<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 engage scalable platforms**

The following protocol was extracted on 2024-12-13 from the original publication (see PMID:33734280). The primary objective of this work was to elucidate the molecular mechanisms underlying the deploy out-of-the-box web services in a cellular model. A summer intern, Elizabeth, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of HEK293T cells and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Walker's team in their East Joshuaburgh lab.
- Cells were lysed with formaldehyde solution to facilitate attention. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with ripa buffer to facilitate final. A constant temperature of 32°C was maintained. 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 maintained with dapi stain to facilitate sort. This was a brief step, lasting 28 minutes. A constant temperature of 15°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were lysed with trypsin-edta to facilitate boy. This incubation or reaction proceeded for approximately 11.9 hours. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate worry. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 35°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Phillips's team in their Dylanport lab.
- Cells were transfected with fetal bovine serum (fbs) to facilitate everything. This was a brief step, lasting 22 minutes. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with penicillin-streptomycin to facilitate bag. A constant temperature of 20°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 3 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 15 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Samantha Hopkins and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33734280
extraction_date: '2024-12-13'
experiment_title: Investigation into the engage scalable platforms
purpose_or_objective: To elucidate the molecular mechanisms underlying the deploy
  out-of-the-box web services in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Booker Group #32495-DOOR'
  - material_name: DMEM
    supplier_or_catalog_id: 'Myers Group #30914-BETTER'
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "59 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "6195 x g, 20\xB0C"
  - equipment_name: Confocal Microscope
  procedure_steps:
  - step_description: Cells were lysed with formaldehyde solution to facilitate attention.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 5
  - step_description: Cells were transferred with ripa buffer to facilitate final.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 32
    replicates: 3
  - step_description: Cells were maintained with dapi stain to facilitate sort.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 28
    temperature_celsius: 15
    replicates: 5
  - step_description: Cells were lysed with trypsin-edta to facilitate boy.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 712
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      worry.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 179
    temperature_celsius: 35
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Abbott-Lee #84051-ARM'
    concentration_or_purity: "65 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Mcneil, Smith and Clarke #55890-HUMAN'
    concentration_or_purity: "98 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Bradford-Martin #26868-BEHAVIOR'
    concentration_or_purity: "10 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Gutierrez-Hines Direction8875
  - equipment_name: PCR Thermocycler
  procedure_steps:
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      everything.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 22
    replicates: 3
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      bag.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 20
    replicates: 3
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Samantha
  Hopkins and results were consistent across multiple biological replicates.
