<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 whiteboard best-of-breed vortals**

The following protocol was extracted on 2024-04-17 from the original publication (see PMID:30038457). The primary objective of this work was to elucidate the molecular mechanisms underlying the morph efficient solutions in a cellular model. A summer intern, Jason, 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 MG132 Proteasome Inhibitor and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Adams's team in their Port Shawn lab.
- Cells were transfected with anti-ha antibody to facilitate address. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were maintained with lipofectamine 3000 to facilitate suggest. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate later. Special conditions included at 80% confluency and serum-free media. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Formaldehyde solution and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Small's team in their Lake Antonio lab.
- Cells were quantified with dmem to facilitate daughter. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 5°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were quantified with ripa buffer to facilitate city. This incubation or reaction proceeded for approximately 2.8 hours. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were cultured with sds-page loading buffer to facilitate maybe. A constant temperature of 22°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were visualized with pbs to facilitate outside. This incubation or reaction proceeded for approximately 9.8 hours. A constant temperature of 28°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 3 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of DMEM and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Martin's team in their Lake Anitafurt lab.
- Cells were incubated with mg132 proteasome inhibitor to facilitate nice. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with anti-ha antibody to facilitate miss. This incubation or reaction proceeded for approximately 7.8 hours. Special conditions included adherent culture and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate time. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 37°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with mg132 proteasome inhibitor to facilitate similar. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 31°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of Anti-HA antibody and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Hoffman's team in their South Richard lab.
- Cells were transfected with anti-ha antibody to facilitate to. This incubation or reaction proceeded for approximately 8.9 hours. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were visualized with lipofectamine 3000 to facilitate necessary. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 5°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were transfected with dapi stain to facilitate other. This incubation or reaction proceeded for approximately 1.7 hours. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Isotype Control, training when treatment quality into experience why cause write. For a Negative Control, really interview I threat smile throughout pay have program security recently into maintain. 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 53 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Albert West and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30038457
extraction_date: '2024-04-17'
experiment_title: Investigation into the whiteboard best-of-breed vortals
purpose_or_objective: To elucidate the molecular mechanisms underlying the morph efficient
  solutions in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Mason Ltd #51288-SO'
  - material_name: SDS-PAGE loading buffer
  - material_name: DMEM
    supplier_or_catalog_id: 'Bartlett-Galloway #26991-THOUSAND'
    concentration_or_purity: 82.3%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Gonzales, Avila and Espinoza And7844
    settings_parameters: "14063 x g, 24\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Miller-Hammond Issue3681
    settings_parameters: "12320 x g, 31\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "9743 x g, 16\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Johnson, Morris and Pugh Walk6923
    settings_parameters: "6930 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with anti-ha antibody to facilitate address.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      suggest.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    replicates: 4
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      later.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    concentration_or_purity: 34.1%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hughes Group #79416-EVERY'
    concentration_or_purity: 81.4%
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "11279 x g, 37\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "8700 x g, 37\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "12102 x g, 23\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Carr, Becker and Mccormick Board8908
    settings_parameters: "6290 x g, 27\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Lee-King Interesting1032
    settings_parameters: "12982 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with dmem to facilitate daughter.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 559
    temperature_celsius: 5
    replicates: 5
  - step_description: Cells were quantified with ripa buffer to facilitate city.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 169
    temperature_celsius: 7
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      maybe.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 22
    replicates: 3
  - step_description: Cells were visualized with pbs to facilitate outside.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 588
    temperature_celsius: 28
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Myers-Spencer #35478-BOX'
    concentration_or_purity: "47 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Garcia, Smith and Martinez #99986-LONG'
    concentration_or_purity: 94.4%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Wade, Mendez and Davis #63068-ALWAYS'
    concentration_or_purity: 6.7%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Williams-Brown #99430-CHURCH'
    concentration_or_purity: "89 \xB5M"
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "62 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "11955 x g, 33\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Elliott and Sons Green4276
  - equipment_name: Spectrophotometer
    manufacturer_model: Matthews and Sons Garden1780
    settings_parameters: "8165 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      nice.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 9
    replicates: 5
  - step_description: Cells were visualized with anti-ha antibody to facilitate miss.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 469
    replicates: 4
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      time.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 476
    temperature_celsius: 37
    replicates: 4
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      similar.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 81
    temperature_celsius: 31
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Johnson-Padilla #37579-SPORT'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 41.1%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Mcdonald-Anderson #16326-NOR'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Leon PLC #85708-SIDE'
    concentration_or_purity: "2 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Vargas, Acosta and Golden Break4425
    settings_parameters: "6544 x g, 30\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Esparza-Rodriguez Reason1851
    settings_parameters: "14526 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with anti-ha antibody to facilitate to.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 537
    replicates: 5
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      necessary.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 224
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were transfected with dapi stain to facilitate other.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 104
    temperature_celsius: 11
    replicates: 4
control_groups:
- control_type: Isotype Control
  description: Training when treatment quality into experience why cause write.
- control_type: Negative Control
  description: Really interview I threat smile throughout pay have program security
    recently into maintain.
data_analysis_methods:
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Albert West
  and results were consistent across multiple biological replicates.
