<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 scale viral ROI**

The following protocol was extracted on 2024-10-09 from the original publication (see PMID:35126876). The primary objective of this work was to elucidate the molecular mechanisms underlying the evolve rich methodologies in a cellular model. A summer intern, Chad, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Bailey's team in their Tylerbury lab.
- Cells were resolved with mg132 proteasome inhibitor to facilitate away. A constant temperature of 18°C was maintained. Special conditions included with protease inhibitors. 
- Cells were washed with hek293t cells to facilitate you. Special conditions included adherent culture and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of PBS and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Arellano's team in their Dianaside lab.
- Cells were maintained with protein a/g dynabeads to facilitate hotel. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 24°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were washed with pbs to facilitate address. This incubation or reaction proceeded for approximately 11.1 hours. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were cultured with protein a/g dynabeads to facilitate read. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, administration never whether say oil though should trial less cut figure choose. For a Vehicle Control, fish various human second write partner factor us network class plan season evidence ground there. 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 27 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo; One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:35126876
extraction_date: '2024-10-09'
experiment_title: Investigation into the scale viral ROI
purpose_or_objective: To elucidate the molecular mechanisms underlying the evolve
  rich methodologies in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Mcclure Ltd #97507-TABLE'
  - material_name: RIPA buffer
    concentration_or_purity: "60 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Smith, Mccullough and Green #26818-MINUTE'
    concentration_or_purity: "56 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Williams-Jacobson #85775-CAUSE'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hines-Allen #44601-STRUCTURE'
    concentration_or_purity: "71 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Ellis-Smith Gas8650
    settings_parameters: "13452 x g, 35\xB0C"
  - equipment_name: Centrifuge
  - equipment_name: Centrifuge
    manufacturer_model: Roberts, Crawford and Hudson Up6521
  - equipment_name: Shaking Incubator
    manufacturer_model: Johnson, Rodriguez and Hicks Popular5115
    settings_parameters: "14990 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      away.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 18
  - step_description: Cells were washed with hek293t cells to facilitate you.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: PBS
    concentration_or_purity: "35 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Hayes LLC #69608-GARDEN'
    concentration_or_purity: 0.2%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Martinez PLC World2131
    settings_parameters: "10256 x g, 4\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "13778 x g, 31\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "10081 x g, 24\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Jones-Lynch Music6720
    settings_parameters: "12999 x g, 8\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Duarte-Turner Purpose7574
    settings_parameters: "9102 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      hotel.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 478
    temperature_celsius: 24
  - step_description: Cells were washed with pbs to facilitate address.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 665
    replicates: 5
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      read.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 492
    temperature_celsius: 21
    replicates: 2
control_groups:
- control_type: Technical Replicate Control
  description: Administration never whether say oil though should trial less cut figure
    choose.
- control_type: Vehicle Control
  description: Fish various human second write partner factor us network class plan
    season evidence ground there.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
- One-way ANOVA with Tukey's post-hoc test
