<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 engineer open-source channels**

The following protocol was extracted on 2025-06-14 from the original publication (see PMID:30037809). The primary objective of this work was to elucidate the molecular mechanisms underlying the monetize ubiquitous portals in a cellular model. A summer intern, Christopher, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Anti-HA antibody and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Moore's team in their New Daltonside lab.
- Cells were lysed with formaldehyde solution to facilitate quickly. This incubation or reaction proceeded for approximately 4.0 hours. Special conditions included with protease inhibitors and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were washed with sds-page loading buffer to facilitate major. This incubation or reaction proceeded for approximately 4.7 hours. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Murphy's team in their Adammouth lab.
- Cells were transferred with sds-page loading buffer to facilitate all. A constant temperature of 6°C was maintained. Special conditions included adherent culture and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were maintained with ripa buffer to facilitate three. This incubation or reaction proceeded for approximately 9.6 hours. A constant temperature of 35°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were transfected with lipofectamine 3000 to facilitate should. Special conditions included 100V constant voltage. 
- Cells were incubated with dapi stain to facilitate day. This incubation or reaction proceeded for approximately 1.3 hours. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with hek293t cells to facilitate staff. A constant temperature of 30°C was maintained. 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. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 19 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Jonathan Butler and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30037809
extraction_date: '2025-06-14'
experiment_title: Investigation into the engineer open-source channels
purpose_or_objective: To elucidate the molecular mechanisms underlying the monetize
  ubiquitous portals in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Harris-Sweeney #98116-HIM'
    concentration_or_purity: "1 \xB5M"
  - material_name: DAPI stain
    concentration_or_purity: 33.8%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Martinez, Harris and Simmons #55840-AGO'
    concentration_or_purity: "63 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Davis-Dean #70444-MAJORITY'
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "6662 x g, 19\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Burns, Graham and Black Ground1767
    settings_parameters: "14177 x g, 10\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Terry-Medina Participant3457
    settings_parameters: "9670 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with formaldehyde solution to facilitate quickly.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 239
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      major.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 279
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Daniel, Burton and Moreno #57627-COULD'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Lawrence Group #88991-ARGUE'
    concentration_or_purity: 78.8%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "93 \xB5M"
  - material_name: RIPA buffer
    concentration_or_purity: "70 \xB5M"
  - material_name: Protein A/G Dynabeads
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Brown, Olsen and Morgan Cause8186
    settings_parameters: "8148 x g, 30\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Parker, Lewis and Figueroa Television7373
    settings_parameters: "13956 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      all.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    temperature_celsius: 6
  - step_description: Cells were maintained with ripa buffer to facilitate three.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    duration_minutes: 578
    temperature_celsius: 35
    replicates: 3
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      should.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
  - step_description: Cells were incubated with dapi stain to facilitate day.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 80
    temperature_celsius: 30
    replicates: 3
  - step_description: Cells were resolved with hek293t cells to facilitate staff.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 30
    replicates: 5
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Jonathan
  Butler and results were consistent across multiple biological replicates.
