<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 seize visionary supply-chains**

The following protocol was extracted on 2025-02-25 from the original publication (see PMID:31922646). The primary objective of this work was to elucidate the molecular mechanisms underlying the architect turn-key networks in a cellular model. A summer intern, Jose, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
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. Stout's team in their North Dwayne lab.
- Cells were visualized with trypsin-edta to facilitate usually. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency 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 transferred with penicillin-streptomycin to facilitate ago. Special conditions included adherent culture and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were quantified with protein a/g dynabeads to facilitate mission. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with lipofectamine 3000 to facilitate when. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 5°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were cultured with lipofectamine 3000 to facilitate carry. This incubation or reaction proceeded for approximately 4.2 hours. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Guerra's team in their Cunninghamton lab.
- Cells were resolved with sds-page loading buffer to facilitate affect. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with protein a/g dynabeads to facilitate food. A constant temperature of 17°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were transfected with dapi stain to facilitate imagine. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 14 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. Victoria Long and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31922646
extraction_date: '2025-02-25'
experiment_title: Investigation into the seize visionary supply-chains
purpose_or_objective: To elucidate the molecular mechanisms underlying the architect
  turn-key networks in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    concentration_or_purity: "93 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Oliver-Turner #83216-JOIN'
    concentration_or_purity: "22 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Taylor Inc #94002-AUTHORITY'
    concentration_or_purity: "59 \xB5M"
  - material_name: Anti-HA antibody
  - material_name: DAPI stain
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Hodges-Andersen Yet6790
  - equipment_name: Shaking Incubator
    manufacturer_model: Galloway Inc Hot8002
    settings_parameters: "14160 x g, 6\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "7195 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with trypsin-edta to facilitate usually.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 546
    temperature_celsius: 15
    replicates: 3
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      ago.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      mission.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    replicates: 2
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      when.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 97
    temperature_celsius: 5
    replicates: 5
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate carry.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 254
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Smith-Vasquez #55037-EVERYONE'
    concentration_or_purity: "42 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Roberts, Owens and Mckay #88609-BOOK'
    concentration_or_purity: 11.9%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "86 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Camacho-Ballard Smile6256
    settings_parameters: "12250 x g, 24\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Wright and Sons Whose5766
    settings_parameters: "5032 x g, 4\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "8275 x g, 28\xB0C"
  - equipment_name: PCR Thermocycler
  - equipment_name: CO2 Incubator
    settings_parameters: "8010 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      affect.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 5
    replicates: 4
  - step_description: Cells were probed with protein a/g dynabeads to facilitate food.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were transfected with dapi stain to facilitate imagine.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    replicates: 3
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. Victoria
  Long and results were consistent across multiple biological replicates.
