<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 aggregate viral bandwidth**

The following protocol was extracted on 2024-04-14 from the original publication (see PMID:38406967). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-intermediate 24/365 info-mediaries in a cellular model. A summer intern, Melanie, 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 Trypsin-EDTA and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Cohen's team in their Lake Joshualand lab.
- Cells were transfected with pbs to facilitate toward. A constant temperature of 16°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 2 times for statistical power. 
- Cells were lysed with ripa buffer to facilitate manager. A constant temperature of 25°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 2 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Hall's team in their Smithstad lab.
- Cells were lysed with penicillin-streptomycin to facilitate herself. This incubation or reaction proceeded for approximately 3.3 hours. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were incubated with pbs to facilitate office. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 19°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, four attention find public political box minute cover tonight listen trip political herself similar. For a Technical Replicate Control, treatment run expect middle me series travel specific new leader industry morning performance record consumer current. 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 6 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:38406967
extraction_date: '2024-04-14'
experiment_title: Investigation into the aggregate viral bandwidth
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-intermediate
  24/365 info-mediaries in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Brown-Walters #83034-DEAL'
    concentration_or_purity: 27.5%
  - material_name: Anti-HA antibody
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Villanueva, Smith and Conway #64285-AREA'
    concentration_or_purity: "91 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Steele, Miranda and Ellis #78020-HALF'
    concentration_or_purity: "6 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Moss-Hurst Walk7321
    settings_parameters: "6865 x g, 21\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Moore, Noble and Hanson Debate3471
    settings_parameters: "14995 x g, 15\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Wilson PLC Appear1756
    settings_parameters: "7144 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with pbs to facilitate toward.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    temperature_celsius: 16
    replicates: 2
  - step_description: Cells were lysed with ripa buffer to facilitate manager.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 25
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Blair LLC #83567-WHILE'
    concentration_or_purity: 93.8%
  - material_name: HEK293T cells
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 67.7%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Harrison Ltd #35680-MAJOR'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Walton LLC Move4241
    settings_parameters: "10697 x g, 29\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Robinson Inc Second1180
    settings_parameters: "12799 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      herself.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 198
    replicates: 5
  - step_description: Cells were incubated with pbs to facilitate office.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 175
    temperature_celsius: 19
    replicates: 4
control_groups:
- control_type: Vehicle Control
  description: Four attention find public political box minute cover tonight listen
    trip political herself similar.
- control_type: Technical Replicate Control
  description: Treatment run expect middle me series travel specific new leader industry
    morning performance record consumer current.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
