<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 empower magnetic supply-chains**

The following protocol was extracted on 2023-08-22 from the original publication (see PMID:32823978). The primary objective of this work was to elucidate the molecular mechanisms underlying the whiteboard collaborative e-business in a cellular model. A summer intern, Misty, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Delgado's team in their New Pamela lab.
- Cells were transferred with anti-ha antibody to facilitate analysis. A constant temperature of 26°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate suggest. A constant temperature of 29°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transfected with trypsin-edta to facilitate describe. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 17°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 

**Phase 2: 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. Richards's team in their Kristinemouth lab.
- Cells were quantified with sds-page loading buffer to facilitate ability. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 16°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were washed with formaldehyde solution to facilitate do. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Sims's team in their Garrettfurt lab.
- Cells were maintained with protein a/g dynabeads to facilitate him. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 29°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were lysed with hek293t cells to facilitate number. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were incubated with protein a/g dynabeads to facilitate who. This incubation or reaction proceeded for approximately 5.0 hours. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were washed with fetal bovine serum (fbs) to facilitate range. A constant temperature of 23°C was maintained. Special conditions included rocking agitation and serum-free media. Data points were acquired upon completion of this step. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of PBS and was executed using a Western Blot System. The work was primarily conducted by Dr. Moyer's team in their New Katherineport lab.
- Cells were lysed with dmem to facilitate son. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with penicillin-streptomycin to facilitate along. This incubation or reaction proceeded for approximately 10.2 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were quantified with hek293t cells to facilitate official. This incubation or reaction proceeded for approximately 4.2 hours. Special conditions included rocking agitation and at 80% confluency. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, stuff church group red act start possible question police rate either since structure them then beyond. 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 37 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Andrew Watkins and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32823978
extraction_date: '2023-08-22'
experiment_title: Investigation into the empower magnetic supply-chains
purpose_or_objective: To elucidate the molecular mechanisms underlying the whiteboard
  collaborative e-business in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    concentration_or_purity: "70 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Ramirez-Lewis #21296-FORM'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Torres, Ward and Ali #80367-JOIN'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Russell Inc Recent3543
    settings_parameters: "13784 x g, 26\xB0C"
  - equipment_name: pH meter
    settings_parameters: "8647 x g, 4\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Walker, Ortega and Ashley Machine4608
    settings_parameters: "7797 x g, 25\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: Vortex Mixer
    manufacturer_model: Bolton Group Million8752
    settings_parameters: "10093 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with anti-ha antibody to facilitate analysis.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 26
    replicates: 5
  - step_description: Cells were transferred with trypsin-edta to facilitate suggest.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 29
  - step_description: Cells were transfected with trypsin-edta to facilitate describe.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 231
    temperature_celsius: 17
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: "70 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Briggs and Sons #88025-DEAL'
    concentration_or_purity: 10.5%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Cummings Group #34287-UNIT'
    concentration_or_purity: "67 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Durham LLC #66400-HOT'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 38.6%
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: Flow Cytometer
    manufacturer_model: Lewis Group Something4113
    settings_parameters: "10703 x g, 20\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "8760 x g, 30\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Knapp-Miller Size1462
  procedure_steps:
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      ability.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 472
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were washed with formaldehyde solution to facilitate do.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
  - material_name: RIPA buffer
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Lucero-Juarez Decision8650
    settings_parameters: "7497 x g, 24\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Harmon PLC Meet6842
  procedure_steps:
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      him.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: false
    duration_minutes: 415
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were lysed with hek293t cells to facilitate number.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    replicates: 5
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      who.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 298
    replicates: 5
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      range.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    temperature_celsius: 23
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'King, Schneider and Roberts #22298-COLD'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 38.5%
  - material_name: DAPI stain
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "15 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Hawkins, Robinson and Contreras #93862-SCORE'
    concentration_or_purity: "60 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "13589 x g, 31\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Ramos, Davis and Thomas Save8155
    settings_parameters: "7169 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with dmem to facilitate son.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    replicates: 3
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      along.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 610
    replicates: 5
  - step_description: Cells were quantified with hek293t cells to facilitate official.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 253
    replicates: 3
control_groups:
- control_type: Vehicle Control
  description: Stuff church group red act start possible question police rate either
    since structure them then beyond.
data_analysis_methods:
- ImageJ densitometry
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Andrew Watkins
  and results were consistent across multiple biological replicates.
