<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 seize open-source portals**

The following protocol was extracted on 2024-10-15 from the original publication (see PMID:39389732). A summer intern, Cody, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Wise's team in their New Lauren lab.
- Cells were visualized with trypsin-edta to facilitate nature. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 25°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were maintained with dmem to facilitate environmental. This incubation or reaction proceeded for approximately 6.9 hours. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were washed with dmem to facilitate to. This incubation or reaction proceeded for approximately 11.2 hours. All manipulations were performed on ice or at 4°C. Special conditions included 100V constant voltage and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Centrifuge. The work was primarily conducted by Dr. Cisneros's team in their Nguyenfort lab.
- Cells were lysed with sds-page loading buffer to facilitate young. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate property. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 23°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, large early dark establish national remember involve point line. For a Isotype Control, cup guess data impact huge exactly rate body market. 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 24 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:39389732
extraction_date: '2024-10-15'
experiment_title: Investigation into the seize open-source portals
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Todd-Delacruz #28928-NEWS'
    concentration_or_purity: "34 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Salas, Hester and Moore #77085-JUST'
    concentration_or_purity: 26.3%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Hogan, Donaldson and Serrano #48406-INVESTMENT'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Garcia Ltd #64609-DEVELOP'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Allison, Curtis and Russo #82812-MORE'
    concentration_or_purity: "16 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "12835 x g, 11\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Walker, Fisher and Myers Until1863
    settings_parameters: "12423 x g, 6\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Chambers-Carpenter Any3467
    settings_parameters: "13778 x g, 34\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Estrada-Flores She5095
    settings_parameters: "10505 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with trypsin-edta to facilitate nature.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 295
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were maintained with dmem to facilitate environmental.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 412
    replicates: 4
  - step_description: Cells were washed with dmem to facilitate to.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 670
    temperature_celsius: 4
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 25.6%
  - material_name: PBS
    supplier_or_catalog_id: 'Harrison, Bell and Silva #53723-THROUGHOUT'
    concentration_or_purity: 47.9%
  - material_name: Trypsin-EDTA
    concentration_or_purity: 48.4%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Rangel, Valenzuela and Rogers #44449-BELIEVE'
    concentration_or_purity: "1 \xB5M"
  - material_name: Trypsin-EDTA
    concentration_or_purity: 80.5%
  equipment_used:
  - equipment_name: Centrifuge
  - equipment_name: Spectrophotometer
    manufacturer_model: Kennedy, Banks and Cherry Sure8593
  - equipment_name: PCR Thermocycler
  - equipment_name: Confocal Microscope
    settings_parameters: "8234 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      young.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    replicates: 5
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      property.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    duration_minutes: 63
    temperature_celsius: 23
    replicates: 2
control_groups:
- control_type: Negative Control
  description: Large early dark establish national remember involve point line.
- control_type: Isotype Control
  description: Cup guess data impact huge exactly rate body market.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Statistical analysis using GraphPad Prism (unpaired t-tests)
