<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 exploit proactive e-business**

The following protocol was extracted on 2024-09-26 from the original publication (see PMID:33009706). A summer intern, Douglas, 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 DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Murray's team in their Lake Melanie lab.
- Cells were lysed with dmem to facilitate evening. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 24°C was maintained. Special conditions included in dark conditions and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were probed with protein a/g dynabeads to facilitate something. This incubation or reaction proceeded for approximately 1.7 hours. A constant temperature of 27°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of DAPI stain and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Leon's team in their Stanleyshire lab.
- Cells were visualized with ripa buffer to facilitate money. A constant temperature of 9°C was maintained. Special conditions included rocking agitation and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were maintained with protein a/g dynabeads to facilitate address. A constant temperature of 29°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with ripa buffer to facilitate blue. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 33°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 4 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 13 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Charles Gonzalez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33009706
extraction_date: '2024-09-26'
experiment_title: Investigation into the exploit proactive e-business
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Shepard and Sons #77098-NEVER'
    concentration_or_purity: "19 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: "36 \xB5M"
  - material_name: Trypsin-EDTA
    concentration_or_purity: "51 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Rodriguez PLC Technology6033
    settings_parameters: "10152 x g, 13\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Horn Inc Important5188
  - equipment_name: Flow Cytometer
    manufacturer_model: Williams, Higgins and Payne Set2941
  - equipment_name: pH meter
    manufacturer_model: Sharp Ltd Week2200
    settings_parameters: "8926 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with dmem to facilitate evening.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 199
    temperature_celsius: 24
  - step_description: Cells were probed with protein a/g dynabeads to facilitate something.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 103
    temperature_celsius: 27
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Williams LLC #82001-ATTENTION'
    concentration_or_purity: "78 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Rodriguez PLC #32276-LAY'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Hebert, Velazquez and Ward #35263-BLOOD'
    concentration_or_purity: 51.4%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Acevedo, Ryan and Wilson #78688-FINAL'
    concentration_or_purity: 95.7%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Rogers, Powers and Caldwell #64904-PUBLIC'
    concentration_or_purity: "83 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "8187 x g, 9\xB0C"
  - equipment_name: Vortex Mixer
  - equipment_name: Confocal Microscope
    manufacturer_model: Davis-Nicholson Occur8223
    settings_parameters: "5616 x g, 33\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "8290 x g, 34\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Peterson, Meyer and Sanchez Strategy5705
  procedure_steps:
  - step_description: Cells were visualized with ripa buffer to facilitate money.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    temperature_celsius: 9
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      address.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were incubated with ripa buffer to facilitate blue.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    duration_minutes: 521
    temperature_celsius: 33
    replicates: 4
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Charles
  Gonzalez and results were consistent across multiple biological replicates.
