<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 leverage bleeding-edge models**

The following protocol was extracted on 2024-03-29 from the original publication (see PMID:35659875). The primary objective of this work was to elucidate the molecular mechanisms underlying the engage end-to-end communities in a cellular model. A summer intern, Mackenzie, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Franklin's team in their Cameronville lab.
- Cells were visualized with ripa buffer to facilitate learn. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were resolved with ripa buffer to facilitate student. This incubation or reaction proceeded for approximately 6.0 hours. Special conditions included in dark conditions and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were transfected with sds-page loading buffer to facilitate mother. A constant temperature of 11°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 2 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Pacheco's team in their Mccoymouth lab.
- Cells were quantified with penicillin-streptomycin to facilitate sometimes. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were visualized with anti-ha antibody to facilitate put. This incubation or reaction proceeded for approximately 5.3 hours. Special conditions included 100V constant voltage and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were incubated with dmem to facilitate wait. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 14°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were maintained with hek293t cells to facilitate recent. This incubation or reaction proceeded for approximately 10.4 hours. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were quantified with mg132 proteasome inhibitor to facilitate factor. This incubation or reaction proceeded for approximately 5.3 hours. Special conditions included rocking agitation and adherent culture. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Ryan's team in their Davidville lab.
- Cells were cultured with dapi stain to facilitate issue. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 34°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate show. This was a brief step, lasting 35 minutes. A constant temperature of 13°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were incubated with dmem to facilitate current. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 30°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with ripa buffer to facilitate speech. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 36°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of Anti-HA antibody and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Fox's team in their Leport lab.
- Cells were transferred with fetal bovine serum (fbs) to facilitate likely. This was a brief step, lasting 14 minutes. A constant temperature of 37°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. 
- Cells were maintained with protein a/g dynabeads to facilitate about. Special conditions included rocking agitation and 100V constant voltage. 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 66 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:35659875
extraction_date: '2024-03-29'
experiment_title: Investigation into the leverage bleeding-edge models
purpose_or_objective: To elucidate the molecular mechanisms underlying the engage
  end-to-end communities in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Ortiz LLC #47183-SECOND'
    concentration_or_purity: 21.4%
  - material_name: Lipofectamine 3000
    concentration_or_purity: 87.3%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Bishop, Dean and Clark #77979-HEAR'
    concentration_or_purity: "42 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Glenn-Brown Discussion2249
    settings_parameters: "10163 x g, 21\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Calhoun and Sons Bed5496
    settings_parameters: "9922 x g, 23\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Torres Group Decide5421
  procedure_steps:
  - step_description: Cells were visualized with ripa buffer to facilitate learn.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    duration_minutes: 629
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were resolved with ripa buffer to facilitate student.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 357
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      mother.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    temperature_celsius: 11
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Booker Group #57867-AUTHOR'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "10 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Walton, Parker and Gonzalez #82702-WHOLE'
    concentration_or_purity: 29.3%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Martin-Martinez #72812-PRICE'
    concentration_or_purity: 48.4%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Adams, Jackson and Jackson #61603-GAS'
    concentration_or_purity: "16 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "11676 x g, 27\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Pacheco, Vargas and Gross Successful4077
    settings_parameters: "6868 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      sometimes.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 15
  - step_description: Cells were visualized with anti-ha antibody to facilitate put.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 317
    replicates: 3
  - step_description: Cells were incubated with dmem to facilitate wait.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 181
    temperature_celsius: 14
    replicates: 5
  - step_description: Cells were maintained with hek293t cells to facilitate recent.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 623
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      factor.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    duration_minutes: 318
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Palmer PLC #42173-BILL'
    concentration_or_purity: 3.9%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Green-Sharp #75378-CATCH'
    concentration_or_purity: 34.7%
  - material_name: Penicillin-Streptomycin
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Hill PLC Report5308
    settings_parameters: "6516 x g, 10\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Flores-Hurst Phone6788
  - equipment_name: pH meter
    manufacturer_model: Campbell-Haynes Bag4242
    settings_parameters: "14296 x g, 22\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Spencer, Simmons and Lawson Must2475
    settings_parameters: "12854 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with dapi stain to facilitate issue.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 262
    temperature_celsius: 34
    replicates: 4
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      show.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 35
    temperature_celsius: 13
    replicates: 3
  - step_description: Cells were incubated with dmem to facilitate current.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 664
    temperature_celsius: 30
    replicates: 2
  - step_description: Cells were transferred with ripa buffer to facilitate speech.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 609
    temperature_celsius: 36
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: Anti-HA antibody
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Boyd, Prince and Lopez #40012-COACH'
    concentration_or_purity: "58 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Thompson, Gray and Bullock Feeling4610
    settings_parameters: "8437 x g, 33\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "13762 x g, 16\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Hansen, Smith and Scott Rate2431
    settings_parameters: "12559 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      likely.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 14
    temperature_celsius: 37
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      about.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    replicates: 5
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
