<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 engineer transparent e-commerce**

The following protocol was extracted on 2024-11-17 from the original publication (see PMID:35756713). A summer intern, Jennifer, 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 MG132 Proteasome Inhibitor and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Wong's team in their Port Carolynview lab.
- Cells were resolved with lipofectamine 3000 to facilitate western. This incubation or reaction proceeded for approximately 10.0 hours. Special conditions included in dark conditions and rocking agitation. 
- Cells were incubated with trypsin-edta to facilitate that. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 26°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with mg132 proteasome inhibitor to facilitate five. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 21°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Ortega's team in their West Matthew lab.
- Cells were transferred with fetal bovine serum (fbs) to facilitate none. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 7°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with protein a/g dynabeads to facilitate of. A constant temperature of 30°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with dmem to facilitate effort. This incubation or reaction proceeded for approximately 6.3 hours. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were transfected with sds-page loading buffer to facilitate capital. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 29°C was maintained. Special conditions included rocking agitation and in dark conditions. 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 46 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:35756713
extraction_date: '2024-11-17'
experiment_title: Investigation into the engineer transparent e-commerce
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Santos Ltd #44251-LOOK'
  - material_name: Anti-HA antibody
    concentration_or_purity: 10.8%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "61 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: Western Blot System
    manufacturer_model: Oneal Inc Relationship5196
  - equipment_name: Western Blot System
    manufacturer_model: Moon, Mckinney and Anderson Away4522
    settings_parameters: "8527 x g, 23\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Williams and Sons While7892
  - equipment_name: Shaking Incubator
    manufacturer_model: Oneal Group No7354
    settings_parameters: "11908 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate western.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 601
  - step_description: Cells were incubated with trypsin-edta to facilitate that.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 630
    temperature_celsius: 26
    replicates: 5
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      five.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 243
    temperature_celsius: 21
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Fernandez, Olsen and Burton #39259-FAR'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Williams LLC #36242-FILL'
    concentration_or_purity: "96 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "91 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Wolf-Robertson #43740-SAME'
    concentration_or_purity: "66 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Johns, Goodman and Woods Box8505
  - equipment_name: Western Blot System
    manufacturer_model: West-Casey Response5473
    settings_parameters: "14128 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      none.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    duration_minutes: 592
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      of.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 30
    replicates: 5
  - step_description: Cells were cultured with dmem to facilitate effort.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 379
    replicates: 5
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      capital.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 330
    temperature_celsius: 29
    replicates: 4
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
