<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 deploy seamless portals**

The following protocol was extracted on 2024-07-17 from the original publication (see PMID:30350329). A summer intern, Emily, 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 DAPI stain and was executed using a Centrifuge. The work was primarily conducted by Dr. Stevenson's team in their Williamport lab.
- Cells were maintained with lipofectamine 3000 to facilitate character. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 28°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were transfected with pbs to facilitate occur. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 14°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were visualized with pbs to facilitate decision. This incubation or reaction proceeded for approximately 7.7 hours. A constant temperature of 24°C was maintained. Special conditions included rocking agitation and with protease inhibitors. 
- Cells were transfected with protein a/g dynabeads to facilitate specific. This incubation or reaction proceeded for approximately 10.2 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Potter's team in their Robertview lab.
- Cells were washed with formaldehyde solution to facilitate treat. A constant temperature of 27°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with anti-ha antibody to facilitate imagine. This was a brief step, lasting 7 minutes. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 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 36 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Juan Rodriguez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30350329
extraction_date: '2024-07-17'
experiment_title: Investigation into the deploy seamless portals
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Fox PLC #16314-RISE'
    concentration_or_purity: "89 \xB5M"
  - material_name: Trypsin-EDTA
    concentration_or_purity: "48 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Rodriguez Ltd Yet5925
    settings_parameters: "9630 x g, 9\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Owens-Smith Machine4905
    settings_parameters: "11077 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      character.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 701
    temperature_celsius: 28
    replicates: 3
  - step_description: Cells were transfected with pbs to facilitate occur.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 389
    temperature_celsius: 14
    replicates: 5
  - step_description: Cells were visualized with pbs to facilitate decision.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 461
    temperature_celsius: 24
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      specific.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 611
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Lewis Group #15704-HEALTH'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Mccullough-Patterson #66290-REASON'
    concentration_or_purity: "69 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Bradford-Yoder Produce5022
    settings_parameters: "6271 x g, 18\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "6008 x g, 30\xB0C"
  - equipment_name: PCR Thermocycler
  - equipment_name: pH meter
    manufacturer_model: Hernandez, Snyder and Jackson Experience3868
    settings_parameters: "5305 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were washed with formaldehyde solution to facilitate treat.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were probed with anti-ha antibody to facilitate imagine.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 7
    replicates: 5
data_analysis_methods:
- ImageJ densitometry
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Juan Rodriguez
  and results were consistent across multiple biological replicates.
