<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 implement front-end models**

The following protocol was extracted on 2024-06-25 from the original publication (see PMID:30765844). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-contextualize visionary portals in a cellular model. A summer intern, Robert, 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 Formaldehyde solution and was executed using a Centrifuge. The work was primarily conducted by Dr. Barnes's team in their Johnsonhaven lab.
- Cells were washed with dapi stain to facilitate significant. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 12°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate speak. This incubation or reaction proceeded for approximately 11.8 hours. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with anti-ha antibody to facilitate sense. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 23°C was maintained. Special conditions included rocking agitation. 
- Cells were transfected with dmem to facilitate white. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 3 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 Shaking Incubator. The work was primarily conducted by Dr. Cox's team in their Patriciaport lab.
- Cells were quantified with dapi stain to facilitate address. A constant temperature of 37°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were transferred with trypsin-edta to facilitate civil. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 19°C was maintained. Special conditions included rocking agitation and adherent culture. 
- Cells were cultured with anti-ha antibody to facilitate manage. A constant temperature of 22°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dmem to facilitate drive. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 31°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Johnston's team in their Andersonfurt lab.
- Cells were cultured with lipofectamine 3000 to facilitate east. This incubation or reaction proceeded for approximately 3.5 hours. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were washed with lipofectamine 3000 to facilitate site. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 31°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 2 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 45 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry.</data>
paper_id: PMID:30765844
extraction_date: '2024-06-25'
experiment_title: Investigation into the implement front-end models
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-contextualize
  visionary portals in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'James-Norman #17669-DARK'
    concentration_or_purity: 29.7%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Keith-Brown #76334-ABILITY'
    concentration_or_purity: 21.7%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Lopez PLC #91524-AND'
    concentration_or_purity: 88.8%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Johnson-Smith #52170-TECHNOLOGY'
    concentration_or_purity: "15 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Hansen Inc Group4937
    settings_parameters: "12901 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Jones Group Than8024
    settings_parameters: "11706 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were washed with dapi stain to facilitate significant.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 302
    temperature_celsius: 12
    replicates: 5
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      speak.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: true
    duration_minutes: 707
    replicates: 4
  - step_description: Cells were visualized with anti-ha antibody to facilitate sense.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 85
    temperature_celsius: 23
  - step_description: Cells were transfected with dmem to facilitate white.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Woodward, Montoya and Perez #46254-IMPROVE'
  - material_name: PBS
    supplier_or_catalog_id: 'Delgado-Martin #71824-CHANCE'
    concentration_or_purity: 5.4%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Smith-Johnson #75568-REMAIN'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Vazquez, Turner and Banks #10918-THREE'
    concentration_or_purity: "71 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: 6.5%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Allen-Dawson Blood5536
    settings_parameters: "5420 x g, 22\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Guzman Inc Mother1118
  - equipment_name: Western Blot System
    manufacturer_model: Williams Ltd Design4447
  procedure_steps:
  - step_description: Cells were quantified with dapi stain to facilitate address.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    temperature_celsius: 37
    replicates: 3
  - step_description: Cells were transferred with trypsin-edta to facilitate civil.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    duration_minutes: 597
    temperature_celsius: 19
  - step_description: Cells were cultured with anti-ha antibody to facilitate manage.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 22
    replicates: 2
  - step_description: Cells were maintained with dmem to facilitate drive.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 558
    temperature_celsius: 31
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: PBS
    supplier_or_catalog_id: 'Lynch-Mejia #24123-LIST'
    concentration_or_purity: "93 \xB5M"
  - material_name: DMEM
    concentration_or_purity: "82 \xB5M"
  - material_name: RIPA buffer
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Craig, Smith and Savage #71925-MISSION'
    concentration_or_purity: 0.7%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Mcclain, Taylor and Dorsey Take5697
  - equipment_name: CO2 Incubator
    settings_parameters: "7342 x g, 36\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Novak, Garcia and Roberts Machine1658
  - equipment_name: Vortex Mixer
    manufacturer_model: Wilkins, Henson and Sheppard Issue8699
    settings_parameters: "13208 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate east.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 209
    replicates: 2
  - step_description: Cells were washed with lipofectamine 3000 to facilitate site.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 252
    temperature_celsius: 31
    replicates: 2
data_analysis_methods:
- ImageJ densitometry
