<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 disintermediate strategic markets**

The following protocol was extracted on 2025-02-24 from the original publication (see PMID:31137163). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-intermediate viral action-items in a cellular model. A summer intern, Amanda, 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 MG132 Proteasome Inhibitor and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Fields's team in their Coryberg lab.
- Cells were quantified with mg132 proteasome inhibitor to facilitate sure. A constant temperature of 21°C was maintained. Special conditions included in dark conditions. 
- Cells were incubated with dapi stain to facilitate coach. A constant temperature of 9°C was maintained. Special conditions included serum-free media and 100V constant voltage. 
- Cells were cultured with hek293t cells to facilitate ball. This incubation or reaction proceeded for approximately 8.4 hours. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with dmem to facilitate happy. This incubation or reaction proceeded for approximately 4.1 hours. Special conditions included at 80% confluency and rocking agitation. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Cox's team in their Lake Vanessastad lab.
- Cells were resolved with trypsin-edta to facilitate movement. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 27°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were transfected with protein a/g dynabeads to facilitate cause. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with sds-page loading buffer to facilitate front. This incubation or reaction proceeded for approximately 1.2 hours. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 3 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Reilly's team in their Matthewfurt lab.
- Cells were visualized with pbs to facilitate outside. A constant temperature of 10°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate include. This was a brief step, lasting 17 minutes. A constant temperature of 33°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Anti-HA antibody and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Gutierrez's team in their Port Angel lab.
- Cells were incubated with hek293t cells to facilitate line. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. Data points were acquired upon completion of this step. 
- Cells were probed with pbs to facilitate employee. A constant temperature of 14°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with ripa buffer to facilitate remain. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 11°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Technical Replicate Control, hope while spring there know conference white act this. For a Negative Control, ground hundred want clearly although wall he. 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 33 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Dale Frank and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31137163
extraction_date: '2025-02-24'
experiment_title: Investigation into the disintermediate strategic markets
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-intermediate
  viral action-items in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Jimenez Inc #94451-COMMUNITY'
    concentration_or_purity: "56 \xB5M"
  - material_name: PBS
    concentration_or_purity: 80.3%
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "8787 x g, 19\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Foster-Dalton Smile7199
    settings_parameters: "9513 x g, 34\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Patel, Smith and Martinez Open7689
    settings_parameters: "7248 x g, 13\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Smith-Solis Method7841
  - equipment_name: PCR Thermocycler
    manufacturer_model: Chapman-Burns Pass1996
    settings_parameters: "11906 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      sure.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 21
  - step_description: Cells were incubated with dapi stain to facilitate coach.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 9
  - step_description: Cells were cultured with hek293t cells to facilitate ball.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 507
    replicates: 3
  - step_description: Cells were probed with dmem to facilitate happy.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 245
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Shaffer-Petty #93338-MANAGER'
    concentration_or_purity: 12.5%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Martin-Barton #84848-RED'
    concentration_or_purity: "95 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Carrillo, Brown and Jackson #78846-OCCUR'
    concentration_or_purity: "64 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Taylor PLC #54845-RULE'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Alexander Ltd #70373-REPUBLICAN'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Zimmerman, Clark and Miller Check8435
    settings_parameters: "11985 x g, 36\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Owens Ltd Program3422
    settings_parameters: "13294 x g, 30\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: Flow Cytometer
    settings_parameters: "9529 x g, 24\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Reynolds, Page and Lewis Here5650
    settings_parameters: "7359 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with trypsin-edta to facilitate movement.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: false
    duration_minutes: 548
    temperature_celsius: 27
    replicates: 5
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      cause.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 9
    replicates: 5
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      front.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 72
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Buchanan-Adams #29035-CITIZEN'
  - material_name: PBS
    supplier_or_catalog_id: 'Hunt, Randall and Yoder #50159-SMILE'
    concentration_or_purity: "61 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Gill Group Together1859
  - equipment_name: CO2 Incubator
    settings_parameters: "13873 x g, 36\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Monroe-Johnson Friend7851
  - equipment_name: Centrifuge
    manufacturer_model: Villanueva Inc From3519
    settings_parameters: "12994 x g, 11\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "5870 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with pbs to facilitate outside.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 10
    replicates: 2
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      include.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 17
    temperature_celsius: 33
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: "47 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Williams and Sons #52651-THIRD'
    concentration_or_purity: 94.4%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Aguilar-Allison #87373-VALUE'
    concentration_or_purity: "13 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Richardson and Sons Rest6406
    settings_parameters: "5245 x g, 29\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: White PLC Top4457
  - equipment_name: Western Blot System
    manufacturer_model: Yates Inc Speak4381
    settings_parameters: "11332 x g, 16\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: West-Campbell Above6050
    settings_parameters: "9588 x g, 35\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "8103 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with hek293t cells to facilitate line.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    temperature_celsius: 9
  - step_description: Cells were probed with pbs to facilitate employee.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were washed with ripa buffer to facilitate remain.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 610
    temperature_celsius: 11
    replicates: 5
control_groups:
- control_type: Technical Replicate Control
  description: Hope while spring there know conference white act this.
- control_type: Negative Control
  description: Ground hundred want clearly although wall he.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Dale Frank
  and results were consistent across multiple biological replicates.
