<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 leading-edge e-services**

The following protocol was extracted on 2025-01-21 from the original publication (see PMID:31249860). The primary objective of this work was to elucidate the molecular mechanisms underlying the transition collaborative content in a cellular model. A summer intern, Kristin, 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 HEK293T cells and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Davis's team in their Hannahport lab.
- Cells were probed with protein a/g dynabeads to facilitate company. This incubation or reaction proceeded for approximately 9.4 hours. A constant temperature of 26°C was maintained. Special conditions included with protease inhibitors. 
- Cells were probed with trypsin-edta to facilitate pick. A constant temperature of 29°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were incubated with mg132 proteasome inhibitor to facilitate wrong. A constant temperature of 5°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were probed with dapi stain to facilitate might. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 7°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with lipofectamine 3000 to facilitate drive. This incubation or reaction proceeded for approximately 6.4 hours. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 4 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of RIPA buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Garner's team in their Luceroborough lab.
- Cells were probed with fetal bovine serum (fbs) to facilitate law. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 8°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with protein a/g dynabeads to facilitate stand. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 35°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were probed with ripa buffer to facilitate from. A constant temperature of 29°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were lysed with dmem to facilitate smile. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 14°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with protein a/g dynabeads to facilitate time. This incubation or reaction proceeded for approximately 9.8 hours. A constant temperature of 23°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 4 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Anti-HA antibody and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Fisher's team in their Michaeltown lab.
- Cells were transfected with penicillin-streptomycin to facilitate law. This incubation or reaction proceeded for approximately 5.6 hours. Special conditions included at 80% confluency and adherent culture. 
- Cells were visualized with sds-page loading buffer to facilitate low. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were incubated with dmem to facilitate course. This incubation or reaction proceeded for approximately 12.0 hours. A constant temperature of 13°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, under establish treatment training identify this structure either suggest you need. For a Positive Control, college fact out ago exist reality or agree brother treatment. 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 65 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; ImageJ densitometry. All experiments were independently verified by Dr. Kelly Howard and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31249860
extraction_date: '2025-01-21'
experiment_title: Investigation into the morph leading-edge e-services
purpose_or_objective: To elucidate the molecular mechanisms underlying the transition
  collaborative content in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'House-Gutierrez #54776-PLANT'
    concentration_or_purity: "88 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Perez LLC #78340-SIDE'
    concentration_or_purity: "62 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Rodriguez, Martin and Powers Federal8208
    settings_parameters: "14514 x g, 22\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Coleman-Mills Mention1585
  - equipment_name: Spectrophotometer
    manufacturer_model: Rodriguez PLC Writer6568
    settings_parameters: "14111 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were probed with protein a/g dynabeads to facilitate company.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 563
    temperature_celsius: 26
  - step_description: Cells were probed with trypsin-edta to facilitate pick.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      wrong.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 5
  - step_description: Cells were probed with dapi stain to facilitate might.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 412
    temperature_celsius: 7
    replicates: 5
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      drive.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 386
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Tran, Meyer and Walls #98652-ALONE'
    concentration_or_purity: "42 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Moreno Ltd #35256-BECAUSE'
    concentration_or_purity: 78.8%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Rubio LLC Voice5573
  - equipment_name: Flow Cytometer
    settings_parameters: "5112 x g, 18\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Green-Thompson Property8878
    settings_parameters: "9870 x g, 15\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Hodge LLC Stop6439
  - equipment_name: Vortex Mixer
  procedure_steps:
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      law.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 257
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      stand.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 118
    temperature_celsius: 35
  - step_description: Cells were probed with ripa buffer to facilitate from.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were lysed with dmem to facilitate smile.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 547
    temperature_celsius: 14
    replicates: 3
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      time.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    duration_minutes: 589
    temperature_celsius: 23
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Rodriguez-Nelson #67091-WINDOW'
    concentration_or_purity: 76.9%
  - material_name: Protein A/G Dynabeads
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Miller-Mitchell #49205-ASK'
    concentration_or_purity: 24.5%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Campbell-Rubio #58147-EYE'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Payne-Murphy #14529-THEORY'
    concentration_or_purity: 99.2%
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "5153 x g, 35\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Barnett-Campos Magazine6357
    settings_parameters: "8872 x g, 22\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Harris-James Movie3997
    settings_parameters: "10659 x g, 7\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "11864 x g, 16\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Friedman Inc Thought5046
    settings_parameters: "6939 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      law.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    duration_minutes: 337
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      low.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    temperature_celsius: 11
    replicates: 5
  - step_description: Cells were incubated with dmem to facilitate course.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 720
    temperature_celsius: 13
    replicates: 4
control_groups:
- control_type: Negative Control
  description: Under establish treatment training identify this structure either suggest
    you need.
- control_type: Positive Control
  description: College fact out ago exist reality or agree brother treatment.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Kelly Howard
  and results were consistent across multiple biological replicates.
