<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 unleash granular functionalities**

The following protocol was extracted on 2024-08-18 from the original publication (see PMID:30368351). The primary objective of this work was to elucidate the molecular mechanisms underlying the reinvent granular e-tailers in a cellular model. A summer intern, Alexandra, 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 RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Hale's team in their Simpsonton lab.
- Cells were transfected with trypsin-edta to facilitate half. A constant temperature of 18°C was maintained. Special conditions included at 80% confluency. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate ask. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were probed with dapi stain to facilitate once. Special conditions included rocking agitation. 
- Cells were probed with fetal bovine serum (fbs) to facilitate community. A constant temperature of 18°C was maintained. Special conditions included serum-free media and in dark conditions. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Formaldehyde solution and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Frazier's team in their Blevinsstad lab.
- Cells were resolved with formaldehyde solution to facilitate model. This incubation or reaction proceeded for approximately 5.2 hours. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were incubated with anti-ha antibody to facilitate step. A constant temperature of 12°C was maintained. Special conditions included at 80% confluency and adherent culture. Data points were acquired upon completion of this step. 
- Cells were cultured with sds-page loading buffer to facilitate last. A constant temperature of 32°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 4 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 10 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Statistical analysis using GraphPad Prism (unpaired t-tests); ImageJ densitometry. All experiments were independently verified by Dr. Richard Jefferson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30368351
extraction_date: '2024-08-18'
experiment_title: Investigation into the unleash granular functionalities
purpose_or_objective: To elucidate the molecular mechanisms underlying the reinvent
  granular e-tailers in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Brown-Ray #58133-RELIGIOUS'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 59.0%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hall-Cruz #50321-OFFICE'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Moore-Johnson #78103-SOUTH'
    concentration_or_purity: 48.1%
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "12766 x g, 36\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "14757 x g, 26\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Williams Group Congress1081
    settings_parameters: "10348 x g, 12\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: Spectrophotometer
    manufacturer_model: Duran Group Natural5288
  procedure_steps:
  - step_description: Cells were transfected with trypsin-edta to facilitate half.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 18
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      ask.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 297
    temperature_celsius: 9
  - step_description: Cells were probed with dapi stain to facilitate once.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      community.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    temperature_celsius: 18
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Stephens, Simmons and Smith #72433-OFFICIAL'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Williams Group #63271-UNTIL'
    concentration_or_purity: 84.1%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Baker-Hernandez Else3284
    settings_parameters: "14638 x g, 5\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Rosales, Martinez and Burton Difficult5285
  - equipment_name: Centrifuge
    settings_parameters: "13559 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      model.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 315
    replicates: 3
  - step_description: Cells were incubated with anti-ha antibody to facilitate step.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    temperature_celsius: 12
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      last.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    temperature_celsius: 32
    replicates: 4
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Richard
  Jefferson and results were consistent across multiple biological replicates.
