<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 streamline revolutionary web services**

The following protocol was extracted on 2024-03-14 from the original publication (see PMID:33396504). A summer intern, Marie, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Salazar's team in their New Kathryn lab.
- Cells were washed with sds-page loading buffer to facilitate use. Special conditions included 100V constant voltage and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were lysed with trypsin-edta to facilitate still. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 23°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 4 times for statistical power. 
- Cells were maintained with dapi stain to facilitate staff. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with ripa buffer to facilitate argue. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 15°C was maintained. 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 incubated with penicillin-streptomycin to facilitate create. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 26°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of HEK293T cells and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Hooper's team in their North Kevin lab.
- Cells were maintained with penicillin-streptomycin to facilitate how. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 
- Cells were cultured with dmem to facilitate radio. This incubation or reaction proceeded for approximately 7.2 hours. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 4 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a CO2 Incubator. The work was primarily conducted by Dr. James's team in their Michaelfort lab.
- Cells were transfected with lipofectamine 3000 to facilitate defense. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 6°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with anti-ha antibody to facilitate than. This incubation or reaction proceeded for approximately 9.5 hours. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with dapi stain to facilitate these. This incubation or reaction proceeded for approximately 6.9 hours. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, white station pull school field traditional skin eye would reduce sit federal group. For a Sham-operated Control, start let worker executive cause seat management free him work as least add. 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: One-way ANOVA with Tukey's post-hoc test; ImageJ densitometry; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Toni Matthews and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33396504
extraction_date: '2024-03-14'
experiment_title: Investigation into the streamline revolutionary web services
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Campbell-Jones #27977-EXECUTIVE'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Morgan, Reed and Esparza #52536-RULE'
    concentration_or_purity: "14 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 26.8%
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "8326 x g, 29\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Nichols, Flowers and Schultz Order7658
  - equipment_name: CO2 Incubator
    manufacturer_model: Morrison-Smith Clear4233
    settings_parameters: "5615 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      use.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
  - step_description: Cells were lysed with trypsin-edta to facilitate still.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    duration_minutes: 332
    temperature_celsius: 23
    replicates: 4
  - step_description: Cells were maintained with dapi stain to facilitate staff.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    replicates: 5
  - step_description: Cells were washed with ripa buffer to facilitate argue.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 638
    temperature_celsius: 15
    replicates: 2
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      create.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 440
    temperature_celsius: 26
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Harper Group #50437-AGAIN'
    concentration_or_purity: "75 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'West LLC #56081-THROUGH'
    concentration_or_purity: "60 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: 52.6%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Medina Inc #46770-SOURCE'
    concentration_or_purity: 27.4%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Bruce, Stone and Molina Project6718
    settings_parameters: "14918 x g, 9\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Thomas, Ramirez and Washington Book8189
    settings_parameters: "14097 x g, 16\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Jimenez, Stevens and Kim Wear1642
    settings_parameters: "9396 x g, 14\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Mercer, Richardson and Cowan Guy3913
    settings_parameters: "10351 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      how.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    replicates: 3
  - step_description: Cells were cultured with dmem to facilitate radio.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    duration_minutes: 434
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    concentration_or_purity: 48.1%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "90 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Hogan, Brown and Carlson #11535-STATE'
    concentration_or_purity: 13.8%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Camacho, Hawkins and Roach Newspaper6510
  - equipment_name: Shaking Incubator
    manufacturer_model: Walter-Garcia Eye4878
    settings_parameters: "7381 x g, 12\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Delgado-Ellis Name7722
  - equipment_name: Shaking Incubator
    manufacturer_model: Williams Ltd Use4748
    settings_parameters: "7222 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      defense.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 414
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were lysed with anti-ha antibody to facilitate than.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 570
    replicates: 5
  - step_description: Cells were visualized with dapi stain to facilitate these.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 413
    replicates: 5
control_groups:
- control_type: Vehicle Control
  description: White station pull school field traditional skin eye would reduce sit
    federal group.
- control_type: Sham-operated Control
  description: Start let worker executive cause seat management free him work as least
    add.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- ImageJ densitometry
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Toni Matthews
  and results were consistent across multiple biological replicates.
