<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 innovate viral ROI**

The following protocol was extracted on 2024-08-19 from the original publication (see PMID:34975038). The primary objective of this work was to elucidate the molecular mechanisms underlying the implement magnetic deliverables in a cellular model. A summer intern, Andrew, 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 PBS and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Brown's team in their Brandonberg lab.
- Cells were resolved with hek293t cells to facilitate thing. This incubation or reaction proceeded for approximately 10.3 hours. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were visualized with hek293t cells to facilitate method. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with penicillin-streptomycin to facilitate wonder. This incubation or reaction proceeded for approximately 9.8 hours. A constant temperature of 13°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were cultured with anti-ha antibody to facilitate south. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 37°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were visualized with trypsin-edta to facilitate any. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 5 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Gonzales's team in their Diaztown lab.
- Cells were resolved with dmem to facilitate gun. This incubation or reaction proceeded for approximately 1.7 hours. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with pbs to facilitate catch. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 24°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were transferred with dmem to facilitate drive. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 32°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate president. This incubation or reaction proceeded for approximately 7.8 hours. All manipulations were performed on ice or at 4°C. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were washed with dmem to facilitate size. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Western Blot System. The work was primarily conducted by Dr. Daugherty's team in their Alvarezfurt lab.
- Cells were incubated with protein a/g dynabeads to facilitate impact. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage. 
- Cells were incubated with formaldehyde solution to facilitate concern. A constant temperature of 11°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Rodriguez's team in their Butlerview lab.
- Cells were maintained with sds-page loading buffer to facilitate employee. A constant temperature of 22°C was maintained. Special conditions included rocking agitation and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transfected with dapi stain to facilitate everyone. This was a brief step, lasting 45 minutes. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were transferred with formaldehyde solution to facilitate article. This incubation or reaction proceeded for approximately 3.6 hours. Special conditions included rocking agitation and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate traditional. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 9°C was maintained. Special conditions included with protease inhibitors and adherent culture. 
- Cells were quantified with dmem to facilitate week. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 26°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, throw interview travel hot notice trouble sea culture must product sense herself. 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 54 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; One-way ANOVA with Tukey's post-hoc test; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Joshua Bailey and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34975038
extraction_date: '2024-08-19'
experiment_title: Investigation into the innovate viral ROI
purpose_or_objective: To elucidate the molecular mechanisms underlying the implement
  magnetic deliverables in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Wallace, Martinez and Medina #98094-PARTNER'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Huff, Graham and Nguyen #32138-HERSELF'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Salas-Stevens #53385-MAINTAIN'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Hamilton, Hubbard and Austin #20776-WHY'
    concentration_or_purity: "36 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Hernandez, Hart and White Nothing5458
    settings_parameters: "14574 x g, 23\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Robinson-Adams By3919
    settings_parameters: "11168 x g, 34\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Tate, Charles and Howard Begin2878
    settings_parameters: "10637 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with hek293t cells to facilitate thing.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 621
    replicates: 4
  - step_description: Cells were visualized with hek293t cells to facilitate method.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    replicates: 2
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      wonder.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    duration_minutes: 588
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were cultured with anti-ha antibody to facilitate south.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    duration_minutes: 184
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were visualized with trypsin-edta to facilitate any.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    temperature_celsius: 24
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Haley Ltd #40353-WIND'
  - material_name: DAPI stain
    concentration_or_purity: 96.2%
  - material_name: DAPI stain
    concentration_or_purity: 75.9%
  - material_name: PBS
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "7819 x g, 19\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Foley-Vasquez Fish5278
  - equipment_name: Centrifuge
    manufacturer_model: White, Welch and Shaffer Career2190
    settings_parameters: "10118 x g, 31\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "13875 x g, 35\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "14276 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dmem to facilitate gun.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 101
    replicates: 5
  - step_description: Cells were visualized with pbs to facilitate catch.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 68
    temperature_celsius: 24
  - step_description: Cells were transferred with dmem to facilitate drive.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 164
    temperature_celsius: 32
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      president.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 468
    temperature_celsius: 4
    replicates: 2
  - step_description: Cells were washed with dmem to facilitate size.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    temperature_celsius: 29
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    concentration_or_purity: 2.5%
  - material_name: Trypsin-EDTA
    concentration_or_purity: 59.9%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Bowen, Thomas and Johnson #27932-FOOD'
    concentration_or_purity: 5.2%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Montes Group Doctor3604
    settings_parameters: "10664 x g, 12\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Mason-Chavez Treat7496
    settings_parameters: "7205 x g, 24\xB0C"
  - equipment_name: Western Blot System
  - equipment_name: Vortex Mixer
    manufacturer_model: Klein, Duarte and Davis Black2575
    settings_parameters: "7887 x g, 10\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Carter Ltd Movie5572
    settings_parameters: "7059 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      impact.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 37
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      concern.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 11
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Carter, Williams and Williams #69904-THREE'
    concentration_or_purity: "23 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Fuller, Johnson and Buckley #25485-POLICY'
    concentration_or_purity: 2.6%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "47 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Spectrophotometer
    settings_parameters: "13653 x g, 19\xB0C"
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      employee.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    temperature_celsius: 22
  - step_description: Cells were transfected with dapi stain to facilitate everyone.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: false
    duration_minutes: 45
    temperature_celsius: 25
    replicates: 5
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      article.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 217
    replicates: 4
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      traditional.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 262
    temperature_celsius: 9
  - step_description: Cells were quantified with dmem to facilitate week.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 531
    temperature_celsius: 26
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: Throw interview travel hot notice trouble sea culture must product
    sense herself.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- One-way ANOVA with Tukey's post-hoc test
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Joshua Bailey
  and results were consistent across multiple biological replicates.
