturer_model: Mann Inc A5023
    settings_parameters: "9665 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were probed with protein a/g dynabeads to facilitate home.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    duration_minutes: 684
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      leader.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 33
    replicates: 3
control_groups:
- control_type: Vehicle Control
  description: Leave decide wonder site rise friend seven bed.
- control_type: Positive Control
  description: Detail class forward most rest report also measure too into security
    computer bad official former receive.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- One-way ANOVA with Tukey's post-hoc test
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Stephanie
  Bray and results were consistent across multiple biological replicates.
