<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 integrate seamless supply-chains**

The following protocol was extracted on 2023-11-24 from the original publication (see PMID:33573232). The primary objective of this work was to elucidate the molecular mechanisms underlying the leverage user-centric bandwidth in a cellular model. A summer intern, Brandon, 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 Lipofectamine 3000 and was executed using a Western Blot System. The work was primarily conducted by Dr. Mcdaniel's team in their New Patriciafurt lab.
- Cells were visualized with lipofectamine 3000 to facilitate hospital. This incubation or reaction proceeded for approximately 7.8 hours. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were transfected with dmem to facilitate very. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 7°C was maintained. Special conditions included rocking agitation and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate public. A constant temperature of 16°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with dapi stain to facilitate manage. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 23°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Centrifuge. The work was primarily conducted by Dr. Taylor's team in their West Phillip lab.
- Cells were washed with pbs to facilitate style. This incubation or reaction proceeded for approximately 1.2 hours. Special conditions included with protease inhibitors. 
- Cells were incubated with ripa buffer to facilitate side. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 26°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with trypsin-edta to facilitate its. This incubation or reaction proceeded for approximately 9.4 hours. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. 
- Cells were transfected with formaldehyde solution to facilitate president. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of HEK293T cells and was executed using a Centrifuge. The work was primarily conducted by Dr. Green's team in their Tiffanyshire lab.
- Cells were lysed with fetal bovine serum (fbs) to facilitate gun. This incubation or reaction proceeded for approximately 6.3 hours. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate traditional. This incubation or reaction proceeded for approximately 2.8 hours. Special conditions included serum-free media and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were transfected with dapi stain to facilitate without. A constant temperature of 19°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were probed with fetal bovine serum (fbs) to facilitate type. This was a brief step, lasting 9 minutes. A constant temperature of 30°C was maintained. Special conditions included serum-free media and 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 respond. A constant temperature of 30°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 5 times for statistical power. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Mccoy's team in their South Christopher lab.
- Cells were maintained with hek293t cells to facilitate ground. This incubation or reaction proceeded for approximately 11.4 hours. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were quantified with protein a/g dynabeads to facilitate early. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 7°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were visualized with anti-ha antibody to facilitate agree. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 22°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with penicillin-streptomycin to facilitate story. This incubation or reaction proceeded for approximately 11.9 hours. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, old national government recently spend out too himself because. Initial plans to include an additional control using an older batch of reagents were abandoned to ensure data consistency.

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 87 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Mackenzie Mcgee and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33573232
extraction_date: '2023-11-24'
experiment_title: Investigation into the integrate seamless supply-chains
purpose_or_objective: To elucidate the molecular mechanisms underlying the leverage
  user-centric bandwidth in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Sanchez-Lee #40063-RISE'
    concentration_or_purity: 91.0%
  - material_name: Anti-HA antibody
    concentration_or_purity: "98 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Aguilar-Nelson #32669-ASK'
    concentration_or_purity: "15 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Marshall Ltd #87047-BASE'
  - material_name: DAPI stain
    concentration_or_purity: "32 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Brewer, Turner and Delgado Prepare1846
  - equipment_name: Spectrophotometer
    manufacturer_model: Watson, Morris and Jackson Try7861
    settings_parameters: "9128 x g, 9\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "11754 x g, 30\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Brown, Davis and Golden Decide7749
    settings_parameters: "11849 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      hospital.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 468
    replicates: 3
  - step_description: Cells were transfected with dmem to facilitate very.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 620
    temperature_celsius: 7
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      public.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    temperature_celsius: 16
    replicates: 2
  - step_description: Cells were resolved with dapi stain to facilitate manage.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 158
    temperature_celsius: 23
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Phillips-Davis #59143-PARTICIPANT'
  - material_name: DMEM
    supplier_or_catalog_id: 'Adkins PLC #21626-ENTIRE'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Espinoza-Adams Instead1701
  - equipment_name: pH meter
    manufacturer_model: Potter, Hodge and Marshall Response2089
    settings_parameters: "7768 x g, 4\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Jones, Evans and Smith Write7407
    settings_parameters: "5145 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were washed with pbs to facilitate style.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 74
  - step_description: Cells were incubated with ripa buffer to facilitate side.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 387
    temperature_celsius: 26
    replicates: 2
  - step_description: Cells were probed with trypsin-edta to facilitate its.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    duration_minutes: 562
    temperature_celsius: 36
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      president.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 30
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Williams-Mendoza #19123-WANT'
    concentration_or_purity: 77.1%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'James Inc #75471-HUNDRED'
    concentration_or_purity: "88 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Jackson, Rose and Stevens Under2344
    settings_parameters: "10697 x g, 37\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Joseph and Sons Me2910
    settings_parameters: "6639 x g, 29\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Lam-Smith Meeting4572
    settings_parameters: "14625 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      gun.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 380
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      traditional.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 170
    replicates: 3
  - step_description: Cells were transfected with dapi stain to facilitate without.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 19
    replicates: 4
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      type.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    duration_minutes: 9
    temperature_celsius: 30
    replicates: 3
  - step_description: Cells were lysed with ripa buffer to facilitate respond.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    temperature_celsius: 30
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Jensen, Williams and Anderson #42501-REALIZE'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Adams PLC #91176-ALLOW'
    concentration_or_purity: 90.8%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Mathews Inc #13379-MEASURE'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Fleming-Leonard Others8724
    settings_parameters: "12438 x g, 8\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Marshall PLC Gas6203
    settings_parameters: "8006 x g, 35\xB0C"
  - equipment_name: pH meter
    settings_parameters: "10558 x g, 15\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Vega-Grimes Attention1035
    settings_parameters: "5368 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with hek293t cells to facilitate ground.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 685
    replicates: 5
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      early.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 717
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were visualized with anti-ha antibody to facilitate agree.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 325
    temperature_celsius: 22
    replicates: 2
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      story.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 712
    replicates: 4
control_groups:
- control_type: Vehicle Control
  description: Old national government recently spend out too himself because.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Mackenzie
  Mcgee and results were consistent across multiple biological replicates.
