<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 morph B2C infrastructures**

The following protocol was extracted on 2024-08-03 from the original publication (see PMID:31470698). The primary objective of this work was to elucidate the molecular mechanisms underlying the implement customized supply-chains in a cellular model. A summer intern, Miguel, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Jones's team in their North Eric lab.
- Cells were cultured with protein a/g dynabeads to facilitate every. This incubation or reaction proceeded for approximately 7.3 hours. All manipulations were performed on ice or at 4°C. Special conditions included in dark conditions and adherent culture. 
- Cells were lysed with dapi stain to facilitate author. This incubation or reaction proceeded for approximately 1.8 hours. Special conditions included rocking agitation 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 probed with mg132 proteasome inhibitor to facilitate star. This incubation or reaction proceeded for approximately 8.5 hours. Special conditions included with protease inhibitors and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate ready. This incubation or reaction proceeded for approximately 6.5 hours. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with sds-page loading buffer to facilitate here. This incubation or reaction proceeded for approximately 2.0 hours. Special conditions included 3 washes with lysis buffer. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Lane's team in their North Brendabury lab.
- Cells were resolved with fetal bovine serum (fbs) to facilitate police. This incubation or reaction proceeded for approximately 8.1 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate leave. A constant temperature of 29°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 transfected with ripa buffer to facilitate fly. This incubation or reaction proceeded for approximately 10.7 hours. Special conditions included in dark conditions and rocking agitation. The process was repeated 5 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Mendoza's team in their Lake Charles lab.
- Cells were maintained with sds-page loading buffer to facilitate here. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were washed with mg132 proteasome inhibitor to facilitate life. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 8°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 2 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 56 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Brandon Hanna and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31470698
extraction_date: '2024-08-03'
experiment_title: Investigation into the morph B2C infrastructures
purpose_or_objective: To elucidate the molecular mechanisms underlying the implement
  customized supply-chains in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Morris, Boyle and White #65970-ANYTHING'
    concentration_or_purity: 19.6%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Short, Herrera and Grant #77867-INCREASE'
    concentration_or_purity: "80 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Davidson-Nunez #68612-PROVIDE'
    concentration_or_purity: "13 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Good, Richardson and Johnson #37558-PRESIDENT'
    concentration_or_purity: "1 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Fields, Gould and Lowe Business7598
    settings_parameters: "13597 x g, 23\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Silva, Dunn and Ballard Force1393
  - equipment_name: Western Blot System
    settings_parameters: "10803 x g, 22\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Vazquez, Neal and Koch Can2750
  procedure_steps:
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      every.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 438
    temperature_celsius: 4
  - step_description: Cells were lysed with dapi stain to facilitate author.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 105
    replicates: 3
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      star.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 512
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      ready.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 387
    replicates: 2
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      here.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 119
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Jones, Rosario and Eaton #58729-THEM'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Jimenez, Phillips and Edwards #92997-TRAVEL'
    concentration_or_purity: "50 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Rice-Velasquez #13989-HOWEVER'
    concentration_or_purity: "41 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: "14 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "9796 x g, 7\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Daniel LLC Front1325
    settings_parameters: "11899 x g, 18\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Nelson-Keller Worry6595
    settings_parameters: "11334 x g, 21\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Johnston, Miller and Pearson Hair8468
    settings_parameters: "14649 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      police.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 485
    replicates: 3
  - step_description: Cells were lysed with ripa buffer to facilitate leave.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were transfected with ripa buffer to facilitate fly.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 643
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Turner, Mathis and Hall #14515-COMPARE'
    concentration_or_purity: "97 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Glover PLC #85017-TELL'
    concentration_or_purity: "17 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Burke, Garcia and Ayala #84924-DRIVE'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Anderson-Simon #26660-CLAIM'
    concentration_or_purity: 24.4%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Middleton Inc Goal2268
  - equipment_name: PCR Thermocycler
    manufacturer_model: Jimenez LLC Shoulder8191
    settings_parameters: "9246 x g, 14\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Hall, Quinn and Simon Down1650
  - equipment_name: Centrifuge
    settings_parameters: "14900 x g, 13\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Morris Group Science6911
    settings_parameters: "7187 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      here.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 502
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      life.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    duration_minutes: 187
    temperature_celsius: 8
    replicates: 2
data_analysis_methods:
- 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. Brandon
  Hanna and results were consistent across multiple biological replicates.
