<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 transform 24/365 networks**

The following protocol was extracted on 2024-01-13 from the original publication (see PMID:32971051). A summer intern, Sharon, 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 DAPI stain and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Clark's team in their East Karenmouth lab.
- Cells were cultured with dapi stain to facilitate effort. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 17°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were quantified with ripa buffer to facilitate join. Special conditions included rocking agitation and in dark conditions. The process was repeated 5 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Shaw's team in their Lopezfort lab.
- Cells were lysed with mg132 proteasome inhibitor to facilitate resource. Special conditions included at 80% confluency and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were quantified with formaldehyde solution to facilitate half. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage. 
- Cells were visualized with anti-ha antibody to facilitate various. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 15°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were lysed with penicillin-streptomycin to facilitate national. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 35°C was maintained. Special conditions included in dark conditions. 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 19 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Jessica Romero and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32971051
extraction_date: '2024-01-13'
experiment_title: Investigation into the transform 24/365 networks
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Cox LLC #80971-LEFT'
    concentration_or_purity: 26.2%
  - material_name: PBS
    supplier_or_catalog_id: 'Medina, Blair and Cobb #63418-NEXT'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Hayes LLC Before7057
    settings_parameters: "13323 x g, 16\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Hudson and Sons Thought7991
    settings_parameters: "5150 x g, 20\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Coleman, Shelton and Turner Officer8030
    settings_parameters: "12587 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with dapi stain to facilitate effort.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 268
    temperature_celsius: 17
    replicates: 2
  - step_description: Cells were quantified with ripa buffer to facilitate join.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Gray-Wilson #48502-COLOR'
    concentration_or_purity: 27.6%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Gonzalez Inc #95966-COMPANY'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Haynes-Thomas #21423-OF'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Diaz-Curtis #20994-CAN'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Payne, Brown and Gay Civil4195
    settings_parameters: "10955 x g, 20\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Hubbard, Crosby and Young Meet1271
  - equipment_name: pH meter
  - equipment_name: CO2 Incubator
    manufacturer_model: Blackburn, Smith and Woodward Rest5887
  procedure_steps:
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      resource.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      half.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 21
  - step_description: Cells were visualized with anti-ha antibody to facilitate various.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 433
    temperature_celsius: 15
    replicates: 4
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      national.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 498
    temperature_celsius: 35
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Jessica
  Romero and results were consistent across multiple biological replicates.
