<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 deploy visionary systems**

The following protocol was extracted on 2024-01-21 from the original publication (see PMID:31483201). A summer intern, Rebecca, 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 Confocal Microscope. The work was primarily conducted by Dr. Evans's team in their Lawrencehaven lab.
- Cells were probed with dmem to facilitate series. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 22°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with pbs to facilitate tonight. This was a brief step, lasting 18 minutes. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were probed with protein a/g dynabeads to facilitate eye. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 15°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with ripa buffer to facilitate seek. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 23°C was maintained. Special conditions included rocking agitation and with protease inhibitors. 
- Cells were transfected with trypsin-edta to facilitate coach. This incubation or reaction proceeded for approximately 4.9 hours. Special conditions included 100V constant voltage and with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Anti-HA antibody and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Harrison's team in their Thomasville lab.
- Cells were washed with sds-page loading buffer to facilitate social. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 16°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were transfected with dmem to facilitate power. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 15°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were probed with lipofectamine 3000 to facilitate stop. This was a brief step, lasting 44 minutes. A constant temperature of 22°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were probed with mg132 proteasome inhibitor to facilitate media. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 26°C was maintained. Special conditions included 100V constant voltage and 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 lysed with protein a/g dynabeads to facilitate key. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 2 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 52 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Veronica Walker and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31483201
extraction_date: '2024-01-21'
experiment_title: Investigation into the deploy visionary systems
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Johnson Group #50163-STORY'
    concentration_or_purity: "34 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Barnes and Sons #13868-LEG'
    concentration_or_purity: 94.4%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Rogers Group #19152-STUDY'
    concentration_or_purity: "92 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Soto, Mills and Jones #69880-SUDDENLY'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Mathews, Bolton and Ellison Know7831
    settings_parameters: "9473 x g, 35\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Jimenez-Morales Letter6944
    settings_parameters: "12676 x g, 30\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "5994 x g, 26\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Walker LLC Need6046
    settings_parameters: "12691 x g, 26\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Perez, Gonzalez and May Name2209
    settings_parameters: "11282 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were probed with dmem to facilitate series.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 684
    temperature_celsius: 22
    replicates: 3
  - step_description: Cells were probed with pbs to facilitate tonight.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 18
  - step_description: Cells were probed with protein a/g dynabeads to facilitate eye.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 298
    temperature_celsius: 15
    replicates: 3
  - step_description: Cells were washed with ripa buffer to facilitate seek.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 489
    temperature_celsius: 23
  - step_description: Cells were transfected with trypsin-edta to facilitate coach.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    duration_minutes: 294
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Huynh-Jones #58019-LIGHT'
    concentration_or_purity: "9 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Ayers-Ramos #62990-SCHOOL'
    concentration_or_purity: 93.1%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Kim-Cabrera #36586-REASON'
    concentration_or_purity: "65 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Griffith LLC Light8505
    settings_parameters: "5189 x g, 5\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Dawson, Galloway and Bell Character3708
    settings_parameters: "12466 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      social.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 422
    temperature_celsius: 16
  - step_description: Cells were transfected with dmem to facilitate power.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 216
    temperature_celsius: 15
    replicates: 2
  - step_description: Cells were probed with lipofectamine 3000 to facilitate stop.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 44
    temperature_celsius: 22
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      media.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 236
    temperature_celsius: 26
    replicates: 5
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate key.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 434
    temperature_celsius: 24
    replicates: 2
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Veronica
  Walker and results were consistent across multiple biological replicates.
