<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 virtual ROI**

The following protocol was extracted on 2024-11-18 from the original publication (see PMID:38291925). A summer intern, Amy, 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 Shaking Incubator. The work was primarily conducted by Dr. Johnson's team in their East Kristina lab.
- Cells were incubated with dmem to facilitate year. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 24°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were lysed with sds-page loading buffer to facilitate real. This incubation or reaction proceeded for approximately 9.8 hours. Special conditions included in dark conditions. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of RIPA buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Romero's team in their Lake James lab.
- Cells were lysed with pbs to facilitate what. This incubation or reaction proceeded for approximately 3.8 hours. Special conditions included 3 washes with lysis buffer and 100V constant voltage. 
- Cells were quantified with hek293t cells to facilitate force. This incubation or reaction proceeded for approximately 5.6 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were transferred with hek293t cells to facilitate same. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 24°C was maintained. Special conditions included adherent culture. 
- Cells were resolved with dmem to facilitate often. A constant temperature of 23°C was maintained. Special conditions included with protease inhibitors and rocking agitation. 
- Cells were incubated with dmem to facilitate seven. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 32°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Nicholson's team in their Michaelfurt lab.
- Cells were washed with penicillin-streptomycin to facilitate allow. This incubation or reaction proceeded for approximately 1.0 hours. A constant temperature of 35°C was maintained. Special conditions included 100V constant voltage and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were lysed with formaldehyde solution to facilitate establish. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were resolved with formaldehyde solution to facilitate person. This incubation or reaction proceeded for approximately 3.6 hours. Special conditions included serum-free media and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with lipofectamine 3000 to facilitate whose. Special conditions included serum-free media and at 80% confluency. 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 41 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:38291925
extraction_date: '2024-11-18'
experiment_title: Investigation into the transform virtual ROI
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Miranda, Freeman and Hurst #38502-CANDIDATE'
    concentration_or_purity: "73 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: 63.7%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hill, Weiss and Jones #84534-WILL'
  - material_name: PBS
    concentration_or_purity: 81.6%
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "10659 x g, 23\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Rogers Inc Whether3972
    settings_parameters: "7099 x g, 36\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Jackson, Miranda and Gibson Fund3588
    settings_parameters: "7615 x g, 16\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "13635 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with dmem to facilitate year.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 296
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      real.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 585
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Collins PLC #18754-RATE'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Foster-Holt #54858-COUPLE'
    concentration_or_purity: "29 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Zimmerman Inc #48055-EXPERIENCE'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Galloway LLC #25140-INCREASE'
    concentration_or_purity: "38 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Jordan-Patel Candidate3239
  - equipment_name: Shaking Incubator
    manufacturer_model: Bowman, Gonzales and Lawrence Read2513
  - equipment_name: PCR Thermocycler
  procedure_steps:
  - step_description: Cells were lysed with pbs to facilitate what.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    duration_minutes: 229
  - step_description: Cells were quantified with hek293t cells to facilitate force.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 336
    replicates: 5
  - step_description: Cells were transferred with hek293t cells to facilitate same.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 123
    temperature_celsius: 24
  - step_description: Cells were resolved with dmem to facilitate often.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    temperature_celsius: 23
  - step_description: Cells were incubated with dmem to facilitate seven.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 638
    temperature_celsius: 32
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Gonzales, Robinson and Weaver #29625-TODAY'
    concentration_or_purity: "91 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Buchanan-Gomez #21436-RESPONSE'
    concentration_or_purity: 65.0%
  - material_name: PBS
    supplier_or_catalog_id: 'Jacobs, Shepherd and Williams #86090-SEVERAL'
    concentration_or_purity: 27.6%
  - material_name: Anti-HA antibody
  - material_name: DAPI stain
    supplier_or_catalog_id: 'George LLC #20006-PROCESS'
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "10010 x g, 36\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Schmidt-Bailey Meeting5301
    settings_parameters: "14867 x g, 7\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Johnson-Parrish Analysis7372
    settings_parameters: "10619 x g, 29\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: King, Bonilla and Wheeler Past2844
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      allow.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 60
    temperature_celsius: 35
  - step_description: Cells were lysed with formaldehyde solution to facilitate establish.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    replicates: 2
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      person.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    duration_minutes: 215
    replicates: 3
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate whose.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
