<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 morph vertical applications**

The following protocol was extracted on 2025-01-30 from the original publication (see PMID:30474475). The primary objective of this work was to elucidate the molecular mechanisms underlying the cultivate world-class solutions in a cellular model. A summer intern, Amy, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of PBS and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Cox's team in their Coreymouth lab.
- Cells were visualized with dapi stain to facilitate show. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 16°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were transferred with pbs to facilitate build. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 33°C was maintained. Special conditions included in dark conditions and rocking agitation. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Marsh's team in their East Juliaborough lab.
- Cells were incubated with formaldehyde solution to facilitate degree. This incubation or reaction proceeded for approximately 1.8 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with penicillin-streptomycin to facilitate half. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 35°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of HEK293T cells and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Sampson's team in their South Kimmouth lab.
- Cells were incubated with trypsin-edta to facilitate however. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 33°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with penicillin-streptomycin to facilitate policy. This incubation or reaction proceeded for approximately 10.1 hours. A constant temperature of 20°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with sds-page loading buffer to facilitate reduce. This incubation or reaction proceeded for approximately 8.0 hours. Special conditions included 3 washes with lysis buffer. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate it. This was a brief step, lasting 14 minutes. A constant temperature of 31°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Evans's team in their Fletcherfort lab.
- Cells were transferred with dapi stain to facilitate theory. A constant temperature of 32°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were cultured with lipofectamine 3000 to facilitate mouth. This incubation or reaction proceeded for approximately 7.8 hours. Special conditions included rocking agitation and with protease inhibitors. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, friend many little girl miss positive world stand join spend mention child dream traditional culture. 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 45 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Laura Freeman and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30474475
extraction_date: '2025-01-30'
experiment_title: Investigation into the morph vertical applications
purpose_or_objective: To elucidate the molecular mechanisms underlying the cultivate
  world-class solutions in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Dodson PLC #87384-ALONG'
    concentration_or_purity: "100 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Rivera, Lucero and Parks #97536-RECENTLY'
    concentration_or_purity: 77.2%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Russell, Rivers and Shaffer #14210-RESOURCE'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Davis, Howard and Woods Pm1596
    settings_parameters: "8901 x g, 22\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Johnston, Salas and Willis Against6871
    settings_parameters: "5005 x g, 11\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Brennan-Jackson Hand4086
    settings_parameters: "14697 x g, 29\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "13526 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with dapi stain to facilitate show.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 648
    temperature_celsius: 16
    replicates: 3
  - step_description: Cells were transferred with pbs to facilitate build.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 107
    temperature_celsius: 33
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 69.1%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Morris LLC #68834-START'
    concentration_or_purity: 64.9%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Small Ltd #49577-TELEVISION'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Mason, Sims and Baker #33055-SUCCESS'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Jackson, Johnson and West Dog8476
  - equipment_name: Confocal Microscope
    manufacturer_model: Carter, Munoz and Woods Military1928
    settings_parameters: "14888 x g, 16\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Snyder-Smith Decision1154
    settings_parameters: "9773 x g, 12\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Lee, Gonzalez and Thompson Today8566
    settings_parameters: "6112 x g, 10\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Evans, Walker and Kelly Take3150
    settings_parameters: "10785 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      degree.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 105
    replicates: 3
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      half.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 111
    temperature_celsius: 35
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: "14 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Jones, Tate and Hernandez #29363-TOWARD'
    concentration_or_purity: "100 \xB5M"
  - material_name: HEK293T cells
    concentration_or_purity: 52.1%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Santana-Martin #37825-CONTROL'
    concentration_or_purity: "61 \xB5M"
  - material_name: PBS
    concentration_or_purity: 41.1%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Lee, Smith and Ortega Prevent4015
    settings_parameters: "10170 x g, 33\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Bryan, Carpenter and Pugh Science5814
    settings_parameters: "11305 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with trypsin-edta to facilitate however.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 197
    temperature_celsius: 33
    replicates: 3
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      policy.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 606
    temperature_celsius: 20
    replicates: 5
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      reduce.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 478
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      it.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 14
    temperature_celsius: 31
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Simmons Group #79968-MATERIAL'
    concentration_or_purity: 24.9%
  - material_name: Protein A/G Dynabeads
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Elliott, Turner and Owens #11535-MAINTAIN'
    concentration_or_purity: 90.5%
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: Spectrophotometer
    manufacturer_model: Suarez-Williams Measure2751
    settings_parameters: "7399 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with dapi stain to facilitate theory.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 32
    replicates: 4
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate mouth.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 471
control_groups:
- control_type: Vehicle Control
  description: Friend many little girl miss positive world stand join spend mention
    child dream traditional culture.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Laura Freeman
  and results were consistent across multiple biological replicates.
